Probabilistic Model for Untargeted Peak Detection in LC-MS Using Bayesian Statistics.

PubMed

Woldegebriel, Michael; Vivó-Truyols, Gabriel

2015-07-21

We introduce a novel Bayesian probabilistic peak detection algorithm for liquid chromatography-mass spectroscopy (LC-MS). The final probabilistic result allows the user to make a final decision about which points in a chromatogram are affected by a chromatographic peak and which ones are only affected by noise. The use of probabilities contrasts with the traditional method in which a binary answer is given, relying on a threshold. By contrast, with the Bayesian peak detection presented here, the values of probability can be further propagated into other preprocessing steps, which will increase (or decrease) the importance of chromatographic regions into the final results. The present work is based on the use of the statistical overlap theory of component overlap from Davis and Giddings (Davis, J. M.; Giddings, J. Anal. Chem. 1983, 55, 418-424) as prior probability in the Bayesian formulation. The algorithm was tested on LC-MS Orbitrap data and was able to successfully distinguish chemical noise from actual peaks without any data preprocessing.

Encoding probabilistic brain atlases using Bayesian inference.

PubMed

Van Leemput, Koen

2009-06-01

This paper addresses the problem of creating probabilistic brain atlases from manually labeled training data. Probabilistic atlases are typically constructed by counting the relative frequency of occurrence of labels in corresponding locations across the training images. However, such an "averaging" approach generalizes poorly to unseen cases when the number of training images is limited, and provides no principled way of aligning the training datasets using deformable registration. In this paper, we generalize the generative image model implicitly underlying standard "average" atlases, using mesh-based representations endowed with an explicit deformation model. Bayesian inference is used to infer the optimal model parameters from the training data, leading to a simultaneous group-wise registration and atlas estimation scheme that encompasses standard averaging as a special case. We also use Bayesian inference to compare alternative atlas models in light of the training data, and show how this leads to a data compression problem that is intuitive to interpret and computationally feasible. Using this technique, we automatically determine the optimal amount of spatial blurring, the best deformation field flexibility, and the most compact mesh representation. We demonstrate, using 2-D training datasets, that the resulting models are better at capturing the structure in the training data than conventional probabilistic atlases. We also present experiments of the proposed atlas construction technique in 3-D, and show the resulting atlases' potential in fully-automated, pulse sequence-adaptive segmentation of 36 neuroanatomical structures in brain MRI scans.

Bayesian Monte Carlo and Maximum Likelihood Approach for Uncertainty Estimation and Risk Management: Application to Lake Oxygen Recovery Model

EPA Science Inventory

Model uncertainty estimation and risk assessment is essential to environmental management and informed decision making on pollution mitigation strategies. In this study, we apply a probabilistic methodology, which combines Bayesian Monte Carlo simulation and Maximum Likelihood e...

Model based inference from microvascular measurements: Combining experimental measurements and model predictions using a Bayesian probabilistic approach

PubMed Central

Rasmussen, Peter M.; Smith, Amy F.; Sakadžić, Sava; Boas, David A.; Pries, Axel R.; Secomb, Timothy W.; Østergaard, Leif

2017-01-01

Objective In vivo imaging of the microcirculation and network-oriented modeling have emerged as powerful means of studying microvascular function and understanding its physiological significance. Network-oriented modeling may provide the means of summarizing vast amounts of data produced by high-throughput imaging techniques in terms of key, physiological indices. To estimate such indices with sufficient certainty, however, network-oriented analysis must be robust to the inevitable presence of uncertainty due to measurement errors as well as model errors. Methods We propose the Bayesian probabilistic data analysis framework as a means of integrating experimental measurements and network model simulations into a combined and statistically coherent analysis. The framework naturally handles noisy measurements and provides posterior distributions of model parameters as well as physiological indices associated with uncertainty. Results We applied the analysis framework to experimental data from three rat mesentery networks and one mouse brain cortex network. We inferred distributions for more than five hundred unknown pressure and hematocrit boundary conditions. Model predictions were consistent with previous analyses, and remained robust when measurements were omitted from model calibration. Conclusion Our Bayesian probabilistic approach may be suitable for optimizing data acquisition and for analyzing and reporting large datasets acquired as part of microvascular imaging studies. PMID:27987383

Probabilistic inversion of expert assessments to inform projections about Antarctic ice sheet responses.

PubMed

Fuller, Robert William; Wong, Tony E; Keller, Klaus

2017-01-01

The response of the Antarctic ice sheet (AIS) to changing global temperatures is a key component of sea-level projections. Current projections of the AIS contribution to sea-level changes are deeply uncertain. This deep uncertainty stems, in part, from (i) the inability of current models to fully resolve key processes and scales, (ii) the relatively sparse available data, and (iii) divergent expert assessments. One promising approach to characterizing the deep uncertainty stemming from divergent expert assessments is to combine expert assessments, observations, and simple models by coupling probabilistic inversion and Bayesian inversion. Here, we present a proof-of-concept study that uses probabilistic inversion to fuse a simple AIS model and diverse expert assessments. We demonstrate the ability of probabilistic inversion to infer joint prior probability distributions of model parameters that are consistent with expert assessments. We then confront these inferred expert priors with instrumental and paleoclimatic observational data in a Bayesian inversion. These additional constraints yield tighter hindcasts and projections. We use this approach to quantify how the deep uncertainty surrounding expert assessments affects the joint probability distributions of model parameters and future projections.

Bayesian probabilistic population projections for all countries.

PubMed

Raftery, Adrian E; Li, Nan; Ševčíková, Hana; Gerland, Patrick; Heilig, Gerhard K

2012-08-28

Projections of countries' future populations, broken down by age and sex, are widely used for planning and research. They are mostly done deterministically, but there is a widespread need for probabilistic projections. We propose a bayesian method for probabilistic population projections for all countries. The total fertility rate and female and male life expectancies at birth are projected probabilistically using bayesian hierarchical models estimated via Markov chain Monte Carlo using United Nations population data for all countries. These are then converted to age-specific rates and combined with a cohort component projection model. This yields probabilistic projections of any population quantity of interest. The method is illustrated for five countries of different demographic stages, continents and sizes. The method is validated by an out of sample experiment in which data from 1950-1990 are used for estimation, and applied to predict 1990-2010. The method appears reasonably accurate and well calibrated for this period. The results suggest that the current United Nations high and low variants greatly underestimate uncertainty about the number of oldest old from about 2050 and that they underestimate uncertainty for high fertility countries and overstate uncertainty for countries that have completed the demographic transition and whose fertility has started to recover towards replacement level, mostly in Europe. The results also indicate that the potential support ratio (persons aged 20-64 per person aged 65+) will almost certainly decline dramatically in most countries over the coming decades.

Probabilistic machine learning and artificial intelligence.

PubMed

Ghahramani, Zoubin

2015-05-28

How can a machine learn from experience? Probabilistic modelling provides a framework for understanding what learning is, and has therefore emerged as one of the principal theoretical and practical approaches for designing machines that learn from data acquired through experience. The probabilistic framework, which describes how to represent and manipulate uncertainty about models and predictions, has a central role in scientific data analysis, machine learning, robotics, cognitive science and artificial intelligence. This Review provides an introduction to this framework, and discusses some of the state-of-the-art advances in the field, namely, probabilistic programming, Bayesian optimization, data compression and automatic model discovery.

Probabilistic machine learning and artificial intelligence

NASA Astrophysics Data System (ADS)

Ghahramani, Zoubin

2015-05-01

How can a machine learn from experience? Probabilistic modelling provides a framework for understanding what learning is, and has therefore emerged as one of the principal theoretical and practical approaches for designing machines that learn from data acquired through experience. The probabilistic framework, which describes how to represent and manipulate uncertainty about models and predictions, has a central role in scientific data analysis, machine learning, robotics, cognitive science and artificial intelligence. This Review provides an introduction to this framework, and discusses some of the state-of-the-art advances in the field, namely, probabilistic programming, Bayesian optimization, data compression and automatic model discovery.

Probabilistic sensitivity analysis for decision trees with multiple branches: use of the Dirichlet distribution in a Bayesian framework.

PubMed

Briggs, Andrew H; Ades, A E; Price, Martin J

2003-01-01

In structuring decision models of medical interventions, it is commonly recommended that only 2 branches be used for each chance node to avoid logical inconsistencies that can arise during sensitivity analyses if the branching probabilities do not sum to 1. However, information may be naturally available in an unconditional form, and structuring a tree in conditional form may complicate rather than simplify the sensitivity analysis of the unconditional probabilities. Current guidance emphasizes using probabilistic sensitivity analysis, and a method is required to provide probabilistic probabilities over multiple branches that appropriately represents uncertainty while satisfying the requirement that mutually exclusive event probabilities should sum to 1. The authors argue that the Dirichlet distribution, the multivariate equivalent of the beta distribution, is appropriate for this purpose and illustrate its use for generating a fully probabilistic transition matrix for a Markov model. Furthermore, they demonstrate that by adopting a Bayesian approach, the problem of observing zero counts for transitions of interest can be overcome.

Revealing the ISO/IEC 9126-1 Clique Tree for COTS Software Evaluation

NASA Technical Reports Server (NTRS)

Morris, A. Terry

2007-01-01

Previous research has shown that acyclic dependency models, if they exist, can be extracted from software quality standards and that these models can be used to assess software safety and product quality. In the case of commercial off-the-shelf (COTS) software, the extracted dependency model can be used in a probabilistic Bayesian network context for COTS software evaluation. Furthermore, while experts typically employ Bayesian networks to encode domain knowledge, secondary structures (clique trees) from Bayesian network graphs can be used to determine the probabilistic distribution of any software variable (attribute) using any clique that contains that variable. Secondary structures, therefore, provide insight into the fundamental nature of graphical networks. This paper will apply secondary structure calculations to reveal the clique tree of the acyclic dependency model extracted from the ISO/IEC 9126-1 software quality standard. Suggestions will be provided to describe how the clique tree may be exploited to aid efficient transformation of an evaluation model.

Finding Useful Questions: On Bayesian Diagnosticity, Probability, Impact, and Information Gain

ERIC Educational Resources Information Center

Nelson, Jonathan D.

2005-01-01

Several norms for how people should assess a question's usefulness have been proposed, notably Bayesian diagnosticity, information gain (mutual information), Kullback-Liebler distance, probability gain (error minimization), and impact (absolute change). Several probabilistic models of previous experiments on categorization, covariation assessment,…

Reasoning in Reference Games: Individual- vs. Population-Level Probabilistic Modeling

PubMed Central

Franke, Michael; Degen, Judith

2016-01-01

Recent advances in probabilistic pragmatics have achieved considerable success in modeling speakers’ and listeners’ pragmatic reasoning as probabilistic inference. However, these models are usually applied to population-level data, and so implicitly suggest a homogeneous population without individual differences. Here we investigate potential individual differences in Theory-of-Mind related depth of pragmatic reasoning in so-called reference games that require drawing ad hoc Quantity implicatures of varying complexity. We show by Bayesian model comparison that a model that assumes a heterogenous population is a better predictor of our data, especially for comprehension. We discuss the implications for the treatment of individual differences in probabilistic models of language use. PMID:27149675

Probabilistic numerical methods for PDE-constrained Bayesian inverse problems

NASA Astrophysics Data System (ADS)

Cockayne, Jon; Oates, Chris; Sullivan, Tim; Girolami, Mark

2017-06-01

This paper develops meshless methods for probabilistically describing discretisation error in the numerical solution of partial differential equations. This construction enables the solution of Bayesian inverse problems while accounting for the impact of the discretisation of the forward problem. In particular, this drives statistical inferences to be more conservative in the presence of significant solver error. Theoretical results are presented describing rates of convergence for the posteriors in both the forward and inverse problems. This method is tested on a challenging inverse problem with a nonlinear forward model.

Stan: A Probabilistic Programming Language for Bayesian Inference and Optimization

ERIC Educational Resources Information Center

Gelman, Andrew; Lee, Daniel; Guo, Jiqiang

2015-01-01

Stan is a free and open-source C++ program that performs Bayesian inference or optimization for arbitrary user-specified models and can be called from the command line, R, Python, Matlab, or Julia and has great promise for fitting large and complex statistical models in many areas of application. We discuss Stan from users' and developers'…

Probabilistic inversion of expert assessments to inform projections about Antarctic ice sheet responses

PubMed Central

Wong, Tony E.; Keller, Klaus

2017-01-01

The response of the Antarctic ice sheet (AIS) to changing global temperatures is a key component of sea-level projections. Current projections of the AIS contribution to sea-level changes are deeply uncertain. This deep uncertainty stems, in part, from (i) the inability of current models to fully resolve key processes and scales, (ii) the relatively sparse available data, and (iii) divergent expert assessments. One promising approach to characterizing the deep uncertainty stemming from divergent expert assessments is to combine expert assessments, observations, and simple models by coupling probabilistic inversion and Bayesian inversion. Here, we present a proof-of-concept study that uses probabilistic inversion to fuse a simple AIS model and diverse expert assessments. We demonstrate the ability of probabilistic inversion to infer joint prior probability distributions of model parameters that are consistent with expert assessments. We then confront these inferred expert priors with instrumental and paleoclimatic observational data in a Bayesian inversion. These additional constraints yield tighter hindcasts and projections. We use this approach to quantify how the deep uncertainty surrounding expert assessments affects the joint probability distributions of model parameters and future projections. PMID:29287095

A Bayesian joint probability modeling approach for seasonal forecasting of streamflows at multiple sites

NASA Astrophysics Data System (ADS)

Wang, Q. J.; Robertson, D. E.; Chiew, F. H. S.

2009-05-01

Seasonal forecasting of streamflows can be highly valuable for water resources management. In this paper, a Bayesian joint probability (BJP) modeling approach for seasonal forecasting of streamflows at multiple sites is presented. A Box-Cox transformed multivariate normal distribution is proposed to model the joint distribution of future streamflows and their predictors such as antecedent streamflows and El Niño-Southern Oscillation indices and other climate indicators. Bayesian inference of model parameters and uncertainties is implemented using Markov chain Monte Carlo sampling, leading to joint probabilistic forecasts of streamflows at multiple sites. The model provides a parametric structure for quantifying relationships between variables, including intersite correlations. The Box-Cox transformed multivariate normal distribution has considerable flexibility for modeling a wide range of predictors and predictands. The Bayesian inference formulated allows the use of data that contain nonconcurrent and missing records. The model flexibility and data-handling ability means that the BJP modeling approach is potentially of wide practical application. The paper also presents a number of statistical measures and graphical methods for verification of probabilistic forecasts of continuous variables. Results for streamflows at three river gauges in the Murrumbidgee River catchment in southeast Australia show that the BJP modeling approach has good forecast quality and that the fitted model is consistent with observed data.

Bayesian probabilistic population projections for all countries

PubMed Central

Raftery, Adrian E.; Li, Nan; Ševčíková, Hana; Gerland, Patrick; Heilig, Gerhard K.

2012-01-01

Projections of countries’ future populations, broken down by age and sex, are widely used for planning and research. They are mostly done deterministically, but there is a widespread need for probabilistic projections. We propose a Bayesian method for probabilistic population projections for all countries. The total fertility rate and female and male life expectancies at birth are projected probabilistically using Bayesian hierarchical models estimated via Markov chain Monte Carlo using United Nations population data for all countries. These are then converted to age-specific rates and combined with a cohort component projection model. This yields probabilistic projections of any population quantity of interest. The method is illustrated for five countries of different demographic stages, continents and sizes. The method is validated by an out of sample experiment in which data from 1950–1990 are used for estimation, and applied to predict 1990–2010. The method appears reasonably accurate and well calibrated for this period. The results suggest that the current United Nations high and low variants greatly underestimate uncertainty about the number of oldest old from about 2050 and that they underestimate uncertainty for high fertility countries and overstate uncertainty for countries that have completed the demographic transition and whose fertility has started to recover towards replacement level, mostly in Europe. The results also indicate that the potential support ratio (persons aged 20–64 per person aged 65+) will almost certainly decline dramatically in most countries over the coming decades. PMID:22908249

A Bayesian Approach to Interactive Retrieval

ERIC Educational Resources Information Center

Tague, Jean M.

1973-01-01

A probabilistic model for interactive retrieval is presented. Bayesian statistical decision theory principles are applied: use of prior and sample information about the relationship of document descriptions to query relevance; maximization of expected value of a utility function, to the problem of optimally restructuring search strategies in an…

A Guide to the Literature on Learning Graphical Models

NASA Technical Reports Server (NTRS)

Buntine, Wray L.; Friedland, Peter (Technical Monitor)

1994-01-01

This literature review discusses different methods under the general rubric of learning Bayesian networks from data, and more generally, learning probabilistic graphical models. Because many problems in artificial intelligence, statistics and neural networks can be represented as a probabilistic graphical model, this area provides a unifying perspective on learning. This paper organizes the research in this area along methodological lines of increasing complexity.

Probabilistic Space Weather Forecasting: a Bayesian Perspective

NASA Astrophysics Data System (ADS)

Camporeale, E.; Chandorkar, M.; Borovsky, J.; Care', A.

2017-12-01

Most of the Space Weather forecasts, both at operational and research level, are not probabilistic in nature. Unfortunately, a prediction that does not provide a confidence level is not very useful in a decision-making scenario. Nowadays, forecast models range from purely data-driven, machine learning algorithms, to physics-based approximation of first-principle equations (and everything that sits in between). Uncertainties pervade all such models, at every level: from the raw data to finite-precision implementation of numerical methods. The most rigorous way of quantifying the propagation of uncertainties is by embracing a Bayesian probabilistic approach. One of the simplest and most robust machine learning technique in the Bayesian framework is Gaussian Process regression and classification. Here, we present the application of Gaussian Processes to the problems of the DST geomagnetic index forecast, the solar wind type classification, and the estimation of diffusion parameters in radiation belt modeling. In each of these very diverse problems, the GP approach rigorously provide forecasts in the form of predictive distributions. In turn, these distributions can be used as input for ensemble simulations in order to quantify the amplification of uncertainties. We show that we have achieved excellent results in all of the standard metrics to evaluate our models, with very modest computational cost.

A Bayesian network approach to the database search problem in criminal proceedings

PubMed Central

2012-01-01

Background The ‘database search problem’, that is, the strengthening of a case - in terms of probative value - against an individual who is found as a result of a database search, has been approached during the last two decades with substantial mathematical analyses, accompanied by lively debate and centrally opposing conclusions. This represents a challenging obstacle in teaching but also hinders a balanced and coherent discussion of the topic within the wider scientific and legal community. This paper revisits and tracks the associated mathematical analyses in terms of Bayesian networks. Their derivation and discussion for capturing probabilistic arguments that explain the database search problem are outlined in detail. The resulting Bayesian networks offer a distinct view on the main debated issues, along with further clarity. Methods As a general framework for representing and analyzing formal arguments in probabilistic reasoning about uncertain target propositions (that is, whether or not a given individual is the source of a crime stain), this paper relies on graphical probability models, in particular, Bayesian networks. This graphical probability modeling approach is used to capture, within a single model, a series of key variables, such as the number of individuals in a database, the size of the population of potential crime stain sources, and the rarity of the corresponding analytical characteristics in a relevant population. Results This paper demonstrates the feasibility of deriving Bayesian network structures for analyzing, representing, and tracking the database search problem. The output of the proposed models can be shown to agree with existing but exclusively formulaic approaches. Conclusions The proposed Bayesian networks allow one to capture and analyze the currently most well-supported but reputedly counter-intuitive and difficult solution to the database search problem in a way that goes beyond the traditional, purely formulaic expressions. The method’s graphical environment, along with its computational and probabilistic architectures, represents a rich package that offers analysts and discussants with additional modes of interaction, concise representation, and coherent communication. PMID:22849390

bnstruct: an R package for Bayesian Network structure learning in the presence of missing data.

PubMed

Franzin, Alberto; Sambo, Francesco; Di Camillo, Barbara

2017-04-15

A Bayesian Network is a probabilistic graphical model that encodes probabilistic dependencies between a set of random variables. We introduce bnstruct, an open source R package to (i) learn the structure and the parameters of a Bayesian Network from data in the presence of missing values and (ii) perform reasoning and inference on the learned Bayesian Networks. To the best of our knowledge, there is no other open source software that provides methods for all of these tasks, particularly the manipulation of missing data, which is a common situation in practice. The software is implemented in R and C and is available on CRAN under a GPL licence. francesco.sambo@unipd.it. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Hierarchical Bayesian Modeling of Fluid-Induced Seismicity

NASA Astrophysics Data System (ADS)

Broccardo, M.; Mignan, A.; Wiemer, S.; Stojadinovic, B.; Giardini, D.

2017-11-01

In this study, we present a Bayesian hierarchical framework to model fluid-induced seismicity. The framework is based on a nonhomogeneous Poisson process with a fluid-induced seismicity rate proportional to the rate of injected fluid. The fluid-induced seismicity rate model depends upon a set of physically meaningful parameters and has been validated for six fluid-induced case studies. In line with the vision of hierarchical Bayesian modeling, the rate parameters are considered as random variables. We develop both the Bayesian inference and updating rules, which are used to develop a probabilistic forecasting model. We tested the Basel 2006 fluid-induced seismic case study to prove that the hierarchical Bayesian model offers a suitable framework to coherently encode both epistemic uncertainty and aleatory variability. Moreover, it provides a robust and consistent short-term seismic forecasting model suitable for online risk quantification and mitigation.

Bayesian networks in neuroscience: a survey.

PubMed

Bielza, Concha; Larrañaga, Pedro

2014-01-01

Bayesian networks are a type of probabilistic graphical models lie at the intersection between statistics and machine learning. They have been shown to be powerful tools to encode dependence relationships among the variables of a domain under uncertainty. Thanks to their generality, Bayesian networks can accommodate continuous and discrete variables, as well as temporal processes. In this paper we review Bayesian networks and how they can be learned automatically from data by means of structure learning algorithms. Also, we examine how a user can take advantage of these networks for reasoning by exact or approximate inference algorithms that propagate the given evidence through the graphical structure. Despite their applicability in many fields, they have been little used in neuroscience, where they have focused on specific problems, like functional connectivity analysis from neuroimaging data. Here we survey key research in neuroscience where Bayesian networks have been used with different aims: discover associations between variables, perform probabilistic reasoning over the model, and classify new observations with and without supervision. The networks are learned from data of any kind-morphological, electrophysiological, -omics and neuroimaging-, thereby broadening the scope-molecular, cellular, structural, functional, cognitive and medical- of the brain aspects to be studied.

Bayesian networks in neuroscience: a survey

PubMed Central

Bielza, Concha; Larrañaga, Pedro

2014-01-01

Bayesian networks are a type of probabilistic graphical models lie at the intersection between statistics and machine learning. They have been shown to be powerful tools to encode dependence relationships among the variables of a domain under uncertainty. Thanks to their generality, Bayesian networks can accommodate continuous and discrete variables, as well as temporal processes. In this paper we review Bayesian networks and how they can be learned automatically from data by means of structure learning algorithms. Also, we examine how a user can take advantage of these networks for reasoning by exact or approximate inference algorithms that propagate the given evidence through the graphical structure. Despite their applicability in many fields, they have been little used in neuroscience, where they have focused on specific problems, like functional connectivity analysis from neuroimaging data. Here we survey key research in neuroscience where Bayesian networks have been used with different aims: discover associations between variables, perform probabilistic reasoning over the model, and classify new observations with and without supervision. The networks are learned from data of any kind–morphological, electrophysiological, -omics and neuroimaging–, thereby broadening the scope–molecular, cellular, structural, functional, cognitive and medical– of the brain aspects to be studied. PMID:25360109

Bayesian Probabilistic Projections of Life Expectancy for All Countries

PubMed Central

Raftery, Adrian E.; Chunn, Jennifer L.; Gerland, Patrick; Ševčíková, Hana

2014-01-01

We propose a Bayesian hierarchical model for producing probabilistic forecasts of male period life expectancy at birth for all the countries of the world from the present to 2100. Such forecasts would be an input to the production of probabilistic population projections for all countries, which is currently being considered by the United Nations. To evaluate the method, we did an out-of-sample cross-validation experiment, fitting the model to the data from 1950–1995, and using the estimated model to forecast for the subsequent ten years. The ten-year predictions had a mean absolute error of about 1 year, about 40% less than the current UN methodology. The probabilistic forecasts were calibrated, in the sense that (for example) the 80% prediction intervals contained the truth about 80% of the time. We illustrate our method with results from Madagascar (a typical country with steadily improving life expectancy), Latvia (a country that has had a mortality crisis), and Japan (a leading country). We also show aggregated results for South Asia, a region with eight countries. Free publicly available R software packages called bayesLife and bayesDem are available to implement the method. PMID:23494599

Using Bayesian Model Averaging (BMA) to calibrate probabilistic surface temperature forecasts over Iran

NASA Astrophysics Data System (ADS)

Soltanzadeh, I.; Azadi, M.; Vakili, G. A.

2011-07-01

Using Bayesian Model Averaging (BMA), an attempt was made to obtain calibrated probabilistic numerical forecasts of 2-m temperature over Iran. The ensemble employs three limited area models (WRF, MM5 and HRM), with WRF used with five different configurations. Initial and boundary conditions for MM5 and WRF are obtained from the National Centers for Environmental Prediction (NCEP) Global Forecast System (GFS) and for HRM the initial and boundary conditions come from analysis of Global Model Europe (GME) of the German Weather Service. The resulting ensemble of seven members was run for a period of 6 months (from December 2008 to May 2009) over Iran. The 48-h raw ensemble outputs were calibrated using BMA technique for 120 days using a 40 days training sample of forecasts and relative verification data. The calibrated probabilistic forecasts were assessed using rank histogram and attribute diagrams. Results showed that application of BMA improved the reliability of the raw ensemble. Using the weighted ensemble mean forecast as a deterministic forecast it was found that the deterministic-style BMA forecasts performed usually better than the best member's deterministic forecast.

PyMC: Bayesian Stochastic Modelling in Python

PubMed Central

Patil, Anand; Huard, David; Fonnesbeck, Christopher J.

2010-01-01

This user guide describes a Python package, PyMC, that allows users to efficiently code a probabilistic model and draw samples from its posterior distribution using Markov chain Monte Carlo techniques. PMID:21603108

When mechanism matters: Bayesian forecasting using models of ecological diffusion

USGS Publications Warehouse

Hefley, Trevor J.; Hooten, Mevin B.; Russell, Robin E.; Walsh, Daniel P.; Powell, James A.

2017-01-01

Ecological diffusion is a theory that can be used to understand and forecast spatio-temporal processes such as dispersal, invasion, and the spread of disease. Hierarchical Bayesian modelling provides a framework to make statistical inference and probabilistic forecasts, using mechanistic ecological models. To illustrate, we show how hierarchical Bayesian models of ecological diffusion can be implemented for large data sets that are distributed densely across space and time. The hierarchical Bayesian approach is used to understand and forecast the growth and geographic spread in the prevalence of chronic wasting disease in white-tailed deer (Odocoileus virginianus). We compare statistical inference and forecasts from our hierarchical Bayesian model to phenomenological regression-based methods that are commonly used to analyse spatial occurrence data. The mechanistic statistical model based on ecological diffusion led to important ecological insights, obviated a commonly ignored type of collinearity, and was the most accurate method for forecasting.

Enhancing Flood Prediction Reliability Using Bayesian Model Averaging

NASA Astrophysics Data System (ADS)

Liu, Z.; Merwade, V.

2017-12-01

Uncertainty analysis is an indispensable part of modeling the hydrology and hydrodynamics of non-idealized environmental systems. Compared to reliance on prediction from one model simulation, using on ensemble of predictions that consider uncertainty from different sources is more reliable. In this study, Bayesian model averaging (BMA) is applied to Black River watershed in Arkansas and Missouri by combining multi-model simulations to get reliable deterministic water stage and probabilistic inundation extent predictions. The simulation ensemble is generated from 81 LISFLOOD-FP subgrid model configurations that include uncertainty from channel shape, channel width, channel roughness and discharge. Model simulation outputs are trained with observed water stage data during one flood event, and BMA prediction ability is validated for another flood event. Results from this study indicate that BMA does not always outperform all members in the ensemble, but it provides relatively robust deterministic flood stage predictions across the basin. Station based BMA (BMA_S) water stage prediction has better performance than global based BMA (BMA_G) prediction which is superior to the ensemble mean prediction. Additionally, high-frequency flood inundation extent (probability greater than 60%) in BMA_G probabilistic map is more accurate than the probabilistic flood inundation extent based on equal weights.

Bayesian Probabilistic Projection of International Migration.

PubMed

Azose, Jonathan J; Raftery, Adrian E

2015-10-01

We propose a method for obtaining joint probabilistic projections of migration for all countries, broken down by age and sex. Joint trajectories for all countries are constrained to satisfy the requirement of zero global net migration. We evaluate our model using out-of-sample validation and compare point projections to the projected migration rates from a persistence model similar to the method used in the United Nations' World Population Prospects, and also to a state-of-the-art gravity model.

Boosting probabilistic graphical model inference by incorporating prior knowledge from multiple sources.

PubMed

Praveen, Paurush; Fröhlich, Holger

2013-01-01

Inferring regulatory networks from experimental data via probabilistic graphical models is a popular framework to gain insights into biological systems. However, the inherent noise in experimental data coupled with a limited sample size reduces the performance of network reverse engineering. Prior knowledge from existing sources of biological information can address this low signal to noise problem by biasing the network inference towards biologically plausible network structures. Although integrating various sources of information is desirable, their heterogeneous nature makes this task challenging. We propose two computational methods to incorporate various information sources into a probabilistic consensus structure prior to be used in graphical model inference. Our first model, called Latent Factor Model (LFM), assumes a high degree of correlation among external information sources and reconstructs a hidden variable as a common source in a Bayesian manner. The second model, a Noisy-OR, picks up the strongest support for an interaction among information sources in a probabilistic fashion. Our extensive computational studies on KEGG signaling pathways as well as on gene expression data from breast cancer and yeast heat shock response reveal that both approaches can significantly enhance the reconstruction accuracy of Bayesian Networks compared to other competing methods as well as to the situation without any prior. Our framework allows for using diverse information sources, like pathway databases, GO terms and protein domain data, etc. and is flexible enough to integrate new sources, if available.

Time-reversal and Bayesian inversion

NASA Astrophysics Data System (ADS)

Debski, Wojciech

2017-04-01

Probabilistic inversion technique is superior to the classical optimization-based approach in all but one aspects. It requires quite exhaustive computations which prohibit its use in huge size inverse problems like global seismic tomography or waveform inversion to name a few. The advantages of the approach are, however, so appealing that there is an ongoing continuous afford to make the large inverse task as mentioned above manageable with the probabilistic inverse approach. One of the perspective possibility to achieve this goal relays on exploring the internal symmetry of the seismological modeling problems in hand - a time reversal and reciprocity invariance. This two basic properties of the elastic wave equation when incorporating into the probabilistic inversion schemata open a new horizons for Bayesian inversion. In this presentation we discuss the time reversal symmetry property, its mathematical aspects and propose how to combine it with the probabilistic inverse theory into a compact, fast inversion algorithm. We illustrate the proposed idea with the newly developed location algorithm TRMLOC and discuss its efficiency when applied to mining induced seismic data.

Acoustic emission based damage localization in composites structures using Bayesian identification

NASA Astrophysics Data System (ADS)

Kundu, A.; Eaton, M. J.; Al-Jumali, S.; Sikdar, S.; Pullin, R.

2017-05-01

Acoustic emission based damage detection in composite structures is based on detection of ultra high frequency packets of acoustic waves emitted from damage sources (such as fibre breakage, fatigue fracture, amongst others) with a network of distributed sensors. This non-destructive monitoring scheme requires solving an inverse problem where the measured signals are linked back to the location of the source. This in turn enables rapid deployment of mitigative measures. The presence of significant amount of uncertainty associated with the operating conditions and measurements makes the problem of damage identification quite challenging. The uncertainties stem from the fact that the measured signals are affected by the irregular geometries, manufacturing imprecision, imperfect boundary conditions, existing damages/structural degradation, amongst others. This work aims to tackle these uncertainties within a framework of automated probabilistic damage detection. The method trains a probabilistic model of the parametrized input and output model of the acoustic emission system with experimental data to give probabilistic descriptors of damage locations. A response surface modelling the acoustic emission as a function of parametrized damage signals collected from sensors would be calibrated with a training dataset using Bayesian inference. This is used to deduce damage locations in the online monitoring phase. During online monitoring, the spatially correlated time data is utilized in conjunction with the calibrated acoustic emissions model to infer the probabilistic description of the acoustic emission source within a hierarchical Bayesian inference framework. The methodology is tested on a composite structure consisting of carbon fibre panel with stiffeners and damage source behaviour has been experimentally simulated using standard H-N sources. The methodology presented in this study would be applicable in the current form to structural damage detection under varying operational loads and would be investigated in future studies.

Probabilistic inference using linear Gaussian importance sampling for hybrid Bayesian networks

NASA Astrophysics Data System (ADS)

Sun, Wei; Chang, K. C.

2005-05-01

Probabilistic inference for Bayesian networks is in general NP-hard using either exact algorithms or approximate methods. However, for very complex networks, only the approximate methods such as stochastic sampling could be used to provide a solution given any time constraint. There are several simulation methods currently available. They include logic sampling (the first proposed stochastic method for Bayesian networks, the likelihood weighting algorithm) the most commonly used simulation method because of its simplicity and efficiency, the Markov blanket scoring method, and the importance sampling algorithm. In this paper, we first briefly review and compare these available simulation methods, then we propose an improved importance sampling algorithm called linear Gaussian importance sampling algorithm for general hybrid model (LGIS). LGIS is aimed for hybrid Bayesian networks consisting of both discrete and continuous random variables with arbitrary distributions. It uses linear function and Gaussian additive noise to approximate the true conditional probability distribution for continuous variable given both its parents and evidence in a Bayesian network. One of the most important features of the newly developed method is that it can adaptively learn the optimal important function from the previous samples. We test the inference performance of LGIS using a 16-node linear Gaussian model and a 6-node general hybrid model. The performance comparison with other well-known methods such as Junction tree (JT) and likelihood weighting (LW) shows that LGIS-GHM is very promising.

Ensemble Bayesian forecasting system Part I: Theory and algorithms

NASA Astrophysics Data System (ADS)

Herr, Henry D.; Krzysztofowicz, Roman

2015-05-01

The ensemble Bayesian forecasting system (EBFS), whose theory was published in 2001, is developed for the purpose of quantifying the total uncertainty about a discrete-time, continuous-state, non-stationary stochastic process such as a time series of stages, discharges, or volumes at a river gauge. The EBFS is built of three components: an input ensemble forecaster (IEF), which simulates the uncertainty associated with random inputs; a deterministic hydrologic model (of any complexity), which simulates physical processes within a river basin; and a hydrologic uncertainty processor (HUP), which simulates the hydrologic uncertainty (an aggregate of all uncertainties except input). It works as a Monte Carlo simulator: an ensemble of time series of inputs (e.g., precipitation amounts) generated by the IEF is transformed deterministically through a hydrologic model into an ensemble of time series of outputs, which is next transformed stochastically by the HUP into an ensemble of time series of predictands (e.g., river stages). Previous research indicated that in order to attain an acceptable sampling error, the ensemble size must be on the order of hundreds (for probabilistic river stage forecasts and probabilistic flood forecasts) or even thousands (for probabilistic stage transition forecasts). The computing time needed to run the hydrologic model this many times renders the straightforward simulations operationally infeasible. This motivates the development of the ensemble Bayesian forecasting system with randomization (EBFSR), which takes full advantage of the analytic meta-Gaussian HUP and generates multiple ensemble members after each run of the hydrologic model; this auxiliary randomization reduces the required size of the meteorological input ensemble and makes it operationally feasible to generate a Bayesian ensemble forecast of large size. Such a forecast quantifies the total uncertainty, is well calibrated against the prior (climatic) distribution of predictand, possesses a Bayesian coherence property, constitutes a random sample of the predictand, and has an acceptable sampling error-which makes it suitable for rational decision making under uncertainty.

Bayesian Action-Perception loop modeling: Application to trajectory generation and recognition using internal motor simulation

NASA Astrophysics Data System (ADS)

Gilet, Estelle; Diard, Julien; Palluel-Germain, Richard; Bessière, Pierre

2011-03-01

This paper is about modeling perception-action loops and, more precisely, the study of the influence of motor knowledge during perception tasks. We use the Bayesian Action-Perception (BAP) model, which deals with the sensorimotor loop involved in reading and writing cursive isolated letters and includes an internal simulation of movement loop. By using this probabilistic model we simulate letter recognition, both with and without internal motor simulation. Comparison of their performance yields an experimental prediction, which we set forth.

Bayesian methods for characterizing unknown parameters of material models

DOE PAGES

Emery, J. M.; Grigoriu, M. D.; Field Jr., R. V.

2016-02-04

A Bayesian framework is developed for characterizing the unknown parameters of probabilistic models for material properties. In this framework, the unknown parameters are viewed as random and described by their posterior distributions obtained from prior information and measurements of quantities of interest that are observable and depend on the unknown parameters. The proposed Bayesian method is applied to characterize an unknown spatial correlation of the conductivity field in the definition of a stochastic transport equation and to solve this equation by Monte Carlo simulation and stochastic reduced order models (SROMs). As a result, the Bayesian method is also employed tomore » characterize unknown parameters of material properties for laser welds from measurements of peak forces sustained by these welds.« less

Bayesian methods for characterizing unknown parameters of material models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Emery, J. M.; Grigoriu, M. D.; Field Jr., R. V.

A Bayesian framework is developed for characterizing the unknown parameters of probabilistic models for material properties. In this framework, the unknown parameters are viewed as random and described by their posterior distributions obtained from prior information and measurements of quantities of interest that are observable and depend on the unknown parameters. The proposed Bayesian method is applied to characterize an unknown spatial correlation of the conductivity field in the definition of a stochastic transport equation and to solve this equation by Monte Carlo simulation and stochastic reduced order models (SROMs). As a result, the Bayesian method is also employed tomore » characterize unknown parameters of material properties for laser welds from measurements of peak forces sustained by these welds.« less

A Computationally-Efficient Inverse Approach to Probabilistic Strain-Based Damage Diagnosis

NASA Technical Reports Server (NTRS)

Warner, James E.; Hochhalter, Jacob D.; Leser, William P.; Leser, Patrick E.; Newman, John A

2016-01-01

This work presents a computationally-efficient inverse approach to probabilistic damage diagnosis. Given strain data at a limited number of measurement locations, Bayesian inference and Markov Chain Monte Carlo (MCMC) sampling are used to estimate probability distributions of the unknown location, size, and orientation of damage. Substantial computational speedup is obtained by replacing a three-dimensional finite element (FE) model with an efficient surrogate model. The approach is experimentally validated on cracked test specimens where full field strains are determined using digital image correlation (DIC). Access to full field DIC data allows for testing of different hypothetical sensor arrangements, facilitating the study of strain-based diagnosis effectiveness as the distance between damage and measurement locations increases. The ability of the framework to effectively perform both probabilistic damage localization and characterization in cracked plates is demonstrated and the impact of measurement location on uncertainty in the predictions is shown. Furthermore, the analysis time to produce these predictions is orders of magnitude less than a baseline Bayesian approach with the FE method by utilizing surrogate modeling and effective numerical sampling approaches.

Bayesian Analysis of a Reduced-Form Air Quality Model

EPA Science Inventory

Numerical air quality models are being used for assessing emission control strategies for improving ambient pollution levels across the globe. This paper applies probabilistic modeling to evaluate the effectiveness of emission reduction scenarios aimed at lowering ground-level oz...

The development of a probabilistic approach to forecast coastal change

USGS Publications Warehouse

Lentz, Erika E.; Hapke, Cheryl J.; Rosati, Julie D.; Wang, Ping; Roberts, Tiffany M.

2011-01-01

This study demonstrates the applicability of a Bayesian probabilistic model as an effective tool in predicting post-storm beach changes along sandy coastlines. Volume change and net shoreline movement are modeled for two study sites at Fire Island, New York in response to two extratropical storms in 2007 and 2009. Both study areas include modified areas adjacent to unmodified areas in morphologically different segments of coast. Predicted outcomes are evaluated against observed changes to test model accuracy and uncertainty along 163 cross-shore transects. Results show strong agreement in the cross validation of predictions vs. observations, with 70-82% accuracies reported. Although no consistent spatial pattern in inaccurate predictions could be determined, the highest prediction uncertainties appeared in locations that had been recently replenished. Further testing and model refinement are needed; however, these initial results show that Bayesian networks have the potential to serve as important decision-support tools in forecasting coastal change.

Incorporating Resilience into Dynamic Social Models

DTIC Science & Technology

2016-07-20

solved by simply using the information provided by the scenario. Instead, additional knowledge is required from relevant fields that study these...resilience function by leveraging Bayesian Knowledge Bases (BKBs), a probabilistic reasoning network framework[5],[6]. BKBs allow for inferencing...reasoning network framework based on Bayesian Knowledge Bases (BKBs). BKBs are central to our social resilience framework as they are used to

Nonadditive entropy maximization is inconsistent with Bayesian updating

NASA Astrophysics Data System (ADS)

Pressé, Steve

2014-11-01

The maximum entropy method—used to infer probabilistic models from data—is a special case of Bayes's model inference prescription which, in turn, is grounded in basic propositional logic. By contrast to the maximum entropy method, the compatibility of nonadditive entropy maximization with Bayes's model inference prescription has never been established. Here we demonstrate that nonadditive entropy maximization is incompatible with Bayesian updating and discuss the immediate implications of this finding. We focus our attention on special cases as illustrations.

Nonadditive entropy maximization is inconsistent with Bayesian updating.

PubMed

Pressé, Steve

2014-11-01

The maximum entropy method-used to infer probabilistic models from data-is a special case of Bayes's model inference prescription which, in turn, is grounded in basic propositional logic. By contrast to the maximum entropy method, the compatibility of nonadditive entropy maximization with Bayes's model inference prescription has never been established. Here we demonstrate that nonadditive entropy maximization is incompatible with Bayesian updating and discuss the immediate implications of this finding. We focus our attention on special cases as illustrations.

A Bayesian framework based on a Gaussian mixture model and radial-basis-function Fisher discriminant analysis (BayGmmKda V1.1) for spatial prediction of floods

NASA Astrophysics Data System (ADS)

Tien Bui, Dieu; Hoang, Nhat-Duc

2017-09-01

In this study, a probabilistic model, named as BayGmmKda, is proposed for flood susceptibility assessment in a study area in central Vietnam. The new model is a Bayesian framework constructed by a combination of a Gaussian mixture model (GMM), radial-basis-function Fisher discriminant analysis (RBFDA), and a geographic information system (GIS) database. In the Bayesian framework, GMM is used for modeling the data distribution of flood-influencing factors in the GIS database, whereas RBFDA is utilized to construct a latent variable that aims at enhancing the model performance. As a result, the posterior probabilistic output of the BayGmmKda model is used as flood susceptibility index. Experiment results showed that the proposed hybrid framework is superior to other benchmark models, including the adaptive neuro-fuzzy inference system and the support vector machine. To facilitate the model implementation, a software program of BayGmmKda has been developed in MATLAB. The BayGmmKda program can accurately establish a flood susceptibility map for the study region. Accordingly, local authorities can overlay this susceptibility map onto various land-use maps for the purpose of land-use planning or management.

Evaluating Mixture Modeling for Clustering: Recommendations and Cautions

ERIC Educational Resources Information Center

Steinley, Douglas; Brusco, Michael J.

2011-01-01

This article provides a large-scale investigation into several of the properties of mixture-model clustering techniques (also referred to as latent class cluster analysis, latent profile analysis, model-based clustering, probabilistic clustering, Bayesian classification, unsupervised learning, and finite mixture models; see Vermunt & Magdison,…

Modeling the Evolution of Beliefs Using an Attentional Focus Mechanism

PubMed Central

Marković, Dimitrije; Gläscher, Jan; Bossaerts, Peter; O’Doherty, John; Kiebel, Stefan J.

2015-01-01

For making decisions in everyday life we often have first to infer the set of environmental features that are relevant for the current task. Here we investigated the computational mechanisms underlying the evolution of beliefs about the relevance of environmental features in a dynamical and noisy environment. For this purpose we designed a probabilistic Wisconsin card sorting task (WCST) with belief solicitation, in which subjects were presented with stimuli composed of multiple visual features. At each moment in time a particular feature was relevant for obtaining reward, and participants had to infer which feature was relevant and report their beliefs accordingly. To test the hypothesis that attentional focus modulates the belief update process, we derived and fitted several probabilistic and non-probabilistic behavioral models, which either incorporate a dynamical model of attentional focus, in the form of a hierarchical winner-take-all neuronal network, or a diffusive model, without attention-like features. We used Bayesian model selection to identify the most likely generative model of subjects’ behavior and found that attention-like features in the behavioral model are essential for explaining subjects’ responses. Furthermore, we demonstrate a method for integrating both connectionist and Bayesian models of decision making within a single framework that allowed us to infer hidden belief processes of human subjects. PMID:26495984

Bayesian analysis of rare events

NASA Astrophysics Data System (ADS)

Straub, Daniel; Papaioannou, Iason; Betz, Wolfgang

2016-06-01

In many areas of engineering and science there is an interest in predicting the probability of rare events, in particular in applications related to safety and security. Increasingly, such predictions are made through computer models of physical systems in an uncertainty quantification framework. Additionally, with advances in IT, monitoring and sensor technology, an increasing amount of data on the performance of the systems is collected. This data can be used to reduce uncertainty, improve the probability estimates and consequently enhance the management of rare events and associated risks. Bayesian analysis is the ideal method to include the data into the probabilistic model. It ensures a consistent probabilistic treatment of uncertainty, which is central in the prediction of rare events, where extrapolation from the domain of observation is common. We present a framework for performing Bayesian updating of rare event probabilities, termed BUS. It is based on a reinterpretation of the classical rejection-sampling approach to Bayesian analysis, which enables the use of established methods for estimating probabilities of rare events. By drawing upon these methods, the framework makes use of their computational efficiency. These methods include the First-Order Reliability Method (FORM), tailored importance sampling (IS) methods and Subset Simulation (SuS). In this contribution, we briefly review these methods in the context of the BUS framework and investigate their applicability to Bayesian analysis of rare events in different settings. We find that, for some applications, FORM can be highly efficient and is surprisingly accurate, enabling Bayesian analysis of rare events with just a few model evaluations. In a general setting, BUS implemented through IS and SuS is more robust and flexible.

Identification of failure type in corroded pipelines: a bayesian probabilistic approach.

PubMed

Breton, T; Sanchez-Gheno, J C; Alamilla, J L; Alvarez-Ramirez, J

2010-07-15

Spillover of hazardous materials from transport pipelines can lead to catastrophic events with serious and dangerous environmental impact, potential fire events and human fatalities. The problem is more serious for large pipelines when the construction material is under environmental corrosion conditions, as in the petroleum and gas industries. In this way, predictive models can provide a suitable framework for risk evaluation, maintenance policies and substitution procedure design that should be oriented to reduce increased hazards. This work proposes a bayesian probabilistic approach to identify and predict the type of failure (leakage or rupture) for steel pipelines under realistic corroding conditions. In the first step of the modeling process, the mechanical performance of the pipe is considered for establishing conditions under which either leakage or rupture failure can occur. In the second step, experimental burst tests are used to introduce a mean probabilistic boundary defining a region where the type of failure is uncertain. In the boundary vicinity, the failure discrimination is carried out with a probabilistic model where the events are considered as random variables. In turn, the model parameters are estimated with available experimental data and contrasted with a real catastrophic event, showing good discrimination capacity. The results are discussed in terms of policies oriented to inspection and maintenance of large-size pipelines in the oil and gas industry. 2010 Elsevier B.V. All rights reserved.

A Probabilistic Model of Social Working Memory for Information Retrieval in Social Interactions.

PubMed

Li, Liyuan; Xu, Qianli; Gan, Tian; Tan, Cheston; Lim, Joo-Hwee

2018-05-01

Social working memory (SWM) plays an important role in navigating social interactions. Inspired by studies in psychology, neuroscience, cognitive science, and machine learning, we propose a probabilistic model of SWM to mimic human social intelligence for personal information retrieval (IR) in social interactions. First, we establish a semantic hierarchy as social long-term memory to encode personal information. Next, we propose a semantic Bayesian network as the SWM, which integrates the cognitive functions of accessibility and self-regulation. One subgraphical model implements the accessibility function to learn the social consensus about IR-based on social information concept, clustering, social context, and similarity between persons. Beyond accessibility, one more layer is added to simulate the function of self-regulation to perform the personal adaptation to the consensus based on human personality. Two learning algorithms are proposed to train the probabilistic SWM model on a raw dataset of high uncertainty and incompleteness. One is an efficient learning algorithm of Newton's method, and the other is a genetic algorithm. Systematic evaluations show that the proposed SWM model is able to learn human social intelligence effectively and outperforms the baseline Bayesian cognitive model. Toward real-world applications, we implement our model on Google Glass as a wearable assistant for social interaction.

Uncertainty Estimation in Tsunami Initial Condition From Rapid Bayesian Finite Fault Modeling

NASA Astrophysics Data System (ADS)

Benavente, R. F.; Dettmer, J.; Cummins, P. R.; Urrutia, A.; Cienfuegos, R.

2017-12-01

It is well known that kinematic rupture models for a given earthquake can present discrepancies even when similar datasets are employed in the inversion process. While quantifying this variability can be critical when making early estimates of the earthquake and triggered tsunami impact, "most likely models" are normally used for this purpose. In this work, we quantify the uncertainty of the tsunami initial condition for the great Illapel earthquake (Mw = 8.3, 2015, Chile). We focus on utilizing data and inversion methods that are suitable to rapid source characterization yet provide meaningful and robust results. Rupture models from teleseismic body and surface waves as well as W-phase are derived and accompanied by Bayesian uncertainty estimates from linearized inversion under positivity constraints. We show that robust and consistent features about the rupture kinematics appear when working within this probabilistic framework. Moreover, by using static dislocation theory, we translate the probabilistic slip distributions into seafloor deformation which we interpret as a tsunami initial condition. After considering uncertainty, our probabilistic seafloor deformation models obtained from different data types appear consistent with each other providing meaningful results. We also show that selecting just a single "representative" solution from the ensemble of initial conditions for tsunami propagation may lead to overestimating information content in the data. Our results suggest that rapid, probabilistic rupture models can play a significant role during emergency response by providing robust information about the extent of the disaster.

Boosting Probabilistic Graphical Model Inference by Incorporating Prior Knowledge from Multiple Sources

PubMed Central

Praveen, Paurush; Fröhlich, Holger

2013-01-01

Inferring regulatory networks from experimental data via probabilistic graphical models is a popular framework to gain insights into biological systems. However, the inherent noise in experimental data coupled with a limited sample size reduces the performance of network reverse engineering. Prior knowledge from existing sources of biological information can address this low signal to noise problem by biasing the network inference towards biologically plausible network structures. Although integrating various sources of information is desirable, their heterogeneous nature makes this task challenging. We propose two computational methods to incorporate various information sources into a probabilistic consensus structure prior to be used in graphical model inference. Our first model, called Latent Factor Model (LFM), assumes a high degree of correlation among external information sources and reconstructs a hidden variable as a common source in a Bayesian manner. The second model, a Noisy-OR, picks up the strongest support for an interaction among information sources in a probabilistic fashion. Our extensive computational studies on KEGG signaling pathways as well as on gene expression data from breast cancer and yeast heat shock response reveal that both approaches can significantly enhance the reconstruction accuracy of Bayesian Networks compared to other competing methods as well as to the situation without any prior. Our framework allows for using diverse information sources, like pathway databases, GO terms and protein domain data, etc. and is flexible enough to integrate new sources, if available. PMID:23826291

Bayesian estimation of Karhunen–Loève expansions; A random subspace approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chowdhary, Kenny; Najm, Habib N.

One of the most widely-used statistical procedures for dimensionality reduction of high dimensional random fields is Principal Component Analysis (PCA), which is based on the Karhunen-Lo eve expansion (KLE) of a stochastic process with finite variance. The KLE is analogous to a Fourier series expansion for a random process, where the goal is to find an orthogonal transformation for the data such that the projection of the data onto this orthogonal subspace is optimal in the L 2 sense, i.e, which minimizes the mean square error. In practice, this orthogonal transformation is determined by performing an SVD (Singular Value Decomposition)more » on the sample covariance matrix or on the data matrix itself. Sampling error is typically ignored when quantifying the principal components, or, equivalently, basis functions of the KLE. Furthermore, it is exacerbated when the sample size is much smaller than the dimension of the random field. In this paper, we introduce a Bayesian KLE procedure, allowing one to obtain a probabilistic model on the principal components, which can account for inaccuracies due to limited sample size. The probabilistic model is built via Bayesian inference, from which the posterior becomes the matrix Bingham density over the space of orthonormal matrices. We use a modified Gibbs sampling procedure to sample on this space and then build a probabilistic Karhunen-Lo eve expansions over random subspaces to obtain a set of low-dimensional surrogates of the stochastic process. We illustrate this probabilistic procedure with a finite dimensional stochastic process inspired by Brownian motion.« less

Bayesian estimation of Karhunen–Loève expansions; A random subspace approach

DOE PAGES

Chowdhary, Kenny; Najm, Habib N.

2016-04-13

One of the most widely-used statistical procedures for dimensionality reduction of high dimensional random fields is Principal Component Analysis (PCA), which is based on the Karhunen-Lo eve expansion (KLE) of a stochastic process with finite variance. The KLE is analogous to a Fourier series expansion for a random process, where the goal is to find an orthogonal transformation for the data such that the projection of the data onto this orthogonal subspace is optimal in the L 2 sense, i.e, which minimizes the mean square error. In practice, this orthogonal transformation is determined by performing an SVD (Singular Value Decomposition)more » on the sample covariance matrix or on the data matrix itself. Sampling error is typically ignored when quantifying the principal components, or, equivalently, basis functions of the KLE. Furthermore, it is exacerbated when the sample size is much smaller than the dimension of the random field. In this paper, we introduce a Bayesian KLE procedure, allowing one to obtain a probabilistic model on the principal components, which can account for inaccuracies due to limited sample size. The probabilistic model is built via Bayesian inference, from which the posterior becomes the matrix Bingham density over the space of orthonormal matrices. We use a modified Gibbs sampling procedure to sample on this space and then build a probabilistic Karhunen-Lo eve expansions over random subspaces to obtain a set of low-dimensional surrogates of the stochastic process. We illustrate this probabilistic procedure with a finite dimensional stochastic process inspired by Brownian motion.« less

A probabilistic process model for pelagic marine ecosystems informed by Bayesian inverse analysis

EPA Science Inventory

Marine ecosystems are complex systems with multiple pathways that produce feedback cycles, which may lead to unanticipated effects. Models abstract this complexity and allow us to predict, understand, and hypothesize. In ecological models, however, the paucity of empirical data...

Data-driven Modeling of Metal-oxide Sensors with Dynamic Bayesian Networks

NASA Astrophysics Data System (ADS)

Gosangi, Rakesh; Gutierrez-Osuna, Ricardo

2011-09-01

We present a data-driven probabilistic framework to model the transient response of MOX sensors modulated with a sequence of voltage steps. Analytical models of MOX sensors are usually built based on the physico-chemical properties of the sensing materials. Although building these models provides an insight into the sensor behavior, they also require a thorough understanding of the underlying operating principles. Here we propose a data-driven approach to characterize the dynamical relationship between sensor inputs and outputs. Namely, we use dynamic Bayesian networks (DBNs), probabilistic models that represent temporal relations between a set of random variables. We identify a set of control variables that influence the sensor responses, create a graphical representation that captures the causal relations between these variables, and finally train the model with experimental data. We validated the approach on experimental data in terms of predictive accuracy and classification performance. Our results show that DBNs can accurately predict the dynamic response of MOX sensors, as well as capture the discriminatory information present in the sensor transients.

Bayesian networks and information theory for audio-visual perception modeling.

PubMed

Besson, Patricia; Richiardi, Jonas; Bourdin, Christophe; Bringoux, Lionel; Mestre, Daniel R; Vercher, Jean-Louis

2010-09-01

Thanks to their different senses, human observers acquire multiple information coming from their environment. Complex cross-modal interactions occur during this perceptual process. This article proposes a framework to analyze and model these interactions through a rigorous and systematic data-driven process. This requires considering the general relationships between the physical events or factors involved in the process, not only in quantitative terms, but also in term of the influence of one factor on another. We use tools from information theory and probabilistic reasoning to derive relationships between the random variables of interest, where the central notion is that of conditional independence. Using mutual information analysis to guide the model elicitation process, a probabilistic causal model encoded as a Bayesian network is obtained. We exemplify the method by using data collected in an audio-visual localization task for human subjects, and we show that it yields a well-motivated model with good predictive ability. The model elicitation process offers new prospects for the investigation of the cognitive mechanisms of multisensory perception.

Incorporating networks in a probabilistic graphical model to find drivers for complex human diseases.

PubMed

Mezlini, Aziz M; Goldenberg, Anna

2017-10-01

Discovering genetic mechanisms driving complex diseases is a hard problem. Existing methods often lack power to identify the set of responsible genes. Protein-protein interaction networks have been shown to boost power when detecting gene-disease associations. We introduce a Bayesian framework, Conflux, to find disease associated genes from exome sequencing data using networks as a prior. There are two main advantages to using networks within a probabilistic graphical model. First, networks are noisy and incomplete, a substantial impediment to gene discovery. Incorporating networks into the structure of a probabilistic models for gene inference has less impact on the solution than relying on the noisy network structure directly. Second, using a Bayesian framework we can keep track of the uncertainty of each gene being associated with the phenotype rather than returning a fixed list of genes. We first show that using networks clearly improves gene detection compared to individual gene testing. We then show consistently improved performance of Conflux compared to the state-of-the-art diffusion network-based method Hotnet2 and a variety of other network and variant aggregation methods, using randomly generated and literature-reported gene sets. We test Hotnet2 and Conflux on several network configurations to reveal biases and patterns of false positives and false negatives in each case. Our experiments show that our novel Bayesian framework Conflux incorporates many of the advantages of the current state-of-the-art methods, while offering more flexibility and improved power in many gene-disease association scenarios.

Specifying and Refining a Complex Measurement Model.

ERIC Educational Resources Information Center

Levy, Roy; Mislevy, Robert J.

This paper aims to describe a Bayesian approach to modeling and estimating cognitive models both in terms of statistical machinery and actual instrument development. Such a method taps the knowledge of experts to provide initial estimates for the probabilistic relationships among the variables in a multivariate latent variable model and refines…

A Bayesian Framework for False Belief Reasoning in Children: A Rational Integration of Theory-Theory and Simulation Theory

PubMed Central

Asakura, Nobuhiko; Inui, Toshio

2016-01-01

Two apparently contrasting theories have been proposed to account for the development of children's theory of mind (ToM): theory-theory and simulation theory. We present a Bayesian framework that rationally integrates both theories for false belief reasoning. This framework exploits two internal models for predicting the belief states of others: one of self and one of others. These internal models are responsible for simulation-based and theory-based reasoning, respectively. The framework further takes into account empirical studies of a developmental ToM scale (e.g., Wellman and Liu, 2004): developmental progressions of various mental state understandings leading up to false belief understanding. By representing the internal models and their interactions as a causal Bayesian network, we formalize the model of children's false belief reasoning as probabilistic computations on the Bayesian network. This model probabilistically weighs and combines the two internal models and predicts children's false belief ability as a multiplicative effect of their early-developed abilities to understand the mental concepts of diverse beliefs and knowledge access. Specifically, the model predicts that children's proportion of correct responses on a false belief task can be closely approximated as the product of their proportions correct on the diverse belief and knowledge access tasks. To validate this prediction, we illustrate that our model provides good fits to a variety of ToM scale data for preschool children. We discuss the implications and extensions of our model for a deeper understanding of developmental progressions of children's ToM abilities. PMID:28082941

A Bayesian Framework for False Belief Reasoning in Children: A Rational Integration of Theory-Theory and Simulation Theory.

PubMed

Asakura, Nobuhiko; Inui, Toshio

2016-01-01

Two apparently contrasting theories have been proposed to account for the development of children's theory of mind (ToM): theory-theory and simulation theory. We present a Bayesian framework that rationally integrates both theories for false belief reasoning. This framework exploits two internal models for predicting the belief states of others: one of self and one of others. These internal models are responsible for simulation-based and theory-based reasoning, respectively. The framework further takes into account empirical studies of a developmental ToM scale (e.g., Wellman and Liu, 2004): developmental progressions of various mental state understandings leading up to false belief understanding. By representing the internal models and their interactions as a causal Bayesian network, we formalize the model of children's false belief reasoning as probabilistic computations on the Bayesian network. This model probabilistically weighs and combines the two internal models and predicts children's false belief ability as a multiplicative effect of their early-developed abilities to understand the mental concepts of diverse beliefs and knowledge access. Specifically, the model predicts that children's proportion of correct responses on a false belief task can be closely approximated as the product of their proportions correct on the diverse belief and knowledge access tasks. To validate this prediction, we illustrate that our model provides good fits to a variety of ToM scale data for preschool children. We discuss the implications and extensions of our model for a deeper understanding of developmental progressions of children's ToM abilities.

Variational Bayesian Inversion of Quasi-Localized Seismic Attributes for the Spatial Distribution of Geological Facies

NASA Astrophysics Data System (ADS)

Nawaz, Muhammad Atif; Curtis, Andrew

2018-04-01

We introduce a new Bayesian inversion method that estimates the spatial distribution of geological facies from attributes of seismic data, by showing how the usual probabilistic inverse problem can be solved using an optimization framework still providing full probabilistic results. Our mathematical model consists of seismic attributes as observed data, which are assumed to have been generated by the geological facies. The method infers the post-inversion (posterior) probability density of the facies plus some other unknown model parameters, from the seismic attributes and geological prior information. Most previous research in this domain is based on the localized likelihoods assumption, whereby the seismic attributes at a location are assumed to depend on the facies only at that location. Such an assumption is unrealistic because of imperfect seismic data acquisition and processing, and fundamental limitations of seismic imaging methods. In this paper, we relax this assumption: we allow probabilistic dependence between seismic attributes at a location and the facies in any neighbourhood of that location through a spatial filter. We term such likelihoods quasi-localized.

Supernova Cosmology Inference with Probabilistic Photometric Redshifts (SCIPPR)

NASA Astrophysics Data System (ADS)

Peters, Christina; Malz, Alex; Hlozek, Renée

2018-01-01

The Bayesian Estimation Applied to Multiple Species (BEAMS) framework employs probabilistic supernova type classifications to do photometric SN cosmology. This work extends BEAMS to replace high-confidence spectroscopic redshifts with photometric redshift probability density functions, a capability that will be essential in the era the Large Synoptic Survey Telescope and other next-generation photometric surveys where it will not be possible to perform spectroscopic follow up on every SN. We present the Supernova Cosmology Inference with Probabilistic Photometric Redshifts (SCIPPR) Bayesian hierarchical model for constraining the cosmological parameters from photometric lightcurves and host galaxy photometry, which includes selection effects and is extensible to uncertainty in the redshift-dependent supernova type proportions. We create a pair of realistic mock catalogs of joint posteriors over supernova type, redshift, and distance modulus informed by photometric supernova lightcurves and over redshift from simulated host galaxy photometry. We perform inference under our model to obtain a joint posterior probability distribution over the cosmological parameters and compare our results with other methods, namely: a spectroscopic subset, a subset of high probability photometrically classified supernovae, and reducing the photometric redshift probability to a single measurement and error bar.

Bayesian Estimation of Small Effects in Exercise and Sports Science.

PubMed

Mengersen, Kerrie L; Drovandi, Christopher C; Robert, Christian P; Pyne, David B; Gore, Christopher J

2016-01-01

The aim of this paper is to provide a Bayesian formulation of the so-called magnitude-based inference approach to quantifying and interpreting effects, and in a case study example provide accurate probabilistic statements that correspond to the intended magnitude-based inferences. The model is described in the context of a published small-scale athlete study which employed a magnitude-based inference approach to compare the effect of two altitude training regimens (live high-train low (LHTL), and intermittent hypoxic exposure (IHE)) on running performance and blood measurements of elite triathletes. The posterior distributions, and corresponding point and interval estimates, for the parameters and associated effects and comparisons of interest, were estimated using Markov chain Monte Carlo simulations. The Bayesian analysis was shown to provide more direct probabilistic comparisons of treatments and able to identify small effects of interest. The approach avoided asymptotic assumptions and overcame issues such as multiple testing. Bayesian analysis of unscaled effects showed a probability of 0.96 that LHTL yields a substantially greater increase in hemoglobin mass than IHE, a 0.93 probability of a substantially greater improvement in running economy and a greater than 0.96 probability that both IHE and LHTL yield a substantially greater improvement in maximum blood lactate concentration compared to a Placebo. The conclusions are consistent with those obtained using a 'magnitude-based inference' approach that has been promoted in the field. The paper demonstrates that a fully Bayesian analysis is a simple and effective way of analysing small effects, providing a rich set of results that are straightforward to interpret in terms of probabilistic statements.

Probabilistic Prognosis of Non-Planar Fatigue Crack Growth

NASA Technical Reports Server (NTRS)

Leser, Patrick E.; Newman, John A.; Warner, James E.; Leser, William P.; Hochhalter, Jacob D.; Yuan, Fuh-Gwo

2016-01-01

Quantifying the uncertainty in model parameters for the purpose of damage prognosis can be accomplished utilizing Bayesian inference and damage diagnosis data from sources such as non-destructive evaluation or structural health monitoring. The number of samples required to solve the Bayesian inverse problem through common sampling techniques (e.g., Markov chain Monte Carlo) renders high-fidelity finite element-based damage growth models unusable due to prohibitive computation times. However, these types of models are often the only option when attempting to model complex damage growth in real-world structures. Here, a recently developed high-fidelity crack growth model is used which, when compared to finite element-based modeling, has demonstrated reductions in computation times of three orders of magnitude through the use of surrogate models and machine learning. The model is flexible in that only the expensive computation of the crack driving forces is replaced by the surrogate models, leaving the remaining parameters accessible for uncertainty quantification. A probabilistic prognosis framework incorporating this model is developed and demonstrated for non-planar crack growth in a modified, edge-notched, aluminum tensile specimen. Predictions of remaining useful life are made over time for five updates of the damage diagnosis data, and prognostic metrics are utilized to evaluate the performance of the prognostic framework. Challenges specific to the probabilistic prognosis of non-planar fatigue crack growth are highlighted and discussed in the context of the experimental results.

Précis of bayesian rationality: The probabilistic approach to human reasoning.

PubMed

Oaksford, Mike; Chater, Nick

2009-02-01

According to Aristotle, humans are the rational animal. The borderline between rationality and irrationality is fundamental to many aspects of human life including the law, mental health, and language interpretation. But what is it to be rational? One answer, deeply embedded in the Western intellectual tradition since ancient Greece, is that rationality concerns reasoning according to the rules of logic--the formal theory that specifies the inferential connections that hold with certainty between propositions. Piaget viewed logical reasoning as defining the end-point of cognitive development; and contemporary psychology of reasoning has focussed on comparing human reasoning against logical standards. Bayesian Rationality argues that rationality is defined instead by the ability to reason about uncertainty. Although people are typically poor at numerical reasoning about probability, human thought is sensitive to subtle patterns of qualitative Bayesian, probabilistic reasoning. In Chapters 1-4 of Bayesian Rationality (Oaksford & Chater 2007), the case is made that cognition in general, and human everyday reasoning in particular, is best viewed as solving probabilistic, rather than logical, inference problems. In Chapters 5-7 the psychology of "deductive" reasoning is tackled head-on: It is argued that purportedly "logical" reasoning problems, revealing apparently irrational behaviour, are better understood from a probabilistic point of view. Data from conditional reasoning, Wason's selection task, and syllogistic inference are captured by recasting these problems probabilistically. The probabilistic approach makes a variety of novel predictions which have been experimentally confirmed. The book considers the implications of this work, and the wider "probabilistic turn" in cognitive science and artificial intelligence, for understanding human rationality.

Predicting coastal cliff erosion using a Bayesian probabilistic model

USGS Publications Warehouse

Hapke, Cheryl J.; Plant, Nathaniel G.

2010-01-01

Regional coastal cliff retreat is difficult to model due to the episodic nature of failures and the along-shore variability of retreat events. There is a growing demand, however, for predictive models that can be used to forecast areas vulnerable to coastal erosion hazards. Increasingly, probabilistic models are being employed that require data sets of high temporal density to define the joint probability density function that relates forcing variables (e.g. wave conditions) and initial conditions (e.g. cliff geometry) to erosion events. In this study we use a multi-parameter Bayesian network to investigate correlations between key variables that control and influence variations in cliff retreat processes. The network uses Bayesian statistical methods to estimate event probabilities using existing observations. Within this framework, we forecast the spatial distribution of cliff retreat along two stretches of cliffed coast in Southern California. The input parameters are the height and slope of the cliff, a descriptor of material strength based on the dominant cliff-forming lithology, and the long-term cliff erosion rate that represents prior behavior. The model is forced using predicted wave impact hours. Results demonstrate that the Bayesian approach is well-suited to the forward modeling of coastal cliff retreat, with the correct outcomes forecast in 70–90% of the modeled transects. The model also performs well in identifying specific locations of high cliff erosion, thus providing a foundation for hazard mapping. This approach can be employed to predict cliff erosion at time-scales ranging from storm events to the impacts of sea-level rise at the century-scale.

Impact assessment of extreme storm events using a Bayesian network

USGS Publications Warehouse

den Heijer, C.(Kees); Knipping, Dirk T.J.A.; Plant, Nathaniel G.; van Thiel de Vries, Jaap S. M.; Baart, Fedor; van Gelder, Pieter H. A. J. M.

2012-01-01

This paper describes an investigation on the usefulness of Bayesian Networks in the safety assessment of dune coasts. A network has been created that predicts the erosion volume based on hydraulic boundary conditions and a number of cross-shore profile indicators. Field measurement data along a large part of the Dutch coast has been used to train the network. Corresponding storm impact on the dunes was calculated with an empirical dune erosion model named duros+. Comparison between the Bayesian Network predictions and the original duros+ results, here considered as observations, results in a skill up to 0.88, provided that the training data covers the range of predictions. Hence, the predictions from a deterministic model (duros+) can be captured in a probabilistic model (Bayesian Network) such that both the process knowledge and uncertainties can be included in impact and vulnerability assessments.

Bayesian analysis of rare events

DOE Office of Scientific and Technical Information (OSTI.GOV)

Straub, Daniel, E-mail: straub@tum.de; Papaioannou, Iason; Betz, Wolfgang

2016-06-01

In many areas of engineering and science there is an interest in predicting the probability of rare events, in particular in applications related to safety and security. Increasingly, such predictions are made through computer models of physical systems in an uncertainty quantification framework. Additionally, with advances in IT, monitoring and sensor technology, an increasing amount of data on the performance of the systems is collected. This data can be used to reduce uncertainty, improve the probability estimates and consequently enhance the management of rare events and associated risks. Bayesian analysis is the ideal method to include the data into themore » probabilistic model. It ensures a consistent probabilistic treatment of uncertainty, which is central in the prediction of rare events, where extrapolation from the domain of observation is common. We present a framework for performing Bayesian updating of rare event probabilities, termed BUS. It is based on a reinterpretation of the classical rejection-sampling approach to Bayesian analysis, which enables the use of established methods for estimating probabilities of rare events. By drawing upon these methods, the framework makes use of their computational efficiency. These methods include the First-Order Reliability Method (FORM), tailored importance sampling (IS) methods and Subset Simulation (SuS). In this contribution, we briefly review these methods in the context of the BUS framework and investigate their applicability to Bayesian analysis of rare events in different settings. We find that, for some applications, FORM can be highly efficient and is surprisingly accurate, enabling Bayesian analysis of rare events with just a few model evaluations. In a general setting, BUS implemented through IS and SuS is more robust and flexible.« less

The meta-Gaussian Bayesian Processor of forecasts and associated preliminary experiments

NASA Astrophysics Data System (ADS)

Chen, Fajing; Jiao, Meiyan; Chen, Jing

2013-04-01

Public weather services are trending toward providing users with probabilistic weather forecasts, in place of traditional deterministic forecasts. Probabilistic forecasting techniques are continually being improved to optimize available forecasting information. The Bayesian Processor of Forecast (BPF), a new statistical method for probabilistic forecast, can transform a deterministic forecast into a probabilistic forecast according to the historical statistical relationship between observations and forecasts generated by that forecasting system. This technique accounts for the typical forecasting performance of a deterministic forecasting system in quantifying the forecast uncertainty. The meta-Gaussian likelihood model is suitable for a variety of stochastic dependence structures with monotone likelihood ratios. The meta-Gaussian BPF adopting this kind of likelihood model can therefore be applied across many fields, including meteorology and hydrology. The Bayes theorem with two continuous random variables and the normal-linear BPF are briefly introduced. The meta-Gaussian BPF for a continuous predictand using a single predictor is then presented and discussed. The performance of the meta-Gaussian BPF is tested in a preliminary experiment. Control forecasts of daily surface temperature at 0000 UTC at Changsha and Wuhan stations are used as the deterministic forecast data. These control forecasts are taken from ensemble predictions with a 96-h lead time generated by the National Meteorological Center of the China Meteorological Administration, the European Centre for Medium-Range Weather Forecasts, and the US National Centers for Environmental Prediction during January 2008. The results of the experiment show that the meta-Gaussian BPF can transform a deterministic control forecast of surface temperature from any one of the three ensemble predictions into a useful probabilistic forecast of surface temperature. These probabilistic forecasts quantify the uncertainty of the control forecast; accordingly, the performance of the probabilistic forecasts differs based on the source of the underlying deterministic control forecasts.

Flood quantile estimation at ungauged sites by Bayesian networks

NASA Astrophysics Data System (ADS)

Mediero, L.; Santillán, D.; Garrote, L.

2012-04-01

Estimating flood quantiles at a site for which no observed measurements are available is essential for water resources planning and management. Ungauged sites have no observations about the magnitude of floods, but some site and basin characteristics are known. The most common technique used is the multiple regression analysis, which relates physical and climatic basin characteristic to flood quantiles. Regression equations are fitted from flood frequency data and basin characteristics at gauged sites. Regression equations are a rigid technique that assumes linear relationships between variables and cannot take the measurement errors into account. In addition, the prediction intervals are estimated in a very simplistic way from the variance of the residuals in the estimated model. Bayesian networks are a probabilistic computational structure taken from the field of Artificial Intelligence, which have been widely and successfully applied to many scientific fields like medicine and informatics, but application to the field of hydrology is recent. Bayesian networks infer the joint probability distribution of several related variables from observations through nodes, which represent random variables, and links, which represent causal dependencies between them. A Bayesian network is more flexible than regression equations, as they capture non-linear relationships between variables. In addition, the probabilistic nature of Bayesian networks allows taking the different sources of estimation uncertainty into account, as they give a probability distribution as result. A homogeneous region in the Tagus Basin was selected as case study. A regression equation was fitted taking the basin area, the annual maximum 24-hour rainfall for a given recurrence interval and the mean height as explanatory variables. Flood quantiles at ungauged sites were estimated by Bayesian networks. Bayesian networks need to be learnt from a huge enough data set. As observational data are reduced, a stochastic generator of synthetic data was developed. Synthetic basin characteristics were randomised, keeping the statistical properties of observed physical and climatic variables in the homogeneous region. The synthetic flood quantiles were stochastically generated taking the regression equation as basis. The learnt Bayesian network was validated by the reliability diagram, the Brier Score and the ROC diagram, which are common measures used in the validation of probabilistic forecasts. Summarising, the flood quantile estimations through Bayesian networks supply information about the prediction uncertainty as a probability distribution function of discharges is given as result. Therefore, the Bayesian network model has application as a decision support for water resources and planning management.

