Science.gov

Sample records for hierarchical bayesian models

  1. Hierarchical Bayesian model updating for structural identification

    NASA Astrophysics Data System (ADS)

    Behmanesh, Iman; Moaveni, Babak; Lombaert, Geert; Papadimitriou, Costas

    2015-12-01

    A new probabilistic finite element (FE) model updating technique based on Hierarchical Bayesian modeling is proposed for identification of civil structural systems under changing ambient/environmental conditions. The performance of the proposed technique is investigated for (1) uncertainty quantification of model updating parameters, and (2) probabilistic damage identification of the structural systems. Accurate estimation of the uncertainty in modeling parameters such as mass or stiffness is a challenging task. Several Bayesian model updating frameworks have been proposed in the literature that can successfully provide the "parameter estimation uncertainty" of model parameters with the assumption that there is no underlying inherent variability in the updating parameters. However, this assumption may not be valid for civil structures where structural mass and stiffness have inherent variability due to different sources of uncertainty such as changing ambient temperature, temperature gradient, wind speed, and traffic loads. Hierarchical Bayesian model updating is capable of predicting the overall uncertainty/variability of updating parameters by assuming time-variability of the underlying linear system. A general solution based on Gibbs Sampler is proposed to estimate the joint probability distributions of the updating parameters. The performance of the proposed Hierarchical approach is evaluated numerically for uncertainty quantification and damage identification of a 3-story shear building model. Effects of modeling errors and incomplete modal data are considered in the numerical study.

  2. A Hierarchical Bayesian Model for Crowd Emotions.

    PubMed

    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

  3. 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

  4. Constructive Epistemic Modeling: A Hierarchical Bayesian Model Averaging Method

    NASA Astrophysics Data System (ADS)

    Tsai, F. T. C.; Elshall, A. S.

    2014-12-01

    Constructive epistemic modeling is the idea that our understanding of a natural system through a scientific model is a mental construct that continually develops through learning about and from the model. Using the hierarchical Bayesian model averaging (HBMA) method [1], this study shows that segregating different uncertain model components through a BMA tree of posterior model probabilities, model prediction, within-model variance, between-model variance and total model variance serves as a learning tool [2]. First, the BMA tree of posterior model probabilities permits the comparative evaluation of the candidate propositions of each uncertain model component. Second, systemic model dissection is imperative for understanding the individual contribution of each uncertain model component to the model prediction and variance. Third, the hierarchical representation of the between-model variance facilitates the prioritization of the contribution of each uncertain model component to the overall model uncertainty. We illustrate these concepts using the groundwater modeling of a siliciclastic aquifer-fault system. The sources of uncertainty considered are from geological architecture, formation dip, boundary conditions and model parameters. The study shows that the HBMA analysis helps in advancing knowledge about the model rather than forcing the model to fit a particularly understanding or merely averaging several candidate models. [1] Tsai, F. T.-C., and A. S. Elshall (2013), Hierarchical Bayesian model averaging for hydrostratigraphic modeling: Uncertainty segregation and comparative evaluation. Water Resources Research, 49, 5520-5536, doi:10.1002/wrcr.20428. [2] Elshall, A.S., and F. T.-C. Tsai (2014). Constructive epistemic modeling of groundwater flow with geological architecture and boundary condition uncertainty under Bayesian paradigm, Journal of Hydrology, 517, 105-119, doi: 10.1016/j.jhydrol.2014.05.027.

  5. Road network safety evaluation using Bayesian hierarchical joint model.

    PubMed

    Wang, Jie; Huang, Helai

    2016-05-01

    Safety and efficiency are commonly regarded as two significant performance indicators of transportation systems. In practice, road network planning has focused on road capacity and transport efficiency whereas the safety level of a road network has received little attention in the planning stage. This study develops a Bayesian hierarchical joint model for road network safety evaluation to help planners take traffic safety into account when planning a road network. The proposed model establishes relationships between road network risk and micro-level variables related to road entities and traffic volume, as well as socioeconomic, trip generation and network density variables at macro level which are generally used for long term transportation plans. In addition, network spatial correlation between intersections and their connected road segments is also considered in the model. A road network is elaborately selected in order to compare the proposed hierarchical joint model with a previous joint model and a negative binomial model. According to the results of the model comparison, the hierarchical joint model outperforms the joint model and negative binomial model in terms of the goodness-of-fit and predictive performance, which indicates the reasonableness of considering the hierarchical data structure in crash prediction and analysis. Moreover, both random effects at the TAZ level and the spatial correlation between intersections and their adjacent segments are found to be significant, supporting the employment of the hierarchical joint model as an alternative in road-network-level safety modeling as well. PMID:26945109

  6. Hierarchical Bayesian spatial models for multispecies conservation planning and monitoring.

    PubMed

    Carroll, Carlos; Johnson, Devin S; Dunk, Jeffrey R; Zielinski, William J

    2010-12-01

    Biologists who develop and apply habitat models are often familiar with the statistical challenges posed by their data's spatial structure but are unsure of whether the use of complex spatial models will increase the utility of model results in planning. We compared the relative performance of nonspatial and hierarchical Bayesian spatial models for three vertebrate and invertebrate taxa of conservation concern (Church's sideband snails [Monadenia churchi], red tree voles [Arborimus longicaudus], and Pacific fishers [Martes pennanti pacifica]) that provide examples of a range of distributional extents and dispersal abilities. We used presence-absence data derived from regional monitoring programs to develop models with both landscape and site-level environmental covariates. We used Markov chain Monte Carlo algorithms and a conditional autoregressive or intrinsic conditional autoregressive model framework to fit spatial models. The fit of Bayesian spatial models was between 35 and 55% better than the fit of nonspatial analogue models. Bayesian spatial models outperformed analogous models developed with maximum entropy (Maxent) methods. Although the best spatial and nonspatial models included similar environmental variables, spatial models provided estimates of residual spatial effects that suggested how ecological processes might structure distribution patterns. Spatial models built from presence-absence data improved fit most for localized endemic species with ranges constrained by poorly known biogeographic factors and for widely distributed species suspected to be strongly affected by unmeasured environmental variables or population processes. By treating spatial effects as a variable of interest rather than a nuisance, hierarchical Bayesian spatial models, especially when they are based on a common broad-scale spatial lattice (here the national Forest Inventory and Analysis grid of 24 km(2) hexagons), can increase the relevance of habitat models to multispecies

  7. Dissecting Magnetar Variability with Bayesian Hierarchical Models

    NASA Astrophysics Data System (ADS)

    Huppenkothen, Daniela; Brewer, Brendon J.; Hogg, David W.; Murray, Iain; Frean, Marcus; Elenbaas, Chris; Watts, Anna L.; Levin, Yuri; van der Horst, Alexander J.; Kouveliotou, Chryssa

    2015-09-01

    Neutron stars are a prime laboratory for testing physical processes under conditions of strong gravity, high density, and extreme magnetic fields. Among the zoo of neutron star phenomena, magnetars stand out for their bursting behavior, ranging from extremely bright, rare giant flares to numerous, less energetic recurrent bursts. The exact trigger and emission mechanisms for these bursts are not known; favored models involve either a crust fracture and subsequent energy release into the magnetosphere, or explosive reconnection of magnetic field lines. In the absence of a predictive model, understanding the physical processes responsible for magnetar burst variability is difficult. Here, we develop an empirical model that decomposes magnetar bursts into a superposition of small spike-like features with a simple functional form, where the number of model components is itself part of the inference problem. The cascades of spikes that we model might be formed by avalanches of reconnection, or crust rupture aftershocks. Using Markov Chain Monte Carlo sampling augmented with reversible jumps between models with different numbers of parameters, we characterize the posterior distributions of the model parameters and the number of components per burst. We relate these model parameters to physical quantities in the system, and show for the first time that the variability within a burst does not conform to predictions from ideas of self-organized criticality. We also examine how well the properties of the spikes fit the predictions of simplified cascade models for the different trigger mechanisms.

  8. Goodness-of-fit diagnostics for Bayesian hierarchical models.

    PubMed

    Yuan, Ying; Johnson, Valen E

    2012-03-01

    This article proposes methodology for assessing goodness of fit in Bayesian hierarchical models. The methodology is based on comparing values of pivotal discrepancy measures (PDMs), computed using parameter values drawn from the posterior distribution, to known reference distributions. Because the resulting diagnostics can be calculated from standard output of Markov chain Monte Carlo algorithms, their computational costs are minimal. Several simulation studies are provided, each of which suggests that diagnostics based on PDMs have higher statistical power than comparable posterior-predictive diagnostic checks in detecting model departures. The proposed methodology is illustrated in a clinical application; an application to discrete data is described in supplementary material. PMID:22050079

  9. Inversion of hierarchical Bayesian models using Gaussian processes.

    PubMed

    Lomakina, Ekaterina I; Paliwal, Saee; Diaconescu, Andreea O; Brodersen, Kay H; Aponte, Eduardo A; Buhmann, Joachim M; Stephan, Klaas E

    2015-09-01

    Over the past decade, computational approaches to neuroimaging have increasingly made use of hierarchical Bayesian models (HBMs), either for inferring on physiological mechanisms underlying fMRI data (e.g., dynamic causal modelling, DCM) or for deriving computational trajectories (from behavioural data) which serve as regressors in general linear models. However, an unresolved problem is that standard methods for inverting the hierarchical Bayesian model are either very slow, e.g. Markov Chain Monte Carlo Methods (MCMC), or are vulnerable to local minima in non-convex optimisation problems, such as variational Bayes (VB). This article considers Gaussian process optimisation (GPO) as an alternative approach for global optimisation of sufficiently smooth and efficiently evaluable objective functions. GPO avoids being trapped in local extrema and can be computationally much more efficient than MCMC. Here, we examine the benefits of GPO for inverting HBMs commonly used in neuroimaging, including DCM for fMRI and the Hierarchical Gaussian Filter (HGF). Importantly, to achieve computational efficiency despite high-dimensional optimisation problems, we introduce a novel combination of GPO and local gradient-based search methods. The utility of this GPO implementation for DCM and HGF is evaluated against MCMC and VB, using both synthetic data from simulations and empirical data. Our results demonstrate that GPO provides parameter estimates with equivalent or better accuracy than the other techniques, but at a fraction of the computational cost required for MCMC. We anticipate that GPO will prove useful for robust and efficient inversion of high-dimensional and nonlinear models of neuroimaging data. PMID:26048619

  10. A unified Bayesian hierarchical model for MRI tissue classification.

    PubMed

    Feng, Dai; Liang, Dong; Tierney, Luke

    2014-04-15

    Various works have used magnetic resonance imaging (MRI) tissue classification extensively to study a number of neurological and psychiatric disorders. Various noise characteristics and other artifacts make this classification a challenging task. Instead of splitting the procedure into different steps, we extend a previous work to develop a unified Bayesian hierarchical model, which addresses both the partial volume effect and intensity non-uniformity, the two major acquisition artifacts, simultaneously. We adopted a normal mixture model with the means and variances depending on the tissue types of voxels to model the observed intensity values. We modeled the relationship among the components of the index vector of tissue types by a hidden Markov model, which captures the spatial similarity of voxels. Furthermore, we addressed the partial volume effect by construction of a higher resolution image in which each voxel is divided into subvoxels. Finally, We achieved the bias field correction by using a Gaussian Markov random field model with a band precision matrix designed in light of image filtering. Sparse matrix methods and parallel computations based on conditional independence are exploited to improve the speed of the Markov chain Monte Carlo simulation. The unified model provides more accurate tissue classification results for both simulated and real data sets. PMID:24738112

  11. Hierarchical Bayesian Model Averaging for Chance Constrained Remediation Designs

    NASA Astrophysics Data System (ADS)

    Chitsazan, N.; Tsai, F. T.

    2012-12-01

    Groundwater remediation designs are heavily relying on simulation models which are subjected to various sources of uncertainty in their predictions. To develop a robust remediation design, it is crucial to understand the effect of uncertainty sources. In this research, we introduce a hierarchical Bayesian model averaging (HBMA) framework to segregate and prioritize sources of uncertainty in a multi-layer frame, where each layer targets a source of uncertainty. The HBMA framework provides an insight to uncertainty priorities and propagation. In addition, HBMA allows evaluating model weights in different hierarchy levels and assessing the relative importance of models in each level. To account for uncertainty, we employ a chance constrained (CC) programming for stochastic remediation design. Chance constrained programming was implemented traditionally to account for parameter uncertainty. Recently, many studies suggested that model structure uncertainty is not negligible compared to parameter uncertainty. Using chance constrained programming along with HBMA can provide a rigorous tool for groundwater remediation designs under uncertainty. In this research, the HBMA-CC was applied to a remediation design in a synthetic aquifer. The design was to develop a scavenger well approach to mitigate saltwater intrusion toward production wells. HBMA was employed to assess uncertainties from model structure, parameter estimation and kriging interpolation. An improved harmony search optimization method was used to find the optimal location of the scavenger well. We evaluated prediction variances of chloride concentration at the production wells through the HBMA framework. The results showed that choosing the single best model may lead to a significant error in evaluating prediction variances for two reasons. First, considering the single best model, variances that stem from uncertainty in the model structure will be ignored. Second, considering the best model with non

  12. A Bayesian hierarchical diffusion model decomposition of performance in Approach–Avoidance Tasks

    PubMed Central

    Krypotos, Angelos-Miltiadis; Beckers, Tom; Kindt, Merel; Wagenmakers, Eric-Jan

    2015-01-01

    Common methods for analysing response time (RT) tasks, frequently used across different disciplines of psychology, suffer from a number of limitations such as the failure to directly measure the underlying latent processes of interest and the inability to take into account the uncertainty associated with each individual's point estimate of performance. Here, we discuss a Bayesian hierarchical diffusion model and apply it to RT data. This model allows researchers to decompose performance into meaningful psychological processes and to account optimally for individual differences and commonalities, even with relatively sparse data. We highlight the advantages of the Bayesian hierarchical diffusion model decomposition by applying it to performance on Approach–Avoidance Tasks, widely used in the emotion and psychopathology literature. Model fits for two experimental data-sets demonstrate that the model performs well. The Bayesian hierarchical diffusion model overcomes important limitations of current analysis procedures and provides deeper insight in latent psychological processes of interest. PMID:25491372

  13. Bayesian Hierarchical Classes Analysis

    ERIC Educational Resources Information Center

    Leenen, Iwin; Van Mechelen, Iven; Gelman, Andrew; De Knop, Stijn

    2008-01-01

    Hierarchical classes models are models for "N"-way "N"-mode data that represent the association among the "N" modes and simultaneously yield, for each mode, a hierarchical classification of its elements. In this paper we present a stochastic extension of the hierarchical classes model for two-way two-mode binary data. In line with the original…

  14. Hierarchical models and Bayesian analysis of bird survey information

    USGS Publications Warehouse

    Sauer, J.R.; Link, W.A.; Royle, J. Andrew

    2005-01-01

    Summary of bird survey information is a critical component of conservation activities, but often our summaries rely on statistical methods that do not accommodate the limitations of the information. Prioritization of species requires ranking and analysis of species by magnitude of population trend, but often magnitude of trend is a misleading measure of actual decline when trend is poorly estimated. Aggregation of population information among regions is also complicated by varying quality of estimates among regions. Hierarchical models provide a reasonable means of accommodating concerns about aggregation and ranking of quantities of varying precision. In these models the need to consider multiple scales is accommodated by placing distributional assumptions on collections of parameters. For collections of species trends, this allows probability statements to be made about the collections of species-specific parameters, rather than about the estimates. We define and illustrate hierarchical models for two commonly encountered situations in bird conservation: (1) Estimating attributes of collections of species estimates, including ranking of trends, estimating number of species with increasing populations, and assessing population stability with regard to predefined trend magnitudes; and (2) estimation of regional population change, aggregating information from bird surveys over strata. User-friendly computer software makes hierarchical models readily accessible to scientists.

  15. Probabilistic Inference: Task Dependency and Individual Differences of Probability Weighting Revealed by Hierarchical Bayesian Modeling

    PubMed Central

    Boos, Moritz; Seer, Caroline; Lange, Florian; Kopp, Bruno

    2016-01-01

    Cognitive determinants of probabilistic inference were examined using hierarchical Bayesian modeling techniques. A classic urn-ball paradigm served as experimental strategy, involving a factorial two (prior probabilities) by two (likelihoods) design. Five computational models of cognitive processes were compared with the observed behavior. Parameter-free Bayesian posterior probabilities and parameter-free base rate neglect provided inadequate models of probabilistic inference. The introduction of distorted subjective probabilities yielded more robust and generalizable results. A general class of (inverted) S-shaped probability weighting functions had been proposed; however, the possibility of large differences in probability distortions not only across experimental conditions, but also across individuals, seems critical for the model's success. It also seems advantageous to consider individual differences in parameters of probability weighting as being sampled from weakly informative prior distributions of individual parameter values. Thus, the results from hierarchical Bayesian modeling converge with previous results in revealing that probability weighting parameters show considerable task dependency and individual differences. Methodologically, this work exemplifies the usefulness of hierarchical Bayesian modeling techniques for cognitive psychology. Theoretically, human probabilistic inference might be best described as the application of individualized strategic policies for Bayesian belief revision. PMID:27303323

  16. Hierarchical Bayesian Model (HBM) - Derived Estimates of Air Quality for 2007: Annual Report

    EPA Science Inventory

    This report describes EPA's Hierarchical Bayesian model generated (HBM) estimates of ozone (O3) and fine particulate matter (PM2.5 particles with aerodynamic diameter < 2.5 microns)concentrations throughout the continental United States during the 2007 calen...

  17. Hierarchical Bayesian Model (HBM)-Derived Estimates of Air Quality for 2006 - Annual Report

    EPA Science Inventory

    This report describes EPA's Hierarchical Bayesian model-generated (HBM) estimates of O3 and PM2.5 concentrations throughout the continental United States during the 2006 calendar year. HBM estimates provide the spatial and temporal variance of O3 ...

  18. Hierarchical Bayesian Model (HBM)-Derived Estimates of Air Quality for 2001 - Annual Report

    EPA Science Inventory

    This report describes EPA's Hierarchical Bayesian model-generated (HBM) estimates of O3 and PM2.5 concentrations throughout the continental United States during the 2001 calendar year. HBM estimates provide the spatial and temporal variance of O 3...

  19. Hierarchical Bayesian Model (HBM)-Derived Estimates of Air Quality for 2003 – Annual Report

    EPA Science Inventory

    This report describes EPA's Hierarchical Bayesian model-generated (HBM) estimates of O3 and PM2.5 concentrations throughout the continental United States during the 2003 calendar year. HBM estimates provide the spatial and temporal variance of O3 ...

  20. Hierarchical Bayesian Model (HBM)-Derived Estimates of Air Quality for 2005 - Annual Report

    EPA Science Inventory

    This report describes EPA's Hierarchical Bayesian model-generated (HBM) estimates of O3 and PM2.5 concentrations throughout the continental United States during the 2005 calendar year. HBM estimates provide the spatial and temporal variance of O3 ...

  1. Hierarchical Bayesian Model (HBM)-Derived Estimates of Air Quality for 2002– Annual Report

    EPA Science Inventory

    This report describes EPA's Hierarchical Bayesian model-generated (HBM) estimates of O3 and PM2.5 concentrations throughout the continental United States during the 2002 calendar year. HBM estimates provide the spatial and temporal variance of O3 ...

  2. Hierarchical Bayesian Model (HBM) - Derived Estimates of Air Quality for 2008: Annual Report

    EPA Science Inventory

    This report describes EPA’s Hierarchical Bayesian model generated (HBM) estimates of ozone (O3) and fine particulate matter (PM2.5, particles with aerodynamic diameter < 2.5 microns) concentrations throughout the continental United States during the 2007 ca...

  3. Hierarchical Bayesian Model (HBM)-Derived Estimates of Air Quality for 2004 - Annual Report

    EPA Science Inventory

    This report describes EPA's Hierarchical Bayesian model-generated (HBM) estimates of O3 and PM2.5 concentrations throughout the continental United States during the 2004 calendar year. HBM estimates provide the spatial and temporal variance of O3 ...

  4. Point source moment tensor inversion through a Bayesian hierarchical model

    NASA Astrophysics Data System (ADS)

    Mustać, Marija; Tkalčić, Hrvoje

    2016-01-01

    Characterization of seismic sources is an important aspect of seismology. Parameter uncertainties in such inversions are essential for estimating solution robustness, but are rarely available. We have developed a non-linear moment tensor inversion method in a probabilistic Bayesian framework that also accounts for noise in the data. The method is designed for point source inversion using waveform data of moderate-size earthquakes and explosions at regional distances. This probabilistic approach results in an ensemble of models, whose density is proportional to parameter probability distribution and quantifies parameter uncertainties. Furthermore, we invert for noise in the data, allowing it to determine the model complexity. We implement an empirical noise covariance matrix that accounts for interdependence of observational errors present in waveform data. After we demonstrate the feasibility of the approach on synthetic data, we apply it to a Long Valley Caldera, CA, earthquake with a well-documented anomalous (non-double-couple) radiation from previous studies. We confirm a statistically significant isotropic component in the source without a trade-off with the compensated linear vector dipoles component.

  5. Hierarchical Bayesian inverse reinforcement learning.

    PubMed

    Choi, Jaedeug; Kim, Kee-Eung

    2015-04-01

    Inverse reinforcement learning (IRL) is the problem of inferring the underlying reward function from the expert's behavior data. The difficulty in IRL mainly arises in choosing the best reward function since there are typically an infinite number of reward functions that yield the given behavior data as optimal. Another difficulty comes from the noisy behavior data due to sub-optimal experts. We propose a hierarchical Bayesian framework, which subsumes most of the previous IRL algorithms as well as models the sub-optimality of the expert's behavior. Using a number of experiments on a synthetic problem, we demonstrate the effectiveness of our approach including the robustness of our hierarchical Bayesian framework to the sub-optimal expert behavior data. Using a real dataset from taxi GPS traces, we additionally show that our approach predicts the driving behavior with a high accuracy. PMID:25291805

  6. A Bayesian hierarchical surrogate outcome model for multiple sclerosis.

    PubMed

    Pozzi, Luca; Schmidli, Heinz; Ohlssen, David I

    2016-07-01

    The development of novel therapies in multiple sclerosis (MS) is one area where a range of surrogate outcomes are used in various stages of clinical research. While the aim of treatments in MS is to prevent disability, a clinical trial for evaluating a drugs effect on disability progression would require a large sample of patients with many years of follow-up. The early stage of MS is characterized by relapses. To reduce study size and duration, clinical relapses are accepted as primary endpoints in phase III trials. For phase II studies, the primary outcomes are typically lesion counts based on magnetic resonance imaging (MRI), as these are considerably more sensitive than clinical measures for detecting MS activity. Recently, Sormani and colleagues in 'Surrogate endpoints for EDSS worsening in multiple sclerosis' provided a systematic review and used weighted regression analyses to examine the role of either MRI lesions or relapses as trial level surrogate outcomes for disability. We build on this work by developing a Bayesian three-level model, accommodating the two surrogates and the disability endpoint, and properly taking into account that treatment effects are estimated with errors. Specifically, a combination of treatment effects based on MRI lesion count outcomes and clinical relapse was used to develop a study-level surrogate outcome model for the corresponding treatment effects based on disability progression. While the primary aim for developing this model was to support decision-making in drug development, the proposed model may also be considered for future validation. Copyright © 2016 John Wiley & Sons, Ltd. PMID:27061897

  7. Improving Local and Regional Flood Quantile Estimates Using a Hierarchical Bayesian GEV Model

    NASA Astrophysics Data System (ADS)

    Ribeiro Lima, C. H.; Lall, U.; Devineni, N.; Troy, T.