Development and comparison in uncertainty assessment based Bayesian modularization method in hydrological modeling

NASA Astrophysics Data System (ADS)

Li, Lu; Xu, Chong-Yu; Engeland, Kolbjørn

2013-04-01

SummaryWith respect to model calibration, parameter estimation and analysis of uncertainty sources, various regression and probabilistic approaches are used in hydrological modeling. A family of Bayesian methods, which incorporates different sources of information into a single analysis through Bayes' theorem, is widely used for uncertainty assessment. However, none of these approaches can well treat the impact of high flows in hydrological modeling. This study proposes a Bayesian modularization uncertainty assessment approach in which the highest streamflow observations are treated as suspect information that should not influence the inference of the main bulk of the model parameters. This study includes a comprehensive comparison and evaluation of uncertainty assessments by our new Bayesian modularization method and standard Bayesian methods using the Metropolis-Hastings (MH) algorithm with the daily hydrological model WASMOD. Three likelihood functions were used in combination with standard Bayesian method: the AR(1) plus Normal model independent of time (Model 1), the AR(1) plus Normal model dependent on time (Model 2) and the AR(1) plus Multi-normal model (Model 3). The results reveal that the Bayesian modularization method provides the most accurate streamflow estimates measured by the Nash-Sutcliffe efficiency and provide the best in uncertainty estimates for low, medium and entire flows compared to standard Bayesian methods. The study thus provides a new approach for reducing the impact of high flows on the discharge uncertainty assessment of hydrological models via Bayesian method.

A Bayesian Attractor Model for Perceptual Decision Making

PubMed Central

Bitzer, Sebastian; Bruineberg, Jelle; Kiebel, Stefan J.

2015-01-01

Even for simple perceptual decisions, the mechanisms that the brain employs are still under debate. Although current consensus states that the brain accumulates evidence extracted from noisy sensory information, open questions remain about how this simple model relates to other perceptual phenomena such as flexibility in decisions, decision-dependent modulation of sensory gain, or confidence about a decision. We propose a novel approach of how perceptual decisions are made by combining two influential formalisms into a new model. Specifically, we embed an attractor model of decision making into a probabilistic framework that models decision making as Bayesian inference. We show that the new model can explain decision making behaviour by fitting it to experimental data. In addition, the new model combines for the first time three important features: First, the model can update decisions in response to switches in the underlying stimulus. Second, the probabilistic formulation accounts for top-down effects that may explain recent experimental findings of decision-related gain modulation of sensory neurons. Finally, the model computes an explicit measure of confidence which we relate to recent experimental evidence for confidence computations in perceptual decision tasks. PMID:26267143

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pichara, Karim; Protopapas, Pavlos

We present an automatic classification method for astronomical catalogs with missing data. We use Bayesian networks and a probabilistic graphical model that allows us to perform inference to predict missing values given observed data and dependency relationships between variables. To learn a Bayesian network from incomplete data, we use an iterative algorithm that utilizes sampling methods and expectation maximization to estimate the distributions and probabilistic dependencies of variables from data with missing values. To test our model, we use three catalogs with missing data (SAGE, Two Micron All Sky Survey, and UBVI) and one complete catalog (MACHO). We examine howmore » classification accuracy changes when information from missing data catalogs is included, how our method compares to traditional missing data approaches, and at what computational cost. Integrating these catalogs with missing data, we find that classification of variable objects improves by a few percent and by 15% for quasar detection while keeping the computational cost the same.« less

Organism-level models: When mechanisms and statistics fail us

NASA Astrophysics Data System (ADS)

Phillips, M. H.; Meyer, J.; Smith, W. P.; Rockhill, J. K.

2014-03-01

Purpose: To describe the unique characteristics of models that represent the entire course of radiation therapy at the organism level and to highlight the uses to which such models can be put. Methods: At the level of an organism, traditional model-building runs into severe difficulties. We do not have sufficient knowledge to devise a complete biochemistry-based model. Statistical model-building fails due to the vast number of variables and the inability to control many of them in any meaningful way. Finally, building surrogate models, such as animal-based models, can result in excluding some of the most critical variables. Bayesian probabilistic models (Bayesian networks) provide a useful alternative that have the advantages of being mathematically rigorous, incorporating the knowledge that we do have, and being practical. Results: Bayesian networks representing radiation therapy pathways for prostate cancer and head & neck cancer were used to highlight the important aspects of such models and some techniques of model-building. A more specific model representing the treatment of occult lymph nodes in head & neck cancer were provided as an example of how such a model can inform clinical decisions. A model of the possible role of PET imaging in brain cancer was used to illustrate the means by which clinical trials can be modelled in order to come up with a trial design that will have meaningful outcomes. Conclusions: Probabilistic models are currently the most useful approach to representing the entire therapy outcome process.

Probabilistic evaluation of n traces with no putative source: A likelihood ratio based approach in an investigative framework.

PubMed

De March, I; Sironi, E; Taroni, F

2016-09-01

Analysis of marks recovered from different crime scenes can be useful to detect a linkage between criminal cases, even though a putative source for the recovered traces is not available. This particular circumstance is often encountered in the early stage of investigations and thus, the evaluation of evidence association may provide useful information for the investigators. This association is evaluated here from a probabilistic point of view: a likelihood ratio based approach is suggested in order to quantify the strength of the evidence of trace association in the light of two mutually exclusive propositions, namely that the n traces come from a common source or from an unspecified number of sources. To deal with this kind of problem, probabilistic graphical models are used, in form of Bayesian networks and object-oriented Bayesian networks, allowing users to intuitively handle with uncertainty related to the inferential problem. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

A Bayesian-based two-stage inexact optimization method for supporting stream water quality management in the Three Gorges Reservoir region.

PubMed

Hu, X H; Li, Y P; Huang, G H; Zhuang, X W; Ding, X W

2016-05-01

In this study, a Bayesian-based two-stage inexact optimization (BTIO) method is developed for supporting water quality management through coupling Bayesian analysis with interval two-stage stochastic programming (ITSP). The BTIO method is capable of addressing uncertainties caused by insufficient inputs in water quality model as well as uncertainties expressed as probabilistic distributions and interval numbers. The BTIO method is applied to a real case of water quality management for the Xiangxi River basin in the Three Gorges Reservoir region to seek optimal water quality management schemes under various uncertainties. Interval solutions for production patterns under a range of probabilistic water quality constraints have been generated. Results obtained demonstrate compromises between the system benefit and the system failure risk due to inherent uncertainties that exist in various system components. Moreover, information about pollutant emission is accomplished, which would help managers to adjust production patterns of regional industry and local policies considering interactions of water quality requirement, economic benefit, and industry structure.

Bayesian Action–Perception Computational Model: Interaction of Production and Recognition of Cursive Letters

PubMed Central

Gilet, Estelle; Diard, Julien; Bessière, Pierre

2011-01-01

In this paper, we study the collaboration of perception and action representations involved in cursive letter recognition and production. We propose a mathematical formulation for the whole perception–action loop, based on probabilistic modeling and Bayesian inference, which we call the Bayesian Action–Perception (BAP) model. Being a model of both perception and action processes, the purpose of this model is to study the interaction of these processes. More precisely, the model includes a feedback loop from motor production, which implements an internal simulation of movement. Motor knowledge can therefore be involved during perception tasks. In this paper, we formally define the BAP model and show how it solves the following six varied cognitive tasks using Bayesian inference: i) letter recognition (purely sensory), ii) writer recognition, iii) letter production (with different effectors), iv) copying of trajectories, v) copying of letters, and vi) letter recognition (with internal simulation of movements). We present computer simulations of each of these cognitive tasks, and discuss experimental predictions and theoretical developments. PMID:21674043

Bayesian exponential random graph modelling of interhospital patient referral networks.

PubMed

Caimo, Alberto; Pallotti, Francesca; Lomi, Alessandro

2017-08-15

Using original data that we have collected on referral relations between 110 hospitals serving a large regional community, we show how recently derived Bayesian exponential random graph models may be adopted to illuminate core empirical issues in research on relational coordination among healthcare organisations. We show how a rigorous Bayesian computation approach supports a fully probabilistic analytical framework that alleviates well-known problems in the estimation of model parameters of exponential random graph models. We also show how the main structural features of interhospital patient referral networks that prior studies have described can be reproduced with accuracy by specifying the system of local dependencies that produce - but at the same time are induced by - decentralised collaborative arrangements between hospitals. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

A novel Bayesian respiratory motion model to estimate and resolve uncertainty in image-guided cardiac interventions.

PubMed

Peressutti, Devis; Penney, Graeme P; Housden, R James; Kolbitsch, Christoph; Gomez, Alberto; Rijkhorst, Erik-Jan; Barratt, Dean C; Rhode, Kawal S; King, Andrew P

2013-05-01

In image-guided cardiac interventions, respiratory motion causes misalignments between the pre-procedure roadmap of the heart used for guidance and the intra-procedure position of the heart, reducing the accuracy of the guidance information and leading to potentially dangerous consequences. We propose a novel technique for motion-correcting the pre-procedural information that combines a probabilistic MRI-derived affine motion model with intra-procedure real-time 3D echocardiography (echo) images in a Bayesian framework. The probabilistic model incorporates a measure of confidence in its motion estimates which enables resolution of the potentially conflicting information supplied by the model and the echo data. Unlike models proposed so far, our method allows the final motion estimate to deviate from the model-produced estimate according to the information provided by the echo images, so adapting to the complex variability of respiratory motion. The proposed method is evaluated using gold-standard MRI-derived motion fields and simulated 3D echo data for nine volunteers and real 3D live echo images for four volunteers. The Bayesian method is compared to 5 other motion estimation techniques and results show mean/max improvements in estimation accuracy of 10.6%/18.9% for simulated echo images and 20.8%/41.5% for real 3D live echo data, over the best comparative estimation method. Copyright © 2013 Elsevier B.V. All rights reserved.

Data free inference with processed data products

DOE PAGES

Chowdhary, K.; Najm, H. N.

2014-07-12

Here, we consider the context of probabilistic inference of model parameters given error bars or confidence intervals on model output values, when the data is unavailable. We introduce a class of algorithms in a Bayesian framework, relying on maximum entropy arguments and approximate Bayesian computation methods, to generate consistent data with the given summary statistics. Once we obtain consistent data sets, we pool the respective posteriors, to arrive at a single, averaged density on the parameters. This approach allows us to perform accurate forward uncertainty propagation consistent with the reported statistics.

Theory Learning as Stochastic Search in the Language of Thought

ERIC Educational Resources Information Center

Ullman, Tomer D.; Goodman, Noah D.; Tenenbaum, Joshua B.

2012-01-01

We present an algorithmic model for the development of children's intuitive theories within a hierarchical Bayesian framework, where theories are described as sets of logical laws generated by a probabilistic context-free grammar. We contrast our approach with connectionist and other emergentist approaches to modeling cognitive development. While…

A Bayesian Framework for Analysis of Pseudo-Spatial Models of Comparable Engineered Systems with Application to Spacecraft Anomaly Prediction Based on Precedent Data

NASA Astrophysics Data System (ADS)

Ndu, Obibobi Kamtochukwu

To ensure that estimates of risk and reliability inform design and resource allocation decisions in the development of complex engineering systems, early engagement in the design life cycle is necessary. An unfortunate constraint on the accuracy of such estimates at this stage of concept development is the limited amount of high fidelity design and failure information available on the actual system under development. Applying the human ability to learn from experience and augment our state of knowledge to evolve better solutions mitigates this limitation. However, the challenge lies in formalizing a methodology that takes this highly abstract, but fundamentally human cognitive, ability and extending it to the field of risk analysis while maintaining the tenets of generalization, Bayesian inference, and probabilistic risk analysis. We introduce an integrated framework for inferring the reliability, or other probabilistic measures of interest, of a new system or a conceptual variant of an existing system. Abstractly, our framework is based on learning from the performance of precedent designs and then applying the acquired knowledge, appropriately adjusted based on degree of relevance, to the inference process. This dissertation presents a method for inferring properties of the conceptual variant using a pseudo-spatial model that describes the spatial configuration of the family of systems to which the concept belongs. Through non-metric multidimensional scaling, we formulate the pseudo-spatial model based on rank-ordered subjective expert perception of design similarity between systems that elucidate the psychological space of the family. By a novel extension of Kriging methods for analysis of geospatial data to our "pseudo-space of comparable engineered systems", we develop a Bayesian inference model that allows prediction of the probabilistic measure of interest.

Multi-dimensional classification of GABAergic interneurons with Bayesian network-modeled label uncertainty.

PubMed

Mihaljević, Bojan; Bielza, Concha; Benavides-Piccione, Ruth; DeFelipe, Javier; Larrañaga, Pedro

2014-01-01

Interneuron classification is an important and long-debated topic in neuroscience. A recent study provided a data set of digitally reconstructed interneurons classified by 42 leading neuroscientists according to a pragmatic classification scheme composed of five categorical variables, namely, of the interneuron type and four features of axonal morphology. From this data set we now learned a model which can classify interneurons, on the basis of their axonal morphometric parameters, into these five descriptive variables simultaneously. Because of differences in opinion among the neuroscientists, especially regarding neuronal type, for many interneurons we lacked a unique, agreed-upon classification, which we could use to guide model learning. Instead, we guided model learning with a probability distribution over the neuronal type and the axonal features, obtained, for each interneuron, from the neuroscientists' classification choices. We conveniently encoded such probability distributions with Bayesian networks, calling them label Bayesian networks (LBNs), and developed a method to predict them. This method predicts an LBN by forming a probabilistic consensus among the LBNs of the interneurons most similar to the one being classified. We used 18 axonal morphometric parameters as predictor variables, 13 of which we introduce in this paper as quantitative counterparts to the categorical axonal features. We were able to accurately predict interneuronal LBNs. Furthermore, when extracting crisp (i.e., non-probabilistic) predictions from the predicted LBNs, our method outperformed related work on interneuron classification. Our results indicate that our method is adequate for multi-dimensional classification of interneurons with probabilistic labels. Moreover, the introduced morphometric parameters are good predictors of interneuron type and the four features of axonal morphology and thus may serve as objective counterparts to the subjective, categorical axonal features.

Bayesian Probability Theory

NASA Astrophysics Data System (ADS)

von der Linden, Wolfgang; Dose, Volker; von Toussaint, Udo

2014-06-01

Preface; Part I. Introduction: 1. The meaning of probability; 2. Basic definitions; 3. Bayesian inference; 4. Combinatrics; 5. Random walks; 6. Limit theorems; 7. Continuous distributions; 8. The central limit theorem; 9. Poisson processes and waiting times; Part II. Assigning Probabilities: 10. Transformation invariance; 11. Maximum entropy; 12. Qualified maximum entropy; 13. Global smoothness; Part III. Parameter Estimation: 14. Bayesian parameter estimation; 15. Frequentist parameter estimation; 16. The Cramer-Rao inequality; Part IV. Testing Hypotheses: 17. The Bayesian way; 18. The frequentist way; 19. Sampling distributions; 20. Bayesian vs frequentist hypothesis tests; Part V. Real World Applications: 21. Regression; 22. Inconsistent data; 23. Unrecognized signal contributions; 24. Change point problems; 25. Function estimation; 26. Integral equations; 27. Model selection; 28. Bayesian experimental design; Part VI. Probabilistic Numerical Techniques: 29. Numerical integration; 30. Monte Carlo methods; 31. Nested sampling; Appendixes; References; Index.

Groundwater Remediation using Bayesian Information-Gap Decision Theory

NASA Astrophysics Data System (ADS)

O'Malley, D.; Vesselinov, V. V.

2016-12-01

Probabilistic analyses of groundwater remediation scenarios frequently fail because the probability of an adverse, unanticipated event occurring is often high. In general, models of flow and transport in contaminated aquifers are always simpler than reality. Further, when a probabilistic analysis is performed, probability distributions are usually chosen more for convenience than correctness. The Bayesian Information-Gap Decision Theory (BIGDT) was designed to mitigate the shortcomings of the models and probabilistic decision analyses by leveraging a non-probabilistic decision theory - information-gap decision theory. BIGDT considers possible models that have not been explicitly enumerated and does not require us to commit to a particular probability distribution for model and remediation-design parameters. Both the set of possible models and the set of possible probability distributions grow as the degree of uncertainty increases. The fundamental question that BIGDT asks is "How large can these sets be before a particular decision results in an undesirable outcome?". The decision that allows these sets to be the largest is considered to be the best option. In this way, BIGDT enables robust decision-support for groundwater remediation problems. Here we apply BIGDT to in a representative groundwater remediation scenario where different options for hydraulic containment and pump & treat are being considered. BIGDT requires many model runs and for complex models high-performance computing resources are needed. These analyses are carried out on synthetic problems, but are applicable to real-world problems such as LANL site contaminations. BIGDT is implemented in Julia (a high-level, high-performance dynamic programming language for technical computing) and is part of the MADS framework (http://mads.lanl.gov/ and https://github.com/madsjulia/Mads.jl).

Probabilistic estimation of dune retreat on the Gold Coast, Australia

USGS Publications Warehouse

Palmsten, Margaret L.; Splinter, Kristen D.; Plant, Nathaniel G.; Stockdon, Hilary F.

2014-01-01

Sand dunes are an important natural buffer between storm impacts and development backing the beach on the Gold Coast of Queensland, Australia. The ability to forecast dune erosion at a prediction horizon of days to a week would allow efficient and timely response to dune erosion in this highly populated area. Towards this goal, we modified an existing probabilistic dune erosion model for use on the Gold Coast. The original model was trained using observations of dune response from Hurricane Ivan on Santa Rosa Island, Florida, USA (Plant and Stockdon 2012. Probabilistic prediction of barrier-island response to hurricanes, Journal of Geophysical Research, 117(F3), F03015). The model relates dune position change to pre-storm dune elevations, dune widths, and beach widths, along with storm surge and run-up using a Bayesian network. The Bayesian approach captures the uncertainty of inputs and predictions through the conditional probabilities between variables. Three versions of the barrier island response Bayesian network were tested for use on the Gold Coast. One network has the same structure as the original and was trained with the Santa Rosa Island data. The second network has a modified design and was trained using only pre- and post-storm data from 1988-2009 for the Gold Coast. The third version of the network has the same design as the second version of the network and was trained with the combined data from the Gold Coast and Santa Rosa Island. The two networks modified for use on the Gold Coast hindcast dune retreat with equal accuracy. Both networks explained 60% of the observed dune retreat variance, which is comparable to the skill observed by Plant and Stockdon (2012) in the initial Bayesian network application at Santa Rosa Island. The new networks improved predictions relative to application of the original network on the Gold Coast. Dune width was the most important morphologic variable in hindcasting dune retreat, while hydrodynamic variables, surge and run-up elevation, were also important

Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks

PubMed Central

Lähdesmäki, Harri; Hautaniemi, Sampsa; Shmulevich, Ilya; Yli-Harja, Olli

2006-01-01

A significant amount of attention has recently been focused on modeling of gene regulatory networks. Two frequently used large-scale modeling frameworks are Bayesian networks (BNs) and Boolean networks, the latter one being a special case of its recent stochastic extension, probabilistic Boolean networks (PBNs). PBN is a promising model class that generalizes the standard rule-based interactions of Boolean networks into the stochastic setting. Dynamic Bayesian networks (DBNs) is a general and versatile model class that is able to represent complex temporal stochastic processes and has also been proposed as a model for gene regulatory systems. In this paper, we concentrate on these two model classes and demonstrate that PBNs and a certain subclass of DBNs can represent the same joint probability distribution over their common variables. The major benefit of introducing the relationships between the models is that it opens up the possibility of applying the standard tools of DBNs to PBNs and vice versa. Hence, the standard learning tools of DBNs can be applied in the context of PBNs, and the inference methods give a natural way of handling the missing values in PBNs which are often present in gene expression measurements. Conversely, the tools for controlling the stationary behavior of the networks, tools for projecting networks onto sub-networks, and efficient learning schemes can be used for DBNs. In other words, the introduced relationships between the models extend the collection of analysis tools for both model classes. PMID:17415411

Neural network modeling and an uncertainty analysis in Bayesian framework: A case study from the KTB borehole site

NASA Astrophysics Data System (ADS)

Maiti, Saumen; Tiwari, Ram Krishna

2010-10-01

A new probabilistic approach based on the concept of Bayesian neural network (BNN) learning theory is proposed for decoding litho-facies boundaries from well-log data. We show that how a multi-layer-perceptron neural network model can be employed in Bayesian framework to classify changes in litho-log successions. The method is then applied to the German Continental Deep Drilling Program (KTB) well-log data for classification and uncertainty estimation in the litho-facies boundaries. In this framework, a posteriori distribution of network parameter is estimated via the principle of Bayesian probabilistic theory, and an objective function is minimized following the scaled conjugate gradient optimization scheme. For the model development, we inflict a suitable criterion, which provides probabilistic information by emulating different combinations of synthetic data. Uncertainty in the relationship between the data and the model space is appropriately taken care by assuming a Gaussian a priori distribution of networks parameters (e.g., synaptic weights and biases). Prior to applying the new method to the real KTB data, we tested the proposed method on synthetic examples to examine the sensitivity of neural network hyperparameters in prediction. Within this framework, we examine stability and efficiency of this new probabilistic approach using different kinds of synthetic data assorted with different level of correlated noise. Our data analysis suggests that the designed network topology based on the Bayesian paradigm is steady up to nearly 40% correlated noise; however, adding more noise (˜50% or more) degrades the results. We perform uncertainty analyses on training, validation, and test data sets with and devoid of intrinsic noise by making the Gaussian approximation of the a posteriori distribution about the peak model. We present a standard deviation error-map at the network output corresponding to the three types of the litho-facies present over the entire litho-section of the KTB. The comparisons of maximum a posteriori geological sections constructed here, based on the maximum a posteriori probability distribution, with the available geological information and the existing geophysical findings suggest that the BNN results reveal some additional finer details in the KTB borehole data at certain depths, which appears to be of some geological significance. We also demonstrate that the proposed BNN approach is superior to the conventional artificial neural network in terms of both avoiding "over-fitting" and aiding uncertainty estimation, which are vital for meaningful interpretation of geophysical records. Our analyses demonstrate that the BNN-based approach renders a robust means for the classification of complex changes in the litho-facies successions and thus could provide a useful guide for understanding the crustal inhomogeneity and the structural discontinuity in many other tectonically complex regions.

Probabilistic techniques for obtaining accurate patient counts in Clinical Data Warehouses

PubMed Central

Myers, Risa B.; Herskovic, Jorge R.

2011-01-01

Proposal and execution of clinical trials, computation of quality measures and discovery of correlation between medical phenomena are all applications where an accurate count of patients is needed. However, existing sources of this type of patient information, including Clinical Data Warehouses (CDW) may be incomplete or inaccurate. This research explores applying probabilistic techniques, supported by the MayBMS probabilistic database, to obtain accurate patient counts from a clinical data warehouse containing synthetic patient data. We present a synthetic clinical data warehouse (CDW), and populate it with simulated data using a custom patient data generation engine. We then implement, evaluate and compare different techniques for obtaining patients counts. We model billing as a test for the presence of a condition. We compute billing’s sensitivity and specificity both by conducting a “Simulated Expert Review” where a representative sample of records are reviewed and labeled by experts, and by obtaining the ground truth for every record. We compute the posterior probability of a patient having a condition through a “Bayesian Chain”, using Bayes’ Theorem to calculate the probability of a patient having a condition after each visit. The second method is a “one-shot” approach that computes the probability of a patient having a condition based on whether the patient is ever billed for the condition Our results demonstrate the utility of probabilistic approaches, which improve on the accuracy of raw counts. In particular, the simulated review paired with a single application of Bayes’ Theorem produces the best results, with an average error rate of 2.1% compared to 43.7% for the straightforward billing counts. Overall, this research demonstrates that Bayesian probabilistic approaches improve patient counts on simulated patient populations. We believe that total patient counts based on billing data are one of the many possible applications of our Bayesian framework. Use of these probabilistic techniques will enable more accurate patient counts and better results for applications requiring this metric. PMID:21986292

A Bayesian Developmental Approach to Robotic Goal-Based Imitation Learning.

PubMed

Chung, Michael Jae-Yoon; Friesen, Abram L; Fox, Dieter; Meltzoff, Andrew N; Rao, Rajesh P N

2015-01-01

A fundamental challenge in robotics today is building robots that can learn new skills by observing humans and imitating human actions. We propose a new Bayesian approach to robotic learning by imitation inspired by the developmental hypothesis that children use self-experience to bootstrap the process of intention recognition and goal-based imitation. Our approach allows an autonomous agent to: (i) learn probabilistic models of actions through self-discovery and experience, (ii) utilize these learned models for inferring the goals of human actions, and (iii) perform goal-based imitation for robotic learning and human-robot collaboration. Such an approach allows a robot to leverage its increasing repertoire of learned behaviors to interpret increasingly complex human actions and use the inferred goals for imitation, even when the robot has very different actuators from humans. We demonstrate our approach using two different scenarios: (i) a simulated robot that learns human-like gaze following behavior, and (ii) a robot that learns to imitate human actions in a tabletop organization task. In both cases, the agent learns a probabilistic model of its own actions, and uses this model for goal inference and goal-based imitation. We also show that the robotic agent can use its probabilistic model to seek human assistance when it recognizes that its inferred actions are too uncertain, risky, or impossible to perform, thereby opening the door to human-robot collaboration.

A Bayesian Developmental Approach to Robotic Goal-Based Imitation Learning

PubMed Central

Chung, Michael Jae-Yoon; Friesen, Abram L.; Fox, Dieter; Meltzoff, Andrew N.; Rao, Rajesh P. N.

2015-01-01

A fundamental challenge in robotics today is building robots that can learn new skills by observing humans and imitating human actions. We propose a new Bayesian approach to robotic learning by imitation inspired by the developmental hypothesis that children use self-experience to bootstrap the process of intention recognition and goal-based imitation. Our approach allows an autonomous agent to: (i) learn probabilistic models of actions through self-discovery and experience, (ii) utilize these learned models for inferring the goals of human actions, and (iii) perform goal-based imitation for robotic learning and human-robot collaboration. Such an approach allows a robot to leverage its increasing repertoire of learned behaviors to interpret increasingly complex human actions and use the inferred goals for imitation, even when the robot has very different actuators from humans. We demonstrate our approach using two different scenarios: (i) a simulated robot that learns human-like gaze following behavior, and (ii) a robot that learns to imitate human actions in a tabletop organization task. In both cases, the agent learns a probabilistic model of its own actions, and uses this model for goal inference and goal-based imitation. We also show that the robotic agent can use its probabilistic model to seek human assistance when it recognizes that its inferred actions are too uncertain, risky, or impossible to perform, thereby opening the door to human-robot collaboration. PMID:26536366

Assessing State Nuclear Weapons Proliferation: Using Bayesian Network Analysis of Social Factors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coles, Garill A.; Brothers, Alan J.; Olson, Jarrod

A Bayesian network (BN) model of social factors can support proliferation assessments by estimating the likelihood that a state will pursue a nuclear weapon. Social factors including political, economic, nuclear capability, security, and national identity and psychology factors may play as important a role in whether a State pursues nuclear weapons as more physical factors. This paper will show how using Bayesian reasoning on a generic case of a would-be proliferator State can be used to combine evidence that supports proliferation assessment. Theories and analysis by political scientists can be leveraged in a quantitative and transparent way to indicate proliferationmore » risk. BN models facilitate diagnosis and inference in a probabilistic environment by using a network of nodes and acyclic directed arcs between the nodes whose connections, or absence of, indicate probabilistic relevance, or independence. We propose a BN model that would use information from both traditional safeguards and the strengthened safeguards associated with the Additional Protocol to indicate countries with a high risk of proliferating nuclear weapons. This model could be used in a variety of applications such a prioritization tool and as a component of state safeguards evaluations. This paper will discuss the benefits of BN reasoning, the development of Pacific Northwest National Laboratory’s (PNNL) BN state proliferation model and how it could be employed as an analytical tool.« less

A functional-dependencies-based Bayesian networks learning method and its application in a mobile commerce system.

PubMed

Liao, Stephen Shaoyi; Wang, Huai Qing; Li, Qiu Dan; Liu, Wei Yi

2006-06-01

This paper presents a new method for learning Bayesian networks from functional dependencies (FD) and third normal form (3NF) tables in relational databases. The method sets up a linkage between the theory of relational databases and probabilistic reasoning models, which is interesting and useful especially when data are incomplete and inaccurate. The effectiveness and practicability of the proposed method is demonstrated by its implementation in a mobile commerce system.

Probabilistic Models and Generative Neural Networks: Towards an Unified Framework for Modeling Normal and Impaired Neurocognitive Functions

PubMed Central

Testolin, Alberto; Zorzi, Marco

2016-01-01

Connectionist models can be characterized within the more general framework of probabilistic graphical models, which allow to efficiently describe complex statistical distributions involving a large number of interacting variables. This integration allows building more realistic computational models of cognitive functions, which more faithfully reflect the underlying neural mechanisms at the same time providing a useful bridge to higher-level descriptions in terms of Bayesian computations. Here we discuss a powerful class of graphical models that can be implemented as stochastic, generative neural networks. These models overcome many limitations associated with classic connectionist models, for example by exploiting unsupervised learning in hierarchical architectures (deep networks) and by taking into account top-down, predictive processing supported by feedback loops. We review some recent cognitive models based on generative networks, and we point out promising research directions to investigate neuropsychological disorders within this approach. Though further efforts are required in order to fill the gap between structured Bayesian models and more realistic, biophysical models of neuronal dynamics, we argue that generative neural networks have the potential to bridge these levels of analysis, thereby improving our understanding of the neural bases of cognition and of pathologies caused by brain damage. PMID:27468262

Probabilistic Models and Generative Neural Networks: Towards an Unified Framework for Modeling Normal and Impaired Neurocognitive Functions.

PubMed

Testolin, Alberto; Zorzi, Marco

2016-01-01

Connectionist models can be characterized within the more general framework of probabilistic graphical models, which allow to efficiently describe complex statistical distributions involving a large number of interacting variables. This integration allows building more realistic computational models of cognitive functions, which more faithfully reflect the underlying neural mechanisms at the same time providing a useful bridge to higher-level descriptions in terms of Bayesian computations. Here we discuss a powerful class of graphical models that can be implemented as stochastic, generative neural networks. These models overcome many limitations associated with classic connectionist models, for example by exploiting unsupervised learning in hierarchical architectures (deep networks) and by taking into account top-down, predictive processing supported by feedback loops. We review some recent cognitive models based on generative networks, and we point out promising research directions to investigate neuropsychological disorders within this approach. Though further efforts are required in order to fill the gap between structured Bayesian models and more realistic, biophysical models of neuronal dynamics, we argue that generative neural networks have the potential to bridge these levels of analysis, thereby improving our understanding of the neural bases of cognition and of pathologies caused by brain damage.

Estimation of parameter uncertainty for an activated sludge model using Bayesian inference: a comparison with the frequentist method.

PubMed

Zonta, Zivko J; Flotats, Xavier; Magrí, Albert

2014-08-01

The procedure commonly used for the assessment of the parameters included in activated sludge models (ASMs) relies on the estimation of their optimal value within a confidence region (i.e. frequentist inference). Once optimal values are estimated, parameter uncertainty is computed through the covariance matrix. However, alternative approaches based on the consideration of the model parameters as probability distributions (i.e. Bayesian inference), may be of interest. The aim of this work is to apply (and compare) both Bayesian and frequentist inference methods when assessing uncertainty for an ASM-type model, which considers intracellular storage and biomass growth, simultaneously. Practical identifiability was addressed exclusively considering respirometric profiles based on the oxygen uptake rate and with the aid of probabilistic global sensitivity analysis. Parameter uncertainty was thus estimated according to both the Bayesian and frequentist inferential procedures. Results were compared in order to evidence the strengths and weaknesses of both approaches. Since it was demonstrated that Bayesian inference could be reduced to a frequentist approach under particular hypotheses, the former can be considered as a more generalist methodology. Hence, the use of Bayesian inference is encouraged for tackling inferential issues in ASM environments.

A Bayesian computational model for online character recognition and disability assessment during cursive eye writing.

PubMed

Diard, Julien; Rynik, Vincent; Lorenceau, Jean

2013-01-01

This research involves a novel apparatus, in which the user is presented with an illusion inducing visual stimulus. The user perceives illusory movement that can be followed by the eye, so that smooth pursuit eye movements can be sustained in arbitrary directions. Thus, free-flow trajectories of any shape can be traced. In other words, coupled with an eye-tracking device, this apparatus enables "eye writing," which appears to be an original object of study. We adapt a previous model of reading and writing to this context. We describe a probabilistic model called the Bayesian Action-Perception for Eye On-Line model (BAP-EOL). It encodes probabilistic knowledge about isolated letter trajectories, their size, high-frequency components of the produced trajectory, and pupil diameter. We show how Bayesian inference, in this single model, can be used to solve several tasks, like letter recognition and novelty detection (i.e., recognizing when a presented character is not part of the learned database). We are interested in the potential use of the eye writing apparatus by motor impaired patients: the final task we solve by Bayesian inference is disability assessment (i.e., measuring and tracking the evolution of motor characteristics of produced trajectories). Preliminary experimental results are presented, which illustrate the method, showing the feasibility of character recognition in the context of eye writing. We then show experimentally how a model of the unknown character can be used to detect trajectories that are likely to be new symbols, and how disability assessment can be performed by opportunistically observing characteristics of fine motor control, as letter are being traced. Experimental analyses also help identify specificities of eye writing, as compared to handwriting, and the resulting technical challenges.

A Bayesian computational model for online character recognition and disability assessment during cursive eye writing

PubMed Central

Diard, Julien; Rynik, Vincent; Lorenceau, Jean

2013-01-01

This research involves a novel apparatus, in which the user is presented with an illusion inducing visual stimulus. The user perceives illusory movement that can be followed by the eye, so that smooth pursuit eye movements can be sustained in arbitrary directions. Thus, free-flow trajectories of any shape can be traced. In other words, coupled with an eye-tracking device, this apparatus enables “eye writing,” which appears to be an original object of study. We adapt a previous model of reading and writing to this context. We describe a probabilistic model called the Bayesian Action-Perception for Eye On-Line model (BAP-EOL). It encodes probabilistic knowledge about isolated letter trajectories, their size, high-frequency components of the produced trajectory, and pupil diameter. We show how Bayesian inference, in this single model, can be used to solve several tasks, like letter recognition and novelty detection (i.e., recognizing when a presented character is not part of the learned database). We are interested in the potential use of the eye writing apparatus by motor impaired patients: the final task we solve by Bayesian inference is disability assessment (i.e., measuring and tracking the evolution of motor characteristics of produced trajectories). Preliminary experimental results are presented, which illustrate the method, showing the feasibility of character recognition in the context of eye writing. We then show experimentally how a model of the unknown character can be used to detect trajectories that are likely to be new symbols, and how disability assessment can be performed by opportunistically observing characteristics of fine motor control, as letter are being traced. Experimental analyses also help identify specificities of eye writing, as compared to handwriting, and the resulting technical challenges. PMID:24273525

Bayesian Modeling of Perceived Surface Slant from Actively-Generated and Passively-Observed Optic Flow

PubMed Central

Caudek, Corrado; Fantoni, Carlo; Domini, Fulvio

2011-01-01

We measured perceived depth from the optic flow (a) when showing a stationary physical or virtual object to observers who moved their head at a normal or slower speed, and (b) when simulating the same optic flow on a computer and presenting it to stationary observers. Our results show that perceived surface slant is systematically distorted, for both the active and the passive viewing of physical or virtual surfaces. These distortions are modulated by head translation speed, with perceived slant increasing directly with the local velocity gradient of the optic flow. This empirical result allows us to determine the relative merits of two alternative approaches aimed at explaining perceived surface slant in active vision: an “inverse optics” model that takes head motion information into account, and a probabilistic model that ignores extra-retinal signals. We compare these two approaches within the framework of the Bayesian theory. The “inverse optics” Bayesian model produces veridical slant estimates if the optic flow and the head translation velocity are measured with no error; because of the influence of a “prior” for flatness, the slant estimates become systematically biased as the measurement errors increase. The Bayesian model, which ignores the observer's motion, always produces distorted estimates of surface slant. Interestingly, the predictions of this second model, not those of the first one, are consistent with our empirical findings. The present results suggest that (a) in active vision perceived surface slant may be the product of probabilistic processes which do not guarantee the correct solution, and (b) extra-retinal signals may be mainly used for a better measurement of retinal information. PMID:21533197

Bayesian network modelling of upper gastrointestinal bleeding

NASA Astrophysics Data System (ADS)

Aisha, Nazziwa; Shohaimi, Shamarina; Adam, Mohd Bakri

2013-09-01

Bayesian networks are graphical probabilistic models that represent causal and other relationships between domain variables. In the context of medical decision making, these models have been explored to help in medical diagnosis and prognosis. In this paper, we discuss the Bayesian network formalism in building medical support systems and we learn a tree augmented naive Bayes Network (TAN) from gastrointestinal bleeding data. The accuracy of the TAN in classifying the source of gastrointestinal bleeding into upper or lower source is obtained. The TAN achieves a high classification accuracy of 86% and an area under curve of 92%. A sensitivity analysis of the model shows relatively high levels of entropy reduction for color of the stool, history of gastrointestinal bleeding, consistency and the ratio of blood urea nitrogen to creatinine. The TAN facilitates the identification of the source of GIB and requires further validation.

Multiscale hidden Markov models for photon-limited imaging

NASA Astrophysics Data System (ADS)

Nowak, Robert D.

1999-06-01

Photon-limited image analysis is often hindered by low signal-to-noise ratios. A novel Bayesian multiscale modeling and analysis method is developed in this paper to assist in these challenging situations. In addition to providing a very natural and useful framework for modeling an d processing images, Bayesian multiscale analysis is often much less computationally demanding compared to classical Markov random field models. This paper focuses on a probabilistic graph model called the multiscale hidden Markov model (MHMM), which captures the key inter-scale dependencies present in natural image intensities. The MHMM framework presented here is specifically designed for photon-limited imagin applications involving Poisson statistics, and applications to image intensity analysis are examined.

Bayesian Fundamentalism or Enlightenment? On the explanatory status and theoretical contributions of Bayesian models of cognition.

PubMed

Jones, Matt; Love, Bradley C

2011-08-01

The prominence of Bayesian modeling of cognition has increased recently largely because of mathematical advances in specifying and deriving predictions from complex probabilistic models. Much of this research aims to demonstrate that cognitive behavior can be explained from rational principles alone, without recourse to psychological or neurological processes and representations. We note commonalities between this rational approach and other movements in psychology - namely, Behaviorism and evolutionary psychology - that set aside mechanistic explanations or make use of optimality assumptions. Through these comparisons, we identify a number of challenges that limit the rational program's potential contribution to psychological theory. Specifically, rational Bayesian models are significantly unconstrained, both because they are uninformed by a wide range of process-level data and because their assumptions about the environment are generally not grounded in empirical measurement. The psychological implications of most Bayesian models are also unclear. Bayesian inference itself is conceptually trivial, but strong assumptions are often embedded in the hypothesis sets and the approximation algorithms used to derive model predictions, without a clear delineation between psychological commitments and implementational details. Comparing multiple Bayesian models of the same task is rare, as is the realization that many Bayesian models recapitulate existing (mechanistic level) theories. Despite the expressive power of current Bayesian models, we argue they must be developed in conjunction with mechanistic considerations to offer substantive explanations of cognition. We lay out several means for such an integration, which take into account the representations on which Bayesian inference operates, as well as the algorithms and heuristics that carry it out. We argue this unification will better facilitate lasting contributions to psychological theory, avoiding the pitfalls that have plagued previous theoretical movements.

Machine Learning

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chikkagoudar, Satish; Chatterjee, Samrat; Thomas, Dennis G.

The absence of a robust and unified theory of cyber dynamics presents challenges and opportunities for using machine learning based data-driven approaches to further the understanding of the behavior of such complex systems. Analysts can also use machine learning approaches to gain operational insights. In order to be operationally beneficial, cybersecurity machine learning based models need to have the ability to: (1) represent a real-world system, (2) infer system properties, and (3) learn and adapt based on expert knowledge and observations. Probabilistic models and Probabilistic graphical models provide these necessary properties and are further explored in this chapter. Bayesian Networksmore » and Hidden Markov Models are introduced as an example of a widely used data driven classification/modeling strategy.« less

Bayesian modeling of the mass and density of asteroids

NASA Astrophysics Data System (ADS)

Dotson, Jessie L.; Mathias, Donovan

2017-10-01

Mass and density are two of the fundamental properties of any object. In the case of near earth asteroids, knowledge about the mass of an asteroid is essential for estimating the risk due to (potential) impact and planning possible mitigation options. The density of an asteroid can illuminate the structure of the asteroid. A low density can be indicative of a rubble pile structure whereas a higher density can imply a monolith and/or higher metal content. The damage resulting from an impact of an asteroid with Earth depends on its interior structure in addition to its total mass, and as a result, density is a key parameter to understanding the risk of asteroid impact. Unfortunately, measuring the mass and density of asteroids is challenging and often results in measurements with large uncertainties. In the absence of mass / density measurements for a specific object, understanding the range and distribution of likely values can facilitate probabilistic assessments of structure and impact risk. Hierarchical Bayesian models have recently been developed to investigate the mass - radius relationship of exoplanets (Wolfgang, Rogers & Ford 2016) and to probabilistically forecast the mass of bodies large enough to establish hydrostatic equilibrium over a range of 9 orders of magnitude in mass (from planemos to main sequence stars; Chen & Kipping 2017). Here, we extend this approach to investigate the mass and densities of asteroids. Several candidate Bayesian models are presented, and their performance is assessed relative to a synthetic asteroid population. In addition, a preliminary Bayesian model for probablistically forecasting masses and densities of asteroids is presented. The forecasting model is conditioned on existing asteroid data and includes observational errors, hyper-parameter uncertainties and intrinsic scatter.

Using Bayesian Networks for Candidate Generation in Consistency-based Diagnosis

NASA Technical Reports Server (NTRS)

Narasimhan, Sriram; Mengshoel, Ole

2008-01-01

Consistency-based diagnosis relies heavily on the assumption that discrepancies between model predictions and sensor observations can be detected accurately. When sources of uncertainty like sensor noise and model abstraction exist robust schemes have to be designed to make a binary decision on whether predictions are consistent with observations. This risks the occurrence of false alarms and missed alarms when an erroneous decision is made. Moreover when multiple sensors (with differing sensing properties) are available the degree of match between predictions and observations can be used to guide the search for fault candidates. In this paper we propose a novel approach to handle this problem using Bayesian networks. In the consistency- based diagnosis formulation, automatically generated Bayesian networks are used to encode a probabilistic measure of fit between predictions and observations. A Bayesian network inference algorithm is used to compute most probable fault candidates.

Learning Bayesian Networks from Correlated Data

NASA Astrophysics Data System (ADS)

Bae, Harold; Monti, Stefano; Montano, Monty; Steinberg, Martin H.; Perls, Thomas T.; Sebastiani, Paola

2016-05-01

Bayesian networks are probabilistic models that represent complex distributions in a modular way and have become very popular in many fields. There are many methods to build Bayesian networks from a random sample of independent and identically distributed observations. However, many observational studies are designed using some form of clustered sampling that introduces correlations between observations within the same cluster and ignoring this correlation typically inflates the rate of false positive associations. We describe a novel parameterization of Bayesian networks that uses random effects to model the correlation within sample units and can be used for structure and parameter learning from correlated data without inflating the Type I error rate. We compare different learning metrics using simulations and illustrate the method in two real examples: an analysis of genetic and non-genetic factors associated with human longevity from a family-based study, and an example of risk factors for complications of sickle cell anemia from a longitudinal study with repeated measures.

Propagation of the velocity model uncertainties to the seismic event location

NASA Astrophysics Data System (ADS)

Gesret, A.; Desassis, N.; Noble, M.; Romary, T.; Maisons, C.

2015-01-01

Earthquake hypocentre locations are crucial in many domains of application (academic and industrial) as seismic event location maps are commonly used to delineate faults or fractures. The interpretation of these maps depends on location accuracy and on the reliability of the associated uncertainties. The largest contribution to location and uncertainty errors is due to the fact that the velocity model errors are usually not correctly taken into account. We propose a new Bayesian formulation that integrates properly the knowledge on the velocity model into the formulation of the probabilistic earthquake location. In this work, the velocity model uncertainties are first estimated with a Bayesian tomography of active shot data. We implement a sampling Monte Carlo type algorithm to generate velocity models distributed according to the posterior distribution. In a second step, we propagate the velocity model uncertainties to the seismic event location in a probabilistic framework. This enables to obtain more reliable hypocentre locations as well as their associated uncertainties accounting for picking and velocity model uncertainties. We illustrate the tomography results and the gain in accuracy of earthquake location for two synthetic examples and one real data case study in the context of induced microseismicity.

Bayesian Inference for NASA Probabilistic Risk and Reliability Analysis

NASA Technical Reports Server (NTRS)

Dezfuli, Homayoon; Kelly, Dana; Smith, Curtis; Vedros, Kurt; Galyean, William

2009-01-01

This document, Bayesian Inference for NASA Probabilistic Risk and Reliability Analysis, is intended to provide guidelines for the collection and evaluation of risk and reliability-related data. It is aimed at scientists and engineers familiar with risk and reliability methods and provides a hands-on approach to the investigation and application of a variety of risk and reliability data assessment methods, tools, and techniques. This document provides both: A broad perspective on data analysis collection and evaluation issues. A narrow focus on the methods to implement a comprehensive information repository. The topics addressed herein cover the fundamentals of how data and information are to be used in risk and reliability analysis models and their potential role in decision making. Understanding these topics is essential to attaining a risk informed decision making environment that is being sought by NASA requirements and procedures such as 8000.4 (Agency Risk Management Procedural Requirements), NPR 8705.05 (Probabilistic Risk Assessment Procedures for NASA Programs and Projects), and the System Safety requirements of NPR 8715.3 (NASA General Safety Program Requirements).

Opinion Dynamics with Confirmation Bias

PubMed Central

Allahverdyan, Armen E.; Galstyan, Aram

2014-01-01

Background Confirmation bias is the tendency to acquire or evaluate new information in a way that is consistent with one's preexisting beliefs. It is omnipresent in psychology, economics, and even scientific practices. Prior theoretical research of this phenomenon has mainly focused on its economic implications possibly missing its potential connections with broader notions of cognitive science. Methodology/Principal Findings We formulate a (non-Bayesian) model for revising subjective probabilistic opinion of a confirmationally-biased agent in the light of a persuasive opinion. The revision rule ensures that the agent does not react to persuasion that is either far from his current opinion or coincides with it. We demonstrate that the model accounts for the basic phenomenology of the social judgment theory, and allows to study various phenomena such as cognitive dissonance and boomerang effect. The model also displays the order of presentation effect–when consecutively exposed to two opinions, the preference is given to the last opinion (recency) or the first opinion (primacy) –and relates recency to confirmation bias. Finally, we study the model in the case of repeated persuasion and analyze its convergence properties. Conclusions The standard Bayesian approach to probabilistic opinion revision is inadequate for describing the observed phenomenology of persuasion process. The simple non-Bayesian model proposed here does agree with this phenomenology and is capable of reproducing a spectrum of effects observed in psychology: primacy-recency phenomenon, boomerang effect and cognitive dissonance. We point out several limitations of the model that should motivate its future development. PMID:25007078

A Tutorial in Bayesian Potential Outcomes Mediation Analysis.

PubMed

Miočević, Milica; Gonzalez, Oscar; Valente, Matthew J; MacKinnon, David P

2018-01-01

Statistical mediation analysis is used to investigate intermediate variables in the relation between independent and dependent variables. Causal interpretation of mediation analyses is challenging because randomization of subjects to levels of the independent variable does not rule out the possibility of unmeasured confounders of the mediator to outcome relation. Furthermore, commonly used frequentist methods for mediation analysis compute the probability of the data given the null hypothesis, which is not the probability of a hypothesis given the data as in Bayesian analysis. Under certain assumptions, applying the potential outcomes framework to mediation analysis allows for the computation of causal effects, and statistical mediation in the Bayesian framework gives indirect effects probabilistic interpretations. This tutorial combines causal inference and Bayesian methods for mediation analysis so the indirect and direct effects have both causal and probabilistic interpretations. Steps in Bayesian causal mediation analysis are shown in the application to an empirical example.

Mixture Modeling for Background and Sources Separation in x-ray Astronomical Images

NASA Astrophysics Data System (ADS)

Guglielmetti, Fabrizia; Fischer, Rainer; Dose, Volker

2004-11-01

A probabilistic technique for the joint estimation of background and sources in high-energy astrophysics is described. Bayesian probability theory is applied to gain insight into the coexistence of background and sources through a probabilistic two-component mixture model, which provides consistent uncertainties of background and sources. The present analysis is applied to ROSAT PSPC data (0.1-2.4 keV) in Survey Mode. A background map is modelled using a Thin-Plate spline. Source probability maps are obtained for each pixel (45 arcsec) independently and for larger correlation lengths, revealing faint and extended sources. We will demonstrate that the described probabilistic method allows for detection improvement of faint extended celestial sources compared to the Standard Analysis Software System (SASS) used for the production of the ROSAT All-Sky Survey (RASS) catalogues.

Deductive Updating Is Not Bayesian

ERIC Educational Resources Information Center

Markovits, Henry; Brisson, Janie; de Chantal, Pier-Luc

2015-01-01

One of the major debates concerning the nature of inferential reasoning is between counterexample-based theories such as mental model theory and probabilistic theories. This study looks at conclusion updating after the addition of statistical information to examine the hypothesis that deductive reasoning cannot be explained by probabilistic…

Using Stan for Item Response Theory Models

ERIC Educational Resources Information Center

Ames, Allison J.; Au, Chi Hang

2018-01-01

Stan is a flexible probabilistic programming language providing full Bayesian inference through Hamiltonian Monte Carlo algorithms. The benefits of Hamiltonian Monte Carlo include improved efficiency and faster inference, when compared to other MCMC software implementations. Users can interface with Stan through a variety of computing…

A Transferrable Belief Model Representation for Physical Security of Nuclear Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

David Gerts

This work analyzed various probabilistic methods such as classic statistics, Bayesian inference, possibilistic theory, and Dempster-Shafer theory of belief functions for the potential insight offered into the physical security of nuclear materials as well as more broad application to nuclear non-proliferation automated decision making theory. A review of the fundamental heuristic and basic limitations of each of these methods suggested that the Dempster-Shafer theory of belief functions may offer significant capability. Further examination of the various interpretations of Dempster-Shafer theory, such as random set, generalized Bayesian, and upper/lower probability demonstrate some limitations. Compared to the other heuristics, the transferrable beliefmore » model (TBM), one of the leading interpretations of Dempster-Shafer theory, can improve the automated detection of the violation of physical security using sensors and human judgment. The improvement is shown to give a significant heuristic advantage over other probabilistic options by demonstrating significant successes for several classic gedanken experiments.« less

Circularly-symmetric complex normal ratio distribution for scalar transmissibility functions. Part III: Application to statistical modal analysis

NASA Astrophysics Data System (ADS)

Yan, Wang-Ji; Ren, Wei-Xin

2018-01-01

This study applies the theoretical findings of circularly-symmetric complex normal ratio distribution Yan and Ren (2016) [1,2] to transmissibility-based modal analysis from a statistical viewpoint. A probabilistic model of transmissibility function in the vicinity of the resonant frequency is formulated in modal domain, while some insightful comments are offered. It theoretically reveals that the statistics of transmissibility function around the resonant frequency is solely dependent on 'noise-to-signal' ratio and mode shapes. As a sequel to the development of the probabilistic model of transmissibility function in modal domain, this study poses the process of modal identification in the context of Bayesian framework by borrowing a novel paradigm. Implementation issues unique to the proposed approach are resolved by Lagrange multiplier approach. Also, this study explores the possibility of applying Bayesian analysis in distinguishing harmonic components and structural ones. The approaches are verified through simulated data and experimentally testing data. The uncertainty behavior due to variation of different factors is also discussed in detail.

A probabilistic model framework for evaluating year-to-year variation in crop productivity

NASA Astrophysics Data System (ADS)

Yokozawa, M.; Iizumi, T.; Tao, F.

2008-12-01

Most models describing the relation between crop productivity and weather condition have so far been focused on mean changes of crop yield. For keeping stable food supply against abnormal weather as well as climate change, evaluating the year-to-year variations in crop productivity rather than the mean changes is more essential. We here propose a new framework of probabilistic model based on Bayesian inference and Monte Carlo simulation. As an example, we firstly introduce a model on paddy rice production in Japan. It is called PRYSBI (Process- based Regional rice Yield Simulator with Bayesian Inference; Iizumi et al., 2008). The model structure is the same as that of SIMRIW, which was developed and used widely in Japan. The model includes three sub- models describing phenological development, biomass accumulation and maturing of rice crop. These processes are formulated to include response nature of rice plant to weather condition. This model inherently was developed to predict rice growth and yield at plot paddy scale. We applied it to evaluate the large scale rice production with keeping the same model structure. Alternatively, we assumed the parameters as stochastic variables. In order to let the model catch up actual yield at larger scale, model parameters were determined based on agricultural statistical data of each prefecture of Japan together with weather data averaged over the region. The posterior probability distribution functions (PDFs) of parameters included in the model were obtained using Bayesian inference. The MCMC (Markov Chain Monte Carlo) algorithm was conducted to numerically solve the Bayesian theorem. For evaluating the year-to-year changes in rice growth/yield under this framework, we firstly iterate simulations with set of parameter values sampled from the estimated posterior PDF of each parameter and then take the ensemble mean weighted with the posterior PDFs. We will also present another example for maize productivity in China. The framework proposed here provides us information on uncertainties, possibilities and limitations on future improvements in crop model as well.

Probabilistic Inference in General Graphical Models through Sampling in Stochastic Networks of Spiking Neurons

PubMed Central

Pecevski, Dejan; Buesing, Lars; Maass, Wolfgang

2011-01-01

An important open problem of computational neuroscience is the generic organization of computations in networks of neurons in the brain. We show here through rigorous theoretical analysis that inherent stochastic features of spiking neurons, in combination with simple nonlinear computational operations in specific network motifs and dendritic arbors, enable networks of spiking neurons to carry out probabilistic inference through sampling in general graphical models. In particular, it enables them to carry out probabilistic inference in Bayesian networks with converging arrows (“explaining away”) and with undirected loops, that occur in many real-world tasks. Ubiquitous stochastic features of networks of spiking neurons, such as trial-to-trial variability and spontaneous activity, are necessary ingredients of the underlying computational organization. We demonstrate through computer simulations that this approach can be scaled up to neural emulations of probabilistic inference in fairly large graphical models, yielding some of the most complex computations that have been carried out so far in networks of spiking neurons. PMID:22219717

Don't Fear Optimality: Sampling for Probabilistic-Logic Sequence Models

NASA Astrophysics Data System (ADS)

Thon, Ingo

One of the current challenges in artificial intelligence is modeling dynamic environments that change due to the actions or activities undertaken by people or agents. The task of inferring hidden states, e.g. the activities or intentions of people, based on observations is called filtering. Standard probabilistic models such as Dynamic Bayesian Networks are able to solve this task efficiently using approximative methods such as particle filters. However, these models do not support logical or relational representations. The key contribution of this paper is the upgrade of a particle filter algorithm for use with a probabilistic logical representation through the definition of a proposal distribution. The performance of the algorithm depends largely on how well this distribution fits the target distribution. We adopt the idea of logical compilation into Binary Decision Diagrams for sampling. This allows us to use the optimal proposal distribution which is normally prohibitively slow.

Risk assessment of turbine rotor failure using probabilistic ultrasonic non-destructive evaluations

NASA Astrophysics Data System (ADS)

Guan, Xuefei; Zhang, Jingdan; Zhou, S. Kevin; Rasselkorde, El Mahjoub; Abbasi, Waheed A.

2014-02-01

The study presents a method and application of risk assessment methodology for turbine rotor fatigue failure using probabilistic ultrasonic nondestructive evaluations. A rigorous probabilistic modeling for ultrasonic flaw sizing is developed by incorporating the model-assisted probability of detection, and the probability density function (PDF) of the actual flaw size is derived. Two general scenarios, namely the ultrasonic inspection with an identified flaw indication and the ultrasonic inspection without flaw indication, are considered in the derivation. To perform estimations for fatigue reliability and remaining useful life, uncertainties from ultrasonic flaw sizing and fatigue model parameters are systematically included and quantified. The model parameter PDF is estimated using Bayesian parameter estimation and actual fatigue testing data. The overall method is demonstrated using a realistic application of steam turbine rotor, and the risk analysis under given safety criteria is provided to support maintenance planning.

From least squares to multilevel modeling: A graphical introduction to Bayesian inference

NASA Astrophysics Data System (ADS)

Loredo, Thomas J.

2016-01-01

This tutorial presentation will introduce some of the key ideas and techniques involved in applying Bayesian methods to problems in astrostatistics. The focus will be on the big picture: understanding the foundations (interpreting probability, Bayes's theorem, the law of total probability and marginalization), making connections to traditional methods (propagation of errors, least squares, chi-squared, maximum likelihood, Monte Carlo simulation), and highlighting problems where a Bayesian approach can be particularly powerful (Poisson processes, density estimation and curve fitting with measurement error). The "graphical" component of the title reflects an emphasis on pictorial representations of some of the math, but also on the use of graphical models (multilevel or hierarchical models) for analyzing complex data. Code for some examples from the talk will be available to participants, in Python and in the Stan probabilistic programming language.

Statistical modelling of networked human-automation performance using working memory capacity.

PubMed

Ahmed, Nisar; de Visser, Ewart; Shaw, Tyler; Mohamed-Ameen, Amira; Campbell, Mark; Parasuraman, Raja

2014-01-01

This study examines the challenging problem of modelling the interaction between individual attentional limitations and decision-making performance in networked human-automation system tasks. Analysis of real experimental data from a task involving networked supervision of multiple unmanned aerial vehicles by human participants shows that both task load and network message quality affect performance, but that these effects are modulated by individual differences in working memory (WM) capacity. These insights were used to assess three statistical approaches for modelling and making predictions with real experimental networked supervisory performance data: classical linear regression, non-parametric Gaussian processes and probabilistic Bayesian networks. It is shown that each of these approaches can help designers of networked human-automated systems cope with various uncertainties in order to accommodate future users by linking expected operating conditions and performance from real experimental data to observable cognitive traits like WM capacity. Practitioner Summary: Working memory (WM) capacity helps account for inter-individual variability in operator performance in networked unmanned aerial vehicle supervisory tasks. This is useful for reliable performance prediction near experimental conditions via linear models; robust statistical prediction beyond experimental conditions via Gaussian process models and probabilistic inference about unknown task conditions/WM capacities via Bayesian network models.

The Diagnostic Challenge Competition: Probabilistic Techniques for Fault Diagnosis in Electrical Power Systems

NASA Technical Reports Server (NTRS)

Ricks, Brian W.; Mengshoel, Ole J.

2009-01-01

Reliable systems health management is an important research area of NASA. A health management system that can accurately and quickly diagnose faults in various on-board systems of a vehicle will play a key role in the success of current and future NASA missions. We introduce in this paper the ProDiagnose algorithm, a diagnostic algorithm that uses a probabilistic approach, accomplished with Bayesian Network models compiled to Arithmetic Circuits, to diagnose these systems. We describe the ProDiagnose algorithm, how it works, and the probabilistic models involved. We show by experimentation on two Electrical Power Systems based on the ADAPT testbed, used in the Diagnostic Challenge Competition (DX 09), that ProDiagnose can produce results with over 96% accuracy and less than 1 second mean diagnostic time.

Probabilistic prediction of barrier-island response to hurricanes

USGS Publications Warehouse

Plant, Nathaniel G.; Stockdon, Hilary F.

2012-01-01

Prediction of barrier-island response to hurricane attack is important for assessing the vulnerability of communities, infrastructure, habitat, and recreational assets to the impacts of storm surge, waves, and erosion. We have demonstrated that a conceptual model intended to make qualitative predictions of the type of beach response to storms (e.g., beach erosion, dune erosion, dune overwash, inundation) can be reformulated in a Bayesian network to make quantitative predictions of the morphologic response. In an application of this approach at Santa Rosa Island, FL, predicted dune-crest elevation changes in response to Hurricane Ivan explained about 20% to 30% of the observed variance. An extended Bayesian network based on the original conceptual model, which included dune elevations, storm surge, and swash, but with the addition of beach and dune widths as input variables, showed improved skill compared to the original model, explaining 70% of dune elevation change variance and about 60% of dune and shoreline position change variance. This probabilistic approach accurately represented prediction uncertainty (measured with the log likelihood ratio), and it outperformed the baseline prediction (i.e., the prior distribution based on the observations). Finally, sensitivity studies demonstrated that degrading the resolution of the Bayesian network or removing data from the calibration process reduced the skill of the predictions by 30% to 40%. The reduction in skill did not change conclusions regarding the relative importance of the input variables, and the extended model's skill always outperformed the original model.

Bayesian modeling of consumer behavior in the presence of anonymous visits

NASA Astrophysics Data System (ADS)

Novak, Julie Esther

Tailoring content to consumers has become a hallmark of marketing and digital media, particularly as it has become easier to identify customers across usage or purchase occasions. However, across a wide variety of contexts, companies find that customers do not consistently identify themselves, leaving a substantial fraction of anonymous visits. We develop a Bayesian hierarchical model that allows us to probabilistically assign anonymous sessions to users. These probabilistic assignments take into account a customer's demographic information, frequency of visitation, activities taken when visiting, and times of arrival. We present two studies, one with synthetic and one with real data, where we demonstrate improved performance over two popular practices (nearest-neighbor matching and deleting the anonymous visits) due to increased efficiency and reduced bias driven by the non-ignorability of which types of events are more likely to be anonymous. Using our proposed model, we avoid potential bias in understanding the effect of a firm's marketing on its customers, improve inference about the total number of customers in the dataset, and provide more precise targeted marketing to both previously observed and unobserved customers.

Reconstructing constructivism: causal models, Bayesian learning mechanisms, and the theory theory.

PubMed

Gopnik, Alison; Wellman, Henry M

2012-11-01

We propose a new version of the "theory theory" grounded in the computational framework of probabilistic causal models and Bayesian learning. Probabilistic models allow a constructivist but rigorous and detailed approach to cognitive development. They also explain the learning of both more specific causal hypotheses and more abstract framework theories. We outline the new theoretical ideas, explain the computational framework in an intuitive and nontechnical way, and review an extensive but relatively recent body of empirical results that supports these ideas. These include new studies of the mechanisms of learning. Children infer causal structure from statistical information, through their own actions on the world and through observations of the actions of others. Studies demonstrate these learning mechanisms in children from 16 months to 4 years old and include research on causal statistical learning, informal experimentation through play, and imitation and informal pedagogy. They also include studies of the variability and progressive character of intuitive theory change, particularly theory of mind. These studies investigate both the physical and the psychological and social domains. We conclude with suggestions for further collaborative projects between developmental and computational cognitive scientists.

Cholinergic stimulation enhances Bayesian belief updating in the deployment of spatial attention.

PubMed

Vossel, Simone; Bauer, Markus; Mathys, Christoph; Adams, Rick A; Dolan, Raymond J; Stephan, Klaas E; Friston, Karl J

2014-11-19

The exact mechanisms whereby the cholinergic neurotransmitter system contributes to attentional processing remain poorly understood. Here, we applied computational modeling to psychophysical data (obtained from a spatial attention task) under a psychopharmacological challenge with the cholinesterase inhibitor galantamine (Reminyl). This allowed us to characterize the cholinergic modulation of selective attention formally, in terms of hierarchical Bayesian inference. In a placebo-controlled, within-subject, crossover design, 16 healthy human subjects performed a modified version of Posner's location-cueing task in which the proportion of validly and invalidly cued targets (percentage of cue validity, % CV) changed over time. Saccadic response speeds were used to estimate the parameters of a hierarchical Bayesian model to test whether cholinergic stimulation affected the trial-wise updating of probabilistic beliefs that underlie the allocation of attention or whether galantamine changed the mapping from those beliefs to subsequent eye movements. Behaviorally, galantamine led to a greater influence of probabilistic context (% CV) on response speed than placebo. Crucially, computational modeling suggested this effect was due to an increase in the rate of belief updating about cue validity (as opposed to the increased sensitivity of behavioral responses to those beliefs). We discuss these findings with respect to cholinergic effects on hierarchical cortical processing and in relation to the encoding of expected uncertainty or precision. Copyright © 2014 the authors 0270-6474/14/3415735-08$15.00/0.

Bayesian Decision Theoretical Framework for Clustering

ERIC Educational Resources Information Center

Chen, Mo

2011-01-01

In this thesis, we establish a novel probabilistic framework for the data clustering problem from the perspective of Bayesian decision theory. The Bayesian decision theory view justifies the important questions: what is a cluster and what a clustering algorithm should optimize. We prove that the spectral clustering (to be specific, the…

Robust nonlinear system identification: Bayesian mixture of experts using the t-distribution

NASA Astrophysics Data System (ADS)

Baldacchino, Tara; Worden, Keith; Rowson, Jennifer

2017-02-01

A novel variational Bayesian mixture of experts model for robust regression of bifurcating and piece-wise continuous processes is introduced. The mixture of experts model is a powerful model which probabilistically splits the input space allowing different models to operate in the separate regions. However, current methods have no fail-safe against outliers. In this paper, a robust mixture of experts model is proposed which consists of Student-t mixture models at the gates and Student-t distributed experts, trained via Bayesian inference. The Student-t distribution has heavier tails than the Gaussian distribution, and so it is more robust to outliers, noise and non-normality in the data. Using both simulated data and real data obtained from the Z24 bridge this robust mixture of experts performs better than its Gaussian counterpart when outliers are present. In particular, it provides robustness to outliers in two forms: unbiased parameter regression models, and robustness to overfitting/complex models.

Precise Network Modeling of Systems Genetics Data Using the Bayesian Network Webserver.

PubMed

Ziebarth, Jesse D; Cui, Yan

2017-01-01

The Bayesian Network Webserver (BNW, http://compbio.uthsc.edu/BNW ) is an integrated platform for Bayesian network modeling of biological datasets. It provides a web-based network modeling environment that seamlessly integrates advanced algorithms for probabilistic causal modeling and reasoning with Bayesian networks. BNW is designed for precise modeling of relatively small networks that contain less than 20 nodes. The structure learning algorithms used by BNW guarantee the discovery of the best (most probable) network structure given the data. To facilitate network modeling across multiple biological levels, BNW provides a very flexible interface that allows users to assign network nodes into different tiers and define the relationships between and within the tiers. This function is particularly useful for modeling systems genetics datasets that often consist of multiscalar heterogeneous genotype-to-phenotype data. BNW enables users to, within seconds or minutes, go from having a simply formatted input file containing a dataset to using a network model to make predictions about the interactions between variables and the potential effects of experimental interventions. In this chapter, we will introduce the functions of BNW and show how to model systems genetics datasets with BNW.

Uncertainty plus Prior Equals Rational Bias: An Intuitive Bayesian Probability Weighting Function

ERIC Educational Resources Information Center

Fennell, John; Baddeley, Roland

2012-01-01

Empirical research has shown that when making choices based on probabilistic options, people behave as if they overestimate small probabilities, underestimate large probabilities, and treat positive and negative outcomes differently. These distortions have been modeled using a nonlinear probability weighting function, which is found in several…

Learning of state-space models with highly informative observations: A tempered sequential Monte Carlo solution

NASA Astrophysics Data System (ADS)

Svensson, Andreas; Schön, Thomas B.; Lindsten, Fredrik

2018-05-01

Probabilistic (or Bayesian) modeling and learning offers interesting possibilities for systematic representation of uncertainty using probability theory. However, probabilistic learning often leads to computationally challenging problems. Some problems of this type that were previously intractable can now be solved on standard personal computers thanks to recent advances in Monte Carlo methods. In particular, for learning of unknown parameters in nonlinear state-space models, methods based on the particle filter (a Monte Carlo method) have proven very useful. A notoriously challenging problem, however, still occurs when the observations in the state-space model are highly informative, i.e. when there is very little or no measurement noise present, relative to the amount of process noise. The particle filter will then struggle in estimating one of the basic components for probabilistic learning, namely the likelihood p (data | parameters). To this end we suggest an algorithm which initially assumes that there is substantial amount of artificial measurement noise present. The variance of this noise is sequentially decreased in an adaptive fashion such that we, in the end, recover the original problem or possibly a very close approximation of it. The main component in our algorithm is a sequential Monte Carlo (SMC) sampler, which gives our proposed method a clear resemblance to the SMC2 method. Another natural link is also made to the ideas underlying the approximate Bayesian computation (ABC). We illustrate it with numerical examples, and in particular show promising results for a challenging Wiener-Hammerstein benchmark problem.

Application of dynamic uncertain causality graph in spacecraft fault diagnosis: Logic cycle

NASA Astrophysics Data System (ADS)

Yao, Quanying; Zhang, Qin; Liu, Peng; Yang, Ping; Zhu, Ma; Wang, Xiaochen

2017-04-01

Intelligent diagnosis system are applied to fault diagnosis in spacecraft. Dynamic Uncertain Causality Graph (DUCG) is a new probability graphic model with many advantages. In the knowledge expression of spacecraft fault diagnosis, feedback among variables is frequently encountered, which may cause directed cyclic graphs (DCGs). Probabilistic graphical models (PGMs) such as bayesian network (BN) have been widely applied in uncertain causality representation and probabilistic reasoning, but BN does not allow DCGs. In this paper, DUGG is applied to fault diagnosis in spacecraft: introducing the inference algorithm for the DUCG to deal with feedback. Now, DUCG has been tested in 16 typical faults with 100% diagnosis accuracy.

Bayesian networks of age estimation and classification based on dental evidence: A study on the third molar mineralization.

PubMed

Sironi, Emanuele; Pinchi, Vilma; Pradella, Francesco; Focardi, Martina; Bozza, Silvia; Taroni, Franco

2018-04-01

Not only does the Bayesian approach offer a rational and logical environment for evidence evaluation in a forensic framework, but it also allows scientists to coherently deal with uncertainty related to a collection of multiple items of evidence, due to its flexible nature. Such flexibility might come at the expense of elevated computational complexity, which can be handled by using specific probabilistic graphical tools, namely Bayesian networks. In the current work, such probabilistic tools are used for evaluating dental evidence related to the development of third molars. A set of relevant properties characterizing the graphical models are discussed and Bayesian networks are implemented to deal with the inferential process laying beyond the estimation procedure, as well as to provide age estimates. Such properties include operationality, flexibility, coherence, transparence and sensitivity. A data sample composed of Italian subjects was employed for the analysis; results were in agreement with previous studies in terms of point estimate and age classification. The influence of the prior probability elicitation in terms of Bayesian estimate and classifies was also analyzed. Findings also supported the opportunity to take into consideration multiple teeth in the evaluative procedure, since it can be shown this results in an increased robustness towards the prior probability elicitation process, as well as in more favorable outcomes from a forensic perspective. Copyright © 2018 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Public opinion by a poll process: model study and Bayesian view

NASA Astrophysics Data System (ADS)

Lee, Hyun Keun; Kim, Yong Woon

2018-05-01

We study the formation of public opinion in a poll process where the current score is open to the public. The voters are assumed to vote probabilistically for or against their own preference considering the group opinion collected up to then in the score. The poll-score probability is found to follow the beta distribution in the large polls limit. We demonstrate that various poll results, even those contradictory to the population preference, are possible with non-zero probability density and that such deviations are readily triggered by initial bias. It is mentioned that our poll model can be understood in the Bayesian viewpoint.

Bayesian quantitative precipitation forecasts in terms of quantiles

NASA Astrophysics Data System (ADS)

Bentzien, Sabrina; Friederichs, Petra

2014-05-01

Ensemble prediction systems (EPS) for numerical weather predictions on the mesoscale are particularly developed to obtain probabilistic guidance for high impact weather. An EPS not only issues a deterministic future state of the atmosphere but a sample of possible future states. Ensemble postprocessing then translates such a sample of forecasts into probabilistic measures. This study focus on probabilistic quantitative precipitation forecasts in terms of quantiles. Quantiles are particular suitable to describe precipitation at various locations, since no assumption is required on the distribution of precipitation. The focus is on the prediction during high-impact events and related to the Volkswagen Stiftung funded project WEX-MOP (Mesoscale Weather Extremes - Theory, Spatial Modeling and Prediction). Quantile forecasts are derived from the raw ensemble and via quantile regression. Neighborhood method and time-lagging are effective tools to inexpensively increase the ensemble spread, which results in more reliable forecasts especially for extreme precipitation events. Since an EPS provides a large amount of potentially informative predictors, a variable selection is required in order to obtain a stable statistical model. A Bayesian formulation of quantile regression allows for inference about the selection of predictive covariates by the use of appropriate prior distributions. Moreover, the implementation of an additional process layer for the regression parameters accounts for spatial variations of the parameters. Bayesian quantile regression and its spatially adaptive extension is illustrated for the German-focused mesoscale weather prediction ensemble COSMO-DE-EPS, which runs (pre)operationally since December 2010 at the German Meteorological Service (DWD). Objective out-of-sample verification uses the quantile score (QS), a weighted absolute error between quantile forecasts and observations. The QS is a proper scoring function and can be decomposed into reliability, resolutions and uncertainty parts. A quantile reliability plot gives detailed insights in the predictive performance of the quantile forecasts.