    2013-12-01

    Flood risk management usually relies on local and regional flood frequency analysis, which tends to suffer from lack of data and parameter uncertainties. Here we estimate local and regional Generalized Extreme Value (GEV) distribution parameters in a hierarchical Bayesian framework, which helps reduce uncertainties by pooling more information in the estimation process and provides a simple topology to propagate model and parameter uncertainties to flood quantile estimates. As prior information for the Bayesian model, it is assumed for each site that the GEV location and scale parameters come from independent log-normal distributions, whose mean parameter follows the well known log-log scaling law with the drainage area. The shape parameter for each site is shrunk towards a common mean. Non-informative prior distributions are assumed for the hyperparameters and the MCMC method is used to sample from the posterior distributions. The model is tested using annual maximum series from 20 streamflow gauges located in an 83.000 km2 basin in southeastern Brazil. The results show a significant improvement of flood quantile estimates over the traditional GEV model, particularly for sites with few data. For return periods within the range of the data (around 50 years), the Bayesian credible intervals for the flood quantiles are narrower than the classical confidence limits based on the delta method. As the return period increases beyond the range of the data, the confidence limits from the delta method become unreliable and the Bayesian credible intervals provide a way to estimate satisfactory confidence bands for the flood quantiles considering the parameter uncertainties. In order to evaluate the applicability of the proposed hierarchical Bayesian model for flood frequency regional analysis, we estimate flood quantiles for three randomly chosen out-of-sample sites and compare with classical estimates using the index flood method. The posterior distributions of the scaling

  8. Technical Note: Probabilistically constraining proxy age-depth models within a Bayesian hierarchical reconstruction model

    NASA Astrophysics Data System (ADS)

    Werner, J. P.; Tingley, M. P.

    2014-12-01

    Reconstructions of late-Holocene climate rely heavily upon proxies that are assumed to be accurately dated by layer counting, such as measurement on tree rings, ice cores, and varved lake sediments. Considerable advances may be achievable if time uncertain proxies could be included within these multiproxy reconstructions, and if time uncertainties were recognized and correctly modeled for proxies commonly treated as free of age model errors. Current approaches to accounting for time uncertainty are generally limited to repeating the reconstruction using each of an ensemble of age models, thereby inflating the final estimated uncertainty - in effect, each possible age model is given equal weighting. Uncertainties can be reduced by exploiting the inferred space-time covariance structure of the climate to re-weight the possible age models. Here we demonstrate how Bayesian Hierarchical climate reconstruction models can be augmented to account for time uncertain proxies. Critically, while a priori all age models are given equal probability of being correct, the probabilities associated with the age models are formally updated within the Bayesian framework, thereby reducing uncertainties. Numerical experiments show that updating the age-model probabilities decreases uncertainty in the climate reconstruction, as compared with the current de-facto standard of sampling over all age models, provided there is sufficient information from other data sources in the region of the time-uncertain proxy. This approach can readily be generalized to non-layer counted proxies, such as those derived from marine sediments.

  9. Technical Note: Probabilistically constraining proxy age-depth models within a Bayesian hierarchical reconstruction model

    NASA Astrophysics Data System (ADS)

    Werner, J. P.; Tingley, M. P.

    2015-03-01

    Reconstructions of the late-Holocene climate rely heavily upon proxies that are assumed to be accurately dated by layer counting, such as measurements of tree rings, ice cores, and varved lake sediments. Considerable advances could be achieved if time-uncertain proxies were able to be included within these multiproxy reconstructions, and if time uncertainties were recognized and correctly modeled for proxies commonly treated as free of age model errors. Current approaches for accounting for time uncertainty are generally limited to repeating the reconstruction using each one of an ensemble of age models, thereby inflating the final estimated uncertainty - in effect, each possible age model is given equal weighting. Uncertainties can be reduced by exploiting the inferred space-time covariance structure of the climate to re-weight the possible age models. Here, we demonstrate how Bayesian hierarchical climate reconstruction models can be augmented to account for time-uncertain proxies. Critically, although a priori all age models are given equal probability of being correct, the probabilities associated with the age models are formally updated within the Bayesian framework, thereby reducing uncertainties. Numerical experiments show that updating the age model probabilities decreases uncertainty in the resulting reconstructions, as compared with the current de facto standard of sampling over all age models, provided there is sufficient information from other data sources in the spatial region of the time-uncertain proxy. This approach can readily be generalized to non-layer-counted proxies, such as those derived from marine sediments.

  10. Probabilistically constraining proxy age-depth models within a Bayesian hierarchical reconstruction model

    NASA Astrophysics Data System (ADS)

    Werner, Johannes; Tingley, Martin

    2015-04-01

    Reconstructions of late-Holocene climate rely heavily upon proxies that are assumed to be accurately dated by layer counting, such as measurement on tree rings, ice cores, and varved lake sediments. Considerable advances may be achievable if time uncertain proxies could be included within these multiproxy reconstructions, and if time uncertainties were recognized and correctly modeled for proxies commonly treated as free of age model errors. Current approaches to accounting for time uncertainty are generally limited to repeating the reconstruction using each of an ensemble of age models, thereby inflating the final estimated uncertainty - in effect, each possible age model is given equal weighting. Uncertainties can be reduced by exploiting the inferred space-time covariance structure of the climate to re-weight the possible age models. Here we demonstrate how Bayesian Hierarchical climate reconstruction models can be augmented to account for time uncertain proxies. Critically, while a priori all age models are given equal probability of being correct, the probabilities associated with the age models are formally updated within the Bayesian framework, thereby reducing uncertainties. Numerical experiments show that updating the age model probabilities decreases uncertainty in the climate reconstruction, as compared with the current de-facto standard of sampling over all age models, provided there is sufficient information from other data sources in the region of the time-uncertain proxy. This approach can readily be generalized to non-layer counted proxies, such as those derived from marine sediments. Werner and Tingley, Climate of the Past Discussions (2014)

  11. Climate information based streamflow and rainfall forecasts for Huai River Basin using Hierarchical Bayesian Modeling

    NASA Astrophysics Data System (ADS)

    Chen, X.; Hao, Z.; Devineni, N.; Lall, U.

    2013-09-01

    A Hierarchal Bayesian model for forecasting regional summer rainfall and streamflow season-ahead using exogenous climate variables for East Central China is presented. The model provides estimates of the posterior forecasted probability distribution for 12 rainfall and 2 streamflow stations considering parameter uncertainty, and cross-site correlation. The model has a multilevel structure with regression coefficients modeled from a common multivariate normal distribution results in partial-pooling of information across multiple stations and better representation of parameter and posterior distribution uncertainty. Covariance structure of the residuals across stations is explicitly modeled. Model performance is tested under leave-10-out cross-validation. Frequentist and Bayesian performance metrics used include Receiver Operating Characteristic, Reduction of Error, Coefficient of Efficiency, Rank Probability Skill Scores, and coverage by posterior credible intervals. The ability of the model to reliably forecast regional summer rainfall and streamflow season-ahead offers potential for developing adaptive water risk management strategies.

  12. Climate information based streamflow and rainfall forecasts for Huai River basin using hierarchical Bayesian modeling

    NASA Astrophysics Data System (ADS)

    Chen, X.; Hao, Z.; Devineni, N.; Lall, U.

    2014-04-01

    A Hierarchal Bayesian model is presented for one season-ahead forecasts of summer rainfall and streamflow using exogenous climate variables for east central China. The model provides estimates of the posterior forecasted probability distribution for 12 rainfall and 2 streamflow stations considering parameter uncertainty, and cross-site correlation. The model has a multi-level structure with regression coefficients modeled from a common multi-variate normal distribution resulting in partial pooling of information across multiple stations and better representation of parameter and posterior distribution uncertainty. Covariance structure of the residuals across stations is explicitly modeled. Model performance is tested under leave-10-out cross-validation. Frequentist and Bayesian performance metrics used include receiver operating characteristic, reduction of error, coefficient of efficiency, rank probability skill scores, and coverage by posterior credible intervals. The ability of the model to reliably forecast season-ahead regional summer rainfall and streamflow offers potential for developing adaptive water risk management strategies.

  13. Bayesian Multidimensional IRT Models with a Hierarchical Structure

    ERIC Educational Resources Information Center

    Sheng, Yanyan; Wikle, Christopher K.

    2008-01-01

    As item response models gain increased popularity in large-scale educational and measurement testing situations, many studies have been conducted on the development and applications of unidimensional and multidimensional models. Recently, attention has been paid to IRT-based models with an overall ability dimension underlying several ability…

  14. Hierarchical Bayesian spatio-temporal modeling and entropy-based network design

    NASA Astrophysics Data System (ADS)

    Wu, Y.; Jin, B.; Chan, E.

    2012-12-01

    Typical spatio-temporal data include temperature, precipitation, atmospheric pressure, ozone concentration, personal income, infection prevalence, mosquito populations, among others. To model such data in a given region by hierarchical Bayesian kriging is undertaken in this paper. In addition, an environmental network design problem is also explored. For demonstration, we consider the ozone concentrations in the Toronto region of Ontario, Canada. There are many missing observations in the data. To proceed, we first formulate the hierarchical spatio-temporal model in terms of observed data. We then fill in some missing observations such that the data has the staircase structure. Thus, in light of Le and Zidek (2006), we model the ozone concentrations in Toronto region by hierarchical Bayesian kriging and derive a conditional predictive distribution of the ozone concentrations over unknown locations. To decide if a new monitoring station needs to be added or an existing station can be closed down, we solve this environmental network design problem by using the principle of maximum entropy.

  15. BAYESIAN HIERARCHICAL MODELING FOR SIGNALING PATHWAY INFERENCE FROM SINGLE CELL INTERVENTIONAL DATA1

    PubMed Central

    Luo, Ruiyan; Zhao, Hongyu

    2011-01-01

    Recent technological advances have made it possible to simultaneously measure multiple protein activities at the single cell level. With such data collected under different stimulatory or inhibitory conditions, it is possible to infer the causal relationships among proteins from single cell interventional data. In this article we propose a Bayesian hierarchical modeling framework to infer the signaling pathway based on the posterior distributions of parameters in the model. Under this framework, we consider network sparsity and model the existence of an association between two proteins both at the overall level across all experiments and at each individual experimental level. This allows us to infer the pairs of proteins that are associated with each other and their causal relationships. We also explicitly consider both intrinsic noise and measurement error. Markov chain Monte Carlo is implemented for statistical inference. We demonstrate that this hierarchical modeling can effectively pool information from different interventional experiments through simulation studies and real data analysis. PMID:22162986

  16. Gas turbine engine prognostics using Bayesian hierarchical models: A variational approach

    NASA Astrophysics Data System (ADS)

    Zaidan, Martha A.; Mills, Andrew R.; Harrison, Robert F.; Fleming, Peter J.

    2016-03-01

    Prognostics is an emerging requirement of modern health monitoring that aims to increase the fidelity of failure-time predictions by the appropriate use of sensory and reliability information. In the aerospace industry it is a key technology to reduce life-cycle costs, improve reliability and asset availability for a diverse fleet of gas turbine engines. In this work, a Bayesian hierarchical model is selected to utilise fleet data from multiple assets to perform probabilistic estimation of remaining useful life (RUL) for civil aerospace gas turbine engines. The hierarchical formulation allows Bayesian updates of an individual predictive model to be made, based upon data received asynchronously from a fleet of assets with different in-service lives and for the entry of new assets into the fleet. In this paper, variational inference is applied to the hierarchical formulation to overcome the computational and convergence concerns that are raised by the numerical sampling techniques needed for inference in the original formulation. The algorithm is tested on synthetic data, where the quality of approximation is shown to be satisfactory with respect to prediction performance, computational speed, and ease of use. A case study of in-service gas turbine engine data demonstrates the value of integrating fleet data for accurately predicting degradation trajectories of assets.

  17. Calibration of Automatically Generated Items Using Bayesian Hierarchical Modeling.

    ERIC Educational Resources Information Center

    Johnson, Matthew S.; Sinharay, Sandip

    For complex educational assessments, there is an increasing use of "item families," which are groups of related items. However, calibration or scoring for such an assessment requires fitting models that take into account the dependence structure inherent among the items that belong to the same item family. C. Glas and W. van der Linden (2001)…

  18. Calibration of Polytomous Item Families Using Bayesian Hierarchical Modeling

    ERIC Educational Resources Information Center

    Johnson, Matthew S.; Sinharay, Sandip

    2005-01-01

    For complex educational assessments, there is an increasing use of item families, which are groups of related items. Calibration or scoring in an assessment involving item families requires models that can take into account the dependence structure inherent among the items that belong to the same item family. This article extends earlier works in…

  19. Hierarchical Bayesian model averaging for hydrostratigraphic modeling: Uncertainty segregation and comparative evaluation

    NASA Astrophysics Data System (ADS)

    Tsai, Frank T.-C.; Elshall, Ahmed S.

    2013-09-01

    Analysts are often faced with competing propositions for each uncertain model component. How can we judge that we select a correct proposition(s) for an uncertain model component out of numerous possible propositions? We introduce the hierarchical Bayesian model averaging (HBMA) method as a multimodel framework for uncertainty analysis. The HBMA allows for segregating, prioritizing, and evaluating different sources of uncertainty and their corresponding competing propositions through a hierarchy of BMA models that forms a BMA tree. We apply the HBMA to conduct uncertainty analysis on the reconstructed hydrostratigraphic architectures of the Baton Rouge aquifer-fault system, Louisiana. Due to uncertainty in model data, structure, and parameters, multiple possible hydrostratigraphic models are produced and calibrated as base models. The study considers four sources of uncertainty. With respect to data uncertainty, the study considers two calibration data sets. With respect to model structure, the study considers three different variogram models, two geological stationarity assumptions and two fault conceptualizations. The base models are produced following a combinatorial design to allow for uncertainty segregation. Thus, these four uncertain model components with their corresponding competing model propositions result in 24 base models. The results show that the systematic dissection of the uncertain model components along with their corresponding competing propositions allows for detecting the robust model propositions and the major sources of uncertainty.

  20. A Hierarchical Bayesian Model to Quantify Uncertainty of Stream Water Temperature Forecasts

    PubMed Central

    Bal, Guillaume; Rivot, Etienne; Baglinière, Jean-Luc; White, Jonathan; Prévost, Etienne

    2014-01-01

    Providing generic and cost effective modelling approaches to reconstruct and forecast freshwater temperature using predictors as air temperature and water discharge is a prerequisite to understanding ecological processes underlying the impact of water temperature and of global warming on continental aquatic ecosystems. Using air temperature as a simple linear predictor of water temperature can lead to significant bias in forecasts as it does not disentangle seasonality and long term trends in the signal. Here, we develop an alternative approach based on hierarchical Bayesian statistical time series modelling of water temperature, air temperature and water discharge using seasonal sinusoidal periodic signals and time varying means and amplitudes. Fitting and forecasting performances of this approach are compared with that of simple linear regression between water and air temperatures using i) an emotive simulated example, ii) application to three French coastal streams with contrasting bio-geographical conditions and sizes. The time series modelling approach better fit data and does not exhibit forecasting bias in long term trends contrary to the linear regression. This new model also allows for more accurate forecasts of water temperature than linear regression together with a fair assessment of the uncertainty around forecasting. Warming of water temperature forecast by our hierarchical Bayesian model was slower and more uncertain than that expected with the classical regression approach. These new forecasts are in a form that is readily usable in further ecological analyses and will allow weighting of outcomes from different scenarios to manage climate change impacts on freshwater wildlife. PMID:25541732

  1. Relating Memory To Functional Performance In Normal Aging to Dementia Using Hierarchical Bayesian Cognitive Processing Models

    PubMed Central

    Shankle, William R.; Pooley, James P.; Steyvers, Mark; Hara, Junko; Mangrola, Tushar; Reisberg, Barry; Lee, Michael D.

    2012-01-01

    Determining how cognition affects functional abilities is important in Alzheimer’s disease and related disorders (ADRD). 280 patients (normal or ADRD) received a total of 1,514 assessments using the Functional Assessment Staging Test (FAST) procedure and the MCI Screen (MCIS). A hierarchical Bayesian cognitive processing (HBCP) model was created by embedding a signal detection theory (SDT) model of the MCIS delayed recognition memory task into a hierarchical Bayesian framework. The SDT model used latent parameters of discriminability (memory process) and response bias (executive function) to predict, simultaneously, recognition memory performance for each patient and each FAST severity group. The observed recognition memory data did not distinguish the six FAST severity stages, but the latent parameters completely separated them. The latent parameters were also used successfully to transform the ordinal FAST measure into a continuous measure reflecting the underlying continuum of functional severity. HBCP models applied to recognition memory data from clinical practice settings accurately translated a latent measure of cognition to a continuous measure of functional severity for both individuals and FAST groups. Such a translation links two levels of brain information processing, and may enable more accurate correlations with other levels, such as those characterized by biomarkers. PMID:22407225

  2. A Bayesian hierarchical model for reconstructing relative sea level: from raw data to rates of change

    NASA Astrophysics Data System (ADS)

    Cahill, Niamh; Kemp, Andrew C.; Horton, Benjamin P.; Parnell, Andrew C.

    2016-02-01

    We present a Bayesian hierarchical model for reconstructing the continuous and dynamic evolution of relative sea-level (RSL) change with quantified uncertainty. The reconstruction is produced from biological (foraminifera) and geochemical (δ13C) sea-level indicators preserved in dated cores of salt-marsh sediment. Our model is comprised of three modules: (1) a new Bayesian transfer (B-TF) function for the calibration of biological indicators into tidal elevation, which is flexible enough to formally accommodate additional proxies; (2) an existing chronology developed using the Bchron age-depth model, and (3) an existing Errors-In-Variables integrated Gaussian process (EIV-IGP) model for estimating rates of sea-level change. Our approach is illustrated using a case study of Common Era sea-level variability from New Jersey, USA We develop a new B-TF using foraminifera, with and without the additional (δ13C) proxy and compare our results to those from a widely used weighted-averaging transfer function (WA-TF). The formal incorporation of a second proxy into the B-TF model results in smaller vertical uncertainties and improved accuracy for reconstructed RSL. The vertical uncertainty from the multi-proxy B-TF is ˜ 28 % smaller on average compared to the WA-TF. When evaluated against historic tide-gauge measurements, the multi-proxy B-TF most accurately reconstructs the RSL changes observed in the instrumental record (mean square error = 0.003 m2). The Bayesian hierarchical model provides a single, unifying framework for reconstructing and analyzing sea-level change through time. This approach is suitable for reconstructing other paleoenvironmental variables (e.g., temperature) using biological proxies.

  3. Bayesian hierarchical modeling for a non-randomized, longitudinal fall prevention trial with spatially correlated observations

    PubMed Central

    Murphy, T. E.; Allore, H. G.; Leo-Summers, L.; Carlin, B. P.

    2012-01-01

    Because randomization of participants is often not feasible in community-based health interventions, non-randomized designs are commonly employed. Non-randomized designs may have experimental units that are spatial in nature, such as zip codes that are characterized by aggregate statistics from sources like the U.S. census and the Centers for Medicare and Medicaid Services. A perennial concern with non-randomized designs is that even after careful balancing of influential covariates, bias may arise from unmeasured factors. In addition to facilitating the analysis of interventional designs based on spatial units, Bayesian hierarchical modeling can quantify unmeasured variability with spatially correlated residual terms. Graphical analysis of these spatial residuals demonstrates whether variability from unmeasured covariates is likely to bias the estimates of interventional effect. The Connecticut Collaboration for Fall Prevention is the first large-scale longitudinal trial of a community-wide healthcare intervention designed to prevent injurious falls in older adults. Over a two-year evaluation phase, this trial demonstrated a rate of fall-related utilization at hospitals and emergency departments by persons 70 years and older in the intervention area that was 11 per cent less than that of the usual care area, and a 9 per cent lower rate of utilization from serious injuries. We describe the Bayesian hierarchical analysis of this non-randomized intervention with emphasis on its spatial and longitudinal characteristics. We also compare several models, using posterior predictive simulations and maps of spatial residuals. PMID:21294148

  4. A Bayesian hierarchical model with spatial variable selection: the effect of weather on insurance claims

    PubMed Central

    Scheel, Ida; Ferkingstad, Egil; Frigessi, Arnoldo; Haug, Ola; Hinnerichsen, Mikkel; Meze-Hausken, Elisabeth

    2013-01-01

    Climate change will affect the insurance industry. We develop a Bayesian hierarchical statistical approach to explain and predict insurance losses due to weather events at a local geographic scale. The number of weather-related insurance claims is modelled by combining generalized linear models with spatially smoothed variable selection. Using Gibbs sampling and reversible jump Markov chain Monte Carlo methods, this model is fitted on daily weather and insurance data from each of the 319 municipalities which constitute southern and central Norway for the period 1997–2006. Precise out-of-sample predictions validate the model. Our results show interesting regional patterns in the effect of different weather covariates. In addition to being useful for insurance pricing, our model can be used for short-term predictions based on weather forecasts and for long-term predictions based on downscaled climate models. PMID:23396890

  5. A Bayesian Hierarchical Modeling Scheme for Estimating Erosion Rates Under Current Climate Conditions

    NASA Astrophysics Data System (ADS)

    Lowman, L.; Barros, A. P.

    2014-12-01

    Computational modeling of surface erosion processes is inherently difficult because of the four-dimensional nature of the problem and the multiple temporal and spatial scales that govern individual mechanisms. Landscapes are modified via surface and fluvial erosion and exhumation, each of which takes place over a range of time scales. Traditional field measurements of erosion/exhumation rates are scale dependent, often valid for a single point-wise location or averaging over large aerial extents and periods with intense and mild erosion. We present a method of remotely estimating erosion rates using a Bayesian hierarchical model based upon the stream power erosion law (SPEL). A Bayesian approach allows for estimating erosion rates using the deterministic relationship given by the SPEL and data on channel slopes and precipitation at the basin and sub-basin scale. The spatial scale associated with this framework is the elevation class, where each class is characterized by distinct morphologic behavior observed through different modes in the distribution of basin outlet elevations. Interestingly, the distributions of first-order outlets are similar in shape and extent to the distribution of precipitation events (i.e. individual storms) over a 14-year period between 1998-2011. We demonstrate an application of the Bayesian hierarchical modeling framework for five basins and one intermontane basin located in the central Andes between 5S and 20S. Using remotely sensed data of current annual precipitation rates from the Tropical Rainfall Measuring Mission (TRMM) and topography from a high resolution (3 arc-seconds) digital elevation map (DEM), our erosion rate estimates are consistent with decadal-scale estimates based on landslide mapping and sediment flux observations and 1-2 orders of magnitude larger than most millennial and million year timescale estimates from thermochronology and cosmogenic nuclides.

  6. Likelihood-free inference of population structure and local adaptation in a Bayesian hierarchical model.

    PubMed

    Bazin, Eric; Dawson, Kevin J; Beaumont, Mark A

    2010-06-01

    We address the problem of finding evidence of natural selection from genetic data, accounting for the confounding effects of demographic history. In the absence of natural selection, gene genealogies should all be sampled from the same underlying distribution, often approximated by a coalescent model. Selection at a particular locus will lead to a modified genealogy, and this motivates a number of recent approaches for detecting the effects of natural selection in the genome as "outliers" under some models. The demographic history of a population affects the sampling distribution of genealogies, and therefore the observed genotypes and the classification of outliers. Since we cannot see genealogies directly, we have to infer them from the observed data under some model of mutation and demography. Thus the accuracy of an outlier-based approach depends to a greater or a lesser extent on the uncertainty about the demographic and mutational model. A natural modeling framework for this type of problem is provided by Bayesian hierarchical models, in which parameters, such as mutation rates and selection coefficients, are allowed to vary across loci. It has proved quite difficult computationally to implement fully probabilistic genealogical models with complex demographies, and this has motivated the development of approximations such as approximate Bayesian computation (ABC). In ABC the data are compressed into summary statistics, and computation of the likelihood function is replaced by simulation of data under the model. In a hierarchical setting one may be interested both in hyperparameters and parameters, and there may be very many of the latter--for example, in a genetic model, these may be parameters describing each of many loci or populations. This poses a problem for ABC in that one then requires summary statistics for each locus, which, if used naively, leads to a consequent difficulty in conditional density estimation. We develop a general method for applying

  7. Prion amplification and hierarchical Bayesian modeling refine detection of prion infection.

    PubMed

    Wyckoff, A Christy; Galloway, Nathan; Meyerett-Reid, Crystal; Powers, Jenny; Spraker, Terry; Monello, Ryan J; Pulford, Bruce; Wild, Margaret; Antolin, Michael; VerCauteren, Kurt; Zabel, Mark

    2015-01-01

    Prions are unique infectious agents that replicate without a genome and cause neurodegenerative diseases that include chronic wasting disease (CWD) of cervids. Immunohistochemistry (IHC) is currently considered the gold standard for diagnosis of a prion infection but may be insensitive to early or sub-clinical CWD that are important to understanding CWD transmission and ecology. We assessed the potential of serial protein misfolding cyclic amplification (sPMCA) to improve detection of CWD prior to the onset of clinical signs. We analyzed tissue samples from free-ranging Rocky Mountain elk (Cervus elaphus nelsoni) and used hierarchical Bayesian analysis to estimate the specificity and sensitivity of IHC and sPMCA conditional on simultaneously estimated disease states. Sensitivity estimates were higher for sPMCA (99.51%, credible interval (CI) 97.15-100%) than IHC of obex (brain stem, 76.56%, CI 57.00-91.46%) or retropharyngeal lymph node (90.06%, CI 74.13-98.70%) tissues, or both (98.99%, CI 90.01-100%). Our hierarchical Bayesian model predicts the prevalence of prion infection in this elk population to be 18.90% (CI 15.50-32.72%), compared to previous estimates of 12.90%. Our data reveal a previously unidentified sub-clinical prion-positive portion of the elk population that could represent silent carriers capable of significantly impacting CWD ecology. PMID:25665713

  8. Prion Amplification and Hierarchical Bayesian Modeling Refine Detection of Prion Infection

    NASA Astrophysics Data System (ADS)

    Wyckoff, A. Christy; Galloway, Nathan; Meyerett-Reid, Crystal; Powers, Jenny; Spraker, Terry; Monello, Ryan J.; Pulford, Bruce; Wild, Margaret; Antolin, Michael; Vercauteren, Kurt; Zabel, Mark

    2015-02-01

    Prions are unique infectious agents that replicate without a genome and cause neurodegenerative diseases that include chronic wasting disease (CWD) of cervids. Immunohistochemistry (IHC) is currently considered the gold standard for diagnosis of a prion infection but may be insensitive to early or sub-clinical CWD that are important to understanding CWD transmission and ecology. We assessed the potential of serial protein misfolding cyclic amplification (sPMCA) to improve detection of CWD prior to the onset of clinical signs. We analyzed tissue samples from free-ranging Rocky Mountain elk (Cervus elaphus nelsoni) and used hierarchical Bayesian analysis to estimate the specificity and sensitivity of IHC and sPMCA conditional on simultaneously estimated disease states. Sensitivity estimates were higher for sPMCA (99.51%, credible interval (CI) 97.15-100%) than IHC of obex (brain stem, 76.56%, CI 57.00-91.46%) or retropharyngeal lymph node (90.06%, CI 74.13-98.70%) tissues, or both (98.99%, CI 90.01-100%). Our hierarchical Bayesian model predicts the prevalence of prion infection in this elk population to be 18.90% (CI 15.50-32.72%), compared to previous estimates of 12.90%. Our data reveal a previously unidentified sub-clinical prion-positive portion of the elk population that could represent silent carriers capable of significantly impacting CWD ecology.

  9. Estimating effectiveness in HIV prevention trials with a Bayesian hierarchical compound Poisson frailty model.

    PubMed

    Coley, Rebecca Yates; Brown, Elizabeth R

    2016-07-10

    Inconsistent results in recent HIV prevention trials of pre-exposure prophylactic interventions may be due to heterogeneity in risk among study participants. Intervention effectiveness is most commonly estimated with the Cox model, which compares event times between populations. When heterogeneity is present, this population-level measure underestimates intervention effectiveness for individuals who are at risk. We propose a likelihood-based Bayesian hierarchical model that estimates the individual-level effectiveness of candidate interventions by accounting for heterogeneity in risk with a compound Poisson-distributed frailty term. This model reflects the mechanisms of HIV risk and allows that some participants are not exposed to HIV and, therefore, have no risk of seroconversion during the study. We assess model performance via simulation and apply the model to data from an HIV prevention trial. Copyright © 2016 John Wiley & Sons, Ltd. PMID:26869051

  10. A hierarchical Bayesian model averaging framework for groundwater prediction under uncertainty.

    PubMed

    Chitsazan, Nima; Tsai, Frank T-C

    2015-01-01

    Groundwater prediction models are subjected to various sources of uncertainty. This study introduces a hierarchical Bayesian model averaging (HBMA) method to segregate and prioritize sources of uncertainty in a hierarchical structure and conduct BMA for concentration prediction. A BMA tree of models is developed to understand the impact of individual sources of uncertainty and uncertainty propagation to model predictions. HBMA evaluates the relative importance of different modeling propositions at each level in the BMA tree of model weights. The HBMA method is applied to chloride concentration prediction for the "1,500-foot" sand of the Baton Rouge area, Louisiana from 2005 to 2029. The groundwater head data from 1990 to 2004 is used for model calibration. Four sources of uncertainty are considered and resulted in 180 flow and transport models for concentration prediction. The results show that prediction variances of concentration from uncertain model elements are much higher than the prediction variance from uncertain model parameters. The HBMA method is able to quantify the contributions of individual sources of uncertainty to the total uncertainty. PMID:24890644

  11. A spectral-spatial-dynamic hierarchical Bayesian (SSD-HB) model for estimating soybean yield

    NASA Astrophysics Data System (ADS)

    Kazama, Yoriko; Kujirai, Toshihiro

    2014-10-01

    A method called a "spectral-spatial-dynamic hierarchical-Bayesian (SSD-HB) model," which can deal with many parameters (such as spectral and weather information all together) by reducing the occurrence of multicollinearity, is proposed. Experiments conducted on soybean yields in Brazil fields with a RapidEye satellite image indicate that the proposed SSD-HB model can predict soybean yield with a higher degree of accuracy than other estimation methods commonly used in remote-sensing applications. In the case of the SSD-HB model, the mean absolute error between estimated yield of the target area and actual yield is 0.28 t/ha, compared to 0.34 t/ha when conventional PLS regression was applied, showing the potential effectiveness of the proposed model.

  12. Radar coincidence imaging with phase error using Bayesian hierarchical prior modeling

    NASA Astrophysics Data System (ADS)

    Zhou, Xiaoli; Wang, Hongqiang; Cheng, Yongqiang; Qin, Yuliang

    2016-01-01

    Radar coincidence imaging (RCI) is a high-resolution imaging technique without the limitation of relative motion between target and radar. In sparsity-driven RCI, the prior knowledge of imaging model requires to be known accurately. However, the phase error generally exists as a model error, which may cause inaccuracies of the model and defocus the image. The problem is formulated using Bayesian hierarchical prior modeling, and the self-calibration variational message passing (SC-VMP) algorithm is proposed to improve the performance of RCI with phase error. The algorithm determines the phase error as part of the imaging process. The scattering coefficient and phase error are iteratively estimated using VMP and Newton's method, respectively. Simulation results show that the proposed algorithm can estimate the phase error accurately and improve the imaging quality significantly.

  13. Bayesian Hierarchical Models for Protein Networks in Single-Cell Mass Cytometry

    PubMed Central

    Mitra, Riten; Müller, Peter; Qiu, Peng; Ji, Yuan

    2014-01-01

    We propose a class of hierarchical models to investigate the protein functional network of cellular markers. We consider a novel data set from single-cell proteomics. The data are generated from single-cell mass cytometry experiments, in which protein expression is measured within an individual cell for multiple markers. Tens of thousands of cells are measured serving as biological replicates. Applying the Bayesian models, we report protein functional networks under different experimental conditions and the differences between the networks, ie, differential networks. We also present the differential network in a novel fashion that allows direct observation of the links between the experimental agent and its putative targeted proteins based on posterior inference. Our method serves as a powerful tool for studying molecular interactions at cellular level. PMID:25574129

  14. A Bayesian hierarchical model for reconstructing relative sea level: from raw data to rates of change

    NASA Astrophysics Data System (ADS)

    Cahill, N.; Kemp, A. C.; Horton, B. P.; Parnell, A. C.

    2015-10-01

    We present a holistic Bayesian hierarchical model for reconstructing the continuous and dynamic evolution of relative sea-level (RSL) change with fully quantified uncertainty. The reconstruction is produced from biological (foraminifera) and geochemical (δ13C) sea-level indicators preserved in dated cores of salt-marsh sediment. Our model is comprised of three modules: (1) A Bayesian transfer function for the calibration of foraminifera into tidal elevation, which is flexible enough to formally accommodate additional proxies (in this case bulk-sediment δ13C values), (2) A chronology developed from an existing Bchron age-depth model, and (3) An existing errors-in-variables integrated Gaussian process (EIV-IGP) model for estimating rates of sea-level change. We illustrate our approach using a case study of Common Era sea-level variability from New Jersey. USA We develop a new Bayesian transfer function (B-TF), with and without the δ13C proxy and compare our results to those from a widely-used weighted-averaging transfer function (WA-TF). The formal incorporation of a second proxy into the B-TF model results in smaller vertical uncertainties and improved accuracy for reconstructed RSL. The vertical uncertainty from the multi-proxy B-TF is ∼ 28 % smaller on average compared to the WA-TF. When evaluated against historic tide-gauge measurements, the multi-proxy B-TF most accurately reconstructs the RSL changes observed in the instrumental record (MSE = 0.003 m2). The holistic model provides a single, unifying framework for reconstructing and analysing sea level through time. This approach is suitable for reconstructing other paleoenvironmental variables using biological proxies.

  15. Hierarchical Bayesian Markov switching models with application to predicting spawning success of shovelnose sturgeon

    USGS Publications Warehouse

    Holan, S.H.; Davis, G.M.; Wildhaber, M.L.; DeLonay, A.J.; Papoulias, D.M.

    2009-01-01

    The timing of spawning in fish is tightly linked to environmental factors; however, these factors are not very well understood for many species. Specifically, little information is available to guide recruitment efforts for endangered species such as the sturgeon. Therefore, we propose a Bayesian hierarchical model for predicting the success of spawning of the shovelnose sturgeon which uses both biological and behavioural (longitudinal) data. In particular, we use data that were produced from a tracking study that was conducted in the Lower Missouri River. The data that were produced from this study consist of biological variables associated with readiness to spawn along with longitudinal behavioural data collected by using telemetry and archival data storage tags. These high frequency data are complex both biologically and in the underlying behavioural process. To accommodate such complexity we developed a hierarchical linear regression model that uses an eigenvalue predictor, derived from the transition probability matrix of a two-state Markov switching model with generalized auto-regressive conditional heteroscedastic dynamics. Finally, to minimize the computational burden that is associated with estimation of this model, a parallel computing approach is proposed. ?? Journal compilation 2009 Royal Statistical Society.

  16. A Bayesian Hierarchical Model for Estimation of Abundance and Spatial Density of Aedes aegypti

    PubMed Central

    Villela, Daniel A. M.; Codeço, Claudia T.; Figueiredo, Felipe; Garcia, Gabriela A.; Maciel-de-Freitas, Rafael; Struchiner, Claudio J.

    2015-01-01

    Strategies to minimize dengue transmission commonly rely on vector control, which aims to maintain Ae. aegypti density below a theoretical threshold. Mosquito abundance is traditionally estimated from mark-release-recapture (MRR) experiments, which lack proper analysis regarding accurate vector spatial distribution and population density. Recently proposed strategies to control vector-borne diseases involve replacing the susceptible wild population by genetically modified individuals’ refractory to the infection by the pathogen. Accurate measurements of mosquito abundance in time and space are required to optimize the success of such interventions. In this paper, we present a hierarchical probabilistic model for the estimation of population abundance and spatial distribution from typical mosquito MRR experiments, with direct application to the planning of these new control strategies. We perform a Bayesian analysis using the model and data from two MRR experiments performed in a neighborhood of Rio de Janeiro, Brazil, during both low- and high-dengue transmission seasons. The hierarchical model indicates that mosquito spatial distribution is clustered during the winter (0.99 mosquitoes/premise 95% CI: 0.80–1.23) and more homogeneous during the high abundance period (5.2 mosquitoes/premise 95% CI: 4.3–5.9). The hierarchical model also performed better than the commonly used Fisher-Ford’s method, when using simulated data. The proposed model provides a formal treatment of the sources of uncertainty associated with the estimation of mosquito abundance imposed by the sampling design. Our approach is useful in strategies such as population suppression or the displacement of wild vector populations by refractory Wolbachia-infected mosquitoes, since the invasion dynamics have been shown to follow threshold conditions dictated by mosquito abundance. The presence of spatially distributed abundance hotspots is also formally addressed under this modeling framework and

  17. Hierarchical Bayesian model for rare variant association analysis integrating genotype uncertainty in human sequence data.

    PubMed

    He, Liang; Pitkäniemi, Janne; Sarin, Antti-Pekka; Salomaa, Veikko; Sillanpää, Mikko J; Ripatti, Samuli

    2015-02-01

    Next-generation sequencing (NGS) has led to the study of rare genetic variants, which possibly explain the missing heritability for complex diseases. Most existing methods for rare variant (RV) association detection do not account for the common presence of sequencing errors in NGS data. The errors can largely affect the power and perturb the accuracy of association tests due to rare observations of minor alleles. We developed a hierarchical Bayesian approach to estimate the association between RVs and complex diseases. Our integrated framework combines the misclassification probability with shrinkage-based Bayesian variable selection. It allows for flexibility in handling neutral and protective RVs with measurement error, and is robust enough for detecting causal RVs with a wide spectrum of minor allele frequency (MAF). Imputation uncertainty and MAF are incorporated into the integrated framework to achieve the optimal statistical power. We demonstrate that sequencing error does significantly affect the findings, and our proposed model can take advantage of it to improve statistical power in both simulated and real data. We further show that our model outperforms existing methods, such as sequence kernel association test (SKAT). Finally, we illustrate the behavior of the proposed method using a Finnish low-density lipoprotein cholesterol study, and show that it identifies an RV known as FH North Karelia in LDLR gene with three carriers in 1,155 individuals, which is missed by both SKAT and Granvil. PMID:25395270

  18. 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.

  19. Bayesian hierarchical models for multivariate nonlinear spatio-temporal dynamical processes in the atmosphere and ocean

    NASA Astrophysics Data System (ADS)

    Leeds, W. B.; Wikle, C. K.

    2012-12-01

    Spatio-temporal statistical models, and in particular Bayesian hierarchical models (BHMs), have become increasingly popular as means of representing natural processes such as climate and weather that evolve over space and time. Hierarchical models make it possible to specify separate, conditional probability distributions that account for uncertainty in the observations, the underlying process, and parameters in situations when specifying these sources of uncertainty in a joint probability distribution may be difficult. As a result, BHMs are a natural setting for climatologists, meteorologists, and other environmental scientists to incorporate scientific information (e.g., PDEs, IDEs, etc.) a priori into a rigorous statistical framework that accounts for error in measurements, uncertainty in the understanding of the true underlying process, and uncertainty in the parameters that describe the process. While much work has been done in the development of statistical models for linear dynamic spatio-temporal processes, statistical modeling for nonlinear (and particularly, multivariate nonlinear) spatio-temporal dynamical processes is still a relatively open area of inquiry. As a result, general statistical models for environmental scientists to model complicated nonlinear processes is limited. We address this limitation in the methodology by introducing a multivariate "general quadratic nonlinear" framework for modeling multivariate, nonlinear spatio-temporal random processes inside of a BHM in a way that is especially applicable for problems in the ocean and atmospheric sciences. We show that in addition to the fact that this model addresses the previously mentioned sources of uncertainty for a wide spectrum of multivariate, nonlinear spatio-temporal processes, it is also a natural framework for data assimilation, allowing for the fusing of observations with computer models, computer model emulators, computer model output, or "mechanistically motivated" statistical

  20. Application of hierarchical Bayesian unmixing models in river sediment source apportionment

    NASA Astrophysics Data System (ADS)

    Blake, Will; Smith, Hugh; Navas, Ana; Bodé, Samuel; Goddard, Rupert; Zou Kuzyk, Zou; Lennard, Amy; Lobb, David; Owens, Phil; Palazon, Leticia; Petticrew, Ellen; Gaspar, Leticia; Stock, Brian; Boeckx, Pacsal; Semmens, Brice

    2016-04-01

    Fingerprinting and unmixing concepts are used widely across environmental disciplines for forensic evaluation of pollutant sources. In aquatic and marine systems, this includes tracking the source of organic and inorganic pollutants in water and linking problem sediment to soil erosion and land use sources. It is, however, the particular complexity of ecological systems that has driven creation of the most sophisticated mixing models, primarily to (i) evaluate diet composition in complex ecological food webs, (ii) inform population structure and (iii) explore animal movement. In the context of the new hierarchical Bayesian unmixing model, MIXSIAR, developed to characterise intra-population niche variation in ecological systems, we evaluate the linkage between ecological 'prey' and 'consumer' concepts and river basin sediment 'source' and sediment 'mixtures' to exemplify the value of ecological modelling tools to river basin science. Recent studies have outlined advantages presented by Bayesian unmixing approaches in handling complex source and mixture datasets while dealing appropriately with uncertainty in parameter probability distributions. MixSIAR is unique in that it allows individual fixed and random effects associated with mixture hierarchy, i.e. factors that might exert an influence on model outcome for mixture groups, to be explored within the source-receptor framework. This offers new and powerful ways of interpreting river basin apportionment data. In this contribution, key components of the model are evaluated in the context of common experimental designs for sediment fingerprinting studies namely simple, nested and distributed catchment sampling programmes. Illustrative examples using geochemical and compound specific stable isotope datasets are presented and used to discuss best practice with specific attention to (1) the tracer selection process, (2) incorporation of fixed effects relating to sample timeframe and sediment type in the modelling

  1. A Bayesian hierarchical approach to model seasonal algal variability along an upstream to downstream river gradient

    NASA Astrophysics Data System (ADS)

    Cha, YoonKyung; Soon Park, Seok; Won Lee, Hye; Stow, Craig A.

    2016-01-01

    Modeling to accurately predict river phytoplankton distribution and abundance is important in water quality and resource management. Nevertheless, the complex nature of eutrophication processes in highly connected river systems makes the task challenging. To model dynamics of river phytoplankton, represented by chlorophyll a (Chl a) concentration, we propose a Bayesian hierarchical model that explicitly accommodates seasonality and upstream-downstream spatial gradient in the structure. The utility of our model is demonstrated with an application to the Nakdong River (South Korea), which is a eutrophic, intensively regulated river, but functions as an irreplaceable water source for more than 13 million people. Chl a is modeled with two manageable factors, river flow, and total phosphorus (TP) concentration. Our model results highlight the importance of taking seasonal and spatial context into account when describing flow regimes and phosphorus delivery in rivers. A contrasting positive Chl a-flow relationship across stations versus negative Chl a-flow slopes that arose when Chl a was modeled on a station-month basis is an illustration of Simpson's paradox, which necessitates modeling Chl a-flow relationships decomposed into seasonal and spatial components. Similar Chl a-TP slopes among stations and months suggest that, with the flow effect removed, positive TP effects on Chl a are uniform regardless of the season and station in the river. Our model prediction successfully captured the shift in the spatial and monthly patterns of Chl a.

  2. Prediction and structural uncertainty analyses of artificial neural networks using hierarchical Bayesian model averaging

    NASA Astrophysics Data System (ADS)

    Chitsazan, Nima; Nadiri, Ata Allah; Tsai, Frank T.-C.

    2015-09-01

    This study adopts a hierarchical Bayesian model averaging (HBMA) method to analyze prediction uncertainty resulted from uncertain components in artificial neural networks (ANNs). The HBMA is an ensemble method for prediction and is used to segregate the sources of model structure uncertainty in ANNs and investigate their variance contributions to total prediction variance. Specific sources of uncertainty considered in ANNs include the uncertainty in neural network weights and biases (model parameters), uncertainty of selecting an activation function for the hidden layer, and uncertainty of selecting a number of hidden layer nodes (model structure). Prediction uncertainties due to uncertain inputs and ANN model parameters are represented by within-model variance. Prediction uncertainties due to uncertain activation function and uncertain number of nodes for the hidden layer are represented by between-model variance. The method is demonstrated through a study that employs ANNs to predict fluoride concentration in the aquifers of the Maku area, Azarbaijan, Iran. The results show that uncertain inputs and ANN model parameters produces the most prediction variance, followed by prediction variances from uncertain number of hidden layer nodes and uncertain activation function.

  3. Full Bayesian hierarchical light curve modeling of core-collapse supernova populations

    NASA Astrophysics Data System (ADS)

    Sanders, Nathan; Betancourt, Michael; Soderberg, Alicia Margarita

    2016-06-01

    While wide field surveys have yielded remarkable quantities of photometry of transient objects, including supernovae, light curves reconstructed from this data suffer from several characteristic problems. Because most transients are discovered near the detection limit, signal to noise is generally poor; because coverage is limited to the observing season, light curves are often incomplete; and because temporal sampling can be uneven across filters, these problems can be exacerbated at any one wavelength. While the prevailing approach of modeling individual light curves independently is successful at recovering inferences for the objects with the highest quality observations, it typically neglects a substantial portion of the data and can introduce systematic biases. Joint modeling of the light curves of transient populations enables direct inference on population-level characteristics as well as superior measurements for individual objects. We present a new hierarchical Bayesian model for supernova light curves, where information inferred from observations of every individual light curve in a sample is partially pooled across objects to constrain population-level hyperparameters. Using an efficient Hamiltonian Monte Carlo sampling technique, the model posterior can be explored to enable marginalization over weakly-identified hyperparameters through full Bayesian inference. We demonstrate our technique on the Pan-STARRS1 (PS1) Type IIP supernova light curve sample published by Sanders et al. (2015), consisting of nearly 20,000 individual photometric observations of more than 70 supernovae in five photometric filters. We discuss the Stan probabilistic programming language used to implement the model, computational challenges, and prospects for future work including generalization to multiple supernova types. We also discuss scientific results from the PS1 dataset including a new relation between the peak magnitude and decline rate of SNe IIP, a new perspective on the

  4. Multimethod, multistate Bayesian hierarchical modeling approach for use in regional monitoring of wolves.

    PubMed

    Jiménez, José; García, Emilio J; Llaneza, Luis; Palacios, Vicente; González, Luis Mariano; García-Domínguez, Francisco; Múñoz-Igualada, Jaime; López-Bao, José Vicente

    2016-08-01

    In many cases, the first step in large-carnivore management is to obtain objective, reliable, and cost-effective estimates of population parameters through procedures that are reproducible over time. However, monitoring predators over large areas is difficult, and the data have a high level of uncertainty. We devised a practical multimethod and multistate modeling approach based on Bayesian hierarchical-site-occupancy models that combined multiple survey methods to estimate different population states for use in monitoring large predators at a regional scale. We used wolves (Canis lupus) as our model species and generated reliable estimates of the number of sites with wolf reproduction (presence of pups). We used 2 wolf data sets from Spain (Western Galicia in 2013 and Asturias in 2004) to test the approach. Based on howling surveys, the naïve estimation (i.e., estimate based only on observations) of the number of sites with reproduction was 9 and 25 sites in Western Galicia and Asturias, respectively. Our model showed 33.4 (SD 9.6) and 34.4 (3.9) sites with wolf reproduction, respectively. The number of occupied sites with wolf reproduction was 0.67 (SD 0.19) and 0.76 (0.11), respectively. This approach can be used to design more cost-effective monitoring programs (i.e., to define the sampling effort needed per site). Our approach should inspire well-coordinated surveys across multiple administrative borders and populations and lead to improved decision making for management of large carnivores on a landscape level. The use of this Bayesian framework provides a simple way to visualize the degree of uncertainty around population-parameter estimates and thus provides managers and stakeholders an intuitive approach to interpreting monitoring results. Our approach can be widely applied to large spatial scales in wildlife monitoring where detection probabilities differ between population states and where several methods are being used to estimate different population

  5. Estimating the Term Structure With a Semiparametric Bayesian Hierarchical Model: An Application to Corporate Bonds1

    PubMed Central

    Cruz-Marcelo, Alejandro; Ensor, Katherine B.; Rosner, Gary L.