Distributed Bayesian Computation and Self-Organized Learning in Sheets of Spiking Neurons with Local Lateral Inhibition

PubMed Central

Bill, Johannes; Buesing, Lars; Habenschuss, Stefan; Nessler, Bernhard; Maass, Wolfgang; Legenstein, Robert

2015-01-01

During the last decade, Bayesian probability theory has emerged as a framework in cognitive science and neuroscience for describing perception, reasoning and learning of mammals. However, our understanding of how probabilistic computations could be organized in the brain, and how the observed connectivity structure of cortical microcircuits supports these calculations, is rudimentary at best. In this study, we investigate statistical inference and self-organized learning in a spatially extended spiking network model, that accommodates both local competitive and large-scale associative aspects of neural information processing, under a unified Bayesian account. Specifically, we show how the spiking dynamics of a recurrent network with lateral excitation and local inhibition in response to distributed spiking input, can be understood as sampling from a variational posterior distribution of a well-defined implicit probabilistic model. This interpretation further permits a rigorous analytical treatment of experience-dependent plasticity on the network level. Using machine learning theory, we derive update rules for neuron and synapse parameters which equate with Hebbian synaptic and homeostatic intrinsic plasticity rules in a neural implementation. In computer simulations, we demonstrate that the interplay of these plasticity rules leads to the emergence of probabilistic local experts that form distributed assemblies of similarly tuned cells communicating through lateral excitatory connections. The resulting sparse distributed spike code of a well-adapted network carries compressed information on salient input features combined with prior experience on correlations among them. Our theory predicts that the emergence of such efficient representations benefits from network architectures in which the range of local inhibition matches the spatial extent of pyramidal cells that share common afferent input. PMID:26284370

A solution to the static frame validation challenge problem using Bayesian model selection

DOE PAGES

Grigoriu, M. D.; Field, R. V.

2007-12-23

Within this paper, we provide a solution to the static frame validation challenge problem (see this issue) in a manner that is consistent with the guidelines provided by the Validation Challenge Workshop tasking document. The static frame problem is constructed such that variability in material properties is known to be the only source of uncertainty in the system description, but there is ignorance on the type of model that best describes this variability. Hence both types of uncertainty, aleatoric and epistemic, are present and must be addressed. Our approach is to consider a collection of competing probabilistic models for themore » material properties, and calibrate these models to the information provided; models of different levels of complexity and numerical efficiency are included in the analysis. A Bayesian formulation is used to select the optimal model from the collection, which is then used for the regulatory assessment. Lastly, bayesian credible intervals are used to provide a measure of confidence to our regulatory assessment.« less

Prediction of road accidents: A Bayesian hierarchical approach.

PubMed

Deublein, Markus; Schubert, Matthias; Adey, Bryan T; Köhler, Jochen; Faber, Michael H

2013-03-01

In this paper a novel methodology for the prediction of the occurrence of road accidents is presented. The methodology utilizes a combination of three statistical methods: (1) gamma-updating of the occurrence rates of injury accidents and injured road users, (2) hierarchical multivariate Poisson-lognormal regression analysis taking into account correlations amongst multiple dependent model response variables and effects of discrete accident count data e.g. over-dispersion, and (3) Bayesian inference algorithms, which are applied by means of data mining techniques supported by Bayesian Probabilistic Networks in order to represent non-linearity between risk indicating and model response variables, as well as different types of uncertainties which might be present in the development of the specific models. Prior Bayesian Probabilistic Networks are first established by means of multivariate regression analysis of the observed frequencies of the model response variables, e.g. the occurrence of an accident, and observed values of the risk indicating variables, e.g. degree of road curvature. Subsequently, parameter learning is done using updating algorithms, to determine the posterior predictive probability distributions of the model response variables, conditional on the values of the risk indicating variables. The methodology is illustrated through a case study using data of the Austrian rural motorway network. In the case study, on randomly selected road segments the methodology is used to produce a model to predict the expected number of accidents in which an injury has occurred and the expected number of light, severe and fatally injured road users. Additionally, the methodology is used for geo-referenced identification of road sections with increased occurrence probabilities of injury accident events on a road link between two Austrian cities. It is shown that the proposed methodology can be used to develop models to estimate the occurrence of road accidents for any road network provided that the required data are available. Copyright © 2012 Elsevier Ltd. All rights reserved.

Probabilistic mapping of descriptive health status responses onto health state utilities using Bayesian networks: an empirical analysis converting SF-12 into EQ-5D utility index in a national US sample.

PubMed

Le, Quang A; Doctor, Jason N

2011-05-01

As quality-adjusted life years have become the standard metric in health economic evaluations, mapping health-profile or disease-specific measures onto preference-based measures to obtain quality-adjusted life years has become a solution when health utilities are not directly available. However, current mapping methods are limited due to their predictive validity, reliability, and/or other methodological issues. We employ probability theory together with a graphical model, called a Bayesian network, to convert health-profile measures into preference-based measures and to compare the results to those estimated with current mapping methods. A sample of 19,678 adults who completed both the 12-item Short Form Health Survey (SF-12v2) and EuroQoL 5D (EQ-5D) questionnaires from the 2003 Medical Expenditure Panel Survey was split into training and validation sets. Bayesian networks were constructed to explore the probabilistic relationships between each EQ-5D domain and 12 items of the SF-12v2. The EQ-5D utility scores were estimated on the basis of the predicted probability of each response level of the 5 EQ-5D domains obtained from the Bayesian inference process using the following methods: Monte Carlo simulation, expected utility, and most-likely probability. Results were then compared with current mapping methods including multinomial logistic regression, ordinary least squares, and censored least absolute deviations. The Bayesian networks consistently outperformed other mapping models in the overall sample (mean absolute error=0.077, mean square error=0.013, and R overall=0.802), in different age groups, number of chronic conditions, and ranges of the EQ-5D index. Bayesian networks provide a new robust and natural approach to map health status responses into health utility measures for health economic evaluations.

Collection Fusion Using Bayesian Estimation of a Linear Regression Model in Image Databases on the Web.

ERIC Educational Resources Information Center

Kim, Deok-Hwan; Chung, Chin-Wan

2003-01-01

Discusses the collection fusion problem of image databases, concerned with retrieving relevant images by content based retrieval from image databases distributed on the Web. Focuses on a metaserver which selects image databases supporting similarity measures and proposes a new algorithm which exploits a probabilistic technique using Bayesian…

Markov Random Fields, Stochastic Quantization and Image Analysis

DTIC Science & Technology

1990-01-01

Markov random fields based on the lattice Z2 have been extensively used in image analysis in a Bayesian framework as a-priori models for the...of Image Analysis can be given some fundamental justification then there is a remarkable connection between Probabilistic Image Analysis , Statistical Mechanics and Lattice-based Euclidean Quantum Field Theory.

Probabilistic Assessment of Planet Habitability and Biosignatures

NASA Astrophysics Data System (ADS)

Bixel, A.; Apai, D.

2017-11-01

We have computed probabilistic constraints on the bulk properties of Proxima Cen b informed by priors from Kepler and RV follow-up. We will extend this approach into a Bayesian framework to assess the habitability of directly imaged planets.

Research on probabilistic information processing

NASA Technical Reports Server (NTRS)

Edwards, W.

1973-01-01

The work accomplished on probabilistic information processing (PIP) is reported. The research proposals and decision analysis are discussed along with the results of research on MSC setting, multiattribute utilities, and Bayesian research. Abstracts of reports concerning the PIP research are included.

Global sensitivity analysis, probabilistic calibration, and predictive assessment for the data assimilation linked ecosystem carbon model

DOE PAGES

Safta, C.; Ricciuto, Daniel M.; Sargsyan, Khachik; ...

2015-07-01

In this paper we propose a probabilistic framework for an uncertainty quantification (UQ) study of a carbon cycle model and focus on the comparison between steady-state and transient simulation setups. A global sensitivity analysis (GSA) study indicates the parameters and parameter couplings that are important at different times of the year for quantities of interest (QoIs) obtained with the data assimilation linked ecosystem carbon (DALEC) model. We then employ a Bayesian approach and a statistical model error term to calibrate the parameters of DALEC using net ecosystem exchange (NEE) observations at the Harvard Forest site. The calibration results are employedmore » in the second part of the paper to assess the predictive skill of the model via posterior predictive checks.« less

Bayesian flood forecasting methods: A review

NASA Astrophysics Data System (ADS)

Han, Shasha; Coulibaly, Paulin

2017-08-01

Over the past few decades, floods have been seen as one of the most common and largely distributed natural disasters in the world. If floods could be accurately forecasted in advance, then their negative impacts could be greatly minimized. It is widely recognized that quantification and reduction of uncertainty associated with the hydrologic forecast is of great importance for flood estimation and rational decision making. Bayesian forecasting system (BFS) offers an ideal theoretic framework for uncertainty quantification that can be developed for probabilistic flood forecasting via any deterministic hydrologic model. It provides suitable theoretical structure, empirically validated models and reasonable analytic-numerical computation method, and can be developed into various Bayesian forecasting approaches. This paper presents a comprehensive review on Bayesian forecasting approaches applied in flood forecasting from 1999 till now. The review starts with an overview of fundamentals of BFS and recent advances in BFS, followed with BFS application in river stage forecasting and real-time flood forecasting, then move to a critical analysis by evaluating advantages and limitations of Bayesian forecasting methods and other predictive uncertainty assessment approaches in flood forecasting, and finally discusses the future research direction in Bayesian flood forecasting. Results show that the Bayesian flood forecasting approach is an effective and advanced way for flood estimation, it considers all sources of uncertainties and produces a predictive distribution of the river stage, river discharge or runoff, thus gives more accurate and reliable flood forecasts. Some emerging Bayesian forecasting methods (e.g. ensemble Bayesian forecasting system, Bayesian multi-model combination) were shown to overcome limitations of single model or fixed model weight and effectively reduce predictive uncertainty. In recent years, various Bayesian flood forecasting approaches have been developed and widely applied, but there is still room for improvements. Future research in the context of Bayesian flood forecasting should be on assimilation of various sources of newly available information and improvement of predictive performance assessment methods.

Computational Approaches to Spatial Orientation: From Transfer Functions to Dynamic Bayesian Inference

PubMed Central

MacNeilage, Paul R.; Ganesan, Narayan; Angelaki, Dora E.

2008-01-01

Spatial orientation is the sense of body orientation and self-motion relative to the stationary environment, fundamental to normal waking behavior and control of everyday motor actions including eye movements, postural control, and locomotion. The brain achieves spatial orientation by integrating visual, vestibular, and somatosensory signals. Over the past years, considerable progress has been made toward understanding how these signals are processed by the brain using multiple computational approaches that include frequency domain analysis, the concept of internal models, observer theory, Bayesian theory, and Kalman filtering. Here we put these approaches in context by examining the specific questions that can be addressed by each technique and some of the scientific insights that have resulted. We conclude with a recent application of particle filtering, a probabilistic simulation technique that aims to generate the most likely state estimates by incorporating internal models of sensor dynamics and physical laws and noise associated with sensory processing as well as prior knowledge or experience. In this framework, priors for low angular velocity and linear acceleration can explain the phenomena of velocity storage and frequency segregation, both of which have been modeled previously using arbitrary low-pass filtering. How Kalman and particle filters may be implemented by the brain is an emerging field. Unlike past neurophysiological research that has aimed to characterize mean responses of single neurons, investigations of dynamic Bayesian inference should attempt to characterize population activities that constitute probabilistic representations of sensory and prior information. PMID:18842952

Spatial Bayesian belief networks as a planning decision tool for mapping ecosystem services trade-offs on forested landscapes.

PubMed

Gonzalez-Redin, Julen; Luque, Sandra; Poggio, Laura; Smith, Ron; Gimona, Alessandro

2016-01-01

An integrated methodology, based on linking Bayesian belief networks (BBN) with GIS, is proposed for combining available evidence to help forest managers evaluate implications and trade-offs between forest production and conservation measures to preserve biodiversity in forested habitats. A Bayesian belief network is a probabilistic graphical model that represents variables and their dependencies through specifying probabilistic relationships. In spatially explicit decision problems where it is difficult to choose appropriate combinations of interventions, the proposed integration of a BBN with GIS helped to facilitate shared understanding of the human-landscape relationships, while fostering collective management that can be incorporated into landscape planning processes. Trades-offs become more and more relevant in these landscape contexts where the participation of many and varied stakeholder groups is indispensable. With these challenges in mind, our integrated approach incorporates GIS-based data with expert knowledge to consider two different land use interests - biodiversity value for conservation and timber production potential - with the focus on a complex mountain landscape in the French Alps. The spatial models produced provided different alternatives of suitable sites that can be used by policy makers in order to support conservation priorities while addressing management options. The approach provided provide a common reasoning language among different experts from different backgrounds while helped to identify spatially explicit conflictive areas. Copyright © 2015 Elsevier Inc. All rights reserved.

scoringRules - A software package for probabilistic model evaluation

NASA Astrophysics Data System (ADS)

Lerch, Sebastian; Jordan, Alexander; Krüger, Fabian

2016-04-01

Models in the geosciences are generally surrounded by uncertainty, and being able to quantify this uncertainty is key to good decision making. Accordingly, probabilistic forecasts in the form of predictive distributions have become popular over the last decades. With the proliferation of probabilistic models arises the need for decision theoretically principled tools to evaluate the appropriateness of models and forecasts in a generalized way. Various scoring rules have been developed over the past decades to address this demand. Proper scoring rules are functions S(F,y) which evaluate the accuracy of a forecast distribution F , given that an outcome y was observed. As such, they allow to compare alternative models, a crucial ability given the variety of theories, data sources and statistical specifications that is available in many situations. This poster presents the software package scoringRules for the statistical programming language R, which contains functions to compute popular scoring rules such as the continuous ranked probability score for a variety of distributions F that come up in applied work. Two main classes are parametric distributions like normal, t, or gamma distributions, and distributions that are not known analytically, but are indirectly described through a sample of simulation draws. For example, Bayesian forecasts produced via Markov Chain Monte Carlo take this form. Thereby, the scoringRules package provides a framework for generalized model evaluation that both includes Bayesian as well as classical parametric models. The scoringRules package aims to be a convenient dictionary-like reference for computing scoring rules. We offer state of the art implementations of several known (but not routinely applied) formulas, and implement closed-form expressions that were previously unavailable. Whenever more than one implementation variant exists, we offer statistically principled default choices.

Recursive Bayesian recurrent neural networks for time-series modeling.

PubMed

Mirikitani, Derrick T; Nikolaev, Nikolay

2010-02-01

This paper develops a probabilistic approach to recursive second-order training of recurrent neural networks (RNNs) for improved time-series modeling. A general recursive Bayesian Levenberg-Marquardt algorithm is derived to sequentially update the weights and the covariance (Hessian) matrix. The main strengths of the approach are a principled handling of the regularization hyperparameters that leads to better generalization, and stable numerical performance. The framework involves the adaptation of a noise hyperparameter and local weight prior hyperparameters, which represent the noise in the data and the uncertainties in the model parameters. Experimental investigations using artificial and real-world data sets show that RNNs equipped with the proposed approach outperform standard real-time recurrent learning and extended Kalman training algorithms for recurrent networks, as well as other contemporary nonlinear neural models, on time-series modeling.

On the Origins of Suboptimality in Human Probabilistic Inference

PubMed Central

Acerbi, Luigi; Vijayakumar, Sethu; Wolpert, Daniel M.

2014-01-01

Humans have been shown to combine noisy sensory information with previous experience (priors), in qualitative and sometimes quantitative agreement with the statistically-optimal predictions of Bayesian integration. However, when the prior distribution becomes more complex than a simple Gaussian, such as skewed or bimodal, training takes much longer and performance appears suboptimal. It is unclear whether such suboptimality arises from an imprecise internal representation of the complex prior, or from additional constraints in performing probabilistic computations on complex distributions, even when accurately represented. Here we probe the sources of suboptimality in probabilistic inference using a novel estimation task in which subjects are exposed to an explicitly provided distribution, thereby removing the need to remember the prior. Subjects had to estimate the location of a target given a noisy cue and a visual representation of the prior probability density over locations, which changed on each trial. Different classes of priors were examined (Gaussian, unimodal, bimodal). Subjects' performance was in qualitative agreement with the predictions of Bayesian Decision Theory although generally suboptimal. The degree of suboptimality was modulated by statistical features of the priors but was largely independent of the class of the prior and level of noise in the cue, suggesting that suboptimality in dealing with complex statistical features, such as bimodality, may be due to a problem of acquiring the priors rather than computing with them. We performed a factorial model comparison across a large set of Bayesian observer models to identify additional sources of noise and suboptimality. Our analysis rejects several models of stochastic behavior, including probability matching and sample-averaging strategies. Instead we show that subjects' response variability was mainly driven by a combination of a noisy estimation of the parameters of the priors, and by variability in the decision process, which we represent as a noisy or stochastic posterior. PMID:24945142

Reconstructing constructivism: Causal models, Bayesian learning mechanisms and the theory theory

PubMed Central

Gopnik, Alison; Wellman, Henry M.

2012-01-01

We propose a new version of the “theory theory” grounded in the computational framework of probabilistic causal models and Bayesian learning. Probabilistic models allow a constructivist but rigorous and detailed approach to cognitive development. They also explain the learning of both more specific causal hypotheses and more abstract framework theories. We outline the new theoretical ideas, explain the computational framework in an intuitive and non-technical way, and review an extensive but relatively recent body of empirical results that supports these ideas. These include new studies of the mechanisms of learning. Children infer causal structure from statistical information, through their own actions on the world and through observations of the actions of others. Studies demonstrate these learning mechanisms in children from 16 months to 4 years old and include research on causal statistical learning, informal experimentation through play, and imitation and informal pedagogy. They also include studies of the variability and progressive character of intuitive theory change, particularly theory of mind. These studies investigate both the physical and psychological and social domains. We conclude with suggestions for further collaborative projects between developmental and computational cognitive scientists. PMID:22582739

Combining MLC and SVM Classifiers for Learning Based Decision Making: Analysis and Evaluations

PubMed Central

Zhang, Yi; Ren, Jinchang; Jiang, Jianmin

2015-01-01

Maximum likelihood classifier (MLC) and support vector machines (SVM) are two commonly used approaches in machine learning. MLC is based on Bayesian theory in estimating parameters of a probabilistic model, whilst SVM is an optimization based nonparametric method in this context. Recently, it is found that SVM in some cases is equivalent to MLC in probabilistically modeling the learning process. In this paper, MLC and SVM are combined in learning and classification, which helps to yield probabilistic output for SVM and facilitate soft decision making. In total four groups of data are used for evaluations, covering sonar, vehicle, breast cancer, and DNA sequences. The data samples are characterized in terms of Gaussian/non-Gaussian distributed and balanced/unbalanced samples which are then further used for performance assessment in comparing the SVM and the combined SVM-MLC classifier. Interesting results are reported to indicate how the combined classifier may work under various conditions. PMID:26089862

Combining MLC and SVM Classifiers for Learning Based Decision Making: Analysis and Evaluations.

PubMed

Zhang, Yi; Ren, Jinchang; Jiang, Jianmin

2015-01-01

Maximum likelihood classifier (MLC) and support vector machines (SVM) are two commonly used approaches in machine learning. MLC is based on Bayesian theory in estimating parameters of a probabilistic model, whilst SVM is an optimization based nonparametric method in this context. Recently, it is found that SVM in some cases is equivalent to MLC in probabilistically modeling the learning process. In this paper, MLC and SVM are combined in learning and classification, which helps to yield probabilistic output for SVM and facilitate soft decision making. In total four groups of data are used for evaluations, covering sonar, vehicle, breast cancer, and DNA sequences. The data samples are characterized in terms of Gaussian/non-Gaussian distributed and balanced/unbalanced samples which are then further used for performance assessment in comparing the SVM and the combined SVM-MLC classifier. Interesting results are reported to indicate how the combined classifier may work under various conditions.

bayesPop: Probabilistic Population Projections

PubMed Central

Ševčíková, Hana; Raftery, Adrian E.

2016-01-01

We describe bayesPop, an R package for producing probabilistic population projections for all countries. This uses probabilistic projections of total fertility and life expectancy generated by Bayesian hierarchical models. It produces a sample from the joint posterior predictive distribution of future age- and sex-specific population counts, fertility rates and mortality rates, as well as future numbers of births and deaths. It provides graphical ways of summarizing this information, including trajectory plots and various kinds of probabilistic population pyramids. An expression language is introduced which allows the user to produce the predictive distribution of a wide variety of derived population quantities, such as the median age or the old age dependency ratio. The package produces aggregated projections for sets of countries, such as UN regions or trading blocs. The methodology has been used by the United Nations to produce their most recent official population projections for all countries, published in the World Population Prospects. PMID:28077933

Bayesian outcome-based strategy classification.

PubMed

Lee, Michael D

2016-03-01

Hilbig and Moshagen (Psychonomic Bulletin & Review, 21, 1431-1443, 2014) recently developed a method for making inferences about the decision processes people use in multi-attribute forced choice tasks. Their paper makes a number of worthwhile theoretical and methodological contributions. Theoretically, they provide an insightful psychological motivation for a probabilistic extension of the widely-used "weighted additive" (WADD) model, and show how this model, as well as other important models like "take-the-best" (TTB), can and should be expressed in terms of meaningful priors. Methodologically, they develop an inference approach based on the Minimum Description Length (MDL) principles that balances both the goodness-of-fit and complexity of the decision models they consider. This paper aims to preserve these useful contributions, but provide a complementary Bayesian approach with some theoretical and methodological advantages. We develop a simple graphical model, implemented in JAGS, that allows for fully Bayesian inferences about which models people use to make decisions. To demonstrate the Bayesian approach, we apply it to the models and data considered by Hilbig and Moshagen (Psychonomic Bulletin & Review, 21, 1431-1443, 2014), showing how a prior predictive analysis of the models, and posterior inferences about which models people use and the parameter settings at which they use them, can contribute to our understanding of human decision making.

Optimal speech motor control and token-to-token variability: a Bayesian modeling approach.

PubMed

Patri, Jean-François; Diard, Julien; Perrier, Pascal

2015-12-01

The remarkable capacity of the speech motor system to adapt to various speech conditions is due to an excess of degrees of freedom, which enables producing similar acoustical properties with different sets of control strategies. To explain how the central nervous system selects one of the possible strategies, a common approach, in line with optimal motor control theories, is to model speech motor planning as the solution of an optimality problem based on cost functions. Despite the success of this approach, one of its drawbacks is the intrinsic contradiction between the concept of optimality and the observed experimental intra-speaker token-to-token variability. The present paper proposes an alternative approach by formulating feedforward optimal control in a probabilistic Bayesian modeling framework. This is illustrated by controlling a biomechanical model of the vocal tract for speech production and by comparing it with an existing optimal control model (GEPPETO). The essential elements of this optimal control model are presented first. From them the Bayesian model is constructed in a progressive way. Performance of the Bayesian model is evaluated based on computer simulations and compared to the optimal control model. This approach is shown to be appropriate for solving the speech planning problem while accounting for variability in a principled way.

What do we gain with Probabilistic Flood Loss Models?

NASA Astrophysics Data System (ADS)

Schroeter, K.; Kreibich, H.; Vogel, K.; Merz, B.; Lüdtke, S.

2015-12-01

The reliability of flood loss models is a prerequisite for their practical usefulness. Oftentimes, traditional uni-variate damage models as for instance depth-damage curves fail to reproduce the variability of observed flood damage. Innovative multi-variate probabilistic modelling approaches are promising to capture and quantify the uncertainty involved and thus to improve the basis for decision making. In this study we compare the predictive capability of two probabilistic modelling approaches, namely Bagging Decision Trees and Bayesian Networks and traditional stage damage functions which are cast in a probabilistic framework. For model evaluation we use empirical damage data which are available from computer aided telephone interviews that were respectively compiled after the floods in 2002, 2005, 2006 and 2013 in the Elbe and Danube catchments in Germany. We carry out a split sample test by sub-setting the damage records. One sub-set is used to derive the models and the remaining records are used to evaluate the predictive performance of the model. Further we stratify the sample according to catchments which allows studying model performance in a spatial transfer context. Flood damage estimation is carried out on the scale of the individual buildings in terms of relative damage. The predictive performance of the models is assessed in terms of systematic deviations (mean bias), precision (mean absolute error) as well as in terms of reliability which is represented by the proportion of the number of observations that fall within the 95-quantile and 5-quantile predictive interval. The reliability of the probabilistic predictions within validation runs decreases only slightly and achieves a very good coverage of observations within the predictive interval. Probabilistic models provide quantitative information about prediction uncertainty which is crucial to assess the reliability of model predictions and improves the usefulness of model results.

CPT-based probabilistic and deterministic assessment of in situ seismic soil liquefaction potential

USGS Publications Warehouse

Moss, R.E.S.; Seed, R.B.; Kayen, R.E.; Stewart, J.P.; Der Kiureghian, A.; Cetin, K.O.

2006-01-01

This paper presents a complete methodology for both probabilistic and deterministic assessment of seismic soil liquefaction triggering potential based on the cone penetration test (CPT). A comprehensive worldwide set of CPT-based liquefaction field case histories were compiled and back analyzed, and the data then used to develop probabilistic triggering correlations. Issues investigated in this study include improved normalization of CPT resistance measurements for the influence of effective overburden stress, and adjustment to CPT tip resistance for the potential influence of "thin" liquefiable layers. The effects of soil type and soil character (i.e., "fines" adjustment) for the new correlations are based on a combination of CPT tip and sleeve resistance. To quantify probability for performancebased engineering applications, Bayesian "regression" methods were used, and the uncertainties of all variables comprising both the seismic demand and the liquefaction resistance were estimated and included in the analysis. The resulting correlations were developed using a Bayesian framework and are presented in both probabilistic and deterministic formats. The results are compared to previous probabilistic and deterministic correlations. ?? 2006 ASCE.

Age estimation by assessment of pulp chamber volume: a Bayesian network for the evaluation of dental evidence.

PubMed

Sironi, Emanuele; Taroni, Franco; Baldinotti, Claudio; Nardi, Cosimo; Norelli, Gian-Aristide; Gallidabino, Matteo; Pinchi, Vilma

2017-11-14

The present study aimed to investigate the performance of a Bayesian method in the evaluation of dental age-related evidence collected by means of a geometrical approximation procedure of the pulp chamber volume. Measurement of this volume was based on three-dimensional cone beam computed tomography images. The Bayesian method was applied by means of a probabilistic graphical model, namely a Bayesian network. Performance of that method was investigated in terms of accuracy and bias of the decisional outcomes. Influence of an informed elicitation of the prior belief of chronological age was also studied by means of a sensitivity analysis. Outcomes in terms of accuracy were adequate with standard requirements for forensic adult age estimation. Findings also indicated that the Bayesian method does not show a particular tendency towards under- or overestimation of the age variable. Outcomes of the sensitivity analysis showed that results on estimation are improved with a ration elicitation of the prior probabilities of age.

Bayesian inference of radiation belt loss timescales.

NASA Astrophysics Data System (ADS)

Camporeale, E.; Chandorkar, M.

2017-12-01

Electron fluxes in the Earth's radiation belts are routinely studied using the classical quasi-linear radial diffusion model. Although this simplified linear equation has proven to be an indispensable tool in understanding the dynamics of the radiation belt, it requires specification of quantities such as the diffusion coefficient and electron loss timescales that are never directly measured. Researchers have so far assumed a-priori parameterisations for radiation belt quantities and derived the best fit using satellite data. The state of the art in this domain lacks a coherent formulation of this problem in a probabilistic framework. We present some recent progress that we have made in performing Bayesian inference of radial diffusion parameters. We achieve this by making extensive use of the theory connecting Gaussian Processes and linear partial differential equations, and performing Markov Chain Monte Carlo sampling of radial diffusion parameters. These results are important for understanding the role and the propagation of uncertainties in radiation belt simulations and, eventually, for providing a probabilistic forecast of energetic electron fluxes in a Space Weather context.

Bayesian networks improve causal environmental assessments for evidence-based policy

EPA Science Inventory

Rule-based weight of evidence approaches to ecological risk assessment may not account for uncertainties and generally lack probabilistic integration of lines of evidence. Bayesian networks allow causal inferences to be made from evidence by including causal knowledge about the p...

A Bayesian Hierarchical Model for Glacial Dynamics Based on the Shallow Ice Approximation and its Evaluation Using Analytical Solutions

NASA Astrophysics Data System (ADS)

Gopalan, Giri; Hrafnkelsson, Birgir; Aðalgeirsdóttir, Guðfinna; Jarosch, Alexander H.; Pálsson, Finnur

2018-03-01

Bayesian hierarchical modeling can assist the study of glacial dynamics and ice flow properties. This approach will allow glaciologists to make fully probabilistic predictions for the thickness of a glacier at unobserved spatio-temporal coordinates, and it will also allow for the derivation of posterior probability distributions for key physical parameters such as ice viscosity and basal sliding. The goal of this paper is to develop a proof of concept for a Bayesian hierarchical model constructed, which uses exact analytical solutions for the shallow ice approximation (SIA) introduced by Bueler et al. (2005). A suite of test simulations utilizing these exact solutions suggests that this approach is able to adequately model numerical errors and produce useful physical parameter posterior distributions and predictions. A byproduct of the development of the Bayesian hierarchical model is the derivation of a novel finite difference method for solving the SIA partial differential equation (PDE). An additional novelty of this work is the correction of numerical errors induced through a numerical solution using a statistical model. This error correcting process models numerical errors that accumulate forward in time and spatial variation of numerical errors between the dome, interior, and margin of a glacier.

A Bayesian method for using simulator data to enhance human error probabilities assigned by existing HRA methods

DOE PAGES

Groth, Katrina M.; Smith, Curtis L.; Swiler, Laura P.

2014-04-05

In the past several years, several international agencies have begun to collect data on human performance in nuclear power plant simulators [1]. This data provides a valuable opportunity to improve human reliability analysis (HRA), but there improvements will not be realized without implementation of Bayesian methods. Bayesian methods are widely used in to incorporate sparse data into models in many parts of probabilistic risk assessment (PRA), but Bayesian methods have not been adopted by the HRA community. In this article, we provide a Bayesian methodology to formally use simulator data to refine the human error probabilities (HEPs) assigned by existingmore » HRA methods. We demonstrate the methodology with a case study, wherein we use simulator data from the Halden Reactor Project to update the probability assignments from the SPAR-H method. The case study demonstrates the ability to use performance data, even sparse data, to improve existing HRA methods. Furthermore, this paper also serves as a demonstration of the value of Bayesian methods to improve the technical basis of HRA.« less

Bayesian Assessment of the Uncertainties of Estimates of a Conceptual Rainfall-Runoff Model Parameters

NASA Astrophysics Data System (ADS)

Silva, F. E. O. E.; Naghettini, M. D. C.; Fernandes, W.

2014-12-01

This paper evaluated the uncertainties associated with the estimation of the parameters of a conceptual rainfall-runoff model, through the use of Bayesian inference techniques by Monte Carlo simulation. The Pará River sub-basin, located in the upper São Francisco river basin, in southeastern Brazil, was selected for developing the studies. In this paper, we used the Rio Grande conceptual hydrologic model (EHR/UFMG, 2001) and the Markov Chain Monte Carlo simulation method named DREAM (VRUGT, 2008a). Two probabilistic models for the residues were analyzed: (i) the classic [Normal likelihood - r ≈ N (0, σ²)]; and (ii) a generalized likelihood (SCHOUPS & VRUGT, 2010), in which it is assumed that the differences between observed and simulated flows are correlated, non-stationary, and distributed as a Skew Exponential Power density. The assumptions made for both models were checked to ensure that the estimation of uncertainties in the parameters was not biased. The results showed that the Bayesian approach proved to be adequate to the proposed objectives, enabling and reinforcing the importance of assessing the uncertainties associated with hydrological modeling.

Probabilistic risk assessment for a loss of coolant accident in McMaster Nuclear Reactor and application of reliability physics model for modeling human reliability

NASA Astrophysics Data System (ADS)

Ha, Taesung

A probabilistic risk assessment (PRA) was conducted for a loss of coolant accident, (LOCA) in the McMaster Nuclear Reactor (MNR). A level 1 PRA was completed including event sequence modeling, system modeling, and quantification. To support the quantification of the accident sequence identified, data analysis using the Bayesian method and human reliability analysis (HRA) using the accident sequence evaluation procedure (ASEP) approach were performed. Since human performance in research reactors is significantly different from that in power reactors, a time-oriented HRA model (reliability physics model) was applied for the human error probability (HEP) estimation of the core relocation. This model is based on two competing random variables: phenomenological time and performance time. The response surface and direct Monte Carlo simulation with Latin Hypercube sampling were applied for estimating the phenomenological time, whereas the performance time was obtained from interviews with operators. An appropriate probability distribution for the phenomenological time was assigned by statistical goodness-of-fit tests. The human error probability (HEP) for the core relocation was estimated from these two competing quantities: phenomenological time and operators' performance time. The sensitivity of each probability distribution in human reliability estimation was investigated. In order to quantify the uncertainty in the predicted HEPs, a Bayesian approach was selected due to its capability of incorporating uncertainties in model itself and the parameters in that model. The HEP from the current time-oriented model was compared with that from the ASEP approach. Both results were used to evaluate the sensitivity of alternative huinan reliability modeling for the manual core relocation in the LOCA risk model. This exercise demonstrated the applicability of a reliability physics model supplemented with a. Bayesian approach for modeling human reliability and its potential usefulness of quantifying model uncertainty as sensitivity analysis in the PRA model.

Effects of additional data on Bayesian clustering.

PubMed

Yamazaki, Keisuke

2017-10-01

Hierarchical probabilistic models, such as mixture models, are used for cluster analysis. These models have two types of variables: observable and latent. In cluster analysis, the latent variable is estimated, and it is expected that additional information will improve the accuracy of the estimation of the latent variable. Many proposed learning methods are able to use additional data; these include semi-supervised learning and transfer learning. However, from a statistical point of view, a complex probabilistic model that encompasses both the initial and additional data might be less accurate due to having a higher-dimensional parameter. The present paper presents a theoretical analysis of the accuracy of such a model and clarifies which factor has the greatest effect on its accuracy, the advantages of obtaining additional data, and the disadvantages of increasing the complexity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Multi-model ensemble hydrologic prediction using Bayesian model averaging

NASA Astrophysics Data System (ADS)

Duan, Qingyun; Ajami, Newsha K.; Gao, Xiaogang; Sorooshian, Soroosh

2007-05-01

Multi-model ensemble strategy is a means to exploit the diversity of skillful predictions from different models. This paper studies the use of Bayesian model averaging (BMA) scheme to develop more skillful and reliable probabilistic hydrologic predictions from multiple competing predictions made by several hydrologic models. BMA is a statistical procedure that infers consensus predictions by weighing individual predictions based on their probabilistic likelihood measures, with the better performing predictions receiving higher weights than the worse performing ones. Furthermore, BMA provides a more reliable description of the total predictive uncertainty than the original ensemble, leading to a sharper and better calibrated probability density function (PDF) for the probabilistic predictions. In this study, a nine-member ensemble of hydrologic predictions was used to test and evaluate the BMA scheme. This ensemble was generated by calibrating three different hydrologic models using three distinct objective functions. These objective functions were chosen in a way that forces the models to capture certain aspects of the hydrograph well (e.g., peaks, mid-flows and low flows). Two sets of numerical experiments were carried out on three test basins in the US to explore the best way of using the BMA scheme. In the first set, a single set of BMA weights was computed to obtain BMA predictions, while the second set employed multiple sets of weights, with distinct sets corresponding to different flow intervals. In both sets, the streamflow values were transformed using Box-Cox transformation to ensure that the probability distribution of the prediction errors is approximately Gaussian. A split sample approach was used to obtain and validate the BMA predictions. The test results showed that BMA scheme has the advantage of generating more skillful and equally reliable probabilistic predictions than original ensemble. The performance of the expected BMA predictions in terms of daily root mean square error (DRMS) and daily absolute mean error (DABS) is generally superior to that of the best individual predictions. Furthermore, the BMA predictions employing multiple sets of weights are generally better than those using single set of weights.

Data analysis using scale-space filtering and Bayesian probabilistic reasoning

NASA Technical Reports Server (NTRS)

Kulkarni, Deepak; Kutulakos, Kiriakos; Robinson, Peter

1991-01-01

This paper describes a program for analysis of output curves from Differential Thermal Analyzer (DTA). The program first extracts probabilistic qualitative features from a DTA curve of a soil sample, and then uses Bayesian probabilistic reasoning to infer the mineral in the soil. The qualifier module employs a simple and efficient extension of scale-space filtering suitable for handling DTA data. We have observed that points can vanish from contours in the scale-space image when filtering operations are not highly accurate. To handle the problem of vanishing points, perceptual organizations heuristics are used to group the points into lines. Next, these lines are grouped into contours by using additional heuristics. Probabilities are associated with these contours using domain-specific correlations. A Bayes tree classifier processes probabilistic features to infer the presence of different minerals in the soil. Experiments show that the algorithm that uses domain-specific correlation to infer qualitative features outperforms a domain-independent algorithm that does not.

Bayesian Knowledge Fusion in Prognostics and Health Management—A Case Study

NASA Astrophysics Data System (ADS)

Rabiei, Masoud; Modarres, Mohammad; Mohammad-Djafari, Ali

2011-03-01

In the past few years, a research effort has been in progress at University of Maryland to develop a Bayesian framework based on Physics of Failure (PoF) for risk assessment and fleet management of aging airframes. Despite significant achievements in modelling of crack growth behavior using fracture mechanics, it is still of great interest to find practical techniques for monitoring the crack growth instances using nondestructive inspection and to integrate such inspection results with the fracture mechanics models to improve the predictions. The ultimate goal of this effort is to develop an integrated probabilistic framework for utilizing all of the available information to come up with enhanced (less uncertain) predictions for structural health of the aircraft in future missions. Such information includes material level fatigue models and test data, health monitoring measurements and inspection field data. In this paper, a case study of using Bayesian fusion technique for integrating information from multiple sources in a structural health management problem is presented.

How to interpret the results of medical time series data analysis: Classical statistical approaches versus dynamic Bayesian network modeling.

PubMed

Onisko, Agnieszka; Druzdzel, Marek J; Austin, R Marshall

2016-01-01

Classical statistics is a well-established approach in the analysis of medical data. While the medical community seems to be familiar with the concept of a statistical analysis and its interpretation, the Bayesian approach, argued by many of its proponents to be superior to the classical frequentist approach, is still not well-recognized in the analysis of medical data. The goal of this study is to encourage data analysts to use the Bayesian approach, such as modeling with graphical probabilistic networks, as an insightful alternative to classical statistical analysis of medical data. This paper offers a comparison of two approaches to analysis of medical time series data: (1) classical statistical approach, such as the Kaplan-Meier estimator and the Cox proportional hazards regression model, and (2) dynamic Bayesian network modeling. Our comparison is based on time series cervical cancer screening data collected at Magee-Womens Hospital, University of Pittsburgh Medical Center over 10 years. The main outcomes of our comparison are cervical cancer risk assessments produced by the three approaches. However, our analysis discusses also several aspects of the comparison, such as modeling assumptions, model building, dealing with incomplete data, individualized risk assessment, results interpretation, and model validation. Our study shows that the Bayesian approach is (1) much more flexible in terms of modeling effort, and (2) it offers an individualized risk assessment, which is more cumbersome for classical statistical approaches.

A Bayesian connectivity-based approach to constructing probabilistic gene regulatory networks.

PubMed

Zhou, Xiaobo; Wang, Xiaodong; Pal, Ranadip; Ivanov, Ivan; Bittner, Michael; Dougherty, Edward R

2004-11-22

We have hypothesized that the construction of transcriptional regulatory networks using a method that optimizes connectivity would lead to regulation consistent with biological expectations. A key expectation is that the hypothetical networks should produce a few, very strong attractors, highly similar to the original observations, mimicking biological state stability and determinism. Another central expectation is that, since it is expected that the biological control is distributed and mutually reinforcing, interpretation of the observations should lead to a very small number of connection schemes. We propose a fully Bayesian approach to constructing probabilistic gene regulatory networks (PGRNs) that emphasizes network topology. The method computes the possible parent sets of each gene, the corresponding predictors and the associated probabilities based on a nonlinear perceptron model, using a reversible jump Markov chain Monte Carlo (MCMC) technique, and an MCMC method is employed to search the network configurations to find those with the highest Bayesian scores to construct the PGRN. The Bayesian method has been used to construct a PGRN based on the observed behavior of a set of genes whose expression patterns vary across a set of melanoma samples exhibiting two very different phenotypes with respect to cell motility and invasiveness. Key biological features have been faithfully reflected in the model. Its steady-state distribution contains attractors that are either identical or very similar to the states observed in the data, and many of the attractors are singletons, which mimics the biological propensity to stably occupy a given state. Most interestingly, the connectivity rules for the most optimal generated networks constituting the PGRN are remarkably similar, as would be expected for a network operating on a distributed basis, with strong interactions between the components.

A comparison of Monte Carlo-based Bayesian parameter estimation methods for stochastic models of genetic networks

PubMed Central

Zaikin, Alexey; Míguez, Joaquín

2017-01-01

We compare three state-of-the-art Bayesian inference methods for the estimation of the unknown parameters in a stochastic model of a genetic network. In particular, we introduce a stochastic version of the paradigmatic synthetic multicellular clock model proposed by Ullner et al., 2007. By introducing dynamical noise in the model and assuming that the partial observations of the system are contaminated by additive noise, we enable a principled mechanism to represent experimental uncertainties in the synthesis of the multicellular system and pave the way for the design of probabilistic methods for the estimation of any unknowns in the model. Within this setup, we tackle the Bayesian estimation of a subset of the model parameters. Specifically, we compare three Monte Carlo based numerical methods for the approximation of the posterior probability density function of the unknown parameters given a set of partial and noisy observations of the system. The schemes we assess are the particle Metropolis-Hastings (PMH) algorithm, the nonlinear population Monte Carlo (NPMC) method and the approximate Bayesian computation sequential Monte Carlo (ABC-SMC) scheme. We present an extensive numerical simulation study, which shows that while the three techniques can effectively solve the problem there are significant differences both in estimation accuracy and computational efficiency. PMID:28797087

Methods for Probabilistic Fault Diagnosis: An Electrical Power System Case Study

NASA Technical Reports Server (NTRS)

Ricks, Brian W.; Mengshoel, Ole J.

2009-01-01

Health management systems that more accurately and quickly diagnose faults that may occur in different technical systems on-board a vehicle will play a key role in the success of future NASA missions. We discuss in this paper the diagnosis of abrupt continuous (or parametric) faults within the context of probabilistic graphical models, more specifically Bayesian networks that are compiled to arithmetic circuits. This paper extends our previous research, within the same probabilistic setting, on diagnosis of abrupt discrete faults. Our approach and diagnostic algorithm ProDiagnose are domain-independent; however we use an electrical power system testbed called ADAPT as a case study. In one set of ADAPT experiments, performed as part of the 2009 Diagnostic Challenge, our system turned out to have the best performance among all competitors. In a second set of experiments, we show how we have recently further significantly improved the performance of the probabilistic model of ADAPT. While these experiments are obtained for an electrical power system testbed, we believe they can easily be transitioned to real-world systems, thus promising to increase the success of future NASA missions.

A Bayesian Approach to Determination of F, D, and Z Values Used in Steam Sterilization Validation.

PubMed

Faya, Paul; Stamey, James D; Seaman, John W

2017-01-01

For manufacturers of sterile drug products, steam sterilization is a common method used to provide assurance of the sterility of manufacturing equipment and products. The validation of sterilization processes is a regulatory requirement and relies upon the estimation of key resistance parameters of microorganisms. Traditional methods have relied upon point estimates for the resistance parameters. In this paper, we propose a Bayesian method for estimation of the well-known D T , z , and F o values that are used in the development and validation of sterilization processes. A Bayesian approach allows the uncertainty about these values to be modeled using probability distributions, thereby providing a fully risk-based approach to measures of sterility assurance. An example is given using the survivor curve and fraction negative methods for estimation of resistance parameters, and we present a means by which a probabilistic conclusion can be made regarding the ability of a process to achieve a specified sterility criterion. LAY ABSTRACT: For manufacturers of sterile drug products, steam sterilization is a common method used to provide assurance of the sterility of manufacturing equipment and products. The validation of sterilization processes is a regulatory requirement and relies upon the estimation of key resistance parameters of microorganisms. Traditional methods have relied upon point estimates for the resistance parameters. In this paper, we propose a Bayesian method for estimation of the critical process parameters that are evaluated in the development and validation of sterilization processes. A Bayesian approach allows the uncertainty about these parameters to be modeled using probability distributions, thereby providing a fully risk-based approach to measures of sterility assurance. An example is given using the survivor curve and fraction negative methods for estimation of resistance parameters, and we present a means by which a probabilistic conclusion can be made regarding the ability of a process to achieve a specified sterility criterion. © PDA, Inc. 2017.

Bayesian network modeling applied to coastal geomorphology: lessons learned from a decade of experimentation and application

NASA Astrophysics Data System (ADS)

Plant, N. G.; Thieler, E. R.; Gutierrez, B.; Lentz, E. E.; Zeigler, S. L.; Van Dongeren, A.; Fienen, M. N.

2016-12-01

We evaluate the strengths and weaknesses of Bayesian networks that have been used to address scientific and decision-support questions related to coastal geomorphology. We will provide an overview of coastal geomorphology research that has used Bayesian networks and describe what this approach can do and when it works (or fails to work). Over the past decade, Bayesian networks have been formulated to analyze the multi-variate structure and evolution of coastal morphology and associated human and ecological impacts. The approach relates observable system variables to each other by estimating discrete correlations. The resulting Bayesian-networks make predictions that propagate errors, conduct inference via Bayes rule, or both. In scientific applications, the model results are useful for hypothesis testing, using confidence estimates to gage the strength of tests while applications to coastal resource management are aimed at decision-support, where the probabilities of desired ecosystems outcomes are evaluated. The range of Bayesian-network applications to coastal morphology includes emulation of high-resolution wave transformation models to make oceanographic predictions, morphologic response to storms and/or sea-level rise, groundwater response to sea-level rise and morphologic variability, habitat suitability for endangered species, and assessment of monetary or human-life risk associated with storms. All of these examples are based on vast observational data sets, numerical model output, or both. We will discuss the progression of our experiments, which has included testing whether the Bayesian-network approach can be implemented and is appropriate for addressing basic and applied scientific problems and evaluating the hindcast and forecast skill of these implementations. We will present and discuss calibration/validation tests that are used to assess the robustness of Bayesian-network models and we will compare these results to tests of other models. This will demonstrate how Bayesian networks are used to extract new insights about coastal morphologic behavior, assess impacts to societal and ecological systems, and communicate probabilistic predictions to decision makers.

A novel approach for pilot error detection using Dynamic Bayesian Networks.

PubMed

Saada, Mohamad; Meng, Qinggang; Huang, Tingwen

2014-06-01

In the last decade Dynamic Bayesian Networks (DBNs) have become one type of the most attractive probabilistic modelling framework extensions of Bayesian Networks (BNs) for working under uncertainties from a temporal perspective. Despite this popularity not many researchers have attempted to study the use of these networks in anomaly detection or the implications of data anomalies on the outcome of such models. An abnormal change in the modelled environment's data at a given time, will cause a trailing chain effect on data of all related environment variables in current and consecutive time slices. Albeit this effect fades with time, it still can have an ill effect on the outcome of such models. In this paper we propose an algorithm for pilot error detection, using DBNs as the modelling framework for learning and detecting anomalous data. We base our experiments on the actions of an aircraft pilot, and a flight simulator is created for running the experiments. The proposed anomaly detection algorithm has achieved good results in detecting pilot errors and effects on the whole system.

Bayesian anomaly detection in monitoring data applying relevance vector machine

NASA Astrophysics Data System (ADS)

Saito, Tomoo

2011-04-01

A method for automatically classifying the monitoring data into two categories, normal and anomaly, is developed in order to remove anomalous data included in the enormous amount of monitoring data, applying the relevance vector machine (RVM) to a probabilistic discriminative model with basis functions and their weight parameters whose posterior PDF (probabilistic density function) conditional on the learning data set is given by Bayes' theorem. The proposed framework is applied to actual monitoring data sets containing some anomalous data collected at two buildings in Tokyo, Japan, which shows that the trained models discriminate anomalous data from normal data very clearly, giving high probabilities of being normal to normal data and low probabilities of being normal to anomalous data.

A Model-Based Probabilistic Inversion Framework for Wire Fault Detection Using TDR

NASA Technical Reports Server (NTRS)

Schuet, Stefan R.; Timucin, Dogan A.; Wheeler, Kevin R.

2010-01-01

Time-domain reflectometry (TDR) is one of the standard methods for diagnosing faults in electrical wiring and interconnect systems, with a long-standing history focused mainly on hardware development of both high-fidelity systems for laboratory use and portable hand-held devices for field deployment. While these devices can easily assess distance to hard faults such as sustained opens or shorts, their ability to assess subtle but important degradation such as chafing remains an open question. This paper presents a unified framework for TDR-based chafing fault detection in lossy coaxial cables by combining an S-parameter based forward modeling approach with a probabilistic (Bayesian) inference algorithm. Results are presented for the estimation of nominal and faulty cable parameters from laboratory data.

Predicting Drug Safety and Communicating Risk: Benefits of a Bayesian Approach.

PubMed

Lazic, Stanley E; Edmunds, Nicholas; Pollard, Christopher E

2018-03-01

Drug toxicity is a major source of attrition in drug discovery and development. Pharmaceutical companies routinely use preclinical data to predict clinical outcomes and continue to invest in new assays to improve predictions. However, there are many open questions about how to make the best use of available data, combine diverse data, quantify risk, and communicate risk and uncertainty to enable good decisions. The costs of suboptimal decisions are clear: resources are wasted and patients may be put at risk. We argue that Bayesian methods provide answers to all of these problems and use hERG-mediated QT prolongation as a case study. Benefits of Bayesian machine learning models include intuitive probabilistic statements of risk that incorporate all sources of uncertainty, the option to include diverse data and external information, and visualizations that have a clear link between the output from a statistical model and what this means for risk. Furthermore, Bayesian methods are easy to use with modern software, making their adoption for safety screening straightforward. We include R and Python code to encourage the adoption of these methods.

Reconstruction of metabolic pathways by combining probabilistic graphical model-based and knowledge-based methods

PubMed Central

2014-01-01

Automatic reconstruction of metabolic pathways for an organism from genomics and transcriptomics data has been a challenging and important problem in bioinformatics. Traditionally, known reference pathways can be mapped into an organism-specific ones based on its genome annotation and protein homology. However, this simple knowledge-based mapping method might produce incomplete pathways and generally cannot predict unknown new relations and reactions. In contrast, ab initio metabolic network construction methods can predict novel reactions and interactions, but its accuracy tends to be low leading to a lot of false positives. Here we combine existing pathway knowledge and a new ab initio Bayesian probabilistic graphical model together in a novel fashion to improve automatic reconstruction of metabolic networks. Specifically, we built a knowledge database containing known, individual gene / protein interactions and metabolic reactions extracted from existing reference pathways. Known reactions and interactions were then used as constraints for Bayesian network learning methods to predict metabolic pathways. Using individual reactions and interactions extracted from different pathways of many organisms to guide pathway construction is new and improves both the coverage and accuracy of metabolic pathway construction. We applied this probabilistic knowledge-based approach to construct the metabolic networks from yeast gene expression data and compared its results with 62 known metabolic networks in the KEGG database. The experiment showed that the method improved the coverage of metabolic network construction over the traditional reference pathway mapping method and was more accurate than pure ab initio methods. PMID:25374614

Probabilistic dose-response modeling: case study using dichloromethane PBPK model results.

PubMed

Marino, Dale J; Starr, Thomas B

2007-12-01

A revised assessment of dichloromethane (DCM) has recently been reported that examines the influence of human genetic polymorphisms on cancer risks using deterministic PBPK and dose-response modeling in the mouse combined with probabilistic PBPK modeling in humans. This assessment utilized Bayesian techniques to optimize kinetic variables in mice and humans with mean values from posterior distributions used in the deterministic modeling in the mouse. To supplement this research, a case study was undertaken to examine the potential impact of probabilistic rather than deterministic PBPK and dose-response modeling in mice on subsequent unit risk factor (URF) determinations. Four separate PBPK cases were examined based on the exposure regimen of the NTP DCM bioassay. These were (a) Same Mouse (single draw of all PBPK inputs for both treatment groups); (b) Correlated BW-Same Inputs (single draw of all PBPK inputs for both treatment groups except for bodyweights (BWs), which were entered as correlated variables); (c) Correlated BW-Different Inputs (separate draws of all PBPK inputs for both treatment groups except that BWs were entered as correlated variables); and (d) Different Mouse (separate draws of all PBPK inputs for both treatment groups). Monte Carlo PBPK inputs reflect posterior distributions from Bayesian calibration in the mouse that had been previously reported. A minimum of 12,500 PBPK iterations were undertaken, in which dose metrics, i.e., mg DCM metabolized by the GST pathway/L tissue/day for lung and liver were determined. For dose-response modeling, these metrics were combined with NTP tumor incidence data that were randomly selected from binomial distributions. Resultant potency factors (0.1/ED(10)) were coupled with probabilistic PBPK modeling in humans that incorporated genetic polymorphisms to derive URFs. Results show that there was relatively little difference, i.e., <10% in central tendency and upper percentile URFs, regardless of the case evaluated. Independent draws of PBPK inputs resulted in the slightly higher URFs. Results were also comparable to corresponding values from the previously reported deterministic mouse PBPK and dose-response modeling approach that used LED(10)s to derive potency factors. This finding indicated that the adjustment from ED(10) to LED(10) in the deterministic approach for DCM compensated for variability resulting from probabilistic PBPK and dose-response modeling in the mouse. Finally, results show a similar degree of variability in DCM risk estimates from a number of different sources including the current effort even though these estimates were developed using very different techniques. Given the variety of different approaches involved, 95th percentile-to-mean risk estimate ratios of 2.1-4.1 represent reasonable bounds on variability estimates regarding probabilistic assessments of DCM.

A note on probabilistic models over strings: the linear algebra approach.

PubMed

Bouchard-Côté, Alexandre

2013-12-01

Probabilistic models over strings have played a key role in developing methods that take into consideration indels as phylogenetically informative events. There is an extensive literature on using automata and transducers on phylogenies to do inference on these probabilistic models, in which an important theoretical question is the complexity of computing the normalization of a class of string-valued graphical models. This question has been investigated using tools from combinatorics, dynamic programming, and graph theory, and has practical applications in Bayesian phylogenetics. In this work, we revisit this theoretical question from a different point of view, based on linear algebra. The main contribution is a set of results based on this linear algebra view that facilitate the analysis and design of inference algorithms on string-valued graphical models. As an illustration, we use this method to give a new elementary proof of a known result on the complexity of inference on the "TKF91" model, a well-known probabilistic model over strings. Compared to previous work, our proving method is easier to extend to other models, since it relies on a novel weak condition, triangular transducers, which is easy to establish in practice. The linear algebra view provides a concise way of describing transducer algorithms and their compositions, opens the possibility of transferring fast linear algebra libraries (for example, based on GPUs), as well as low rank matrix approximation methods, to string-valued inference problems.

Comparing Bayesian stable isotope mixing models: Which tools are best for sediments?

NASA Astrophysics Data System (ADS)

Morris, David; Macko, Stephen

2016-04-01

Bayesian stable isotope mixing models have received much attention as a means of coping with multiple sources and uncertainty in isotope ecology (e.g. Phillips et al., 2014), enabling the probabilistic determination of the contributions made by each food source to the total diet of the organism in question. We have applied these techniques to marine sediments for the first time. The sediments of the Chukchi Sea and Beaufort Sea offer an opportunity to utilize these models for organic geochemistry, as there are three likely sources of organic carbon; pelagic phytoplankton, sea ice algae and terrestrial material from rivers and coastal erosion, as well as considerable variation in the marine δ13C values. Bayesian mixing models using bulk δ13C and δ15N data from Shelf Basin Interaction samples allow for the probabilistic determination of the contributions made by each of the sources to the organic carbon budget, and can be compared with existing source contribution estimates based upon biomarker models (e.g. Belicka & Harvey, 2009, Faux, Belicka, & Rodger Harvey, 2011). The δ13C of this preserved material varied from -22.1 to -16.7‰ (mean -19.4±1.3‰), while δ15N varied from 4.1 to 7.6‰ (mean 5.7±1.1‰). Using the SIAR model, we found that water column productivity was the source of between 50 and 70% of the organic carbon buried in this portion of the western Arctic with the remainder mainly supplied by sea ice algal productivity (25-35%) and terrestrial inputs (15%). With many mixing models now available, this study will compare SIAR with MixSIAR and the new FRUITS model. Monte Carlo modeling of the mixing polygon will be used to validate the models, and hierarchical models will be utilised to glean more information from the data set.

Bayesian probabilistic approach for inverse source determination from limited and noisy chemical or biological sensor concentration measurements

NASA Astrophysics Data System (ADS)

Yee, Eugene

2007-04-01

Although a great deal of research effort has been focused on the forward prediction of the dispersion of contaminants (e.g., chemical and biological warfare agents) released into the turbulent atmosphere, much less work has been directed toward the inverse prediction of agent source location and strength from the measured concentration, even though the importance of this problem for a number of practical applications is obvious. In general, the inverse problem of source reconstruction is ill-posed and unsolvable without additional information. It is demonstrated that a Bayesian probabilistic inferential framework provides a natural and logically consistent method for source reconstruction from a limited number of noisy concentration data. In particular, the Bayesian approach permits one to incorporate prior knowledge about the source as well as additional information regarding both model and data errors. The latter enables a rigorous determination of the uncertainty in the inference of the source parameters (e.g., spatial location, emission rate, release time, etc.), hence extending the potential of the methodology as a tool for quantitative source reconstruction. A model (or, source-receptor relationship) that relates the source distribution to the concentration data measured by a number of sensors is formulated, and Bayesian probability theory is used to derive the posterior probability density function of the source parameters. A computationally efficient methodology for determination of the likelihood function for the problem, based on an adjoint representation of the source-receptor relationship, is described. Furthermore, we describe the application of efficient stochastic algorithms based on Markov chain Monte Carlo (MCMC) for sampling from the posterior distribution of the source parameters, the latter of which is required to undertake the Bayesian computation. The Bayesian inferential methodology for source reconstruction is validated against real dispersion data for two cases involving contaminant dispersion in highly disturbed flows over urban and complex environments where the idealizations of horizontal homogeneity and/or temporal stationarity in the flow cannot be applied to simplify the problem. Furthermore, the methodology is applied to the case of reconstruction of multiple sources.

Probabilistic Common Spatial Patterns for Multichannel EEG Analysis

PubMed Central

Chen, Zhe; Gao, Xiaorong; Li, Yuanqing; Brown, Emery N.; Gao, Shangkai

2015-01-01

Common spatial patterns (CSP) is a well-known spatial filtering algorithm for multichannel electroencephalogram (EEG) analysis. In this paper, we cast the CSP algorithm in a probabilistic modeling setting. Specifically, probabilistic CSP (P-CSP) is proposed as a generic EEG spatio-temporal modeling framework that subsumes the CSP and regularized CSP algorithms. The proposed framework enables us to resolve the overfitting issue of CSP in a principled manner. We derive statistical inference algorithms that can alleviate the issue of local optima. In particular, an efficient algorithm based on eigendecomposition is developed for maximum a posteriori (MAP) estimation in the case of isotropic noise. For more general cases, a variational algorithm is developed for group-wise sparse Bayesian learning for the P-CSP model and for automatically determining the model size. The two proposed algorithms are validated on a simulated data set. Their practical efficacy is also demonstrated by successful applications to single-trial classifications of three motor imagery EEG data sets and by the spatio-temporal pattern analysis of one EEG data set recorded in a Stroop color naming task. PMID:26005228

A comparison of machine learning and Bayesian modelling for molecular serotyping.

PubMed

Newton, Richard; Wernisch, Lorenz

2017-08-11

Streptococcus pneumoniae is a human pathogen that is a major cause of infant mortality. Identifying the pneumococcal serotype is an important step in monitoring the impact of vaccines used to protect against disease. Genomic microarrays provide an effective method for molecular serotyping. Previously we developed an empirical Bayesian model for the classification of serotypes from a molecular serotyping array. With only few samples available, a model driven approach was the only option. In the meanwhile, several thousand samples have been made available to us, providing an opportunity to investigate serotype classification by machine learning methods, which could complement the Bayesian model. We compare the performance of the original Bayesian model with two machine learning algorithms: Gradient Boosting Machines and Random Forests. We present our results as an example of a generic strategy whereby a preliminary probabilistic model is complemented or replaced by a machine learning classifier once enough data are available. Despite the availability of thousands of serotyping arrays, a problem encountered when applying machine learning methods is the lack of training data containing mixtures of serotypes; due to the large number of possible combinations. Most of the available training data comprises samples with only a single serotype. To overcome the lack of training data we implemented an iterative analysis, creating artificial training data of serotype mixtures by combining raw data from single serotype arrays. With the enhanced training set the machine learning algorithms out perform the original Bayesian model. However, for serotypes currently lacking sufficient training data the best performing implementation was a combination of the results of the Bayesian Model and the Gradient Boosting Machine. As well as being an effective method for classifying biological data, machine learning can also be used as an efficient method for revealing subtle biological insights, which we illustrate with an example.

A Web-Based System for Bayesian Benchmark Dose Estimation.

PubMed

Shao, Kan; Shapiro, Andrew J

2018-01-11

Benchmark dose (BMD) modeling is an important step in human health risk assessment and is used as the default approach to identify the point of departure for risk assessment. A probabilistic framework for dose-response assessment has been proposed and advocated by various institutions and organizations; therefore, a reliable tool is needed to provide distributional estimates for BMD and other important quantities in dose-response assessment. We developed an online system for Bayesian BMD (BBMD) estimation and compared results from this software with U.S. Environmental Protection Agency's (EPA's) Benchmark Dose Software (BMDS). The system is built on a Bayesian framework featuring the application of Markov chain Monte Carlo (MCMC) sampling for model parameter estimation and BMD calculation, which makes the BBMD system fundamentally different from the currently prevailing BMD software packages. In addition to estimating the traditional BMDs for dichotomous and continuous data, the developed system is also capable of computing model-averaged BMD estimates. A total of 518 dichotomous and 108 continuous data sets extracted from the U.S. EPA's Integrated Risk Information System (IRIS) database (and similar databases) were used as testing data to compare the estimates from the BBMD and BMDS programs. The results suggest that the BBMD system may outperform the BMDS program in a number of aspects, including fewer failed BMD and BMDL calculations and estimates. The BBMD system is a useful alternative tool for estimating BMD with additional functionalities for BMD analysis based on most recent research. Most importantly, the BBMD has the potential to incorporate prior information to make dose-response modeling more reliable and can provide distributional estimates for important quantities in dose-response assessment, which greatly facilitates the current trend for probabilistic risk assessment. https://doi.org/10.1289/EHP1289.

Bayesian network models for error detection in radiotherapy plans

NASA Astrophysics Data System (ADS)

Kalet, Alan M.; Gennari, John H.; Ford, Eric C.; Phillips, Mark H.

2015-04-01

The purpose of this study is to design and develop a probabilistic network for detecting errors in radiotherapy plans for use at the time of initial plan verification. Our group has initiated a multi-pronged approach to reduce these errors. We report on our development of Bayesian models of radiotherapy plans. Bayesian networks consist of joint probability distributions that define the probability of one event, given some set of other known information. Using the networks, we find the probability of obtaining certain radiotherapy parameters, given a set of initial clinical information. A low probability in a propagated network then corresponds to potential errors to be flagged for investigation. To build our networks we first interviewed medical physicists and other domain experts to identify the relevant radiotherapy concepts and their associated interdependencies and to construct a network topology. Next, to populate the network’s conditional probability tables, we used the Hugin Expert software to learn parameter distributions from a subset of de-identified data derived from a radiation oncology based clinical information database system. These data represent 4990 unique prescription cases over a 5 year period. Under test case scenarios with approximately 1.5% introduced error rates, network performance produced areas under the ROC curve of 0.88, 0.98, and 0.89 for the lung, brain and female breast cancer error detection networks, respectively. Comparison of the brain network to human experts performance (AUC of 0.90 ± 0.01) shows the Bayes network model performs better than domain experts under the same test conditions. Our results demonstrate the feasibility and effectiveness of comprehensive probabilistic models as part of decision support systems for improved detection of errors in initial radiotherapy plan verification procedures.

A Hierarchical Bayesian Model for Crowd Emotions

PubMed Central

Urizar, Oscar J.; Baig, Mirza S.; Barakova, Emilia I.; Regazzoni, Carlo S.; Marcenaro, Lucio; Rauterberg, Matthias

2016-01-01

Estimation of emotions is an essential aspect in developing intelligent systems intended for crowded environments. However, emotion estimation in crowds remains a challenging problem due to the complexity in which human emotions are manifested and the capability of a system to perceive them in such conditions. This paper proposes a hierarchical Bayesian model to learn in unsupervised manner the behavior of individuals and of the crowd as a single entity, and explore the relation between behavior and emotions to infer emotional states. Information about the motion patterns of individuals are described using a self-organizing map, and a hierarchical Bayesian network builds probabilistic models to identify behaviors and infer the emotional state of individuals and the crowd. This model is trained and tested using data produced from simulated scenarios that resemble real-life environments. The conducted experiments tested the efficiency of our method to learn, detect and associate behaviors with emotional states yielding accuracy levels of 74% for individuals and 81% for the crowd, similar in performance with existing methods for pedestrian behavior detection but with novel concepts regarding the analysis of crowds. PMID:27458366

Topics in Computational Bayesian Statistics With Applications to Hierarchical Models in Astronomy and Sociology

NASA Astrophysics Data System (ADS)

Sahai, Swupnil

This thesis includes three parts. The overarching theme is how to analyze structured hierarchical data, with applications to astronomy and sociology. The first part discusses how expectation propagation can be used to parallelize the computation when fitting big hierarchical bayesian models. This methodology is then used to fit a novel, nonlinear mixture model to ultraviolet radiation from various regions of the observable universe. The second part discusses how the Stan probabilistic programming language can be used to numerically integrate terms in a hierarchical bayesian model. This technique is demonstrated on supernovae data to significantly speed up convergence to the posterior distribution compared to a previous study that used a Gibbs-type sampler. The third part builds a formal latent kernel representation for aggregate relational data as a way to more robustly estimate the mixing characteristics of agents in a network. In particular, the framework is applied to sociology surveys to estimate, as a function of ego age, the age and sex composition of the personal networks of individuals in the United States.

Bayesian Inference for Source Reconstruction: A Real-World Application

PubMed Central

Yee, Eugene; Hoffman, Ian; Ungar, Kurt

2014-01-01

This paper applies a Bayesian probabilistic inferential methodology for the reconstruction of the location and emission rate from an actual contaminant source (emission from the Chalk River Laboratories medical isotope production facility) using a small number of activity concentration measurements of a noble gas (Xenon-133) obtained from three stations that form part of the International Monitoring System radionuclide network. The sampling of the resulting posterior distribution of the source parameters is undertaken using a very efficient Markov chain Monte Carlo technique that utilizes a multiple-try differential evolution adaptive Metropolis algorithm with an archive of past states. It is shown that the principal difficulty in the reconstruction lay in the correct specification of the model errors (both scale and structure) for use in the Bayesian inferential methodology. In this context, two different measurement models for incorporation of the model error of the predicted concentrations are considered. The performance of both of these measurement models with respect to their accuracy and precision in the recovery of the source parameters is compared and contrasted. PMID:27379292

Learning In networks

NASA Technical Reports Server (NTRS)

Buntine, Wray L.

1995-01-01

Intelligent systems require software incorporating probabilistic reasoning, and often times learning. Networks provide a framework and methodology for creating this kind of software. This paper introduces network models based on chain graphs with deterministic nodes. Chain graphs are defined as a hierarchical combination of Bayesian and Markov networks. To model learning, plates on chain graphs are introduced to model independent samples. The paper concludes by discussing various operations that can be performed on chain graphs with plates as a simplification process or to generate learning algorithms.

Bayesian uncertainty quantification in linear models for diffusion MRI.

PubMed

Sjölund, Jens; Eklund, Anders; Özarslan, Evren; Herberthson, Magnus; Bånkestad, Maria; Knutsson, Hans

2018-03-29

Diffusion MRI (dMRI) is a valuable tool in the assessment of tissue microstructure. By fitting a model to the dMRI signal it is possible to derive various quantitative features. Several of the most popular dMRI signal models are expansions in an appropriately chosen basis, where the coefficients are determined using some variation of least-squares. However, such approaches lack any notion of uncertainty, which could be valuable in e.g. group analyses. In this work, we use a probabilistic interpretation of linear least-squares methods to recast popular dMRI models as Bayesian ones. This makes it possible to quantify the uncertainty of any derived quantity. In particular, for quantities that are affine functions of the coefficients, the posterior distribution can be expressed in closed-form. We simulated measurements from single- and double-tensor models where the correct values of several quantities are known, to validate that the theoretically derived quantiles agree with those observed empirically. We included results from residual bootstrap for comparison and found good agreement. The validation employed several different models: Diffusion Tensor Imaging (DTI), Mean Apparent Propagator MRI (MAP-MRI) and Constrained Spherical Deconvolution (CSD). We also used in vivo data to visualize maps of quantitative features and corresponding uncertainties, and to show how our approach can be used in a group analysis to downweight subjects with high uncertainty. In summary, we convert successful linear models for dMRI signal estimation to probabilistic models, capable of accurate uncertainty quantification. Copyright © 2018 Elsevier Inc. All rights reserved.

Probabilistic segmentation and intensity estimation for microarray images.

PubMed

Gottardo, Raphael; Besag, Julian; Stephens, Matthew; Murua, Alejandro

2006-01-01

We describe a probabilistic approach to simultaneous image segmentation and intensity estimation for complementary DNA microarray experiments. The approach overcomes several limitations of existing methods. In particular, it (a) uses a flexible Markov random field approach to segmentation that allows for a wider range of spot shapes than existing methods, including relatively common 'doughnut-shaped' spots; (b) models the image directly as background plus hybridization intensity, and estimates the two quantities simultaneously, avoiding the common logical error that estimates of foreground may be less than those of the corresponding background if the two are estimated separately; and (c) uses a probabilistic modeling approach to simultaneously perform segmentation and intensity estimation, and to compute spot quality measures. We describe two approaches to parameter estimation: a fast algorithm, based on the expectation-maximization and the iterated conditional modes algorithms, and a fully Bayesian framework. These approaches produce comparable results, and both appear to offer some advantages over other methods. We use an HIV experiment to compare our approach to two commercial software products: Spot and Arrayvision.

Applications of Bayesian spectrum representation in acoustics

NASA Astrophysics Data System (ADS)

Botts, Jonathan M.

This dissertation utilizes a Bayesian inference framework to enhance the solution of inverse problems where the forward model maps to acoustic spectra. A Bayesian solution to filter design inverts a acoustic spectra to pole-zero locations of a discrete-time filter model. Spatial sound field analysis with a spherical microphone array is a data analysis problem that requires inversion of spatio-temporal spectra to directions of arrival. As with many inverse problems, a probabilistic analysis results in richer solutions than can be achieved with ad-hoc methods. In the filter design problem, the Bayesian inversion results in globally optimal coefficient estimates as well as an estimate the most concise filter capable of representing the given spectrum, within a single framework. This approach is demonstrated on synthetic spectra, head-related transfer function spectra, and measured acoustic reflection spectra. The Bayesian model-based analysis of spatial room impulse responses is presented as an analogous problem with equally rich solution. The model selection mechanism provides an estimate of the number of arrivals, which is necessary to properly infer the directions of simultaneous arrivals. Although, spectrum inversion problems are fairly ubiquitous, the scope of this dissertation has been limited to these two and derivative problems. The Bayesian approach to filter design is demonstrated on an artificial spectrum to illustrate the model comparison mechanism and then on measured head-related transfer functions to show the potential range of application. Coupled with sampling methods, the Bayesian approach is shown to outperform least-squares filter design methods commonly used in commercial software, confirming the need for a global search of the parameter space. The resulting designs are shown to be comparable to those that result from global optimization methods, but the Bayesian approach has the added advantage of a filter length estimate within the same unified framework. The application to reflection data is useful for representing frequency-dependent impedance boundaries in finite difference acoustic simulations. Furthermore, since the filter transfer function is a parametric model, it can be modified to incorporate arbitrary frequency weighting and account for the band-limited nature of measured reflection spectra. Finally, the model is modified to compensate for dispersive error in the finite difference simulation, from the filter design process. Stemming from the filter boundary problem, the implementation of pressure sources in finite difference simulation is addressed in order to assure that schemes properly converge. A class of parameterized source functions is proposed and shown to offer straightforward control of residual error in the simulation. Guided by the notion that the solution to be approximated affects the approximation error, sources are designed which reduce residual dispersive error to the size of round-off errors. The early part of a room impulse response can be characterized by a series of isolated plane waves. Measured with an array of microphones, plane waves map to a directional response of the array or spatial intensity map. Probabilistic inversion of this response results in estimates of the number and directions of image source arrivals. The model-based inversion is shown to avoid ambiguities associated with peak-finding or inspection of the spatial intensity map. For this problem, determining the number of arrivals in a given frame is critical for properly inferring the state of the sound field. This analysis is effectively compression of the spatial room response, which is useful for analysis or encoding of the spatial sound field. Parametric, model-based formulations of these problems enhance the solution in all cases, and a Bayesian interpretation provides a principled approach to model comparison and parameter estimation. v

SIG-VISA: Signal-based Vertically Integrated Seismic Monitoring

NASA Astrophysics Data System (ADS)

Moore, D.; Mayeda, K. M.; Myers, S. C.; Russell, S.

2013-12-01

Traditional seismic monitoring systems rely on discrete detections produced by station processing software; however, while such detections may constitute a useful summary of station activity, they discard large amounts of information present in the original recorded signal. We present SIG-VISA (Signal-based Vertically Integrated Seismic Analysis), a system for seismic monitoring through Bayesian inference on seismic signals. By directly modeling the recorded signal, our approach incorporates additional information unavailable to detection-based methods, enabling higher sensitivity and more accurate localization using techniques such as waveform matching. SIG-VISA's Bayesian forward model of seismic signal envelopes includes physically-derived models of travel times and source characteristics as well as Gaussian process (kriging) statistical models of signal properties that combine interpolation of historical data with extrapolation of learned physical trends. Applying Bayesian inference, we evaluate the model on earthquakes as well as the 2009 DPRK test event, demonstrating a waveform matching effect as part of the probabilistic inference, along with results on event localization and sensitivity. In particular, we demonstrate increased sensitivity from signal-based modeling, in which the SIGVISA signal model finds statistical evidence for arrivals even at stations for which the IMS station processing failed to register any detection.

Probing the Small-scale Structure in Strongly Lensed Systems via Transdimensional Inference

NASA Astrophysics Data System (ADS)

Daylan, Tansu; Cyr-Racine, Francis-Yan; Diaz Rivero, Ana; Dvorkin, Cora; Finkbeiner, Douglas P.