    2011-01-01

    The term structure of interest rates is used to price defaultable bonds and credit derivatives, as well as to infer the quality of bonds for risk management purposes. We introduce a model that jointly estimates term structures by means of a Bayesian hierarchical model with a prior probability model based on Dirichlet process mixtures. The modeling methodology borrows strength across term structures for purposes of estimation. The main advantage of our framework is its ability to produce reliable estimators at the company level even when there are only a few bonds per company. After describing the proposed model, we discuss an empirical application in which the term structure of 197 individual companies is estimated. The sample of 197 consists of 143 companies with only one or two bonds. In-sample and out-of-sample tests are used to quantify the improvement in accuracy that results from approximating the term structure of corporate bonds with estimators by company rather than by credit rating, the latter being a popular choice in the financial literature. A complete description of a Markov chain Monte Carlo (MCMC) scheme for the proposed model is available as Supplementary Material. PMID:21765566

  6. Estimating the Term Structure With a Semiparametric Bayesian Hierarchical Model: An Application to Corporate Bonds.

    PubMed

    Cruz-Marcelo, Alejandro; Ensor, Katherine B; Rosner, Gary L

    2011-06-01

    The term structure of interest rates is used to price defaultable bonds and credit derivatives, as well as to infer the quality of bonds for risk management purposes. We introduce a model that jointly estimates term structures by means of a Bayesian hierarchical model with a prior probability model based on Dirichlet process mixtures. The modeling methodology borrows strength across term structures for purposes of estimation. The main advantage of our framework is its ability to produce reliable estimators at the company level even when there are only a few bonds per company. After describing the proposed model, we discuss an empirical application in which the term structure of 197 individual companies is estimated. The sample of 197 consists of 143 companies with only one or two bonds. In-sample and out-of-sample tests are used to quantify the improvement in accuracy that results from approximating the term structure of corporate bonds with estimators by company rather than by credit rating, the latter being a popular choice in the financial literature. A complete description of a Markov chain Monte Carlo (MCMC) scheme for the proposed model is available as Supplementary Material. PMID:21765566

  7. A Bayesian hierarchical framework for modeling brain connectivity for neuroimaging data.

    PubMed

    Chen, Shuo; Bowman, F DuBois; Mayberg, Helen S

    2016-06-01

    We propose a novel Bayesian hierarchical model for brain imaging data that unifies voxel-level (the most localized unit of measure) and region-level brain connectivity analyses, and yields population-level inferences. Functional connectivity generally refers to associations in brain activity between distinct locations. The first level of our model summarizes brain connectivity for cross-region voxel pairs using a two-component mixture model consisting of connected and nonconnected voxels. We use the proportion of connected voxel pairs to define a new measure of connectivity strength, which reflects the breadth of between-region connectivity. Furthermore, we evaluate the impact of clinical covariates on connectivity between region-pairs at a population level. We perform parameter estimation using Markov chain Monte Carlo (MCMC) techniques, which can be executed quickly relative to the number of model parameters. We apply our method to resting-state functional magnetic resonance imaging (fMRI) data from 32 subjects with major depression and simulated data to demonstrate the properties of our method. PMID:26501687

  8. A Bayesian hierarchical model with novel prior specifications for estimating HIV testing rates

    PubMed Central

    An, Qian; Kang, Jian; Song, Ruiguang; Hall, H. Irene

    2016-01-01

    Human immunodeficiency virus (HIV) infection is a severe infectious disease actively spreading globally, and acquired immunodeficiency syndrome (AIDS) is an advanced stage of HIV infection. The HIV testing rate, that is, the probability that an AIDS-free HIV infected person seeks a test for HIV during a particular time interval, given no previous positive test has been obtained prior to the start of the time, is an important parameter for public health. In this paper, we propose a Bayesian hierarchical model with two levels of hierarchy to estimate the HIV testing rate using annual AIDS and AIDS-free HIV diagnoses data. At level one, we model the latent number of HIV infections for each year using a Poisson distribution with the intensity parameter representing the HIV incidence rate. At level two, the annual numbers of AIDS and AIDS-free HIV diagnosed cases and all undiagnosed cases stratified by the HIV infections at different years are modeled using a multinomial distribution with parameters including the HIV testing rate. We propose a new class of priors for the HIV incidence rate and HIV testing rate taking into account the temporal dependence of these parameters to improve the estimation accuracy. We develop an efficient posterior computation algorithm based on the adaptive rejection metropolis sampling technique. We demonstrate our model using simulation studies and the analysis of the national HIV surveillance data in the USA. PMID:26567891

  9. A Bayesian hierarchical model with novel prior specifications for estimating HIV testing rates.

    PubMed

    An, Qian; Kang, Jian; Song, Ruiguang; Hall, H Irene

    2016-04-30

    Human immunodeficiency virus (HIV) infection is a severe infectious disease actively spreading globally, and acquired immunodeficiency syndrome (AIDS) is an advanced stage of HIV infection. The HIV testing rate, that is, the probability that an AIDS-free HIV infected person seeks a test for HIV during a particular time interval, given no previous positive test has been obtained prior to the start of the time, is an important parameter for public health. In this paper, we propose a Bayesian hierarchical model with two levels of hierarchy to estimate the HIV testing rate using annual AIDS and AIDS-free HIV diagnoses data. At level one, we model the latent number of HIV infections for each year using a Poisson distribution with the intensity parameter representing the HIV incidence rate. At level two, the annual numbers of AIDS and AIDS-free HIV diagnosed cases and all undiagnosed cases stratified by the HIV infections at different years are modeled using a multinomial distribution with parameters including the HIV testing rate. We propose a new class of priors for the HIV incidence rate and HIV testing rate taking into account the temporal dependence of these parameters to improve the estimation accuracy. We develop an efficient posterior computation algorithm based on the adaptive rejection metropolis sampling technique. We demonstrate our model using simulation studies and the analysis of the national HIV surveillance data in the USA. PMID:26567891

  10. Testing comparative phylogeographic models of marine vicariance and dispersal using a hierarchical Bayesian approach

    PubMed Central

    2008-01-01

    Background Marine allopatric speciation is an enigma because pelagic larval dispersal can potentially connect disjunct populations thereby preventing reproductive and morphological divergence. Here we present a new hierarchical approximate Bayesian computation model (HABC) that tests two hypotheses of marine allopatric speciation: 1.) "soft vicariance", where a speciation involves fragmentation of a large widespread ancestral species range that was previously connected by long distance gene flow; and 2.) peripatric colonization, where speciations in peripheral archipelagos emerge from sweepstakes colonizations from central source regions. The HABC approach analyzes all the phylogeographic datasets at once in order to make across taxon-pair inferences about biogeographic processes while explicitly allowing for uncertainty in the demographic differences within each taxon-pair. Our method uses comparative phylogeographic data that consists of single locus mtDNA sequences from multiple co-distributed taxa containing pairs of central and peripheral populations. We use the method on two comparative phylogeographic data sets consisting of cowrie gastropod endemics co-distributed in the Hawaiian (11 taxon-pairs) and Marquesan archipelagos (7 taxon-pairs). Results Given the Marquesan data, we find strong evidence of simultaneous colonization across all seven cowrie gastropod endemics co-distributed in the Marquesas. In contrast, the lower sample sizes in the Hawaiian data lead to greater uncertainty associated with the Hawaiian estimates. Although, the hyper-parameter estimates point to soft vicariance in a subset of the 11 Hawaiian taxon-pairs, the hyper-prior and hyper-posterior are too similar to make a definitive conclusion. Both results are not inconsistent with what is known about the geologic history of the archipelagos. Simulations verify that our method can successfully distinguish these two histories across a wide range of conditions given sufficient sampling

  11. Monitoring schistosomiasis risk in East China over space and time using a Bayesian hierarchical modeling approach.

    PubMed

    Hu, Yi; Ward, Michael P; Xia, Congcong; Li, Rui; Sun, Liqian; Lynn, Henry; Gao, Fenghua; Wang, Qizhi; Zhang, Shiqing; Xiong, Chenglong; Zhang, Zhijie; Jiang, Qingwu

    2016-01-01

    Schistosomiasis remains a major public health problem and causes substantial economic impact in east China, particularly along the Yangtze River Basin. Disease forecasting and surveillance can assist in the development and implementation of more effective intervention measures to control disease. In this study, we applied a Bayesian hierarchical spatio-temporal model to describe trends in schistosomiasis risk in Anhui Province, China, using annual parasitological and environmental data for the period 1997-2010. A computationally efficient approach-Integrated Nested Laplace Approximation-was used for model inference. A zero-inflated, negative binomial model best described the spatio-temporal dynamics of schistosomiasis risk. It predicted that the disease risk would generally be low and stable except for some specific, local areas during the period 2011-2014. High-risk counties were identified in the forecasting maps: three in which the risk remained high, and two in which risk would become high. The results indicated that schistosomiasis risk has been reduced to consistently low levels throughout much of this region of China; however, some counties were identified in which progress in schistosomiasis control was less than satisfactory. Whilst maintaining overall control, specific interventions in the future should focus on these refractive counties as part of a strategy to eliminate schistosomiasis from this region. PMID:27053447

  12. Monitoring schistosomiasis risk in East China over space and time using a Bayesian hierarchical modeling approach

    PubMed Central

    Hu, Yi; Ward, Michael P.; Xia, Congcong; Li, Rui; Sun, Liqian; Lynn, Henry; Gao, Fenghua; Wang, Qizhi; Zhang, Shiqing; Xiong, Chenglong; Zhang, Zhijie; Jiang, Qingwu

    2016-01-01

    Schistosomiasis remains a major public health problem and causes substantial economic impact in east China, particularly along the Yangtze River Basin. Disease forecasting and surveillance can assist in the development and implementation of more effective intervention measures to control disease. In this study, we applied a Bayesian hierarchical spatio-temporal model to describe trends in schistosomiasis risk in Anhui Province, China, using annual parasitological and environmental data for the period 1997–2010. A computationally efficient approach–Integrated Nested Laplace Approximation–was used for model inference. A zero-inflated, negative binomial model best described the spatio-temporal dynamics of schistosomiasis risk. It predicted that the disease risk would generally be low and stable except for some specific, local areas during the period 2011–2014. High-risk counties were identified in the forecasting maps: three in which the risk remained high, and two in which risk would become high. The results indicated that schistosomiasis risk has been reduced to consistently low levels throughout much of this region of China; however, some counties were identified in which progress in schistosomiasis control was less than satisfactory. Whilst maintaining overall control, specific interventions in the future should focus on these refractive counties as part of a strategy to eliminate schistosomiasis from this region. PMID:27053447

  13. Hierarchical Bayesian modelling of mobility metrics for hazard model input calibration

    NASA Astrophysics Data System (ADS)

    Calder, Eliza; Ogburn, Sarah; Spiller, Elaine; Rutarindwa, Regis; Berger, Jim

    2015-04-01

    In this work we present a method to constrain flow mobility input parameters for pyroclastic flow models using hierarchical Bayes modeling of standard mobility metrics such as H/L and flow volume etc. The advantage of hierarchical modeling is that it can leverage the information in global dataset for a particular mobility metric in order to reduce the uncertainty in modeling of an individual volcano, especially important where individual volcanoes have only sparse datasets. We use compiled pyroclastic flow runout data from Colima, Merapi, Soufriere Hills, Unzen and Semeru volcanoes, presented in an open-source database FlowDat (https://vhub.org/groups/massflowdatabase). While the exact relationship between flow volume and friction varies somewhat between volcanoes, dome collapse flows originating from the same volcano exhibit similar mobility relationships. Instead of fitting separate regression models for each volcano dataset, we use a variation of the hierarchical linear model (Kass and Steffey, 1989). The model presents a hierarchical structure with two levels; all dome collapse flows and dome collapse flows at specific volcanoes. The hierarchical model allows us to assume that the flows at specific volcanoes share a common distribution of regression slopes, then solves for that distribution. We present comparisons of the 95% confidence intervals on the individual regression lines for the data set from each volcano as well as those obtained from the hierarchical model. The results clearly demonstrate the advantage of considering global datasets using this technique. The technique developed is demonstrated here for mobility metrics, but can be applied to many other global datasets of volcanic parameters. In particular, such methods can provide a means to better contain parameters for volcanoes for which we only have sparse data, a ubiquitous problem in volcanology.

  14. Hierarchical Bayesian Model Averaging for Non-Uniqueness and Uncertainty Analysis of Artificial Neural Networks

    NASA Astrophysics Data System (ADS)

    Fijani, E.; Chitsazan, N.; Nadiri, A.; Tsai, F. T.; Asghari Moghaddam, A.

    2012-12-01

    Artificial Neural Networks (ANNs) have been widely used to estimate concentration of chemicals in groundwater systems. However, estimation uncertainty is rarely discussed in the literature. Uncertainty in ANN output stems from three sources: ANN inputs, ANN parameters (weights and biases), and ANN structures. Uncertainty in ANN inputs may come from input data selection and/or input data error. ANN parameters are naturally uncertain because they are maximum-likelihood estimated. ANN structure is also uncertain because there is no unique ANN model given a specific case. Therefore, multiple plausible AI models are generally resulted for a study. One might ask why good models have to be ignored in favor of the best model in traditional estimation. What is the ANN estimation variance? How do the variances from different ANN models accumulate to the total estimation variance? To answer these questions we propose a Hierarchical Bayesian Model Averaging (HBMA) framework. Instead of choosing one ANN model (the best ANN model) for estimation, HBMA averages outputs of all plausible ANN models. The model weights are based on the evidence of data. Therefore, the HBMA avoids overconfidence on the single best ANN model. In addition, HBMA is able to analyze uncertainty propagation through aggregation of ANN models in a hierarchy framework. This method is applied for estimation of fluoride concentration in the Poldasht plain and the Bazargan plain in Iran. Unusually high fluoride concentration in the Poldasht and Bazargan plains has caused negative effects on the public health. Management of this anomaly requires estimation of fluoride concentration distribution in the area. The results show that the HBMA provides a knowledge-decision-based framework that facilitates analyzing and quantifying ANN estimation uncertainties from different sources. In addition HBMA allows comparative evaluation of the realizations for each source of uncertainty by segregating the uncertainty sources in

  15. Estimating the distribution of sensorimotor synchronization data: A Bayesian hierarchical modeling approach.

    PubMed

    Bååth, Rasmus

    2016-06-01

    The sensorimotor synchronization paradigm is used when studying the coordination of rhythmic motor responses with a pacing stimulus and is an important paradigm in the study of human timing and time perception. Two measures of performance frequently calculated using sensorimotor synchronization data are the average offset and variability of the stimulus-to-response asynchronies-the offsets between the stimuli and the motor responses. Here it is shown that assuming that asynchronies are normally distributed when estimating these measures can result in considerable underestimation of both the average offset and variability. This is due to a tendency for the distribution of the asynchronies to be bimodal and left skewed when the interstimulus interval is longer than 2 s. It is argued that (1) this asymmetry is the result of the distribution of the asynchronies being a mixture of two types of responses-predictive and reactive-and (2) the main interest in a sensorimotor synchronization study is the predictive responses. A Bayesian hierarchical modeling approach is proposed in which sensorimotor synchronization data are modeled as coming from a right-censored normal distribution that effectively separates the predictive responses from the reactive responses. Evaluation using both simulated data and experimental data from a study by Repp and Doggett (2007) showed that the proposed approach produces more precise estimates of the average offset and variability, with considerably less underestimation. PMID:25931279

  16. A hierarchical Bayesian model for flexible module discovery in three-way time-series data

    PubMed Central

    Amar, David; Yekutieli, Daniel; Maron-Katz, Adi; Hendler, Talma; Shamir, Ron

    2015-01-01

    Motivation: Detecting modules of co-ordinated activity is fundamental in the analysis of large biological studies. For two-dimensional data (e.g. genes × patients), this is often done via clustering or biclustering. More recently, studies monitoring patients over time have added another dimension. Analysis is much more challenging in this case, especially when time measurements are not synchronized. New methods that can analyze three-way data are thus needed. Results: We present a new algorithm for finding coherent and flexible modules in three-way data. Our method can identify both core modules that appear in multiple patients and patient-specific augmentations of these core modules that contain additional genes. Our algorithm is based on a hierarchical Bayesian data model and Gibbs sampling. The algorithm outperforms extant methods on simulated and on real data. The method successfully dissected key components of septic shock response from time series measurements of gene expression. Detected patient-specific module augmentations were informative for disease outcome. In analyzing brain functional magnetic resonance imaging time series of subjects at rest, it detected the pertinent brain regions involved. Availability and implementation: R code and data are available at http://acgt.cs.tau.ac.il/twigs/. Contact: rshamir@tau.ac.il Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26072479

  17. Establishing a connection between hydrologic model parameters and physical catchment signatures for improved hierarchical Bayesian modeling in ungauged catchments

    NASA Astrophysics Data System (ADS)

    Marshall, L. A.; Weber, K.; Smith, T. J.; Greenwood, M. C.; Sharma, A.

    2012-12-01

    In an effort to improve hydrologic analysis in areas with limited data, hydrologists often seek to link catchments where little to no data collection occurs to catchments that are gauged. Various metrics and methods have been proposed to identify such relationships, in the hope that "surrogate" catchments might provide information for those catchments that are hydrologically similar. In this study we present a statistical analysis of over 150 catchments located in southeast Australia to examine the relationship between a hydrological model and certain catchment metrics. A conceptual rainfall-runoff model is optimized for each of the catchments and hierarchical clustering is performed to link catchments based on their calibrated model parameters. Clustering has been used in recent hydrologic studies but catchments are often clustered based on physical characteristics alone. Usually there is little evidence to suggest that such "surrogate" data approaches provide sufficiently similar model predictions. Beginning with model parameters and working backwards, we hope to establish if there is a relationship between the model parameters and physical characteristics for improved model predictions in the ungauged catchment. To analyze relationships, permutational multivariate analysis of variance tests are used that suggest which hydrologic metrics are most appropriate for discriminating between calibrated catchment clusters. Additional analysis is performed to determine which cluster pairs show significant differences for various metrics. We further examine the extent to which these results may be insightful for a hierarchical Bayesian modeling approach that is aimed at generating model predictions at an ungauged site. The method, known as Bayes Empirical Bayes (BEB) works to pool information from similar catchments to generate informed probability distributions for each model parameter at a data-limited catchment of interest. We demonstrate the effect of selecting

  18. Estimating temporal trend in the presence of spatial complexity: a Bayesian hierarchical model for a wetland plant population undergoing restoration.

    PubMed

    Rodhouse, Thomas J; Irvine, Kathryn M; Vierling, Kerri T; Vierling, Lee A

    2011-01-01

    Monitoring programs that evaluate restoration and inform adaptive management are important for addressing environmental degradation. These efforts may be well served by spatially explicit hierarchical approaches to modeling because of unavoidable spatial structure inherited from past land use patterns and other factors. We developed bayesian hierarchical models to estimate trends from annual density counts observed in a spatially structured wetland forb (Camassia quamash [camas]) population following the cessation of grazing and mowing on the study area, and in a separate reference population of camas. The restoration site was bisected by roads and drainage ditches, resulting in distinct subpopulations ("zones") with different land use histories. We modeled this spatial structure by fitting zone-specific intercepts and slopes. We allowed spatial covariance parameters in the model to vary by zone, as in stratified kriging, accommodating anisotropy and improving computation and biological interpretation. Trend estimates provided evidence of a positive effect of passive restoration, and the strength of evidence was influenced by the amount of spatial structure in the model. Allowing trends to vary among zones and accounting for topographic heterogeneity increased precision of trend estimates. Accounting for spatial autocorrelation shifted parameter coefficients in ways that varied among zones depending on strength of statistical shrinkage, autocorrelation and topographic heterogeneity--a phenomenon not widely described. Spatially explicit estimates of trend from hierarchical models will generally be more useful to land managers than pooled regional estimates and provide more realistic assessments of uncertainty. The ability to grapple with historical contingency is an appealing benefit of this approach. PMID:22163047

  19. Estimating temporal trend in the presence of spatial complexity: A Bayesian hierarchical model for a wetland plant population undergoing restoration

    USGS Publications Warehouse

    Rodhouse, T.J.; Irvine, K.M.; Vierling, K.T.; Vierling, L.A.

    2011-01-01

    Monitoring programs that evaluate restoration and inform adaptive management are important for addressing environmental degradation. These efforts may be well served by spatially explicit hierarchical approaches to modeling because of unavoidable spatial structure inherited from past land use patterns and other factors. We developed Bayesian hierarchical models to estimate trends from annual density counts observed in a spatially structured wetland forb (Camassia quamash [camas]) population following the cessation of grazing and mowing on the study area, and in a separate reference population of camas. The restoration site was bisected by roads and drainage ditches, resulting in distinct subpopulations ("zones") with different land use histories. We modeled this spatial structure by fitting zone-specific intercepts and slopes. We allowed spatial covariance parameters in the model to vary by zone, as in stratified kriging, accommodating anisotropy and improving computation and biological interpretation. Trend estimates provided evidence of a positive effect of passive restoration, and the strength of evidence was influenced by the amount of spatial structure in the model. Allowing trends to vary among zones and accounting for topographic heterogeneity increased precision of trend estimates. Accounting for spatial autocorrelation shifted parameter coefficients in ways that varied among zones depending on strength of statistical shrinkage, autocorrelation and topographic heterogeneity-a phenomenon not widely described. Spatially explicit estimates of trend from hierarchical models will generally be more useful to land managers than pooled regional estimates and provide more realistic assessments of uncertainty. The ability to grapple with historical contingency is an appealing benefit of this approach.

  20. Fully Bayesian hierarchical modelling in two stages, with application to meta-analysis

    PubMed Central

    Lunn, David; Barrett, Jessica; Sweeting, Michael; Thompson, Simon

    2013-01-01

    Meta-analysis is often undertaken in two stages, with each study analysed separately in stage 1 and estimates combined across studies in stage 2. The study-specific estimates are assumed to arise from normal distributions with known variances equal to their corresponding estimates. In contrast, a one-stage analysis estimates all parameters simultaneously. A Bayesian one-stage approach offers additional advantages, such as the acknowledgement of uncertainty in all parameters and greater flexibility. However, there are situations when a two-stage strategy is compelling, e.g. when study-specific analyses are complex and/or time consuming. We present a novel method for fitting the full Bayesian model in two stages, hence benefiting from its advantages while retaining the convenience and flexibility of a two-stage approach. Using Markov chain Monte Carlo methods, posteriors for the parameters of interest are derived separately for each study. These are then used as proposal distributions in a computationally efficient second stage. We illustrate these ideas on a small binomial data set; we also analyse motivating data on the growth and rupture of abdominal aortic aneurysms. The two-stage Bayesian approach closely reproduces a one-stage analysis when it can be undertaken, but can also be easily carried out when a one-stage approach is difficult or impossible. PMID:24223435

  1. Does Mortality Vary between Asian Subgroups in New Zealand: An Application of Hierarchical Bayesian Modelling

    PubMed Central

    Jatrana, Santosh; Richardson, Ken; Blakely, Tony; Dayal, Saira

    2014-01-01

    The aim of this paper was to see whether all-cause and cause-specific mortality rates vary between Asian ethnic subgroups, and whether overseas born Asian subgroup mortality rate ratios varied by nativity and duration of residence. We used hierarchical Bayesian methods to allow for sparse data in the analysis of linked census-mortality data for 25–75 year old New Zealanders. We found directly standardised posterior all-cause and cardiovascular mortality rates were highest for the Indian ethnic group, significantly so when compared with those of Chinese ethnicity. In contrast, cancer mortality rates were lowest for ethnic Indians. Asian overseas born subgroups have about 70% of the mortality rate of their New Zealand born Asian counterparts, a result that showed little variation by Asian subgroup or cause of death. Within the overseas born population, all-cause mortality rates for migrants living 0–9 years in New Zealand were about 60% of the mortality rate of those living more than 25 years in New Zealand regardless of ethnicity. The corresponding figure for cardiovascular mortality rates was 50%. However, while Chinese cancer mortality rates increased with duration of residence, Indian and Other Asian cancer mortality rates did not. Future research on the mechanisms of worsening of health with increased time spent in the host country is required to improve the understanding of the process, and would assist the policy-makers and health planners. PMID:25140523

  2. Does mortality vary between Asian subgroups in New Zealand: an application of hierarchical Bayesian modelling.

    PubMed

    Jatrana, Santosh; Richardson, Ken; Blakely, Tony; Dayal, Saira

    2014-01-01

    The aim of this paper was to see whether all-cause and cause-specific mortality rates vary between Asian ethnic subgroups, and whether overseas born Asian subgroup mortality rate ratios varied by nativity and duration of residence. We used hierarchical Bayesian methods to allow for sparse data in the analysis of linked census-mortality data for 25-75 year old New Zealanders. We found directly standardised posterior all-cause and cardiovascular mortality rates were highest for the Indian ethnic group, significantly so when compared with those of Chinese ethnicity. In contrast, cancer mortality rates were lowest for ethnic Indians. Asian overseas born subgroups have about 70% of the mortality rate of their New Zealand born Asian counterparts, a result that showed little variation by Asian subgroup or cause of death. Within the overseas born population, all-cause mortality rates for migrants living 0-9 years in New Zealand were about 60% of the mortality rate of those living more than 25 years in New Zealand regardless of ethnicity. The corresponding figure for cardiovascular mortality rates was 50%. However, while Chinese cancer mortality rates increased with duration of residence, Indian and Other Asian cancer mortality rates did not. Future research on the mechanisms of worsening of health with increased time spent in the host country is required to improve the understanding of the process, and would assist the policy-makers and health planners. PMID:25140523

  3. Mapping brucellosis increases relative to elk density using hierarchical Bayesian models

    USGS Publications Warehouse

    Cross, Paul C.; Heisey, Dennis M.; Scurlock, Brandon M.; Edwards, William H.; Brennan, Angela; Ebinger, Michael R.

    2010-01-01

    The relationship between host density and parasite transmission is central to the effectiveness of many disease management strategies. Few studies, however, have empirically estimated this relationship particularly in large mammals. We applied hierarchical Bayesian methods to a 19-year dataset of over 6400 brucellosis tests of adult female elk (Cervus elaphus) in northwestern Wyoming. Management captures that occurred from January to March were over two times more likely to be seropositive than hunted elk that were killed in September to December, while accounting for site and year effects. Areas with supplemental feeding grounds for elk had higher seroprevalence in 1991 than other regions, but by 2009 many areas distant from the feeding grounds were of comparable seroprevalence. The increases in brucellosis seroprevalence were correlated with elk densities at the elk management unit, or hunt area, scale (mean 2070 km2; range = [95–10237]). The data, however, could not differentiate among linear and non-linear effects of host density. Therefore, control efforts that focus on reducing elk densities at a broad spatial scale were only weakly supported. Additional research on how a few, large groups within a region may be driving disease dynamics is needed for more targeted and effective management interventions. Brucellosis appears to be expanding its range into new regions and elk populations, which is likely to further complicate the United States brucellosis eradication program. This study is an example of how the dynamics of host populations can affect their ability to serve as disease reservoirs.

  4. Mapping Brucellosis Increases Relative to Elk Density Using Hierarchical Bayesian Models

    PubMed Central

    Cross, Paul C.; Heisey, Dennis M.; Scurlock, Brandon M.; Edwards, William H.; Ebinger, Michael R.; Brennan, Angela

    2010-01-01

    The relationship between host density and parasite transmission is central to the effectiveness of many disease management strategies. Few studies, however, have empirically estimated this relationship particularly in large mammals. We applied hierarchical Bayesian methods to a 19-year dataset of over 6400 brucellosis tests of adult female elk (Cervus elaphus) in northwestern Wyoming. Management captures that occurred from January to March were over two times more likely to be seropositive than hunted elk that were killed in September to December, while accounting for site and year effects. Areas with supplemental feeding grounds for elk had higher seroprevalence in 1991 than other regions, but by 2009 many areas distant from the feeding grounds were of comparable seroprevalence. The increases in brucellosis seroprevalence were correlated with elk densities at the elk management unit, or hunt area, scale (mean 2070 km2; range  = [95–10237]). The data, however, could not differentiate among linear and non-linear effects of host density. Therefore, control efforts that focus on reducing elk densities at a broad spatial scale were only weakly supported. Additional research on how a few, large groups within a region may be driving disease dynamics is needed for more targeted and effective management interventions. Brucellosis appears to be expanding its range into new regions and elk populations, which is likely to further complicate the United States brucellosis eradication program. This study is an example of how the dynamics of host populations can affect their ability to serve as disease reservoirs. PMID:20428240

  5. Estimating the spatiotemporal distribution of geochemical parameters associated with biostimulation using spectral induced polarization data and hierarchical Bayesian models

    NASA Astrophysics Data System (ADS)

    Chen, Jinsong; Hubbard, Susan S.; Williams, Kenneth H.; Flores Orozco, AdriáN.; Kemna, Andreas

    2012-05-01

    We developed a hierarchical Bayesian model to estimate the spatiotemporal distribution of aqueous geochemical parameters associated with in-situ bioremediation using surface spectral induced polarization (SIP) data and borehole geochemical measurements collected during a bioremediation experiment at a uranium-contaminated site near Rifle, Colorado (USA). The SIP data were first inverted for Cole-Cole parameters, including chargeability, time constant, resistivity at the DC frequency, and dependence factor, at each pixel of two-dimensional grids using a previously developed stochastic method. Correlations between the inverted Cole-Cole parameters and the wellbore-based groundwater chemistry measurements indicative of key metabolic processes within the aquifer (e.g., ferrous iron, sulfate, uranium) were established and used as a basis for petrophysical model development. The developed Bayesian model consists of three levels of statistical submodels: (1) data model, providing links between geochemical and geophysical attributes, (2) process model, describing the spatial and temporal variability of geochemical properties in the subsurface system, and (3) parameter model, describing prior distributions of various parameters and initial conditions. The unknown parameters were estimated using Markov chain Monte Carlo methods. By combining the temporally distributed geochemical data with the spatially distributed geophysical data, we obtained the spatiotemporal distribution of ferrous iron, sulfate, and sulfide, and their associated uncertainty information. The obtained results can be used to assess the efficacy of the bioremediation treatment over space and time and to constrain reactive transport models.

  6. Estimating the Sizes of Populations At Risk of HIV Infection From Multiple Data Sources Using a Bayesian Hierarchical Model

    PubMed Central

    Bao, Le; Raftery, Adrian E.; Reddy, Amala

    2014-01-01

    In most countries in the world outside of sub-Saharan Africa, HIV is largely concentrated in sub-populations whose behavior puts them at higher risk of contracting and transmitting HIV, such as people who inject drugs, sex workers and men who have sex with men. Estimating the size of these sub-populations is important for assessing overall HIV prevalence and designing effective interventions. We present a Bayesian hierarchical model for estimating the sizes of local and national HIV key affected populations. The model incorporates multiple commonly used data sources including mapping data, surveys, interventions, capture-recapture data, estimates or guesstimates from organizations, and expert opinion. The proposed model is used to estimate the numbers of people who inject drugs in Bangladesh. PMID:26015851

  7. Improving inferences from short-term ecological studies with Bayesian hierarchical modeling: white-headed woodpeckers in managed forests

    PubMed Central

    Linden, Daniel W; Roloff, Gary J

    2015-01-01

    Pilot studies are often used to design short-term research projects and long-term ecological monitoring programs, but data are sometimes discarded when they do not match the eventual survey design. Bayesian hierarchical modeling provides a convenient framework for integrating multiple data sources while explicitly separating sample variation into observation and ecological state processes. Such an approach can better estimate state uncertainty and improve inferences from short-term studies in dynamic systems. We used a dynamic multistate occupancy model to estimate the probabilities of occurrence and nesting for white-headed woodpeckers Picoides albolarvatus in recent harvest units within managed forests of northern California, USA. Our objectives were to examine how occupancy states and state transitions were related to forest management practices, and how the probabilities changed over time. Using Gibbs variable selection, we made inferences using multiple model structures and generated model-averaged estimates. Probabilities of white-headed woodpecker occurrence and nesting were high in 2009 and 2010, and the probability that nesting persisted at a site was positively related to the snag density in harvest units. Prior-year nesting resulted in higher probabilities of subsequent occurrence and nesting. We demonstrate the benefit of forest management practices that increase the density of retained snags in harvest units for providing white-headed woodpecker nesting habitat. While including an additional year of data from our pilot study did not drastically alter management recommendations, it changed the interpretation of the mechanism behind the observed dynamics. Bayesian hierarchical modeling has the potential to maximize the utility of studies based on small sample sizes while fully accounting for measurement error and both estimation and model uncertainty, thereby improving the ability of observational data to inform conservation and management strategies

  8. Improving inferences from short-term ecological studies with Bayesian hierarchical modeling: white-headed woodpeckers in managed forests.

    PubMed

    Linden, Daniel W; Roloff, Gary J

    2015-08-01

    Pilot studies are often used to design short-term research projects and long-term ecological monitoring programs, but data are sometimes discarded when they do not match the eventual survey design. Bayesian hierarchical modeling provides a convenient framework for integrating multiple data sources while explicitly separating sample variation into observation and ecological state processes. Such an approach can better estimate state uncertainty and improve inferences from short-term studies in dynamic systems. We used a dynamic multistate occupancy model to estimate the probabilities of occurrence and nesting for white-headed woodpeckers Picoides albolarvatus in recent harvest units within managed forests of northern California, USA. Our objectives were to examine how occupancy states and state transitions were related to forest management practices, and how the probabilities changed over time. Using Gibbs variable selection, we made inferences using multiple model structures and generated model-averaged estimates. Probabilities of white-headed woodpecker occurrence and nesting were high in 2009 and 2010, and the probability that nesting persisted at a site was positively related to the snag density in harvest units. Prior-year nesting resulted in higher probabilities of subsequent occurrence and nesting. We demonstrate the benefit of forest management practices that increase the density of retained snags in harvest units for providing white-headed woodpecker nesting habitat. While including an additional year of data from our pilot study did not drastically alter management recommendations, it changed the interpretation of the mechanism behind the observed dynamics. Bayesian hierarchical modeling has the potential to maximize the utility of studies based on small sample sizes while fully accounting for measurement error and both estimation and model uncertainty, thereby improving the ability of observational data to inform conservation and management strategies

  9. Hierarchical Bayesian modeling of spatio-temporal patterns of lung cancer incidence risk in Georgia, USA: 2000-2007

    NASA Astrophysics Data System (ADS)

    Yin, Ping; Mu, Lan; Madden, Marguerite; Vena, John E.

    2014-10-01

    Lung cancer is the second most commonly diagnosed cancer in both men and women in Georgia, USA. However, the spatio-temporal patterns of lung cancer risk in Georgia have not been fully studied. Hierarchical Bayesian models are used here to explore the spatio-temporal patterns of lung cancer incidence risk by race and gender in Georgia for the period of 2000-2007. With the census tract level as the spatial scale and the 2-year period aggregation as the temporal scale, we compare a total of seven Bayesian spatio-temporal models including two under a separate modeling framework and five under a joint modeling framework. One joint model outperforms others based on the deviance information criterion. Results show that the northwest region of Georgia has consistently high lung cancer incidence risk for all population groups during the study period. In addition, there are inverse relationships between the socioeconomic status and the lung cancer incidence risk among all Georgian population groups, and the relationships in males are stronger than those in females. By mapping more reliable variations in lung cancer incidence risk at a relatively fine spatio-temporal scale for different Georgian population groups, our study aims to better support healthcare performance assessment, etiological hypothesis generation, and health policy making.

  10. A Bayesian Hierarchical Model for Reconstructing Sea Level from the Common Era: From Raw Data to Rates of Change

    NASA Astrophysics Data System (ADS)

    Cahill, N.; Kemp, A.; Horton, B.; Parnell, A. C.

    2015-12-01

    We present a holistic Bayesian hierarchical model for reconstructing the continuous and dynamic evolution of relative sea-level change with fully quantified uncertainty. The reconstruction is produced from biological (foraminifera) and geochemical (δ13C) sea-level indicators preserved in dated cores of salt-marsh sediment. The model is comprised of three modules: (1) A Bayesian transfer function for the calibration of foraminifera into tidal elevation, which is flexible enough to formally accommodate additional proxies (in this case bulk-sediment δ13C values). (2) A chronology developed from a Bchron age-depth model. (3) An errors-in-variables integrated Gaussian process (EIV-IGP) model for estimating rates of sea-level change. We illustrate our approach using a case study of Common Era sea-level variability from New Jersey, USA. Results from our new Bayesian transfer function (B-TF), with and without the δ13C proxy, are compared to those from a widely-used weighted-averaging transfer function (WA-TF). The incorporation of secondary proxy information into the model in a formalized way results in smaller vertical uncertainties for reconstructed relative sea level. The vertical uncertainty from the multi proxy B-TF is ~30% smaller on average compared to the WA-TF. We evaluate the performance of both transfer functions by comparing reconstructed relative sea level to historic tide-gauge measurements. The multi proxy B-TF most accurately reconstructs the relative sea-level changes observed in the tide-gauge record. The holistic model provides a single, unifying framework for reconstructing and analysing sea level through time.

  11. Bayesian hierarchical model for multiple repeated measures and survival data: an application to Parkinson's disease.

    PubMed

    Luo, Sheng; Wang, Jue

    2014-10-30

    Multilevel item response theory models have been increasingly used to analyze the multivariate longitudinal data of mixed types (e.g., continuous and categorical) in clinical studies. To address the possible correlation between multivariate longitudinal measures and time to terminal events (e.g., death and dropout), joint models that consist of a multilevel item response theory submodel and a survival submodel have been previously developed. However, in multisite studies, multiple patients are recruited and treated by the same clinical site. There can be a significant site correlation because of common environmental and socioeconomic status, and similar quality of care within site. In this article, we develop and study several hierarchical joint models with the hazard of terminal events dependent on shared random effects from various levels. We conduct extensive simulation study to evaluate the performance of various models under different scenarios. The proposed hierarchical joint models are applied to the motivating deprenyl and tocopherol antioxidative therapy of Parkinsonism study to investigate the effect of tocopherol in slowing Parkinson's disease progression. PMID:24935619

  12. Bayesian hierarchical models suggest oldest known plant-visiting bat was omnivorous.

    PubMed

    Yohe, Laurel R; Velazco, Paúl M; Rojas, Danny; Gerstner, Beth E; Simmons, Nancy B; Dávalos, Liliana M

    2015-11-01

    The earliest record of plant visiting in bats dates to the Middle Miocene of La Venta, the world's most diverse tropical palaeocommunity. Palynephyllum antimaster is known from molars that indicate nectarivory. Skull length, an important indicator of key traits such as body size, bite force and trophic specialization, remains unknown. We developed Bayesian models to infer skull length based on dental measurements. These models account for variation within and between species, variation between clades, and phylogenetic error structure. Models relating skull length to trophic level for nectarivorous bats were then used to infer the diet of the fossil. The skull length estimate for Palynephyllum places it among the larger lonchophylline bats. The inferred diet suggests Palynephyllum fed on nectar and insects, similar to its living relatives. Omnivory has persisted since the mid-Miocene. This is the first study to corroborate with fossil data that highly specialized nectarivory in bats requires an omnivorous transition. PMID:26559512

  13. A hierarchical Bayesian model for embedding larval drift and habitat models in integrated life cycles for exploited fish.

    PubMed

    Rochette, S; Le Pape, O; Vigneau, J; Rivot, E

    2013-10-01

    This paper proposes a hierarchical Bayesian framework for modeling the life cycle of marine exploited fish with a spatial perspective. The application was developed for a nursery-dependent fish species, the common sole (Solea solea), on the Eastern Channel population (Western Europe). The approach combined processes of different natures and various sources of observations within an integrated framework for life-cycle modeling: (1) outputs of an individual-based model for larval drift and survival that provided yearly estimates of the dispersion and mortality of eggs and larvae, from spawning grounds to settlement in several coastal nurseries; (2) a habitat suitability model, based on juvenile trawl surveys coupled with a geographic information system, to estimate juvenile densities and surface areas of suitable juvenile habitat in each nursery sector; (3) a statistical catch-at-age model for the estimation of the numbers-at-age and the fishing mortality on subadults and adults. The approach provided estimates of hidden variables and parameters of key biological significance. A simulation approach provided insight to the robustness of the approach when only weak data are available. Estimates of spawning biomass, fishing mortality, and recruitment were close to the estimations derived from stock-assessment working groups. In addition, the model quantified mortality along the life cycle, and estimated site-specific density-dependent mortalities between settled larvae and age-0 juveniles in each nursery ground. This provided a better understanding of the productivity and the specific contribution of each nursery ground toward recruitment and population renewal. Perspectives include further development of the modeling framework on the common sole and applications to other fish species to disentangle the effects of multiple interacting stress factors (e.g., estuarine and coastal nursery habitat degradation, fishing pressure) on population renewal and to develop risk

  14. Analyzing large-scale conservation interventions with Bayesian hierarchical models: a case study of supplementing threatened Pacific salmon.

    PubMed

    Scheuerell, Mark D; Buhle, Eric R; Semmens, Brice X; Ford, Michael J; Cooney, Tom; Carmichael, Richard W

    2015-05-01

    Myriad human activities increasingly threaten the existence of many species. A variety of conservation interventions such as habitat restoration, protected areas, and captive breeding have been used to prevent extinctions. Evaluating the effectiveness of these interventions requires appropriate statistical methods, given the quantity and quality of available data. Historically, analysis of variance has been used with some form of predetermined before-after control-impact design to estimate the effects of large-scale experiments or conservation interventions. However, ad hoc retrospective study designs or the presence of random effects at multiple scales may preclude the use of these tools. We evaluated the effects of a large-scale supplementation program on the density of adult Chinook salmon Oncorhynchus tshawytscha from the Snake River basin in the northwestern United States currently listed under the U.S. Endangered Species Act. We analyzed 43 years of data from 22 populations, accounting for random effects across time and space using a form of Bayesian hierarchical time-series model common in analyses of financial markets. We found that varying degrees of supplementation over a period of 25 years increased the density of natural-origin adults, on average, by 0-8% relative to nonsupplementation years. Thirty-nine of the 43 year effects were at least two times larger in magnitude than the mean supplementation effect, suggesting common environmental variables play a more important role in driving interannual variability in adult density. Additional residual variation in density varied considerably across the region, but there was no systematic difference between supplemented and reference populations. Our results demonstrate the power of hierarchical Bayesian models to detect the diffuse effects of management interventions and to quantitatively describe the variability of intervention success. Nevertheless, our study could not address whether ecological factors

  15. Analyzing large-scale conservation interventions with Bayesian hierarchical models: a case study of supplementing threatened Pacific salmon

    PubMed Central

    Scheuerell, Mark D; Buhle, Eric R; Semmens, Brice X; Ford, Michael J; Cooney, Tom; Carmichael, Richard W

    2015-01-01

    Myriad human activities increasingly threaten the existence of many species. A variety of conservation interventions such as habitat restoration, protected areas, and captive breeding have been used to prevent extinctions. Evaluating the effectiveness of these interventions requires appropriate statistical methods, given the quantity and quality of available data. Historically, analysis of variance has been used with some form of predetermined before-after control-impact design to estimate the effects of large-scale experiments or conservation interventions. However, ad hoc retrospective study designs or the presence of random effects at multiple scales may preclude the use of these tools. We evaluated the effects of a large-scale supplementation program on the density of adult Chinook salmon Oncorhynchus tshawytscha from the Snake River basin in the northwestern United States currently listed under the U.S. Endangered Species Act. We analyzed 43 years of data from 22 populations, accounting for random effects across time and space using a form of Bayesian hierarchical time-series model common in analyses of financial markets. We found that varying degrees of supplementation over a period of 25 years increased the density of natural-origin adults, on average, by 0–8% relative to nonsupplementation years. Thirty-nine of the 43 year effects were at least two times larger in magnitude than the mean supplementation effect, suggesting common environmental variables play a more important role in driving interannual variability in adult density. Additional residual variation in density varied considerably across the region, but there was no systematic difference between supplemented and reference populations. Our results demonstrate the power of hierarchical Bayesian models to detect the diffuse effects of management interventions and to quantitatively describe the variability of intervention success. Nevertheless, our study could not address whether ecological

  16. A BAYESIAN HIERARCHICAL SPATIAL POINT PROCESS MODEL FOR MULTI-TYPE NEUROIMAGING META-ANALYSIS

    PubMed Central

    Kang, Jian; Nichols, Thomas E.; Wager, Tor D.; Johnson, Timothy D.

    2014-01-01

    Neuroimaging meta-analysis is an important tool for finding consistent effects over studies that each usually have 20 or fewer subjects. Interest in meta-analysis in brain mapping is also driven by a recent focus on so-called “reverse inference”: where as traditional “forward inference” identifies the regions of the brain involved in a task, a reverse inference identifies the cognitive processes that a task engages. Such reverse inferences, however, requires a set of meta-analysis, one for each possible cognitive domain. However, existing methods for neuroimaging meta-analysis have significant limitations. Commonly used methods for neuroimaging meta-analysis are not model based, do not provide interpretable parameter estimates, and only produce null hypothesis inferences; further, they are generally designed for a single group of studies and cannot produce reverse inferences. In this work we address these limitations by adopting a non-parametric Bayesian approach for meta analysis data from multiple classes or types of studies. In particular, foci from each type of study are modeled as a cluster process driven by a random intensity function that is modeled as a kernel convolution of a gamma random field. The type-specific gamma random fields are linked and modeled as a realization of a common gamma random field, shared by all types, that induces correlation between study types and mimics the behavior of a univariate mixed effects model. We illustrate our model on simulation studies and a meta analysis of five emotions from 219 studies and check model fit by a posterior predictive assessment. In addition, we implement reverse inference by using the model to predict study type from a newly presented study. We evaluate this predictive performance via leave-one-out cross validation that is efficiently implemented using importance sampling techniques. PMID:25426185

  17. Bayesian inversion of microtremor array dispersion data with hierarchical trans-dimensional earth and autoregressive error models

    NASA Astrophysics Data System (ADS)

    Molnar, S.; Dettmer, J.; Steininger, G.; Dosso, S. E.; Cassidy, J. F.