2018-02-01

Strong lensing is a sensitive probe of the small-scale density fluctuations in the Universe. We implement a pipeline to model strongly lensed systems using probabilistic cataloging, which is a transdimensional, hierarchical, and Bayesian framework to sample from a metamodel (union of models with different dimensionality) consistent with observed photon count maps. Probabilistic cataloging allows one to robustly characterize modeling covariances within and across lens models with different numbers of subhalos. Unlike traditional cataloging of subhalos, it does not require model subhalos to improve the goodness of fit above the detection threshold. Instead, it allows the exploitation of all information contained in the photon count maps—for instance, when constraining the subhalo mass function. We further show that, by not including these small subhalos in the lens model, fixed-dimensional inference methods can significantly mismodel the data. Using a simulated Hubble Space Telescope data set, we show that the subhalo mass function can be probed even when many subhalos in the sample catalogs are individually below the detection threshold and would be absent in a traditional catalog. The implemented software, Probabilistic Cataloger (PCAT) is made publicly available at https://github.com/tdaylan/pcat.

A Bayesian network to predict vulnerability to sea-level rise: data report

USGS Publications Warehouse

Gutierrez, Benjamin T.; Plant, Nathaniel G.; Thieler, E. Robert

2011-01-01

During the 21st century, sea-level rise is projected to have a wide range of effects on coastal environments, development, and infrastructure. Consequently, there has been an increased focus on developing modeling or other analytical approaches to evaluate potential impacts to inform coastal management. This report provides the data that were used to develop and evaluate the performance of a Bayesian network designed to predict long-term shoreline change due to sea-level rise. The data include local rates of relative sea-level rise, wave height, tide range, geomorphic classification, coastal slope, and shoreline-change rate compiled as part of the U.S. Geological Survey Coastal Vulnerability Index for the U.S. Atlantic coast. In this project, the Bayesian network is used to define relationships among driving forces, geologic constraints, and coastal responses. Using this information, the Bayesian network is used to make probabilistic predictions of shoreline change in response to different future sea-level-rise scenarios.

Multimodel Ensemble Methods for Prediction of Wake-Vortex Transport and Decay Originating NASA

NASA Technical Reports Server (NTRS)

Korner, Stephan; Ahmad, Nashat N.; Holzapfel, Frank; VanValkenburg, Randal L.

2017-01-01

Several multimodel ensemble methods are selected and further developed to improve the deterministic and probabilistic prediction skills of individual wake-vortex transport and decay models. The different multimodel ensemble methods are introduced, and their suitability for wake applications is demonstrated. The selected methods include direct ensemble averaging, Bayesian model averaging, and Monte Carlo simulation. The different methodologies are evaluated employing data from wake-vortex field measurement campaigns conducted in the United States and Germany.

WE-H-BRC-06: A Unified Machine-Learning Based Probabilistic Model for Automated Anomaly Detection in the Treatment Plan Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang, X; Liu, S; Kalet, A

Purpose: The purpose of this work was to investigate the ability of a machine-learning based probabilistic approach to detect radiotherapy treatment plan anomalies given initial disease classes information. Methods In total we obtained 1112 unique treatment plans with five plan parameters and disease information from a Mosaiq treatment management system database for use in the study. The plan parameters include prescription dose, fractions, fields, modality and techniques. The disease information includes disease site, and T, M and N disease stages. A Bayesian network method was employed to model the probabilistic relationships between tumor disease information, plan parameters and an anomalymore » flag. A Bayesian learning method with Dirichlet prior was useed to learn the joint probabilities between dependent variables in error-free plan data and data with artificially induced anomalies. In the study, we randomly sampled data with anomaly in a specified anomaly space.We tested the approach with three groups of plan anomalies – improper concurrence of values of all five plan parameters and values of any two out of five parameters, and all single plan parameter value anomalies. Totally, 16 types of plan anomalies were covered by the study. For each type, we trained an individual Bayesian network. Results: We found that the true positive rate (recall) and positive predictive value (precision) to detect concurrence anomalies of five plan parameters in new patient cases were 94.45±0.26% and 93.76±0.39% respectively. To detect other 15 types of plan anomalies, the average recall and precision were 93.61±2.57% and 93.78±3.54% respectively. The computation time to detect the plan anomaly of each type in a new plan is ∼0.08 seconds. Conclusion: The proposed method for treatment plan anomaly detection was found effective in the initial tests. The results suggest that this type of models could be applied to develop plan anomaly detection tools to assist manual and automated plan checks. The senior author received research grants from ViewRay Inc. and Varian Medical System.« less

Monitoring Human Development Goals: A Straightforward (Bayesian) Methodology for Cross-National Indices

ERIC Educational Resources Information Center

Abayomi, Kobi; Pizarro, Gonzalo

2013-01-01

We offer a straightforward framework for measurement of progress, across many dimensions, using cross-national social indices, which we classify as linear combinations of multivariate country level data onto a univariate score. We suggest a Bayesian approach which yields probabilistic (confidence type) intervals for the point estimates of country…

A Bayesian Multilevel Model for Microcystin Prediction in ...

EPA Pesticide Factsheets

The frequency of cyanobacteria blooms in North American lakes is increasing. A major concernwith rising cyanobacteria blooms is microcystin, a common cyanobacterial hepatotoxin. Toexplore the conditions that promote high microcystin concentrations, we analyzed the US EPANational Lake Assessment (NLA) dataset collected in the summer of 2007. The NLA datasetis reported for nine eco-regions. We used the results of random forest modeling as a means ofvariable selection from which we developed a Bayesian multilevel model of microcystin concentrations.Model parameters under a multilevel modeling framework are eco-region specific, butthey are also assumed to be exchangeable across eco-regions for broad continental scaling. Theexchangeability assumption ensures that both the common patterns and eco-region specific featureswill be reflected in the model. Furthermore, the method incorporates appropriate estimatesof uncertainty. Our preliminary results show associations between microcystin and turbidity, totalnutrients, and N:P ratios. The NLA 2012 will be used for Bayesian updating. The results willhelp develop management strategies to alleviate microcystin impacts and improve lake quality. This work provides a probabilistic framework for predicting microcystin presences in lakes. It would allow for insights to be made about how changes in nutrient concentrations could potentially change toxin levels.

Probabilistic Damage Characterization Using the Computationally-Efficient Bayesian Approach

NASA Technical Reports Server (NTRS)

Warner, James E.; Hochhalter, Jacob D.

2016-01-01

This work presents a computationally-ecient approach for damage determination that quanti es uncertainty in the provided diagnosis. Given strain sensor data that are polluted with measurement errors, Bayesian inference is used to estimate the location, size, and orientation of damage. This approach uses Bayes' Theorem to combine any prior knowledge an analyst may have about the nature of the damage with information provided implicitly by the strain sensor data to form a posterior probability distribution over possible damage states. The unknown damage parameters are then estimated based on samples drawn numerically from this distribution using a Markov Chain Monte Carlo (MCMC) sampling algorithm. Several modi cations are made to the traditional Bayesian inference approach to provide signi cant computational speedup. First, an ecient surrogate model is constructed using sparse grid interpolation to replace a costly nite element model that must otherwise be evaluated for each sample drawn with MCMC. Next, the standard Bayesian posterior distribution is modi ed using a weighted likelihood formulation, which is shown to improve the convergence of the sampling process. Finally, a robust MCMC algorithm, Delayed Rejection Adaptive Metropolis (DRAM), is adopted to sample the probability distribution more eciently. Numerical examples demonstrate that the proposed framework e ectively provides damage estimates with uncertainty quanti cation and can yield orders of magnitude speedup over standard Bayesian approaches.

Bayesian wavelet PCA methodology for turbomachinery damage diagnosis under uncertainty

NASA Astrophysics Data System (ADS)

Xu, Shengli; Jiang, Xiaomo; Huang, Jinzhi; Yang, Shuhua; Wang, Xiaofang

2016-12-01

Centrifugal compressor often suffers various defects such as impeller cracking, resulting in forced outage of the total plant. Damage diagnostics and condition monitoring of such a turbomachinery system has become an increasingly important and powerful tool to prevent potential failure in components and reduce unplanned forced outage and further maintenance costs, while improving reliability, availability and maintainability of a turbomachinery system. This paper presents a probabilistic signal processing methodology for damage diagnostics using multiple time history data collected from different locations of a turbomachine, considering data uncertainty and multivariate correlation. The proposed methodology is based on the integration of three advanced state-of-the-art data mining techniques: discrete wavelet packet transform, Bayesian hypothesis testing, and probabilistic principal component analysis. The multiresolution wavelet analysis approach is employed to decompose a time series signal into different levels of wavelet coefficients. These coefficients represent multiple time-frequency resolutions of a signal. Bayesian hypothesis testing is then applied to each level of wavelet coefficient to remove possible imperfections. The ratio of posterior odds Bayesian approach provides a direct means to assess whether there is imperfection in the decomposed coefficients, thus avoiding over-denoising. Power spectral density estimated by the Welch method is utilized to evaluate the effectiveness of Bayesian wavelet cleansing method. Furthermore, the probabilistic principal component analysis approach is developed to reduce dimensionality of multiple time series and to address multivariate correlation and data uncertainty for damage diagnostics. The proposed methodology and generalized framework is demonstrated with a set of sensor data collected from a real-world centrifugal compressor with impeller cracks, through both time series and contour analyses of vibration signal and principal components.

Bayesian Processor of Output for Probabilistic Quantitative Precipitation Forecasting

NASA Astrophysics Data System (ADS)

Krzysztofowicz, R.; Maranzano, C. J.

2006-05-01

The Bayesian Processor of Output (BPO) is a new, theoretically-based technique for probabilistic forecasting of weather variates. It processes output from a numerical weather prediction (NWP) model and optimally fuses it with climatic data in order to quantify uncertainty about a predictand. The BPO is being tested by producing Probabilistic Quantitative Precipitation Forecasts (PQPFs) for a set of climatically diverse stations in the contiguous U.S. For each station, the PQPFs are produced for the same 6-h, 12-h, and 24-h periods up to 84- h ahead for which operational forecasts are produced by the AVN-MOS (Model Output Statistics technique applied to output fields from the Global Spectral Model run under the code name AVN). The inputs into the BPO are estimated as follows. The prior distribution is estimated from a (relatively long) climatic sample of the predictand; this sample is retrieved from the archives of the National Climatic Data Center. The family of the likelihood functions is estimated from a (relatively short) joint sample of the predictor vector and the predictand; this sample is retrieved from the same archive that the Meteorological Development Laboratory of the National Weather Service utilized to develop the AVN-MOS system. This talk gives a tutorial introduction to the principles and procedures behind the BPO, and highlights some results from the testing: a numerical example of the estimation of the BPO, and a comparative verification of the BPO forecasts and the MOS forecasts. It concludes with a list of demonstrated attributes of the BPO (vis- à-vis the MOS): more parsimonious definitions of predictors, more efficient extraction of predictive information, better representation of the distribution function of predictand, and equal or better performance (in terms of calibration and informativeness).

Speech Enhancement Using Gaussian Scale Mixture Models

PubMed Central

Hao, Jiucang; Lee, Te-Won; Sejnowski, Terrence J.

2011-01-01

This paper presents a novel probabilistic approach to speech enhancement. Instead of a deterministic logarithmic relationship, we assume a probabilistic relationship between the frequency coefficients and the log-spectra. The speech model in the log-spectral domain is a Gaussian mixture model (GMM). The frequency coefficients obey a zero-mean Gaussian whose covariance equals to the exponential of the log-spectra. This results in a Gaussian scale mixture model (GSMM) for the speech signal in the frequency domain, since the log-spectra can be regarded as scaling factors. The probabilistic relation between frequency coefficients and log-spectra allows these to be treated as two random variables, both to be estimated from the noisy signals. Expectation-maximization (EM) was used to train the GSMM and Bayesian inference was used to compute the posterior signal distribution. Because exact inference of this full probabilistic model is computationally intractable, we developed two approaches to enhance the efficiency: the Laplace method and a variational approximation. The proposed methods were applied to enhance speech corrupted by Gaussian noise and speech-shaped noise (SSN). For both approximations, signals reconstructed from the estimated frequency coefficients provided higher signal-to-noise ratio (SNR) and those reconstructed from the estimated log-spectra produced lower word recognition error rate because the log-spectra fit the inputs to the recognizer better. Our algorithms effectively reduced the SSN, which algorithms based on spectral analysis were not able to suppress. PMID:21359139

None of the above: A Bayesian account of the detection of novel categories.

PubMed

Navarro, Daniel J; Kemp, Charles

2017-10-01

Every time we encounter a new object, action, or event, there is some chance that we will need to assign it to a novel category. We describe and evaluate a class of probabilistic models that detect when an object belongs to a category that has not previously been encountered. The models incorporate a prior distribution that is influenced by the distribution of previous objects among categories, and we present 2 experiments that demonstrate that people are also sensitive to this distributional information. Two additional experiments confirm that distributional information is combined with similarity when both sources of information are available. We compare our approach to previous models of unsupervised categorization and to several heuristic-based models, and find that a hierarchical Bayesian approach provides the best account of our data. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

A Flexible Hierarchical Bayesian Modeling Technique for Risk Analysis of Major Accidents.

PubMed

Yu, Hongyang; Khan, Faisal; Veitch, Brian

2017-09-01

Safety analysis of rare events with potentially catastrophic consequences is challenged by data scarcity and uncertainty. Traditional causation-based approaches, such as fault tree and event tree (used to model rare event), suffer from a number of weaknesses. These include the static structure of the event causation, lack of event occurrence data, and need for reliable prior information. In this study, a new hierarchical Bayesian modeling based technique is proposed to overcome these drawbacks. The proposed technique can be used as a flexible technique for risk analysis of major accidents. It enables both forward and backward analysis in quantitative reasoning and the treatment of interdependence among the model parameters. Source-to-source variability in data sources is also taken into account through a robust probabilistic safety analysis. The applicability of the proposed technique has been demonstrated through a case study in marine and offshore industry. © 2017 Society for Risk Analysis.

A unified probabilistic framework for spontaneous facial action modeling and understanding.

PubMed

Tong, Yan; Chen, Jixu; Ji, Qiang

2010-02-01

Facial expression is a natural and powerful means of human communication. Recognizing spontaneous facial actions, however, is very challenging due to subtle facial deformation, frequent head movements, and ambiguous and uncertain facial motion measurements. Because of these challenges, current research in facial expression recognition is limited to posed expressions and often in frontal view. A spontaneous facial expression is characterized by rigid head movements and nonrigid facial muscular movements. More importantly, it is the coherent and consistent spatiotemporal interactions among rigid and nonrigid facial motions that produce a meaningful facial expression. Recognizing this fact, we introduce a unified probabilistic facial action model based on the Dynamic Bayesian network (DBN) to simultaneously and coherently represent rigid and nonrigid facial motions, their spatiotemporal dependencies, and their image measurements. Advanced machine learning methods are introduced to learn the model based on both training data and subjective prior knowledge. Given the model and the measurements of facial motions, facial action recognition is accomplished through probabilistic inference by systematically integrating visual measurements with the facial action model. Experiments show that compared to the state-of-the-art techniques, the proposed system yields significant improvements in recognizing both rigid and nonrigid facial motions, especially for spontaneous facial expressions.

Estimating uncertainties in complex joint inverse problems

NASA Astrophysics Data System (ADS)

Afonso, Juan Carlos

2016-04-01

Sources of uncertainty affecting geophysical inversions can be classified either as reflective (i.e. the practitioner is aware of her/his ignorance) or non-reflective (i.e. the practitioner does not know that she/he does not know!). Although we should be always conscious of the latter, the former are the ones that, in principle, can be estimated either empirically (by making measurements or collecting data) or subjectively (based on the experience of the researchers). For complex parameter estimation problems in geophysics, subjective estimation of uncertainty is the most common type. In this context, probabilistic (aka Bayesian) methods are commonly claimed to offer a natural and realistic platform from which to estimate model uncertainties. This is because in the Bayesian approach, errors (whatever their nature) can be naturally included as part of the global statistical model, the solution of which represents the actual solution to the inverse problem. However, although we agree that probabilistic inversion methods are the most powerful tool for uncertainty estimation, the common claim that they produce "realistic" or "representative" uncertainties is not always justified. Typically, ALL UNCERTAINTY ESTIMATES ARE MODEL DEPENDENT, and therefore, besides a thorough characterization of experimental uncertainties, particular care must be paid to the uncertainty arising from model errors and input uncertainties. We recall here two quotes by G. Box and M. Gunzburger, respectively, of special significance for inversion practitioners and for this session: "…all models are wrong, but some are useful" and "computational results are believed by no one, except the person who wrote the code". In this presentation I will discuss and present examples of some problems associated with the estimation and quantification of uncertainties in complex multi-observable probabilistic inversions, and how to address them. Although the emphasis will be on sources of uncertainty related to the forward and statistical models, I will also address other uncertainties associated with data and uncertainty propagation.

Modeling Women's Menstrual Cycles using PICI Gates in Bayesian Network.

PubMed

Zagorecki, Adam; Łupińska-Dubicka, Anna; Voortman, Mark; Druzdzel, Marek J

2016-03-01

A major difficulty in building Bayesian network (BN) models is the size of conditional probability tables, which grow exponentially in the number of parents. One way of dealing with this problem is through parametric conditional probability distributions that usually require only a number of parameters that is linear in the number of parents. In this paper, we introduce a new class of parametric models, the Probabilistic Independence of Causal Influences (PICI) models, that aim at lowering the number of parameters required to specify local probability distributions, but are still capable of efficiently modeling a variety of interactions. A subset of PICI models is decomposable and this leads to significantly faster inference as compared to models that cannot be decomposed. We present an application of the proposed method to learning dynamic BNs for modeling a woman's menstrual cycle. We show that PICI models are especially useful for parameter learning from small data sets and lead to higher parameter accuracy than when learning CPTs.

The probabilistic convolution tree: efficient exact Bayesian inference for faster LC-MS/MS protein inference.

PubMed

Serang, Oliver

2014-01-01

Exact Bayesian inference can sometimes be performed efficiently for special cases where a function has commutative and associative symmetry of its inputs (called "causal independence"). For this reason, it is desirable to exploit such symmetry on big data sets. Here we present a method to exploit a general form of this symmetry on probabilistic adder nodes by transforming those probabilistic adder nodes into a probabilistic convolution tree with which dynamic programming computes exact probabilities. A substantial speedup is demonstrated using an illustration example that can arise when identifying splice forms with bottom-up mass spectrometry-based proteomics. On this example, even state-of-the-art exact inference algorithms require a runtime more than exponential in the number of splice forms considered. By using the probabilistic convolution tree, we reduce the runtime to O(k log(k)2) and the space to O(k log(k)) where k is the number of variables joined by an additive or cardinal operator. This approach, which can also be used with junction tree inference, is applicable to graphs with arbitrary dependency on counting variables or cardinalities and can be used on diverse problems and fields like forward error correcting codes, elemental decomposition, and spectral demixing. The approach also trivially generalizes to multiple dimensions.

The Probabilistic Convolution Tree: Efficient Exact Bayesian Inference for Faster LC-MS/MS Protein Inference

PubMed Central

Serang, Oliver

2014-01-01

Exact Bayesian inference can sometimes be performed efficiently for special cases where a function has commutative and associative symmetry of its inputs (called “causal independence”). For this reason, it is desirable to exploit such symmetry on big data sets. Here we present a method to exploit a general form of this symmetry on probabilistic adder nodes by transforming those probabilistic adder nodes into a probabilistic convolution tree with which dynamic programming computes exact probabilities. A substantial speedup is demonstrated using an illustration example that can arise when identifying splice forms with bottom-up mass spectrometry-based proteomics. On this example, even state-of-the-art exact inference algorithms require a runtime more than exponential in the number of splice forms considered. By using the probabilistic convolution tree, we reduce the runtime to and the space to where is the number of variables joined by an additive or cardinal operator. This approach, which can also be used with junction tree inference, is applicable to graphs with arbitrary dependency on counting variables or cardinalities and can be used on diverse problems and fields like forward error correcting codes, elemental decomposition, and spectral demixing. The approach also trivially generalizes to multiple dimensions. PMID:24626234

A Bayesian network model to assess the public health risk associated with wet weather sewer overflows discharging into waterways.

PubMed

Goulding, R; Jayasuriya, N; Horan, E

2012-10-15

Overflows from sanitary sewers during wet weather, which occur when the hydraulic capacity of the sewer system is exceeded, are considered a potential threat to the ecological and public health of the waterways which receive these overflows. As a result, water retailers in Australia and internationally commit significant resources to manage and abate sewer overflows. However, whilst some studies have contributed to an increased understanding of the impacts and risks associated with these events, they are relatively few in number and there still is a general lack of knowledge in this area. A Bayesian network model to assess the public health risk associated with wet weather sewer overflows is presented in this paper. The Bayesian network approach is shown to provide significant benefits in the assessment of public health risks associated with wet weather sewer overflows. In particular, the ability for the model to account for the uncertainty inherent in sewer overflow events and subsequent impacts through the use of probabilities is a valuable function. In addition, the paper highlights the benefits of the probabilistic inference function of the Bayesian network in prioritising management options to minimise public health risks associated with sewer overflows. Copyright © 2012. Published by Elsevier Ltd.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brewer, Brendon J.; Foreman-Mackey, Daniel; Hogg, David W., E-mail: bj.brewer@auckland.ac.nz

We present and implement a probabilistic (Bayesian) method for producing catalogs from images of stellar fields. The method is capable of inferring the number of sources N in the image and can also handle the challenges introduced by noise, overlapping sources, and an unknown point-spread function. The luminosity function of the stars can also be inferred, even when the precise luminosity of each star is uncertain, via the use of a hierarchical Bayesian model. The computational feasibility of the method is demonstrated on two simulated images with different numbers of stars. We find that our method successfully recovers the inputmore » parameter values along with principled uncertainties even when the field is crowded. We also compare our results with those obtained from the SExtractor software. While the two approaches largely agree about the fluxes of the bright stars, the Bayesian approach provides more accurate inferences about the faint stars and the number of stars, particularly in the crowded case.« less

Applying Bayesian belief networks in rapid response situations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gibson, William L; Deborah, Leishman, A.; Van Eeckhout, Edward

2008-01-01

The authors have developed an enhanced Bayesian analysis tool called the Integrated Knowledge Engine (IKE) for monitoring and surveillance. The enhancements are suited for Rapid Response Situations where decisions must be made based on uncertain and incomplete evidence from many diverse and heterogeneous sources. The enhancements extend the probabilistic results of the traditional Bayesian analysis by (1) better quantifying uncertainty arising from model parameter uncertainty and uncertain evidence, (2) optimizing the collection of evidence to reach conclusions more quickly, and (3) allowing the analyst to determine the influence of the remaining evidence that cannot be obtained in the time allowed.more » These extended features give the analyst and decision maker a better comprehension of the adequacy of the acquired evidence and hence the quality of the hurried decisions. They also describe two example systems where the above features are highlighted.« less

Models and simulation of 3D neuronal dendritic trees using Bayesian networks.

PubMed

López-Cruz, Pedro L; Bielza, Concha; Larrañaga, Pedro; Benavides-Piccione, Ruth; DeFelipe, Javier

2011-12-01

Neuron morphology is crucial for neuronal connectivity and brain information processing. Computational models are important tools for studying dendritic morphology and its role in brain function. We applied a class of probabilistic graphical models called Bayesian networks to generate virtual dendrites from layer III pyramidal neurons from three different regions of the neocortex of the mouse. A set of 41 morphological variables were measured from the 3D reconstructions of real dendrites and their probability distributions used in a machine learning algorithm to induce the model from the data. A simulation algorithm is also proposed to obtain new dendrites by sampling values from Bayesian networks. The main advantage of this approach is that it takes into account and automatically locates the relationships between variables in the data instead of using predefined dependencies. Therefore, the methodology can be applied to any neuronal class while at the same time exploiting class-specific properties. Also, a Bayesian network was defined for each part of the dendrite, allowing the relationships to change in the different sections and to model heterogeneous developmental factors or spatial influences. Several univariate statistical tests and a novel multivariate test based on Kullback-Leibler divergence estimation confirmed that virtual dendrites were similar to real ones. The analyses of the models showed relationships that conform to current neuroanatomical knowledge and support model correctness. At the same time, studying the relationships in the models can help to identify new interactions between variables related to dendritic morphology.

Probabilistic methods for sensitivity analysis and calibration in the NASA challenge problem

DOE PAGES

Safta, Cosmin; Sargsyan, Khachik; Najm, Habib N.; ...

2015-01-01

In this study, a series of algorithms are proposed to address the problems in the NASA Langley Research Center Multidisciplinary Uncertainty Quantification Challenge. A Bayesian approach is employed to characterize and calibrate the epistemic parameters based on the available data, whereas a variance-based global sensitivity analysis is used to rank the epistemic and aleatory model parameters. A nested sampling of the aleatory–epistemic space is proposed to propagate uncertainties from model parameters to output quantities of interest.

Probabilistic methods for sensitivity analysis and calibration in the NASA challenge problem

DOE Office of Scientific and Technical Information (OSTI.GOV)

Safta, Cosmin; Sargsyan, Khachik; Najm, Habib N.

In this study, a series of algorithms are proposed to address the problems in the NASA Langley Research Center Multidisciplinary Uncertainty Quantification Challenge. A Bayesian approach is employed to characterize and calibrate the epistemic parameters based on the available data, whereas a variance-based global sensitivity analysis is used to rank the epistemic and aleatory model parameters. A nested sampling of the aleatory–epistemic space is proposed to propagate uncertainties from model parameters to output quantities of interest.

XID+: Next generation XID development

NASA Astrophysics Data System (ADS)

Hurley, Peter

2017-04-01

XID+ is a prior-based source extraction tool which carries out photometry in the Herschel SPIRE (Spectral and Photometric Imaging Receiver) maps at the positions of known sources. It uses a probabilistic Bayesian framework that provides a natural framework in which to include prior information, and uses the Bayesian inference tool Stan to obtain the full posterior probability distribution on flux estimates.

CTPPL: A Continuous Time Probabilistic Programming Language

DTIC Science & Technology

2009-07-01

recent years there has been a flurry of interest in continuous time models, mostly focused on continuous time Bayesian networks ( CTBNs ) [Nodelman, 2007... CTBNs are built on homogenous Markov processes. A homogenous Markov pro- cess is a finite state, continuous time process, consisting of an initial...q1 : xn()] ... Some state transitions can produce emissions. In a CTBN , each variable has a conditional inten- sity matrix Qu for every combination of

The Challenges of Credible Thermal Protection System Reliability Quantification

NASA Technical Reports Server (NTRS)

Green, Lawrence L.

2013-01-01

The paper discusses several of the challenges associated with developing a credible reliability estimate for a human-rated crew capsule thermal protection system. The process of developing such a credible estimate is subject to the quantification, modeling and propagation of numerous uncertainties within a probabilistic analysis. The development of specific investment recommendations, to improve the reliability prediction, among various potential testing and programmatic options is then accomplished through Bayesian analysis.

Uncertainty and the Social Cost of Methane Using Bayesian Constrained Climate Models

NASA Astrophysics Data System (ADS)

Errickson, F. C.; Anthoff, D.; Keller, K.

2016-12-01

Social cost estimates of greenhouse gases are important for the design of sound climate policies and are also plagued by uncertainty. One major source of uncertainty stems from the simplified representation of the climate system used in the integrated assessment models that provide these social cost estimates. We explore how uncertainty over the social cost of methane varies with the way physical processes and feedbacks in the methane cycle are modeled by (i) coupling three different methane models to a simple climate model, (ii) using MCMC to perform a Bayesian calibration of the three coupled climate models that simulates direct sampling from the joint posterior probability density function (pdf) of model parameters, and (iii) producing probabilistic climate projections that are then used to calculate the Social Cost of Methane (SCM) with the DICE and FUND integrated assessment models. We find that including a temperature feedback in the methane cycle acts as an additional constraint during the calibration process and results in a correlation between the tropospheric lifetime of methane and several climate model parameters. This correlation is not seen in the models lacking this feedback. Several of the estimated marginal pdfs of the model parameters also exhibit different distributional shapes and expected values depending on the methane model used. As a result, probabilistic projections of the climate system out to the year 2300 exhibit different levels of uncertainty and magnitudes of warming for each of the three models under an RCP8.5 scenario. We find these differences in climate projections result in differences in the distributions and expected values for our estimates of the SCM. We also examine uncertainty about the SCM by performing a Monte Carlo analysis using a distribution for the climate sensitivity while holding all other climate model parameters constant. Our SCM estimates using the Bayesian calibration are lower and exhibit less uncertainty about extremely high values in the right tail of the distribution compared to the Monte Carlo approach. This finding has important climate policy implications and suggests previous work that accounts for climate model uncertainty by only varying the climate sensitivity parameter may overestimate the SCM.

NasoNet, modeling the spread of nasopharyngeal cancer with networks of probabilistic events in discrete time.

PubMed

Galán, S F; Aguado, F; Díez, F J; Mira, J

2002-07-01

The spread of cancer is a non-deterministic dynamic process. As a consequence, the design of an assistant system for the diagnosis and prognosis of the extent of a cancer should be based on a representation method that deals with both uncertainty and time. The ultimate goal is to know the stage of development of a cancer in a patient before selecting the appropriate treatment. A network of probabilistic events in discrete time (NPEDT) is a type of Bayesian network for temporal reasoning that models the causal mechanisms associated with the time evolution of a process. This paper describes NasoNet, a system that applies NPEDTs to the diagnosis and prognosis of nasopharyngeal cancer. We have made use of temporal noisy gates to model the dynamic causal interactions that take place in the domain. The methodology we describe is general enough to be applied to any other type of cancer.

Probabilistic hindcasts and projections of the coupled climate, carbon cycle and Atlantic meridional overturning circulation system: a Bayesian fusion of century-scale observations with a simple model

NASA Astrophysics Data System (ADS)

Urban, Nathan M.; Keller, Klaus

2010-10-01

How has the Atlantic Meridional Overturning Circulation (AMOC) varied over the past centuries and what is the risk of an anthropogenic AMOC collapse? We report probabilistic projections of the future climate which improve on previous AMOC projection studies by (i) greatly expanding the considered observational constraints and (ii) carefully sampling the tail areas of the parameter probability distribution function (pdf). We use a Bayesian inversion to constrain a simple model of the coupled climate, carbon cycle and AMOC systems using observations to derive multicentury hindcasts and projections. Our hindcasts show considerable skill in representing the observational constraints. We show that robust AMOC risk estimates can require carefully sampling the parameter pdfs. We find a low probability of experiencing an AMOC collapse within the 21st century for a business-as-usual emissions scenario. The probability of experiencing an AMOC collapse within two centuries is 1/10. The probability of crossing a forcing threshold and triggering a future AMOC collapse (by 2300) is approximately 1/30 in the 21st century and over 1/3 in the 22nd. Given the simplicity of the model structure and uncertainty in the forcing assumptions, our analysis should be considered a proof of concept and the quantitative conclusions subject to severe caveats.

Comparing models for quantitative risk assessment: an application to the European Registry of foreign body injuries in children.

PubMed

Berchialla, Paola; Scarinzi, Cecilia; Snidero, Silvia; Gregori, Dario

2016-08-01

Risk Assessment is the systematic study of decisions subject to uncertain consequences. An increasing interest has been focused on modeling techniques like Bayesian Networks since their capability of (1) combining in the probabilistic framework different type of evidence including both expert judgments and objective data; (2) overturning previous beliefs in the light of the new information being received and (3) making predictions even with incomplete data. In this work, we proposed a comparison among Bayesian Networks and other classical Quantitative Risk Assessment techniques such as Neural Networks, Classification Trees, Random Forests and Logistic Regression models. Hybrid approaches, combining both Classification Trees and Bayesian Networks, were also considered. Among Bayesian Networks, a clear distinction between purely data-driven approach and combination of expert knowledge with objective data is made. The aim of this paper consists in evaluating among this models which best can be applied, in the framework of Quantitative Risk Assessment, to assess the safety of children who are exposed to the risk of inhalation/insertion/aspiration of consumer products. The issue of preventing injuries in children is of paramount importance, in particular where product design is involved: quantifying the risk associated to product characteristics can be of great usefulness in addressing the product safety design regulation. Data of the European Registry of Foreign Bodies Injuries formed the starting evidence for risk assessment. Results showed that Bayesian Networks appeared to have both the ease of interpretability and accuracy in making prediction, even if simpler models like logistic regression still performed well. © The Author(s) 2013.

A Mixtures-of-Trees Framework for Multi-Label Classification

PubMed Central

Hong, Charmgil; Batal, Iyad; Hauskrecht, Milos

2015-01-01

We propose a new probabilistic approach for multi-label classification that aims to represent the class posterior distribution P(Y|X). Our approach uses a mixture of tree-structured Bayesian networks, which can leverage the computational advantages of conditional tree-structured models and the abilities of mixtures to compensate for tree-structured restrictions. We develop algorithms for learning the model from data and for performing multi-label predictions using the learned model. Experiments on multiple datasets demonstrate that our approach outperforms several state-of-the-art multi-label classification methods. PMID:25927011

Uncertainty quantification in capacitive RF MEMS switches

NASA Astrophysics Data System (ADS)

Pax, Benjamin J.

Development of radio frequency micro electrical-mechanical systems (RF MEMS) has led to novel approaches to implement electrical circuitry. The introduction of capacitive MEMS switches, in particular, has shown promise in low-loss, low-power devices. However, the promise of MEMS switches has not yet been completely realized. RF-MEMS switches are known to fail after only a few months of operation, and nominally similar designs show wide variability in lifetime. Modeling switch operation using nominal or as-designed parameters cannot predict the statistical spread in the number of cycles to failure, and probabilistic methods are necessary. A Bayesian framework for calibration, validation and prediction offers an integrated approach to quantifying the uncertainty in predictions of MEMS switch performance. The objective of this thesis is to use the Bayesian framework to predict the creep-related deflection of the PRISM RF-MEMS switch over several thousand hours of operation. The PRISM switch used in this thesis is the focus of research at Purdue's PRISM center, and is a capacitive contacting RF-MEMS switch. It employs a fixed-fixed nickel membrane which is electrostatically actuated by applying voltage between the membrane and a pull-down electrode. Creep plays a central role in the reliability of this switch. The focus of this thesis is on the creep model, which is calibrated against experimental data measured for a frog-leg varactor fabricated and characterized at Purdue University. Creep plasticity is modeled using plate element theory with electrostatic forces being generated using either parallel plate approximations where appropriate, or solving for the full 3D potential field. For the latter, structure-electrostatics interaction is determined through immersed boundary method. A probabilistic framework using generalized polynomial chaos (gPC) is used to create surrogate models to mitigate the costly full physics simulations, and Bayesian calibration and forward propagation of uncertainty are performed using this surrogate model. The first step in the analysis is Bayesian calibration of the creep related parameters. A computational model of the frog-leg varactor is created, and the computed creep deflection of the device over 800 hours is used to generate a surrogate model using a polynomial chaos expansion in Hermite polynomials. Parameters related to the creep phenomenon are calibrated using Bayesian calibration with experimental deflection data from the frog-leg device. The calibrated input distributions are subsequently propagated through a surrogate gPC model for the PRISM MEMS switch to produce probability density functions of the maximum membrane deflection of the membrane over several thousand hours. The assumptions related to the Bayesian calibration and forward propagation are analyzed to determine the sensitivity to these assumptions of the calibrated input distributions and propagated output distributions of the PRISM device. The work is an early step in understanding the role of geometric variability, model uncertainty, numerical errors and experimental uncertainties in the long-term performance of RF-MEMS.

Testing for ontological errors in probabilistic forecasting models of natural systems

PubMed Central

Marzocchi, Warner; Jordan, Thomas H.

2014-01-01

Probabilistic forecasting models describe the aleatory variability of natural systems as well as our epistemic uncertainty about how the systems work. Testing a model against observations exposes ontological errors in the representation of a system and its uncertainties. We clarify several conceptual issues regarding the testing of probabilistic forecasting models for ontological errors: the ambiguity of the aleatory/epistemic dichotomy, the quantification of uncertainties as degrees of belief, the interplay between Bayesian and frequentist methods, and the scientific pathway for capturing predictability. We show that testability of the ontological null hypothesis derives from an experimental concept, external to the model, that identifies collections of data, observed and not yet observed, that are judged to be exchangeable when conditioned on a set of explanatory variables. These conditional exchangeability judgments specify observations with well-defined frequencies. Any model predicting these behaviors can thus be tested for ontological error by frequentist methods; e.g., using P values. In the forecasting problem, prior predictive model checking, rather than posterior predictive checking, is desirable because it provides more severe tests. We illustrate experimental concepts using examples from probabilistic seismic hazard analysis. Severe testing of a model under an appropriate set of experimental concepts is the key to model validation, in which we seek to know whether a model replicates the data-generating process well enough to be sufficiently reliable for some useful purpose, such as long-term seismic forecasting. Pessimistic views of system predictability fail to recognize the power of this methodology in separating predictable behaviors from those that are not. PMID:25097265

Bayesian characterization of uncertainty in species interaction strengths.

PubMed

Wolf, Christopher; Novak, Mark; Gitelman, Alix I

2017-06-01

Considerable effort has been devoted to the estimation of species interaction strengths. This effort has focused primarily on statistical significance testing and obtaining point estimates of parameters that contribute to interaction strength magnitudes, leaving the characterization of uncertainty associated with those estimates unconsidered. We consider a means of characterizing the uncertainty of a generalist predator's interaction strengths by formulating an observational method for estimating a predator's prey-specific per capita attack rates as a Bayesian statistical model. This formulation permits the explicit incorporation of multiple sources of uncertainty. A key insight is the informative nature of several so-called non-informative priors that have been used in modeling the sparse data typical of predator feeding surveys. We introduce to ecology a new neutral prior and provide evidence for its superior performance. We use a case study to consider the attack rates in a New Zealand intertidal whelk predator, and we illustrate not only that Bayesian point estimates can be made to correspond with those obtained by frequentist approaches, but also that estimation uncertainty as described by 95% intervals is more useful and biologically realistic using the Bayesian method. In particular, unlike in bootstrap confidence intervals, the lower bounds of the Bayesian posterior intervals for attack rates do not include zero when a predator-prey interaction is in fact observed. We conclude that the Bayesian framework provides a straightforward, probabilistic characterization of interaction strength uncertainty, enabling future considerations of both the deterministic and stochastic drivers of interaction strength and their impact on food webs.

Predictors of Outcome in Traumatic Brain Injury: New Insight Using Receiver Operating Curve Indices and Bayesian Network Analysis.

PubMed

Zador, Zsolt; Sperrin, Matthew; King, Andrew T

2016-01-01

Traumatic brain injury remains a global health problem. Understanding the relative importance of outcome predictors helps optimize our treatment strategies by informing assessment protocols, clinical decisions and trial designs. In this study we establish importance ranking for outcome predictors based on receiver operating indices to identify key predictors of outcome and create simple predictive models. We then explore the associations between key outcome predictors using Bayesian networks to gain further insight into predictor importance. We analyzed the corticosteroid randomization after significant head injury (CRASH) trial database of 10008 patients and included patients for whom demographics, injury characteristics, computer tomography (CT) findings and Glasgow Outcome Scale (GCS) were recorded (total of 13 predictors, which would be available to clinicians within a few hours following the injury in 6945 patients). Predictions of clinical outcome (death or severe disability at 6 months) were performed using logistic regression models with 5-fold cross validation. Predictive performance was measured using standardized partial area (pAUC) under the receiver operating curve (ROC) and we used Delong test for comparisons. Variable importance ranking was based on pAUC targeted at specificity (pAUCSP) and sensitivity (pAUCSE) intervals of 90-100%. Probabilistic associations were depicted using Bayesian networks. Complete AUC analysis showed very good predictive power (AUC = 0.8237, 95% CI: 0.8138-0.8336) for the complete model. Specificity focused importance ranking highlighted age, pupillary, motor responses, obliteration of basal cisterns/3rd ventricle and midline shift. Interestingly when targeting model sensitivity, the highest-ranking variables were age, severe extracranial injury, verbal response, hematoma on CT and motor response. Simplified models, which included only these key predictors, had similar performance (pAUCSP = 0.6523, 95% CI: 0.6402-0.6641 and pAUCSE = 0.6332, 95% CI: 0.62-0.6477) compared to the complete models (pAUCSP = 0.6664, 95% CI: 0.6543-0.679, pAUCSE = 0.6436, 95% CI: 0.6289-0.6585, de Long p value 0.1165 and 0.3448 respectively). Bayesian networks showed the predictors that did not feature in the simplified models were associated with those that did. We demonstrate that importance based variable selection allows simplified predictive models to be created while maintaining prediction accuracy. Variable selection targeting specificity confirmed key components of clinical assessment in TBI whereas sensitivity based ranking suggested extracranial injury as one of the important predictors. These results help refine our approach to head injury assessment, decision-making and outcome prediction targeted at model sensitivity and specificity. Bayesian networks proved to be a comprehensive tool for depicting probabilistic associations for key predictors giving insight into why the simplified model has maintained accuracy.

Probabilistic Elastic Part Model: A Pose-Invariant Representation for Real-World Face Verification.

PubMed

Li, Haoxiang; Hua, Gang

2018-04-01

Pose variation remains to be a major challenge for real-world face recognition. We approach this problem through a probabilistic elastic part model. We extract local descriptors (e.g., LBP or SIFT) from densely sampled multi-scale image patches. By augmenting each descriptor with its location, a Gaussian mixture model (GMM) is trained to capture the spatial-appearance distribution of the face parts of all face images in the training corpus, namely the probabilistic elastic part (PEP) model. Each mixture component of the GMM is confined to be a spherical Gaussian to balance the influence of the appearance and the location terms, which naturally defines a part. Given one or multiple face images of the same subject, the PEP-model builds its PEP representation by sequentially concatenating descriptors identified by each Gaussian component in a maximum likelihood sense. We further propose a joint Bayesian adaptation algorithm to adapt the universally trained GMM to better model the pose variations between the target pair of faces/face tracks, which consistently improves face verification accuracy. Our experiments show that we achieve state-of-the-art face verification accuracy with the proposed representations on the Labeled Face in the Wild (LFW) dataset, the YouTube video face database, and the CMU MultiPIE dataset.

A Bayesian Multilevel Model for Microcystin Prediction in ...

EPA Pesticide Factsheets

The frequency of cyanobacteria blooms in North American lakes is increasing. A major concern with rising cyanobacteria blooms is microcystin, a common cyanobacterial hepatotoxin. To explore the conditions that promote high microcystin concentrations, we analyzed the US EPA National Lake Assessment (NLA) dataset collected in the summer of 2007. The NLA dataset is reported for nine eco-regions. We used the results of random forest modeling as a means ofvariable selection from which we developed a Bayesian multilevel model of microcystin concentrations. Model parameters under a multilevel modeling framework are eco-region specific, butthey are also assumed to be exchangeable across eco-regions for broad continental scaling. The exchangeability assumption ensures that both the common patterns and eco-region specific features will be reflected in the model. Furthermore, the method incorporates appropriate estimates of uncertainty. Our preliminary results show associations between microcystin and turbidity, total nutrients, and N:P ratios. Upon release of a comparable 2012 NLA dataset, we will apply Bayesian updating. The results will help develop management strategies to alleviate microcystin impacts and improve lake quality. This work provides a probabilistic framework for predicting microcystin presences in lakes. It would allow for insights to be made about how changes in nutrient concentrations could potentially change toxin levels.

Quantum-Like Bayesian Networks for Modeling Decision Making

PubMed Central

Moreira, Catarina; Wichert, Andreas

2016-01-01

In this work, we explore an alternative quantum structure to perform quantum probabilistic inferences to accommodate the paradoxical findings of the Sure Thing Principle. We propose a Quantum-Like Bayesian Network, which consists in replacing classical probabilities by quantum probability amplitudes. However, since this approach suffers from the problem of exponential growth of quantum parameters, we also propose a similarity heuristic that automatically fits quantum parameters through vector similarities. This makes the proposed model general and predictive in contrast to the current state of the art models, which cannot be generalized for more complex decision scenarios and that only provide an explanatory nature for the observed paradoxes. In the end, the model that we propose consists in a nonparametric method for estimating inference effects from a statistical point of view. It is a statistical model that is simpler than the previous quantum dynamic and quantum-like models proposed in the literature. We tested the proposed network with several empirical data from the literature, mainly from the Prisoner's Dilemma game and the Two Stage Gambling game. The results obtained show that the proposed quantum Bayesian Network is a general method that can accommodate violations of the laws of classical probability theory and make accurate predictions regarding human decision-making in these scenarios. PMID:26858669

Bayesian analysis of the flutter margin method in aeroelasticity

DOE PAGES

Khalil, Mohammad; Poirel, Dominique; Sarkar, Abhijit

2016-08-27

A Bayesian statistical framework is presented for Zimmerman and Weissenburger flutter margin method which considers the uncertainties in aeroelastic modal parameters. The proposed methodology overcomes the limitations of the previously developed least-square based estimation technique which relies on the Gaussian approximation of the flutter margin probability density function (pdf). Using the measured free-decay responses at subcritical (preflutter) airspeeds, the joint non-Gaussain posterior pdf of the modal parameters is sampled using the Metropolis–Hastings (MH) Markov chain Monte Carlo (MCMC) algorithm. The posterior MCMC samples of the modal parameters are then used to obtain the flutter margin pdfs and finally the fluttermore » speed pdf. The usefulness of the Bayesian flutter margin method is demonstrated using synthetic data generated from a two-degree-of-freedom pitch-plunge aeroelastic model. The robustness of the statistical framework is demonstrated using different sets of measurement data. In conclusion, it will be shown that the probabilistic (Bayesian) approach reduces the number of test points required in providing a flutter speed estimate for a given accuracy and precision.« less

Probabilistic short-term volcanic hazard in phases of unrest: A case study for tephra fallout

NASA Astrophysics Data System (ADS)

Selva, Jacopo; Costa, Antonio; Sandri, Laura; Macedonio, Giovanni; Marzocchi, Warner

2014-12-01

During volcanic crises, volcanologists estimate the impact of possible imminent eruptions usually through deterministic modeling of the effects of one or a few preestablished scenarios. Despite such an approach may bring an important information to the decision makers, the sole use of deterministic scenarios does not allow scientists to properly take into consideration all uncertainties, and it cannot be used to assess quantitatively the risk because the latter unavoidably requires a probabilistic approach. We present a model based on the concept of Bayesian event tree (hereinafter named BET_VH_ST, standing for Bayesian event tree for short-term volcanic hazard), for short-term near-real-time probabilistic volcanic hazard analysis formulated for any potential hazardous phenomenon accompanying an eruption. The specific goal of BET_VH_ST is to produce a quantitative assessment of the probability of exceedance of any potential level of intensity for a given volcanic hazard due to eruptions within restricted time windows (hours to days) in any area surrounding the volcano, accounting for all natural and epistemic uncertainties. BET_VH_ST properly assesses the conditional probability at each level of the event tree accounting for any relevant information derived from the monitoring system, theoretical models, and the past history of the volcano, propagating any relevant epistemic uncertainty underlying these assessments. As an application example of the model, we apply BET_VH_ST to assess short-term volcanic hazard related to tephra loading during Major Emergency Simulation Exercise, a major exercise at Mount Vesuvius that took place from 19 to 23 October 2006, consisting in a blind simulation of Vesuvius reactivation, from the early warning phase up to the final eruption, including the evacuation of a sample of about 2000 people from the area at risk. The results show that BET_VH_ST is able to produce short-term forecasts of the impact of tephra fall during a rapidly evolving crisis, accurately accounting for and propagating all uncertainties and enabling rational decision making under uncertainty.

Application of the Approximate Bayesian Computation methods in the stochastic estimation of atmospheric contamination parameters for mobile sources

NASA Astrophysics Data System (ADS)

Kopka, Piotr; Wawrzynczak, Anna; Borysiewicz, Mieczyslaw

2016-11-01

In this paper the Bayesian methodology, known as Approximate Bayesian Computation (ABC), is applied to the problem of the atmospheric contamination source identification. The algorithm input data are on-line arriving concentrations of the released substance registered by the distributed sensors network. This paper presents the Sequential ABC algorithm in detail and tests its efficiency in estimation of probabilistic distributions of atmospheric release parameters of a mobile contamination source. The developed algorithms are tested using the data from Over-Land Atmospheric Diffusion (OLAD) field tracer experiment. The paper demonstrates estimation of seven parameters characterizing the contamination source, i.e.: contamination source starting position (x,y), the direction of the motion of the source (d), its velocity (v), release rate (q), start time of release (ts) and its duration (td). The online-arriving new concentrations dynamically update the probability distributions of search parameters. The atmospheric dispersion Second-order Closure Integrated PUFF (SCIPUFF) Model is used as the forward model to predict the concentrations at the sensors locations.

A Joint Gaussian Process Model for Active Visual Recognition with Expertise Estimation in Crowdsourcing

PubMed Central

Long, Chengjiang; Hua, Gang; Kapoor, Ashish

2015-01-01

We present a noise resilient probabilistic model for active learning of a Gaussian process classifier from crowds, i.e., a set of noisy labelers. It explicitly models both the overall label noise and the expertise level of each individual labeler with two levels of flip models. Expectation propagation is adopted for efficient approximate Bayesian inference of our probabilistic model for classification, based on which, a generalized EM algorithm is derived to estimate both the global label noise and the expertise of each individual labeler. The probabilistic nature of our model immediately allows the adoption of the prediction entropy for active selection of data samples to be labeled, and active selection of high quality labelers based on their estimated expertise to label the data. We apply the proposed model for four visual recognition tasks, i.e., object category recognition, multi-modal activity recognition, gender recognition, and fine-grained classification, on four datasets with real crowd-sourced labels from the Amazon Mechanical Turk. The experiments clearly demonstrate the efficacy of the proposed model. In addition, we extend the proposed model with the Predictive Active Set Selection Method to speed up the active learning system, whose efficacy is verified by conducting experiments on the first three datasets. The results show our extended model can not only preserve a higher accuracy, but also achieve a higher efficiency. PMID:26924892

Modular Bayesian Networks with Low-Power Wearable Sensors for Recognizing Eating Activities.

PubMed

Kim, Kee-Hoon; Cho, Sung-Bae

2017-12-11

Recently, recognizing a user's daily activity using a smartphone and wearable sensors has become a popular issue. However, in contrast with the ideal definition of an experiment, there could be numerous complex activities in real life with respect to its various background and contexts: time, space, age, culture, and so on. Recognizing these complex activities with limited low-power sensors, considering the power and memory constraints of the wearable environment and the user's obtrusiveness at once is not an easy problem, although it is very crucial for the activity recognizer to be practically useful. In this paper, we recognize activity of eating, which is one of the most typical examples of a complex activity, using only daily low-power mobile and wearable sensors. To organize the related contexts systemically, we have constructed the context model based on activity theory and the "Five W's", and propose a Bayesian network with 88 nodes to predict uncertain contexts probabilistically. The structure of the proposed Bayesian network is designed by a modular and tree-structured approach to reduce the time complexity and increase the scalability. To evaluate the proposed method, we collected the data with 10 different activities from 25 volunteers of various ages, occupations, and jobs, and have obtained 79.71% accuracy, which outperforms other conventional classifiers by 7.54-14.4%. Analyses of the results showed that our probabilistic approach could also give approximate results even when one of contexts or sensor values has a very heterogeneous pattern or is missing.

Synaptic and nonsynaptic plasticity approximating probabilistic inference

PubMed Central

Tully, Philip J.; Hennig, Matthias H.; Lansner, Anders

2014-01-01

Learning and memory operations in neural circuits are believed to involve molecular cascades of synaptic and nonsynaptic changes that lead to a diverse repertoire of dynamical phenomena at higher levels of processing. Hebbian and homeostatic plasticity, neuromodulation, and intrinsic excitability all conspire to form and maintain memories. But it is still unclear how these seemingly redundant mechanisms could jointly orchestrate learning in a more unified system. To this end, a Hebbian learning rule for spiking neurons inspired by Bayesian statistics is proposed. In this model, synaptic weights and intrinsic currents are adapted on-line upon arrival of single spikes, which initiate a cascade of temporally interacting memory traces that locally estimate probabilities associated with relative neuronal activation levels. Trace dynamics enable synaptic learning to readily demonstrate a spike-timing dependence, stably return to a set-point over long time scales, and remain competitive despite this stability. Beyond unsupervised learning, linking the traces with an external plasticity-modulating signal enables spike-based reinforcement learning. At the postsynaptic neuron, the traces are represented by an activity-dependent ion channel that is shown to regulate the input received by a postsynaptic cell and generate intrinsic graded persistent firing levels. We show how spike-based Hebbian-Bayesian learning can be performed in a simulated inference task using integrate-and-fire (IAF) neurons that are Poisson-firing and background-driven, similar to the preferred regime of cortical neurons. Our results support the view that neurons can represent information in the form of probability distributions, and that probabilistic inference could be a functional by-product of coupled synaptic and nonsynaptic mechanisms operating over several timescales. The model provides a biophysical realization of Bayesian computation by reconciling several observed neural phenomena whose functional effects are only partially understood in concert. PMID:24782758

Towards Real-time, On-board, Hardware-Supported Sensor and Software Health Management for Unmanned Aerial Systems

NASA Technical Reports Server (NTRS)

Schumann, Johann; Rozier, Kristin Y.; Reinbacher, Thomas; Mengshoel, Ole J.; Mbaya, Timmy; Ippolito, Corey

2013-01-01

Unmanned aerial systems (UASs) can only be deployed if they can effectively complete their missions and respond to failures and uncertain environmental conditions while maintaining safety with respect to other aircraft as well as humans and property on the ground. In this paper, we design a real-time, on-board system health management (SHM) capability to continuously monitor sensors, software, and hardware components for detection and diagnosis of failures and violations of safety or performance rules during the flight of a UAS. Our approach to SHM is three-pronged, providing: (1) real-time monitoring of sensor and/or software signals; (2) signal analysis, preprocessing, and advanced on the- fly temporal and Bayesian probabilistic fault diagnosis; (3) an unobtrusive, lightweight, read-only, low-power realization using Field Programmable Gate Arrays (FPGAs) that avoids overburdening limited computing resources or costly re-certification of flight software due to instrumentation. Our implementation provides a novel approach of combining modular building blocks, integrating responsive runtime monitoring of temporal logic system safety requirements with model-based diagnosis and Bayesian network-based probabilistic analysis. We demonstrate this approach using actual data from the NASA Swift UAS, an experimental all-electric aircraft.

Characterization and Quantification of Uncertainty in the NARCCAP Regional Climate Model Ensemble and Application to Impacts on Water Systems

NASA Astrophysics Data System (ADS)

Mearns, L. O.; Sain, S. R.; McGinnis, S. A.; Steinschneider, S.; Brown, C. M.

2015-12-01

In this talk we present the development of a joint Bayesian Probabilistic Model for the climate change results of the North American Regional Climate Change Assessment Program (NARCCAP) that uses a unique prior in the model formulation. We use the climate change results (joint distribution of seasonal temperature and precipitation changes (future vs. current)) from the global climate models (GCMs) that provided boundary conditions for the six different regional climate models used in the program as informative priors for the bivariate Bayesian Model. The two variables involved are seasonal temperature and precipitation over sub-regions (i.e., Bukovsky Regions) of the full NARCCAP domain. The basic approach to the joint Bayesian hierarchical model follows the approach of Tebaldi and Sansó (2009). We compare model results using informative (i.e., GCM information) as well as uninformative priors. We apply these results to the Water Evaluation and Planning System (WEAP) model for the Colorado Springs Utility in Colorado. We investigate the layout of the joint pdfs in the context of the water model sensitivities to ranges of temperature and precipitation results to determine the likelihoods of future climate conditions that cannot be accommodated by possible adaptation options. Comparisons may also be made with joint pdfs formed from the CMIP5 collection of global climate models and empirically downscaled to the region of interest.

Confronting uncertainty in flood damage predictions

NASA Astrophysics Data System (ADS)

Schröter, Kai; Kreibich, Heidi; Vogel, Kristin; Merz, Bruno

2015-04-01

Reliable flood damage models are a prerequisite for the practical usefulness of the model results. Oftentimes, traditional uni-variate damage models as for instance depth-damage curves fail to reproduce the variability of observed flood damage. Innovative multi-variate probabilistic modelling approaches are promising to capture and quantify the uncertainty involved and thus to improve the basis for decision making. In this study we compare the predictive capability of two probabilistic modelling approaches, namely Bagging Decision Trees and Bayesian Networks. For model evaluation we use empirical damage data which are available from computer aided telephone interviews that were respectively compiled after the floods in 2002, 2005 and 2006, in the Elbe and Danube catchments in Germany. We carry out a split sample test by sub-setting the damage records. One sub-set is used to derive the models and the remaining records are used to evaluate the predictive performance of the model. Further we stratify the sample according to catchments which allows studying model performance in a spatial transfer context. Flood damage estimation is carried out on the scale of the individual buildings in terms of relative damage. The predictive performance of the models is assessed in terms of systematic deviations (mean bias), precision (mean absolute error) as well as in terms of reliability which is represented by the proportion of the number of observations that fall within the 95-quantile and 5-quantile predictive interval. The reliability of the probabilistic predictions within validation runs decreases only slightly and achieves a very good coverage of observations within the predictive interval. Probabilistic models provide quantitative information about prediction uncertainty which is crucial to assess the reliability of model predictions and improves the usefulness of model results.

BN-FLEMOps pluvial - A probabilistic multi-variable loss estimation model for pluvial floods

NASA Astrophysics Data System (ADS)

Roezer, V.; Kreibich, H.; Schroeter, K.; Doss-Gollin, J.; Lall, U.; Merz, B.

2017-12-01

Pluvial flood events, such as in Copenhagen (Denmark) in 2011, Beijing (China) in 2012 or Houston (USA) in 2016, have caused severe losses to urban dwellings in recent years. These floods are caused by storm events with high rainfall rates well above the design levels of urban drainage systems, which lead to inundation of streets and buildings. A projected increase in frequency and intensity of heavy rainfall events in many areas and an ongoing urbanization may increase pluvial flood losses in the future. For an efficient risk assessment and adaptation to pluvial floods, a quantification of the flood risk is needed. Few loss models have been developed particularly for pluvial floods. These models usually use simple waterlevel- or rainfall-loss functions and come with very high uncertainties. To account for these uncertainties and improve the loss estimation, we present a probabilistic multi-variable loss estimation model for pluvial floods based on empirical data. The model was developed in a two-step process using a machine learning approach and a comprehensive database comprising 783 records of direct building and content damage of private households. The data was gathered through surveys after four different pluvial flood events in Germany between 2005 and 2014. In a first step, linear and non-linear machine learning algorithms, such as tree-based and penalized regression models were used to identify the most important loss influencing factors among a set of 55 candidate variables. These variables comprise hydrological and hydraulic aspects, early warning, precaution, building characteristics and the socio-economic status of the household. In a second step, the most important loss influencing variables were used to derive a probabilistic multi-variable pluvial flood loss estimation model based on Bayesian Networks. Two different networks were tested: a score-based network learned from the data and a network based on expert knowledge. Loss predictions are made through Bayesian inference using Markov chain Monte Carlo (MCMC) sampling. With the ability to cope with incomplete information and use expert knowledge, as well as inherently providing quantitative uncertainty information, it is shown that loss models based on BNs are superior to deterministic approaches for pluvial flood risk assessment.

A Bayesian state-space approach for damage detection and classification

NASA Astrophysics Data System (ADS)

Dzunic, Zoran; Chen, Justin G.; Mobahi, Hossein; Büyüköztürk, Oral; Fisher, John W.

2017-11-01

The problem of automatic damage detection in civil structures is complex and requires a system that can interpret collected sensor data into meaningful information. We apply our recently developed switching Bayesian model for dependency analysis to the problems of damage detection and classification. The model relies on a state-space approach that accounts for noisy measurement processes and missing data, which also infers the statistical temporal dependency between measurement locations signifying the potential flow of information within the structure. A Gibbs sampling algorithm is used to simultaneously infer the latent states, parameters of the state dynamics, the dependence graph, and any changes in behavior. By employing a fully Bayesian approach, we are able to characterize uncertainty in these variables via their posterior distribution and provide probabilistic estimates of the occurrence of damage or a specific damage scenario. We also implement a single class classification method which is more realistic for most real world situations where training data for a damaged structure is not available. We demonstrate the methodology with experimental test data from a laboratory model structure and accelerometer data from a real world structure during different environmental and excitation conditions.

Uncertainty analysis of depth predictions from seismic reflection data using Bayesian statistics

NASA Astrophysics Data System (ADS)

Michelioudakis, Dimitrios G.; Hobbs, Richard W.; Caiado, Camila C. S.

2018-03-01

Estimating the depths of target horizons from seismic reflection data is an important task in exploration geophysics. To constrain these depths we need a reliable and accurate velocity model. Here, we build an optimum 2D seismic reflection data processing flow focused on pre - stack deghosting filters and velocity model building and apply Bayesian methods, including Gaussian process emulation and Bayesian History Matching (BHM), to estimate the uncertainties of the depths of key horizons near the borehole DSDP-258 located in the Mentelle Basin, south west of Australia, and compare the results with the drilled core from that well. Following this strategy, the tie between the modelled and observed depths from DSDP-258 core was in accordance with the ± 2σ posterior credibility intervals and predictions for depths to key horizons were made for the two new drill sites, adjacent the existing borehole of the area. The probabilistic analysis allowed us to generate multiple realizations of pre-stack depth migrated images, these can be directly used to better constrain interpretation and identify potential risk at drill sites. The method will be applied to constrain the drilling targets for the upcoming International Ocean Discovery Program (IODP), leg 369.

Uncertainty analysis of depth predictions from seismic reflection data using Bayesian statistics

NASA Astrophysics Data System (ADS)

Michelioudakis, Dimitrios G.; Hobbs, Richard W.; Caiado, Camila C. S.

2018-06-01

Estimating the depths of target horizons from seismic reflection data is an important task in exploration geophysics. To constrain these depths we need a reliable and accurate velocity model. Here, we build an optimum 2-D seismic reflection data processing flow focused on pre-stack deghosting filters and velocity model building and apply Bayesian methods, including Gaussian process emulation and Bayesian History Matching, to estimate the uncertainties of the depths of key horizons near the Deep Sea Drilling Project (DSDP) borehole 258 (DSDP-258) located in the Mentelle Basin, southwest of Australia, and compare the results with the drilled core from that well. Following this strategy, the tie between the modelled and observed depths from DSDP-258 core was in accordance with the ±2σ posterior credibility intervals and predictions for depths to key horizons were made for the two new drill sites, adjacent to the existing borehole of the area. The probabilistic analysis allowed us to generate multiple realizations of pre-stack depth migrated images, these can be directly used to better constrain interpretation and identify potential risk at drill sites. The method will be applied to constrain the drilling targets for the upcoming International Ocean Discovery Program, leg 369.

Efficient Effects-Based Military Planning Final Report

DTIC Science & Technology

2010-11-13

using probabilistic infer- ence methods,” in Proc. 8th Annu. Conf. Uncertainty Artificial Intelli - gence (UAI), Stanford, CA. San Mateo, CA: Morgan...Imprecise Probabilities, the 24th Conference on Uncertainty in Artificial Intelligence (UAI), 2008. 7. Yan Tong and Qiang Ji, Learning Bayesian Networks...Bayesian Networks using Constraints Cassio P. de Campos cassiopc@acm.org Dalle Molle Institute for Artificial Intelligence Galleria 2, Manno 6928

Bayesian Monte Carlo and Maximum Likelihood Approach for ...

EPA Pesticide Factsheets

Model uncertainty estimation and risk assessment is essential to environmental management and informed decision making on pollution mitigation strategies. In this study, we apply a probabilistic methodology, which combines Bayesian Monte Carlo simulation and Maximum Likelihood estimation (BMCML) to calibrate a lake oxygen recovery model. We first derive an analytical solution of the differential equation governing lake-averaged oxygen dynamics as a function of time-variable wind speed. Statistical inferences on model parameters and predictive uncertainty are then drawn by Bayesian conditioning of the analytical solution on observed daily wind speed and oxygen concentration data obtained from an earlier study during two recovery periods on a eutrophic lake in upper state New York. The model is calibrated using oxygen recovery data for one year and statistical inferences were validated using recovery data for another year. Compared with essentially two-step, regression and optimization approach, the BMCML results are more comprehensive and performed relatively better in predicting the observed temporal dissolved oxygen levels (DO) in the lake. BMCML also produced comparable calibration and validation results with those obtained using popular Markov Chain Monte Carlo technique (MCMC) and is computationally simpler and easier to implement than the MCMC. Next, using the calibrated model, we derive an optimal relationship between liquid film-transfer coefficien

Asking better questions: How presentation formats influence information search.

PubMed

Wu, Charley M; Meder, Björn; Filimon, Flavia; Nelson, Jonathan D

2017-08-01

While the influence of presentation formats have been widely studied in Bayesian reasoning tasks, we present the first systematic investigation of how presentation formats influence information search decisions. Four experiments were conducted across different probabilistic environments, where subjects (N = 2,858) chose between 2 possible search queries, each with binary probabilistic outcomes, with the goal of maximizing classification accuracy. We studied 14 different numerical and visual formats for presenting information about the search environment, constructed across 6 design features that have been prominently related to improvements in Bayesian reasoning accuracy (natural frequencies, posteriors, complement, spatial extent, countability, and part-to-whole information). The posterior variants of the icon array and bar graph formats led to the highest proportion of correct responses, and were substantially better than the standard probability format. Results suggest that presenting information in terms of posterior probabilities and visualizing natural frequencies using spatial extent (a perceptual feature) were especially helpful in guiding search decisions, although environments with a mixture of probabilistic and certain outcomes were challenging across all formats. Subjects who made more accurate probability judgments did not perform better on the search task, suggesting that simple decision heuristics may be used to make search decisions without explicitly applying Bayesian inference to compute probabilities. We propose a new take-the-difference (TTD) heuristic that identifies the accuracy-maximizing query without explicit computation of posterior probabilities. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Bayesian Analysis for Risk Assessment of Selected Medical Events in Support of the Integrated Medical Model Effort

NASA Technical Reports Server (NTRS)

Gilkey, Kelly M.; Myers, Jerry G.; McRae, Michael P.; Griffin, Elise A.; Kallrui, Aditya S.

2012-01-01

The Exploration Medical Capability project is creating a catalog of risk assessments using the Integrated Medical Model (IMM). The IMM is a software-based system intended to assist mission planners in preparing for spaceflight missions by helping them to make informed decisions about medical preparations and supplies needed for combating and treating various medical events using Probabilistic Risk Assessment. The objective is to use statistical analyses to inform the IMM decision tool with estimated probabilities of medical events occurring during an exploration mission. Because data regarding astronaut health are limited, Bayesian statistical analysis is used. Bayesian inference combines prior knowledge, such as data from the general U.S. population, the U.S. Submarine Force, or the analog astronaut population located at the NASA Johnson Space Center, with observed data for the medical condition of interest. The posterior results reflect the best evidence for specific medical events occurring in flight. Bayes theorem provides a formal mechanism for combining available observed data with data from similar studies to support the quantification process. The IMM team performed Bayesian updates on the following medical events: angina, appendicitis, atrial fibrillation, atrial flutter, dental abscess, dental caries, dental periodontal disease, gallstone disease, herpes zoster, renal stones, seizure, and stroke.

Bayesian Estimation and Inference Using Stochastic Electronics

PubMed Central

Thakur, Chetan Singh; Afshar, Saeed; Wang, Runchun M.; Hamilton, Tara J.; Tapson, Jonathan; van Schaik, André

2016-01-01

In this paper, we present the implementation of two types of Bayesian inference problems to demonstrate the potential of building probabilistic algorithms in hardware using single set of building blocks with the ability to perform these computations in real time. The first implementation, referred to as the BEAST (Bayesian Estimation and Stochastic Tracker), demonstrates a simple problem where an observer uses an underlying Hidden Markov Model (HMM) to track a target in one dimension. In this implementation, sensors make noisy observations of the target position at discrete time steps. The tracker learns the transition model for target movement, and the observation model for the noisy sensors, and uses these to estimate the target position by solving the Bayesian recursive equation online. We show the tracking performance of the system and demonstrate how it can learn the observation model, the transition model, and the external distractor (noise) probability interfering with the observations. In the second implementation, referred to as the Bayesian INference in DAG (BIND), we show how inference can be performed in a Directed Acyclic Graph (DAG) using stochastic circuits. We show how these building blocks can be easily implemented using simple digital logic gates. An advantage of the stochastic electronic implementation is that it is robust to certain types of noise, which may become an issue in integrated circuit (IC) technology with feature sizes in the order of tens of nanometers due to their low noise margin, the effect of high-energy cosmic rays and the low supply voltage. In our framework, the flipping of random individual bits would not affect the system performance because information is encoded in a bit stream. PMID:27047326

Bayesian Estimation and Inference Using Stochastic Electronics.

PubMed

Thakur, Chetan Singh; Afshar, Saeed; Wang, Runchun M; Hamilton, Tara J; Tapson, Jonathan; van Schaik, André

2016-01-01

In this paper, we present the implementation of two types of Bayesian inference problems to demonstrate the potential of building probabilistic algorithms in hardware using single set of building blocks with the ability to perform these computations in real time. The first implementation, referred to as the BEAST (Bayesian Estimation and Stochastic Tracker), demonstrates a simple problem where an observer uses an underlying Hidden Markov Model (HMM) to track a target in one dimension. In this implementation, sensors make noisy observations of the target position at discrete time steps. The tracker learns the transition model for target movement, and the observation model for the noisy sensors, and uses these to estimate the target position by solving the Bayesian recursive equation online. We show the tracking performance of the system and demonstrate how it can learn the observation model, the transition model, and the external distractor (noise) probability interfering with the observations. In the second implementation, referred to as the Bayesian INference in DAG (BIND), we show how inference can be performed in a Directed Acyclic Graph (DAG) using stochastic circuits. We show how these building blocks can be easily implemented using simple digital logic gates. An advantage of the stochastic electronic implementation is that it is robust to certain types of noise, which may become an issue in integrated circuit (IC) technology with feature sizes in the order of tens of nanometers due to their low noise margin, the effect of high-energy cosmic rays and the low supply voltage. In our framework, the flipping of random individual bits would not affect the system performance because information is encoded in a bit stream.

Probabilistic classifiers with high-dimensional data

PubMed Central

Kim, Kyung In; Simon, Richard

2011-01-01

For medical classification problems, it is often desirable to have a probability associated with each class. Probabilistic classifiers have received relatively little attention for small n large p classification problems despite of their importance in medical decision making. In this paper, we introduce 2 criteria for assessment of probabilistic classifiers: well-calibratedness and refinement and develop corresponding evaluation measures. We evaluated several published high-dimensional probabilistic classifiers and developed 2 extensions of the Bayesian compound covariate classifier. Based on simulation studies and analysis of gene expression microarray data, we found that proper probabilistic classification is more difficult than deterministic classification. It is important to ensure that a probabilistic classifier is well calibrated or at least not “anticonservative” using the methods developed here. We provide this evaluation for several probabilistic classifiers and also evaluate their refinement as a function of sample size under weak and strong signal conditions. We also present a cross-validation method for evaluating the calibration and refinement of any probabilistic classifier on any data set. PMID:21087946

PyBetVH: A Python tool for probabilistic volcanic hazard assessment and for generation of Bayesian hazard curves and maps

NASA Astrophysics Data System (ADS)

Tonini, Roberto; Sandri, Laura; Anne Thompson, Mary

2015-06-01

PyBetVH is a completely new, free, open-source and cross-platform software implementation of the Bayesian Event Tree for Volcanic Hazard (BET_VH), a tool for estimating the probability of any magmatic hazardous phenomenon occurring in a selected time frame, accounting for all the uncertainties. New capabilities of this implementation include the ability to calculate hazard curves which describe the distribution of the exceedance probability as a function of intensity (e.g., tephra load) on a grid of points covering the target area. The computed hazard curves are (i) absolute (accounting for the probability of eruption in a given time frame, and for all the possible vent locations and eruptive sizes) and (ii) Bayesian (computed at different percentiles, in order to quantify the epistemic uncertainty). Such curves allow representation of the full information contained in the probabilistic volcanic hazard assessment (PVHA) and are well suited to become a main input to quantitative risk analyses. PyBetVH allows for interactive visualization of both the computed hazard curves, and the corresponding Bayesian hazard/probability maps. PyBetVH is designed to minimize the efforts of end users, making PVHA results accessible to people who may be less experienced in probabilistic methodologies, e.g. decision makers. The broad compatibility of Python language has also allowed PyBetVH to be installed on the VHub cyber-infrastructure, where it can be run online or downloaded at no cost. PyBetVH can be used to assess any type of magmatic hazard from any volcano. Here we illustrate how to perform a PVHA through PyBetVH using the example of analyzing tephra fallout from the Okataina Volcanic Centre (OVC), New Zealand, and highlight the range of outputs that the tool can generate.

A Bayesian modelling framework for tornado occurrences in North America

NASA Astrophysics Data System (ADS)

Cheng, Vincent Y. S.; Arhonditsis, George B.; Sills, David M. L.; Gough, William A.; Auld, Heather

2015-03-01

Tornadoes represent one of nature’s most hazardous phenomena that have been responsible for significant destruction and devastating fatalities. Here we present a Bayesian modelling approach for elucidating the spatiotemporal patterns of tornado activity in North America. Our analysis shows a significant increase in the Canadian Prairies and the Northern Great Plains during the summer, indicating a clear transition of tornado activity from the United States to Canada. The linkage between monthly-averaged atmospheric variables and likelihood of tornado events is characterized by distinct seasonality; the convective available potential energy is the predominant factor in the summer; vertical wind shear appears to have a strong signature primarily in the winter and secondarily in the summer; and storm relative environmental helicity is most influential in the spring. The present probabilistic mapping can be used to draw inference on the likelihood of tornado occurrence in any location in North America within a selected time period of the year.

A Bayesian modelling framework for tornado occurrences in North America.

PubMed

Cheng, Vincent Y S; Arhonditsis, George B; Sills, David M L; Gough, William A; Auld, Heather

2015-03-25

Tornadoes represent one of nature's most hazardous phenomena that have been responsible for significant destruction and devastating fatalities. Here we present a Bayesian modelling approach for elucidating the spatiotemporal patterns of tornado activity in North America. Our analysis shows a significant increase in the Canadian Prairies and the Northern Great Plains during the summer, indicating a clear transition of tornado activity from the United States to Canada. The linkage between monthly-averaged atmospheric variables and likelihood of tornado events is characterized by distinct seasonality; the convective available potential energy is the predominant factor in the summer; vertical wind shear appears to have a strong signature primarily in the winter and secondarily in the summer; and storm relative environmental helicity is most influential in the spring. The present probabilistic mapping can be used to draw inference on the likelihood of tornado occurrence in any location in North America within a selected time period of the year.

Integrated software health management for aerospace guidance, navigation, and control systems: A probabilistic reasoning approach

NASA Astrophysics Data System (ADS)

Mbaya, Timmy

Embedded Aerospace Systems have to perform safety and mission critical operations in a real-time environment where timing and functional correctness are extremely important. Guidance, Navigation, and Control (GN&C) systems substantially rely on complex software interfacing with hardware in real-time; any faults in software or hardware, or their interaction could result in fatal consequences. Integrated Software Health Management (ISWHM) provides an approach for detection and diagnosis of software failures while the software is in operation. The ISWHM approach is based on probabilistic modeling of software and hardware sensors using a Bayesian network. To meet memory and timing constraints of real-time embedded execution, the Bayesian network is compiled into an Arithmetic Circuit, which is used for on-line monitoring. This type of system monitoring, using an ISWHM, provides automated reasoning capabilities that compute diagnoses in a timely manner when failures occur. This reasoning capability enables time-critical mitigating decisions and relieves the human agent from the time-consuming and arduous task of foraging through a multitude of isolated---and often contradictory---diagnosis data. For the purpose of demonstrating the relevance of ISWHM, modeling and reasoning is performed on a simple simulated aerospace system running on a real-time operating system emulator, the OSEK/Trampoline platform. Models for a small satellite and an F-16 fighter jet GN&C (Guidance, Navigation, and Control) system have been implemented. Analysis of the ISWHM is then performed by injecting faults and analyzing the ISWHM's diagnoses.

Long-range dismount activity classification: LODAC

NASA Astrophysics Data System (ADS)

Garagic, Denis; Peskoe, Jacob; Liu, Fang; Cuevas, Manuel; Freeman, Andrew M.; Rhodes, Bradley J.

2014-06-01

Continuous classification of dismount types (including gender, age, ethnicity) and their activities (such as walking, running) evolving over space and time is challenging. Limited sensor resolution (often exacerbated as a function of platform standoff distance) and clutter from shadows in dense target environments, unfavorable environmental conditions, and the normal properties of real data all contribute to the challenge. The unique and innovative aspect of our approach is a synthesis of multimodal signal processing with incremental non-parametric, hierarchical Bayesian machine learning methods to create a new kind of target classification architecture. This architecture is designed from the ground up to optimally exploit correlations among the multiple sensing modalities (multimodal data fusion) and rapidly and continuously learns (online self-tuning) patterns of distinct classes of dismounts given little a priori information. This increases classification performance in the presence of challenges posed by anti-access/area denial (A2/AD) sensing. To fuse multimodal features, Long-range Dismount Activity Classification (LODAC) develops a novel statistical information theoretic approach for multimodal data fusion that jointly models multimodal data (i.e., a probabilistic model for cross-modal signal generation) and discovers the critical cross-modal correlations by identifying components (features) with maximal mutual information (MI) which is efficiently estimated using non-parametric entropy models. LODAC develops a generic probabilistic pattern learning and classification framework based on a new class of hierarchical Bayesian learning algorithms for efficiently discovering recurring patterns (classes of dismounts) in multiple simultaneous time series (sensor modalities) at multiple levels of feature granularity.

A Practical Probabilistic Graphical Modeling Tool for Weighing ...

EPA Pesticide Factsheets

Past weight-of-evidence frameworks for adverse ecological effects have provided soft-scoring procedures for judgments based on the quality and measured attributes of evidence. Here, we provide a flexible probabilistic structure for weighing and integrating lines of evidence for ecological risk determinations. Probabilistic approaches can provide both a quantitative weighing of lines of evidence and methods for evaluating risk and uncertainty. The current modeling structure wasdeveloped for propagating uncertainties in measured endpoints and their influence on the plausibility of adverse effects. To illustrate the approach, we apply the model framework to the sediment quality triad using example lines of evidence for sediment chemistry measurements, bioassay results, and in situ infauna diversity of benthic communities using a simplified hypothetical case study. We then combine the three lines evidence and evaluate sensitivity to the input parameters, and show how uncertainties are propagated and how additional information can be incorporated to rapidly update the probability of impacts. The developed network model can be expanded to accommodate additional lines of evidence, variables and states of importance, and different types of uncertainties in the lines of evidence including spatial and temporal as well as measurement errors. We provide a flexible Bayesian network structure for weighing and integrating lines of evidence for ecological risk determinations

A model-based test for treatment effects with probabilistic classifications.

PubMed

Cavagnaro, Daniel R; Davis-Stober, Clintin P

2018-05-21

Within modern psychology, computational and statistical models play an important role in describing a wide variety of human behavior. Model selection analyses are typically used to classify individuals according to the model(s) that best describe their behavior. These classifications are inherently probabilistic, which presents challenges for performing group-level analyses, such as quantifying the effect of an experimental manipulation. We answer this challenge by presenting a method for quantifying treatment effects in terms of distributional changes in model-based (i.e., probabilistic) classifications across treatment conditions. The method uses hierarchical Bayesian mixture modeling to incorporate classification uncertainty at the individual level into the test for a treatment effect at the group level. We illustrate the method with several worked examples, including a reanalysis of the data from Kellen, Mata, and Davis-Stober (2017), and analyze its performance more generally through simulation studies. Our simulations show that the method is both more powerful and less prone to type-1 errors than Fisher's exact test when classifications are uncertain. In the special case where classifications are deterministic, we find a near-perfect power-law relationship between the Bayes factor, derived from our method, and the p value obtained from Fisher's exact test. We provide code in an online supplement that allows researchers to apply the method to their own data. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Lung Cancer Assistant: a hybrid clinical decision support application for lung cancer care.

PubMed

Sesen, M Berkan; Peake, Michael D; Banares-Alcantara, Rene; Tse, Donald; Kadir, Timor; Stanley, Roz; Gleeson, Fergus; Brady, Michael

2014-09-06

Multidisciplinary team (MDT) meetings are becoming the model of care for cancer patients worldwide. While MDTs have improved the quality of cancer care, the meetings impose substantial time pressure on the members, who generally attend several such MDTs. We describe Lung Cancer Assistant (LCA), a clinical decision support (CDS) prototype designed to assist the experts in the treatment selection decisions in the lung cancer MDTs. A novel feature of LCA is its ability to provide rule-based and probabilistic decision support within a single platform. The guideline-based CDS is based on clinical guideline rules, while the probabilistic CDS is based on a Bayesian network trained on the English Lung Cancer Audit Database (LUCADA). We assess rule-based and probabilistic recommendations based on their concordances with the treatments recorded in LUCADA. Our results reveal that the guideline rule-based recommendations perform well in simulating the recorded treatments with exact and partial concordance rates of 0.57 and 0.79, respectively. On the other hand, the exact and partial concordance rates achieved with probabilistic results are relatively poorer with 0.27 and 0.76. However, probabilistic decision support fulfils a complementary role in providing accurate survival estimations. Compared to recorded treatments, both CDS approaches promote higher resection rates and multimodality treatments.

A Copula-Based Conditional Probabilistic Forecast Model for Wind Power Ramps

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hodge, Brian S; Krishnan, Venkat K; Zhang, Jie

Efficient management of wind ramping characteristics can significantly reduce wind integration costs for balancing authorities. By considering the stochastic dependence of wind power ramp (WPR) features, this paper develops a conditional probabilistic wind power ramp forecast (cp-WPRF) model based on Copula theory. The WPRs dataset is constructed by extracting ramps from a large dataset of historical wind power. Each WPR feature (e.g., rate, magnitude, duration, and start-time) is separately forecasted by considering the coupling effects among different ramp features. To accurately model the marginal distributions with a copula, a Gaussian mixture model (GMM) is adopted to characterize the WPR uncertaintymore » and features. The Canonical Maximum Likelihood (CML) method is used to estimate parameters of the multivariable copula. The optimal copula model is chosen based on the Bayesian information criterion (BIC) from each copula family. Finally, the best conditions based cp-WPRF model is determined by predictive interval (PI) based evaluation metrics. Numerical simulations on publicly available wind power data show that the developed copula-based cp-WPRF model can predict WPRs with a high level of reliability and sharpness.« less

Prediction in Health Domain Using Bayesian Networks Optimization Based on Induction Learning Techniques

NASA Astrophysics Data System (ADS)

Felgaer, Pablo; Britos, Paola; García-Martínez, Ramón

A Bayesian network is a directed acyclic graph in which each node represents a variable and each arc a probabilistic dependency; they are used to provide: a compact form to represent the knowledge and flexible methods of reasoning. Obtaining it from data is a learning process that is divided in two steps: structural learning and parametric learning. In this paper we define an automatic learning method that optimizes the Bayesian networks applied to classification, using a hybrid method of learning that combines the advantages of the induction techniques of the decision trees (TDIDT-C4.5) with those of the Bayesian networks. The resulting method is applied to prediction in health domain.

Perspective: Stochastic magnetic devices for cognitive computing

NASA Astrophysics Data System (ADS)

Roy, Kaushik; Sengupta, Abhronil; Shim, Yong

2018-06-01

Stochastic switching of nanomagnets can potentially enable probabilistic cognitive hardware consisting of noisy neural and synaptic components. Furthermore, computational paradigms inspired from the Ising computing model require stochasticity for achieving near-optimality in solutions to various types of combinatorial optimization problems such as the Graph Coloring Problem or the Travelling Salesman Problem. Achieving optimal solutions in such problems are computationally exhaustive and requires natural annealing to arrive at the near-optimal solutions. Stochastic switching of devices also finds use in applications involving Deep Belief Networks and Bayesian Inference. In this article, we provide a multi-disciplinary perspective across the stack of devices, circuits, and algorithms to illustrate how the stochastic switching dynamics of spintronic devices in the presence of thermal noise can provide a direct mapping to the computational units of such probabilistic intelligent systems.

Probabilistic Low-Rank Multitask Learning.

PubMed

Kong, Yu; Shao, Ming; Li, Kang; Fu, Yun

2018-03-01

In this paper, we consider the problem of learning multiple related tasks simultaneously with the goal of improving the generalization performance of individual tasks. The key challenge is to effectively exploit the shared information across multiple tasks as well as preserve the discriminative information for each individual task. To address this, we propose a novel probabilistic model for multitask learning (MTL) that can automatically balance between low-rank and sparsity constraints. The former assumes a low-rank structure of the underlying predictive hypothesis space to explicitly capture the relationship of different tasks and the latter learns the incoherent sparse patterns private to each task. We derive and perform inference via variational Bayesian methods. Experimental results on both regression and classification tasks on real-world applications demonstrate the effectiveness of the proposed method in dealing with the MTL problems.

Combining Bayesian Networks and Agent Based Modeling to develop a decision-support model in Vietnam

NASA Astrophysics Data System (ADS)

Nong, Bao Anh; Ertsen, Maurits; Schoups, Gerrit

2016-04-01

Complexity and uncertainty in natural resources management have been focus themes in recent years. Within these debates, with the aim to define an approach feasible for water management practice, we are developing an integrated conceptual modeling framework for simulating decision-making processes of citizens, in our case in the Day river area, Vietnam. The model combines Bayesian Networks (BNs) and Agent-Based Modeling (ABM). BNs are able to combine both qualitative data from consultants / experts / stakeholders, and quantitative data from observations on different phenomena or outcomes from other models. Further strengths of BNs are that the relationship between variables in the system is presented in a graphical interface, and that components of uncertainty are explicitly related to their probabilistic dependencies. A disadvantage is that BNs cannot easily identify the feedback of agents in the system once changes appear. Hence, ABM was adopted to represent the reaction among stakeholders under changes. The modeling framework is developed as an attempt to gain better understanding about citizen's behavior and factors influencing their decisions in order to reduce uncertainty in the implementation of water management policy.

Bayes in biological anthropology.

PubMed

Konigsberg, Lyle W; Frankenberg, Susan R

2013-12-01

In this article, we both contend and illustrate that biological anthropologists, particularly in the Americas, often think like Bayesians but act like frequentists when it comes to analyzing a wide variety of data. In other words, while our research goals and perspectives are rooted in probabilistic thinking and rest on prior knowledge, we often proceed to use statistical hypothesis tests and confidence interval methods unrelated (or tenuously related) to the research questions of interest. We advocate for applying Bayesian analyses to a number of different bioanthropological questions, especially since many of the programming and computational challenges to doing so have been overcome in the past two decades. To facilitate such applications, this article explains Bayesian principles and concepts, and provides concrete examples of Bayesian computer simulations and statistics that address questions relevant to biological anthropology, focusing particularly on bioarchaeology and forensic anthropology. It also simultaneously reviews the use of Bayesian methods and inference within the discipline to date. This article is intended to act as primer to Bayesian methods and inference in biological anthropology, explaining the relationships of various methods to likelihoods or probabilities and to classical statistical models. Our contention is not that traditional frequentist statistics should be rejected outright, but that there are many situations where biological anthropology is better served by taking a Bayesian approach. To this end it is hoped that the examples provided in this article will assist researchers in choosing from among the broad array of statistical methods currently available. Copyright © 2013 Wiley Periodicals, Inc.

Probabilistic models in human sensorimotor control

PubMed Central

Wolpert, Daniel M.

2009-01-01

Sensory and motor uncertainty form a fundamental constraint on human sensorimotor control. Bayesian decision theory (BDT) has emerged as a unifying framework to understand how the central nervous system performs optimal estimation and control in the face of such uncertainty. BDT has two components: Bayesian statistics and decision theory. Here we review Bayesian statistics and show how it applies to estimating the state of the world and our own body. Recent results suggest that when learning novel tasks we are able to learn the statistical properties of both the world and our own sensory apparatus so as to perform estimation using Bayesian statistics. We review studies which suggest that humans can combine multiple sources of information to form maximum likelihood estimates, can incorporate prior beliefs about possible states of the world so as to generate maximum a posteriori estimates and can use Kalman filter-based processes to estimate time-varying states. Finally, we review Bayesian decision theory in motor control and how the central nervous system processes errors to determine loss functions and optimal actions. We review results that suggest we plan movements based on statistics of our actions that result from signal-dependent noise on our motor outputs. Taken together these studies provide a statistical framework for how the motor system performs in the presence of uncertainty. PMID:17628731

Tracking composite material damage evolution using Bayesian filtering and flash thermography data

NASA Astrophysics Data System (ADS)

Gregory, Elizabeth D.; Holland, Steve D.

2016-05-01

We propose a method for tracking the condition of a composite part using Bayesian filtering of ash thermography data over the lifetime of the part. In this demonstration, composite panels were fabricated; impacted to induce subsurface delaminations; and loaded in compression over multiple time steps, causing the delaminations to grow in size. Flash thermography data was collected between each damage event to serve as a time history of the part. The ash thermography indicated some areas of damage but provided little additional information as to the exact nature or depth of the damage. Computed tomography (CT) data was also collected after each damage event and provided a high resolution volume model of damage that acted as truth. After each cycle, the condition estimate, from the ash thermography data and the Bayesian filter, was compared to 'ground truth'. The Bayesian process builds on the lifetime history of ash thermography scans and can give better estimates of material condition as compared to the most recent scan alone, which is common practice in the aerospace industry. Bayesian inference provides probabilistic estimates of damage condition that are updated as each new set of data becomes available. The method was tested on simulated data and then on an experimental data set.

Quantitative analysis of breast cancer diagnosis using a probabilistic modelling approach.

PubMed

Liu, Shuo; Zeng, Jinshu; Gong, Huizhou; Yang, Hongqin; Zhai, Jia; Cao, Yi; Liu, Junxiu; Luo, Yuling; Li, Yuhua; Maguire, Liam; Ding, Xuemei

2018-01-01

Breast cancer is the most prevalent cancer in women in most countries of the world. Many computer-aided diagnostic methods have been proposed, but there are few studies on quantitative discovery of probabilistic dependencies among breast cancer data features and identification of the contribution of each feature to breast cancer diagnosis. This study aims to fill this void by utilizing a Bayesian network (BN) modelling approach. A K2 learning algorithm and statistical computation methods are used to construct BN structure and assess the obtained BN model. The data used in this study were collected from a clinical ultrasound dataset derived from a Chinese local hospital and a fine-needle aspiration cytology (FNAC) dataset from UCI machine learning repository. Our study suggested that, in terms of ultrasound data, cell shape is the most significant feature for breast cancer diagnosis, and the resistance index presents a strong probabilistic dependency on blood signals. With respect to FNAC data, bare nuclei are the most important discriminating feature of malignant and benign breast tumours, and uniformity of both cell size and cell shape are tightly interdependent. The BN modelling approach can support clinicians in making diagnostic decisions based on the significant features identified by the model, especially when some other features are missing for specific patients. The approach is also applicable to other healthcare data analytics and data modelling for disease diagnosis. Copyright © 2017 Elsevier Ltd. All rights reserved.

The integration of probabilistic information during sensorimotor estimation is unimpaired in children with Cerebral Palsy

PubMed Central

Sokhey, Taegh; Gaebler-Spira, Deborah; Kording, Konrad P.

2017-01-01

Background It is important to understand the motor deficits of children with Cerebral Palsy (CP). Our understanding of this motor disorder can be enriched by computational models of motor control. One crucial stage in generating movement involves combining uncertain information from different sources, and deficits in this process could contribute to reduced motor function in children with CP. Healthy adults can integrate previously-learned information (prior) with incoming sensory information (likelihood) in a close-to-optimal way when estimating object location, consistent with the use of Bayesian statistics. However, there are few studies investigating how children with CP perform sensorimotor integration. We compare sensorimotor estimation in children with CP and age-matched controls using a model-based analysis to understand the process. Methods and findings We examined Bayesian sensorimotor integration in children with CP, aged between 5 and 12 years old, with Gross Motor Function Classification System (GMFCS) levels 1–3 and compared their estimation behavior with age-matched typically-developing (TD) children. We used a simple sensorimotor estimation task which requires participants to combine probabilistic information from different sources: a likelihood distribution (current sensory information) with a prior distribution (learned target information). In order to examine sensorimotor integration, we quantified how participants weighed statistical information from the two sources (prior and likelihood) and compared this to the statistical optimal weighting. We found that the weighing of statistical information in children with CP was as statistically efficient as that of TD children. Conclusions We conclude that Bayesian sensorimotor integration is not impaired in children with CP and therefore, does not contribute to their motor deficits. Future research has the potential to enrich our understanding of motor disorders by investigating the stages of motor processing set out by computational models. Therapeutic interventions should exploit the ability of children with CP to use statistical information. PMID:29186196

Generative diffeomorphic modelling of large MRI data sets for probabilistic template construction.

PubMed

Blaiotta, Claudia; Freund, Patrick; Cardoso, M Jorge; Ashburner, John

2018-02-01

In this paper we present a hierarchical generative model of medical image data, which can capture simultaneously the variability of both signal intensity and anatomical shapes across large populations. Such a model has a direct application for learning average-shaped probabilistic tissue templates in a fully automated manner. While in principle the generality of the proposed Bayesian approach makes it suitable to address a wide range of medical image computing problems, our work focuses primarily on neuroimaging applications. In particular we validate the proposed method on both real and synthetic brain MR scans including the cervical cord and demonstrate that it yields accurate alignment of brain and spinal cord structures, as compared to state-of-the-art tools for medical image registration. At the same time we illustrate how the resulting tissue probability maps can readily be used to segment, bias correct and spatially normalise unseen data, which are all crucial pre-processing steps for MR imaging studies. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Bayesian inference and assessment for rare-event bycatch in marine fisheries: a drift gillnet fishery case study.

PubMed

Martin, Summer L; Stohs, Stephen M; Moore, Jeffrey E

2015-03-01

Fisheries bycatch is a global threat to marine megafauna. Environmental laws require bycatch assessment for protected species, but this is difficult when bycatch is rare. Low bycatch rates, combined with low observer coverage, may lead to biased, imprecise estimates when using standard ratio estimators. Bayesian model-based approaches incorporate uncertainty, produce less volatile estimates, and enable probabilistic evaluation of estimates relative to management thresholds. Here, we demonstrate a pragmatic decision-making process that uses Bayesian model-based inferences to estimate the probability of exceeding management thresholds for bycatch in fisheries with < 100% observer coverage. Using the California drift gillnet fishery as a case study, we (1) model rates of rare-event bycatch and mortality using Bayesian Markov chain Monte Carlo estimation methods and 20 years of observer data; (2) predict unobserved counts of bycatch and mortality; (3) infer expected annual mortality; (4) determine probabilities of mortality exceeding regulatory thresholds; and (5) classify the fishery as having low, medium, or high bycatch impact using those probabilities. We focused on leatherback sea turtles (Dermochelys coriacea) and humpback whales (Megaptera novaeangliae). Candidate models included Poisson or zero-inflated Poisson likelihood, fishing effort, and a bycatch rate that varied with area, time, or regulatory regime. Regulatory regime had the strongest effect on leatherback bycatch, with the highest levels occurring prior to a regulatory change. Area had the strongest effect on humpback bycatch. Cumulative bycatch estimates for the 20-year period were 104-242 leatherbacks (52-153 deaths) and 6-50 humpbacks (0-21 deaths). The probability of exceeding a regulatory threshold under the U.S. Marine Mammal Protection Act (Potential Biological Removal, PBR) of 0.113 humpback deaths was 0.58, warranting a "medium bycatch impact" classification of the fishery. No PBR thresholds exist for leatherbacks, but the probability of exceeding an anticipated level of two deaths per year, stated as part of a U.S. Endangered Species Act assessment process, was 0.0007. The approach demonstrated here would allow managers to objectively and probabilistically classify fisheries with respect to bycatch impacts on species that have population-relevant mortality reference points, and declare with a stipulated level of certainty that bycatch did or did not exceed estimated upper bounds.

Shear-wave velocity-based probabilistic and deterministic assessment of seismic soil liquefaction potential

USGS Publications Warehouse

Kayen, R.; Moss, R.E.S.; Thompson, E.M.; Seed, R.B.; Cetin, K.O.; Der Kiureghian, A.; Tanaka, Y.; Tokimatsu, K.

2013-01-01

Shear-wave velocity (Vs) offers a means to determine the seismic resistance of soil to liquefaction by a fundamental soil property. This paper presents the results of an 11-year international project to gather new Vs site data and develop probabilistic correlations for seismic soil liquefaction occurrence. Toward that objective, shear-wave velocity test sites were identified, and measurements made for 301 new liquefaction field case histories in China, Japan, Taiwan, Greece, and the United States over a decade. The majority of these new case histories reoccupy those previously investigated by penetration testing. These new data are combined with previously published case histories to build a global catalog of 422 case histories of Vs liquefaction performance. Bayesian regression and structural reliability methods facilitate a probabilistic treatment of the Vs catalog for performance-based engineering applications. Where possible, uncertainties of the variables comprising both the seismic demand and the soil capacity were estimated and included in the analysis, resulting in greatly reduced overall model uncertainty relative to previous studies. The presented data set and probabilistic analysis also help resolve the ancillary issues of adjustment for soil fines content and magnitude scaling factors.

Approximate string matching algorithms for limited-vocabulary OCR output correction

NASA Astrophysics Data System (ADS)

Lasko, Thomas A.; Hauser, Susan E.

2000-12-01

Five methods for matching words mistranslated by optical character recognition to their most likely match in a reference dictionary were tested on data from the archives of the National Library of Medicine. The methods, including an adaptation of the cross correlation algorithm, the generic edit distance algorithm, the edit distance algorithm with a probabilistic substitution matrix, Bayesian analysis, and Bayesian analysis on an actively thinned reference dictionary were implemented and their accuracy rates compared. Of the five, the Bayesian algorithm produced the most correct matches (87%), and had the advantage of producing scores that have a useful and practical interpretation.

Learning coefficient of generalization error in Bayesian estimation and vandermonde matrix-type singularity.

PubMed

Aoyagi, Miki; Nagata, Kenji

2012-06-01

The term algebraic statistics arises from the study of probabilistic models and techniques for statistical inference using methods from algebra and geometry (Sturmfels, 2009 ). The purpose of our study is to consider the generalization error and stochastic complexity in learning theory by using the log-canonical threshold in algebraic geometry. Such thresholds correspond to the main term of the generalization error in Bayesian estimation, which is called a learning coefficient (Watanabe, 2001a , 2001b ). The learning coefficient serves to measure the learning efficiencies in hierarchical learning models. In this letter, we consider learning coefficients for Vandermonde matrix-type singularities, by using a new approach: focusing on the generators of the ideal, which defines singularities. We give tight new bound values of learning coefficients for the Vandermonde matrix-type singularities and the explicit values with certain conditions. By applying our results, we can show the learning coefficients of three-layered neural networks and normal mixture models.

Mixed linear-non-linear inversion of crustal deformation data: Bayesian inference of model, weighting and regularization parameters

NASA Astrophysics Data System (ADS)

Fukuda, Jun'ichi; Johnson, Kaj M.

2010-06-01

We present a unified theoretical framework and solution method for probabilistic, Bayesian inversions of crustal deformation data. The inversions involve multiple data sets with unknown relative weights, model parameters that are related linearly or non-linearly through theoretic models to observations, prior information on model parameters and regularization priors to stabilize underdetermined problems. To efficiently handle non-linear inversions in which some of the model parameters are linearly related to the observations, this method combines both analytical least-squares solutions and a Monte Carlo sampling technique. In this method, model parameters that are linearly and non-linearly related to observations, relative weights of multiple data sets and relative weights of prior information and regularization priors are determined in a unified Bayesian framework. In this paper, we define the mixed linear-non-linear inverse problem, outline the theoretical basis for the method, provide a step-by-step algorithm for the inversion, validate the inversion method using synthetic data and apply the method to two real data sets. We apply the method to inversions of multiple geodetic data sets with unknown relative data weights for interseismic fault slip and locking depth. We also apply the method to the problem of estimating the spatial distribution of coseismic slip on faults with unknown fault geometry, relative data weights and smoothing regularization weight.

Probabilistically modeling lava flows with MOLASSES

NASA Astrophysics Data System (ADS)

Richardson, J. A.; Connor, L.; Connor, C.; Gallant, E.

2017-12-01

Modeling lava flows through Cellular Automata methods enables a computationally inexpensive means to quickly forecast lava flow paths and ultimate areal extents. We have developed a lava flow simulator, MOLASSES, that forecasts lava flow inundation over an elevation model from a point source eruption. This modular code can be implemented in a deterministic fashion with given user inputs that will produce a single lava flow simulation. MOLASSES can also be implemented in a probabilistic fashion where given user inputs define parameter distributions that are randomly sampled to create many lava flow simulations. This probabilistic approach enables uncertainty in input data to be expressed in the model results and MOLASSES outputs a probability map of inundation instead of a determined lava flow extent. Since the code is comparatively fast, we use it probabilistically to investigate where potential vents are located that may impact specific sites and areas, as well as the unconditional probability of lava flow inundation of sites or areas from any vent. We have validated the MOLASSES code to community-defined benchmark tests and to the real world lava flows at Tolbachik (2012-2013) and Pico do Fogo (2014-2015). To determine the efficacy of the MOLASSES simulator at accurately and precisely mimicking the inundation area of real flows, we report goodness of fit using both model sensitivity and the Positive Predictive Value, the latter of which is a Bayesian posterior statistic. Model sensitivity is often used in evaluating lava flow simulators, as it describes how much of the lava flow was successfully modeled by the simulation. We argue that the positive predictive value is equally important in determining how good a simulator is, as it describes the percentage of the simulation space that was actually inundated by lava.

A probabilistic method for streamflow projection and associated uncertainty analysis in a data sparse alpine region

NASA Astrophysics Data System (ADS)

Ren, Weiwei; Yang, Tao; Shi, Pengfei; Xu, Chong-yu; Zhang, Ke; Zhou, Xudong; Shao, Quanxi; Ciais, Philippe

2018-06-01

Climate change imposes profound influence on regional hydrological cycle and water security in many alpine regions worldwide. Investigating regional climate impacts using watershed scale hydrological models requires a large number of input data such as topography, meteorological and hydrological data. However, data scarcity in alpine regions seriously restricts evaluation of climate change impacts on water cycle using conventional approaches based on global or regional climate models, statistical downscaling methods and hydrological models. Therefore, this study is dedicated to development of a probabilistic model to replace the conventional approaches for streamflow projection. The probabilistic model was built upon an advanced Bayesian Neural Network (BNN) approach directly fed by the large-scale climate predictor variables and tested in a typical data sparse alpine region, the Kaidu River basin in Central Asia. Results show that BNN model performs better than the general methods across a number of statistical measures. The BNN method with flexible model structures by active indicator functions, which reduce the dependence on the initial specification for the input variables and the number of hidden units, can work well in a data limited region. Moreover, it can provide more reliable streamflow projections with a robust generalization ability. Forced by the latest bias-corrected GCM scenarios, streamflow projections for the 21st century under three RCP emission pathways were constructed and analyzed. Briefly, the proposed probabilistic projection approach could improve runoff predictive ability over conventional methods and provide better support to water resources planning and management under data limited conditions as well as enable a facilitated climate change impact analysis on runoff and water resources in alpine regions worldwide.

Development of a Probabilistic Decision-Support Model to Forecast Coastal Resilience

NASA Astrophysics Data System (ADS)

Wilson, K.; Safak, I.; Brenner, O.; Lentz, E. E.; Hapke, C. J.

2016-02-01

Site-specific forecasts of coastal change are a valuable management tool in preparing for and assessing storm-driven impacts in coastal areas. More specifically, understanding the likelihood of storm impacts, recovery following events, and the alongshore variability of both is central in evaluating vulnerability and resiliency of barrier islands. We introduce a probabilistic modeling framework that integrates hydrodynamic, anthropogenic, and morphologic components of the barrier system to evaluate coastal change at Fire Island, New York. The model is structured on a Bayesian network (BN), which utilizes observations to learn statistical relationships between system variables. In addition to predictive ability, probabilistic models convey the level of confidence associated with a prediction, an important consideration for coastal managers. Our model predicts the likelihood of morphologic change on the upper beach based on several decades of beach monitoring data. A coupled hydrodynamic BN combines probabilistic and deterministic modeling approaches; by querying nearly two decades of nested-grid wave simulations that account for both distant swells and local seas, we produce scenarios of event and seasonal wave climates. The wave scenarios of total water level - a sum of run up, surge and tide - and anthropogenic modification are the primary drivers of morphologic change in our model structure. Preliminary results show the hydrodynamic BN is able to reproduce time series of total water levels, a critical validation process before generating scenarios, and forecasts of geomorphic change over three month intervals are up to 70% accurate. Predictions of storm-induced change and recovery are linked to evaluate zones of persistent vulnerability or resilience and will help managers target restoration efforts, identify areas most vulnerable to habitat degradation, and highlight resilient zones that may best support relocation of critical infrastructure.

Probabilistic (Bayesian) Modeling of Gene Expression in Transplant Glomerulopathy

DTIC Science & Technology

2010-01-01

Mengel M, Mihatsch MJ, Nankivell BJ, Nickeleit V, Papadimitriou JC, Platt JL, Randhawa P, Roberts I, Salinas-Madriga L, Salomon DR, Seron D, Sheaff...8217CAN’), Am J Transplant 2007, 7:518-526 14. Solez K, Colvin RB, Racusen LC, Haas M, Sis B, Mengel M, Halloran PF, Baldwin W, Banfi G, Collins AB...Transplant 2009, 9:517-526 29. Mengel M, Bock O, Priess M, Haller H, Kreipe H, Gwinner W: Expression of pro- and antifibrotic genes in protocol biopsies

Modular Bayesian Networks with Low-Power Wearable Sensors for Recognizing Eating Activities

PubMed Central

Kim, Kee-Hoon

2017-01-01

Recently, recognizing a user’s daily activity using a smartphone and wearable sensors has become a popular issue. However, in contrast with the ideal definition of an experiment, there could be numerous complex activities in real life with respect to its various background and contexts: time, space, age, culture, and so on. Recognizing these complex activities with limited low-power sensors, considering the power and memory constraints of the wearable environment and the user’s obtrusiveness at once is not an easy problem, although it is very crucial for the activity recognizer to be practically useful. In this paper, we recognize activity of eating, which is one of the most typical examples of a complex activity, using only daily low-power mobile and wearable sensors. To organize the related contexts systemically, we have constructed the context model based on activity theory and the “Five W’s”, and propose a Bayesian network with 88 nodes to predict uncertain contexts probabilistically. The structure of the proposed Bayesian network is designed by a modular and tree-structured approach to reduce the time complexity and increase the scalability. To evaluate the proposed method, we collected the data with 10 different activities from 25 volunteers of various ages, occupations, and jobs, and have obtained 79.71% accuracy, which outperforms other conventional classifiers by 7.54–14.4%. Analyses of the results showed that our probabilistic approach could also give approximate results even when one of contexts or sensor values has a very heterogeneous pattern or is missing. PMID:29232937

Robust Bayesian Algorithm for Targeted Compound Screening in Forensic Toxicology.

PubMed

Woldegebriel, Michael; Gonsalves, John; van Asten, Arian; Vivó-Truyols, Gabriel

2016-02-16

As part of forensic toxicological investigation of cases involving unexpected death of an individual, targeted or untargeted xenobiotic screening of post-mortem samples is normally conducted. To this end, liquid chromatography (LC) coupled to high-resolution mass spectrometry (MS) is typically employed. For data analysis, almost all commonly applied algorithms are threshold-based (frequentist). These algorithms examine the value of a certain measurement (e.g., peak height) to decide whether a certain xenobiotic of interest (XOI) is present/absent, yielding a binary output. Frequentist methods pose a problem when several sources of information [e.g., shape of the chromatographic peak, isotopic distribution, estimated mass-to-charge ratio (m/z), adduct, etc.] need to be combined, requiring the approach to make arbitrary decisions at substep levels of data analysis. We hereby introduce a novel Bayesian probabilistic algorithm for toxicological screening. The method tackles the problem with a different strategy. It is not aimed at reaching a final conclusion regarding the presence of the XOI, but it estimates its probability. The algorithm effectively and efficiently combines all possible pieces of evidence from the chromatogram and calculates the posterior probability of the presence/absence of XOI features. This way, the model can accommodate more information by updating the probability if extra evidence is acquired. The final probabilistic result assists the end user to make a final decision with respect to the presence/absence of the xenobiotic. The Bayesian method was validated and found to perform better (in terms of false positives and false negatives) than the vendor-supplied software package.

Quantum Inference on Bayesian Networks

NASA Astrophysics Data System (ADS)

Yoder, Theodore; Low, Guang Hao; Chuang, Isaac

2014-03-01

Because quantum physics is naturally probabilistic, it seems reasonable to expect physical systems to describe probabilities and their evolution in a natural fashion. Here, we use quantum computation to speedup sampling from a graphical probability model, the Bayesian network. A specialization of this sampling problem is approximate Bayesian inference, where the distribution on query variables is sampled given the values e of evidence variables. Inference is a key part of modern machine learning and artificial intelligence tasks, but is known to be NP-hard. Classically, a single unbiased sample is obtained from a Bayesian network on n variables with at most m parents per node in time (nmP(e) - 1 / 2) , depending critically on P(e) , the probability the evidence might occur in the first place. However, by implementing a quantum version of rejection sampling, we obtain a square-root speedup, taking (n2m P(e) -1/2) time per sample. The speedup is the result of amplitude amplification, which is proving to be broadly applicable in sampling and machine learning tasks. In particular, we provide an explicit and efficient circuit construction that implements the algorithm without the need for oracle access.

Identifying biological concepts from a protein-related corpus with a probabilistic topic model

PubMed Central

Zheng, Bin; McLean, David C; Lu, Xinghua

2006-01-01

Background Biomedical literature, e.g., MEDLINE, contains a wealth of knowledge regarding functions of proteins. Major recurring biological concepts within such text corpora represent the domains of this body of knowledge. The goal of this research is to identify the major biological topics/concepts from a corpus of protein-related MEDLINE© titles and abstracts by applying a probabilistic topic model. Results The latent Dirichlet allocation (LDA) model was applied to the corpus. Based on the Bayesian model selection, 300 major topics were extracted from the corpus. The majority of identified topics/concepts was found to be semantically coherent and most represented biological objects or concepts. The identified topics/concepts were further mapped to the controlled vocabulary of the Gene Ontology (GO) terms based on mutual information. Conclusion The major and recurring biological concepts within a collection of MEDLINE documents can be extracted by the LDA model. The identified topics/concepts provide parsimonious and semantically-enriched representation of the texts in a semantic space with reduced dimensionality and can be used to index text. PMID:16466569

Incremental Bayesian Category Learning From Natural Language.

PubMed

Frermann, Lea; Lapata, Mirella

2016-08-01

Models of category learning have been extensively studied in cognitive science and primarily tested on perceptual abstractions or artificial stimuli. In this paper, we focus on categories acquired from natural language stimuli, that is, words (e.g., chair is a member of the furniture category). We present a Bayesian model that, unlike previous work, learns both categories and their features in a single process. We model category induction as two interrelated subproblems: (a) the acquisition of features that discriminate among categories, and (b) the grouping of concepts into categories based on those features. Our model learns categories incrementally using particle filters, a sequential Monte Carlo method commonly used for approximate probabilistic inference that sequentially integrates newly observed data and can be viewed as a plausible mechanism for human learning. Experimental results show that our incremental learner obtains meaningful categories which yield a closer fit to behavioral data compared to related models while at the same time acquiring features which characterize the learned categories. (An earlier version of this work was published in Frermann and Lapata .). Copyright © 2015 Cognitive Science Society, Inc.

Variational Bayesian Learning for Wavelet Independent Component Analysis

NASA Astrophysics Data System (ADS)

Roussos, E.; Roberts, S.; Daubechies, I.

2005-11-01

In an exploratory approach to data analysis, it is often useful to consider the observations as generated from a set of latent generators or "sources" via a generally unknown mapping. For the noisy overcomplete case, where we have more sources than observations, the problem becomes extremely ill-posed. Solutions to such inverse problems can, in many cases, be achieved by incorporating prior knowledge about the problem, captured in the form of constraints. This setting is a natural candidate for the application of the Bayesian methodology, allowing us to incorporate "soft" constraints in a natural manner. The work described in this paper is mainly driven by problems in functional magnetic resonance imaging of the brain, for the neuro-scientific goal of extracting relevant "maps" from the data. This can be stated as a `blind' source separation problem. Recent experiments in the field of neuroscience show that these maps are sparse, in some appropriate sense. The separation problem can be solved by independent component analysis (ICA), viewed as a technique for seeking sparse components, assuming appropriate distributions for the sources. We derive a hybrid wavelet-ICA model, transforming the signals into a domain where the modeling assumption of sparsity of the coefficients with respect to a dictionary is natural. We follow a graphical modeling formalism, viewing ICA as a probabilistic generative model. We use hierarchical source and mixing models and apply Bayesian inference to the problem. This allows us to perform model selection in order to infer the complexity of the representation, as well as automatic denoising. Since exact inference and learning in such a model is intractable, we follow a variational Bayesian mean-field approach in the conjugate-exponential family of distributions, for efficient unsupervised learning in multi-dimensional settings. The performance of the proposed algorithm is demonstrated on some representative experiments.

Uncertainty plus prior equals rational bias: an intuitive Bayesian probability weighting function.

PubMed

Fennell, John; Baddeley, Roland

2012-10-01

Empirical research has shown that when making choices based on probabilistic options, people behave as if they overestimate small probabilities, underestimate large probabilities, and treat positive and negative outcomes differently. These distortions have been modeled using a nonlinear probability weighting function, which is found in several nonexpected utility theories, including rank-dependent models and prospect theory; here, we propose a Bayesian approach to the probability weighting function and, with it, a psychological rationale. In the real world, uncertainty is ubiquitous and, accordingly, the optimal strategy is to combine probability statements with prior information using Bayes' rule. First, we show that any reasonable prior on probabilities leads to 2 of the observed effects; overweighting of low probabilities and underweighting of high probabilities. We then investigate 2 plausible kinds of priors: informative priors based on previous experience and uninformative priors of ignorance. Individually, these priors potentially lead to large problems of bias and inefficiency, respectively; however, when combined using Bayesian model comparison methods, both forms of prior can be applied adaptively, gaining the efficiency of empirical priors and the robustness of ignorance priors. We illustrate this for the simple case of generic good and bad options, using Internet blogs to estimate the relevant priors of inference. Given this combined ignorant/informative prior, the Bayesian probability weighting function is not only robust and efficient but also matches all of the major characteristics of the distortions found in empirical research. PsycINFO Database Record (c) 2012 APA, all rights reserved.

Resident Space Object Characterization and Behavior Understanding via Machine Learning and Ontology-based Bayesian Networks

NASA Astrophysics Data System (ADS)

Furfaro, R.; Linares, R.; Gaylor, D.; Jah, M.; Walls, R.

2016-09-01

In this paper, we present an end-to-end approach that employs machine learning techniques and Ontology-based Bayesian Networks (BN) to characterize the behavior of resident space objects. State-of-the-Art machine learning architectures (e.g. Extreme Learning Machines, Convolutional Deep Networks) are trained on physical models to learn the Resident Space Object (RSO) features in the vectorized energy and momentum states and parameters. The mapping from measurements to vectorized energy and momentum states and parameters enables behavior characterization via clustering in the features space and subsequent RSO classification. Additionally, Space Object Behavioral Ontologies (SOBO) are employed to define and capture the domain knowledge-base (KB) and BNs are constructed from the SOBO in a semi-automatic fashion to execute probabilistic reasoning over conclusions drawn from trained classifiers and/or directly from processed data. Such an approach enables integrating machine learning classifiers and probabilistic reasoning to support higher-level decision making for space domain awareness applications. The innovation here is to use these methods (which have enjoyed great success in other domains) in synergy so that it enables a "from data to discovery" paradigm by facilitating the linkage and fusion of large and disparate sources of information via a Big Data Science and Analytics framework.

Application of Fragment Ion Information as Further Evidence in Probabilistic Compound Screening Using Bayesian Statistics and Machine Learning: A Leap Toward Automation.

PubMed

Woldegebriel, Michael; Zomer, Paul; Mol, Hans G J; Vivó-Truyols, Gabriel

2016-08-02

In this work, we introduce an automated, efficient, and elegant model to combine all pieces of evidence (e.g., expected retention times, peak shapes, isotope distributions, fragment-to-parent ratio) obtained from liquid chromatography-tandem mass spectrometry (LC-MS/MS/MS) data for screening purposes. Combining all these pieces of evidence requires a careful assessment of the uncertainties in the analytical system as well as all possible outcomes. To-date, the majority of the existing algorithms are highly dependent on user input parameters. Additionally, the screening process is tackled as a deterministic problem. In this work we present a Bayesian framework to deal with the combination of all these pieces of evidence. Contrary to conventional algorithms, the information is treated in a probabilistic way, and a final probability assessment of the presence/absence of a compound feature is computed. Additionally, all the necessary parameters except the chromatographic band broadening for the method are learned from the data in training and learning phase of the algorithm, avoiding the introduction of a large number of user-defined parameters. The proposed method was validated with a large data set and has shown improved sensitivity and specificity in comparison to a threshold-based commercial software package.

BUMPER v1.0: a Bayesian user-friendly model for palaeo-environmental reconstruction

NASA Astrophysics Data System (ADS)

Holden, Philip B.; Birks, H. John B.; Brooks, Stephen J.; Bush, Mark B.; Hwang, Grace M.; Matthews-Bird, Frazer; Valencia, Bryan G.; van Woesik, Robert

2017-02-01

We describe the Bayesian user-friendly model for palaeo-environmental reconstruction (BUMPER), a Bayesian transfer function for inferring past climate and other environmental variables from microfossil assemblages. BUMPER is fully self-calibrating, straightforward to apply, and computationally fast, requiring ˜ 2 s to build a 100-taxon model from a 100-site training set on a standard personal computer. We apply the model's probabilistic framework to generate thousands of artificial training sets under ideal assumptions. We then use these to demonstrate the sensitivity of reconstructions to the characteristics of the training set, considering assemblage richness, taxon tolerances, and the number of training sites. We find that a useful guideline for the size of a training set is to provide, on average, at least 10 samples of each taxon. We demonstrate general applicability to real data, considering three different organism types (chironomids, diatoms, pollen) and different reconstructed variables. An identically configured model is used in each application, the only change being the input files that provide the training-set environment and taxon-count data. The performance of BUMPER is shown to be comparable with weighted average partial least squares (WAPLS) in each case. Additional artificial datasets are constructed with similar characteristics to the real data, and these are used to explore the reasons for the differing performances of the different training sets.

The Dopaminergic Midbrain Encodes the Expected Certainty about Desired Outcomes.

PubMed

Schwartenbeck, Philipp; FitzGerald, Thomas H B; Mathys, Christoph; Dolan, Ray; Friston, Karl

2015-10-01

Dopamine plays a key role in learning; however, its exact function in decision making and choice remains unclear. Recently, we proposed a generic model based on active (Bayesian) inference wherein dopamine encodes the precision of beliefs about optimal policies. Put simply, dopamine discharges reflect the confidence that a chosen policy will lead to desired outcomes. We designed a novel task to test this hypothesis, where subjects played a "limited offer" game in a functional magnetic resonance imaging experiment. Subjects had to decide how long to wait for a high offer before accepting a low offer, with the risk of losing everything if they waited too long. Bayesian model comparison showed that behavior strongly supported active inference, based on surprise minimization, over classical utility maximization schemes. Furthermore, midbrain activity, encompassing dopamine projection neurons, was accurately predicted by trial-by-trial variations in model-based estimates of precision. Our findings demonstrate that human subjects infer both optimal policies and the precision of those inferences, and thus support the notion that humans perform hierarchical probabilistic Bayesian inference. In other words, subjects have to infer both what they should do as well as how confident they are in their choices, where confidence may be encoded by dopaminergic firing. © The Author 2014. Published by Oxford University Press.

The Dopaminergic Midbrain Encodes the Expected Certainty about Desired Outcomes

PubMed Central

Schwartenbeck, Philipp; FitzGerald, Thomas H. B.; Mathys, Christoph; Dolan, Ray; Friston, Karl

2015-01-01

Dopamine plays a key role in learning; however, its exact function in decision making and choice remains unclear. Recently, we proposed a generic model based on active (Bayesian) inference wherein dopamine encodes the precision of beliefs about optimal policies. Put simply, dopamine discharges reflect the confidence that a chosen policy will lead to desired outcomes. We designed a novel task to test this hypothesis, where subjects played a “limited offer” game in a functional magnetic resonance imaging experiment. Subjects had to decide how long to wait for a high offer before accepting a low offer, with the risk of losing everything if they waited too long. Bayesian model comparison showed that behavior strongly supported active inference, based on surprise minimization, over classical utility maximization schemes. Furthermore, midbrain activity, encompassing dopamine projection neurons, was accurately predicted by trial-by-trial variations in model-based estimates of precision. Our findings demonstrate that human subjects infer both optimal policies and the precision of those inferences, and thus support the notion that humans perform hierarchical probabilistic Bayesian inference. In other words, subjects have to infer both what they should do as well as how confident they are in their choices, where confidence may be encoded by dopaminergic firing. PMID:25056572

Flooding Fragility Experiments and Prediction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Curtis L.; Tahhan, Antonio; Muchmore, Cody

2016-09-01

This report describes the work that has been performed on flooding fragility, both the experimental tests being carried out and the probabilistic fragility predictive models being produced in order to use the text results. Flooding experiments involving full-scale doors have commenced in the Portal Evaluation Tank. The goal of these experiments is to develop a full-scale component flooding experiment protocol and to acquire data that can be used to create Bayesian regression models representing the fragility of these components. This work is in support of the Risk-Informed Safety Margin Characterization (RISMC) Pathway external hazards evaluation research and development.

From multi-disciplinary monitoring observation to probabilistic eruption forecasting: a Bayesian view

NASA Astrophysics Data System (ADS)

Marzocchi, W.

2011-12-01

Eruption forecasting is the probability of eruption in a specific time-space-magnitude window. The use of probabilities to track the evolution of a phase of unrest is unavoidable for two main reasons: first, eruptions are intrinsically unpredictable in a deterministic sense, and, second, probabilities represent a quantitative tool that can be rationally used by decision-makers (this is usually done in many other fields). The primary information for the probability assessment during a phase of unrest come from monitoring data of different quantities, such as the seismic activity, ground deformation, geochemical signatures, and so on. Nevertheless, the probabilistic forecast based on monitoring data presents two main difficulties. First, many high-risk volcanoes do not have monitoring pre-eruptive and unrest databases, making impossible a probabilistic assessment based on the frequency of past observations. The ongoing project WOVOdat (led by Christopher Newhall) is trying to tackle this limitation creating a sort of worldwide epidemiological database that may cope with the lack of monitoring pre-eruptive and unrest databases for a specific volcano using observations of 'analogs' volcanoes. Second, the quantity and quality of monitoring data are rapidly increasing in many volcanoes, creating strongly inhomogeneous dataset. In these cases, classical statistical analysis can be performed on high quality monitoring observations only for (usually too) short periods of time, or alternatively using only few specific monitoring data that are available for longer times (such as the number of earthquakes), therefore neglecting a lot of information carried out by the most recent kind of monitoring. Here, we explore a possible strategy to cope with these limitations. In particular, we present a Bayesian strategy that merges different kinds of information. In this approach, all relevant monitoring observations are embedded into a probabilistic scheme through expert opinion, conceptual models, and, possibly, real past data. After discussing all scientific and philosophical aspects of such approach, we present some applications for Campi Flegrei and Vesuvius.

Learning abstract visual concepts via probabilistic program induction in a Language of Thought.

PubMed

Overlan, Matthew C; Jacobs, Robert A; Piantadosi, Steven T

2017-11-01

The ability to learn abstract concepts is a powerful component of human cognition. It has been argued that variable binding is the key element enabling this ability, but the computational aspects of variable binding remain poorly understood. Here, we address this shortcoming by formalizing the Hierarchical Language of Thought (HLOT) model of rule learning. Given a set of data items, the model uses Bayesian inference to infer a probability distribution over stochastic programs that implement variable binding. Because the model makes use of symbolic variables as well as Bayesian inference and programs with stochastic primitives, it combines many of the advantages of both symbolic and statistical approaches to cognitive modeling. To evaluate the model, we conducted an experiment in which human subjects viewed training items and then judged which test items belong to the same concept as the training items. We found that the HLOT model provides a close match to human generalization patterns, significantly outperforming two variants of the Generalized Context Model, one variant based on string similarity and the other based on visual similarity using features from a deep convolutional neural network. Additional results suggest that variable binding happens automatically, implying that binding operations do not add complexity to peoples' hypothesized rules. Overall, this work demonstrates that a cognitive model combining symbolic variables with Bayesian inference and stochastic program primitives provides a new perspective for understanding people's patterns of generalization. Copyright © 2017 Elsevier B.V. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

La Russa, D

Purpose: The purpose of this project is to develop a robust method of parameter estimation for a Poisson-based TCP model using Bayesian inference. Methods: Bayesian inference was performed using the PyMC3 probabilistic programming framework written in Python. A Poisson-based TCP regression model that accounts for clonogen proliferation was fit to observed rates of local relapse as a function of equivalent dose in 2 Gy fractions for a population of 623 stage-I non-small-cell lung cancer patients. The Slice Markov Chain Monte Carlo sampling algorithm was used to sample the posterior distributions, and was initiated using the maximum of the posterior distributionsmore » found by optimization. The calculation of TCP with each sample step required integration over the free parameter α, which was performed using an adaptive 24-point Gauss-Legendre quadrature. Convergence was verified via inspection of the trace plot and posterior distribution for each of the fit parameters, as well as with comparisons of the most probable parameter values with their respective maximum likelihood estimates. Results: Posterior distributions for α, the standard deviation of α (σ), the average tumour cell-doubling time (Td), and the repopulation delay time (Tk), were generated assuming α/β = 10 Gy, and a fixed clonogen density of 10{sup 7} cm−{sup 3}. Posterior predictive plots generated from samples from these posterior distributions are in excellent agreement with the observed rates of local relapse used in the Bayesian inference. The most probable values of the model parameters also agree well with maximum likelihood estimates. Conclusion: A robust method of performing Bayesian inference of TCP data using a complex TCP model has been established.« less

Opportunities of probabilistic flood loss models

NASA Astrophysics Data System (ADS)

Schröter, Kai; Kreibich, Heidi; Lüdtke, Stefan; Vogel, Kristin; Merz, Bruno

2016-04-01

Oftentimes, traditional uni-variate damage models as for instance depth-damage curves fail to reproduce the variability of observed flood damage. However, reliable flood damage models are a prerequisite for the practical usefulness of the model results. Innovative multi-variate probabilistic modelling approaches are promising to capture and quantify the uncertainty involved and thus to improve the basis for decision making. In this study we compare the predictive capability of two probabilistic modelling approaches, namely Bagging Decision Trees and Bayesian Networks and traditional stage damage functions. For model evaluation we use empirical damage data which are available from computer aided telephone interviews that were respectively compiled after the floods in 2002, 2005, 2006 and 2013 in the Elbe and Danube catchments in Germany. We carry out a split sample test by sub-setting the damage records. One sub-set is used to derive the models and the remaining records are used to evaluate the predictive performance of the model. Further we stratify the sample according to catchments which allows studying model performance in a spatial transfer context. Flood damage estimation is carried out on the scale of the individual buildings in terms of relative damage. The predictive performance of the models is assessed in terms of systematic deviations (mean bias), precision (mean absolute error) as well as in terms of sharpness of the predictions the reliability which is represented by the proportion of the number of observations that fall within the 95-quantile and 5-quantile predictive interval. The comparison of the uni-variable Stage damage function and the multivariable model approach emphasises the importance to quantify predictive uncertainty. With each explanatory variable, the multi-variable model reveals an additional source of uncertainty. However, the predictive performance in terms of precision (mbe), accuracy (mae) and reliability (HR) is clearly improved in comparison to uni-variable Stage damage function. Overall, Probabilistic models provide quantitative information about prediction uncertainty which is crucial to assess the reliability of model predictions and improves the usefulness of model results.

Two-dimensional probabilistic inversion of plane-wave electromagnetic data: methodology, model constraints and joint inversion with electrical resistivity data

NASA Astrophysics Data System (ADS)

Rosas-Carbajal, Marina; Linde, Niklas; Kalscheuer, Thomas; Vrugt, Jasper A.

2014-03-01

Probabilistic inversion methods based on Markov chain Monte Carlo (MCMC) simulation are well suited to quantify parameter and model uncertainty of nonlinear inverse problems. Yet, application of such methods to CPU-intensive forward models can be a daunting task, particularly if the parameter space is high dimensional. Here, we present a 2-D pixel-based MCMC inversion of plane-wave electromagnetic (EM) data. Using synthetic data, we investigate how model parameter uncertainty depends on model structure constraints using different norms of the likelihood function and the model constraints, and study the added benefits of joint inversion of EM and electrical resistivity tomography (ERT) data. Our results demonstrate that model structure constraints are necessary to stabilize the MCMC inversion results of a highly discretized model. These constraints decrease model parameter uncertainty and facilitate model interpretation. A drawback is that these constraints may lead to posterior distributions that do not fully include the true underlying model, because some of its features exhibit a low sensitivity to the EM data, and hence are difficult to resolve. This problem can be partly mitigated if the plane-wave EM data is augmented with ERT observations. The hierarchical Bayesian inverse formulation introduced and used herein is able to successfully recover the probabilistic properties of the measurement data errors and a model regularization weight. Application of the proposed inversion methodology to field data from an aquifer demonstrates that the posterior mean model realization is very similar to that derived from a deterministic inversion with similar model constraints.

A New Bayesian Approach for Estimating the Presence of a Suspected Compound in Routine Screening Analysis.

PubMed

Woldegebriel, Michael; Vivó-Truyols, Gabriel

2016-10-04

A novel method for compound identification in liquid chromatography-high resolution mass spectrometry (LC-HRMS) is proposed. The method, based on Bayesian statistics, accommodates all possible uncertainties involved, from instrumentation up to data analysis into a single model yielding the probability of the compound of interest being present/absent in the sample. This approach differs from the classical methods in two ways. First, it is probabilistic (instead of deterministic); hence, it computes the probability that the compound is (or is not) present in a sample. Second, it answers the hypothesis "the compound is present", opposed to answering the question "the compound feature is present". This second difference implies a shift in the way data analysis is tackled, since the probability of interfering compounds (i.e., isomers and isobaric compounds) is also taken into account.

Probabilistic liquefaction triggering based on the cone penetration test

USGS Publications Warehouse

Moss, R.E.S.; Seed, R.B.; Kayen, R.E.; Stewart, J.P.; Tokimatsu, K.

2005-01-01

Performance-based earthquake engineering requires a probabilistic treatment of potential failure modes in order to accurately quantify the overall stability of the system. This paper is a summary of the application portions of the probabilistic liquefaction triggering correlations proposed recently proposed by Moss and co-workers. To enable probabilistic treatment of liquefaction triggering, the variables comprising the seismic load and the liquefaction resistance were treated as inherently uncertain. Supporting data from an extensive Cone Penetration Test (CPT)-based liquefaction case history database were used to develop a probabilistic correlation. The methods used to measure the uncertainty of the load and resistance variables, how the interactions of these variables were treated using Bayesian updating, and how reliability analysis was applied to produce curves of equal probability of liquefaction are presented. The normalization for effective overburden stress, the magnitude correlated duration weighting factor, and the non-linear shear mass participation factor used are also discussed.

A decision aid for intensity-modulated radiation-therapy plan selection in prostate cancer based on a prognostic Bayesian network and a Markov model.

PubMed

Smith, Wade P; Doctor, Jason; Meyer, Jürgen; Kalet, Ira J; Phillips, Mark H

2009-06-01

The prognosis of cancer patients treated with intensity-modulated radiation-therapy (IMRT) is inherently uncertain, depends on many decision variables, and requires that a physician balance competing objectives: maximum tumor control with minimal treatment complications. In order to better deal with the complex and multiple objective nature of the problem we have combined a prognostic probabilistic model with multi-attribute decision theory which incorporates patient preferences for outcomes. The response to IMRT for prostate cancer was modeled. A Bayesian network was used for prognosis for each treatment plan. Prognoses included predicting local tumor control, regional spread, distant metastases, and normal tissue complications resulting from treatment. A Markov model was constructed and used to calculate a quality-adjusted life-expectancy which aids in the multi-attribute decision process. Our method makes explicit the tradeoffs patients face between quality and quantity of life. This approach has advantages over current approaches because with our approach risks of health outcomes and patient preferences determine treatment decisions.

Taking error into account when fitting models using Approximate Bayesian Computation.

PubMed

van der Vaart, Elske; Prangle, Dennis; Sibly, Richard M

2018-03-01

Stochastic computer simulations are often the only practical way of answering questions relating to ecological management. However, due to their complexity, such models are difficult to calibrate and evaluate. Approximate Bayesian Computation (ABC) offers an increasingly popular approach to this problem, widely applied across a variety of fields. However, ensuring the accuracy of ABC's estimates has been difficult. Here, we obtain more accurate estimates by incorporating estimation of error into the ABC protocol. We show how this can be done where the data consist of repeated measures of the same quantity and errors may be assumed to be normally distributed and independent. We then derive the correct acceptance probabilities for a probabilistic ABC algorithm, and update the coverage test with which accuracy is assessed. We apply this method, which we call error-calibrated ABC, to a toy example and a realistic 14-parameter simulation model of earthworms that is used in environmental risk assessment. A comparison with exact methods and the diagnostic coverage test show that our approach improves estimation of parameter values and their credible intervals for both models. © 2017 by the Ecological Society of America.

Bayesian Analysis of the Glacial-Interglacial Methane Increase Constrained by Stable Isotopes and Earth System Modeling

NASA Astrophysics Data System (ADS)

Hopcroft, Peter O.; Valdes, Paul J.; Kaplan, Jed O.

2018-04-01

The observed rise in atmospheric methane (CH4) from 375 ppbv during the Last Glacial Maximum (LGM: 21,000 years ago) to 680 ppbv during the late preindustrial era is not well understood. Atmospheric chemistry considerations implicate an increase in CH4 sources, but process-based estimates fail to reproduce the required amplitude. CH4 stable isotopes provide complementary information that can help constrain the underlying causes of the increase. We combine Earth System model simulations of the late preindustrial and LGM CH4 cycles, including process-based estimates of the isotopic discrimination of vegetation, in a box model of atmospheric CH4 and its isotopes. Using a Bayesian approach, we show how model-based constraints and ice core observations may be combined in a consistent probabilistic framework. The resultant posterior distributions point to a strong reduction in wetland and other biogenic CH4 emissions during the LGM, with a modest increase in the geological source, or potentially natural or anthropogenic fires, accounting for the observed enrichment of δ13CH4.

Smsynth: AN Imagery Synthesis System for Soil Moisture Retrieval

NASA Astrophysics Data System (ADS)

Cao, Y.; Xu, L.; Peng, J.

2018-04-01

Soil moisture (SM) is a important variable in various research areas, such as weather and climate forecasting, agriculture, drought and flood monitoring and prediction, and human health. An ongoing challenge in estimating SM via synthetic aperture radar (SAR) is the development of the retrieval SM methods, especially the empirical models needs as training samples a lot of measurements of SM and soil roughness parameters which are very difficult to acquire. As such, it is difficult to develop empirical models using realistic SAR imagery and it is necessary to develop methods to synthesis SAR imagery. To tackle this issue, a SAR imagery synthesis system based on the SM named SMSynth is presented, which can simulate radar signals that are realistic as far as possible to the real SAR imagery. In SMSynth, SAR backscatter coefficients for each soil type are simulated via the Oh model under the Bayesian framework, where the spatial correlation is modeled by the Markov random field (MRF) model. The backscattering coefficients simulated based on the designed soil parameters and sensor parameters are added into the Bayesian framework through the data likelihood where the soil parameters and sensor parameters are set as realistic as possible to the circumstances on the ground and in the validity range of the Oh model. In this way, a complete and coherent Bayesian probabilistic framework is established. Experimental results show that SMSynth is capable of generating realistic SAR images that suit the needs of a large amount of training samples of empirical models.

Lip-reading aids word recognition most in moderate noise: a Bayesian explanation using high-dimensional feature space.

PubMed

Ma, Wei Ji; Zhou, Xiang; Ross, Lars A; Foxe, John J; Parra, Lucas C

2009-01-01

Watching a speaker's facial movements can dramatically enhance our ability to comprehend words, especially in noisy environments. From a general doctrine of combining information from different sensory modalities (the principle of inverse effectiveness), one would expect that the visual signals would be most effective at the highest levels of auditory noise. In contrast, we find, in accord with a recent paper, that visual information improves performance more at intermediate levels of auditory noise than at the highest levels, and we show that a novel visual stimulus containing only temporal information does the same. We present a Bayesian model of optimal cue integration that can explain these conflicts. In this model, words are regarded as points in a multidimensional space and word recognition is a probabilistic inference process. When the dimensionality of the feature space is low, the Bayesian model predicts inverse effectiveness; when the dimensionality is high, the enhancement is maximal at intermediate auditory noise levels. When the auditory and visual stimuli differ slightly in high noise, the model makes a counterintuitive prediction: as sound quality increases, the proportion of reported words corresponding to the visual stimulus should first increase and then decrease. We confirm this prediction in a behavioral experiment. We conclude that auditory-visual speech perception obeys the same notion of optimality previously observed only for simple multisensory stimuli.

Probabilistic multi-resolution human classification

NASA Astrophysics Data System (ADS)

Tu, Jun; Ran, H.

2006-02-01

Recently there has been some interest in using infrared cameras for human detection because of the sharply decreasing prices of infrared cameras. The training data used in our work for developing the probabilistic template consists images known to contain humans in different poses and orientation but having the same height. Multiresolution templates are performed. They are based on contour and edges. This is done so that the model does not learn the intensity variations among the background pixels and intensity variations among the foreground pixels. Each template at every level is then translated so that the centroid of the non-zero pixels matches the geometrical center of the image. After this normalization step, for each pixel of the template, the probability of it being pedestrian is calculated based on the how frequently it appears as 1 in the training data. We also use periodicity gait to verify the pedestrian in a Bayesian manner for the whole blob in a probabilistic way. The videos had quite a lot of variations in the scenes, sizes of people, amount of occlusions and clutter in the backgrounds as is clearly evident. Preliminary experiments show the robustness.

A Probabilistic Approach for Real-Time Volcano Surveillance

NASA Astrophysics Data System (ADS)

Cannavo, F.; Cannata, A.; Cassisi, C.; Di Grazia, G.; Maronno, P.; Montalto, P.; Prestifilippo, M.; Privitera, E.; Gambino, S.; Coltelli, M.

2016-12-01

Continuous evaluation of the state of potentially dangerous volcanos plays a key role for civil protection purposes. Presently, real-time surveillance of most volcanoes worldwide is essentially delegated to one or more human experts in volcanology, who interpret data coming from different kind of monitoring networks. Unfavorably, the coupling of highly non-linear and complex volcanic dynamic processes leads to measurable effects that can show a large variety of different behaviors. Moreover, due to intrinsic uncertainties and possible failures in some recorded data, the volcano state needs to be expressed in probabilistic terms, thus making the fast volcano state assessment sometimes impracticable for the personnel on duty at the control rooms. With the aim of aiding the personnel on duty in volcano surveillance, we present a probabilistic graphical model to estimate automatically the ongoing volcano state from all the available different kind of measurements. The model consists of a Bayesian network able to represent a set of variables and their conditional dependencies via a directed acyclic graph. The model variables are both the measurements and the possible states of the volcano through the time. The model output is an estimation of the probability distribution of the feasible volcano states. We tested the model on the Mt. Etna (Italy) case study by considering a long record of multivariate data from 2011 to 2015 and cross-validated it. Results indicate that the proposed model is effective and of great power for decision making purposes.

Fully probabilistic earthquake source inversion on teleseismic scales

NASA Astrophysics Data System (ADS)

Stähler, Simon; Sigloch, Karin

2017-04-01

Seismic source inversion is a non-linear problem in seismology where not just the earthquake parameters but also estimates of their uncertainties are of great practical importance. We have developed a method of fully Bayesian inference for source parameters, based on measurements of waveform cross-correlation between broadband, teleseismic body-wave observations and their modelled counterparts. This approach yields not only depth and moment tensor estimates but also source time functions. These unknowns are parameterised efficiently by harnessing as prior knowledge solutions from a large number of non-Bayesian inversions. The source time function is expressed as a weighted sum of a small number of empirical orthogonal functions, which were derived from a catalogue of >1000 source time functions (STFs) by a principal component analysis. We use a likelihood model based on the cross-correlation misfit between observed and predicted waveforms. The resulting ensemble of solutions provides full uncertainty and covariance information for the source parameters, and permits propagating these source uncertainties into travel time estimates used for seismic tomography. The computational effort is such that routine, global estimation of earthquake mechanisms and source time functions from teleseismic broadband waveforms is feasible. A prerequisite for Bayesian inference is the proper characterisation of the noise afflicting the measurements. We show that, for realistic broadband body-wave seismograms, the systematic error due to an incomplete physical model affects waveform misfits more strongly than random, ambient background noise. In this situation, the waveform cross-correlation coefficient CC, or rather its decorrelation D = 1 - CC, performs more robustly as a misfit criterion than ℓp norms, more commonly used as sample-by-sample measures of misfit based on distances between individual time samples. From a set of over 900 user-supervised, deterministic earthquake source solutions treated as a quality-controlled reference, we derive the noise distribution on signal decorrelation D of the broadband seismogram fits between observed and modelled waveforms. The noise on D is found to approximately follow a log-normal distribution, a fortunate fact that readily accommodates the formulation of an empirical likelihood function for D for our multivariate problem. The first and second moments of this multivariate distribution are shown to depend mostly on the signal-to-noise ratio (SNR) of the CC measurements and on the back-azimuthal distances of seismic stations. References: Stähler, S. C. and Sigloch, K.: Fully probabilistic seismic source inversion - Part 1: Efficient parameterisation, Solid Earth, 5, 1055-1069, doi:10.5194/se-5-1055-2014, 2014. Stähler, S. C. and Sigloch, K.: Fully probabilistic seismic source inversion - Part 2: Modelling errors and station covariances, Solid Earth, 7, 1521-1536, doi:10.5194/se-7-1521-2016, 2016.

Decoding brain activity using a large-scale probabilistic functional-anatomical atlas of human cognition

PubMed Central

Jones, Michael N.

2017-01-01

A central goal of cognitive neuroscience is to decode human brain activity—that is, to infer mental processes from observed patterns of whole-brain activation. Previous decoding efforts have focused on classifying brain activity into a small set of discrete cognitive states. To attain maximal utility, a decoding framework must be open-ended, systematic, and context-sensitive—that is, capable of interpreting numerous brain states, presented in arbitrary combinations, in light of prior information. Here we take steps towards this objective by introducing a probabilistic decoding framework based on a novel topic model—Generalized Correspondence Latent Dirichlet Allocation—that learns latent topics from a database of over 11,000 published fMRI studies. The model produces highly interpretable, spatially-circumscribed topics that enable flexible decoding of whole-brain images. Importantly, the Bayesian nature of the model allows one to “seed” decoder priors with arbitrary images and text—enabling researchers, for the first time, to generate quantitative, context-sensitive interpretations of whole-brain patterns of brain activity. PMID:29059185

A regional-scale ecological risk framework for environmental flow evaluations

NASA Astrophysics Data System (ADS)

O'Brien, Gordon C.; Dickens, Chris; Hines, Eleanor; Wepener, Victor; Stassen, Retha; Quayle, Leo; Fouchy, Kelly; MacKenzie, James; Graham, P. Mark; Landis, Wayne G.

2018-02-01

Environmental flow (E-flow) frameworks advocate holistic, regional-scale, probabilistic E-flow assessments that consider flow and non-flow drivers of change in a socio-ecological context as best practice. Regional-scale ecological risk assessments of multiple stressors to social and ecological endpoints, which address ecosystem dynamism, have been undertaken internationally at different spatial scales using the relative-risk model since the mid-1990s. With the recent incorporation of Bayesian belief networks into the relative-risk model, a robust regional-scale ecological risk assessment approach is available that can contribute to achieving the best practice recommendations of E-flow frameworks. PROBFLO is a holistic E-flow assessment method that incorporates the relative-risk model and Bayesian belief networks (BN-RRM) into a transparent probabilistic modelling tool that addresses uncertainty explicitly. PROBFLO has been developed to evaluate the socio-ecological consequences of historical, current and future water resource use scenarios and generate E-flow requirements on regional spatial scales. The approach has been implemented in two regional-scale case studies in Africa where its flexibility and functionality has been demonstrated. In both case studies the evidence-based outcomes facilitated informed environmental management decision making, with trade-off considerations in the context of social and ecological aspirations. This paper presents the PROBFLO approach as applied to the Senqu River catchment in Lesotho and further developments and application in the Mara River catchment in Kenya and Tanzania. The 10 BN-RRM procedural steps incorporated in PROBFLO are demonstrated with examples from both case studies. PROBFLO can contribute to the adaptive management of water resources and contribute to the allocation of resources for sustainable use of resources and address protection requirements.

The Probabilistic Admissible Region with Additional Constraints

NASA Astrophysics Data System (ADS)

Roscoe, C.; Hussein, I.; Wilkins, M.; Schumacher, P.

The admissible region, in the space surveillance field, is defined as the set of physically acceptable orbits (e.g., orbits with negative energies) consistent with one or more observations of a space object. Given additional constraints on orbital semimajor axis, eccentricity, etc., the admissible region can be constrained, resulting in the constrained admissible region (CAR). Based on known statistics of the measurement process, one can replace hard constraints with a probabilistic representation of the admissible region. This results in the probabilistic admissible region (PAR), which can be used for orbit initiation in Bayesian tracking and prioritization of tracks in a multiple hypothesis tracking framework. The PAR concept was introduced by the authors at the 2014 AMOS conference. In that paper, a Monte Carlo approach was used to show how to construct the PAR in the range/range-rate space based on known statistics of the measurement, semimajor axis, and eccentricity. An expectation-maximization algorithm was proposed to convert the particle cloud into a Gaussian Mixture Model (GMM) representation of the PAR. This GMM can be used to initialize a Bayesian filter. The PAR was found to be significantly non-uniform, invalidating an assumption frequently made in CAR-based filtering approaches. Using the GMM or particle cloud representations of the PAR, orbits can be prioritized for propagation in a multiple hypothesis tracking (MHT) framework. In this paper, the authors focus on expanding the PAR methodology to allow additional constraints, such as a constraint on perigee altitude, to be modeled in the PAR. This requires re-expressing the joint probability density function for the attributable vector as well as the (constrained) orbital parameters and range and range-rate. The final PAR is derived by accounting for any interdependencies between the parameters. Noting that the concepts presented are general and can be applied to any measurement scenario, the idea will be illustrated using a short-arc, angles-only observation scenario.

Clarifying the Hubble constant tension with a Bayesian hierarchical model of the local distance ladder

NASA Astrophysics Data System (ADS)

Feeney, Stephen M.; Mortlock, Daniel J.; Dalmasso, Niccolò

2018-05-01

Estimates of the Hubble constant, H0, from the local distance ladder and from the cosmic microwave background (CMB) are discrepant at the ˜3σ level, indicating a potential issue with the standard Λ cold dark matter (ΛCDM) cosmology. A probabilistic (i.e. Bayesian) interpretation of this tension requires a model comparison calculation, which in turn depends strongly on the tails of the H0 likelihoods. Evaluating the tails of the local H0 likelihood requires the use of non-Gaussian distributions to faithfully represent anchor likelihoods and outliers, and simultaneous fitting of the complete distance-ladder data set to ensure correct uncertainty propagation. We have hence developed a Bayesian hierarchical model of the full distance ladder that does not rely on Gaussian distributions and allows outliers to be modelled without arbitrary data cuts. Marginalizing over the full ˜3000-parameter joint posterior distribution, we find H0 = (72.72 ± 1.67) km s-1 Mpc-1 when applied to the outlier-cleaned Riess et al. data, and (73.15 ± 1.78) km s-1 Mpc-1 with supernova outliers reintroduced (the pre-cut Cepheid data set is not available). Using our precise evaluation of the tails of the H0 likelihood, we apply Bayesian model comparison to assess the evidence for deviation from ΛCDM given the distance-ladder and CMB data. The odds against ΛCDM are at worst ˜10:1 when considering the Planck 2015 XIII data, regardless of outlier treatment, considerably less dramatic than naïvely implied by the 2.8σ discrepancy. These odds become ˜60:1 when an approximation to the more-discrepant Planck Intermediate XLVI likelihood is included.

Analysis of femtosecond pump-probe photoelectron-photoion coincidence measurements applying Bayesian probability theory

NASA Astrophysics Data System (ADS)

Rumetshofer, M.; Heim, P.; Thaler, B.; Ernst, W. E.; Koch, M.; von der Linden, W.

2018-06-01

Ultrafast dynamical processes in photoexcited molecules can be observed with pump-probe measurements, in which information about the dynamics is obtained from the transient signal associated with the excited state. Background signals provoked by pump and/or probe pulses alone often obscure these excited-state signals. Simple subtraction of pump-only and/or probe-only measurements from the pump-probe measurement, as commonly applied, results in a degradation of the signal-to-noise ratio and, in the case of coincidence detection, the danger of overrated background subtraction. Coincidence measurements additionally suffer from false coincidences, requiring long data-acquisition times to keep erroneous signals at an acceptable level. Here we present a probabilistic approach based on Bayesian probability theory that overcomes these problems. For a pump-probe experiment with photoelectron-photoion coincidence detection, we reconstruct the interesting excited-state spectrum from pump-probe and pump-only measurements. This approach allows us to treat background and false coincidences consistently and on the same footing. We demonstrate that the Bayesian formalism has the following advantages over simple signal subtraction: (i) the signal-to-noise ratio is significantly increased, (ii) the pump-only contribution is not overestimated, (iii) false coincidences are excluded, (iv) prior knowledge, such as positivity, is consistently incorporated, (v) confidence intervals are provided for the reconstructed spectrum, and (vi) it is applicable to any experimental situation and noise statistics. Most importantly, by accounting for false coincidences, the Bayesian approach allows us to run experiments at higher ionization rates, resulting in a significant reduction of data acquisition times. The probabilistic approach is thoroughly scrutinized by challenging mock data. The application to pump-probe coincidence measurements on acetone molecules enables quantitative interpretations about the molecular decay dynamics and fragmentation behavior. All results underline the superiority of a consistent probabilistic approach over ad hoc estimations.