    2013-12-01

    This paper applies hierarchical, trans-dimensional Bayesian models for earth and residual-error parametrizations to the inversion of microtremor array dispersion data for shear-wave velocity (Vs) structure. The earth is parametrized in terms of flat-lying, homogeneous layers and residual errors are parametrized with a first-order autoregressive data-error model. The inversion accounts for the limited knowledge of the optimal earth and residual error model parametrization (e.g. the number of layers in the Vs profile) in the resulting Vs parameter uncertainty estimates. The assumed earth model parametrization influences estimates of parameter values and uncertainties due to different parametrizations leading to different ranges of data predictions. The support of the data for a particular model is often non-unique and several parametrizations may be supported. A trans-dimensional formulation accounts for this non-uniqueness by including a model-indexing parameter as an unknown so that groups of models (identified by the index) are considered in the results. In addition, serial residual-error correlations are addressed by augmenting the geophysical forward model with a hierarchical autoregressive error model that can account for a wide range of error processes with a small number of parameters. Hence, the limited knowledge about the true statistical distribution of data errors is also accounted for in the earth model parameter estimates, resulting in more realistic uncertainties and parameter values. Hierarchical autoregressive error models do not rely on point estimates of the model vector to estimate residual-error statistics, and have no requirement for computing the inverse or determinant of a covariance matrix. This approach is particularly useful for trans-dimensional inverse problems, as point estimates may not be representative of the state space that spans multiple subspaces of different dimensions. The autoregressive process is restricted to first order and

  18. A hierarchical Bayesian regional model for nonstationary precipitation extremes in Northern California conditioned on tropical moisture exports

    NASA Astrophysics Data System (ADS)

    Steinschneider, Scott; Lall, Upmanu

    2015-03-01

    Warm, moist, and longitudinally confined tropical air masses are being linked to some of the most extreme precipitation and flooding events in the midlatitudes. The interannual frequency and intensity of such atmospheric rivers (ARs), or tropical moisture exports (TMEs), are connected to the risk of extreme precipitation events in areas where moisture convergence occurs. This study presents a nonstationary, regional frequency analysis of precipitation extremes in Northern California that is conditioned on the interannual variability of TMEs entering the region. Parameters of a multisite peaks-over-threshold model are allowed to vary conditional on the integrated moisture delivery from TMEs over the area. Parameters are also related to time-invariant, local characteristics to facilitate regionalization to ungaged sites. The model is developed and calibrated in a hierarchical Bayesian framework to support partial pooling and enhance regionalization skill. The model is cross validated along with two alternative, increasingly parsimonious formulations to assess the additional skill provided by the covariates. Climate diagnostics are also used to better understand the instances where TMEs fail to explain variations in rainfall extremes to provide a path forward for further model improvement. The modeling structure is designed to link seasonal forecasting and long-term projections of TMEs directly to regional models of extremes used for risk estimation. Results suggest that the inclusion of TME-based information greatly improves the characterization of extremes, particularly for their frequency of occurrence. Diagnostics indicate that the model could be further improved by considering an index for frontal systems as an additional covariate.

  19. Individual differences in social information gathering revealed through Bayesian hierarchical models

    PubMed Central

    Pearson, John M.; Watson, Karli K.; Klein, Jeffrey T.; Ebitz, R. Becket; Platt, Michael L.

    2013-01-01

    As studies of the neural circuits underlying choice expand to include more complicated behaviors, analysis of behaviors elicited in laboratory paradigms has grown increasingly difficult. Social behaviors present a particular challenge, since inter- and intra-individual variation are expected to play key roles. However, due to limitations on data collection, studies must often choose between pooling data across all subjects or using individual subjects' data in isolation. Hierarchical models mediate between these two extremes by modeling individual subjects as drawn from a population distribution, allowing the population at large to serve as prior information about individuals' behavior. Here, we apply this method to data collected across multiple experimental sessions from a set of rhesus macaques performing a social information valuation task. We show that, while the values of social images vary markedly between individuals and between experimental sessions for the same individual, individuals also differentially value particular categories of social images. Furthermore, we demonstrate covariance between values for image categories within individuals and find evidence suggesting that magnitudes of stimulus values tend to diminish over time. PMID:24062635

  20. Hierarchical Bayesian random intercept model-based cross-level interaction decomposition for truck driver injury severity investigations.

    PubMed

    Chen, Cong; Zhang, Guohui; Tian, Zong; Bogus, Susan M; Yang, Yin

    2015-12-01

    Traffic crashes occurring on rural roadways induce more severe injuries and fatalities than those in urban areas, especially when there are trucks involved. Truck drivers are found to suffer higher potential of crash injuries compared with other occupational labors. Besides, unobserved heterogeneity in crash data analysis is a critical issue that needs to be carefully addressed. In this study, a hierarchical Bayesian random intercept model decomposing cross-level interaction effects as unobserved heterogeneity is developed to examine the posterior probabilities of truck driver injuries in rural truck-involved crashes. The interaction effects contributing to truck driver injury outcomes are investigated based on two-year rural truck-involved crashes in New Mexico from 2010 to 2011. The analysis results indicate that the cross-level interaction effects play an important role in predicting truck driver injury severities, and the proposed model produces comparable performance with the traditional random intercept model and the mixed logit model even after penalization by high model complexity. It is revealed that factors including road grade, number of vehicles involved in a crash, maximum vehicle damage in a crash, vehicle actions, driver age, seatbelt use, and driver under alcohol or drug influence, as well as a portion of their cross-level interaction effects with other variables are significantly associated with truck driver incapacitating injuries and fatalities. These findings are helpful to understand the respective or joint impacts of these attributes on truck driver injury patterns in rural truck-involved crashes. PMID:26454045

  1. Analysis of gene expression data of the NCl 60 cancer cell lines using Bayesian hierarchical effects model

    NASA Astrophysics Data System (ADS)

    Lee, Jae K.; Scherf, Uwe; Smith, Lawrence H.; Tanabe, Lorraine; Weinstein, John N.

    2001-06-01

    From the end of the last decade, NCI has been performing large screening of anticancer drug compounds and molecular targets on a pool of 60 cell lines of various types of cancer. In particular, a complete set of cDNA expression array data on the 60 cell lines are now available. To discover differentially-expressed genes in each type of cancer cell lines, we need to estimate a large number of genetic parameters, especially interaction effects for all combinations of cancer types and genes, by decomposing the total variance into biological and array instrumental components. This error decomposition is important to identify subtle genes with low biological variability. An innovative statistical method is required for simultaneously estimating more than 100,000 parameters of interaction effects and error components. We propose a Bayesian statistical approach based on the construction of a hierarchical model adopting parameterization of a liner effects model. The estimation of the model parameters is performed by Markov Chain Monte Carlo, a recent computer- intensive statistical resampling technique. We have identified novel genes whose effects have not been revealed by the previous clustering approaches to the gene expression data.

  2. Bayesian Hierarchical Multiresolution Hazard Model for the Study of Time-Dependent Failure Patterns in Early Stage Breast Cancer

    PubMed Central

    Dukić, Vanja; Dignam, James

    2011-01-01

    The multiresolution estimator, developed originally in engineering applications as a wavelet-based method for density estimation, has been recently extended and adapted for estimation of hazard functions (Bouman et al. 2005, 2007). Using the multiresolution hazard (MRH) estimator in the Bayesian framework, we are able to incorporate any a priori desired shape and amount of smoothness in the hazard function. The MRH method’s main appeal is in its relatively simple estimation and inference procedures, making it possible to obtain simultaneous confidence bands on the hazard function over the entire time span of interest. Moreover, these confidence bands properly reflect the multiple sources of uncertainty, such as multiple centers or heterogeneity in the patient population. Also, rather than the commonly employed approach of estimating covariate effects and the hazard function separately, the Bayesian MRH method estimates all of these parameters jointly, thus resulting in properly adjusted inference about any of the quantities. In this paper, we extend the previously proposed MRH methods (Bouman et al. 2005, 2007) into the hierarchical multiresolution hazard setting (HMRH), to accommodate the case of separate hazard rate functions within each of several strata as well as some common covariate effects across all strata while accounting for within-stratum correlation. We apply this method to examine patterns of tumor recurrence after treatment for early stage breast cancer, using data from two large-scale randomized clinical trials that have substantially influenced breast cancer treatment standards. We implement the proposed model to estimate the recurrence hazard and explore how the shape differs between patients grouped by a key tumor characteristic (estrogen receptor status) and treatment types, after adjusting for other important patient characteristics such as age, tumor size and progesterone level. We also comment on whether the hazards exhibit nonmonotonic

  3. Relative age and birthplace effect in Japanese professional sports: a quantitative evaluation using a Bayesian hierarchical Poisson model.

    PubMed

    Ishigami, Hideaki

    2016-01-01

    Relative age effect (RAE) in sports has been well documented. Recent studies investigate the effect of birthplace in addition to the RAE. The first objective of this study was to show the magnitude of the RAE in two major professional sports in Japan, baseball and soccer. Second, we examined the birthplace effect and compared its magnitude with that of the RAE. The effect sizes were estimated using a Bayesian hierarchical Poisson model with the number of players as dependent variable. The RAEs were 9.0% and 7.7% per month for soccer and baseball, respectively. These estimates imply that children born in the first month of a school year have about three times greater chance of becoming a professional player than those born in the last month of the year. Over half of the difference in likelihoods of becoming a professional player between birthplaces was accounted for by weather conditions, with the likelihood decreasing by 1% per snow day. An effect of population size was not detected in the data. By investigating different samples, we demonstrated that using quarterly data leads to underestimation and that the age range of sampled athletes should be set carefully. PMID:25917193

  4. Using hierarchical Bayesian binary probit models to analyze crash injury severity on high speed facilities with real-time traffic data.

    PubMed

    Yu, Rongjie; Abdel-Aty, Mohamed

    2014-01-01

    Severe crashes are causing serious social and economic loss, and because of this, reducing crash injury severity has become one of the key objectives of the high speed facilities' (freeway and expressway) management. Traditional crash injury severity analysis utilized data mainly from crash reports concerning the crash occurrence information, drivers' characteristics and roadway geometric related variables. In this study, real-time traffic and weather data were introduced to analyze the crash injury severity. The space mean speeds captured by the Automatic Vehicle Identification (AVI) system on the two roadways were used as explanatory variables in this study; and data from a mountainous freeway (I-70 in Colorado) and an urban expressway (State Road 408 in Orlando) have been used to identify the analysis result's consistence. Binary probit (BP) models were estimated to classify the non-severe (property damage only) crashes and severe (injury and fatality) crashes. Firstly, Bayesian BP models' results were compared to the results from Maximum Likelihood Estimation BP models and it was concluded that Bayesian inference was superior with more significant variables. Then different levels of hierarchical Bayesian BP models were developed with random effects accounting for the unobserved heterogeneity at segment level and crash individual level, respectively. Modeling results from both studied locations demonstrate that large variations of speed prior to the crash occurrence would increase the likelihood of severe crash occurrence. Moreover, with considering unobserved heterogeneity in the Bayesian BP models, the model goodness-of-fit has improved substantially. Finally, possible future applications of the model results and the hierarchical Bayesian probit models were discussed. PMID:24172082

  5. Top-Down Feedback in an HMAX-Like Cortical Model of Object Perception Based on Hierarchical Bayesian Networks and Belief Propagation

    PubMed Central

    Dura-Bernal, Salvador; Wennekers, Thomas; Denham, Susan L.

    2012-01-01

    Hierarchical generative models, such as Bayesian networks, and belief propagation have been shown to provide a theoretical framework that can account for perceptual processes, including feedforward recognition and feedback modulation. The framework explains both psychophysical and physiological experimental data and maps well onto the hierarchical distributed cortical anatomy. However, the complexity required to model cortical processes makes inference, even using approximate methods, very computationally expensive. Thus, existing object perception models based on this approach are typically limited to tree-structured networks with no loops, use small toy examples or fail to account for certain perceptual aspects such as invariance to transformations or feedback reconstruction. In this study we develop a Bayesian network with an architecture similar to that of HMAX, a biologically-inspired hierarchical model of object recognition, and use loopy belief propagation to approximate the model operations (selectivity and invariance). Crucially, the resulting Bayesian network extends the functionality of HMAX by including top-down recursive feedback. Thus, the proposed model not only achieves successful feedforward recognition invariant to noise, occlusions, and changes in position and size, but is also able to reproduce modulatory effects such as illusory contour completion and attention. Our novel and rigorous methodology covers key aspects such as learning using a layerwise greedy algorithm, combining feedback information from multiple parents and reducing the number of operations required. Overall, this work extends an established model of object recognition to include high-level feedback modulation, based on state-of-the-art probabilistic approaches. The methodology employed, consistent with evidence from the visual cortex, can be potentially generalized to build models of hierarchical perceptual organization that include top-down and bottom-up interactions, for

  6. Joint Segmentation and Deconvolution of Ultrasound Images Using a Hierarchical Bayesian Model Based on Generalized Gaussian Priors.

    PubMed

    Zhao, Ningning; Basarab, Adrian; Kouame, Denis; Tourneret, Jean-Yves

    2016-08-01

    This paper proposes a joint segmentation and deconvolution Bayesian method for medical ultrasound (US) images. Contrary to piecewise homogeneous images, US images exhibit heavy characteristic speckle patterns correlated with the tissue structures. The generalized Gaussian distribution (GGD) has been shown to be one of the most relevant distributions for characterizing the speckle in US images. Thus, we propose a GGD-Potts model defined by a label map coupling US image segmentation and deconvolution. The Bayesian estimators of the unknown model parameters, including the US image, the label map, and all the hyperparameters are difficult to be expressed in a closed form. Thus, we investigate a Gibbs sampler to generate samples distributed according to the posterior of interest. These generated samples are finally used to compute the Bayesian estimators of the unknown parameters. The performance of the proposed Bayesian model is compared with the existing approaches via several experiments conducted on realistic synthetic data and in vivo US images. PMID:27187959

  7. Genetic evidence for long-term population decline in a savannah-dwelling primate: inferences from a hierarchical bayesian model.

    PubMed

    Storz, Jay F; Beaumont, Mark A; Alberts, Susan C

    2002-11-01

    The purpose of this study was to test for evidence that savannah baboons (Papio cynocephalus) underwent a population expansion in concert with a hypothesized expansion of African human and chimpanzee populations during the late Pleistocene. The rationale is that any type of environmental event sufficient to cause simultaneous population expansions in African humans and chimpanzees would also be expected to affect other codistributed mammals. To test for genetic evidence of population expansion or contraction, we performed a coalescent analysis of multilocus microsatellite data using a hierarchical Bayesian model. Markov chain Monte Carlo (MCMC) simulations were used to estimate the posterior probability density of demographic and genealogical parameters. The model was designed to allow interlocus variation in mutational and demographic parameters, which made it possible to detect aberrant patterns of variation at individual loci that could result from heterogeneity in mutational dynamics or from the effects of selection at linked sites. Results of the MCMC simulations were consistent with zero variance in demographic parameters among loci, but there was evidence for a 10- to 20-fold difference in mutation rate between the most slowly and most rapidly evolving loci. Results of the model provided strong evidence that savannah baboons have undergone a long-term historical decline in population size. The mode of the highest posterior density for the joint distribution of current and ancestral population size indicated a roughly eightfold contraction over the past 1,000 to 250,000 years. These results indicate that savannah baboons apparently did not share a common demographic history with other codistributed primate species. PMID:12411607

  8. Assessing risk profiles for Salmonella serotypes in breeding pig operations in Portugal using a Bayesian hierarchical model

    PubMed Central

    2012-01-01

    Background The EU Regulation No 2160/2003 imposes a reduction in the prevalence of Salmonella in pigs. The efficiency of control programmes for Salmonella in pigs, reported among the EU Member States, varies and definitive eradication seems very difficult. Control measures currently recommended for Salmonella are not serotype-specific. Is it possible that the risk factors for different Salmonella serotypes are different? The aim of this study was to investigate potential risk factors for two groups of Salmonella sp serotypes using pen faecal samples from breeding pig holdings representative of the Portuguese pig sector. Methods The data used come from the Baseline Survey for the Prevalence of Salmonella in breeding pigs in Portugal. A total of 1670 pen faecal samples from 167 herds were tested, and 170 samples were positive for Salmonella. The presence of Salmonella in each sample (outcome variable) was classified in three categories: i) no Salmonella, ii) Salmonella Typhimurium or S. Typhimurium-like strains with the antigenic formula: 1,4,5,12:i:-, , and iii) other serotypes. Along with the sample collection, a questionnaire concerning herd management and potential risk factors was utilised. The data have a “natural” hierarchical structure so a categorical multilevel analysis of the dataset was carried out using a Bayesian hierarchical model. The model was estimated using Markov Chain Monte Carlo methods, implemented in the software WinBUGS. Results The significant associations found (when compared to category “no Salmonella”), for category “serotype Typhimurium or S. Typhimurium-like strains with the antigenic formula: 1,4,5,12:i:-” were: age of breeding sows, size of the herd, number of pigs/pen and source of semen. For the category “other serotypes” the significant associations found were: control of rodents, region of the country, source of semen, breeding sector room and source of feed. Conclusions The risk factors significantly associated

  9. Pollen-Climate Calibration, Characterization of Statistical Uncertainty, and Forward Modeling for Integration Into Bayesian Hierarchical Climate Reconstruction

    NASA Astrophysics Data System (ADS)

    Wahl, E. R.

    2008-12-01

    as much information as the multi-taxonomic MAT in well-selected regions, the ratio inverse model is used as the starting point for developing a temperature-pollen forward model. Such a forward model can be directly incorporated into a Bayesian hierarchical model (BHM) framework: the reason for seeking a taxonomically simplified pollen model is itself driven by computational considerations within the BHM. The BHM framework thus allows pollen- derived climate information to contribute multi-decadal to centennial information into a simultaneous reconstruction framework that also incorporates annually-resolved climate information from tree ring sources and centennial to multi-centennial information from borehole reconstructions. In the forward model, the pine and oak pollen counts are treated as binomial random variables with expected values (p) and (1-p), conditional on the calibration temperature values and the total counts (n) used to determine the ratios. Model parameters and (p) values have been estimated using a binomial logistic form of the generalized linear model. Comparison of the estimated conditional expected (p) values with the associated calibration ratio/temperature relationships shows good performance for the SW N American test case, with little (but non- 0) bias and good overall tracking (R2 = 0.79). (4) The results from (3) indicate that appropriate forward models can be developed for a suite of sites in North America with temporally dense, well-dated fossil pollen records over the past 2ka, and then incorporated into the BHM. Modeling results for the suite of sites will be presented.

  10. Estimation of Coast-Wide Population Trends of Marbled Murrelets in Canada Using a Bayesian Hierarchical Model.

    PubMed

    Bertram, Douglas F; Drever, Mark C; McAllister, Murdoch K; Schroeder, Bernard K; Lindsay, David J; Faust, Deborah A

    2015-01-01

    Species at risk with secretive breeding behaviours, low densities, and wide geographic range pose a significant challenge to conservation actions because population trends are difficult to detect. Such is the case with the Marbled Murrelet (Brachyramphus marmoratus), a seabird listed as 'Threatened' by the Species at Risk Act in Canada largely due to the loss of its old growth forest nesting habitat. We report the first estimates of population trend of Marbled Murrelets in Canada derived from a monitoring program that uses marine radar to detect birds as they enter forest watersheds during 923 dawn surveys at 58 radar monitoring stations within the six Marbled Murrelet Conservation Regions on coastal British Columbia, Canada, 1996-2013. Temporal trends in radar counts were analyzed with a hierarchical Bayesian multivariate modeling approach that controlled for variation in tilt of the radar unit and day of year, included year-specific deviations from the overall trend ('year effects'), and allowed for trends to be estimated at three spatial scales. A negative overall trend of -1.6%/yr (95% credibility interval: -3.2%, 0.01%) indicated moderate evidence for a coast-wide decline, although trends varied strongly among the six conservation regions. Negative annual trends were detected in East Vancouver Island (-9%/yr) and South Mainland Coast (-3%/yr) Conservation Regions. Over a quarter of the year effects were significantly different from zero, and the estimated standard deviation in common-shared year effects between sites within each region was about 50% per year. This large common-shared interannual variation in counts may have been caused by regional movements of birds related to changes in marine conditions that affect the availability of prey. PMID:26258803

  11. Estimation of Coast-Wide Population Trends of Marbled Murrelets in Canada Using a Bayesian Hierarchical Model

    PubMed Central

    Schroeder, Bernard K.; Lindsay, David J.; Faust, Deborah A.

    2015-01-01

    Species at risk with secretive breeding behaviours, low densities, and wide geographic range pose a significant challenge to conservation actions because population trends are difficult to detect. Such is the case with the Marbled Murrelet (Brachyramphus marmoratus), a seabird listed as ‘Threatened’ by the Species at Risk Act in Canada largely due to the loss of its old growth forest nesting habitat. We report the first estimates of population trend of Marbled Murrelets in Canada derived from a monitoring program that uses marine radar to detect birds as they enter forest watersheds during 923 dawn surveys at 58 radar monitoring stations within the six Marbled Murrelet Conservation Regions on coastal British Columbia, Canada, 1996–2013. Temporal trends in radar counts were analyzed with a hierarchical Bayesian multivariate modeling approach that controlled for variation in tilt of the radar unit and day of year, included year-specific deviations from the overall trend (‘year effects’), and allowed for trends to be estimated at three spatial scales. A negative overall trend of -1.6%/yr (95% credibility interval: -3.2%, 0.01%) indicated moderate evidence for a coast-wide decline, although trends varied strongly among the six conservation regions. Negative annual trends were detected in East Vancouver Island (-9%/yr) and South Mainland Coast (-3%/yr) Conservation Regions. Over a quarter of the year effects were significantly different from zero, and the estimated standard deviation in common-shared year effects between sites within each region was about 50% per year. This large common-shared interannual variation in counts may have been caused by regional movements of birds related to changes in marine conditions that affect the availability of prey. PMID:26258803

  12. Effects of management intervention on post-disturbance community composition: an experimental analysis using bayesian hierarchical models.

    PubMed

    Giovanini, Jack; Kroll, Andrew J; Jones, Jay E; Altman, Bob; Arnett, Edward B

    2013-01-01

    As human demand for ecosystem products increases, management intervention may become more frequent after environmental disturbances. Evaluations of ecological responses to cumulative effects of management interventions and natural disturbances provide critical decision-support tools for managers who strive to balance environmental conservation and economic development. We conducted an experiment to evaluate the effects of salvage logging on avian community composition in lodgepole pine (Pinus contorta) forests affected by beetle outbreaks in Oregon, USA, 1996-1998. Treatments consisted of the removal of lodgepole pine snags only, and live trees were not harvested. We used a bayesian hierarchical model to quantify occupancy dynamics for 27 breeding species, while accounting for variation in the detection process. We examined how magnitude and precision of treatment effects varied when incorporating prior information from a separate intervention study that occurred in a similar ecological system. Regardless of which prior we evaluated, we found no evidence that the harvest treatment had a negative impact on species richness, with an estimated average of 0.2-2.2 more species in harvested stands than unharvested stands. Estimated average similarity between control and treatment stands ranged from 0.82-0.87 (1 indicating complete similarity between a pair of stands) and suggested that treatment stands did not contain novel assemblies of species responding to the harvesting prescription. Estimated treatment effects were positive for twenty-four (90%) of the species, although the credible intervals contained 0 in all cases. These results suggest that, unlike most post-fire salvage logging prescriptions, selective harvesting after beetle outbreaks may meet multiple management objectives, including the maintenance of avian community richness comparable to what is found in unharvested stands. Our results provide managers with prescription alternatives to respond to severe

  13. Effects of Management Intervention on Post-Disturbance Community Composition: An Experimental Analysis Using Bayesian Hierarchical Models

    PubMed Central

    Giovanini, Jack; Kroll, Andrew J.; Jones, Jay E.; Altman, Bob; Arnett, Edward B.