The influence of emotions on cognitive control: feelings and beliefs—where do they meet?

PubMed Central

Harlé, Katia M.; Shenoy, Pradeep; Paulus, Martin P.

2013-01-01

The influence of emotion on higher-order cognitive functions, such as attention allocation, planning, and decision-making, is a growing area of research with important clinical applications. In this review, we provide a computational framework to conceptualize emotional influences on inhibitory control, an important building block of executive functioning. We first summarize current neuro-cognitive models of inhibitory control and show how Bayesian ideal observer models can help reframe inhibitory control as a dynamic decision-making process. Finally, we propose a Bayesian framework to study emotional influences on inhibitory control, providing several hypotheses that may be useful to conceptualize inhibitory control biases in mental illness such as depression and anxiety. To do so, we consider the neurocognitive literature pertaining to how affective states can bias inhibitory control, with particular attention to how valence and arousal may independently impact inhibitory control by biasing probabilistic representations of information (i.e., beliefs) and valuation processes (e.g., speed-error tradeoffs). PMID:24065901

Real-time realizations of the Bayesian Infrasonic Source Localization Method

NASA Astrophysics Data System (ADS)

Pinsky, V.; Arrowsmith, S.; Hofstetter, A.; Nippress, A.

2015-12-01

The Bayesian Infrasonic Source Localization method (BISL), introduced by Mordak et al. (2010) and upgraded by Marcillo et al. (2014) is destined for the accurate estimation of the atmospheric event origin at local, regional and global scales by the seismic and infrasonic networks and arrays. The BISL is based on probabilistic models of the source-station infrasonic signal propagation time, picking time and azimuth estimate merged with a prior knowledge about celerity distribution. It requires at each hypothetical source location, integration of the product of the corresponding source-station likelihood functions multiplied by a prior probability density function of celerity over the multivariate parameter space. The present BISL realization is generally time-consuming procedure based on numerical integration. The computational scheme proposed simplifies the target function so that integrals are taken exactly and are represented via standard functions. This makes the procedure much faster and realizable in real-time without practical loss of accuracy. The procedure executed as PYTHON-FORTRAN code demonstrates high performance on a set of the model and real data.

Accuracy of latent-variable estimation in Bayesian semi-supervised learning.

PubMed

Yamazaki, Keisuke

2015-09-01

Hierarchical probabilistic models, such as Gaussian mixture models, are widely used for unsupervised learning tasks. These models consist of observable and latent variables, which represent the observable data and the underlying data-generation process, respectively. Unsupervised learning tasks, such as cluster analysis, are regarded as estimations of latent variables based on the observable ones. The estimation of latent variables in semi-supervised learning, where some labels are observed, will be more precise than that in unsupervised, and one of the concerns is to clarify the effect of the labeled data. However, there has not been sufficient theoretical analysis of the accuracy of the estimation of latent variables. In a previous study, a distribution-based error function was formulated, and its asymptotic form was calculated for unsupervised learning with generative models. It has been shown that, for the estimation of latent variables, the Bayes method is more accurate than the maximum-likelihood method. The present paper reveals the asymptotic forms of the error function in Bayesian semi-supervised learning for both discriminative and generative models. The results show that the generative model, which uses all of the given data, performs better when the model is well specified. Copyright © 2015 Elsevier Ltd. All rights reserved.

Combining information from multiple flood projections in a hierarchical Bayesian framework

NASA Astrophysics Data System (ADS)

Le Vine, Nataliya

2016-04-01

This study demonstrates, in the context of flood frequency analysis, the potential of a recently proposed hierarchical Bayesian approach to combine information from multiple models. The approach explicitly accommodates shared multimodel discrepancy as well as the probabilistic nature of the flood estimates, and treats the available models as a sample from a hypothetical complete (but unobserved) set of models. The methodology is applied to flood estimates from multiple hydrological projections (the Future Flows Hydrology data set) for 135 catchments in the UK. The advantages of the approach are shown to be: (1) to ensure adequate "baseline" with which to compare future changes; (2) to reduce flood estimate uncertainty; (3) to maximize use of statistical information in circumstances where multiple weak predictions individually lack power, but collectively provide meaningful information; (4) to diminish the importance of model consistency when model biases are large; and (5) to explicitly consider the influence of the (model performance) stationarity assumption. Moreover, the analysis indicates that reducing shared model discrepancy is the key to further reduction of uncertainty in the flood frequency analysis. The findings are of value regarding how conclusions about changing exposure to flooding are drawn, and to flood frequency change attribution studies.

Bayesian Estimation of Thermonuclear Reaction Rates for Deuterium+Deuterium Reactions

NASA Astrophysics Data System (ADS)

Gómez Iñesta, Á.; Iliadis, C.; Coc, A.

2017-11-01

The study of d+d reactions is of major interest since their reaction rates affect the predicted abundances of D, 3He, and 7Li. In particular, recent measurements of primordial D/H ratios call for reduced uncertainties in the theoretical abundances predicted by Big Bang nucleosynthesis (BBN). Different authors have studied reactions involved in BBN by incorporating new experimental data and a careful treatment of systematic and probabilistic uncertainties. To analyze the experimental data, Coc et al. used results of ab initio models for the theoretical calculation of the energy dependence of S-factors in conjunction with traditional statistical methods based on χ 2 minimization. Bayesian methods have now spread to many scientific fields and provide numerous advantages in data analysis. Astrophysical S-factors and reaction rates using Bayesian statistics were calculated by Iliadis et al. Here we present a similar analysis for two d+d reactions, d(d, n)3He and d(d, p)3H, that has been translated into a total decrease of the predicted D/H value by 0.16%.

A Bayesian Machine Learning Model for Estimating Building Occupancy from Open Source Data

DOE PAGES

Stewart, Robert N.; Urban, Marie L.; Duchscherer, Samantha E.; ...

2016-01-01

Understanding building occupancy is critical to a wide array of applications including natural hazards loss analysis, green building technologies, and population distribution modeling. Due to the expense of directly monitoring buildings, scientists rely in addition on a wide and disparate array of ancillary and open source information including subject matter expertise, survey data, and remote sensing information. These data are fused using data harmonization methods which refer to a loose collection of formal and informal techniques for fusing data together to create viable content for building occupancy estimation. In this paper, we add to the current state of the artmore » by introducing the Population Data Tables (PDT), a Bayesian based informatics system for systematically arranging data and harmonization techniques into a consistent, transparent, knowledge learning framework that retains in the final estimation uncertainty emerging from data, expert judgment, and model parameterization. PDT probabilistically estimates ambient occupancy in units of people/1000ft2 for over 50 building types at the national and sub-national level with the goal of providing global coverage. The challenge of global coverage led to the development of an interdisciplinary geospatial informatics system tool that provides the framework for capturing, storing, and managing open source data, handling subject matter expertise, carrying out Bayesian analytics as well as visualizing and exporting occupancy estimation results. We present the PDT project, situate the work within the larger community, and report on the progress of this multi-year project.Understanding building occupancy is critical to a wide array of applications including natural hazards loss analysis, green building technologies, and population distribution modeling. Due to the expense of directly monitoring buildings, scientists rely in addition on a wide and disparate array of ancillary and open source information including subject matter expertise, survey data, and remote sensing information. These data are fused using data harmonization methods which refer to a loose collection of formal and informal techniques for fusing data together to create viable content for building occupancy estimation. In this paper, we add to the current state of the art by introducing the Population Data Tables (PDT), a Bayesian model and informatics system for systematically arranging data and harmonization techniques into a consistent, transparent, knowledge learning framework that retains in the final estimation uncertainty emerging from data, expert judgment, and model parameterization. PDT probabilistically estimates ambient occupancy in units of people/1000 ft 2 for over 50 building types at the national and sub-national level with the goal of providing global coverage. The challenge of global coverage led to the development of an interdisciplinary geospatial informatics system tool that provides the framework for capturing, storing, and managing open source data, handling subject matter expertise, carrying out Bayesian analytics as well as visualizing and exporting occupancy estimation results. We present the PDT project, situate the work within the larger community, and report on the progress of this multi-year project.« less

Bayesian networks and statistical analysis application to analyze the diagnostic test accuracy

NASA Astrophysics Data System (ADS)

Orzechowski, P.; Makal, Jaroslaw; Onisko, A.

2005-02-01

The computer aided BPH diagnosis system based on Bayesian network is described in the paper. First result are compared to a given statistical method. Different statistical methods are used successfully in medicine for years. However, the undoubted advantages of probabilistic methods make them useful in application in newly created systems which are frequent in medicine, but do not have full and competent knowledge. The article presents advantages of the computer aided BPH diagnosis system in clinical practice for urologists.

A Bayesian elicitation of veterinary beliefs regarding systemic dry cow therapy: variation and importance for clinical trial design.

PubMed

Higgins, H M; Dryden, I L; Green, M J

2012-09-15

The two key aims of this research were: (i) to conduct a probabilistic elicitation to quantify the variation in veterinarians' beliefs regarding the efficacy of systemic antibiotics when used as an adjunct to intra-mammary dry cow therapy and (ii) to investigate (in a Bayesian statistical framework) the strength of future research evidence required (in theory) to change the beliefs of practising veterinary surgeons regarding the efficacy of systemic antibiotics, given their current clinical beliefs. The beliefs of 24 veterinarians in 5 practices in England were quantified as probability density functions. Classic multidimensional scaling revealed major variations in beliefs both within and between veterinary practices which included: confident optimism, confident pessimism and considerable uncertainty. Of the 9 veterinarians interviewed holding further cattle qualifications, 6 shared a confidently pessimistic belief in the efficacy of systemic therapy and whilst 2 were more optimistic, they were also more uncertain. A Bayesian model based on a synthetic dataset from a randomised clinical trial (showing no benefit with systemic therapy) predicted how each of the 24 veterinarians' prior beliefs would alter as the size of the clinical trial increased, assuming that practitioners would update their beliefs rationally in accordance with Bayes' theorem. The study demonstrated the usefulness of probabilistic elicitation for evaluating the diversity and strength of practitioners' beliefs. The major variation in beliefs observed raises interest in the veterinary profession's approach to prescribing essential medicines. Results illustrate the importance of eliciting prior beliefs when designing clinical trials in order to increase the chance that trial data are of sufficient strength to alter the clinical beliefs of practitioners and do not merely serve to satisfy researchers. Copyright © 2012 Elsevier B.V. All rights reserved.

Hypothesis Testing as an Act of Rationality

NASA Astrophysics Data System (ADS)

Nearing, Grey

2017-04-01

Statistical hypothesis testing is ad hoc in two ways. First, setting probabilistic rejection criteria is, as Neyman (1957) put it, an act of will rather than an act of rationality. Second, physical theories like conservation laws do not inherently admit probabilistic predictions, and so we must use what are called epistemic bridge principles to connect model predictions with the actual methods of hypothesis testing. In practice, these bridge principles are likelihood functions, error functions, or performance metrics. I propose that the reason we are faced with these problems is because we have historically failed to account for a fundamental component of basic logic - namely the portion of logic that explains how epistemic states evolve in the presence of empirical data. This component of Cox' (1946) calculitic logic is called information theory (Knuth, 2005), and adding information theory our hypothetico-deductive account of science yields straightforward solutions to both of the above problems. This also yields a straightforward method for dealing with Popper's (1963) problem of verisimilitude by facilitating a quantitative approach to measuring process isomorphism. In practice, this involves data assimilation. Finally, information theory allows us to reliably bound measures of epistemic uncertainty, thereby avoiding the problem of Bayesian incoherency under misspecified priors (Grünwald, 2006). I therefore propose solutions to four of the fundamental problems inherent in both hypothetico-deductive and/or Bayesian hypothesis testing. - Neyman (1957) Inductive Behavior as a Basic Concept of Philosophy of Science. - Cox (1946) Probability, Frequency and Reasonable Expectation. - Knuth (2005) Lattice Duality: The Origin of Probability and Entropy. - Grünwald (2006). Bayesian Inconsistency under Misspecification. - Popper (1963) Conjectures and Refutations: The Growth of Scientific Knowledge.

Bayesian inference of T Tauri star properties using multi-wavelength survey photometry

NASA Astrophysics Data System (ADS)

Barentsen, Geert; Vink, J. S.; Drew, J. E.; Sale, S. E.

2013-03-01

There are many pertinent open issues in the area of star and planet formation. Large statistical samples of young stars across star-forming regions are needed to trigger a breakthrough in our understanding, but most optical studies are based on a wide variety of spectrographs and analysis methods, which introduces large biases. Here we show how graphical Bayesian networks can be employed to construct a hierarchical probabilistic model which allows pre-main-sequence ages, masses, accretion rates and extinctions to be estimated using two widely available photometric survey data bases (Isaac Newton Telescope Photometric Hα Survey r'/Hα/i' and Two Micron All Sky Survey J-band magnitudes). Because our approach does not rely on spectroscopy, it can easily be applied to ho-mogeneously study the large number of clusters for which Gaia will yield membership lists. We explain how the analysis is carried out using the Markov chain Monte Carlo method and provide PYTHON source code. We then demonstrate its use on 587 known low-mass members of the star-forming region NGC 2264 (Cone Nebula), arriving at a median age of 3.0 Myr, an accretion fraction of 20 ± 2 per cent and a median accretion rate of 10-8.4 M⊙ yr-1. The Bayesian analysis formulated in this work delivers results which are in agreement with spectroscopic studies already in the literature, but achieves this with great efficiency by depending only on photometry. It is a significant step forward from previous photometric studies because the probabilistic approach ensures that nuisance parameters, such as extinction and distance, are fully included in the analysis with a clear picture on any degeneracies.

Modelling multi-hazard hurricane damages on an urbanized coast with a Bayesian Network approach

USGS Publications Warehouse

van Verseveld, H.C.W.; Van Dongeren, A. R.; Plant, Nathaniel G.; Jäger, W.S.; den Heijer, C.

2015-01-01

Hurricane flood impacts to residential buildings in coastal zones are caused by a number of hazards, such as inundation, overflow currents, erosion, and wave attack. However, traditional hurricane damage models typically make use of stage-damage functions, where the stage is related to flooding depth only. Moreover, these models are deterministic and do not consider the large amount of uncertainty associated with both the processes themselves and with the predictions. This uncertainty becomes increasingly important when multiple hazards (flooding, wave attack, erosion, etc.) are considered simultaneously. This paper focusses on establishing relationships between observed damage and multiple hazard indicators in order to make better probabilistic predictions. The concept consists of (1) determining Local Hazard Indicators (LHIs) from a hindcasted storm with use of a nearshore morphodynamic model, XBeach, and (2) coupling these LHIs and building characteristics to the observed damages. We chose a Bayesian Network approach in order to make this coupling and used the LHIs ‘Inundation depth’, ‘Flow velocity’, ‘Wave attack’, and ‘Scour depth’ to represent flooding, current, wave impacts, and erosion related hazards.The coupled hazard model was tested against four thousand damage observations from a case site at the Rockaway Peninsula, NY, that was impacted by Hurricane Sandy in late October, 2012. The model was able to accurately distinguish ‘Minor damage’ from all other outcomes 95% of the time and could distinguish areas that were affected by the storm, but not severely damaged, 68% of the time. For the most heavily damaged buildings (‘Major Damage’ and ‘Destroyed’), projections of the expected damage underestimated the observed damage. The model demonstrated that including multiple hazards doubled the prediction skill, with Log-Likelihood Ratio test (a measure of improved accuracy and reduction in uncertainty) scores between 0.02 and 0.17 when only one hazard is considered and a score of 0.37 when multiple hazards are considered simultaneously. The LHIs with the most predictive skill were ‘Inundation depth’ and ‘Wave attack’. The Bayesian Network approach has several advantages over the market-standard stage-damage functions: the predictive capacity of multiple indicators can be combined; probabilistic predictions can be obtained, which include uncertainty; and quantitative as well as descriptive information can be used simultaneously.

Uncertainty Quantification of Hypothesis Testing for the Integrated Knowledge Engine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cuellar, Leticia

2012-05-31

The Integrated Knowledge Engine (IKE) is a tool of Bayesian analysis, based on Bayesian Belief Networks or Bayesian networks for short. A Bayesian network is a graphical model (directed acyclic graph) that allows representing the probabilistic structure of many variables assuming a localized type of dependency called the Markov property. The Markov property in this instance makes any node or random variable to be independent of any non-descendant node given information about its parent. A direct consequence of this property is that it is relatively easy to incorporate new evidence and derive the appropriate consequences, which in general is notmore » an easy or feasible task. Typically we use Bayesian networks as predictive models for a small subset of the variables, either the leave nodes or the root nodes. In IKE, since most applications deal with diagnostics, we are interested in predicting the likelihood of the root nodes given new observations on any of the children nodes. The root nodes represent the various possible outcomes of the analysis, and an important problem is to determine when we have gathered enough evidence to lean toward one of these particular outcomes. This document presents criteria to decide when the evidence gathered is sufficient to draw a particular conclusion or decide in favor of a particular outcome by quantifying the uncertainty in the conclusions that are drawn from the data. The material in this document is organized as follows: Section 2 presents briefly a forensics Bayesian network, and we explore evaluating the information provided by new evidence by looking first at the posterior distribution of the nodes of interest, and then at the corresponding posterior odds ratios. Section 3 presents a third alternative: Bayes Factors. In section 4 we finalize by showing the relation between the posterior odds ratios and Bayes factors and showing examples these cases, and in section 5 we conclude by providing clear guidelines of how to use these for the type of Bayesian networks used in IKE.« less

ensembleBMA: An R Package for Probabilistic Forecasting using Ensembles and Bayesian Model Averaging

DTIC Science & Technology

2007-08-15

library is used to allow addition of the legend and map outline to the plot. > bluescale <- function(n) hsv (4/6, s = seq(from = 1 /8, to = 1 , length = n...v = 1 ) > plotBMAforecast( probFreeze290104, lon=srftGridData$lon, lat =srftGridData$ lat , type="image", col=bluescale(100)) > title("Probability of...probPrecip130103) # used to determine zlim in plots [ 1 ] 0.02832709 0.99534860 > plotBMAforecast( probPrecip130103[,Ŕ"], lon=prcpGridData$lon, lat

A robust multi-kernel change detection framework for detecting leaf beetle defoliation using Landsat 7 ETM+ data

NASA Astrophysics Data System (ADS)

Anees, Asim; Aryal, Jagannath; O'Reilly, Małgorzata M.; Gale, Timothy J.; Wardlaw, Tim

2016-12-01

A robust non-parametric framework, based on multiple Radial Basic Function (RBF) kernels, is proposed in this study, for detecting land/forest cover changes using Landsat 7 ETM+ images. One of the widely used frameworks is to find change vectors (difference image) and use a supervised classifier to differentiate between change and no-change. The Bayesian Classifiers e.g. Maximum Likelihood Classifier (MLC), Naive Bayes (NB), are widely used probabilistic classifiers which assume parametric models, e.g. Gaussian function, for the class conditional distributions. However, their performance can be limited if the data set deviates from the assumed model. The proposed framework exploits the useful properties of Least Squares Probabilistic Classifier (LSPC) formulation i.e. non-parametric and probabilistic nature, to model class posterior probabilities of the difference image using a linear combination of a large number of Gaussian kernels. To this end, a simple technique, based on 10-fold cross-validation is also proposed for tuning model parameters automatically instead of selecting a (possibly) suboptimal combination from pre-specified lists of values. The proposed framework has been tested and compared with Support Vector Machine (SVM) and NB for detection of defoliation, caused by leaf beetles (Paropsisterna spp.) in Eucalyptus nitens and Eucalyptus globulus plantations of two test areas, in Tasmania, Australia, using raw bands and band combination indices of Landsat 7 ETM+. It was observed that due to multi-kernel non-parametric formulation and probabilistic nature, the LSPC outperforms parametric NB with Gaussian assumption in change detection framework, with Overall Accuracy (OA) ranging from 93.6% (κ = 0.87) to 97.4% (κ = 0.94) against 85.3% (κ = 0.69) to 93.4% (κ = 0.85), and is more robust to changing data distributions. Its performance was comparable to SVM, with added advantages of being probabilistic and capable of handling multi-class problems naturally with its original formulation.

Risk of fire occurrence in arid and semi-arid ecosystems of Iran: an investigation using Bayesian belief networks.

PubMed

Bashari, Hossein; Naghipour, Ali Asghar; Khajeddin, Seyed Jamaleddin; Sangoony, Hamed; Tahmasebi, Pejman

2016-09-01

Identifying areas that have a high risk of burning is a main component of fire management planning. Although the available tools can predict the fire risks, these are poor in accommodating uncertainties in their predictions. In this study, we accommodated uncertainty in wildfire prediction using Bayesian belief networks (BBNs). An influence diagram was developed to identify the factors influencing wildfire in arid and semi-arid areas of Iran, and it was populated with probabilities to produce a BBNs model. The behavior of the model was tested using scenario and sensitivity analysis. Land cover/use, mean annual rainfall, mean annual temperature, elevation, and livestock density were recognized as the main variables determining wildfire occurrence. The produced model had good accuracy as its ROC area under the curve was 0.986. The model could be applied in both predictive and diagnostic analysis for answering "what if" and "how" questions. The probabilistic relationships within the model can be updated over time using observation and monitoring data. The wildfire BBN model may be updated as new knowledge emerges; hence, it can be used to support the process of adaptive management.

A tesselated probabilistic representation for spatial robot perception and navigation

NASA Technical Reports Server (NTRS)

Elfes, Alberto

1989-01-01

The ability to recover robust spatial descriptions from sensory information and to efficiently utilize these descriptions in appropriate planning and problem-solving activities are crucial requirements for the development of more powerful robotic systems. Traditional approaches to sensor interpretation, with their emphasis on geometric models, are of limited use for autonomous mobile robots operating in and exploring unknown and unstructured environments. Here, researchers present a new approach to robot perception that addresses such scenarios using a probabilistic tesselated representation of spatial information called the Occupancy Grid. The Occupancy Grid is a multi-dimensional random field that maintains stochastic estimates of the occupancy state of each cell in the grid. The cell estimates are obtained by interpreting incoming range readings using probabilistic models that capture the uncertainty in the spatial information provided by the sensor. A Bayesian estimation procedure allows the incremental updating of the map using readings taken from several sensors over multiple points of view. An overview of the Occupancy Grid framework is given, and its application to a number of problems in mobile robot mapping and navigation are illustrated. It is argued that a number of robotic problem-solving activities can be performed directly on the Occupancy Grid representation. Some parallels are drawn between operations on Occupancy Grids and related image processing operations.

Functional mechanisms of probabilistic inference in feature- and space-based attentional systems.

PubMed

Dombert, Pascasie L; Kuhns, Anna; Mengotti, Paola; Fink, Gereon R; Vossel, Simone

2016-11-15

Humans flexibly attend to features or locations and these processes are influenced by the probability of sensory events. We combined computational modeling of response times with fMRI to compare the functional correlates of (re-)orienting, and the modulation by probabilistic inference in spatial and feature-based attention systems. Twenty-four volunteers performed two task versions with spatial or color cues. Percentage of cue validity changed unpredictably. A hierarchical Bayesian model was used to derive trial-wise estimates of probability-dependent attention, entering the fMRI analysis as parametric regressors. Attentional orienting activated a dorsal frontoparietal network in both tasks, without significant parametric modulation. Spatially invalid trials activated a bilateral frontoparietal network and the precuneus, while invalid feature trials activated the left intraparietal sulcus (IPS). Probability-dependent attention modulated activity in the precuneus, left posterior IPS, middle occipital gyrus, and right temporoparietal junction for spatial attention, and in the left anterior IPS for feature-based and spatial attention. These findings provide novel insights into the generality and specificity of the functional basis of attentional control. They suggest that probabilistic inference can distinctively affect each attentional subsystem, but that there is an overlap in the left IPS, which responds to both spatial and feature-based expectancy violations. Copyright © 2016 Elsevier Inc. All rights reserved.

Dynamic Uncertain Causality Graph for Knowledge Representation and Probabilistic Reasoning: Directed Cyclic Graph and Joint Probability Distribution.

PubMed

Zhang, Qin

2015-07-01

Probabilistic graphical models (PGMs) such as Bayesian network (BN) have been widely applied in uncertain causality representation and probabilistic reasoning. Dynamic uncertain causality graph (DUCG) is a newly presented model of PGMs, which can be applied to fault diagnosis of large and complex industrial systems, disease diagnosis, and so on. The basic methodology of DUCG has been previously presented, in which only the directed acyclic graph (DAG) was addressed. However, the mathematical meaning of DUCG was not discussed. In this paper, the DUCG with directed cyclic graphs (DCGs) is addressed. In contrast, BN does not allow DCGs, as otherwise the conditional independence will not be satisfied. The inference algorithm for the DUCG with DCGs is presented, which not only extends the capabilities of DUCG from DAGs to DCGs but also enables users to decompose a large and complex DUCG into a set of small, simple sub-DUCGs, so that a large and complex knowledge base can be easily constructed, understood, and maintained. The basic mathematical definition of a complete DUCG with or without DCGs is proved to be a joint probability distribution (JPD) over a set of random variables. The incomplete DUCG as a part of a complete DUCG may represent a part of JPD. Examples are provided to illustrate the methodology.

A fast combination method in DSmT and its application to recommender system

PubMed Central

Liu, Yihai

2018-01-01

In many applications involving epistemic uncertainties usually modeled by belief functions, it is often necessary to approximate general (non-Bayesian) basic belief assignments (BBAs) to subjective probabilities (called Bayesian BBAs). This necessity occurs if one needs to embed the fusion result in a system based on the probabilistic framework and Bayesian inference (e.g. tracking systems), or if one needs to make a decision in the decision making problems. In this paper, we present a new fast combination method, called modified rigid coarsening (MRC), to obtain the final Bayesian BBAs based on hierarchical decomposition (coarsening) of the frame of discernment. Regarding this method, focal elements with probabilities are coarsened efficiently to reduce computational complexity in the process of combination by using disagreement vector and a simple dichotomous approach. In order to prove the practicality of our approach, this new approach is applied to combine users’ soft preferences in recommender systems (RSs). Additionally, in order to make a comprehensive performance comparison, the proportional conflict redistribution rule #6 (PCR6) is regarded as a baseline in a range of experiments. According to the results of experiments, MRC is more effective in accuracy of recommendations compared to original Rigid Coarsening (RC) method and comparable in computational time. PMID:29351297

Planetary micro-rover operations on Mars using a Bayesian framework for inference and control

NASA Astrophysics Data System (ADS)

Post, Mark A.; Li, Junquan; Quine, Brendan M.

2016-03-01

With the recent progress toward the application of commercially-available hardware to small-scale space missions, it is now becoming feasible for groups of small, efficient robots based on low-power embedded hardware to perform simple tasks on other planets in the place of large-scale, heavy and expensive robots. In this paper, we describe design and programming of the Beaver micro-rover developed for Northern Light, a Canadian initiative to send a small lander and rover to Mars to study the Martian surface and subsurface. For a small, hardware-limited rover to handle an uncertain and mostly unknown environment without constant management by human operators, we use a Bayesian network of discrete random variables as an abstraction of expert knowledge about the rover and its environment, and inference operations for control. A framework for efficient construction and inference into a Bayesian network using only the C language and fixed-point mathematics on embedded hardware has been developed for the Beaver to make intelligent decisions with minimal sensor data. We study the performance of the Beaver as it probabilistically maps a simple outdoor environment with sensor models that include uncertainty. Results indicate that the Beaver and other small and simple robotic platforms can make use of a Bayesian network to make intelligent decisions in uncertain planetary environments.

Remembrance of inferences past: Amortization in human hypothesis generation.

PubMed

Dasgupta, Ishita; Schulz, Eric; Goodman, Noah D; Gershman, Samuel J

2018-05-21

Bayesian models of cognition assume that people compute probability distributions over hypotheses. However, the required computations are frequently intractable or prohibitively expensive. Since people often encounter many closely related distributions, selective reuse of computations (amortized inference) is a computationally efficient use of the brain's limited resources. We present three experiments that provide evidence for amortization in human probabilistic reasoning. When sequentially answering two related queries about natural scenes, participants' responses to the second query systematically depend on the structure of the first query. This influence is sensitive to the content of the queries, only appearing when the queries are related. Using a cognitive load manipulation, we find evidence that people amortize summary statistics of previous inferences, rather than storing the entire distribution. These findings support the view that the brain trades off accuracy and computational cost, to make efficient use of its limited cognitive resources to approximate probabilistic inference. Copyright © 2018 Elsevier B.V. All rights reserved.

Hamiltonian Monte Carlo acceleration using surrogate functions with random bases.

PubMed

Zhang, Cheng; Shahbaba, Babak; Zhao, Hongkai

2017-11-01

For big data analysis, high computational cost for Bayesian methods often limits their applications in practice. In recent years, there have been many attempts to improve computational efficiency of Bayesian inference. Here we propose an efficient and scalable computational technique for a state-of-the-art Markov chain Monte Carlo methods, namely, Hamiltonian Monte Carlo. The key idea is to explore and exploit the structure and regularity in parameter space for the underlying probabilistic model to construct an effective approximation of its geometric properties. To this end, we build a surrogate function to approximate the target distribution using properly chosen random bases and an efficient optimization process. The resulting method provides a flexible, scalable, and efficient sampling algorithm, which converges to the correct target distribution. We show that by choosing the basis functions and optimization process differently, our method can be related to other approaches for the construction of surrogate functions such as generalized additive models or Gaussian process models. Experiments based on simulated and real data show that our approach leads to substantially more efficient sampling algorithms compared to existing state-of-the-art methods.

Review of Reliability-Based Design Optimization Approach and Its Integration with Bayesian Method

NASA Astrophysics Data System (ADS)

Zhang, Xiangnan

2018-03-01

A lot of uncertain factors lie in practical engineering, such as external load environment, material property, geometrical shape, initial condition, boundary condition, etc. Reliability method measures the structural safety condition and determine the optimal design parameter combination based on the probabilistic theory. Reliability-based design optimization (RBDO) is the most commonly used approach to minimize the structural cost or other performance under uncertainty variables which combines the reliability theory and optimization. However, it cannot handle the various incomplete information. The Bayesian approach is utilized to incorporate this kind of incomplete information in its uncertainty quantification. In this paper, the RBDO approach and its integration with Bayesian method are introduced.

Implementing Bayesian networks with embedded stochastic MRAM

NASA Astrophysics Data System (ADS)

Faria, Rafatul; Camsari, Kerem Y.; Datta, Supriyo

2018-04-01

Magnetic tunnel junctions (MTJ's) with low barrier magnets have been used to implement random number generators (RNG's) and it has recently been shown that such an MTJ connected to the drain of a conventional transistor provides a three-terminal tunable RNG or a p-bit. In this letter we show how this p-bit can be used to build a p-circuit that emulates a Bayesian network (BN), such that the correlations in real world variables can be obtained from electrical measurements on the corresponding circuit nodes. The p-circuit design proceeds in two steps: the BN is first translated into a behavioral model, called Probabilistic Spin Logic (PSL), defined by dimensionless biasing (h) and interconnection (J) coefficients, which are then translated into electronic circuit elements. As a benchmark example, we mimic a family tree of three generations and show that the genetic relatedness calculated from a SPICE-compatible circuit simulator matches well-known results.

Probabilistic Volcanic Multi-Hazard Assessment at Somma-Vesuvius (Italy): coupling Bayesian Belief Networks with a physical model for lahar propagation

NASA Astrophysics Data System (ADS)

Tierz, Pablo; Woodhouse, Mark; Phillips, Jeremy; Sandri, Laura; Selva, Jacopo; Marzocchi, Warner; Odbert, Henry

2017-04-01

Volcanoes are extremely complex physico-chemical systems where magma formed at depth breaks into the planet's surface resulting in major hazards from local to global scales. Volcano physics are dominated by non-linearities, and complicated spatio-temporal interrelationships which make volcanic hazards stochastic (i.e. not deterministic) by nature. In this context, probabilistic assessments are required to quantify the large uncertainties related to volcanic hazards. Moreover, volcanoes are typically multi-hazard environments where different hazardous processes can occur whether simultaneously or in succession. In particular, explosive volcanoes are able to accumulate, through tephra fallout and Pyroclastic Density Currents (PDCs), large amounts of pyroclastic material into the drainage basins surrounding the volcano. This addition of fresh particulate material alters the local/regional hydrogeological equilibrium and increases the frequency and magnitude of sediment-rich aqueous flows, commonly known as lahars. The initiation and volume of rain-triggered lahars may depend on: rainfall intensity and duration; antecedent rainfall; terrain slope; thickness, permeability and hydraulic diffusivity of the tephra deposit; etc. Quantifying these complex interrelationships (and their uncertainties), in a tractable manner, requires a structured but flexible probabilistic approach. A Bayesian Belief Network (BBN) is a directed acyclic graph that allows the representation of the joint probability distribution for a set of uncertain variables in a compact and efficient way, by exploiting unconditional and conditional independences between these variables. Once constructed and parametrized, the BBN uses Bayesian inference to perform causal (e.g. forecast) and/or evidential reasoning (e.g. explanation) about query variables, given some evidence. In this work, we illustrate how BBNs can be used to model the influence of several variables on the generation of rain-triggered lahars and, finally, assess the probability of occurrence of lahars of different volumes. The information utilized to parametrize the BBNs includes: (1) datasets of lahar observations; (2) numerical modelling of tephra fallout and PDCs; and (3) literature data. The BBN framework provides an opportunity to quantitatively combine these different types of evidence and use them to derive a rational approach to lahar forecasting. Lastly, we couple the BBN assessments with a shallow-water physical model for lahar propagation in order to attach probabilities to the simulated hazard footprints. We develop our methodology at Somma-Vesuvius (Italy), an explosive volcano prone to rain-triggered lahars or debris flows whether right after an eruption or during inter-eruptive periods. Accounting for the variability in tephra-fallout and dense-PDC propagation and the main geomorphological features of the catchments around Somma-Vesuvius, the areas most likely of forming medium-large lahars are the flanks of the volcano and the Sarno mountains towards the east.

Observations and Bayesian location methodology of transient acoustic signals (likely blue whales) in the Indian Ocean, using a hydrophone triplet.

PubMed

Le Bras, Ronan J; Kuzma, Heidi; Sucic, Victor; Bokelmann, Götz

2016-05-01

A notable sequence of calls was encountered, spanning several days in January 2003, in the central part of the Indian Ocean on a hydrophone triplet recording acoustic data at a 250 Hz sampling rate. This paper presents signal processing methods applied to the waveform data to detect, group, extract amplitude and bearing estimates for the recorded signals. An approximate location for the source of the sequence of calls is inferred from extracting the features from the waveform. As the source approaches the hydrophone triplet, the source level (SL) of the calls is estimated at 187 ± 6 dB re: 1 μPa-1 m in the 15-60 Hz frequency range. The calls are attributed to a subgroup of blue whales, Balaenoptera musculus, with a characteristic acoustic signature. A Bayesian location method using probabilistic models for bearing and amplitude is demonstrated on the calls sequence. The method is applied to the case of detection at a single triad of hydrophones and results in a probability distribution map for the origin of the calls. It can be extended to detections at multiple triads and because of the Bayesian formulation, additional modeling complexity can be built-in as needed.

Toward improved prediction of the bedrock depth underneath hillslopes: Bayesian inference of the bottom-up control hypothesis using high-resolution topographic data

NASA Astrophysics Data System (ADS)

Gomes, Guilherme J. C.; Vrugt, Jasper A.; Vargas, Eurípedes A.

2016-04-01

The depth to bedrock controls a myriad of processes by influencing subsurface flow paths, erosion rates, soil moisture, and water uptake by plant roots. As hillslope interiors are very difficult and costly to illuminate and access, the topography of the bedrock surface is largely unknown. This essay is concerned with the prediction of spatial patterns in the depth to bedrock (DTB) using high-resolution topographic data, numerical modeling, and Bayesian analysis. Our DTB model builds on the bottom-up control on fresh-bedrock topography hypothesis of Rempe and Dietrich (2014) and includes a mass movement and bedrock-valley morphology term to extent the usefulness and general applicability of the model. We reconcile the DTB model with field observations using Bayesian analysis with the DREAM algorithm. We investigate explicitly the benefits of using spatially distributed parameter values to account implicitly, and in a relatively simple way, for rock mass heterogeneities that are very difficult, if not impossible, to characterize adequately in the field. We illustrate our method using an artificial data set of bedrock depth observations and then evaluate our DTB model with real-world data collected at the Papagaio river basin in Rio de Janeiro, Brazil. Our results demonstrate that the DTB model predicts accurately the observed bedrock depth data. The posterior mean DTB simulation is shown to be in good agreement with the measured data. The posterior prediction uncertainty of the DTB model can be propagated forward through hydromechanical models to derive probabilistic estimates of factors of safety.

An ecosystem service approach to support integrated pond management: a case study using Bayesian belief networks--highlighting opportunities and risks.

PubMed

Landuyt, Dries; Lemmens, Pieter; D'hondt, Rob; Broekx, Steven; Liekens, Inge; De Bie, Tom; Declerck, Steven A J; De Meester, Luc; Goethals, Peter L M

2014-12-01

Freshwater ponds deliver a broad range of ecosystem services (ESS). Taking into account this broad range of services to attain cost-effective ESS delivery is an important challenge facing integrated pond management. To assess the strengths and weaknesses of an ESS approach to support decisions in integrated pond management, we applied it on a small case study in Flanders, Belgium. A Bayesian belief network model was developed to assess ESS delivery under three alternative pond management scenarios: intensive fish farming (IFF), extensive fish farming (EFF) and nature conservation management (NCM). A probabilistic cost-benefit analysis was performed that includes both costs associated with pond management practices and benefits associated with ESS delivery. Whether or not a particular ESS is included in the analysis affects the identification of the most preferable management scenario by the model. Assessing the delivery of a more complete set of ecosystem services tends to shift the results away from intensive management to more biodiversity-oriented management scenarios. The proposed methodology illustrates the potential of Bayesian belief networks. BBNs facilitate knowledge integration and their modular nature encourages future model expansion to more encompassing sets of services. Yet, we also illustrate the key weaknesses of such exercises, being that the choice whether or not to include a particular ecosystem service may determine the suggested optimal management practice. Copyright © 2014 Elsevier Ltd. All rights reserved.

Exploratory study on a statistical method to analyse time resolved data obtained during nanomaterial exposure measurements

NASA Astrophysics Data System (ADS)

Clerc, F.; Njiki-Menga, G.-H.; Witschger, O.

2013-04-01

Most of the measurement strategies that are suggested at the international level to assess workplace exposure to nanomaterials rely on devices measuring, in real time, airborne particles concentrations (according different metrics). Since none of the instruments to measure aerosols can distinguish a particle of interest to the background aerosol, the statistical analysis of time resolved data requires special attention. So far, very few approaches have been used for statistical analysis in the literature. This ranges from simple qualitative analysis of graphs to the implementation of more complex statistical models. To date, there is still no consensus on a particular approach and the current period is always looking for an appropriate and robust method. In this context, this exploratory study investigates a statistical method to analyse time resolved data based on a Bayesian probabilistic approach. To investigate and illustrate the use of the this statistical method, particle number concentration data from a workplace study that investigated the potential for exposure via inhalation from cleanout operations by sandpapering of a reactor producing nanocomposite thin films have been used. In this workplace study, the background issue has been addressed through the near-field and far-field approaches and several size integrated and time resolved devices have been used. The analysis of the results presented here focuses only on data obtained with two handheld condensation particle counters. While one was measuring at the source of the released particles, the other one was measuring in parallel far-field. The Bayesian probabilistic approach allows a probabilistic modelling of data series, and the observed task is modelled in the form of probability distributions. The probability distributions issuing from time resolved data obtained at the source can be compared with the probability distributions issuing from the time resolved data obtained far-field, leading in a quantitative estimation of the airborne particles released at the source when the task is performed. Beyond obtained results, this exploratory study indicates that the analysis of the results requires specific experience in statistics.

Bayesian population receptive field modelling.

PubMed

Zeidman, Peter; Silson, Edward Harry; Schwarzkopf, Dietrich Samuel; Baker, Chris Ian; Penny, Will

2017-09-08

We introduce a probabilistic (Bayesian) framework and associated software toolbox for mapping population receptive fields (pRFs) based on fMRI data. This generic approach is intended to work with stimuli of any dimension and is demonstrated and validated in the context of 2D retinotopic mapping. The framework enables the experimenter to specify generative (encoding) models of fMRI timeseries, in which experimental stimuli enter a pRF model of neural activity, which in turns drives a nonlinear model of neurovascular coupling and Blood Oxygenation Level Dependent (BOLD) response. The neuronal and haemodynamic parameters are estimated together on a voxel-by-voxel or region-of-interest basis using a Bayesian estimation algorithm (variational Laplace). This offers several novel contributions to receptive field modelling. The variance/covariance of parameters are estimated, enabling receptive fields to be plotted while properly representing uncertainty about pRF size and location. Variability in the haemodynamic response across the brain is accounted for. Furthermore, the framework introduces formal hypothesis testing to pRF analysis, enabling competing models to be evaluated based on their log model evidence (approximated by the variational free energy), which represents the optimal tradeoff between accuracy and complexity. Using simulations and empirical data, we found that parameters typically used to represent pRF size and neuronal scaling are strongly correlated, which is taken into account by the Bayesian methods we describe when making inferences. We used the framework to compare the evidence for six variants of pRF model using 7 T functional MRI data and we found a circular Difference of Gaussians (DoG) model to be the best explanation for our data overall. We hope this framework will prove useful for mapping stimulus spaces with any number of dimensions onto the anatomy of the brain. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Toward a probabilistic acoustic emission source location algorithm: A Bayesian approach

NASA Astrophysics Data System (ADS)

Schumacher, Thomas; Straub, Daniel; Higgins, Christopher

2012-09-01

Acoustic emissions (AE) are stress waves initiated by sudden strain releases within a solid body. These can be caused by internal mechanisms such as crack opening or propagation, crushing, or rubbing of crack surfaces. One application for the AE technique in the field of Structural Engineering is Structural Health Monitoring (SHM). With piezo-electric sensors mounted to the surface of the structure, stress waves can be detected, recorded, and stored for later analysis. An important step in quantitative AE analysis is the estimation of the stress wave source locations. Commonly, source location results are presented in a rather deterministic manner as spatial and temporal points, excluding information about uncertainties and errors. Due to variability in the material properties and uncertainty in the mathematical model, measures of uncertainty are needed beyond best-fit point solutions for source locations. This paper introduces a novel holistic framework for the development of a probabilistic source location algorithm. Bayesian analysis methods with Markov Chain Monte Carlo (MCMC) simulation are employed where all source location parameters are described with posterior probability density functions (PDFs). The proposed methodology is applied to an example employing data collected from a realistic section of a reinforced concrete bridge column. The selected approach is general and has the advantage that it can be extended and refined efficiently. Results are discussed and future steps to improve the algorithm are suggested.

A Bayesian model averaging approach with non-informative priors for cost-effectiveness analyses.

PubMed

Conigliani, Caterina

2010-07-20

We consider the problem of assessing new and existing technologies for their cost-effectiveness in the case where data on both costs and effects are available from a clinical trial, and we address it by means of the cost-effectiveness acceptability curve. The main difficulty in these analyses is that cost data usually exhibit highly skew and heavy-tailed distributions, so that it can be extremely difficult to produce realistic probabilistic models for the underlying population distribution. Here, in order to integrate the uncertainty about the model into the analysis of cost data and into cost-effectiveness analyses, we consider an approach based on Bayesian model averaging (BMA) in the particular case of weak prior informations about the unknown parameters of the different models involved in the procedure. The main consequence of this assumption is that the marginal densities required by BMA are undetermined. However, in accordance with the theory of partial Bayes factors and in particular of fractional Bayes factors, we suggest replacing each marginal density with a ratio of integrals that can be efficiently computed via path sampling. Copyright (c) 2010 John Wiley & Sons, Ltd.

Model-based Clustering of Categorical Time Series with Multinomial Logit Classification

NASA Astrophysics Data System (ADS)

Frühwirth-Schnatter, Sylvia; Pamminger, Christoph; Winter-Ebmer, Rudolf; Weber, Andrea

2010-09-01

A common problem in many areas of applied statistics is to identify groups of similar time series in a panel of time series. However, distance-based clustering methods cannot easily be extended to time series data, where an appropriate distance-measure is rather difficult to define, particularly for discrete-valued time series. Markov chain clustering, proposed by Pamminger and Frühwirth-Schnatter [6], is an approach for clustering discrete-valued time series obtained by observing a categorical variable with several states. This model-based clustering method is based on finite mixtures of first-order time-homogeneous Markov chain models. In order to further explain group membership we present an extension to the approach of Pamminger and Frühwirth-Schnatter [6] by formulating a probabilistic model for the latent group indicators within the Bayesian classification rule by using a multinomial logit model. The parameters are estimated for a fixed number of clusters within a Bayesian framework using an Markov chain Monte Carlo (MCMC) sampling scheme representing a (full) Gibbs-type sampler which involves only draws from standard distributions. Finally, an application to a panel of Austrian wage mobility data is presented which leads to an interesting segmentation of the Austrian labour market.

Visual and Auditory Components in the Perception of Asynchronous Audiovisual Speech

PubMed Central

Alcalá-Quintana, Rocío

2015-01-01

Research on asynchronous audiovisual speech perception manipulates experimental conditions to observe their effects on synchrony judgments. Probabilistic models establish a link between the sensory and decisional processes underlying such judgments and the observed data, via interpretable parameters that allow testing hypotheses and making inferences about how experimental manipulations affect such processes. Two models of this type have recently been proposed, one based on independent channels and the other using a Bayesian approach. Both models are fitted here to a common data set, with a subsequent analysis of the interpretation they provide about how experimental manipulations affected the processes underlying perceived synchrony. The data consist of synchrony judgments as a function of audiovisual offset in a speech stimulus, under four within-subjects manipulations of the quality of the visual component. The Bayesian model could not accommodate asymmetric data, was rejected by goodness-of-fit statistics for 8/16 observers, and was found to be nonidentifiable, which renders uninterpretable parameter estimates. The independent-channels model captured asymmetric data, was rejected for only 1/16 observers, and identified how sensory and decisional processes mediating asynchronous audiovisual speech perception are affected by manipulations that only alter the quality of the visual component of the speech signal. PMID:27551361

Coupling of Bayesian Networks with GIS for wildfire risk assessment on natural and agricultural areas of the Mediterranean

NASA Astrophysics Data System (ADS)

Scherb, Anke; Papakosta, Panagiota; Straub, Daniel

2014-05-01

Wildfires cause severe damages to ecosystems, socio-economic assets, and human lives in the Mediterranean. To facilitate coping with wildfire risks, an understanding of the factors influencing wildfire occurrence and behavior (e.g. human activity, weather conditions, topography, fuel loads) and their interaction is of importance, as is the implementation of this knowledge in improved wildfire hazard and risk prediction systems. In this project, a probabilistic wildfire risk prediction model is developed, with integrated fire occurrence and fire propagation probability and potential impact prediction on natural and cultivated areas. Bayesian Networks (BNs) are used to facilitate the probabilistic modeling. The final BN model is a spatial-temporal prediction system at the meso scale (1 km2 spatial and 1 day temporal resolution). The modeled consequences account for potential restoration costs and production losses referred to forests, agriculture, and (semi-) natural areas. BNs and a geographic information system (GIS) are coupled within this project to support a semi-automated BN model parameter learning and the spatial-temporal risk prediction. The coupling also enables the visualization of prediction results by means of daily maps. The BN parameters are learnt for Cyprus with data from 2006-2009. Data from 2010 is used as validation data set. A special focus is put on the performance evaluation of the BN for fire occurrence, which is modeled as binary classifier and thus, could be validated by means of Receiver Operator Characteristic (ROC) curves. With the final best models, AUC values of more than 70% for validation could be achieved, which indicates potential for reliable prediction performance via BN. Maps of selected days in 2010 are shown to illustrate final prediction results. The resulting system can be easily expanded to predict additional expected damages in the mesoscale (e.g. building and infrastructure damages). The system can support planning of preventive measures (e.g. state resources allocation for wildfire prevention and preparedness) and assist recuperation plans of damaged areas.

Aviation Safety Risk Modeling: Lessons Learned From Multiple Knowledge Elicitation Sessions

NASA Technical Reports Server (NTRS)

Luxhoj, J. T.; Ancel, E.; Green, L. L.; Shih, A. T.; Jones, S. M.; Reveley, M. S.

2014-01-01

Aviation safety risk modeling has elements of both art and science. In a complex domain, such as the National Airspace System (NAS), it is essential that knowledge elicitation (KE) sessions with domain experts be performed to facilitate the making of plausible inferences about the possible impacts of future technologies and procedures. This study discusses lessons learned throughout the multiple KE sessions held with domain experts to construct probabilistic safety risk models for a Loss of Control Accident Framework (LOCAF), FLightdeck Automation Problems (FLAP), and Runway Incursion (RI) mishap scenarios. The intent of these safety risk models is to support a portfolio analysis of NASA's Aviation Safety Program (AvSP). These models use the flexible, probabilistic approach of Bayesian Belief Networks (BBNs) and influence diagrams to model the complex interactions of aviation system risk factors. Each KE session had a different set of experts with diverse expertise, such as pilot, air traffic controller, certification, and/or human factors knowledge that was elicited to construct a composite, systems-level risk model. There were numerous "lessons learned" from these KE sessions that deal with behavioral aggregation, conditional probability modeling, object-oriented construction, interpretation of the safety risk results, and model verification/validation that are presented in this paper.

Tractography-Based Score for Learning Effective Connectivity From Multimodal Imaging Data Using Dynamic Bayesian Networks.

PubMed

Dang, Shilpa; Chaudhury, Santanu; Lall, Brejesh; Roy, Prasun K

2018-05-01

Effective connectivity (EC) is the methodology for determining functional-integration among the functionally active segregated regions of the brain. By definition EC is "the causal influence exerted by one neuronal group on another" which is constrained by anatomical connectivity (AC) (axonal connections). AC is necessary for EC but does not fully determine it, because synaptic communication occurs dynamically in a context-dependent fashion. Although there is a vast emerging evidence of structure-function relationship using multimodal imaging studies, till date only a few studies have done joint modeling of the two modalities: functional MRI (fMRI) and diffusion tensor imaging (DTI). We aim to propose a unified probabilistic framework that combines information from both sources to learn EC using dynamic Bayesian networks (DBNs). DBNs are probabilistic graphical temporal models that learn EC in an exploratory fashion. Specifically, we propose a novel anatomically informed (AI) score that evaluates fitness of a given connectivity structure to both DTI and fMRI data simultaneously. The AI score is employed in structure learning of DBN given the data. Experiments with synthetic-data demonstrate the face validity of structure learning with our AI score over anatomically uninformed counterpart. Moreover, real-data results are cross-validated by performing classification-experiments. EC inferred on real fMRI-DTI datasets is found to be consistent with previous literature and show promising results in light of the AC present as compared to other classically used techniques such as Granger-causality. Multimodal analyses provide a more reliable basis for differentiating brain under abnormal/diseased conditions than the single modality analysis.

RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

PubMed Central

Höhna, Sebastian; Landis, Michael J.

2016-01-01

Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite of models. Consequently, users of these software packages are simultaneously forced to use a number of programs for a given study, while also lacking the freedom to explore models that have not been implemented by the developers of those programs. We developed a new open-source software package, RevBayes, to address these problems. RevBayes is entirely based on probabilistic graphical models, a powerful generic framework for specifying and analyzing statistical models. Phylogenetic-graphical models can be specified interactively in RevBayes, piece by piece, using a new succinct and intuitive language called Rev. Rev is similar to the R language and the BUGS model-specification language, and should be easy to learn for most users. The strength of RevBayes is the simplicity with which one can design, specify, and implement new and complex models. Fortunately, this tremendous flexibility does not come at the cost of slower computation; as we demonstrate, RevBayes outperforms competing software for several standard analyses. Compared with other programs, RevBayes has fewer black-box elements. Users need to explicitly specify each part of the model and analysis. Although this explicitness may initially be unfamiliar, we are convinced that this transparency will improve understanding of phylogenetic models in our field. Moreover, it will motivate the search for improvements to existing methods by brazenly exposing the model choices that we make to critical scrutiny. RevBayes is freely available at http://www.RevBayes.com. [Bayesian inference; Graphical models; MCMC; statistical phylogenetics.] PMID:27235697

RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language.

PubMed

Höhna, Sebastian; Landis, Michael J; Heath, Tracy A; Boussau, Bastien; Lartillot, Nicolas; Moore, Brian R; Huelsenbeck, John P; Ronquist, Fredrik

2016-07-01

Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite of models. Consequently, users of these software packages are simultaneously forced to use a number of programs for a given study, while also lacking the freedom to explore models that have not been implemented by the developers of those programs. We developed a new open-source software package, RevBayes, to address these problems. RevBayes is entirely based on probabilistic graphical models, a powerful generic framework for specifying and analyzing statistical models. Phylogenetic-graphical models can be specified interactively in RevBayes, piece by piece, using a new succinct and intuitive language called Rev. Rev is similar to the R language and the BUGS model-specification language, and should be easy to learn for most users. The strength of RevBayes is the simplicity with which one can design, specify, and implement new and complex models. Fortunately, this tremendous flexibility does not come at the cost of slower computation; as we demonstrate, RevBayes outperforms competing software for several standard analyses. Compared with other programs, RevBayes has fewer black-box elements. Users need to explicitly specify each part of the model and analysis. Although this explicitness may initially be unfamiliar, we are convinced that this transparency will improve understanding of phylogenetic models in our field. Moreover, it will motivate the search for improvements to existing methods by brazenly exposing the model choices that we make to critical scrutiny. RevBayes is freely available at http://www.RevBayes.com [Bayesian inference; Graphical models; MCMC; statistical phylogenetics.]. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Machine health prognostics using the Bayesian-inference-based probabilistic indication and high-order particle filtering framework

NASA Astrophysics Data System (ADS)

Yu, Jianbo

2015-12-01

Prognostics is much efficient to achieve zero-downtime performance, maximum productivity and proactive maintenance of machines. Prognostics intends to assess and predict the time evolution of machine health degradation so that machine failures can be predicted and prevented. A novel prognostics system is developed based on the data-model-fusion scheme using the Bayesian inference-based self-organizing map (SOM) and an integration of logistic regression (LR) and high-order particle filtering (HOPF). In this prognostics system, a baseline SOM is constructed to model the data distribution space of healthy machine under an assumption that predictable fault patterns are not available. Bayesian inference-based probability (BIP) derived from the baseline SOM is developed as a quantification indication of machine health degradation. BIP is capable of offering failure probability for the monitored machine, which has intuitionist explanation related to health degradation state. Based on those historic BIPs, the constructed LR and its modeling noise constitute a high-order Markov process (HOMP) to describe machine health propagation. HOPF is used to solve the HOMP estimation to predict the evolution of the machine health in the form of a probability density function (PDF). An on-line model update scheme is developed to adapt the Markov process changes to machine health dynamics quickly. The experimental results on a bearing test-bed illustrate the potential applications of the proposed system as an effective and simple tool for machine health prognostics.

Goal-directed decision making as probabilistic inference: A computational framework and potential neural correlates

PubMed Central

Solway, A.; Botvinick, M.

2013-01-01

Recent work has given rise to the view that reward-based decision making is governed by two key controllers: a habit system, which stores stimulus-response associations shaped by past reward, and a goal-oriented system that selects actions based on their anticipated outcomes. The current literature provides a rich body of computational theory addressing habit formation, centering on temporal-difference learning mechanisms. Less progress has been made toward formalizing the processes involved in goal-directed decision making. We draw on recent work in cognitive neuroscience, animal conditioning, cognitive and developmental psychology and machine learning, to outline a new theory of goal-directed decision making. Our basic proposal is that the brain, within an identifiable network of cortical and subcortical structures, implements a probabilistic generative model of reward, and that goal-directed decision making is effected through Bayesian inversion of this model. We present a set of simulations implementing the account, which address benchmark behavioral and neuroscientific findings, and which give rise to a set of testable predictions. We also discuss the relationship between the proposed framework and other models of decision making, including recent models of perceptual choice, to which our theory bears a direct connection. PMID:22229491

Bayesian Monitoring Systems for the CTBT: Historical Development and New Results

NASA Astrophysics Data System (ADS)

Russell, S.; Arora, N. S.; Moore, D.

2016-12-01

A project at Berkeley, begun in 2009 in collaboration with CTBTO andmore recently with LLNL, has reformulated the global seismicmonitoring problem in a Bayesian framework. A first-generation system,NETVISA, has been built comprising a spatial event prior andgenerative models of event transmission and detection, as well as aMonte Carlo inference algorithm. The probabilistic model allows forseamless integration of various disparate sources of information,including negative information (the absence of detections). Workingfrom arrivals extracted by traditional station processing fromInternational Monitoring System (IMS) data, NETVISA achieves areduction of around 60% in the number of missed events compared withthe currently deployed network processing system. It also finds manyevents that are missed by the human analysts who postprocess the IMSoutput. Recent improvements include the integration of models forinfrasound and hydroacoustic detections and a global depth model fornatural seismicity trained from ISC data. NETVISA is now fullycompatible with the CTBTO operating environment. A second-generation model called SIGVISA extends NETVISA's generativemodel all the way from events to raw signal data, avoiding theerror-prone bottom-up detection phase of station processing. SIGVISA'smodel automatically captures the phenomena underlying existingdetection and location techniques such as multilateration, waveformcorrelation matching, and double-differencing, and integrates theminto a global inference process that also (like NETVISA) handles denovo events. Initial results for the Western US in early 2008 (whenthe transportable US Array was operating) shows that SIGVISA finds,from IMS data only, more than twice the number of events recorded inthe CTBTO Late Event Bulletin (LEB). For mb 1.0-2.5, the ratio is more than10; put another way, for this data set, SIGVISA lowers the detectionthreshold by roughly one magnitude compared to LEB. The broader message of this work is that probabilistic inference basedon a vertically integrated generative model that directly expressesgeophysical knowledge can be a much more effective approach forinterpreting scientific data than the traditional bottom-up processingpipeline.

Source Detection with Bayesian Inference on ROSAT All-Sky Survey Data Sample

NASA Astrophysics Data System (ADS)

Guglielmetti, F.; Voges, W.; Fischer, R.; Boese, G.; Dose, V.

2004-07-01

We employ Bayesian inference for the joint estimation of sources and background on ROSAT All-Sky Survey (RASS) data. The probabilistic method allows for detection improvement of faint extended celestial sources compared to the Standard Analysis Software System (SASS). Background maps were estimated in a single step together with the detection of sources without pixel censoring. Consistent uncertainties of background and sources are provided. The source probability is evaluated for single pixels as well as for pixel domains to enhance source detection of weak and extended sources.

ENSURF: multi-model sea level forecast - implementation and validation results for the IBIROOS and Western Mediterranean regions

NASA Astrophysics Data System (ADS)

Pérez, B.; Brouwer, R.; Beckers, J.; Paradis, D.; Balseiro, C.; Lyons, K.; Cure, M.; Sotillo, M. G.; Hackett, B.; Verlaan, M.; Fanjul, E. A.

2012-03-01

ENSURF (Ensemble SURge Forecast) is a multi-model application for sea level forecast that makes use of several storm surge or circulation models and near-real time tide gauge data in the region, with the following main goals: 1. providing easy access to existing forecasts, as well as to its performance and model validation, by means of an adequate visualization tool; 2. generation of better forecasts of sea level, including confidence intervals, by means of the Bayesian Model Average technique (BMA). The Bayesian Model Average technique generates an overall forecast probability density function (PDF) by making a weighted average of the individual forecasts PDF's; the weights represent the Bayesian likelihood that a model will give the correct forecast and are continuously updated based on the performance of the models during a recent training period. This implies the technique needs the availability of sea level data from tide gauges in near-real time. The system was implemented for the European Atlantic facade (IBIROOS region) and Western Mediterranean coast based on the MATROOS visualization tool developed by Deltares. Results of validation of the different models and BMA implementation for the main harbours are presented for these regions where this kind of activity is performed for the first time. The system is currently operational at Puertos del Estado and has proved to be useful in the detection of calibration problems in some of the circulation models, in the identification of the systematic differences between baroclinic and barotropic models for sea level forecasts and to demonstrate the feasibility of providing an overall probabilistic forecast, based on the BMA method.

Modeling the effectiveness of oil combating from an ecological perspective--a Bayesian network for the Gulf of Finland; the Baltic Sea.

PubMed

Helle, Inari; Lecklin, Tiina; Jolma, Ari; Kuikka, Sakari

2011-01-15

Maritime traffic poses a major threat to marine ecosystems in the form of oil spills. The Gulf of Finland, the easternmost part of the Baltic Sea, has witnessed a rapid increase in oil transportation during the last 15 years. Should a spill occur, the negative ecological impacts may be reduced by oil combating, the effectiveness of which is, however, strongly dependent on prevailing environmental conditions and available technical resources. This poses increased uncertainty related to ecological consequences of future spills. We developed a probabilistic Bayesian network model that can be used to assess the effectiveness of different oil combating strategies in minimizing the negative effects of oil on six species living in the Gulf of Finland. The model can be used for creating different accident scenarios and assessing the performance of various oil combating actions under uncertainty, which enables its use as a supportive tool in decision-making. While the model is confined to the western Gulf of Finland, the methodology is adaptable to other marine areas facing similar risks and challenges related to oil spills. Copyright © 2010 Elsevier B.V. All rights reserved.

Semantic Likelihood Models for Bayesian Inference in Human-Robot Interaction

NASA Astrophysics Data System (ADS)

Sweet, Nicholas

Autonomous systems, particularly unmanned aerial systems (UAS), remain limited in au- tonomous capabilities largely due to a poor understanding of their environment. Current sensors simply do not match human perceptive capabilities, impeding progress towards full autonomy. Recent work has shown the value of humans as sources of information within a human-robot team; in target applications, communicating human-generated 'soft data' to autonomous systems enables higher levels of autonomy through large, efficient information gains. This requires development of a 'human sensor model' that allows soft data fusion through Bayesian inference to update the probabilistic belief representations maintained by autonomous systems. Current human sensor models that capture linguistic inputs as semantic information are limited in their ability to generalize likelihood functions for semantic statements: they may be learned from dense data; they do not exploit the contextual information embedded within groundings; and they often limit human input to restrictive and simplistic interfaces. This work provides mechanisms to synthesize human sensor models from constraints based on easily attainable a priori knowledge, develops compression techniques to capture information-dense semantics, and investigates the problem of capturing and fusing semantic information contained within unstructured natural language. A robotic experimental testbed is also developed to validate the above contributions.

Boosting Bayesian parameter inference of stochastic differential equation models with methods from statistical physics

NASA Astrophysics Data System (ADS)

Albert, Carlo; Ulzega, Simone; Stoop, Ruedi

2016-04-01

Measured time-series of both precipitation and runoff are known to exhibit highly non-trivial statistical properties. For making reliable probabilistic predictions in hydrology, it is therefore desirable to have stochastic models with output distributions that share these properties. When parameters of such models have to be inferred from data, we also need to quantify the associated parametric uncertainty. For non-trivial stochastic models, however, this latter step is typically very demanding, both conceptually and numerically, and always never done in hydrology. Here, we demonstrate that methods developed in statistical physics make a large class of stochastic differential equation (SDE) models amenable to a full-fledged Bayesian parameter inference. For concreteness we demonstrate these methods by means of a simple yet non-trivial toy SDE model. We consider a natural catchment that can be described by a linear reservoir, at the scale of observation. All the neglected processes are assumed to happen at much shorter time-scales and are therefore modeled with a Gaussian white noise term, the standard deviation of which is assumed to scale linearly with the system state (water volume in the catchment). Even for constant input, the outputs of this simple non-linear SDE model show a wealth of desirable statistical properties, such as fat-tailed distributions and long-range correlations. Standard algorithms for Bayesian inference fail, for models of this kind, because their likelihood functions are extremely high-dimensional intractable integrals over all possible model realizations. The use of Kalman filters is illegitimate due to the non-linearity of the model. Particle filters could be used but become increasingly inefficient with growing number of data points. Hamiltonian Monte Carlo algorithms allow us to translate this inference problem to the problem of simulating the dynamics of a statistical mechanics system and give us access to most sophisticated methods that have been developed in the statistical physics community over the last few decades. We demonstrate that such methods, along with automated differentiation algorithms, allow us to perform a full-fledged Bayesian inference, for a large class of SDE models, in a highly efficient and largely automatized manner. Furthermore, our algorithm is highly parallelizable. For our toy model, discretized with a few hundred points, a full Bayesian inference can be performed in a matter of seconds on a standard PC.

Bayesian parameter estimation for chiral effective field theory

NASA Astrophysics Data System (ADS)

Wesolowski, Sarah; Furnstahl, Richard; Phillips, Daniel; Klco, Natalie

2016-09-01

The low-energy constants (LECs) of a chiral effective field theory (EFT) interaction in the two-body sector are fit to observable data using a Bayesian parameter estimation framework. By using Bayesian prior probability distributions (pdfs), we quantify relevant physical expectations such as LEC naturalness and include them in the parameter estimation procedure. The final result is a posterior pdf for the LECs, which can be used to propagate uncertainty resulting from the fit to data to the final observable predictions. The posterior pdf also allows an empirical test of operator redundancy and other features of the potential. We compare results of our framework with other fitting procedures, interpreting the underlying assumptions in Bayesian probabilistic language. We also compare results from fitting all partial waves of the interaction simultaneously to cross section data compared to fitting to extracted phase shifts, appropriately accounting for correlations in the data. Supported in part by the NSF and DOE.

Robust Observation Detection for Single Object Tracking: Deterministic and Probabilistic Patch-Based Approaches

PubMed Central

Zulkifley, Mohd Asyraf; Rawlinson, David; Moran, Bill

2012-01-01

In video analytics, robust observation detection is very important as the content of the videos varies a lot, especially for tracking implementation. Contrary to the image processing field, the problems of blurring, moderate deformation, low illumination surroundings, illumination change and homogenous texture are normally encountered in video analytics. Patch-Based Observation Detection (PBOD) is developed to improve detection robustness to complex scenes by fusing both feature- and template-based recognition methods. While we believe that feature-based detectors are more distinctive, however, for finding the matching between the frames are best achieved by a collection of points as in template-based detectors. Two methods of PBOD—the deterministic and probabilistic approaches—have been tested to find the best mode of detection. Both algorithms start by building comparison vectors at each detected points of interest. The vectors are matched to build candidate patches based on their respective coordination. For the deterministic method, patch matching is done in 2-level test where threshold-based position and size smoothing are applied to the patch with the highest correlation value. For the second approach, patch matching is done probabilistically by modelling the histograms of the patches by Poisson distributions for both RGB and HSV colour models. Then, maximum likelihood is applied for position smoothing while a Bayesian approach is applied for size smoothing. The result showed that probabilistic PBOD outperforms the deterministic approach with average distance error of 10.03% compared with 21.03%. This algorithm is best implemented as a complement to other simpler detection methods due to heavy processing requirement. PMID:23202226

Multivariable and Bayesian Network Analysis of Outcome Predictors in Acute Aneurysmal Subarachnoid Hemorrhage: Review of a Pure Surgical Series in the Post-International Subarachnoid Aneurysm Trial Era.

PubMed

Zador, Zsolt; Huang, Wendy; Sperrin, Matthew; Lawton, Michael T

2018-06-01

Following the International Subarachnoid Aneurysm Trial (ISAT), evolving treatment modalities for acute aneurysmal subarachnoid hemorrhage (aSAH) has changed the case mix of patients undergoing urgent surgical clipping. To update our knowledge on outcome predictors by analyzing admission parameters in a pure surgical series using variable importance ranking and machine learning. We reviewed a single surgeon's case series of 226 patients suffering from aSAH treated with urgent surgical clipping. Predictions were made using logistic regression models, and predictive performance was assessed using areas under the receiver operating curve (AUC). We established variable importance ranking using partial Nagelkerke R2 scores. Probabilistic associations between variables were depicted using Bayesian networks, a method of machine learning. Importance ranking showed that World Federation of Neurosurgical Societies (WFNS) grade and age were the most influential outcome prognosticators. Inclusion of only these 2 predictors was sufficient to maintain model performance compared to when all variables were considered (AUC = 0.8222, 95% confidence interval (CI): 0.7646-0.88 vs 0.8218, 95% CI: 0.7616-0.8821, respectively, DeLong's P = .992). Bayesian networks showed that age and WFNS grade were associated with several variables such as laboratory results and cardiorespiratory parameters. Our study is the first to report early outcomes and formal predictor importance ranking following aSAH in a post-ISAT surgical case series. Models showed good predictive power with fewer relevant predictors than in similar size series. Bayesian networks proved to be a powerful tool in visualizing the widespread association of the 2 key predictors with admission variables, explaining their importance and demonstrating the potential for hypothesis generation.

Uncertainty analysis for effluent trading planning using a Bayesian estimation-based simulation-optimization modeling approach.

PubMed

Zhang, J L; Li, Y P; Huang, G H; Baetz, B W; Liu, J

2017-06-01

In this study, a Bayesian estimation-based simulation-optimization modeling approach (BESMA) is developed for identifying effluent trading strategies. BESMA incorporates nutrient fate modeling with soil and water assessment tool (SWAT), Bayesian estimation, and probabilistic-possibilistic interval programming with fuzzy random coefficients (PPI-FRC) within a general framework. Based on the water quality protocols provided by SWAT, posterior distributions of parameters can be analyzed through Bayesian estimation; stochastic characteristic of nutrient loading can be investigated which provides the inputs for the decision making. PPI-FRC can address multiple uncertainties in the form of intervals with fuzzy random boundaries and the associated system risk through incorporating the concept of possibility and necessity measures. The possibility and necessity measures are suitable for optimistic and pessimistic decision making, respectively. BESMA is applied to a real case of effluent trading planning in the Xiangxihe watershed, China. A number of decision alternatives can be obtained under different trading ratios and treatment rates. The results can not only facilitate identification of optimal effluent-trading schemes, but also gain insight into the effects of trading ratio and treatment rate on decision making. The results also reveal that decision maker's preference towards risk would affect decision alternatives on trading scheme as well as system benefit. Compared with the conventional optimization methods, it is proved that BESMA is advantageous in (i) dealing with multiple uncertainties associated with randomness and fuzziness in effluent-trading planning within a multi-source, multi-reach and multi-period context; (ii) reflecting uncertainties existing in nutrient transport behaviors to improve the accuracy in water quality prediction; and (iii) supporting pessimistic and optimistic decision making for effluent trading as well as promoting diversity of decision alternatives. Copyright © 2017 Elsevier Ltd. All rights reserved.

Applying a probabilistic seismic-petrophysical inversion and two different rock-physics models for reservoir characterization in offshore Nile Delta

NASA Astrophysics Data System (ADS)

Aleardi, Mattia

2018-01-01

We apply a two-step probabilistic seismic-petrophysical inversion for the characterization of a clastic, gas-saturated, reservoir located in offshore Nile Delta. In particular, we discuss and compare the results obtained when two different rock-physics models (RPMs) are employed in the inversion. The first RPM is an empirical, linear model directly derived from the available well log data by means of an optimization procedure. The second RPM is a theoretical, non-linear model based on the Hertz-Mindlin contact theory. The first step of the inversion procedure is a Bayesian linearized amplitude versus angle (AVA) inversion in which the elastic properties, and the associated uncertainties, are inferred from pre-stack seismic data. The estimated elastic properties constitute the input to the second step that is a probabilistic petrophysical inversion in which we account for the noise contaminating the recorded seismic data and the uncertainties affecting both the derived rock-physics models and the estimated elastic parameters. In particular, a Gaussian mixture a-priori distribution is used to properly take into account the facies-dependent behavior of petrophysical properties, related to the different fluid and rock properties of the different litho-fluid classes. In the synthetic and in the field data tests, the very minor differences between the results obtained by employing the two RPMs, and the good match between the estimated properties and well log information, confirm the applicability of the inversion approach and the suitability of the two different RPMs for reservoir characterization in the investigated area.

Bayesian network learning for natural hazard assessments

NASA Astrophysics Data System (ADS)

Vogel, Kristin

2016-04-01

Even though quite different in occurrence and consequences, from a modelling perspective many natural hazards share similar properties and challenges. Their complex nature as well as lacking knowledge about their driving forces and potential effects make their analysis demanding. On top of the uncertainty about the modelling framework, inaccurate or incomplete event observations and the intrinsic randomness of the natural phenomenon add up to different interacting layers of uncertainty, which require a careful handling. Thus, for reliable natural hazard assessments it is crucial not only to capture and quantify involved uncertainties, but also to express and communicate uncertainties in an intuitive way. Decision-makers, who often find it difficult to deal with uncertainties, might otherwise return to familiar (mostly deterministic) proceedings. In the scope of the DFG research training group „NatRiskChange" we apply the probabilistic framework of Bayesian networks for diverse natural hazard and vulnerability studies. The great potential of Bayesian networks was already shown in previous natural hazard assessments. Treating each model component as random variable, Bayesian networks aim at capturing the joint distribution of all considered variables. Hence, each conditional distribution of interest (e.g. the effect of precautionary measures on damage reduction) can be inferred. The (in-)dependencies between the considered variables can be learned purely data driven or be given by experts. Even a combination of both is possible. By translating the (in-)dependences into a graph structure, Bayesian networks provide direct insights into the workings of the system and allow to learn about the underlying processes. Besides numerous studies on the topic, learning Bayesian networks from real-world data remains challenging. In previous studies, e.g. on earthquake induced ground motion and flood damage assessments, we tackled the problems arising with continuous variables and incomplete observations. Further studies rise the challenge of relying on very small data sets. Since parameter estimates for complex models based on few observations are unreliable, it is necessary to focus on simplified, yet still meaningful models. A so called Markov Blanket approach is developed to identify the most relevant model components and to construct a simple Bayesian network based on those findings. Since the proceeding is completely data driven, it can easily be transferred to various applications in natural hazard domains. This study is funded by the Deutsche Forschungsgemeinschaft (DFG) within the research training programme GRK 2043/1 "NatRiskChange - Natural hazards and risks in a changing world" at Potsdam University.

Multi-Detection Events, Probability Density Functions, and Reduced Location Area

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eslinger, Paul W.; Schrom, Brian T.