    2013-01-01

    As human demand for ecosystem products increases, management intervention may become more frequent after environmental disturbances. Evaluations of ecological responses to cumulative effects of management interventions and natural disturbances provide critical decision-support tools for managers who strive to balance environmental conservation and economic development. We conducted an experiment to evaluate the effects of salvage logging on avian community composition in lodgepole pine (Pinus contorta) forests affected by beetle outbreaks in Oregon, USA, 1996–1998. Treatments consisted of the removal of lodgepole pine snags only, and live trees were not harvested. We used a Bayesian hierarchical model to quantify occupancy dynamics for 27 breeding species, while accounting for variation in the detection process. We examined how magnitude and precision of treatment effects varied when incorporating prior information from a separate intervention study that occurred in a similar ecological system. Regardless of which prior we evaluated, we found no evidence that the harvest treatment had a negative impact on species richness, with an estimated average of 0.2–2.2 more species in harvested stands than unharvested stands. Estimated average similarity between control and treatment stands ranged from 0.82–0.87 (1 indicating complete similarity between a pair of stands) and suggested that treatment stands did not contain novel assemblies of species responding to the harvesting prescription. Estimated treatment effects were positive for twenty-four (90%) of the species, although the credible intervals contained 0 in all cases. These results suggest that, unlike most post-fire salvage logging prescriptions, selective harvesting after beetle outbreaks may meet multiple management objectives, including the maintenance of avian community richness comparable to what is found in unharvested stands. Our results provide managers with prescription alternatives to respond to

  14. A Bayesian Approach for Analyzing Hierarchical Data with Missing Outcomes through Structural Equation Models

    ERIC Educational Resources Information Center

    Song, Xin-Yuan; Lee, Sik-Yum

    2008-01-01

    Structural equation models are widely appreciated in behavioral, social, and psychological research to model relations between latent constructs and manifest variables, and to control for measurement errors. Most applications of structural equation models are based on fully observed data that are independently distributed. However, hierarchical…

  15. Evaluation of uncertainties in N2O and NO fluxes from agricultural soil using a hierarchical Bayesian model

    NASA Astrophysics Data System (ADS)

    Nishina, Kazuya; Akiyama, Hiroko; Nishimura, Seiichi; Sudo, Shigeto; Yagi, Kazuyuki

    2012-12-01

    Agricultural soil is the major source of nitrous oxide (N2O) and nitric oxide (NO). However, N2O and NO fluxes from the soil show high spatial and temporal variability. Therefore, traditional statistical tools are insufficient for evaluating the strength of the emissions and determining the environmental and management factors affecting these fluxes. To compensate for the inherent variability of N oxide fluxes in situ, we proposed the application of a hierarchical Bayesian (HB) model based on a simple semi-mechanistic model with a lognormal probability distribution. We applied the HB model to the daily N2O and NO fluxes from an Andosol soil field to which a chemical N fertilizer was applied. In addition, we evaluated the responses of these fluxes to environmental factors and N application. The posterior inference revealed various sensitivities to the soil temperature and water-filled pore space (WFPS) among the N oxide gas fluxes. The N2O flux showed a higher temperature dependency compared with the NO flux. The estimated optimum WFPS of the NO flux (54.1% with credible interval (CI) 95%, from 47.1% to 79.4%) was lower than that of the N2O flux (75.8% with CI 95%, from 54.1% to 98.3%) in this soil sample. Although control plots without N fertilizer application are usually required to calculate the fertilizer-induced emission factor (EF), our HB model could estimate EFs and their uncertainties using posterior simulations (for N2O 0.077% with CI 95% high probability density, from 0.056% to 0.191%; for NO 0.875% with CI 95% high probability density, from 0.552% to 2.05%). Our HB model can be easily applied to the observations of the N2O and NO fluxes because it requires only several explanatory variables and can be used to evaluate the flux uncertainties and responses of the nonlinear N oxide fluxes to environmental factors.

  16. A Survey of Model Evaluation Approaches with a Tutorial on Hierarchical Bayesian Methods

    ERIC Educational Resources Information Center

    Shiffrin, Richard M.; Lee, Michael D.; Kim, Woojae; Wagenmakers, Eric-Jan

    2008-01-01

    This article reviews current methods for evaluating models in the cognitive sciences, including theoretically based approaches, such as Bayes factors and minimum description length measures; simulation approaches, including model mimicry evaluations; and practical approaches, such as validation and generalization measures. This article argues…

  17. An alternative parameterization of Bayesian logistic hierarchical models for mixed treatment comparisons.

    PubMed

    Pechlivanoglou, Petros; Abegaz, Fentaw; Postma, Maarten J; Wit, Ernst

    2015-01-01

    Mixed treatment comparison (MTC) models rely on estimates of relative effectiveness from randomized clinical trials so as to respect randomization across treatment arms. This approach could potentially be simplified by an alternative parameterization of the way effectiveness is modeled. We introduce a treatment-based parameterization of the MTC model that estimates outcomes on both the study and treatment levels. We compare the proposed model to the commonly used MTC models using a simulation study as well as three randomized clinical trial datasets from published systematic reviews comparing (i) treatments on bleeding after cirrhosis, (ii) the impact of antihypertensive drugs in diabetes mellitus, and (iii) smoking cessation strategies. The simulation results suggest similar or sometimes better performance of the treatment-based MTC model. Moreover, from the real data analyses, little differences were observed on the inference extracted from both models. Overall, our proposed MTC approach performed as good, or better, than the commonly applied indirect and MTC models and is simpler, fast, and easier to implement in standard statistical software. PMID:25958984

  18. A Bayesian Hierarchical Modeling Approach to Predicting Flow in Ungauged Basins

    EPA Science Inventory

    Recent innovative approaches to identifying and applying regression-based relationships between land use patterns (such as increasing impervious surface area and decreasing vegetative cover) and rainfall-runoff model parameters represent novel and promising improvements to predic...

  19. Bayesian Hierarchical Semiparametric Modelling of Longitudinal Post-treatment Outcomes from Open Enrolment Therapy Groups

    PubMed Central

    Paddock, Susan M.; Savitsky, Terrance D.

    2013-01-01

    There are several challenges to testing the effectiveness of group therapy-based interventions in alcohol and other drug use (AOD) treatment settings. Enrollment into AOD therapy groups typically occurs on an open (rolling) basis. Changes in therapy group membership induce a complex correlation structure among client outcomes, with relatively small numbers of clients attending each therapy group session. Primary outcomes are measured post-treatment, so each datum reflects the effect of all sessions attended by a client. The number of post-treatment outcomes assessments is typically very limited. The first feature of our modeling approach relaxes the assumption of independent random effects in the standard multiple membership model by employing conditional autoregression (CAR) to model correlation in random therapy group session effects associated with clients’ attendance of common group therapy sessions. A second feature specifies a longitudinal growth model under which the posterior distribution of client-specific random effects, or growth parameters, is modeled non-parametrically. The Dirichlet process prior helps to overcome limitations of standard parametric growth models given limited numbers of longitudinal assessments. We motivate and illustrate our approach with a data set from a study of group cognitive behavioral therapy to reduce depressive symptoms among residential AOD treatment clients. PMID:24353375

  20. Bayesian Hierarchical Semiparametric Modelling of Longitudinal Post-treatment Outcomes from Open Enrolment Therapy Groups.

    PubMed

    Paddock, Susan M; Savitsky, Terrance D

    2013-06-01

    There are several challenges to testing the effectiveness of group therapy-based interventions in alcohol and other drug use (AOD) treatment settings. Enrollment into AOD therapy groups typically occurs on an open (rolling) basis. Changes in therapy group membership induce a complex correlation structure among client outcomes, with relatively small numbers of clients attending each therapy group session. Primary outcomes are measured post-treatment, so each datum reflects the effect of all sessions attended by a client. The number of post-treatment outcomes assessments is typically very limited. The first feature of our modeling approach relaxes the assumption of independent random effects in the standard multiple membership model by employing conditional autoregression (CAR) to model correlation in random therapy group session effects associated with clients' attendance of common group therapy sessions. A second feature specifies a longitudinal growth model under which the posterior distribution of client-specific random effects, or growth parameters, is modeled non-parametrically. The Dirichlet process prior helps to overcome limitations of standard parametric growth models given limited numbers of longitudinal assessments. We motivate and illustrate our approach with a data set from a study of group cognitive behavioral therapy to reduce depressive symptoms among residential AOD treatment clients. PMID:24353375

  1. A Bayesian hierarchical model for maximizing the vascular adhesion of nanoparticles

    NASA Astrophysics Data System (ADS)

    Fronczyk, Kassandra; Guindani, Michele; Vannucci, Marina; Palange, Annalisa; Decuzzi, Paolo

    2014-03-01

    The complex vascular dynamics and wall deposition of systemically injected nanoparticles is regulated by their geometrical properties (size, shape) and biophysical parameters (ligand-receptor bond type and surface density, local shear rates). Although sophisticated computational models have been developed to capture the vascular behavior of nanoparticles, it is increasingly recognized that purely deterministic approaches, where the governing parameters are known a priori and conclusively describe behaviors based on physical characteristics, may be too restrictive to accurately reflect natural processes. Here, a novel computational framework is proposed by coupling the physics dictating the vascular adhesion of nanoparticles with a stochastic model. In particular, two governing parameters (i.e. the ligand-receptor bond length and the ligand surface density on the nanoparticle) are treated as two stochastic quantities, whose values are not fixed a priori but would rather range in defined intervals with a certain probability. This approach is used to predict the deposition of spherical nanoparticles with different radii, ranging from 750 to 6,000 nm, in a parallel plate flow chamber under different flow conditions, with a shear rate ranging from 50 to 90 . It is demonstrated that the resulting stochastic model can predict the experimental data more accurately than the original deterministic model. This approach allows one to increase the predictive power of mathematical models of any natural process by accounting for the experimental and intrinsic biological uncertainties.

  2. A Bayesian hierarchical model for maximizing the vascular adhesion of nanoparticles

    PubMed Central

    Guindani, Michele; Vannucci, Marina; Palange, Annalisa

    2014-01-01

    The complex vascular dynamics and wall deposition of systemically injected nanoparticles is regulated by their geometrical properties (size, shape) and biophysical parameters (ligand-receptor bond type and surface density, local shear rates). Although sophisticated computational models have been developed to capture the vascular behavior of nanoparticles, it is increasingly recognized that purely deterministic approaches, where the governing parameters are known a priori and conclusively describe behaviors based on physical characteristics, may be too restrictive to accurately reflect natural processes. Here, a novel computational framework is proposed by coupling the physics dictating the vascular adhesion of nanoparticles with a stochastic model. In particular, two governing parameters (i.e. the ligand-receptor bond length and the ligand surface density on the nanoparticle) are treated as two stochastic quantities, whose values are not fixed a priori but would rather range in defined intervals with a certain probability. This approach is used to predict the deposition of spherical nanoparticles with different radii, ranging from 750 to 6,000 nm, in a parallel plate flow chamber under different flow conditions, with a shear rate ranging from 50 to 90 sec−1. It is demonstrated that the resulting stochastic model can predict the experimental data more accurately than the original deterministic model. This approach allows one to increase the predictive power of mathematical models of any natural process by accounting for the experimental and intrinsic biological uncertainties. PMID:24833810

  3. Bayesian Hierarchical Air-Sea Interaction Modeling: Application to the Labrador Sea

    NASA Technical Reports Server (NTRS)

    Niiler, Pearn P.

    2002-01-01

    The objectives are to: 1) Organize data from 26 MINIMET drifters in the Labrador Sea, including sensor calibration and error checking of ARGOS transmissions. 2) Produce wind direction, barometer, and sea surface temperature time series. In addition, provide data from historical file of 150 SHARP drifters in the Labrador Sea. 3) Work with data interpretation and data-modeling assimilation issues.

  4. Bayesian Non-Parametric Hierarchical Modeling for Multiple Membership Data in Grouped Attendance Interventions

    PubMed Central

    Savitsky, Terrance D.; Paddock, Susan M.

    2012-01-01

    We develop a dependent Dirichlet process (DDP) model for repeated measures multiple membership (MM) data. This data structure arises in studies under which an intervention is delivered to each client through a sequence of elements which overlap with those of other clients on different occasions. Our interest concentrates on study designs for which the overlaps of sequences occur for clients who receive an intervention in a shared or grouped fashion whose memberships may change over multiple treatment events. Our motivating application focuses on evaluation of the effectiveness of a group therapy intervention with treatment delivered through a sequence of cognitive behavioral therapy session blocks, called modules. An open-enrollment protocol permits entry of clients at the beginning of any new module in a manner that may produce unique MM sequences across clients. We begin with a model that composes an addition of client and multiple membership module random effect terms, which are assumed independent. Our MM DDP model relaxes the assumption of conditionally independent client and module random effects by specifying a collection of random distributions for the client effect parameters that are indexed by the unique set of module attendances. We demonstrate how this construction facilitates examining heterogeneity in the relative effectiveness of group therapy modules over repeated measurement occasions. PMID:24273629

  5. Bayesian Non-Parametric Hierarchical Modeling for Multiple Membership Data in Grouped Attendance Interventions.

    PubMed

    Savitsky, Terrance D; Paddock, Susan M

    2013-06-01

    We develop a dependent Dirichlet process (DDP) model for repeated measures multiple membership (MM) data. This data structure arises in studies under which an intervention is delivered to each client through a sequence of elements which overlap with those of other clients on different occasions. Our interest concentrates on study designs for which the overlaps of sequences occur for clients who receive an intervention in a shared or grouped fashion whose memberships may change over multiple treatment events. Our motivating application focuses on evaluation of the effectiveness of a group therapy intervention with treatment delivered through a sequence of cognitive behavioral therapy session blocks, called modules. An open-enrollment protocol permits entry of clients at the beginning of any new module in a manner that may produce unique MM sequences across clients. We begin with a model that composes an addition of client and multiple membership module random effect terms, which are assumed independent. Our MM DDP model relaxes the assumption of conditionally independent client and module random effects by specifying a collection of random distributions for the client effect parameters that are indexed by the unique set of module attendances. We demonstrate how this construction facilitates examining heterogeneity in the relative effectiveness of group therapy modules over repeated measurement occasions. PMID:24273629

  6. Inferring land use and land cover impact on stream water quality using a Bayesian hierarchical modeling approach in the Xitiaoxi River Watershed, China.

    PubMed

    Wan, Rongrong; Cai, Shanshan; Li, Hengpeng; Yang, Guishan; Li, Zhaofu; Nie, Xiaofei

    2014-01-15

    Lake eutrophication has become a very serious environmental problem in China. If water pollution is to be controlled and ultimately eliminated, it is essential to understand how human activities affect surface water quality. A recently developed technique using the Bayesian hierarchical linear regression model revealed the effects of land use and land cover (LULC) on stream water quality at a watershed scale. Six LULC categories combined with watershed characteristics, including size, slope, and permeability were the variables that were studied. The pollutants of concern were nutrient concentrations of total nitrogen (TN) and total phosphorus (TP), common pollutants found in eutrophication. The monthly monitoring data at 41 sites in the Xitiaoxi Watershed, China during 2009-2010 were used for model demonstration. The results showed that the relationships between LULC and stream water quality are so complicated that the effects are varied over large areas. The models suggested that urban and agricultural land are important sources of TN and TP concentrations, while rural residential land is one of the major sources of TN. Certain agricultural practices (excessive fertilizer application) result in greater concentrations of nutrients in paddy fields, artificial grasslands, and artificial woodlands. This study suggests that Bayesian hierarchical modeling is a powerful tool for examining the complicated relationships between land use and water quality on different scales, and for developing land use and water management policies. PMID:24342905

  7. A Hierarchical Bayesian Model for Estimating Remediation-induced Biogeochemical Transformations Using Spectral Induced Polarization Data: Development and Application to the Contaminated DOE Rifle (CO) Site

    NASA Astrophysics Data System (ADS)

    Chen, J.; Hubbard, S. S.; Williams, K. H.; Tuglus, C.; Flores-Orozco, A.; Kemna, A.

    2010-12-01

    Although in-situ bioremediation is often considered as a key approach for subsurface environmental remediation, monitoring induced biogeochemical processes, needed to evaluate the efficacy of the treatments, is challenging over field relevant scales. In this study, we develop a hierarchical Bayesian model that builds on our previous framework for estimating biogeochemical transformations using geochemical and geophysical data obtained from laboratory column experiments. The new Bayesian model treats the induced biogeochemical transformations as both spatial and temporal (rather than just temporal) processes and combines time-lapse borehole ‘point’ geochemical measurements with inverted surface- or crosshole-based spectral induced polarization (SIP) data. This model consists of three levels of statistical sub-models: (1) data model (or likelihood function), which provides links between the biogeochemical end-products and geophysical attributes, (2) process model, which describes the spatial and temporal variability of biogeochemical properties in the disturbed subsurface systems, and (3) parameter model, which describes the prior distributions of various parameters and initial conditions. The joint posterior probability distribution is explored using Markov Chain Monte Carlo sampling methods to obtain the spatial and temporal distribution of the hidden parameters. We apply the developed Bayesian model to the datasets collected from the uranium-contaminated DOE Rifle site for estimating the spatial and temporal distribution of remediation-induced end products. The datasets consist of time-lapse wellbore aqueous geochemical parameters (including Fe(II), sulfate, sulfide, acetate, uranium, chloride, and bromide concentrations) and surface SIP data collected over 13 frequencies (ranging from 0.065Hz to 256Hz). We first perform statistical analysis on the multivariate data to identify possible patterns (or ‘diagnostic signatures’) of bioremediation, and then we

  8. A Bayesian Hierarchical Approach to Regional Frequency Analysis of Extremes

    NASA Astrophysics Data System (ADS)

    Renard, B.

    2010-12-01

    Rainfall and runoff frequency analysis is a major issue for the hydrological community. The distribution of hydrological extremes varies in space and possibly in time. Describing and understanding this spatiotemporal variability are primary challenges to improve hazard quantification and risk assessment. This presentation proposes a general approach based on a Bayesian hierarchical model, following previous work by Cooley et al. [2007], Micevski [2007], Aryal et al. [2009] or Lima and Lall [2009; 2010]. Such a hierarchical model is made up of two levels: (1) a data level modeling the distribution of observations, and (2) a process level describing the fluctuation of the distribution parameters in space and possibly in time. At the first level of the model, at-site data (e.g., annual maxima series) are modeled with a chosen distribution (e.g., a GEV distribution). Since data from several sites are considered, the joint distribution of a vector of (spatial) observations needs to be derived. This is challenging because data are in general not spatially independent, especially for nearby sites. An elliptical copula is therefore used to formally account for spatial dependence between at-site data. This choice might be questionable in the context of extreme value distributions. However, it is motivated by its applicability in spatial highly dimensional problems, where the joint pdf of a vector of n observations is required to derive the likelihood function (with n possibly amounting to hundreds of sites). At the second level of the model, parameters of the chosen at-site distribution are then modeled by a Gaussian spatial process, whose mean may depend on covariates (e.g. elevation, distance to sea, weather pattern, time). In particular, this spatial process allows estimating parameters at ungauged sites, and deriving the predictive distribution of rainfall/runoff at every pixel/catchment of the studied domain. An application to extreme rainfall series from the French

  9. A Bayesian Hierarchical Model for Spatio-Temporal Prediction and Uncertainty Assessment Using Repeat LiDAR Acquisitions for the Kenai Peninsula, AK, USA

    NASA Astrophysics Data System (ADS)

    Babcock, C. R.; Andersen, H. E.; Finley, A. O.; Cook, B.; Morton, D. C.

    2015-12-01

    Models using repeat LiDAR and field campaigns may be one mechanism to monitor carbon storage and flux in forested regions. Considering the ability of multi-temporal LiDAR to estimate growth, it is not surprising that there is great interest in developing forest carbon monitoring strategies that rely on repeated LiDAR acquisitions. Allowing for sparser field campaigns, LiDAR stands to make monitoring forest carbon cheaper and more efficient than field-only sampling procedures. Here, we look to the spatio-temporally data-rich Kenai Peninsula in Alaska to examine the potential for Bayesian spatio-temporal mapping of forest carbon storage and uncertainty. The framework explored here can predict forest carbon through space and time, while formally propagating uncertainty through to prediction. Bayesian spatio-temporal models are flexible frameworks allowing for forest growth processes to be formally integrated into the model. By incorporating a mechanism for growth---using temporally repeated field and LiDAR data---we can more fully exploit the information-rich inventory network to improve prediction accuracy. LiDAR data for the Kenai Peninsula has been collected on four different occasions---spatially coincident LiDAR strip samples in 2004, 09 and 14, along with a wall-to-wall collection in 2008. There were 436 plots measured twice between 2002 and 2014. LiDAR was acquired at least once over most inventory plots with many having LiDAR collected during 2, 3 or 4 different campaigns. Results from this research will impact how forests are inventoried. It is too expensive to monitor terrestrial carbon using field-only sampling strategies and currently proposed LiDAR model-based techniques lack the ability to properly utilize temporally repeated and misaligned data. Bayesian hierarchical spatio-temporal models offer a solution to these shortcomings and allow for formal predictive error assessment, which is useful for policy development and decision making.

  10. Application of Bayesian Hierarchical Model for Detecting Effective Factors on Growth Failure of Infants Less Than Two Years of Age in a Multicenter Longitudinal Study

    PubMed Central

    Zayeri, Farid; Amini, Maedeh; Moghimbeigi, Abbas; Soltanian, Ali Reza; Kholdi, Nahid; Gholami-Fesharaki, Mohammad

    2016-01-01

    Background Nowadays, one of the major public health problems among children is growth failure. It can be characterized in terms of either inadequate growth or the inability to maintain growth. Objectives The main objective of this study was to examine the effects of some factors on growth failure among a sample of infants less than two years old. Materials and Methods The present longitudinal archival study relied on data gathered from health files from February 2007 to July 2010 for 1,358 children under two years of age, selected from eight health centers in the east and northeast parts of Tehran, Iran. In the present study, growth failure refers to at least a 50 g decrease in an infant’s weight as recorded at each attendance in comparison to the previous measurement. The impacts of risk indicators were assessed using the Bayesian hierarchical logistic regression modeling technique. Results The highest and lowest percentage of growth failure was 5.8% and 0.1%, respectively, in the eleventh and the first month after birth. The obtained results from the Bayesian hierarchical modeling revealed that diarrhea (95% credible interval (CrI): 0.70 - 3.31), discontinuation of breastfeeding (95% CrI: 0.77 - 5.96), and respiratory infections (95% CrI: 2.07 - 4.61) were significant risk factors for growth failure. The random term at the child level was significant (95% CrI: 0.74 - 7.82), while the variation in centers was extremely small (95% CrI: 0.004 - 4.22). Conclusions It was noted that a relatively high prevalence of growth failure was observed in the study sample. For minimizing the impact of significant risk factors on growth failure, the early detection of growth failure and its risk indicators is of great importance. In addition, when the focus of the analysis is on the different nested sources of variability and the data has a hierarchical structure, using a hierarchical modeling approach is recommended to achieve more accurate results.