2016-03-01

Abstract Several efforts have been made in the Comprehensive Nuclear-Test-Ban Treaty (CTBT) community to assess the benefits of combining detections of radionuclides to improve the location estimates available from atmospheric transport modeling (ATM) backtrack calculations. We present a Bayesian estimation approach rather than a simple dilution field of regard approach to allow xenon detections and non-detections to be combined mathematically. This system represents one possible probabilistic approach to radionuclide event formation. Application of this method to a recent interesting radionuclide event shows a substantial reduction in the location uncertainty of that event.

Scientific thinking in young children: theoretical advances, empirical research, and policy implications.

PubMed

Gopnik, Alison

2012-09-28

New theoretical ideas and empirical research show that very young children's learning and thinking are strikingly similar to much learning and thinking in science. Preschoolers test hypotheses against data and make causal inferences; they learn from statistics and informal experimentation, and from watching and listening to others. The mathematical framework of probabilistic models and Bayesian inference can describe this learning in precise ways. These discoveries have implications for early childhood education and policy. In particular, they suggest both that early childhood experience is extremely important and that the trend toward more structured and academic early childhood programs is misguided.

Probabilistic delay differential equation modeling of event-related potentials.

PubMed

Ostwald, Dirk; Starke, Ludger

2016-08-01

"Dynamic causal models" (DCMs) are a promising approach in the analysis of functional neuroimaging data due to their biophysical interpretability and their consolidation of functional-segregative and functional-integrative propositions. In this theoretical note we are concerned with the DCM framework for electroencephalographically recorded event-related potentials (ERP-DCM). Intuitively, ERP-DCM combines deterministic dynamical neural mass models with dipole-based EEG forward models to describe the event-related scalp potential time-series over the entire electrode space. Since its inception, ERP-DCM has been successfully employed to capture the neural underpinnings of a wide range of neurocognitive phenomena. However, in spite of its empirical popularity, the technical literature on ERP-DCM remains somewhat patchy. A number of previous communications have detailed certain aspects of the approach, but no unified and coherent documentation exists. With this technical note, we aim to close this gap and to increase the technical accessibility of ERP-DCM. Specifically, this note makes the following novel contributions: firstly, we provide a unified and coherent review of the mathematical machinery of the latent and forward models constituting ERP-DCM by formulating the approach as a probabilistic latent delay differential equation model. Secondly, we emphasize the probabilistic nature of the model and its variational Bayesian inversion scheme by explicitly deriving the variational free energy function in terms of both the likelihood expectation and variance parameters. Thirdly, we detail and validate the estimation of the model with a special focus on the explicit form of the variational free energy function and introduce a conventional nonlinear optimization scheme for its maximization. Finally, we identify and discuss a number of computational issues which may be addressed in the future development of the approach. Copyright © 2016 Elsevier Inc. All rights reserved.

Optimal decision-making in mammals: insights from a robot study of rodent texture discrimination

PubMed Central

Lepora, Nathan F.; Fox, Charles W.; Evans, Mathew H.; Diamond, Mathew E.; Gurney, Kevin; Prescott, Tony J.

2012-01-01

Texture perception is studied here in a physical model of the rat whisker system consisting of a robot equipped with a biomimetic vibrissal sensor. Investigations of whisker motion in rodents have led to several explanations for texture discrimination, such as resonance or stick-slips. Meanwhile, electrophysiological studies of decision-making in monkeys have suggested a neural mechanism of evidence accumulation to threshold for competing percepts, described by a probabilistic model of Bayesian sequential analysis. For our robot whisker data, we find that variable reaction-time decision-making with sequential analysis performs better than the fixed response-time maximum-likelihood estimation. These probabilistic classifiers also use whatever available features of the whisker signals aid the discrimination, giving improved performance over a single-feature strategy, such as matching the peak power spectra of whisker vibrations. These results cast new light on how the various proposals for texture discrimination in rodents depend on the whisker contact mechanics and suggest the possibility of a common account of decision-making across mammalian species. PMID:22279155

Predicting uncertainty in future marine ice sheet volume using Bayesian statistical methods

NASA Astrophysics Data System (ADS)

Davis, A. D.

2015-12-01

The marine ice instability can trigger rapid retreat of marine ice streams. Recent observations suggest that marine ice systems in West Antarctica have begun retreating. However, unknown ice dynamics, computationally intensive mathematical models, and uncertain parameters in these models make predicting retreat rate and ice volume difficult. In this work, we fuse current observational data with ice stream/shelf models to develop probabilistic predictions of future grounded ice sheet volume. Given observational data (e.g., thickness, surface elevation, and velocity) and a forward model that relates uncertain parameters (e.g., basal friction and basal topography) to these observations, we use a Bayesian framework to define a posterior distribution over the parameters. A stochastic predictive model then propagates uncertainties in these parameters to uncertainty in a particular quantity of interest (QoI)---here, the volume of grounded ice at a specified future time. While the Bayesian approach can in principle characterize the posterior predictive distribution of the QoI, the computational cost of both the forward and predictive models makes this effort prohibitively expensive. To tackle this challenge, we introduce a new Markov chain Monte Carlo method that constructs convergent approximations of the QoI target density in an online fashion, yielding accurate characterizations of future ice sheet volume at significantly reduced computational cost.Our second goal is to attribute uncertainty in these Bayesian predictions to uncertainties in particular parameters. Doing so can help target data collection, for the purpose of constraining the parameters that contribute most strongly to uncertainty in the future volume of grounded ice. For instance, smaller uncertainties in parameters to which the QoI is highly sensitive may account for more variability in the prediction than larger uncertainties in parameters to which the QoI is less sensitive. We use global sensitivity analysis to help answer this question, and make the computation of sensitivity indices computationally tractable using a combination of polynomial chaos and Monte Carlo techniques.

Asking Better Questions: How Presentation Formats Influence Information Search

ERIC Educational Resources Information Center

Wu, Charley M.; Meder, Björn; Filimon, Flavia; Nelson, Jonathan D.

2017-01-01

While the influence of presentation formats have been widely studied in Bayesian reasoning tasks, we present the first systematic investigation of how presentation formats influence information search decisions. Four experiments were conducted across different probabilistic environments, where subjects (N = 2,858) chose between 2 possible search…

Merging information from multi-model flood projections in a hierarchical Bayesian framework

NASA Astrophysics Data System (ADS)

Le Vine, Nataliya

2016-04-01

Multi-model ensembles are becoming widely accepted for flood frequency change analysis. The use of multiple models results in large uncertainty around estimates of flood magnitudes, due to both uncertainty in model selection and natural variability of river flow. The challenge is therefore to extract the most meaningful signal from the multi-model predictions, accounting for both model quality and uncertainties in individual model estimates. The study demonstrates the potential of a recently proposed hierarchical Bayesian approach to combine information from multiple models. The approach facilitates explicit treatment of shared multi-model discrepancy as well as the probabilistic nature of the flood estimates, by treating the available models as a sample from a hypothetical complete (but unobserved) set of models. The advantages of the approach are: 1) to insure an adequate 'baseline' conditions with which to compare future changes; 2) to reduce flood estimate uncertainty; 3) to maximize use of statistical information in circumstances where multiple weak predictions individually lack power, but collectively provide meaningful information; 4) to adjust multi-model consistency criteria when model biases are large; and 5) to explicitly consider the influence of the (model performance) stationarity assumption. Moreover, the analysis indicates that reducing shared model discrepancy is the key to further reduction of uncertainty in the flood frequency analysis. The findings are of value regarding how conclusions about changing exposure to flooding are drawn, and to flood frequency change attribution studies.

Towards Breaking the Histone Code – Bayesian Graphical Models for Histone Modifications

PubMed Central

Mitra, Riten; Müller, Peter; Liang, Shoudan; Xu, Yanxun; Ji, Yuan

2013-01-01

Background Histones are proteins that wrap DNA around in small spherical structures called nucleosomes. Histone modifications (HMs) refer to the post-translational modifications to the histone tails. At a particular genomic locus, each of these HMs can either be present or absent, and the combinatory patterns of the presence or absence of multiple HMs, or the ‘histone codes,’ are believed to co-regulate important biological processes. We aim to use raw data on HM markers at different genomic loci to (1) decode the complex biological network of HMs in a single region and (2) demonstrate how the HM networks differ in different regulatory regions. We suggest that these differences in network attributes form a significant link between histones and genomic functions. Methods and Results We develop a powerful graphical model under Bayesian paradigm. Posterior inference is fully probabilistic, allowing us to compute the probabilities of distinct dependence patterns of the HMs using graphs. Furthermore, our model-based framework allows for easy but important extensions for inference on differential networks under various conditions, such as the different annotations of the genomic locations (e.g., promoters versus insulators). We applied these models to ChIP-Seq data based on CD4+ T lymphocytes. The results confirmed many existing findings and provided a unified tool to generate various promising hypotheses. Differential network analyses revealed new insights on co-regulation of HMs of transcriptional activities in different genomic regions. Conclusions The use of Bayesian graphical models and borrowing strength across different conditions provide high power to infer histone networks and their differences. PMID:23748248

Quantum Graphical Models and Belief Propagation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leifer, M.S.; Perimeter Institute for Theoretical Physics, 31 Caroline Street North, Waterloo Ont., N2L 2Y5; Poulin, D.

Belief Propagation algorithms acting on Graphical Models of classical probability distributions, such as Markov Networks, Factor Graphs and Bayesian Networks, are amongst the most powerful known methods for deriving probabilistic inferences amongst large numbers of random variables. This paper presents a generalization of these concepts and methods to the quantum case, based on the idea that quantum theory can be thought of as a noncommutative, operator-valued, generalization of classical probability theory. Some novel characterizations of quantum conditional independence are derived, and definitions of Quantum n-Bifactor Networks, Markov Networks, Factor Graphs and Bayesian Networks are proposed. The structure of Quantum Markovmore » Networks is investigated and some partial characterization results are obtained, along the lines of the Hammersley-Clifford theorem. A Quantum Belief Propagation algorithm is presented and is shown to converge on 1-Bifactor Networks and Markov Networks when the underlying graph is a tree. The use of Quantum Belief Propagation as a heuristic algorithm in cases where it is not known to converge is discussed. Applications to decoding quantum error correcting codes and to the simulation of many-body quantum systems are described.« less

Explicitly integrating parameter, input, and structure uncertainties into Bayesian Neural Networks for probabilistic hydrologic forecasting

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Xuesong; Liang, Faming; Yu, Beibei

2011-11-09

Estimating uncertainty of hydrologic forecasting is valuable to water resources and other relevant decision making processes. Recently, Bayesian Neural Networks (BNNs) have been proved powerful tools for quantifying uncertainty of streamflow forecasting. In this study, we propose a Markov Chain Monte Carlo (MCMC) framework to incorporate the uncertainties associated with input, model structure, and parameter into BNNs. This framework allows the structure of the neural networks to change by removing or adding connections between neurons and enables scaling of input data by using rainfall multipliers. The results show that the new BNNs outperform the BNNs that only consider uncertainties associatedmore » with parameter and model structure. Critical evaluation of posterior distribution of neural network weights, number of effective connections, rainfall multipliers, and hyper-parameters show that the assumptions held in our BNNs are not well supported. Further understanding of characteristics of different uncertainty sources and including output error into the MCMC framework are expected to enhance the application of neural networks for uncertainty analysis of hydrologic forecasting.« less

Collaborative autonomous sensing with Bayesians in the loop

NASA Astrophysics Data System (ADS)

Ahmed, Nisar

2016-10-01

There is a strong push to develop intelligent unmanned autonomy that complements human reasoning for applications as diverse as wilderness search and rescue, military surveillance, and robotic space exploration. More than just replacing humans for `dull, dirty and dangerous' work, autonomous agents are expected to cope with a whole host of uncertainties while working closely together with humans in new situations. The robotics revolution firmly established the primacy of Bayesian algorithms for tackling challenging perception, learning and decision-making problems. Since the next frontier of autonomy demands the ability to gather information across stretches of time and space that are beyond the reach of a single autonomous agent, the next generation of Bayesian algorithms must capitalize on opportunities to draw upon the sensing and perception abilities of humans-in/on-the-loop. This work summarizes our recent research toward harnessing `human sensors' for information gathering tasks. The basic idea behind is to allow human end users (i.e. non-experts in robotics, statistics, machine learning, etc.) to directly `talk to' the information fusion engine and perceptual processes aboard any autonomous agent. Our approach is grounded in rigorous Bayesian modeling and fusion of flexible semantic information derived from user-friendly interfaces, such as natural language chat and locative hand-drawn sketches. This naturally enables `plug and play' human sensing with existing probabilistic algorithms for planning and perception, and has been successfully demonstrated with human-robot teams in target localization applications.

Attention in a Bayesian Framework

PubMed Central

Whiteley, Louise; Sahani, Maneesh

2012-01-01

The behavioral phenomena of sensory attention are thought to reflect the allocation of a limited processing resource, but there is little consensus on the nature of the resource or why it should be limited. Here we argue that a fundamental bottleneck emerges naturally within Bayesian models of perception, and use this observation to frame a new computational account of the need for, and action of, attention – unifying diverse attentional phenomena in a way that goes beyond previous inferential, probabilistic and Bayesian models. Attentional effects are most evident in cluttered environments, and include both selective phenomena, where attention is invoked by cues that point to particular stimuli, and integrative phenomena, where attention is invoked dynamically by endogenous processing. However, most previous Bayesian accounts of attention have focused on describing relatively simple experimental settings, where cues shape expectations about a small number of upcoming stimuli and thus convey “prior” information about clearly defined objects. While operationally consistent with the experiments it seeks to describe, this view of attention as prior seems to miss many essential elements of both its selective and integrative roles, and thus cannot be easily extended to complex environments. We suggest that the resource bottleneck stems from the computational intractability of exact perceptual inference in complex settings, and that attention reflects an evolved mechanism for approximate inference which can be shaped to refine the local accuracy of perception. We show that this approach extends the simple picture of attention as prior, so as to provide a unified and computationally driven account of both selective and integrative attentional phenomena. PMID:22712010

Visual shape perception as Bayesian inference of 3D object-centered shape representations.

PubMed

Erdogan, Goker; Jacobs, Robert A

2017-11-01

Despite decades of research, little is known about how people visually perceive object shape. We hypothesize that a promising approach to shape perception is provided by a "visual perception as Bayesian inference" framework which augments an emphasis on visual representation with an emphasis on the idea that shape perception is a form of statistical inference. Our hypothesis claims that shape perception of unfamiliar objects can be characterized as statistical inference of 3D shape in an object-centered coordinate system. We describe a computational model based on our theoretical framework, and provide evidence for the model along two lines. First, we show that, counterintuitively, the model accounts for viewpoint-dependency of object recognition, traditionally regarded as evidence against people's use of 3D object-centered shape representations. Second, we report the results of an experiment using a shape similarity task, and present an extensive evaluation of existing models' abilities to account for the experimental data. We find that our shape inference model captures subjects' behaviors better than competing models. Taken as a whole, our experimental and computational results illustrate the promise of our approach and suggest that people's shape representations of unfamiliar objects are probabilistic, 3D, and object-centered. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Structured statistical models of inductive reasoning.

PubMed

Kemp, Charles; Tenenbaum, Joshua B

2009-01-01

Everyday inductive inferences are often guided by rich background knowledge. Formal models of induction should aim to incorporate this knowledge and should explain how different kinds of knowledge lead to the distinctive patterns of reasoning found in different inductive contexts. This article presents a Bayesian framework that attempts to meet both goals and describes [corrected] 4 applications of the framework: a taxonomic model, a spatial model, a threshold model, and a causal model. Each model makes probabilistic inferences about the extensions of novel properties, but the priors for the 4 models are defined over different kinds of structures that capture different relationships between the categories in a domain. The framework therefore shows how statistical inference can operate over structured background knowledge, and the authors argue that this interaction between structure and statistics is critical for explaining the power and flexibility of human reasoning.

Generalized multiple kernel learning with data-dependent priors.

PubMed

Mao, Qi; Tsang, Ivor W; Gao, Shenghua; Wang, Li

2015-06-01

Multiple kernel learning (MKL) and classifier ensemble are two mainstream methods for solving learning problems in which some sets of features/views are more informative than others, or the features/views within a given set are inconsistent. In this paper, we first present a novel probabilistic interpretation of MKL such that maximum entropy discrimination with a noninformative prior over multiple views is equivalent to the formulation of MKL. Instead of using the noninformative prior, we introduce a novel data-dependent prior based on an ensemble of kernel predictors, which enhances the prediction performance of MKL by leveraging the merits of the classifier ensemble. With the proposed probabilistic framework of MKL, we propose a hierarchical Bayesian model to learn the proposed data-dependent prior and classification model simultaneously. The resultant problem is convex and other information (e.g., instances with either missing views or missing labels) can be seamlessly incorporated into the data-dependent priors. Furthermore, a variety of existing MKL models can be recovered under the proposed MKL framework and can be readily extended to incorporate these priors. Extensive experiments demonstrate the benefits of our proposed framework in supervised and semisupervised settings, as well as in tasks with partial correspondence among multiple views.

Bayesian CP Factorization of Incomplete Tensors with Automatic Rank Determination.

PubMed

Zhao, Qibin; Zhang, Liqing; Cichocki, Andrzej

2015-09-01

CANDECOMP/PARAFAC (CP) tensor factorization of incomplete data is a powerful technique for tensor completion through explicitly capturing the multilinear latent factors. The existing CP algorithms require the tensor rank to be manually specified, however, the determination of tensor rank remains a challenging problem especially for CP rank . In addition, existing approaches do not take into account uncertainty information of latent factors, as well as missing entries. To address these issues, we formulate CP factorization using a hierarchical probabilistic model and employ a fully Bayesian treatment by incorporating a sparsity-inducing prior over multiple latent factors and the appropriate hyperpriors over all hyperparameters, resulting in automatic rank determination. To learn the model, we develop an efficient deterministic Bayesian inference algorithm, which scales linearly with data size. Our method is characterized as a tuning parameter-free approach, which can effectively infer underlying multilinear factors with a low-rank constraint, while also providing predictive distributions over missing entries. Extensive simulations on synthetic data illustrate the intrinsic capability of our method to recover the ground-truth of CP rank and prevent the overfitting problem, even when a large amount of entries are missing. Moreover, the results from real-world applications, including image inpainting and facial image synthesis, demonstrate that our method outperforms state-of-the-art approaches for both tensor factorization and tensor completion in terms of predictive performance.

Scheduling structural health monitoring activities for optimizing life-cycle costs and reliability of wind turbines

NASA Astrophysics Data System (ADS)

Hanish Nithin, Anu; Omenzetter, Piotr

2017-04-01

Optimization of the life-cycle costs and reliability of offshore wind turbines (OWTs) is an area of immense interest due to the widespread increase in wind power generation across the world. Most of the existing studies have used structural reliability and the Bayesian pre-posterior analysis for optimization. This paper proposes an extension to the previous approaches in a framework for probabilistic optimization of the total life-cycle costs and reliability of OWTs by combining the elements of structural reliability/risk analysis (SRA), the Bayesian pre-posterior analysis with optimization through a genetic algorithm (GA). The SRA techniques are adopted to compute the probabilities of damage occurrence and failure associated with the deterioration model. The probabilities are used in the decision tree and are updated using the Bayesian analysis. The output of this framework would determine the optimal structural health monitoring and maintenance schedules to be implemented during the life span of OWTs while maintaining a trade-off between the life-cycle costs and risk of the structural failure. Numerical illustrations with a generic deterioration model for one monitoring exercise in the life cycle of a system are demonstrated. Two case scenarios, namely to build initially an expensive and robust or a cheaper but more quickly deteriorating structures and to adopt expensive monitoring system, are presented to aid in the decision-making process.

Using Bayes Model Averaging for Wind Power Forecasts

NASA Astrophysics Data System (ADS)

Preede Revheim, Pål; Beyer, Hans Georg

2014-05-01

For operational purposes predictions of the forecasts of the lumped output of groups of wind farms spread over larger geographic areas will often be of interest. A naive approach is to make forecasts for each individual site and sum them up to get the group forecast. It is however well documented that a better choice is to use a model that also takes advantage of spatial smoothing effects. It might however be the case that some sites tends to more accurately reflect the total output of the region, either in general or for certain wind directions. It will then be of interest giving these a greater influence over the group forecast. Bayesian model averaging (BMA) is a statistical post-processing method for producing probabilistic forecasts from ensembles. Raftery et al. [1] show how BMA can be used for statistical post processing of forecast ensembles, producing PDFs of future weather quantities. The BMA predictive PDF of a future weather quantity is a weighted average of the ensemble members' PDFs, where the weights can be interpreted as posterior probabilities and reflect the ensemble members' contribution to overall forecasting skill over a training period. In Revheim and Beyer [2] the BMA procedure used in Sloughter, Gneiting and Raftery [3] were found to produce fairly accurate PDFs for the future mean wind speed of a group of sites from the single sites wind speeds. However, when the procedure was attempted applied to wind power it resulted in either problems with the estimation of the parameters (mainly caused by longer consecutive periods of no power production) or severe underestimation (mainly caused by problems with reflecting the power curve). In this paper the problems that arose when applying BMA to wind power forecasting is met through two strategies. First, the BMA procedure is run with a combination of single site wind speeds and single site wind power production as input. This solves the problem with longer consecutive periods where the input data does not contain information, but it has the disadvantage of nearly doubling the number of model parameters to be estimated. Second, the BMA procedure is run with group mean wind power as the response variable instead of group mean wind speed. This also solves the problem with longer consecutive periods without information in the input data, but it leaves the power curve to also be estimated from the data. [1] Raftery, A. E., et al. (2005). Using Bayesian Model Averaging to Calibrate Forecast Ensembles. Monthly Weather Review, 133, 1155-1174. [2]Revheim, P. P. and H. G. Beyer (2013). Using Bayesian Model Averaging for wind farm group forecasts. EWEA Wind Power Forecasting Technology Workshop,Rotterdam, 4-5 December 2013. [3]Sloughter, J. M., T. Gneiting and A. E. Raftery (2010). Probabilistic Wind Speed Forecasting Using Ensembles and Bayesian Model Averaging. Journal of the American Statistical Association, Vol. 105, No. 489, 25-35

A Bayesian analysis of the 2016 Pedernales (Ecuador) earthquake rupture process

NASA Astrophysics Data System (ADS)

Gombert, B.; Duputel, Z.; Jolivet, R.; Rivera, L. A.; Simons, M.; Jiang, J.; Liang, C.; Fielding, E. J.

2017-12-01

The 2016 Mw = 7.8 Pedernales earthquake is the largest event to strike Ecuador since 1979. Long period W-phase and Global CMT solutions suggest that slip is not perpendicular to the trench axis, in agreement with the convergence obliquity of the Ecuadorian subduction. In this study, we propose a new co-seismic kinematic slip model obtained from the joint inversion of multiple observations in an unregularized and fully Bayesian framework. We use a comprehensive static dataset composed of several InSAR scenes, GPS static offsets, and tsunami waveforms from two nearby DART stations. The kinematic component of the rupture process is constrained by an extensive network of High-Rate GPS and accelerometers. Our solution includes the ensemble of all plausible models that are consistent with our prior information and fit the available observations within data and prediction uncertainties. We analyse the source process in light of the historical seismicity, in particular the Mw = 7.8 1942 earthquake for which the rupture extent overlaps with the 2016 event. In addition, we conduct a probabilistic comparison of co-seismic slip with a stochastic interseismic coupling model obtained from GPS data, putting a light on the processes at play within the Ecuadorian subduction margin.

Intelligent Hardware-Enabled Sensor and Software Safety and Health Management for Autonomous UAS

NASA Technical Reports Server (NTRS)

Rozier, Kristin Y.; Schumann, Johann; Ippolito, Corey

2015-01-01

Unmanned Aerial Systems (UAS) can only be deployed if they can effectively complete their mission and respond to failures and uncertain environmental conditions while maintaining safety with respect to other aircraft as well as humans and property on the ground. We propose to design a real-time, onboard system health management (SHM) capability to continuously monitor essential system components such as sensors, software, and hardware systems for detection and diagnosis of failures and violations of safety or performance rules during the ight of a UAS. Our approach to SHM is three-pronged, providing: (1) real-time monitoring of sensor and software signals; (2) signal analysis, preprocessing, and advanced on-the- y temporal and Bayesian probabilistic fault diagnosis; (3) an unobtrusive, lightweight, read-only, low-power hardware realization using Field Programmable Gate Arrays (FPGAs) in order to avoid overburdening limited computing resources or costly re-certi cation of ight software due to instrumentation. No currently available SHM capabilities (or combinations of currently existing SHM capabilities) come anywhere close to satisfying these three criteria yet NASA will require such intelligent, hardwareenabled sensor and software safety and health management for introducing autonomous UAS into the National Airspace System (NAS). We propose a novel approach of creating modular building blocks for combining responsive runtime monitoring of temporal logic system safety requirements with model-based diagnosis and Bayesian network-based probabilistic analysis. Our proposed research program includes both developing this novel approach and demonstrating its capabilities using the NASA Swift UAS as a demonstration platform.

A new Bayesian Event Tree tool to track and quantify volcanic unrest and its application to Kawah Ijen volcano

NASA Astrophysics Data System (ADS)

Tonini, Roberto; Sandri, Laura; Rouwet, Dmitri; Caudron, Corentin; Marzocchi, Warner; Suparjan

2016-07-01

Although most of volcanic hazard studies focus on magmatic eruptions, volcanic hazardous events can also occur when no migration of magma can be recognized. Examples are tectonic and hydrothermal unrest that may lead to phreatic eruptions. Recent events (e.g., Ontake eruption on September 2014) have demonstrated that phreatic eruptions are still hard to forecast, despite being potentially very hazardous. For these reasons, it is of paramount importance to identify indicators that define the condition of nonmagmatic unrest, in particular for hydrothermal systems. Often, this type of unrest is driven by movement of fluids, requiring alternative monitoring setups, beyond the classical seismic-geodetic-geochemical architectures. Here we present a new version of the probabilistic BET (Bayesian Event Tree) model, specifically developed to include the forecasting of nonmagmatic unrest and related hazards. The structure of the new event tree differs from the previous schemes by adding a specific branch to detail nonmagmatic unrest outcomes. A further goal of this work consists in providing a user-friendly, open-access, and straightforward tool to handle the probabilistic forecast and visualize the results as possible support during a volcanic crisis. The new event tree and tool are here applied to Kawah Ijen stratovolcano, Indonesia, as exemplificative application. In particular, the tool is set on the basis of monitoring data for the learning period 2000-2010, and is then blindly applied to the test period 2010-2012, during which significant unrest phases occurred.

Dynamic Bayesian Network Modeling of the Interplay between EGFR and Hedgehog Signaling.

PubMed

Fröhlich, Holger; Bahamondez, Gloria; Götschel, Frank; Korf, Ulrike

2015-01-01

Aberrant activation of sonic Hegdehog (SHH) signaling has been found to disrupt cellular differentiation in many human cancers and to increase proliferation. The SHH pathway is known to cross-talk with EGFR dependent signaling. Recent studies experimentally addressed this interplay in Daoy cells, which are presumable a model system for medulloblastoma, a highly malignant brain tumor that predominately occurs in children. Currently ongoing are several clinical trials for different solid cancers, which are designed to validate the clinical benefits of targeting the SHH in combination with other pathways. This has motivated us to investigate interactions between EGFR and SHH dependent signaling in greater depth. To our knowledge, there is no mathematical model describing the interplay between EGFR and SHH dependent signaling in medulloblastoma so far. Here we come up with a fully probabilistic approach using Dynamic Bayesian Networks (DBNs). To build our model, we made use of literature based knowledge describing SHH and EGFR signaling and integrated gene expression (Illumina) and cellular location dependent time series protein expression data (Reverse Phase Protein Arrays). We validated our model by sub-sampling training data and making Bayesian predictions on the left out test data. Our predictions focusing on key transcription factors and p70S6K, showed a high level of concordance with experimental data. Furthermore, the stability of our model was tested by a parametric bootstrap approach. Stable network features were in agreement with published data. Altogether we believe that our model improved our understanding of the interplay between two highly oncogenic signaling pathways in Daoy cells. This may open new perspectives for the future therapy of Hedghog/EGF-dependent solid tumors.

Merging Digital Surface Models Implementing Bayesian Approaches

NASA Astrophysics Data System (ADS)

Sadeq, H.; Drummond, J.; Li, Z.

2016-06-01

In this research different DSMs from different sources have been merged. The merging is based on a probabilistic model using a Bayesian Approach. The implemented data have been sourced from very high resolution satellite imagery sensors (e.g. WorldView-1 and Pleiades). It is deemed preferable to use a Bayesian Approach when the data obtained from the sensors are limited and it is difficult to obtain many measurements or it would be very costly, thus the problem of the lack of data can be solved by introducing a priori estimations of data. To infer the prior data, it is assumed that the roofs of the buildings are specified as smooth, and for that purpose local entropy has been implemented. In addition to the a priori estimations, GNSS RTK measurements have been collected in the field which are used as check points to assess the quality of the DSMs and to validate the merging result. The model has been applied in the West-End of Glasgow containing different kinds of buildings, such as flat roofed and hipped roofed buildings. Both quantitative and qualitative methods have been employed to validate the merged DSM. The validation results have shown that the model was successfully able to improve the quality of the DSMs and improving some characteristics such as the roof surfaces, which consequently led to better representations. In addition to that, the developed model has been compared with the well established Maximum Likelihood model and showed similar quantitative statistical results and better qualitative results. Although the proposed model has been applied on DSMs that were derived from satellite imagery, it can be applied to any other sourced DSMs.

Selection of polynomial chaos bases via Bayesian model uncertainty methods with applications to sparse approximation of PDEs with stochastic inputs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karagiannis, Georgios, E-mail: georgios.karagiannis@pnnl.gov; Lin, Guang, E-mail: guang.lin@pnnl.gov

2014-02-15

Generalized polynomial chaos (gPC) expansions allow us to represent the solution of a stochastic system using a series of polynomial chaos basis functions. The number of gPC terms increases dramatically as the dimension of the random input variables increases. When the number of the gPC terms is larger than that of the available samples, a scenario that often occurs when the corresponding deterministic solver is computationally expensive, evaluation of the gPC expansion can be inaccurate due to over-fitting. We propose a fully Bayesian approach that allows for global recovery of the stochastic solutions, in both spatial and random domains, bymore » coupling Bayesian model uncertainty and regularization regression methods. It allows the evaluation of the PC coefficients on a grid of spatial points, via (1) the Bayesian model average (BMA) or (2) the median probability model, and their construction as spatial functions on the spatial domain via spline interpolation. The former accounts for the model uncertainty and provides Bayes-optimal predictions; while the latter provides a sparse representation of the stochastic solutions by evaluating the expansion on a subset of dominating gPC bases. Moreover, the proposed methods quantify the importance of the gPC bases in the probabilistic sense through inclusion probabilities. We design a Markov chain Monte Carlo (MCMC) sampler that evaluates all the unknown quantities without the need of ad-hoc techniques. The proposed methods are suitable for, but not restricted to, problems whose stochastic solutions are sparse in the stochastic space with respect to the gPC bases while the deterministic solver involved is expensive. We demonstrate the accuracy and performance of the proposed methods and make comparisons with other approaches on solving elliptic SPDEs with 1-, 14- and 40-random dimensions.« less

Improved representation of situational awareness within a dismounted small combat unit constructive simulation

NASA Astrophysics Data System (ADS)

Lee, K. David; Colony, Mike

2011-06-01

Modeling and simulation has been established as a cost-effective means of supporting the development of requirements, exploring doctrinal alternatives, assessing system performance, and performing design trade-off analysis. The Army's constructive simulation for the evaluation of equipment effectiveness in small combat unit operations is currently limited to representation of situation awareness without inclusion of the many uncertainties associated with real world combat environments. The goal of this research is to provide an ability to model situation awareness and decision process uncertainties in order to improve evaluation of the impact of battlefield equipment on ground soldier and small combat unit decision processes. Our Army Probabilistic Inference and Decision Engine (Army-PRIDE) system provides this required uncertainty modeling through the application of two critical techniques that allow Bayesian network technology to be applied to real-time applications. (Object-Oriented Bayesian Network methodology and Object-Oriented Inference technique). In this research, we implement decision process and situation awareness models for a reference scenario using Army-PRIDE and demonstrate its ability to model a variety of uncertainty elements, including: confidence of source, information completeness, and information loss. We also demonstrate that Army-PRIDE improves the realism of the current constructive simulation's decision processes through Monte Carlo simulation.

From Sensory Signals to Modality-Independent Conceptual Representations: A Probabilistic Language of Thought Approach

PubMed Central

Erdogan, Goker; Yildirim, Ilker; Jacobs, Robert A.

2015-01-01

People learn modality-independent, conceptual representations from modality-specific sensory signals. Here, we hypothesize that any system that accomplishes this feat will include three components: a representational language for characterizing modality-independent representations, a set of sensory-specific forward models for mapping from modality-independent representations to sensory signals, and an inference algorithm for inverting forward models—that is, an algorithm for using sensory signals to infer modality-independent representations. To evaluate this hypothesis, we instantiate it in the form of a computational model that learns object shape representations from visual and/or haptic signals. The model uses a probabilistic grammar to characterize modality-independent representations of object shape, uses a computer graphics toolkit and a human hand simulator to map from object representations to visual and haptic features, respectively, and uses a Bayesian inference algorithm to infer modality-independent object representations from visual and/or haptic signals. Simulation results show that the model infers identical object representations when an object is viewed, grasped, or both. That is, the model’s percepts are modality invariant. We also report the results of an experiment in which different subjects rated the similarity of pairs of objects in different sensory conditions, and show that the model provides a very accurate account of subjects’ ratings. Conceptually, this research significantly contributes to our understanding of modality invariance, an important type of perceptual constancy, by demonstrating how modality-independent representations can be acquired and used. Methodologically, it provides an important contribution to cognitive modeling, particularly an emerging probabilistic language-of-thought approach, by showing how symbolic and statistical approaches can be combined in order to understand aspects of human perception. PMID:26554704

Bayesian analysis of the dynamic cosmic web in the SDSS galaxy survey

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leclercq, Florent; Wandelt, Benjamin; Jasche, Jens, E-mail: florent.leclercq@polytechnique.org, E-mail: jasche@iap.fr, E-mail: wandelt@iap.fr

Recent application of the Bayesian algorithm \\textsc(borg) to the Sloan Digital Sky Survey (SDSS) main sample galaxies resulted in the physical inference of the formation history of the observed large-scale structure from its origin to the present epoch. In this work, we use these inferences as inputs for a detailed probabilistic cosmic web-type analysis. To do so, we generate a large set of data-constrained realizations of the large-scale structure using a fast, fully non-linear gravitational model. We then perform a dynamic classification of the cosmic web into four distinct components (voids, sheets, filaments, and clusters) on the basis of themore » tidal field. Our inference framework automatically and self-consistently propagates typical observational uncertainties to web-type classification. As a result, this study produces accurate cosmographic classification of large-scale structure elements in the SDSS volume. By also providing the history of these structure maps, the approach allows an analysis of the origin and growth of the early traces of the cosmic web present in the initial density field and of the evolution of global quantities such as the volume and mass filling fractions of different structures. For the problem of web-type classification, the results described in this work constitute the first connection between theory and observations at non-linear scales including a physical model of structure formation and the demonstrated capability of uncertainty quantification. A connection between cosmology and information theory using real data also naturally emerges from our probabilistic approach. Our results constitute quantitative chrono-cosmography of the complex web-like patterns underlying the observed galaxy distribution.« less

Predicting BCI subject performance using probabilistic spatio-temporal filters.

PubMed

Suk, Heung-Il; Fazli, Siamac; Mehnert, Jan; Müller, Klaus-Robert; Lee, Seong-Whan

2014-01-01

Recently, spatio-temporal filtering to enhance decoding for Brain-Computer-Interfacing (BCI) has become increasingly popular. In this work, we discuss a novel, fully Bayesian-and thereby probabilistic-framework, called Bayesian Spatio-Spectral Filter Optimization (BSSFO) and apply it to a large data set of 80 non-invasive EEG-based BCI experiments. Across the full frequency range, the BSSFO framework allows to analyze which spatio-spectral parameters are common and which ones differ across the subject population. As expected, large variability of brain rhythms is observed between subjects. We have clustered subjects according to similarities in their corresponding spectral characteristics from the BSSFO model, which is found to reflect their BCI performances well. In BCI, a considerable percentage of subjects is unable to use a BCI for communication, due to their missing ability to modulate their brain rhythms-a phenomenon sometimes denoted as BCI-illiteracy or inability. Predicting individual subjects' performance preceding the actual, time-consuming BCI-experiment enhances the usage of BCIs, e.g., by detecting users with BCI inability. This work additionally contributes by using the novel BSSFO method to predict the BCI-performance using only 2 minutes and 3 channels of resting-state EEG data recorded before the actual BCI-experiment. Specifically, by grouping the individual frequency characteristics we have nicely classified them into the subject 'prototypes' (like μ - or β -rhythm type subjects) or users without ability to communicate with a BCI, and then by further building a linear regression model based on the grouping we could predict subjects' performance with the maximum correlation coefficient of 0.581 with the performance later seen in the actual BCI session.

A novel visualisation tool for climate services: a case study of temperature extremes and human mortality in Europe

NASA Astrophysics Data System (ADS)

Lowe, R.; Ballester, J.; Robine, J.; Herrmann, F. R.; Jupp, T. E.; Stephenson, D.; Rodó, X.

2013-12-01

Users of climate information often require probabilistic information on which to base their decisions. However, communicating information contained within a probabilistic forecast presents a challenge. In this paper we demonstrate a novel visualisation technique to display ternary probabilistic forecasts on a map in order to inform decision making. In this method, ternary probabilistic forecasts, which assign probabilities to a set of three outcomes (e.g. low, medium, and high risk), are considered as a point in a triangle of barycentric coordinates. This allows a unique colour to be assigned to each forecast from a continuum of colours defined on the triangle. Colour saturation increases with information gain relative to the reference forecast (i.e. the long term average). This provides additional information to decision makers compared with conventional methods used in seasonal climate forecasting, where one colour is used to represent one forecast category on a forecast map (e.g. red = ';dry'). We use the tool to present climate-related mortality projections across Europe. Temperature and humidity are related to human mortality via location-specific transfer functions, calculated using historical data. Daily mortality data at the NUTS2 level for 16 countries in Europe were obtain from 1998-2005. Transfer functions were calculated for 54 aggregations in Europe, defined using criteria related to population and climatological similarities. Aggregations are restricted to fall within political boundaries to avoid problems related to varying adaptation policies between countries. A statistical model is fit to cold and warm tails to estimate future mortality using forecast temperatures, in a Bayesian probabilistic framework. Using predefined categories of temperature-related mortality risk, we present maps of probabilistic projections for human mortality at seasonal to decadal time scales. We demonstrate the information gained from using this technique compared to more traditional methods to display ternary probabilistic forecasts. This technique allows decision makers to identify areas where the model predicts with certainty area-specific heat waves or cold snaps, in order to effectively target resources to those areas most at risk, for a given season or year. It is hoped that this visualisation tool will facilitate the interpretation of the probabilistic forecasts not only for public health decision makers but also within a multi-sectoral climate service framework.

A label field fusion bayesian model and its penalized maximum rand estimator for image segmentation.

PubMed

Mignotte, Max

2010-06-01

This paper presents a novel segmentation approach based on a Markov random field (MRF) fusion model which aims at combining several segmentation results associated with simpler clustering models in order to achieve a more reliable and accurate segmentation result. The proposed fusion model is derived from the recently introduced probabilistic Rand measure for comparing one segmentation result to one or more manual segmentations of the same image. This non-parametric measure allows us to easily derive an appealing fusion model of label fields, easily expressed as a Gibbs distribution, or as a nonstationary MRF model defined on a complete graph. Concretely, this Gibbs energy model encodes the set of binary constraints, in terms of pairs of pixel labels, provided by each segmentation results to be fused. Combined with a prior distribution, this energy-based Gibbs model also allows for definition of an interesting penalized maximum probabilistic rand estimator with which the fusion of simple, quickly estimated, segmentation results appears as an interesting alternative to complex segmentation models existing in the literature. This fusion framework has been successfully applied on the Berkeley image database. The experiments reported in this paper demonstrate that the proposed method is efficient in terms of visual evaluation and quantitative performance measures and performs well compared to the best existing state-of-the-art segmentation methods recently proposed in the literature.

Fully probabilistic seismic source inversion - Part 2: Modelling errors and station covariances

NASA Astrophysics Data System (ADS)

Stähler, Simon C.; Sigloch, Karin

2016-11-01

Seismic source inversion, a central task in seismology, is concerned with the estimation of earthquake source parameters and their uncertainties. Estimating uncertainties is particularly challenging because source inversion is a non-linear problem. In a companion paper, Stähler and Sigloch (2014) developed a method of fully Bayesian inference for source parameters, based on measurements of waveform cross-correlation between broadband, teleseismic body-wave observations and their modelled counterparts. This approach yields not only depth and moment tensor estimates but also source time functions. A prerequisite for Bayesian inference is the proper characterisation of the noise afflicting the measurements, a problem we address here. We show that, for realistic broadband body-wave seismograms, the systematic error due to an incomplete physical model affects waveform misfits more strongly than random, ambient background noise. In this situation, the waveform cross-correlation coefficient CC, or rather its decorrelation D = 1 - CC, performs more robustly as a misfit criterion than ℓp norms, more commonly used as sample-by-sample measures of misfit based on distances between individual time samples. From a set of over 900 user-supervised, deterministic earthquake source solutions treated as a quality-controlled reference, we derive the noise distribution on signal decorrelation D = 1 - CC of the broadband seismogram fits between observed and modelled waveforms. The noise on D is found to approximately follow a log-normal distribution, a fortunate fact that readily accommodates the formulation of an empirical likelihood function for D for our multivariate problem. The first and second moments of this multivariate distribution are shown to depend mostly on the signal-to-noise ratio (SNR) of the CC measurements and on the back-azimuthal distances of seismic stations. By identifying and quantifying this likelihood function, we make D and thus waveform cross-correlation measurements usable for fully probabilistic sampling strategies, in source inversion and related applications such as seismic tomography.

Probabilistic peak detection for first-order chromatographic data.

PubMed

Lopatka, M; Vivó-Truyols, G; Sjerps, M J

2014-03-19

We present a novel algorithm for probabilistic peak detection in first-order chromatographic data. Unlike conventional methods that deliver a binary answer pertaining to the expected presence or absence of a chromatographic peak, our method calculates the probability of a point being affected by such a peak. The algorithm makes use of chromatographic information (i.e. the expected width of a single peak and the standard deviation of baseline noise). As prior information of the existence of a peak in a chromatographic run, we make use of the statistical overlap theory. We formulate an exhaustive set of mutually exclusive hypotheses concerning presence or absence of different peak configurations. These models are evaluated by fitting a segment of chromatographic data by least-squares. The evaluation of these competing hypotheses can be performed as a Bayesian inferential task. We outline the potential advantages of adopting this approach for peak detection and provide several examples of both improved performance and increased flexibility afforded by our approach. Copyright © 2014 Elsevier B.V. All rights reserved.

Objectively combining AR5 instrumental period and paleoclimate climate sensitivity evidence

NASA Astrophysics Data System (ADS)

Lewis, Nicholas; Grünwald, Peter

2018-03-01

Combining instrumental period evidence regarding equilibrium climate sensitivity with largely independent paleoclimate proxy evidence should enable a more constrained sensitivity estimate to be obtained. Previous, subjective Bayesian approaches involved selection of a prior probability distribution reflecting the investigators' beliefs about climate sensitivity. Here a recently developed approach employing two different statistical methods—objective Bayesian and frequentist likelihood-ratio—is used to combine instrumental period and paleoclimate evidence based on data presented and assessments made in the IPCC Fifth Assessment Report. Probabilistic estimates from each source of evidence are represented by posterior probability density functions (PDFs) of physically-appropriate form that can be uniquely factored into a likelihood function and a noninformative prior distribution. The three-parameter form is shown accurately to fit a wide range of estimated climate sensitivity PDFs. The likelihood functions relating to the probabilistic estimates from the two sources are multiplicatively combined and a prior is derived that is noninformative for inference from the combined evidence. A posterior PDF that incorporates the evidence from both sources is produced using a single-step approach, which avoids the order-dependency that would arise if Bayesian updating were used. Results are compared with an alternative approach using the frequentist signed root likelihood ratio method. Results from these two methods are effectively identical, and provide a 5-95% range for climate sensitivity of 1.1-4.05 K (median 1.87 K).

Capturing changes in flood risk with Bayesian approaches for flood damage assessment

NASA Astrophysics Data System (ADS)

Vogel, Kristin; Schröter, Kai; Kreibich, Heidi; Thieken, Annegret; Müller, Meike; Sieg, Tobias; Laudan, Jonas; Kienzler, Sarah; Weise, Laura; Merz, Bruno; Scherbaum, Frank

2016-04-01

Flood risk is a function of hazard as well as of exposure and vulnerability. All three components are under change over space and time and have to be considered for reliable damage estimations and risk analyses, since this is the basis for an efficient, adaptable risk management. Hitherto, models for estimating flood damage are comparatively simple and cannot sufficiently account for changing conditions. The Bayesian network approach allows for a multivariate modeling of complex systems without relying on expert knowledge about physical constraints. In a Bayesian network each model component is considered to be a random variable. The way of interactions between those variables can be learned from observations or be defined by expert knowledge. Even a combination of both is possible. Moreover, the probabilistic framework captures uncertainties related to the prediction and provides a probability distribution for the damage instead of a point estimate. The graphical representation of Bayesian networks helps to study the change of probabilities for changing circumstances and may thus simplify the communication between scientists and public authorities. In the framework of the DFG-Research Training Group "NatRiskChange" we aim to develop Bayesian networks for flood damage and vulnerability assessments of residential buildings and companies under changing conditions. A Bayesian network learned from data, collected over the last 15 years in flooded regions in the Elbe and Danube catchments (Germany), reveals the impact of many variables like building characteristics, precaution and warning situation on flood damage to residential buildings. While the handling of incomplete and hybrid (discrete mixed with continuous) data are the most challenging issues in the study on residential buildings, a similar study, that focuses on the vulnerability of small to medium sized companies, bears new challenges. Relying on a much smaller data set for the determination of the model parameters, overly complex models should be avoided. A so called Markov Blanket approach aims at the identification of the most relevant factors and constructs a Bayesian network based on those findings. With our approach we want to exploit a major advantage of Bayesian networks which is their ability to consider dependencies not only pairwise, but to capture the joint effects and interactions of driving forces. Hence, the flood damage network does not only show the impact of precaution on the building damage separately, but also reveals the mutual effects of precaution and the quality of warning for a variety of flood settings. Thus, it allows for a consideration of changing conditions and different courses of action and forms a novel and valuable tool for decision support. This study is funded by the Deutsche Forschungsgemeinschaft (DFG) within the research training program GRK 2043/1 "NatRiskChange - Natural hazards and risks in a changing world" at the University of Potsdam.

Bayes and blickets: Effects of knowledge on causal induction in children and adults

PubMed Central

Griffiths, Thomas L.; Sobel, David M.; Tenenbaum, Joshua B.; Gopnik, Alison

2011-01-01

People are adept at inferring novel causal relations, even from only a few observations. Prior knowledge about the probability of encountering causal relations of various types and the nature of the mechanisms relating causes and effects plays a crucial role in these inferences. We test a formal account of how this knowledge can be used and acquired, based on analyzing causal induction as Bayesian inference. Five studies explored the predictions of this account with adults and 4-year-olds, using tasks in which participants learned about the causal properties of a set of objects. The studies varied the two factors that our Bayesian approach predicted should be relevant to causal induction: the prior probability with which causal relations exist, and the assumption of a deterministic or a probabilistic relation between cause and effect. Adults’ judgments (Experiments 1, 2, and 4) were in close correspondence with the quantitative predictions of the model, and children’s judgments (Experiments 3 and 5) agreed qualitatively with this account. PMID:21972897

Developing a Methodology for Eliciting Subjective Probability Estimates During Expert Evaluations of Safety Interventions: Application for Bayesian Belief Networks

NASA Technical Reports Server (NTRS)

Wiegmann, Douglas A.a

2005-01-01

The NASA Aviation Safety Program (AvSP) has defined several products that will potentially modify airline and/or ATC operations, enhance aircraft systems, and improve the identification of potential hazardous situations within the National Airspace System (NAS). Consequently, there is a need to develop methods for evaluating the potential safety benefit of each of these intervention products so that resources can be effectively invested to produce the judgments to develop Bayesian Belief Networks (BBN's) that model the potential impact that specific interventions may have. Specifically, the present report summarizes methodologies for improving the elicitation of probability estimates during expert evaluations of AvSP products for use in BBN's. The work involved joint efforts between Professor James Luxhoj from Rutgers University and researchers at the University of Illinois. The Rutgers' project to develop BBN's received funding by NASA entitled "Probabilistic Decision Support for Evaluating Technology Insertion and Assessing Aviation Safety System Risk." The proposed project was funded separately but supported the existing Rutgers' program.

Bayesian identification of multiple seismic change points and varying seismic rates caused by induced seismicity

NASA Astrophysics Data System (ADS)

Montoya-Noguera, Silvana; Wang, Yu

2017-04-01

The Central and Eastern United States (CEUS) has experienced an abnormal increase in seismic activity, which is believed to be related to anthropogenic activities. The U.S. Geological Survey has acknowledged this situation and developed the CEUS 2016 1 year seismic hazard model using the catalog of 2015 by assuming stationary seismicity in that period. However, due to the nonstationary nature of induced seismicity, it is essential to identify change points for accurate probabilistic seismic hazard analysis (PSHA). We present a Bayesian procedure to identify the most probable change points in seismicity and define their respective seismic rates. It uses prior distributions in agreement with conventional PSHA and updates them with recent data to identify seismicity changes. It can determine the change points in a regional scale and may incorporate different types of information in an objective manner. It is first successfully tested with simulated data, and then it is used to evaluate Oklahoma's regional seismicity.

Sequential inference as a mode of cognition and its correlates in fronto-parietal and hippocampal brain regions

PubMed Central

Friston, Karl J.; Dolan, Raymond J.

2017-01-01

Normative models of human cognition often appeal to Bayesian filtering, which provides optimal online estimates of unknown or hidden states of the world, based on previous observations. However, in many cases it is necessary to optimise beliefs about sequences of states rather than just the current state. Importantly, Bayesian filtering and sequential inference strategies make different predictions about beliefs and subsequent choices, rendering them behaviourally dissociable. Taking data from a probabilistic reversal task we show that subjects’ choices provide strong evidence that they are representing short sequences of states. Between-subject measures of this implicit sequential inference strategy had a neurobiological underpinning and correlated with grey matter density in prefrontal and parietal cortex, as well as the hippocampus. Our findings provide, to our knowledge, the first evidence for sequential inference in human cognition, and by exploiting between-subject variation in this measure we provide pointers to its neuronal substrates. PMID:28486504

Use of Bayesian Networks to Probabilistically Model and Improve the Likelihood of Validation of Microarray Findings by RT-PCR

PubMed Central

English, Sangeeta B.; Shih, Shou-Ching; Ramoni, Marco F.; Smith, Lois E.; Butte, Atul J.

2014-01-01

Though genome-wide technologies, such as microarrays, are widely used, data from these methods are considered noisy; there is still varied success in downstream biological validation. We report a method that increases the likelihood of successfully validating microarray findings using real time RT-PCR, including genes at low expression levels and with small differences. We use a Bayesian network to identify the most relevant sources of noise based on the successes and failures in validation for an initial set of selected genes, and then improve our subsequent selection of genes for validation based on eliminating these sources of noise. The network displays the significant sources of noise in an experiment, and scores the likelihood of validation for every gene. We show how the method can significantly increase validation success rates. In conclusion, in this study, we have successfully added a new automated step to determine the contributory sources of noise that determine successful or unsuccessful downstream biological validation. PMID:18790084

DM-BLD: differential methylation detection using a hierarchical Bayesian model exploiting local dependency.

PubMed

Wang, Xiao; Gu, Jinghua; Hilakivi-Clarke, Leena; Clarke, Robert; Xuan, Jianhua

2017-01-15

The advent of high-throughput DNA methylation profiling techniques has enabled the possibility of accurate identification of differentially methylated genes for cancer research. The large number of measured loci facilitates whole genome methylation study, yet posing great challenges for differential methylation detection due to the high variability in tumor samples. We have developed a novel probabilistic approach, D: ifferential M: ethylation detection using a hierarchical B: ayesian model exploiting L: ocal D: ependency (DM-BLD), to detect differentially methylated genes based on a Bayesian framework. The DM-BLD approach features a joint model to capture both the local dependency of measured loci and the dependency of methylation change in samples. Specifically, the local dependency is modeled by Leroux conditional autoregressive structure; the dependency of methylation changes is modeled by a discrete Markov random field. A hierarchical Bayesian model is developed to fully take into account the local dependency for differential analysis, in which differential states are embedded as hidden variables. Simulation studies demonstrate that DM-BLD outperforms existing methods for differential methylation detection, particularly when the methylation change is moderate and the variability of methylation in samples is high. DM-BLD has been applied to breast cancer data to identify important methylated genes (such as polycomb target genes and genes involved in transcription factor activity) associated with breast cancer recurrence. A Matlab package of DM-BLD is available at http://www.cbil.ece.vt.edu/software.htm CONTACT: Xuan@vt.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A probabilistic method to diagnose faults of air handling units

NASA Astrophysics Data System (ADS)

Dey, Debashis

Air handling unit (AHU) is one of the most extensively used equipment in large commercial buildings. This device is typically customized and lacks quality system integration which can result in hardwire failures and controller errors. Air handling unit Performance Assessment Rules (APAR) is a fault detection tool that uses a set of expert rules derived from mass and energy balances to detect faults in air handling units. APAR is computationally simple enough that it can be embedded in commercial building automation and control systems and relies only upon sensor data and control signals that are commonly available in these systems. Although APAR has many advantages over other methods, for example no training data required and easy to implement commercially, most of the time it is unable to provide the diagnosis of the faults. For instance, a fault on temperature sensor could be fixed bias, drifting bias, inappropriate location, complete failure. Also a fault in mixing box can be return and outdoor damper leak or stuck. In addition, when multiple rules are satisfied the list of faults increases. There is no proper way to have the correct diagnosis for rule based fault detection system. To overcome this limitation we proposed Bayesian Belief Network (BBN) as a diagnostic tool. BBN can be used to simulate diagnostic thinking of FDD experts through a probabilistic way. In this study we developed a new way to detect and diagnose faults in AHU through combining APAR rules and Bayesian Belief network. Bayesian Belief Network is used as a decision support tool for rule based expert system. BBN is highly capable to prioritize faults when multiple rules are satisfied simultaneously. Also it can get information from previous AHU operating conditions and maintenance records to provide proper diagnosis. The proposed model is validated with real time measured data of a campus building at University of Texas at San Antonio (UTSA).The results show that BBN is correctly able to prioritize faults which can be verified by manual investigation.

Bayesian modeling of Clostridium perfringens growth in beef-in-sauce products.

PubMed

Jaloustre, S; Cornu, M; Morelli, E; Noël, V; Delignette-Muller, M L

2011-04-01

Models on Clostridium perfringens growth which have been published to date have all been deterministic. A probabilistic model describing growth under non-isothermal conditions was thus proposed for predicting C. perfringens growth in beef-in-sauce products cooked and distributed in a French hospital. Model parameters were estimated from different types of data from various studies. A Bayesian approach was proposed to model the overall uncertainty regarding parameters and potential variability on the 'work to be done' (h(0)) during the germination, outgrowth and lag phase. Three models which differed according to their description of this parameter h(0) were tested. The model with inter-curve variability on h(0) was found to be the best one, on the basis of goodness-of-fit assessment and validation with literature data on results obtained under non-isothermal conditions. This model was used in two-dimensional Monte Carlo simulations to predict C. perfringens growth throughout the preparation of beef-in-sauce products, using temperature profiles recorded in a hospital kitchen. The median predicted growth was 7.8×10(-2) log(10) cfu·g(-1) (95% credibility interval [2.4×10(-2), 0.8]) despite the fact that for more than 50% of the registered temperature profiles cooling steps were longer than those required by French regulations. Copyright © 2010 Elsevier Ltd. All rights reserved.

A probabilistic model for detecting rigid domains in protein structures.

PubMed

Nguyen, Thach; Habeck, Michael

2016-09-01

Large-scale conformational changes in proteins are implicated in many important biological functions. These structural transitions can often be rationalized in terms of relative movements of rigid domains. There is a need for objective and automated methods that identify rigid domains in sets of protein structures showing alternative conformational states. We present a probabilistic model for detecting rigid-body movements in protein structures. Our model aims to approximate alternative conformational states by a few structural parts that are rigidly transformed under the action of a rotation and a translation. By using Bayesian inference and Markov chain Monte Carlo sampling, we estimate all parameters of the model, including a segmentation of the protein into rigid domains, the structures of the domains themselves, and the rigid transformations that generate the observed structures. We find that our Gibbs sampling algorithm can also estimate the optimal number of rigid domains with high efficiency and accuracy. We assess the power of our method on several thousand entries of the DynDom database and discuss applications to various complex biomolecular systems. The Python source code for protein ensemble analysis is available at: https://github.com/thachnguyen/motion_detection : mhabeck@gwdg.de. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Population viability assessment of salmonids by using probabilistic networks

Treesearch

Danny C. Lee; Bruce E. Rieman

1997-01-01

Public agencies are being asked to quantitatively assess the impact of land management activities on sensitive populations of salmonids. To aid in these assessments, we developed a Bayesian viability assessment procedure (BayVAM) to help characterize land use risks to salmonids in the Pacific Northwest. This procedure incorporates a hybrid approach to viability...

Optimization of nonlinear, non-Gaussian Bayesian filtering for diagnosis and prognosis of monotonic degradation processes

NASA Astrophysics Data System (ADS)

Corbetta, Matteo; Sbarufatti, Claudio; Giglio, Marco; Todd, Michael D.

2018-05-01

The present work critically analyzes the probabilistic definition of dynamic state-space models subject to Bayesian filters used for monitoring and predicting monotonic degradation processes. The study focuses on the selection of the random process, often called process noise, which is a key perturbation source in the evolution equation of particle filtering. Despite the large number of applications of particle filtering predicting structural degradation, the adequacy of the picked process noise has not been investigated. This paper reviews existing process noise models that are typically embedded in particle filters dedicated to monitoring and predicting structural damage caused by fatigue, which is monotonic in nature. The analysis emphasizes that existing formulations of the process noise can jeopardize the performance of the filter in terms of state estimation and remaining life prediction (i.e., damage prognosis). This paper subsequently proposes an optimal and unbiased process noise model and a list of requirements that the stochastic model must satisfy to guarantee high prognostic performance. These requirements are useful for future and further implementations of particle filtering for monotonic system dynamics. The validity of the new process noise formulation is assessed against experimental fatigue crack growth data from a full-scale aeronautical structure using dedicated performance metrics.

Discriminative Relational Topic Models.

PubMed

Chen, Ning; Zhu, Jun; Xia, Fei; Zhang, Bo

2015-05-01

Relational topic models (RTMs) provide a probabilistic generative process to describe both the link structure and document contents for document networks, and they have shown promise on predicting network structures and discovering latent topic representations. However, existing RTMs have limitations in both the restricted model expressiveness and incapability of dealing with imbalanced network data. To expand the scope and improve the inference accuracy of RTMs, this paper presents three extensions: 1) unlike the common link likelihood with a diagonal weight matrix that allows the-same-topic interactions only, we generalize it to use a full weight matrix that captures all pairwise topic interactions and is applicable to asymmetric networks; 2) instead of doing standard Bayesian inference, we perform regularized Bayesian inference (RegBayes) with a regularization parameter to deal with the imbalanced link structure issue in real networks and improve the discriminative ability of learned latent representations; and 3) instead of doing variational approximation with strict mean-field assumptions, we present collapsed Gibbs sampling algorithms for the generalized relational topic models by exploring data augmentation without making restricting assumptions. Under the generic RegBayes framework, we carefully investigate two popular discriminative loss functions, namely, the logistic log-loss and the max-margin hinge loss. Experimental results on several real network datasets demonstrate the significance of these extensions on improving prediction performance.

A rational model of function learning.

PubMed

Lucas, Christopher G; Griffiths, Thomas L; Williams, Joseph J; Kalish, Michael L

2015-10-01

Theories of how people learn relationships between continuous variables have tended to focus on two possibilities: one, that people are estimating explicit functions, or two that they are performing associative learning supported by similarity. We provide a rational analysis of function learning, drawing on work on regression in machine learning and statistics. Using the equivalence of Bayesian linear regression and Gaussian processes, which provide a probabilistic basis for similarity-based function learning, we show that learning explicit rules and using similarity can be seen as two views of one solution to this problem. We use this insight to define a rational model of human function learning that combines the strengths of both approaches and accounts for a wide variety of experimental results.

Whose statistical reasoning is facilitated by a causal structure intervention?

PubMed

McNair, Simon; Feeney, Aidan

2015-02-01

People often struggle when making Bayesian probabilistic estimates on the basis of competing sources of statistical evidence. Recently, Krynski and Tenenbaum (Journal of Experimental Psychology: General, 136, 430-450, 2007) proposed that a causal Bayesian framework accounts for peoples' errors in Bayesian reasoning and showed that, by clarifying the causal relations among the pieces of evidence, judgments on a classic statistical reasoning problem could be significantly improved. We aimed to understand whose statistical reasoning is facilitated by the causal structure intervention. In Experiment 1, although we observed causal facilitation effects overall, the effect was confined to participants high in numeracy. We did not find an overall facilitation effect in Experiment 2 but did replicate the earlier interaction between numerical ability and the presence or absence of causal content. This effect held when we controlled for general cognitive ability and thinking disposition. Our results suggest that clarifying causal structure facilitates Bayesian judgments, but only for participants with sufficient understanding of basic concepts in probability and statistics.

Novel health economic evaluation of a vaccination strategy to prevent HPV-related diseases: the BEST study.

PubMed

Favato, Giampiero; Baio, Gianluca; Capone, Alessandro; Marcellusi, Andrea; Costa, Silvano; Garganese, Giorgia; Picardo, Mauro; Drummond, Mike; Jonsson, Bengt; Scambia, Giovanni; Zweifel, Peter; Mennini, Francesco S

2012-12-01

The development of human papillomavirus (HPV)-related diseases is not understood perfectly and uncertainties associated with commonly utilized probabilistic models must be considered. The study assessed the cost-effectiveness of a quadrivalent-based multicohort HPV vaccination strategy within a Bayesian framework. A full Bayesian multicohort Markov model was used, in which all unknown quantities were associated with suitable probability distributions reflecting the state of currently available knowledge. These distributions were informed by observed data or expert opinion. The model cycle lasted 1 year, whereas the follow-up time horizon was 90 years. Precancerous cervical lesions, cervical cancers, and anogenital warts were considered as outcomes. The base case scenario (2 cohorts of girls aged 12 and 15 y) and other multicohort vaccination strategies (additional cohorts aged 18 and 25 y) were cost-effective, with a discounted cost per quality-adjusted life-year gained that corresponded to €12,013, €13,232, and €15,890 for vaccination programs based on 2, 3, and 4 cohorts, respectively. With multicohort vaccination strategies, the reduction in the number of HPV-related events occurred earlier (range, 3.8-6.4 y) when compared with a single cohort. The analysis of the expected value of information showed that the results of the model were subject to limited uncertainty (cost per patient = €12.6). This methodological approach is designed to incorporate the uncertainty associated with HPV vaccination. Modeling the cost-effectiveness of a multicohort vaccination program with Bayesian statistics confirmed the value for money of quadrivalent-based HPV vaccination. The expected value of information gave the most appropriate and feasible representation of the true value of this program.

Bayesian convolutional neural network based MRI brain extraction on nonhuman primates.

PubMed

Zhao, Gengyan; Liu, Fang; Oler, Jonathan A; Meyerand, Mary E; Kalin, Ned H; Birn, Rasmus M

2018-07-15

Brain extraction or skull stripping of magnetic resonance images (MRI) is an essential step in neuroimaging studies, the accuracy of which can severely affect subsequent image processing procedures. Current automatic brain extraction methods demonstrate good results on human brains, but are often far from satisfactory on nonhuman primates, which are a necessary part of neuroscience research. To overcome the challenges of brain extraction in nonhuman primates, we propose a fully-automated brain extraction pipeline combining deep Bayesian convolutional neural network (CNN) and fully connected three-dimensional (3D) conditional random field (CRF). The deep Bayesian CNN, Bayesian SegNet, is used as the core segmentation engine. As a probabilistic network, it is not only able to perform accurate high-resolution pixel-wise brain segmentation, but also capable of measuring the model uncertainty by Monte Carlo sampling with dropout in the testing stage. Then, fully connected 3D CRF is used to refine the probability result from Bayesian SegNet in the whole 3D context of the brain volume. The proposed method was evaluated with a manually brain-extracted dataset comprising T1w images of 100 nonhuman primates. Our method outperforms six popular publicly available brain extraction packages and three well-established deep learning based methods with a mean Dice coefficient of 0.985 and a mean average symmetric surface distance of 0.220 mm. A better performance against all the compared methods was verified by statistical tests (all p-values < 10 -4 , two-sided, Bonferroni corrected). The maximum uncertainty of the model on nonhuman primate brain extraction has a mean value of 0.116 across all the 100 subjects. The behavior of the uncertainty was also studied, which shows the uncertainty increases as the training set size decreases, the number of inconsistent labels in the training set increases, or the inconsistency between the training set and the testing set increases. Copyright © 2018 Elsevier Inc. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stewart, Robert N.; Urban, Marie L.; Duchscherer, Samantha E.

Understanding building occupancy is critical to a wide array of applications including natural hazards loss analysis, green building technologies, and population distribution modeling. Due to the expense of directly monitoring buildings, scientists rely in addition on a wide and disparate array of ancillary and open source information including subject matter expertise, survey data, and remote sensing information. These data are fused using data harmonization methods which refer to a loose collection of formal and informal techniques for fusing data together to create viable content for building occupancy estimation. In this paper, we add to the current state of the artmore » by introducing the Population Data Tables (PDT), a Bayesian based informatics system for systematically arranging data and harmonization techniques into a consistent, transparent, knowledge learning framework that retains in the final estimation uncertainty emerging from data, expert judgment, and model parameterization. PDT probabilistically estimates ambient occupancy in units of people/1000ft2 for over 50 building types at the national and sub-national level with the goal of providing global coverage. The challenge of global coverage led to the development of an interdisciplinary geospatial informatics system tool that provides the framework for capturing, storing, and managing open source data, handling subject matter expertise, carrying out Bayesian analytics as well as visualizing and exporting occupancy estimation results. We present the PDT project, situate the work within the larger community, and report on the progress of this multi-year project.Understanding building occupancy is critical to a wide array of applications including natural hazards loss analysis, green building technologies, and population distribution modeling. Due to the expense of directly monitoring buildings, scientists rely in addition on a wide and disparate array of ancillary and open source information including subject matter expertise, survey data, and remote sensing information. These data are fused using data harmonization methods which refer to a loose collection of formal and informal techniques for fusing data together to create viable content for building occupancy estimation. In this paper, we add to the current state of the art by introducing the Population Data Tables (PDT), a Bayesian model and informatics system for systematically arranging data and harmonization techniques into a consistent, transparent, knowledge learning framework that retains in the final estimation uncertainty emerging from data, expert judgment, and model parameterization. PDT probabilistically estimates ambient occupancy in units of people/1000 ft 2 for over 50 building types at the national and sub-national level with the goal of providing global coverage. The challenge of global coverage led to the development of an interdisciplinary geospatial informatics system tool that provides the framework for capturing, storing, and managing open source data, handling subject matter expertise, carrying out Bayesian analytics as well as visualizing and exporting occupancy estimation results. We present the PDT project, situate the work within the larger community, and report on the progress of this multi-year project.« less

A Probabilistic Strategy for Understanding Action Selection

PubMed Central

Kim, Byounghoon; Basso, Michele A.

2010-01-01

Brain regions involved in transforming sensory signals into movement commands are the likely sites where decisions are formed. Once formed, a decision must be read-out from the activity of populations of neurons to produce a choice of action. How this occurs remains unresolved. We recorded from four superior colliculus (SC) neurons simultaneously while monkeys performed a target selection task. We implemented three models to gain insight into the computational principles underlying population coding of action selection. We compared the population vector average (PVA), winner-takes-all (WTA) and a Bayesian model, maximum a posteriori estimate (MAP) to determine which predicted choices most often. The probabilistic model predicted more trials correctly than both the WTA and the PVA. The MAP model predicted 81.88% whereas WTA predicted 71.11% and PVA/OLE predicted the least number of trials at 55.71 and 69.47%. Recovering MAP estimates using simulated, non-uniform priors that correlated with monkeys’ choice performance, improved the accuracy of the model by 2.88%. A dynamic analysis revealed that the MAP estimate evolved over time and the posterior probability of the saccade choice reached a maximum at the time of the saccade. MAP estimates also scaled with choice performance accuracy. Although there was overlap in the prediction abilities of all the models, we conclude that movement choice from populations of neurons may be best understood by considering frameworks based on probability. PMID:20147560

High-resolution surface wave tomography of the European crust and uppermost mantle from ambient seismic noise

NASA Astrophysics Data System (ADS)

Lu, Yang; Stehly, Laurent; Paul, Anne; AlpArray Working Group

2018-05-01

Taking advantage of the large number of seismic stations installed in Europe, in particular in the greater Alpine region with the AlpArray experiment, we derive a new high-resolution 3-D shear-wave velocity model of the European crust and uppermost mantle from ambient noise tomography. The correlation of up to four years of continuous vertical-component seismic recordings from 1293 broadband stations (10° W-35° E, 30° N-75° N) provides Rayleigh wave group velocity dispersion data in the period band 5-150 s at more than 0.8 million virtual source-receiver pairs. Two-dimensional Rayleigh wave group velocity maps are estimated using adaptive parameterization to accommodate the strong heterogeneity of path coverage. A probabilistic 3-D shear-wave velocity model, including probability densities for the depth of layer boundaries and S-wave velocity values, is obtained by non-linear Bayesian inversion. A weighted average of the probabilistic model is then used as starting model for the linear inversion step, providing the final Vs model. The resulting S-wave velocity model and Moho depth are validated by comparison with previous geophysical studies. Although surface-wave tomography is weakly sensitive to layer boundaries, vertical cross-sections through our Vs model and the associated probability of presence of interfaces display striking similarities with reference controlled-source (CSS) and receiver-function sections across the Alpine belt. Our model even provides new structural information such as a ˜8 km Moho jump along the CSS ECORS-CROP profile that was not imaged by reflection data due to poor penetration across a heterogeneous upper crust. Our probabilistic and final shear wave velocity models have the potential to become new reference models of the European crust, both for crustal structure probing and geophysical studies including waveform modeling or full waveform inversion.

Decision-theoretic control of EUVE telescope scheduling

NASA Technical Reports Server (NTRS)

Hansson, Othar; Mayer, Andrew

1993-01-01

This paper describes a decision theoretic scheduler (DTS) designed to employ state-of-the-art probabilistic inference technology to speed the search for efficient solutions to constraint-satisfaction problems. Our approach involves assessing the performance of heuristic control strategies that are normally hard-coded into scheduling systems and using probabilistic inference to aggregate this information in light of the features of a given problem. The Bayesian Problem-Solver (BPS) introduced a similar approach to solving single agent and adversarial graph search patterns yielding orders-of-magnitude improvement over traditional techniques. Initial efforts suggest that similar improvements will be realizable when applied to typical constraint-satisfaction scheduling problems.

Experiments with a decision-theoretic scheduler

NASA Technical Reports Server (NTRS)

Hansson, Othar; Holt, Gerhard; Mayer, Andrew

1992-01-01

This paper describes DTS, a decision-theoretic scheduler designed to employ state-of-the-art probabilistic inference technology to speed the search for efficient solutions to constraint-satisfaction problems. Our approach involves assessing the performance of heuristic control strategies that are normally hard-coded into scheduling systems, and using probabilistic inference to aggregate this information in light of features of a given problem. BPS, the Bayesian Problem-Solver, introduced a similar approach to solving single-agent and adversarial graph search problems, yielding orders-of-magnitude improvement over traditional techniques. Initial efforts suggest that similar improvements will be realizable when applied to typical constraint-satisfaction scheduling problems.

Probabilistic Hazard Estimation at a Densely Urbanised Area: the Neaples Volcanoes

NASA Astrophysics Data System (ADS)

de Natale, G.; Mastrolorenzo, G.; Panizza, A.; Pappalardo, L.; Claudia, T.

2005-12-01

The Neaples volcanic area (Southern Italy), including Vesuvius, Campi Flegrei caldera and Ischia island, is the highest risk one in the World, where more than 2 million people live within about 10 km from an active volcanic vent. Such an extreme risk calls for accurate methodologies aimed to quantify it, in a probabilistic way, considering all the available volcanological information as well as modelling results. In fact, simple hazard maps based on the observation of deposits from past eruptions have the major problem that eruptive history generally samples a very limited number of possible outcomes, thus resulting almost meaningless to get the event probability in the area. This work describes a methodology making the best use (from a Bayesian point of view) of volcanological data and modelling results, to compute probabilistic hazard maps from multi-vent explosive eruptions. The method, which follows an approach recently developed by the same authors for pyroclastic flows hazard, has been here improved and extended to compute also fall-out hazard. The application of the method to the Neapolitan volcanic area, including the densely populated city of Naples, allows, for the first time, to get a global picture of the areal distribution for the main hazards from multi-vent explosive eruptions. From a joint consideration of the hazard contributions from all the three volcanic areas, new insight on the volcanic hazard distribution emerges, which will have strong implications for urban and emergency planning in the area.

Hierarchical probabilistic Gabor and MRF segmentation of brain tumours in MRI volumes.

PubMed

Subbanna, Nagesh K; Precup, Doina; Collins, D Louis; Arbel, Tal

2013-01-01

In this paper, we present a fully automated hierarchical probabilistic framework for segmenting brain tumours from multispectral human brain magnetic resonance images (MRIs) using multiwindow Gabor filters and an adapted Markov Random Field (MRF) framework. In the first stage, a customised Gabor decomposition is developed, based on the combined-space characteristics of the two classes (tumour and non-tumour) in multispectral brain MRIs in order to optimally separate tumour (including edema) from healthy brain tissues. A Bayesian framework then provides a coarse probabilistic texture-based segmentation of tumours (including edema) whose boundaries are then refined at the voxel level through a modified MRF framework that carefully separates the edema from the main tumour. This customised MRF is not only built on the voxel intensities and class labels as in traditional MRFs, but also models the intensity differences between neighbouring voxels in the likelihood model, along with employing a prior based on local tissue class transition probabilities. The second inference stage is shown to resolve local inhomogeneities and impose a smoothing constraint, while also maintaining the appropriate boundaries as supported by the local intensity difference observations. The method was trained and tested on the publicly available MICCAI 2012 Brain Tumour Segmentation Challenge (BRATS) Database [1] on both synthetic and clinical volumes (low grade and high grade tumours). Our method performs well compared to state-of-the-art techniques, outperforming the results of the top methods in cases of clinical high grade and low grade tumour core segmentation by 40% and 45% respectively.

Global Infrasound Association Based on Probabilistic Clutter Categorization

NASA Astrophysics Data System (ADS)

Arora, Nimar; Mialle, Pierrick

2016-04-01

The IDC advances its methods and continuously improves its automatic system for the infrasound technology. The IDC focuses on enhancing the automatic system for the identification of valid signals and the optimization of the network detection threshold by identifying ways to refine signal characterization methodology and association criteria. An objective of this study is to reduce the number of associated infrasound arrivals that are rejected from the automatic bulletins when generating the reviewed event bulletins. Indeed, a considerable number of signal detections are due to local clutter sources such as microbaroms, waterfalls, dams, gas flares, surf (ocean breaking waves) etc. These sources are either too diffuse or too local to form events. Worse still, the repetitive nature of this clutter leads to a large number of false event hypotheses due to the random matching of clutter at multiple stations. Previous studies, for example [1], have worked on categorization of clutter using long term trends on detection azimuth, frequency, and amplitude at each station. In this work we continue the same line of reasoning to build a probabilistic model of clutter that is used as part of NETVISA [2], a Bayesian approach to network processing. The resulting model is a fusion of seismic, hydroacoustic and infrasound processing built on a unified probabilistic framework. References: [1] Infrasound categorization Towards a statistics based approach. J. Vergoz, P. Gaillard, A. Le Pichon, N. Brachet, and L. Ceranna. ITW 2011 [2] NETVISA: Network Processing Vertically Integrated Seismic Analysis. N. S. Arora, S. Russell, and E. Sudderth. BSSA 2013

Probabilistic models and uncertainty quantification for the ionization reaction rate of atomic Nitrogen

NASA Astrophysics Data System (ADS)

Miki, K.; Panesi, M.; Prudencio, E. E.; Prudhomme, S.

2012-05-01

The objective in this paper is to analyze some stochastic models for estimating the ionization reaction rate constant of atomic Nitrogen (N + e- → N+ + 2e-). Parameters of the models are identified by means of Bayesian inference using spatially resolved absolute radiance data obtained from the Electric Arc Shock Tube (EAST) wind-tunnel. The proposed methodology accounts for uncertainties in the model parameters as well as physical model inadequacies, providing estimates of the rate constant that reflect both types of uncertainties. We present four different probabilistic models by varying the error structure (either additive or multiplicative) and by choosing different descriptions of the statistical correlation among data points. In order to assess the validity of our methodology, we first present some calibration results obtained with manufactured data and then proceed by using experimental data collected at EAST experimental facility. In order to simulate the radiative signature emitted in the shock-heated air plasma, we use a one-dimensional flow solver with Park's two-temperature model that simulates non-equilibrium effects. We also discuss the implications of the choice of the stochastic model on the estimation of the reaction rate and its uncertainties. Our analysis shows that the stochastic models based on correlated multiplicative errors are the most plausible models among the four models proposed in this study. The rate of the atomic Nitrogen ionization is found to be (6.2 ± 3.3) × 1011 cm3 mol-1 s-1 at 10,000 K.

Hierarchical Bayesian method for mapping biogeochemical hot spots using induced polarization imaging

DOE PAGES

Wainwright, Haruko M.; Flores Orozco, Adrian; Bucker, Matthias; ...

2016-01-29

In floodplain environments, a naturally reduced zone (NRZ) is considered to be a common biogeochemical hot spot, having distinct microbial and geochemical characteristics. Although important for understanding their role in mediating floodplain biogeochemical processes, mapping the subsurface distribution of NRZs over the dimensions of a floodplain is challenging, as conventional wellbore data are typically spatially limited and the distribution of NRZs is heterogeneous. In this work, we present an innovative methodology for the probabilistic mapping of NRZs within a three-dimensional (3-D) subsurface domain using induced polarization imaging, which is a noninvasive geophysical technique. Measurements consist of surface geophysical surveys andmore » drilling-recovered sediments at the U.S. Department of Energy field site near Rifle, CO (USA). Inversion of surface time domain-induced polarization (TDIP) data yielded 3-D images of the complex electrical resistivity, in terms of magnitude and phase, which are associated with mineral precipitation and other lithological properties. By extracting the TDIP data values colocated with wellbore lithological logs, we found that the NRZs have a different distribution of resistivity and polarization from the other aquifer sediments. To estimate the spatial distribution of NRZs, we developed a Bayesian hierarchical model to integrate the geophysical and wellbore data. In addition, the resistivity images were used to estimate hydrostratigraphic interfaces under the floodplain. Validation results showed that the integration of electrical imaging and wellbore data using a Bayesian hierarchical model was capable of mapping spatially heterogeneous interfaces and NRZ distributions thereby providing a minimally invasive means to parameterize a hydrobiogeochemical model of the floodplain.« less

A quantum probability framework for human probabilistic inference.

PubMed

Trueblood, Jennifer S; Yearsley, James M; Pothos, Emmanuel M

2017-09-01

There is considerable variety in human inference (e.g., a doctor inferring the presence of a disease, a juror inferring the guilt of a defendant, or someone inferring future weight loss based on diet and exercise). As such, people display a wide range of behaviors when making inference judgments. Sometimes, people's judgments appear Bayesian (i.e., normative), but in other cases, judgments deviate from the normative prescription of classical probability theory. How can we combine both Bayesian and non-Bayesian influences in a principled way? We propose a unified explanation of human inference using quantum probability theory. In our approach, we postulate a hierarchy of mental representations, from 'fully' quantum to 'fully' classical, which could be adopted in different situations. In our hierarchy of models, moving from the lowest level to the highest involves changing assumptions about compatibility (i.e., how joint events are represented). Using results from 3 experiments, we show that our modeling approach explains 5 key phenomena in human inference including order effects, reciprocity (i.e., the inverse fallacy), memorylessness, violations of the Markov condition, and antidiscounting. As far as we are aware, no existing theory or model can explain all 5 phenomena. We also explore transitions in our hierarchy, examining how representations change from more quantum to more classical. We show that classical representations provide a better account of data as individuals gain familiarity with a task. We also show that representations vary between individuals, in a way that relates to a simple measure of cognitive style, the Cognitive Reflection Test. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Stan : A Probabilistic Programming Language

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carpenter, Bob; Gelman, Andrew; Hoffman, Matthew D.

Stan is a probabilistic programming language for specifying statistical models. A Stan program imperatively defines a log probability function over parameters conditioned on specified data and constants. As of version 2.14.0, Stan provides full Bayesian inference for continuous-variable models through Markov chain Monte Carlo methods such as the No-U-Turn sampler, an adaptive form of Hamiltonian Monte Carlo sampling. Penalized maximum likelihood estimates are calculated using optimization methods such as the limited memory Broyden-Fletcher-Goldfarb-Shanno algorithm. Stan is also a platform for computing log densities and their gradients and Hessians, which can be used in alternative algorithms such as variational Bayes, expectationmore » propagation, and marginal inference using approximate integration. To this end, Stan is set up so that the densities, gradients, and Hessians, along with intermediate quantities of the algorithm such as acceptance probabilities, are easily accessible. Stan can also be called from the command line using the cmdstan package, through R using the rstan package, and through Python using the pystan package. All three interfaces support sampling and optimization-based inference with diagnostics and posterior analysis. rstan and pystan also provide access to log probabilities, gradients, Hessians, parameter transforms, and specialized plotting.« less

Stan : A Probabilistic Programming Language

DOE PAGES

Carpenter, Bob; Gelman, Andrew; Hoffman, Matthew D.; ...

2017-01-01

Stan is a probabilistic programming language for specifying statistical models. A Stan program imperatively defines a log probability function over parameters conditioned on specified data and constants. As of version 2.14.0, Stan provides full Bayesian inference for continuous-variable models through Markov chain Monte Carlo methods such as the No-U-Turn sampler, an adaptive form of Hamiltonian Monte Carlo sampling. Penalized maximum likelihood estimates are calculated using optimization methods such as the limited memory Broyden-Fletcher-Goldfarb-Shanno algorithm. Stan is also a platform for computing log densities and their gradients and Hessians, which can be used in alternative algorithms such as variational Bayes, expectationmore » propagation, and marginal inference using approximate integration. To this end, Stan is set up so that the densities, gradients, and Hessians, along with intermediate quantities of the algorithm such as acceptance probabilities, are easily accessible. Stan can also be called from the command line using the cmdstan package, through R using the rstan package, and through Python using the pystan package. All three interfaces support sampling and optimization-based inference with diagnostics and posterior analysis. rstan and pystan also provide access to log probabilities, gradients, Hessians, parameter transforms, and specialized plotting.« less

The total probabilities from high-resolution ensemble forecasting of floods

NASA Astrophysics Data System (ADS)

Olav Skøien, Jon; Bogner, Konrad; Salamon, Peter; Smith, Paul; Pappenberger, Florian

2015-04-01

Ensemble forecasting has for a long time been used in meteorological modelling, to give an indication of the uncertainty of the forecasts. As meteorological ensemble forecasts often show some bias and dispersion errors, there is a need for calibration and post-processing of the ensembles. Typical methods for this are Bayesian Model Averaging (Raftery et al., 2005) and Ensemble Model Output Statistics (EMOS) (Gneiting et al., 2005). There are also methods for regionalizing these methods (Berrocal et al., 2007) and for incorporating the correlation between lead times (Hemri et al., 2013). To make optimal predictions of floods along the stream network in hydrology, we can easily use the ensemble members as input to the hydrological models. However, some of the post-processing methods will need modifications when regionalizing the forecasts outside the calibration locations, as done by Hemri et al. (2013). We present a method for spatial regionalization of the post-processed forecasts based on EMOS and top-kriging (Skøien et al., 2006). We will also look into different methods for handling the non-normality of runoff and the effect on forecasts skills in general and for floods in particular. Berrocal, V. J., Raftery, A. E. and Gneiting, T.: Combining Spatial Statistical and Ensemble Information in Probabilistic Weather Forecasts, Mon. Weather Rev., 135(4), 1386-1402, doi:10.1175/MWR3341.1, 2007. Gneiting, T., Raftery, A. E., Westveld, A. H. and Goldman, T.: Calibrated Probabilistic Forecasting Using Ensemble Model Output Statistics and Minimum CRPS Estimation, Mon. Weather Rev., 133(5), 1098-1118, doi:10.1175/MWR2904.1, 2005. Hemri, S., Fundel, F. and Zappa, M.: Simultaneous calibration of ensemble river flow predictions over an entire range of lead times, Water Resour. Res., 49(10), 6744-6755, doi:10.1002/wrcr.20542, 2013. Raftery, A. E., Gneiting, T., Balabdaoui, F. and Polakowski, M.: Using Bayesian Model Averaging to Calibrate Forecast Ensembles, Mon. Weather Rev., 133(5), 1155-1174, doi:10.1175/MWR2906.1, 2005. Skøien, J. O., Merz, R. and Blöschl, G.: Top-kriging - Geostatistics on stream networks, Hydrol. Earth Syst. Sci., 10(2), 277-287, 2006.

Validation workflow for a clinical Bayesian network model in multidisciplinary decision making in head and neck oncology treatment.

PubMed

Cypko, Mario A; Stoehr, Matthaeus; Kozniewski, Marcin; Druzdzel, Marek J; Dietz, Andreas; Berliner, Leonard; Lemke, Heinz U

2017-11-01

Oncological treatment is being increasingly complex, and therefore, decision making in multidisciplinary teams is becoming the key activity in the clinical pathways. The increased complexity is related to the number and variability of possible treatment decisions that may be relevant to a patient. In this paper, we describe validation of a multidisciplinary cancer treatment decision in the clinical domain of head and neck oncology. Probabilistic graphical models and corresponding inference algorithms, in the form of Bayesian networks, can support complex decision-making processes by providing a mathematically reproducible and transparent advice. The quality of BN-based advice depends on the quality of the model. Therefore, it is vital to validate the model before it is applied in practice. For an example BN subnetwork of laryngeal cancer with 303 variables, we evaluated 66 patient records. To validate the model on this dataset, a validation workflow was applied in combination with quantitative and qualitative analyses. In the subsequent analyses, we observed four sources of imprecise predictions: incorrect data, incomplete patient data, outvoting relevant observations, and incorrect model. Finally, the four problems were solved by modifying the data and the model. The presented validation effort is related to the model complexity. For simpler models, the validation workflow is the same, although it may require fewer validation methods. The validation success is related to the model's well-founded knowledge base. The remaining laryngeal cancer model may disclose additional sources of imprecise predictions.

Incorporation of GRACE Data into a Bayesian Model for Groundwater Drought Monitoring

NASA Astrophysics Data System (ADS)

Slinski, K.; Hogue, T. S.; McCray, J. E.; Porter, A.

2015-12-01

Groundwater drought, defined as the sustained occurrence of below average availability of groundwater, is marked by below average water levels in aquifers and reduced flows to groundwater-fed rivers and wetlands. The impact of groundwater drought on ecosystems, agriculture, municipal water supply, and the energy sector is an increasingly important global issue. However, current drought monitors heavily rely on precipitation and vegetative stress indices to characterize the timing, duration, and severity of drought events. The paucity of in situ observations of aquifer levels is a substantial obstacle to the development of systems to monitor groundwater drought in drought-prone areas, particularly in developing countries. Observations from the NASA/German Space Agency's Gravity Recovery and Climate Experiment (GRACE) have been used to estimate changes in groundwater storage over areas with sparse point measurements. This study incorporates GRACE total water storage observations into a Bayesian framework to assess the performance of a probabilistic model for monitoring groundwater drought based on remote sensing data. Overall, it is hoped that these methods will improve global drought preparedness and risk reduction by providing information on groundwater drought necessary to manage its impacts on ecosystems, as well as on the agricultural, municipal, and energy sectors.

Structural and parameteric uncertainty quantification in cloud microphysics parameterization schemes

NASA Astrophysics Data System (ADS)

van Lier-Walqui, M.; Morrison, H.; Kumjian, M. R.; Prat, O. P.; Martinkus, C.

2017-12-01

Atmospheric model parameterization schemes employ approximations to represent the effects of unresolved processes. These approximations are a source of error in forecasts, caused in part by considerable uncertainty about the optimal value of parameters within each scheme -- parameteric uncertainty. Furthermore, there is uncertainty regarding the best choice of the overarching structure of the parameterization scheme -- structrual uncertainty. Parameter estimation can constrain the first, but may struggle with the second because structural choices are typically discrete. We address this problem in the context of cloud microphysics parameterization schemes by creating a flexible framework wherein structural and parametric uncertainties can be simultaneously constrained. Our scheme makes no assuptions about drop size distribution shape or the functional form of parametrized process rate terms. Instead, these uncertainties are constrained by observations using a Markov Chain Monte Carlo sampler within a Bayesian inference framework. Our scheme, the Bayesian Observationally-constrained Statistical-physical Scheme (BOSS), has flexibility to predict various sets of prognostic drop size distribution moments as well as varying complexity of process rate formulations. We compare idealized probabilistic forecasts from versions of BOSS with varying levels of structural complexity. This work has applications in ensemble forecasts with model physics uncertainty, data assimilation, and cloud microphysics process studies.

Advanced Computational Framework for Environmental Management ZEM, Version 1.x

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vesselinov, Velimir V.; O'Malley, Daniel; Pandey, Sachin

2016-11-04

Typically environmental management problems require analysis of large and complex data sets originating from concurrent data streams with different data collection frequencies and pedigree. These big data sets require on-the-fly integration into a series of models with different complexity for various types of model analyses where the data are applied as soft and hard model constraints. This is needed to provide fast iterative model analyses based on the latest available data to guide decision-making. Furthermore, the data and model are associated with uncertainties. The uncertainties are probabilistic (e.g. measurement errors) and non-probabilistic (unknowns, e.g. alternative conceptual models characterizing site conditions).more » To address all of these issues, we have developed an integrated framework for real-time data and model analyses for environmental decision-making called ZEM. The framework allows for seamless and on-the-fly integration of data and modeling results for robust and scientifically-defensible decision-making applying advanced decision analyses tools such as Bayesian- Information-Gap Decision Theory (BIG-DT). The framework also includes advanced methods for optimization that are capable of dealing with a large number of unknown model parameters, and surrogate (reduced order) modeling capabilities based on support vector regression techniques. The framework is coded in Julia, a state-of-the-art high-performance programing language (http://julialang.org). The ZEM framework is open-source and can be applied to any environmental management site. The framework will be open-source and released under GPL V3 license.« less

Probabilistic Approaches for Multi-Hazard Risk Assessment of Structures and Systems

NASA Astrophysics Data System (ADS)

Kwag, Shinyoung

Performance assessment of structures, systems, and components for multi-hazard scenarios has received significant attention in recent years. However, the concept of multi-hazard analysis is quite broad in nature and the focus of existing literature varies across a wide range of problems. In some cases, such studies focus on hazards that either occur simultaneously or are closely correlated with each other. For example, seismically induced flooding or seismically induced fires. In other cases, multi-hazard studies relate to hazards that are not dependent or correlated but have strong likelihood of occurrence at different times during the lifetime of a structure. The current approaches for risk assessment need enhancement to account for multi-hazard risks. It must be able to account for uncertainty propagation in a systems-level analysis, consider correlation among events or failure modes, and allow integration of newly available information from continually evolving simulation models, experimental observations, and field measurements. This dissertation presents a detailed study that proposes enhancements by incorporating Bayesian networks and Bayesian updating within a performance-based probabilistic framework. The performance-based framework allows propagation of risk as well as uncertainties in the risk estimates within a systems analysis. Unlike conventional risk assessment techniques such as a fault-tree analysis, a Bayesian network can account for statistical dependencies and correlations among events/hazards. The proposed approach is extended to develop a risk-informed framework for quantitative validation and verification of high fidelity system-level simulation tools. Validation of such simulations can be quite formidable within the context of a multi-hazard risk assessment in nuclear power plants. The efficiency of this approach lies in identification of critical events, components, and systems that contribute to the overall risk. Validation of any event or component on the critical path is relatively more important in a risk-informed environment. Significance of multi-hazard risk is also illustrated for uncorrelated hazards of earthquakes and high winds which may result in competing design objectives. It is also illustrated that the number of computationally intensive nonlinear simulations needed in performance-based risk assessment for external hazards can be significantly reduced by using the power of Bayesian updating in conjunction with the concept of equivalent limit-state.

Probabilistic Gait Classification in Children with Cerebral Palsy: A Bayesian Approach

ERIC Educational Resources Information Center

Van Gestel, Leen; De Laet, Tinne; Di Lello, Enrico; Bruyninckx, Herman; Molenaers, Guy; Van Campenhout, Anja; Aertbelien, Erwin; Schwartz, Mike; Wambacq, Hans; De Cock, Paul; Desloovere, Kaat

2011-01-01

Three-dimensional gait analysis (3DGA) generates a wealth of highly variable data. Gait classifications help to reduce, simplify and interpret this vast amount of 3DGA data and thereby assist and facilitate clinical decision making in the treatment of CP. CP gait is often a mix of several clinically accepted distinct gait patterns. Therefore,…

How many kinds of reasoning? Inference, probability, and natural language semantics.

PubMed

Lassiter, Daniel; Goodman, Noah D

2015-03-01

The "new paradigm" unifying deductive and inductive reasoning in a Bayesian framework (Oaksford & Chater, 2007; Over, 2009) has been claimed to be falsified by results which show sharp differences between reasoning about necessity vs. plausibility (Heit & Rotello, 2010; Rips, 2001; Rotello & Heit, 2009). We provide a probabilistic model of reasoning with modal expressions such as "necessary" and "plausible" informed by recent work in formal semantics of natural language, and show that it predicts the possibility of non-linear response patterns which have been claimed to be problematic. Our model also makes a strong monotonicity prediction, while two-dimensional theories predict the possibility of reversals in argument strength depending on the modal word chosen. Predictions were tested using a novel experimental paradigm that replicates the previously-reported response patterns with a minimal manipulation, changing only one word of the stimulus between conditions. We found a spectrum of reasoning "modes" corresponding to different modal words, and strong support for our model's monotonicity prediction. This indicates that probabilistic approaches to reasoning can account in a clear and parsimonious way for data previously argued to falsify them, as well as new, more fine-grained, data. It also illustrates the importance of careful attention to the semantics of language employed in reasoning experiments. Copyright © 2014 Elsevier B.V. All rights reserved.

BAYESIAN PROTEIN STRUCTURE ALIGNMENT.

PubMed

Rodriguez, Abel; Schmidler, Scott C

The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over evolutionary timescales. A key challenge is the identification and evaluation of structural similarity between proteins; such analysis can aid in understanding the role of newly discovered proteins and help elucidate evolutionary relationships between organisms. Computational biologists have developed many clever algorithmic techniques for comparing protein structures, however, all are based on heuristic optimization criteria, making statistical interpretation somewhat difficult. Here we present a fully probabilistic framework for pairwise structural alignment of proteins. Our approach has several advantages, including the ability to capture alignment uncertainty and to estimate key "gap" parameters which critically affect the quality of the alignment. We show that several existing alignment methods arise as maximum a posteriori estimates under specific choices of prior distributions and error models. Our probabilistic framework is also easily extended to incorporate additional information, which we demonstrate by including primary sequence information to generate simultaneous sequence-structure alignments that can resolve ambiguities obtained using structure alone. This combined model also provides a natural approach for the difficult task of estimating evolutionary distance based on structural alignments. The model is illustrated by comparison with well-established methods on several challenging protein alignment examples.

A Bayesian-Based Approach to Marine Spatial Planning: Evaluating Spatial and Temporal Variance in the Provision of Ecosystem Services Before and After the Establishment Oregon's Marine Protected Areas

NASA Astrophysics Data System (ADS)

Black, B.; Harte, M.; Goldfinger, C.

2017-12-01

Participating in a ten-year monitoring project to assess the ecological, social, and socioeconomic impacts of Oregon's Marine Protected Areas (MPAs), we have worked in partnership with the Oregon Department of Fish and Wildlife (ODFW) to develop a Bayesian geospatial method to evaluate the spatial and temporal variance in the provision of ecosystem services produced by Oregon's MPAs. Probabilistic (Bayesian) approaches to Marine Spatial Planning (MSP) show considerable potential for addressing issues such as uncertainty, cumulative effects, and the need to integrate stakeholder-held information and preferences into decision making processes. To that end, we have created a Bayesian-based geospatial approach to MSP capable of modelling the evolution of the provision of ecosystem services before and after the establishment of Oregon's MPAs. Our approach permits both planners and stakeholders to view expected impacts of differing policies, behaviors, or choices made concerning Oregon's MPAs and surrounding areas in a geospatial (map) format while simultaneously considering multiple parties' beliefs on the policies or uses in question. We quantify the influence of the MPAs as the shift in the spatial distribution of ecosystem services, both inside and outside the protected areas, over time. Once the MPAs' influence on the provision of coastal ecosystem services has been evaluated, it is possible to view these impacts through geovisualization techniques. As a specific example of model use and output, a user could investigate the effects of altering the habitat preferences of a rockfish species over a prescribed period of time (5, 10, 20 years post-harvesting restrictions, etc.) on the relative intensity of spillover from nearby reserves (please see submitted figure). Particular strengths of our Bayesian-based approach include its ability to integrate highly disparate input types (qualitative or quantitative), to accommodate data gaps, address uncertainty, and to investigate temporal and spatial variation. This approach conveys the modeled outcome of proposed policy changes and is also a vehicle through which stakeholders and planners can work together to compare and deliberate on the impacts of policy and management changes, a capacity of considerable utility for planners and stakeholders engaged in MSP.

Learning multisensory representations for auditory-visual transfer of sequence category knowledge: a probabilistic language of thought approach.

PubMed

Yildirim, Ilker; Jacobs, Robert A

2015-06-01

If a person is trained to recognize or categorize objects or events using one sensory modality, the person can often recognize or categorize those same (or similar) objects and events via a novel modality. This phenomenon is an instance of cross-modal transfer of knowledge. Here, we study the Multisensory Hypothesis which states that people extract the intrinsic, modality-independent properties of objects and events, and represent these properties in multisensory representations. These representations underlie cross-modal transfer of knowledge. We conducted an experiment evaluating whether people transfer sequence category knowledge across auditory and visual domains. Our experimental data clearly indicate that we do. We also developed a computational model accounting for our experimental results. Consistent with the probabilistic language of thought approach to cognitive modeling, our model formalizes multisensory representations as symbolic "computer programs" and uses Bayesian inference to learn these representations. Because the model demonstrates how the acquisition and use of amodal, multisensory representations can underlie cross-modal transfer of knowledge, and because the model accounts for subjects' experimental performances, our work lends credence to the Multisensory Hypothesis. Overall, our work suggests that people automatically extract and represent objects' and events' intrinsic properties, and use these properties to process and understand the same (and similar) objects and events when they are perceived through novel sensory modalities.

A Bayesian network modeling approach to forecasting the 21st century worldwide status of polar bears

NASA Astrophysics Data System (ADS)

Amstrup, Steven C.; Marcot, Bruce G.; Douglas, David C.

To inform the U.S. Fish and Wildlife Service decision, whether or not to list polar bears as threatened under the Endangered Species Act (ESA), we projected the status of the world's polar bears (Ursus maritimus) for decades centered on future years 2025, 2050, 2075, and 2095. We defined four ecoregions based on current and projected sea ice conditions: seasonal ice, Canadian Archipelago, polar basin divergent, and polar basin convergent ecoregions. We incorporated general circulation model projections of future sea ice into a Bayesian network (BN) model structured around the factors considered in ESA decisions. This first-generation BN model combined empirical data, interpretations of data, and professional judgments of one polar bear expert into a probabilistic framework that identifies causal links between environmental stressors and polar bear responses. We provide guidance regarding steps necessary to refine the model, including adding inputs from other experts. The BN model projected extirpation of polar bears from the seasonal ice and polar basin divergent ecoregions, where ≈2/3 of the world's polar bears currently occur, by mid century. Projections were less dire in other ecoregions. Decline in ice habitat was the overriding factor driving the model outcomes. Although this is a first-generation model, the dependence of polar bears on sea ice is universally accepted, and the observed sea ice decline is faster than models suggest. Therefore, incorporating judgments of multiple experts in a final model is not expected to fundamentally alter the outlook for polar bears described here.

Bayesian updating in a fault tree model for shipwreck risk assessment.

PubMed

Landquist, H; Rosén, L; Lindhe, A; Norberg, T; Hassellöv, I-M

2017-07-15

Shipwrecks containing oil and other hazardous substances have been deteriorating on the seabeds of the world for many years and are threatening to pollute the marine environment. The status of the wrecks and the potential volume of harmful substances present in the wrecks are affected by a multitude of uncertainties. Each shipwreck poses a unique threat, the nature of which is determined by the structural status of the wreck and possible damage resulting from hazardous activities that could potentially cause a discharge. Decision support is required to ensure the efficiency of the prioritisation process and the allocation of resources required to carry out risk mitigation measures. Whilst risk assessments can provide the requisite decision support, comprehensive methods that take into account key uncertainties related to shipwrecks are limited. The aim of this paper was to develop a method for estimating the probability of discharge of hazardous substances from shipwrecks. The method is based on Bayesian updating of generic information on the hazards posed by different activities in the surroundings of the wreck, with information on site-specific and wreck-specific conditions in a fault tree model. Bayesian updating is performed using Monte Carlo simulations for estimating the probability of a discharge of hazardous substances and formal handling of intrinsic uncertainties. An example application involving two wrecks located off the Swedish coast is presented. Results show the estimated probability of opening, discharge and volume of the discharge for the two wrecks and illustrate the capability of the model to provide decision support. Together with consequence estimations of a discharge of hazardous substances, the suggested model enables comprehensive and probabilistic risk assessments of shipwrecks to be made. Copyright © 2017 Elsevier B.V. All rights reserved.

Inferring on the Intentions of Others by Hierarchical Bayesian Learning

PubMed Central

Diaconescu, Andreea O.; Mathys, Christoph; Weber, Lilian A. E.; Daunizeau, Jean; Kasper, Lars; Lomakina, Ekaterina I.; Fehr, Ernst; Stephan, Klaas E.

2014-01-01

Inferring on others' (potentially time-varying) intentions is a fundamental problem during many social transactions. To investigate the underlying mechanisms, we applied computational modeling to behavioral data from an economic game in which 16 pairs of volunteers (randomly assigned to “player” or “adviser” roles) interacted. The player performed a probabilistic reinforcement learning task, receiving information about a binary lottery from a visual pie chart. The adviser, who received more predictive information, issued an additional recommendation. Critically, the game was structured such that the adviser's incentives to provide helpful or misleading information varied in time. Using a meta-Bayesian modeling framework, we found that the players' behavior was best explained by the deployment of hierarchical learning: they inferred upon the volatility of the advisers' intentions in order to optimize their predictions about the validity of their advice. Beyond learning, volatility estimates also affected the trial-by-trial variability of decisions: participants were more likely to rely on their estimates of advice accuracy for making choices when they believed that the adviser's intentions were presently stable. Finally, our model of the players' inference predicted the players' interpersonal reactivity index (IRI) scores, explicit ratings of the advisers' helpfulness and the advisers' self-reports on their chosen strategy. Overall, our results suggest that humans (i) employ hierarchical generative models to infer on the changing intentions of others, (ii) use volatility estimates to inform decision-making in social interactions, and (iii) integrate estimates of advice accuracy with non-social sources of information. The Bayesian framework presented here can quantify individual differences in these mechanisms from simple behavioral readouts and may prove useful in future clinical studies of maladaptive social cognition. PMID:25187943

Sparse Bayesian learning machine for real-time management of reservoir releases

NASA Astrophysics Data System (ADS)

Khalil, Abedalrazq; McKee, Mac; Kemblowski, Mariush; Asefa, Tirusew

2005-11-01

Water scarcity and uncertainties in forecasting future water availabilities present serious problems for basin-scale water management. These problems create a need for intelligent prediction models that learn and adapt to their environment in order to provide water managers with decision-relevant information related to the operation of river systems. This manuscript presents examples of state-of-the-art techniques for forecasting that combine excellent generalization properties and sparse representation within a Bayesian paradigm. The techniques are demonstrated as decision tools to enhance real-time water management. A relevance vector machine, which is a probabilistic model, has been used in an online fashion to provide confident forecasts given knowledge of some state and exogenous conditions. In practical applications, online algorithms should recognize changes in the input space and account for drift in system behavior. Support vectors machines lend themselves particularly well to the detection of drift and hence to the initiation of adaptation in response to a recognized shift in system structure. The resulting model will normally have a structure and parameterization that suits the information content of the available data. The utility and practicality of this proposed approach have been demonstrated with an application in a real case study involving real-time operation of a reservoir in a river basin in southern Utah.

Modelling Trial-by-Trial Changes in the Mismatch Negativity

PubMed Central

Lieder, Falk; Daunizeau, Jean; Garrido, Marta I.; Friston, Karl J.; Stephan, Klaas E.

2013-01-01

The mismatch negativity (MMN) is a differential brain response to violations of learned regularities. It has been used to demonstrate that the brain learns the statistical structure of its environment and predicts future sensory inputs. However, the algorithmic nature of these computations and the underlying neurobiological implementation remain controversial. This article introduces a mathematical framework with which competing ideas about the computational quantities indexed by MMN responses can be formalized and tested against single-trial EEG data. This framework was applied to five major theories of the MMN, comparing their ability to explain trial-by-trial changes in MMN amplitude. Three of these theories (predictive coding, model adjustment, and novelty detection) were formalized by linking the MMN to different manifestations of the same computational mechanism: approximate Bayesian inference according to the free-energy principle. We thereby propose a unifying view on three distinct theories of the MMN. The relative plausibility of each theory was assessed against empirical single-trial MMN amplitudes acquired from eight healthy volunteers in a roving oddball experiment. Models based on the free-energy principle provided more plausible explanations of trial-by-trial changes in MMN amplitude than models representing the two more traditional theories (change detection and adaptation). Our results suggest that the MMN reflects approximate Bayesian learning of sensory regularities, and that the MMN-generating process adjusts a probabilistic model of the environment according to prediction errors. PMID:23436989

Linking urbanization to the Biological Condition Gradient (BCG) for stream ecosystems in the Northeastern United States using a Bayesian network approach

USGS Publications Warehouse

Kashuba, Roxolana; McMahon, Gerard; Cuffney, Thomas F.; Qian, Song; Reckhow, Kenneth; Gerritsen, Jeroen; Davies, Susan

2012-01-01

In realization of the aforementioned advantages, a Bayesian network model was constructed to characterize the effect of urban development on aquatic macroinvertebrate stream communities through three simultaneous, interacting ecological pathways affecting stream hydrology, habitat, and water quality across watersheds in the Northeastern United States. This model incorporates both empirical data and expert knowledge to calculate the probabilities of attaining desired aquatic ecosystem conditions under different urban stress levels, environmental conditions, and management options. Ecosystem conditions are characterized in terms of standardized Biological Condition Gradient (BCG) management endpoints. This approach to evaluating urban development-induced perturbations in watersheds integrates statistical and mechanistic perspectives, different information sources, and several ecological processes into a comprehensive description of the system that can be used to support decision making. The completed model can be used to infer which management actions would lead to the highest likelihood of desired BCG tier achievement. For example, if best management practices (BMP) were implemented in a highly urbanized watershed to reduce flashiness to medium levels and specific conductance to low levels, the stream would have a 70-percent chance of achieving BCG Tier 3 or better, relative to a 24-percent achievement likelihood for unmanaged high urban land cover. Results are reported probabilistically to account for modeling uncertainty that is inherent in sources such as natural variability and model simplification error.

Bayesian deterministic decision making: a normative account of the operant matching law and heavy-tailed reward history dependency of choices.

PubMed

Saito, Hiroshi; Katahira, Kentaro; Okanoya, Kazuo; Okada, Masato

2014-01-01

The decision making behaviors of humans and animals adapt and then satisfy an "operant matching law" in certain type of tasks. This was first pointed out by Herrnstein in his foraging experiments on pigeons. The matching law has been one landmark for elucidating the underlying processes of decision making and its learning in the brain. An interesting question is whether decisions are made deterministically or probabilistically. Conventional learning models of the matching law are based on the latter idea; they assume that subjects learn choice probabilities of respective alternatives and decide stochastically with the probabilities. However, it is unknown whether the matching law can be accounted for by a deterministic strategy or not. To answer this question, we propose several deterministic Bayesian decision making models that have certain incorrect beliefs about an environment. We claim that a simple model produces behavior satisfying the matching law in static settings of a foraging task but not in dynamic settings. We found that the model that has a belief that the environment is volatile works well in the dynamic foraging task and exhibits undermatching, which is a slight deviation from the matching law observed in many experiments. This model also demonstrates the double-exponential reward history dependency of a choice and a heavier-tailed run-length distribution, as has recently been reported in experiments on monkeys.

Wind power application research on the fusion of the determination and ensemble prediction

NASA Astrophysics Data System (ADS)

Lan, Shi; Lina, Xu; Yuzhu, Hao

2017-07-01

The fused product of wind speed for the wind farm is designed through the use of wind speed products of ensemble prediction from the European Centre for Medium-Range Weather Forecasts (ECMWF) and professional numerical model products on wind power based on Mesoscale Model5 (MM5) and Beijing Rapid Update Cycle (BJ-RUC), which are suitable for short-term wind power forecasting and electric dispatch. The single-valued forecast is formed by calculating the different ensemble statistics of the Bayesian probabilistic forecasting representing the uncertainty of ECMWF ensemble prediction. Using autoregressive integrated moving average (ARIMA) model to improve the time resolution of the single-valued forecast, and based on the Bayesian model averaging (BMA) and the deterministic numerical model prediction, the optimal wind speed forecasting curve and the confidence interval are provided. The result shows that the fusion forecast has made obvious improvement to the accuracy relative to the existing numerical forecasting products. Compared with the 0-24 h existing deterministic forecast in the validation period, the mean absolute error (MAE) is decreased by 24.3 % and the correlation coefficient (R) is increased by 12.5 %. In comparison with the ECMWF ensemble forecast, the MAE is reduced by 11.7 %, and R is increased 14.5 %. Additionally, MAE did not increase with the prolongation of the forecast ahead.

Sensitivity of a Bayesian atmospheric-transport inversion model to spatio-temporal sensor resolution applied to the 2006 North Korean nuclear test

NASA Astrophysics Data System (ADS)

Lundquist, K. A.; Jensen, D. D.; Lucas, D. D.

2017-12-01

Atmospheric source reconstruction allows for the probabilistic estimate of source characteristics of an atmospheric release using observations of the release. Performance of the inversion depends partially on the temporal frequency and spatial scale of the observations. The objective of this study is to quantify the sensitivity of the source reconstruction method to sparse spatial and temporal observations. To this end, simulations of atmospheric transport of noble gasses are created for the 2006 nuclear test at the Punggye-ri nuclear test site. Synthetic observations are collected from the simulation, and are taken as "ground truth". Data denial techniques are used to progressively coarsen the temporal and spatial resolution of the synthetic observations, while the source reconstruction model seeks to recover the true input parameters from the synthetic observations. Reconstructed parameters considered here are source location, source timing and source quantity. Reconstruction is achieved by running an ensemble of thousands of dispersion model runs that sample from a uniform distribution of the input parameters. Machine learning is used to train a computationally-efficient surrogate model from the ensemble simulations. Monte Carlo sampling and Bayesian inversion are then used in conjunction with the surrogate model to quantify the posterior probability density functions of source input parameters. This research seeks to inform decision makers of the tradeoffs between more expensive, high frequency observations and less expensive, low frequency observations.

Guided SAR image despeckling with probabilistic non local weights

NASA Astrophysics Data System (ADS)

Gokul, Jithin; Nair, Madhu S.; Rajan, Jeny

2017-12-01

SAR images are generally corrupted by granular disturbances called speckle, which makes visual analysis and detail extraction a difficult task. Non Local despeckling techniques with probabilistic similarity has been a recent trend in SAR despeckling. To achieve effective speckle suppression without compromising detail preservation, we propose an improvement for the existing Generalized Guided Filter with Bayesian Non-Local Means (GGF-BNLM) method. The proposed method (Guided SAR Image Despeckling with Probabilistic Non Local Weights) replaces parametric constants based on heuristics in GGF-BNLM method with dynamically derived values based on the image statistics for weight computation. Proposed changes make GGF-BNLM method adaptive and as a result, significant improvement is achieved in terms of performance. Experimental analysis on SAR images shows excellent speckle reduction without compromising feature preservation when compared to GGF-BNLM method. Results are also compared with other state-of-the-art and classic SAR depseckling techniques to demonstrate the effectiveness of the proposed method.

Bayesian estimation of magma supply, storage, and eruption rates using a multiphysical volcano model: Kīlauea Volcano, 2000-2012

NASA Astrophysics Data System (ADS)

Anderson, Kyle R.; Poland, Michael P.

2016-08-01

Estimating rates of magma supply to the world's volcanoes remains one of the most fundamental aims of volcanology. Yet, supply rates can be difficult to estimate even at well-monitored volcanoes, in part because observations are noisy and are usually considered independently rather than as part of a holistic system. In this work we demonstrate a technique for probabilistically estimating time-variable rates of magma supply to a volcano through probabilistic constraint on storage and eruption rates. This approach utilizes Bayesian joint inversion of diverse datasets using predictions from a multiphysical volcano model, and independent prior information derived from previous geophysical, geochemical, and geological studies. The solution to the inverse problem takes the form of a probability density function which takes into account uncertainties in observations and prior information, and which we sample using a Markov chain Monte Carlo algorithm. Applying the technique to Kīlauea Volcano, we develop a model which relates magma flow rates with deformation of the volcano's surface, sulfur dioxide emission rates, lava flow field volumes, and composition of the volcano's basaltic magma. This model accounts for effects and processes mostly neglected in previous supply rate estimates at Kīlauea, including magma compressibility, loss of sulfur to the hydrothermal system, and potential magma storage in the volcano's deep rift zones. We jointly invert data and prior information to estimate rates of supply, storage, and eruption during three recent quasi-steady-state periods at the volcano. Results shed new light on the time-variability of magma supply to Kīlauea, which we find to have increased by 35-100% between 2001 and 2006 (from 0.11-0.17 to 0.18-0.28 km3/yr), before subsequently decreasing to 0.08-0.12 km3/yr by 2012. Changes in supply rate directly impact hazard at the volcano, and were largely responsible for an increase in eruption rate of 60-150% between 2001 and 2006, and subsequent decline by as much as 60% by 2012. We also demonstrate the occurrence of temporal changes in the proportion of Kīlauea's magma supply that is stored versus erupted, with the supply ;surge; in 2006 associated with increased accumulation of magma at the summit. Finally, we are able to place some constraints on sulfur concentrations in Kīlauea magma and the scrubbing of sulfur by the volcano's hydrothermal system. Multiphysical, Bayesian constraint on magma flow rates may be used to monitor evolving volcanic hazard not just at Kīlauea but at other volcanoes around the world.

Predictive coarse-graining

NASA Astrophysics Data System (ADS)

Schöberl, Markus; Zabaras, Nicholas; Koutsourelakis, Phaedon-Stelios

2017-03-01

We propose a data-driven, coarse-graining formulation in the context of equilibrium statistical mechanics. In contrast to existing techniques which are based on a fine-to-coarse map, we adopt the opposite strategy by prescribing a probabilistic coarse-to-fine map. This corresponds to a directed probabilistic model where the coarse variables play the role of latent generators of the fine scale (all-atom) data. From an information-theoretic perspective, the framework proposed provides an improvement upon the relative entropy method [1] and is capable of quantifying the uncertainty due to the information loss that unavoidably takes place during the coarse-graining process. Furthermore, it can be readily extended to a fully Bayesian model where various sources of uncertainties are reflected in the posterior of the model parameters. The latter can be used to produce not only point estimates of fine-scale reconstructions or macroscopic observables, but more importantly, predictive posterior distributions on these quantities. Predictive posterior distributions reflect the confidence of the model as a function of the amount of data and the level of coarse-graining. The issues of model complexity and model selection are seamlessly addressed by employing a hierarchical prior that favors the discovery of sparse solutions, revealing the most prominent features in the coarse-grained model. A flexible and parallelizable Monte Carlo - Expectation-Maximization (MC-EM) scheme is proposed for carrying out inference and learning tasks. A comparative assessment of the proposed methodology is presented for a lattice spin system and the SPC/E water model.

Predictive coarse-graining

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schöberl, Markus, E-mail: m.schoeberl@tum.de; Zabaras, Nicholas; Department of Aerospace and Mechanical Engineering, University of Notre Dame, 365 Fitzpatrick Hall, Notre Dame, IN 46556

We propose a data-driven, coarse-graining formulation in the context of equilibrium statistical mechanics. In contrast to existing techniques which are based on a fine-to-coarse map, we adopt the opposite strategy by prescribing a probabilistic coarse-to-fine map. This corresponds to a directed probabilistic model where the coarse variables play the role of latent generators of the fine scale (all-atom) data. From an information-theoretic perspective, the framework proposed provides an improvement upon the relative entropy method and is capable of quantifying the uncertainty due to the information loss that unavoidably takes place during the coarse-graining process. Furthermore, it can be readily extendedmore » to a fully Bayesian model where various sources of uncertainties are reflected in the posterior of the model parameters. The latter can be used to produce not only point estimates of fine-scale reconstructions or macroscopic observables, but more importantly, predictive posterior distributions on these quantities. Predictive posterior distributions reflect the confidence of the model as a function of the amount of data and the level of coarse-graining. The issues of model complexity and model selection are seamlessly addressed by employing a hierarchical prior that favors the discovery of sparse solutions, revealing the most prominent features in the coarse-grained model. A flexible and parallelizable Monte Carlo – Expectation–Maximization (MC-EM) scheme is proposed for carrying out inference and learning tasks. A comparative assessment of the proposed methodology is presented for a lattice spin system and the SPC/E water model.« less

Bayesian tomography and integrated data analysis in fusion diagnostics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Dong, E-mail: lid@swip.ac.cn; Dong, Y. B.; Deng, Wei

2016-11-15

In this article, a Bayesian tomography method using non-stationary Gaussian process for a prior has been introduced. The Bayesian formalism allows quantities which bear uncertainty to be expressed in the probabilistic form so that the uncertainty of a final solution can be fully resolved from the confidence interval of a posterior probability. Moreover, a consistency check of that solution can be performed by checking whether the misfits between predicted and measured data are reasonably within an assumed data error. In particular, the accuracy of reconstructions is significantly improved by using the non-stationary Gaussian process that can adapt to the varyingmore » smoothness of emission distribution. The implementation of this method to a soft X-ray diagnostics on HL-2A has been used to explore relevant physics in equilibrium and MHD instability modes. This project is carried out within a large size inference framework, aiming at an integrated analysis of heterogeneous diagnostics.« less

How might Model-based Probabilities Extracted from Imperfect Models Guide Rational Decisions: The Case for non-probabilistic odds

NASA Astrophysics Data System (ADS)

Smith, Leonard A.

2010-05-01

This contribution concerns "deep" or "second-order" uncertainty, such as the uncertainty in our probability forecasts themselves. It asks the question: "Is it rational to take (or offer) bets using model-based probabilities as if they were objective probabilities?" If not, what alternative approaches for determining odds, perhaps non-probabilistic odds, might prove useful in practice, given the fact we know our models are imperfect? We consider the case where the aim is to provide sustainable odds: not to produce a profit but merely to rationally expect to break even in the long run. In other words, to run a quantified risk of ruin that is relatively small. Thus the cooperative insurance schemes of coastal villages provide a more appropriate parallel than a casino. A "better" probability forecast would lead to lower premiums charged and less volatile fluctuations in the cash reserves of the village. Note that the Bayesian paradigm does not constrain one to interpret model distributions as subjective probabilities, unless one believes the model to be empirically adequate for the task at hand. In geophysics, this is rarely the case. When a probability forecast is interpreted as the objective probability of an event, the odds on that event can be easily computed as one divided by the probability of the event, and one need not favour taking either side of the wager. (Here we are using "odds-for" not "odds-to", the difference being whether of not the stake is returned; odds of one to one are equivalent to odds of two for one.) The critical question is how to compute sustainable odds based on information from imperfect models. We suggest that this breaks the symmetry between the odds-on an event and the odds-against it. While a probability distribution can always be translated into odds, interpreting the odds on a set of events might result in "implied-probabilities" that sum to more than one. And/or the set of odds may be incomplete, not covering all events. We ask whether or not probabilities based on imperfect models can be expected to yield probabilistic odds which are sustainable. Evidence is provided that suggest this is not the case. Even with very good models (good in an Root-Mean-Square sense), the risk of ruin of probabilistic odds is significantly higher than might be expected. Methods for constructing model-based non-probabilistic odds which are sustainable are discussed. The aim here is to be relevant to real world decision support, and so unrealistic assumptions of equal knowledge, equal compute power, or equal access to information are to be avoided. Finally, the use of non-probabilistic odds as a method for communicating deep uncertainty (uncertainty in a probability forecast itself) is discussed in the context of other methods, such as stating one's subjective probability that the models will prove inadequate in each particular instance (that is, the Probability of a "Big Surprise").

Statistical surrogate models for prediction of high-consequence climate change.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Constantine, Paul; Field, Richard V., Jr.; Boslough, Mark Bruce Elrick

2011-09-01

In safety engineering, performance metrics are defined using probabilistic risk assessments focused on the low-probability, high-consequence tail of the distribution of possible events, as opposed to best estimates based on central tendencies. We frame the climate change problem and its associated risks in a similar manner. To properly explore the tails of the distribution requires extensive sampling, which is not possible with existing coupled atmospheric models due to the high computational cost of each simulation. We therefore propose the use of specialized statistical surrogate models (SSMs) for the purpose of exploring the probability law of various climate variables of interest.more » A SSM is different than a deterministic surrogate model in that it represents each climate variable of interest as a space/time random field. The SSM can be calibrated to available spatial and temporal data from existing climate databases, e.g., the Program for Climate Model Diagnosis and Intercomparison (PCMDI), or to a collection of outputs from a General Circulation Model (GCM), e.g., the Community Earth System Model (CESM) and its predecessors. Because of its reduced size and complexity, the realization of a large number of independent model outputs from a SSM becomes computationally straightforward, so that quantifying the risk associated with low-probability, high-consequence climate events becomes feasible. A Bayesian framework is developed to provide quantitative measures of confidence, via Bayesian credible intervals, in the use of the proposed approach to assess these risks.« less

Development of a Bayesian model to estimate health care outcomes in the severely wounded

PubMed Central

Stojadinovic, Alexander; Eberhardt, John; Brown, Trevor S; Hawksworth, Jason S; Gage, Frederick; Tadaki, Douglas K; Forsberg, Jonathan A; Davis, Thomas A; Potter, Benjamin K; Dunne, James R; Elster, E A

2010-01-01

Background: Graphical probabilistic models have the ability to provide insights as to how clinical factors are conditionally related. These models can be used to help us understand factors influencing health care outcomes and resource utilization, and to estimate morbidity and clinical outcomes in trauma patient populations. Study design: Thirty-two combat casualties with severe extremity injuries enrolled in a prospective observational study were analyzed using step-wise machine-learned Bayesian belief network (BBN) and step-wise logistic regression (LR). Models were evaluated using 10-fold cross-validation to calculate area-under-the-curve (AUC) from receiver operating characteristics (ROC) curves. Results: Our BBN showed important associations between various factors in our data set that could not be developed using standard regression methods. Cross-validated ROC curve analysis showed that our BBN model was a robust representation of our data domain and that LR models trained on these findings were also robust: hospital-acquired infection (AUC: LR, 0.81; BBN, 0.79), intensive care unit length of stay (AUC: LR, 0.97; BBN, 0.81), and wound healing (AUC: LR, 0.91; BBN, 0.72) showed strong AUC. Conclusions: A BBN model can effectively represent clinical outcomes and biomarkers in patients hospitalized after severe wounding, and is confirmed by 10-fold cross-validation and further confirmed through logistic regression modeling. The method warrants further development and independent validation in other, more diverse patient populations. PMID:21197361

SU-F-R-44: Modeling Lung SBRT Tumor Response Using Bayesian Network Averaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Diamant, A; Ybarra, N; Seuntjens, J

2016-06-15

Purpose: The prediction of tumor control after a patient receives lung SBRT (stereotactic body radiation therapy) has proven to be challenging, due to the complex interactions between an individual’s biology and dose-volume metrics. Many of these variables have predictive power when combined, a feature that we exploit using a graph modeling approach based on Bayesian networks. This provides a probabilistic framework that allows for accurate and visually intuitive predictive modeling. The aim of this study is to uncover possible interactions between an individual patient’s characteristics and generate a robust model capable of predicting said patient’s treatment outcome. Methods: We investigatedmore » a cohort of 32 prospective patients from multiple institutions whom had received curative SBRT to the lung. The number of patients exhibiting tumor failure was observed to be 7 (event rate of 22%). The serum concentration of 5 biomarkers previously associated with NSCLC (non-small cell lung cancer) was measured pre-treatment. A total of 21 variables were analyzed including: dose-volume metrics with BED (biologically effective dose) correction and clinical variables. A Markov Chain Monte Carlo technique estimated the posterior probability distribution of the potential graphical structures. The probability of tumor failure was then estimated by averaging the top 100 graphs and applying Baye’s rule. Results: The optimal Bayesian model generated throughout this study incorporated the PTV volume, the serum concentration of the biomarker EGFR (epidermal growth factor receptor) and prescription BED. This predictive model recorded an area under the receiver operating characteristic curve of 0.94(1), providing better performance compared to competing methods in other literature. Conclusion: The use of biomarkers in conjunction with dose-volume metrics allows for the generation of a robust predictive model. The preliminary results of this report demonstrate that it is possible to accurately model the prognosis of an individual lung SBRT patient’s treatment.« less

Evaluating the Performance of a Climate-Driven Mortality Model during Heat Waves and Cold Spells in Europe

PubMed Central

Lowe, Rachel; Ballester, Joan; Creswick, James; Robine, Jean-Marie; Herrmann, François R.; Rodó, Xavier

2015-01-01

The impact of climate change on human health is a serious concern. In particular, changes in the frequency and intensity of heat waves and cold spells are of high relevance in terms of mortality and morbidity. This demonstrates the urgent need for reliable early-warning systems to help authorities prepare and respond to emergency situations. In this study, we evaluate the performance of a climate-driven mortality model to provide probabilistic predictions of exceeding emergency mortality thresholds for heat wave and cold spell scenarios. Daily mortality data corresponding to 187 NUTS2 regions across 16 countries in Europe were obtained from 1998–2003. Data were aggregated to 54 larger regions in Europe, defined according to similarities in population structure and climate. Location-specific average mortality rates, at given temperature intervals over the time period, were modelled to account for the increased mortality observed during both high and low temperature extremes and differing comfort temperatures between regions. Model parameters were estimated in a Bayesian framework, in order to generate probabilistic simulations of mortality across Europe for time periods of interest. For the heat wave scenario (1–15 August 2003), the model was successfully able to anticipate the occurrence or non-occurrence of mortality rates exceeding the emergency threshold (75th percentile of the mortality distribution) for 89% of the 54 regions, given a probability decision threshold of 70%. For the cold spell scenario (1–15 January 2003), mortality events in 69% of the regions were correctly anticipated with a probability decision threshold of 70%. By using a more conservative decision threshold of 30%, this proportion increased to 87%. Overall, the model performed better for the heat wave scenario. By replacing observed temperature data in the model with forecast temperature, from state-of-the-art European forecasting systems, probabilistic mortality predictions could potentially be made several months ahead of imminent heat waves and cold spells. PMID:25625407

Evaluating the performance of a climate-driven mortality model during heat waves and cold spells in Europe.

PubMed

Lowe, Rachel; Ballester, Joan; Creswick, James; Robine, Jean-Marie; Herrmann, François R; Rodó, Xavier

2015-01-23

The impact of climate change on human health is a serious concern. In particular, changes in the frequency and intensity of heat waves and cold spells are of high relevance in terms of mortality and morbidity. This demonstrates the urgent need for reliable early-warning systems to help authorities prepare and respond to emergency situations. In this study, we evaluate the performance of a climate-driven mortality model to provide probabilistic predictions of exceeding emergency mortality thresholds for heat wave and cold spell scenarios. Daily mortality data corresponding to 187 NUTS2 regions across 16 countries in Europe were obtained from 1998-2003. Data were aggregated to 54 larger regions in Europe, defined according to similarities in population structure and climate. Location-specific average mortality rates, at given temperature intervals over the time period, were modelled to account for the increased mortality observed during both high and low temperature extremes and differing comfort temperatures between regions. Model parameters were estimated in a Bayesian framework, in order to generate probabilistic simulations of mortality across Europe for time periods of interest. For the heat wave scenario (1-15 August 2003), the model was successfully able to anticipate the occurrence or non-occurrence of mortality rates exceeding the emergency threshold (75th percentile of the mortality distribution) for 89% of the 54 regions, given a probability decision threshold of 70%. For the cold spell scenario (1-15 January 2003), mortality events in 69% of the regions were correctly anticipated with a probability decision threshold of 70%. By using a more conservative decision threshold of 30%, this proportion increased to 87%. Overall, the model performed better for the heat wave scenario. By replacing observed temperature data in the model with forecast temperature, from state-of-the-art European forecasting systems, probabilistic mortality predictions could potentially be made several months ahead of imminent heat waves and cold spells.

Multimodal Speaker Diarization.

PubMed

Noulas, A; Englebienne, G; Krose, B J A

2012-01-01

We present a novel probabilistic framework that fuses information coming from the audio and video modality to perform speaker diarization. The proposed framework is a Dynamic Bayesian Network (DBN) that is an extension of a factorial Hidden Markov Model (fHMM) and models the people appearing in an audiovisual recording as multimodal entities that generate observations in the audio stream, the video stream, and the joint audiovisual space. The framework is very robust to different contexts, makes no assumptions about the location of the recording equipment, and does not require labeled training data as it acquires the model parameters using the Expectation Maximization (EM) algorithm. We apply the proposed model to two meeting videos and a news broadcast video, all of which come from publicly available data sets. The results acquired in speaker diarization are in favor of the proposed multimodal framework, which outperforms the single modality analysis results and improves over the state-of-the-art audio-based speaker diarization.

The method of belief scales as a means for dealing with uncertainty in tough regulatory decisions.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pilch, Martin M.

Modeling and simulation is playing an increasing role in supporting tough regulatory decisions, which are typically characterized by variabilities and uncertainties in the scenarios, input conditions, failure criteria, model parameters, and even model form. Variability exists when there is a statistically significant database that is fully relevant to the application. Uncertainty, on the other hand, is characterized by some degree of ignorance. A simple algebraic problem was used to illustrate how various risk methodologies address variability and uncertainty in a regulatory context. These traditional risk methodologies include probabilistic methods (including frequensic and Bayesian perspectives) and second-order methods where variabilities andmore » uncertainties are treated separately. Representing uncertainties with (subjective) probability distributions and using probabilistic methods to propagate subjective distributions can lead to results that are not logically consistent with available knowledge and that may not be conservative. The Method of Belief Scales (MBS) is developed as a means to logically aggregate uncertain input information and to propagate that information through the model to a set of results that are scrutable, easily interpretable by the nonexpert, and logically consistent with the available input information. The MBS, particularly in conjunction with sensitivity analyses, has the potential to be more computationally efficient than other risk methodologies. The regulatory language must be tailored to the specific risk methodology if ambiguity and conflict are to be avoided.« less

A probabilistic approach to interpreting verbal autopsies: methodology and preliminary validation in Vietnam.

PubMed

Byass, Peter; Huong, Dao Lan; Minh, Hoang Van

2003-01-01

Verbal autopsy (VA) has become an important tool in the past 20 years for determining cause of death in communities where there is no routine registration. In many cases, expert physicians have been used to interpret the VA findings and so assign individual causes of death. However, this is time consuming and not always repeatable. Other approaches such as algorithms and neural networks have been developed in some settings. This paper aims to develop a method that is simple, reliable and consistent, which could represent an advance in VA interpretation. This paper describes the development of a Bayesian probability model for VA interpretation as an attempt to find a better approach. This methodology and a preliminary implementation are described, with an evaluation based on VA material from rural Vietnam. The new model was tested against a series of 189 VA interviews from a rural community in Vietnam. Using this very basic model, over 70% of individual causes of death corresponded with those determined by two physicians increasing to over 80% if those cases ascribed to old age or as being indeterminate by the physicians were excluded. Although there is a clear need to improve the preliminary model and to test more extensively with larger and more varied datasets, these preliminary results suggest that there may be good potential in this probabilistic approach.

Probabilistic parameter estimation of activated sludge processes using Markov Chain Monte Carlo.

PubMed

Sharifi, Soroosh; Murthy, Sudhir; Takács, Imre; Massoudieh, Arash

2014-03-01

One of the most important challenges in making activated sludge models (ASMs) applicable to design problems is identifying the values of its many stoichiometric and kinetic parameters. When wastewater characteristics data from full-scale biological treatment systems are used for parameter estimation, several sources of uncertainty, including uncertainty in measured data, external forcing (e.g. influent characteristics), and model structural errors influence the value of the estimated parameters. This paper presents a Bayesian hierarchical modeling framework for the probabilistic estimation of activated sludge process parameters. The method provides the joint probability density functions (JPDFs) of stoichiometric and kinetic parameters by updating prior information regarding the parameters obtained from expert knowledge and literature. The method also provides the posterior correlations between the parameters, as well as a measure of sensitivity of the different constituents with respect to the parameters. This information can be used to design experiments to provide higher information content regarding certain parameters. The method is illustrated using the ASM1 model to describe synthetically generated data from a hypothetical biological treatment system. The results indicate that data from full-scale systems can narrow down the ranges of some parameters substantially whereas the amount of information they provide regarding other parameters is small, due to either large correlations between some of the parameters or a lack of sensitivity with respect to the parameters. Copyright © 2013 Elsevier Ltd. All rights reserved.

Learning Probabilistic Features for Robotic Navigation Using Laser Sensors

PubMed Central

Aznar, Fidel; Pujol, Francisco A.; Pujol, Mar; Rizo, Ramón; Pujol, María-José

2014-01-01

SLAM is a popular task used by robots and autonomous vehicles to build a map of an unknown environment and, at the same time, to determine their location within the map. This paper describes a SLAM-based, probabilistic robotic system able to learn the essential features of different parts of its environment. Some previous SLAM implementations had computational complexities ranging from O(Nlog(N)) to O(N 2), where N is the number of map features. Unlike these methods, our approach reduces the computational complexity to O(N) by using a model to fuse the information from the sensors after applying the Bayesian paradigm. Once the training process is completed, the robot identifies and locates those areas that potentially match the sections that have been previously learned. After the training, the robot navigates and extracts a three-dimensional map of the environment using a single laser sensor. Thus, it perceives different sections of its world. In addition, in order to make our system able to be used in a low-cost robot, low-complexity algorithms that can be easily implemented on embedded processors or microcontrollers are used. PMID:25415377

Learning probabilistic features for robotic navigation using laser sensors.

PubMed

Aznar, Fidel; Pujol, Francisco A; Pujol, Mar; Rizo, Ramón; Pujol, María-José

2014-01-01

SLAM is a popular task used by robots and autonomous vehicles to build a map of an unknown environment and, at the same time, to determine their location within the map. This paper describes a SLAM-based, probabilistic robotic system able to learn the essential features of different parts of its environment. Some previous SLAM implementations had computational complexities ranging from O(Nlog(N)) to O(N(2)), where N is the number of map features. Unlike these methods, our approach reduces the computational complexity to O(N) by using a model to fuse the information from the sensors after applying the Bayesian paradigm. Once the training process is completed, the robot identifies and locates those areas that potentially match the sections that have been previously learned. After the training, the robot navigates and extracts a three-dimensional map of the environment using a single laser sensor. Thus, it perceives different sections of its world. In addition, in order to make our system able to be used in a low-cost robot, low-complexity algorithms that can be easily implemented on embedded processors or microcontrollers are used.

Dynamic Bayesian Networks as a Probabilistic Metamodel for Combat Simulations

DTIC Science & Technology

2014-09-18

test is commonly used for large data sets and is the method of comparison presented in Section 5.5. 4.3.3 Kullback - Leibler Divergence Goodness of Fit ...methods exist that might improve the results. A goodness of fit test using the Kullback - Leibler Divergence was proposed in the first paper, but still... Kullback - Leibler Divergence Goodness of Fit Test . . .

Common problems in the elicitation and analysis of expert opinion affecting probabilistic safety assessments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meyer, M.A.; Booker, J.M.

1990-01-01

Expert opinion is frequently used in probabilistic safety assessment (PSA), particularly in estimating low probability events. In this paper, we discuss some of the common problems encountered in eliciting and analyzing expert opinion data and offer solutions or recommendations. The problems are: that experts are not naturally Bayesian. People fail to update their existing information to account for new information as it becomes available, as would be predicted by the Bayesian philosophy; that experts cannot be fully calibrated. To calibrate experts, the feedback from the known quantities must be immediate, frequent, and specific to the task; that experts are limitedmore » in the number of things that they can mentally juggle at a time to 7 {plus minus} 2; that data gatherers and analysts can introduce bias by unintentionally causing an altering of the expert's thinking or answers; that the level of detail the data, or granularity, can affect the analyses; and the conditioning effect poses difficulties in gathering and analyzing of the expert data. The data that the expert gives can be conditioned on a variety of factors that can affect the analysis and the interpretation of the results. 31 refs.« less

A Bayesian model for estimating multi-state disease progression.

PubMed

Shen, Shiwen; Han, Simon X; Petousis, Panayiotis; Weiss, Robert E; Meng, Frank; Bui, Alex A T; Hsu, William

2017-02-01

A growing number of individuals who are considered at high risk of cancer are now routinely undergoing population screening. However, noted harms such as radiation exposure, overdiagnosis, and overtreatment underscore the need for better temporal models that predict who should be screened and at what frequency. The mean sojourn time (MST), an average duration period when a tumor can be detected by imaging but with no observable clinical symptoms, is a critical variable for formulating screening policy. Estimation of MST has been long studied using continuous Markov model (CMM) with Maximum likelihood estimation (MLE). However, a lot of traditional methods assume no observation error of the imaging data, which is unlikely and can bias the estimation of the MST. In addition, the MLE may not be stably estimated when data is sparse. Addressing these shortcomings, we present a probabilistic modeling approach for periodic cancer screening data. We first model the cancer state transition using a three state CMM model, while simultaneously considering observation error. We then jointly estimate the MST and observation error within a Bayesian framework. We also consider the inclusion of covariates to estimate individualized rates of disease progression. Our approach is demonstrated on participants who underwent chest x-ray screening in the National Lung Screening Trial (NLST) and validated using posterior predictive p-values and Pearson's chi-square test. Our model demonstrates more accurate and sensible estimates of MST in comparison to MLE. Copyright © 2016 Elsevier Ltd. All rights reserved.

Boosting Bayesian parameter inference of nonlinear stochastic differential equation models by Hamiltonian scale separation.

PubMed

Albert, Carlo; Ulzega, Simone; Stoop, Ruedi

2016-04-01

Parameter inference is a fundamental problem in data-driven modeling. Given observed data that is believed to be a realization of some parameterized model, the aim is to find parameter values that are able to explain the observed data. In many situations, the dominant sources of uncertainty must be included into the model for making reliable predictions. This naturally leads to stochastic models. Stochastic models render parameter inference much harder, as the aim then is to find a distribution of likely parameter values. In Bayesian statistics, which is a consistent framework for data-driven learning, this so-called posterior distribution can be used to make probabilistic predictions. We propose a novel, exact, and very efficient approach for generating posterior parameter distributions for stochastic differential equation models calibrated to measured time series. The algorithm is inspired by reinterpreting the posterior distribution as a statistical mechanics partition function of an object akin to a polymer, where the measurements are mapped on heavier beads compared to those of the simulated data. To arrive at distribution samples, we employ a Hamiltonian Monte Carlo approach combined with a multiple time-scale integration. A separation of time scales naturally arises if either the number of measurement points or the number of simulation points becomes large. Furthermore, at least for one-dimensional problems, we can decouple the harmonic modes between measurement points and solve the fastest part of their dynamics analytically. Our approach is applicable to a wide range of inference problems and is highly parallelizable.

Exact calculation of distributions on integers, with application to sequence alignment.

PubMed

Newberg, Lee A; Lawrence, Charles E

2009-01-01

Computational biology is replete with high-dimensional discrete prediction and inference problems. Dynamic programming recursions can be applied to several of the most important of these, including sequence alignment, RNA secondary-structure prediction, phylogenetic inference, and motif finding. In these problems, attention is frequently focused on some scalar quantity of interest, a score, such as an alignment score or the free energy of an RNA secondary structure. In many cases, score is naturally defined on integers, such as a count of the number of pairing differences between two sequence alignments, or else an integer score has been adopted for computational reasons, such as in the test of significance of motif scores. The probability distribution of the score under an appropriate probabilistic model is of interest, such as in tests of significance of motif scores, or in calculation of Bayesian confidence limits around an alignment. Here we present three algorithms for calculating the exact distribution of a score of this type; then, in the context of pairwise local sequence alignments, we apply the approach so as to find the alignment score distribution and Bayesian confidence limits.

Modelling ecosystem service flows under uncertainty with stochiastic SPAN

USGS Publications Warehouse

Johnson, Gary W.; Snapp, Robert R.; Villa, Ferdinando; Bagstad, Kenneth J.

2012-01-01

Ecosystem service models are increasingly in demand for decision making. However, the data required to run these models are often patchy, missing, outdated, or untrustworthy. Further, communication of data and model uncertainty to decision makers is often either absent or unintuitive. In this work, we introduce a systematic approach to addressing both the data gap and the difficulty in communicating uncertainty through a stochastic adaptation of the Service Path Attribution Networks (SPAN) framework. The SPAN formalism assesses ecosystem services through a set of up to 16 maps, which characterize the services in a study area in terms of flow pathways between ecosystems and human beneficiaries. Although the SPAN algorithms were originally defined deterministically, we present them here in a stochastic framework which combines probabilistic input data with a stochastic transport model in order to generate probabilistic spatial outputs. This enables a novel feature among ecosystem service models: the ability to spatially visualize uncertainty in the model results. The stochastic SPAN model can analyze areas where data limitations are prohibitive for deterministic models. Greater uncertainty in the model inputs (including missing data) should lead to greater uncertainty expressed in the model’s output distributions. By using Bayesian belief networks to fill data gaps and expert-provided trust assignments to augment untrustworthy or outdated information, we can account for uncertainty in input data, producing a model that is still able to run and provide information where strictly deterministic models could not. Taken together, these attributes enable more robust and intuitive modelling of ecosystem services under uncertainty.

Automatized near-real-time short-term Probabilistic Volcanic Hazard Assessment of tephra dispersion before and during eruptions: BET_VHst for Mt. Etna

NASA Astrophysics Data System (ADS)

Selva, Jacopo; Scollo, Simona; Costa, Antonio; Brancato, Alfonso; Prestifilippo, Michele

2015-04-01

Tephra dispersal, even in small amounts, may heavily affect public health and critical infrastructures, such as airports, train and road networks, and electric power supply systems. Probabilistic Volcanic Hazard Assessment (PVHA) represents the most complete scientific contribution for planning rational strategies aimed at managing and mitigating the risk posed by activity during volcanic crises and during eruptions. Short-term PVHA (over time intervals in the order of hours to few days) must account for rapidly changing information coming from the monitoring system, as well as, updated wind forecast, and they must be accomplished in near-real-time. In addition, while during unrest the primary goal is to forecast potential eruptions, during eruptions it is also fundamental to correctly account for the real-time status of the eruption and of tephra dispersal, as well as its potential evolution in the short-term. Here, we present a preliminary application of BET_VHst model (Selva et al. 2014) for Mt. Etna. The model has its roots into present state deterministic procedure, and it deals with the large uncertainty that such procedures typically ignore, like uncertainty on the potential position of the vent and eruptive size, on the possible evolution of volcanological input during ongoing eruptions, as well as, on wind field. Uncertainty is treated by making use of Bayesian inference, alternative modeling procedures for tephra dispersal, and statistical mixing of long- and short-term analyses. References Selva J., Costa A., Sandri L., Macedonio G., Marzocchi W. (2014) Probabilistic short-term volcanic hazard in phases of unrest: a case study for tephra fallout, J. Geophys. Res., 119, doi: 10.1002/2014JB011252

Bayesian networks for satellite payload testing

NASA Astrophysics Data System (ADS)

Przytula, Krzysztof W.; Hagen, Frank; Yung, Kar

1999-11-01

Satellite payloads are fast increasing in complexity, resulting in commensurate growth in cost of manufacturing and operation. A need exists for a software tool, which would assist engineers in production and operation of satellite systems. We have designed and implemented a software tool, which performs part of this task. The tool aids a test engineer in debugging satellite payloads during system testing. At this stage of satellite integration and testing both the tested payload and the testing equipment represent complicated systems consisting of a very large number of components and devices. When an error is detected during execution of a test procedure, the tool presents to the engineer a ranked list of potential sources of the error and a list of recommended further tests. The engineer decides this on this basis if to perform some of the recommended additional test or replace the suspect component. The tool has been installed in payload testing facility. The tool is based on Bayesian networks, a graphical method of representing uncertainty in terms of probabilistic influences. The Bayesian network was configured using detailed flow diagrams of testing procedures and block diagrams of the payload and testing hardware. The conditional and prior probability values were initially obtained from experts and refined in later stages of design. The Bayesian network provided a very informative model of the payload and testing equipment and inspired many new ideas regarding the future test procedures and testing equipment configurations. The tool is the first step in developing a family of tools for various phases of satellite integration and operation.

Performance assessment of a Bayesian Forecasting System (BFS) for real-time flood forecasting

NASA Astrophysics Data System (ADS)

Biondi, D.; De Luca, D. L.

2013-02-01

SummaryThe paper evaluates, for a number of flood events, the performance of a Bayesian Forecasting System (BFS), with the aim of evaluating total uncertainty in real-time flood forecasting. The predictive uncertainty of future streamflow is estimated through the Bayesian integration of two separate processors. The former evaluates the propagation of input uncertainty on simulated river discharge, the latter computes the hydrological uncertainty of actual river discharge associated with all other possible sources of error. A stochastic model and a distributed rainfall-runoff model were assumed, respectively, for rainfall and hydrological response simulations. A case study was carried out for a small basin in the Calabria region (southern Italy). The performance assessment of the BFS was performed with adequate verification tools suited for probabilistic forecasts of continuous variables such as streamflow. Graphical tools and scalar metrics were used to evaluate several attributes of the forecast quality of the entire time-varying predictive distributions: calibration, sharpness, accuracy, and continuous ranked probability score (CRPS). Besides the overall system, which incorporates both sources of uncertainty, other hypotheses resulting from the BFS properties were examined, corresponding to (i) a perfect hydrological model; (ii) a non-informative rainfall forecast for predicting streamflow; and (iii) a perfect input forecast. The results emphasize the importance of using different diagnostic approaches to perform comprehensive analyses of predictive distributions, to arrive at a multifaceted view of the attributes of the prediction. For the case study, the selected criteria revealed the interaction of the different sources of error, in particular the crucial role of the hydrological uncertainty processor when compensating, at the cost of wider forecast intervals, for the unreliable and biased predictive distribution resulting from the Precipitation Uncertainty Processor.

Markov blanket-based approach for learning multi-dimensional Bayesian network classifiers: an application to predict the European Quality of Life-5 Dimensions (EQ-5D) from the 39-item Parkinson's Disease Questionnaire (PDQ-39).

PubMed

Borchani, Hanen; Bielza, Concha; Martı Nez-Martı N, Pablo; Larrañaga, Pedro

2012-12-01

Multi-dimensional Bayesian network classifiers (MBCs) are probabilistic graphical models recently proposed to deal with multi-dimensional classification problems, where each instance in the data set has to be assigned to more than one class variable. In this paper, we propose a Markov blanket-based approach for learning MBCs from data. Basically, it consists of determining the Markov blanket around each class variable using the HITON algorithm, then specifying the directionality over the MBC subgraphs. Our approach is applied to the prediction problem of the European Quality of Life-5 Dimensions (EQ-5D) from the 39-item Parkinson's Disease Questionnaire (PDQ-39) in order to estimate the health-related quality of life of Parkinson's patients. Fivefold cross-validation experiments were carried out on randomly generated synthetic data sets, Yeast data set, as well as on a real-world Parkinson's disease data set containing 488 patients. The experimental study, including comparison with additional Bayesian network-based approaches, back propagation for multi-label learning, multi-label k-nearest neighbor, multinomial logistic regression, ordinary least squares, and censored least absolute deviations, shows encouraging results in terms of predictive accuracy as well as the identification of dependence relationships among class and feature variables. Copyright © 2012 Elsevier Inc. All rights reserved.