  11. Estimation of Gene Expression at Isoform Level from mRNA-Seq Data by Bayesian Hierarchical Modeling

    PubMed Central

    Bhattacharjee, M.; Gupta, Ravi; Davuluri, R. V.

    2012-01-01

    mRNA-Seq is a precise and highly reproducible technique for measurement of transcripts levels and yields sequence information of a transcriptome at a single nucleotide base-level thus enabling us to determine splice junctions and alternative splicing events with high confidence. Often analysis of mRNA-Seq data does not attempt to quantify the expressions at isoform level. In this paper our objective would be use the mRNA-Seq data to infer expression at isoform level, where splicing patterns of a gene is assumed to be known. A Bayesian latent variable based modeling framework is proposed here, where the parameterization enables us to infer at various levels. For example, expression variability of an isoform across different conditions; the model parameterization also allows us to carry out two-sample comparisons, e.g., using a Bayesian t-test, in addition simple presence or absence of an isoform can also be estimated by the use of the latent variables present in the model. In this paper we would carry out inference on isoform expression under different normalization techniques, since it has been recently shown that one of the most prominent sources of variation in differential call using mRNA-Seq data is the normalization method used. The statistical framework is developed for multiple isoforms and easily extends to reads mapping to multiple genes. This could be achieved by slight conceptual modifications in definitions of what we consider as a gene and what as an exon. Additionally proposed framework can be extended by appropriate modeling of the design matrix to infer about yet unknown novel transcripts. However such attempts should be made judiciously since the input date used in the proposed model does not use reads from splice junctions. PMID:23293650

  12. Stochastic Downscaling of Daily Rainfall: Analysis of future hydroclimatic changes and their impact on the Pontinia plain using Nonhomogeneous Hidden Markov Model and Dynamic Hierarchical Bayesian Network Model.

    NASA Astrophysics Data System (ADS)

    Cioffi, Francesco; Devineni, Naresh; Monti, Alessandro; Lall, Upmanu

    2013-04-01

    The Nonhomogeneous Hidden Markov Model is an established technique that usually provides excellent results for the downscaling of multi-site precipitation. However, the selection of the number of states is subjective and results in a model that can be over parameterized and overfit leading to por performance in applications. A dynamic hierarchical Bayesian network model (DHBN) that is continuous and is not based on discretization into states is tested here and compared against NHMM for the downscaling of daily precipitation for Pontinia Plain. This región is a relevant example of coastal area particularly vulnerable to hydrological changes. The winter (October-March) wet season is considered. Weather states and atmospheric variables from CMIP5 GCM are used as exogenous predictors. The daily rainfall occurrence and amount at 32 stations over the region for the winters of 1916-2004 is used as the primary data. Rainfall variability is described in terms of occurrence of 'weather state' as classified by a Hidden Markov Model, and associated to variables representing the main characteristics of large scale atmospheric circulation as obtained by reanalysis data. A nonhomogeneous hidden Markov model (NHHM) and a DHBN model are used to make future projections of the downscaled precipitation as by using the GCM's simulations under different global warming scenarios.The spatial interaction between the sites is modeled through the underlying covariance function and the uncertainty in the model parameters is explicitly represented in their posterior distribution. Preliminary results show that the seasonal statistics are adequately captures for the 20th century runs. The structural differences between the two models are discussed.

  13. Bayesian hierarchical spatial models to improve forest variable prediction and mapping with Light Detection and Ranging data sets

    NASA Astrophysics Data System (ADS)

    Ball, Jessica Lynne

    Light Detection and Ranging (LiDAR) data has shown great potential to estimate spatially explicit forest variables, including above-ground biomass, stem density, tree height, and more. Due to its ability to garner information about the vertical and horizontal structure of forest canopies effectively and efficiently, LiDAR sensors have played a key role in the development of operational air and space-borne instruments capable of gathering information about forest structure at regional, continental, and global scales. Combining LiDAR datasets with field-based validation measurements to build predictive models is becoming an attractive solution to the problem of quantifying and mapping forest structure for private forest land owners and local, state, and federal government entities alike. As with any statistical model using spatially indexed data, the potential to violate modeling assumptions resulting from spatial correlation is high. This thesis explores several different modeling frameworks that aim to accommodate correlation structures within model residuals. The development is motivated using LiDAR and forest inventory datasets. Special attention is paid to estimation and propagation of parameter and model uncertainty through to prediction units. Inference follows a Bayesian statistical paradigm. Results suggest the proposed frameworks help ensure model assumptions are met and prediction performance can be improved by pursuing spatially enabled models.

  14. Bayesian hierarchical grouping: Perceptual grouping as mixture estimation.

    PubMed

    Froyen, Vicky; Feldman, Jacob; Singh, Manish

    2015-10-01

    We propose a novel framework for perceptual grouping based on the idea of mixture models, called Bayesian hierarchical grouping (BHG). In BHG, we assume that the configuration of image elements is generated by a mixture of distinct objects, each of which generates image elements according to some generative assumptions. Grouping, in this framework, means estimating the number and the parameters of the mixture components that generated the image, including estimating which image elements are "owned" by which objects. We present a tractable implementation of the framework, based on the hierarchical clustering approach of Heller and Ghahramani (2005). We illustrate it with examples drawn from a number of classical perceptual grouping problems, including dot clustering, contour integration, and part decomposition. Our approach yields an intuitive hierarchical representation of image elements, giving an explicit decomposition of the image into mixture components, along with estimates of the probability of various candidate decompositions. We show that BHG accounts well for a diverse range of empirical data drawn from the literature. Because BHG provides a principled quantification of the plausibility of grouping interpretations over a wide range of grouping problems, we argue that it provides an appealing unifying account of the elusive Gestalt notion of Prägnanz. PMID:26322548

  15. 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

  16. Poor-data and data-poor species stock assessment using a Bayesian hierarchical approach.

    PubMed

    Jiao, Yan; Cortés, Enric; Andrews, Kate; Guo, Feng

    2011-10-01

    Appropriate inference for stocks or species with low-quality data (poor data) or limited data (data poor) is extremely important. Hierarchical Bayesian methods are especially applicable to small-area, small-sample-size estimation problems because they allow poor-data species to borrow strength from species with good-quality data. We used a hammerhead shark complex as an example to investigate the advantages of using hierarchical Bayesian models in assessing the status of poor-data and data-poor exploited species. The hammerhead shark complex (Sphyrna spp.) along the Atlantic and Gulf of Mexico coasts of the United States is composed of three species: the scalloped hammerhead (S. lewini), the great hammerhead (S. mokarran), and the smooth hammerhead (S. zygaena) sharks. The scalloped hammerhead comprises 70-80% of the catch and has catch and relative abundance data of good quality, whereas great and smooth hammerheads have relative abundance indices that are both limited and of low quality presumably because of low stock density and limited sampling. Four hierarchical Bayesian state-space surplus production models were developed to simulate variability in population growth rates, carrying capacity, and catchability of the species. The results from the hierarchical Bayesian models were considerably more robust than those of the nonhierarchical models. The hierarchical Bayesian approach represents an intermediate strategy between traditional models that assume different population parameters for each species and those that assume all species share identical parameters. Use of the hierarchical Bayesian approach is suggested for future hammerhead shark stock assessments and for modeling fish complexes with species-specific data, because the poor-data species can borrow strength from the species with good data, making the estimation more stable and robust. PMID:22073653

  17. Hierarchical Bayesian mixture modelling for antigen-specific T-cell subtyping in combinatorially encoded flow cytometry studies

    PubMed Central

    Lin, Lin; Chan, Cliburn; Hadrup, Sine R.; Froesig, Thomas M.; Wang, Quanli; West, Mike

    2014-01-01

    Novel uses of automated flow cytometry technology for measuring levels of protein markers on thousands to millions of cells are promoting increasing need for relevant, customized Bayesian mixture modelling approaches in many areas of biomedical research and application. In studies of immune profiling in many biological areas, traditional flow cytometry measures relative levels of abundance of marker proteins using fluorescently labeled tags that identify specific markers by a single-color. One specific and important recent development in this area is the use of combinatorial marker assays in which each marker is targeted with a probe that is labeled with two or more fluorescent tags. The use of several colors enables the identification of, in principle, combinatorially increasingly numbers of subtypes of cells, each identified by a subset of colors. This represents a major advance in the ability to characterize variation in immune responses involving larger numbers of functionally differentiated cell subtypes. We describe novel classes of Markov chain Monte Carlo methods for model fitting that exploit distributed GPU (graphics processing unit) implementation. We discuss issues of cellular subtype identification in this novel, general model framework, and provide a detailed example using simulated data. We then describe application to a data set from an experimental study of antigen-specific T-cell subtyping using combinatorially encoded assays in human blood samples. Summary comments discuss broader questions in applications in immunology, and aspects of statistical computation. PMID:23629459

  18. Exemplars, Prototypes, Similarities, and Rules in Category Representation: An Example of Hierarchical Bayesian Analysis

    ERIC Educational Resources Information Center

    Lee, Michael D.; Vanpaemel, Wolf

    2008-01-01

    This article demonstrates the potential of using hierarchical Bayesian methods to relate models and data in the cognitive sciences. This is done using a worked example that considers an existing model of category representation, the Varying Abstraction Model (VAM), which attempts to infer the representations people use from their behavior in…

  19. Bayesian hierarchical modelling of continuous non-negative longitudinal data with a spike at zero: An application to a study of birds visiting gardens in winter.

    PubMed

    Swallow, Ben; Buckland, Stephen T; King, Ruth; Toms, Mike P

    2016-03-01

    The development of methods for dealing with continuous data with a spike at zero has lagged behind those for overdispersed or zero-inflated count data. We consider longitudinal ecological data corresponding to an annual average of 26 weekly maximum counts of birds, and are hence effectively continuous, bounded below by zero but also with a discrete mass at zero. We develop a Bayesian hierarchical Tweedie regression model that can directly accommodate the excess number of zeros common to this type of data, whilst accounting for both spatial and temporal correlation. Implementation of the model is conducted in a Markov chain Monte Carlo (MCMC) framework, using reversible jump MCMC to explore uncertainty across both parameter and model spaces. This regression modelling framework is very flexible and removes the need to make strong assumptions about mean-variance relationships a priori. It can also directly account for the spike at zero, whilst being easily applicable to other types of data and other model formulations. Whilst a correlative study such as this cannot prove causation, our results suggest that an increase in an avian predator may have led to an overall decrease in the number of one of its prey species visiting garden feeding stations in the United Kingdom. This may reflect a change in behaviour of house sparrows to avoid feeding stations frequented by sparrowhawks, or a reduction in house sparrow population size as a result of sparrowhawk increase. PMID:25737026

  20. Bayesian hierarchical modelling of continuous non‐negative longitudinal data with a spike at zero: An application to a study of birds visiting gardens in winter

    PubMed Central

    Buckland, Stephen T.; King, Ruth; Toms, Mike P.

    2015-01-01

    The development of methods for dealing with continuous data with a spike at zero has lagged behind those for overdispersed or zero‐inflated count data. We consider longitudinal ecological data corresponding to an annual average of 26 weekly maximum counts of birds, and are hence effectively continuous, bounded below by zero but also with a discrete mass at zero. We develop a Bayesian hierarchical Tweedie regression model that can directly accommodate the excess number of zeros common to this type of data, whilst accounting for both spatial and temporal correlation. Implementation of the model is conducted in a Markov chain Monte Carlo (MCMC) framework, using reversible jump MCMC to explore uncertainty across both parameter and model spaces. This regression modelling framework is very flexible and removes the need to make strong assumptions about mean‐variance relationships a priori. It can also directly account for the spike at zero, whilst being easily applicable to other types of data and other model formulations. Whilst a correlative study such as this cannot prove causation, our results suggest that an increase in an avian predator may have led to an overall decrease in the number of one of its prey species visiting garden feeding stations in the United Kingdom. This may reflect a change in behaviour of house sparrows to avoid feeding stations frequented by sparrowhawks, or a reduction in house sparrow population size as a result of sparrowhawk increase. PMID:25737026

  1. Examining the Impact of Prior Models in Transmural Electrophysiological Imaging: A Hierarchical Multiple-Model Bayesian Approach.

    PubMed

    Rahimi, Azar; Sapp, John; Xu, Jingjia; Bajorski, Peter; Horacek, Milan; Wang, Linwei

    2016-01-01

    Noninvasive cardiac electrophysiological (EP) imaging aims to mathematically reconstruct the spatiotemporal dynamics of cardiac sources from body-surface electrocardiographic (ECG) data. This ill-posed problem is often regularized by a fixed constraining model. However, a fixed-model approach enforces the source distribution to follow a pre-assumed structure that does not always match the varying spatiotemporal distribution of actual sources. To understand the model-data relation and examine the impact of prior models, we present a multiple-model approach for volumetric cardiac EP imaging where multiple prior models are included and automatically picked by the available ECG data. Multiple models are incorporated as an Lp-norm prior for sources, where p is an unknown hyperparameter with a prior uniform distribution. To examine how different combinations of models may be favored by different measurement data, the posterior distribution of cardiac sources and hyperparameter p is calculated using a Markov Chain Monte Carlo (MCMC) technique. The importance of multiple-model prior was assessed in two sets of synthetic and real-data experiments, compared to fixed-model priors (using Laplace and Gaussian priors). The results showed that the posterior combination of models (the posterior distribution of p) as determined by the ECG data differed substantially when reconstructing sources with different sizes and structures. While the use of fixed models is best suited in situations where the prior assumption fits the actual source structures, the use of an automatically adaptive set of models may have the ability to better address model-data mismatch and to provide consistent performance in reconstructing sources with different properties. PMID:26259018

  2. Unsupervised Transient Light Curve Analysis via Hierarchical Bayesian Inference

    NASA Astrophysics Data System (ADS)

    Sanders, N. E.; Betancourt, M.; Soderberg, A. M.

    2015-02-01

    Historically, light curve studies of supernovae (SNe) and other transient classes have focused on individual objects with copious and high signal-to-noise observations. In the nascent era of wide field transient searches, objects with detailed observations are decreasing as a fraction of the overall known SN population, and this strategy sacrifices the majority of the information contained in the data about the underlying population of transients. A population level modeling approach, simultaneously fitting all available observations of objects in a transient sub-class of interest, fully mines the data to infer the properties of the population and avoids certain systematic biases. We present a novel hierarchical Bayesian statistical model for population level modeling of transient light curves, and discuss its implementation using an efficient Hamiltonian Monte Carlo technique. As a test case, we apply this model to the Type IIP SN sample from the Pan-STARRS1 Medium Deep Survey, consisting of 18,837 photometric observations of 76 SNe, corresponding to a joint posterior distribution with 9176 parameters under our model. Our hierarchical model fits provide improved constraints on light curve parameters relevant to the physical properties of their progenitor stars relative to modeling individual light curves alone. Moreover, we directly evaluate the probability for occurrence rates of unseen light curve characteristics from the model hyperparameters, addressing observational biases in survey methodology. We view this modeling framework as an unsupervised machine learning technique with the ability to maximize scientific returns from data to be collected by future wide field transient searches like LSST.

  3. UNSUPERVISED TRANSIENT LIGHT CURVE ANALYSIS VIA HIERARCHICAL BAYESIAN INFERENCE

    SciTech Connect

    Sanders, N. E.; Soderberg, A. M.; Betancourt, M.

    2015-02-10

    Historically, light curve studies of supernovae (SNe) and other transient classes have focused on individual objects with copious and high signal-to-noise observations. In the nascent era of wide field transient searches, objects with detailed observations are decreasing as a fraction of the overall known SN population, and this strategy sacrifices the majority of the information contained in the data about the underlying population of transients. A population level modeling approach, simultaneously fitting all available observations of objects in a transient sub-class of interest, fully mines the data to infer the properties of the population and avoids certain systematic biases. We present a novel hierarchical Bayesian statistical model for population level modeling of transient light curves, and discuss its implementation using an efficient Hamiltonian Monte Carlo technique. As a test case, we apply this model to the Type IIP SN sample from the Pan-STARRS1 Medium Deep Survey, consisting of 18,837 photometric observations of 76 SNe, corresponding to a joint posterior distribution with 9176 parameters under our model. Our hierarchical model fits provide improved constraints on light curve parameters relevant to the physical properties of their progenitor stars relative to modeling individual light curves alone. Moreover, we directly evaluate the probability for occurrence rates of unseen light curve characteristics from the model hyperparameters, addressing observational biases in survey methodology. We view this modeling framework as an unsupervised machine learning technique with the ability to maximize scientific returns from data to be collected by future wide field transient searches like LSST.

  4. Using hierarchical Bayesian multi-species mixture models to estimate tandem hoop-net based habitat associations and detection probabilities of fishes in reservoirs

    USGS Publications Warehouse

    Stewart, David R.; Long, James M.

    2015-01-01

    Species distribution models are useful tools to evaluate habitat relationships of fishes. We used hierarchical Bayesian multispecies mixture models to evaluate the relationships of both detection and abundance with habitat of reservoir fishes caught using tandem hoop nets. A total of 7,212 fish from 12 species were captured, and the majority of the catch was composed of Channel Catfish Ictalurus punctatus (46%), Bluegill Lepomis macrochirus(25%), and White Crappie Pomoxis annularis (14%). Detection estimates ranged from 8% to 69%, and modeling results suggested that fishes were primarily influenced by reservoir size and context, water clarity and temperature, and land-use types. Species were differentially abundant within and among habitat types, and some fishes were found to be more abundant in turbid, less impacted (e.g., by urbanization and agriculture) reservoirs with longer shoreline lengths; whereas, other species were found more often in clear, nutrient-rich impoundments that had generally shorter shoreline length and were surrounded by a higher percentage of agricultural land. Our results demonstrated that habitat and reservoir characteristics may differentially benefit species and assemblage structure. This study provides a useful framework for evaluating capture efficiency for not only hoop nets but other gear types used to sample fishes in reservoirs.

  5. Occupancy models for monitoring marine fish: a bayesian hierarchical approach to model imperfect detection with a novel gear combination.

    PubMed

    Coggins, Lewis G; Bacheler, Nathan M; Gwinn, Daniel C

    2014-01-01

    Occupancy models using incidence data collected repeatedly at sites across the range of a population are increasingly employed to infer patterns and processes influencing population distribution and dynamics. While such work is common in terrestrial systems, fewer examples exist in marine applications. This disparity likely exists because the replicate samples required by these models to account for imperfect detection are often impractical to obtain when surveying aquatic organisms, particularly fishes. We employ simultaneous sampling using fish traps and novel underwater camera observations to generate the requisite replicate samples for occupancy models of red snapper, a reef fish species. Since the replicate samples are collected simultaneously by multiple sampling devices, many typical problems encountered when obtaining replicate observations are avoided. Our results suggest that augmenting traditional fish trap sampling with camera observations not only doubled the probability of detecting red snapper in reef habitats off the Southeast coast of the United States, but supplied the necessary observations to infer factors influencing population distribution and abundance while accounting for imperfect detection. We found that detection probabilities tended to be higher for camera traps than traditional fish traps. Furthermore, camera trap detections were influenced by the current direction and turbidity of the water, indicating that collecting data on these variables is important for future monitoring. These models indicate that the distribution and abundance of this species is more heavily influenced by latitude and depth than by micro-scale reef characteristics lending credence to previous characterizations of red snapper as a reef habitat generalist. This study demonstrates the utility of simultaneous sampling devices, including camera traps, in aquatic environments to inform occupancy models and account for imperfect detection when describing factors

  6. Occupancy Models for Monitoring Marine Fish: A Bayesian Hierarchical Approach to Model Imperfect Detection with a Novel Gear Combination

    PubMed Central

    Coggins, Lewis G.; Bacheler, Nathan M.; Gwinn, Daniel C.

    2014-01-01

    Occupancy models using incidence data collected repeatedly at sites across the range of a population are increasingly employed to infer patterns and processes influencing population distribution and dynamics. While such work is common in terrestrial systems, fewer examples exist in marine applications. This disparity likely exists because the replicate samples required by these models to account for imperfect detection are often impractical to obtain when surveying aquatic organisms, particularly fishes. We employ simultaneous sampling using fish traps and novel underwater camera observations to generate the requisite replicate samples for occupancy models of red snapper, a reef fish species. Since the replicate samples are collected simultaneously by multiple sampling devices, many typical problems encountered when obtaining replicate observations are avoided. Our results suggest that augmenting traditional fish trap sampling with camera observations not only doubled the probability of detecting red snapper in reef habitats off the Southeast coast of the United States, but supplied the necessary observations to infer factors influencing population distribution and abundance while accounting for imperfect detection. We found that detection probabilities tended to be higher for camera traps than traditional fish traps. Furthermore, camera trap detections were influenced by the current direction and turbidity of the water, indicating that collecting data on these variables is important for future monitoring. These models indicate that the distribution and abundance of this species is more heavily influenced by latitude and depth than by micro-scale reef characteristics lending credence to previous characterizations of red snapper as a reef habitat generalist. This study demonstrates the utility of simultaneous sampling devices, including camera traps, in aquatic environments to inform occupancy models and account for imperfect detection when describing factors

  7. Recent global methane trends: an investigation using hierarchical Bayesian methods

    NASA Astrophysics Data System (ADS)

    Rigby, M. L.; Stavert, A.; Ganesan, A.; Lunt, M. F.

    2014-12-01

    Following a decade with little growth, methane concentrations began to increase across the globe in 2007, and have continued to rise ever since. The reasons for this renewed growth are currently the subject of much debate. Here, we discuss the recent observed trends, and highlight some of the strengths and weaknesses in current "inverse" methods for quantifying fluxes using observations. In particular, we focus on the outstanding problems of accurately quantifying uncertainties in inverse frameworks. We examine to what extent the recent methane changes can be explained by the current generation of flux models and inventories. We examine the major modes of variability in wetland models along with the Global Fire Emissions Database (GFED) and the Emissions Database for Global Atmospheric Research (EDGAR). Using the Model for Ozone and Related Tracers (MOZART), we determine whether the spatial and temporal atmospheric trends predicted using these emissions can be brought into consistency with in situ atmospheric observations. We use a novel hierarchical Bayesian methodology in which scaling factors applied to the principal components of the flux fields are estimated simultaneously with the uncertainties associated with the a priori fluxes and with model representations of the observations. Using this method, we examine the predictive power of methane flux models for explaining recent fluctuations.

  8. A Robust Deconvolution Method based on Transdimensional Hierarchical Bayesian Inference

    NASA Astrophysics Data System (ADS)

    Kolb, J.; Lekic, V.

    2012-12-01

    Analysis of P-S and S-P conversions allows us to map receiver side crustal and lithospheric structure. This analysis often involves deconvolution of the parent wave field from the scattered wave field as a means of suppressing source-side complexity. A variety of deconvolution techniques exist including damped spectral division, Wiener filtering, iterative time-domain deconvolution, and the multitaper method. All of these techniques require estimates of noise characteristics as input parameters. We present a deconvolution method based on transdimensional Hierarchical Bayesian inference in which both noise magnitude and noise correlation are used as parameters in calculating the likelihood probability distribution. Because the noise for P-S and S-P conversion analysis in terms of receiver functions is a combination of both background noise - which is relatively easy to characterize - and signal-generated noise - which is much more difficult to quantify - we treat measurement errors as an known quantity, characterized by a probability density function whose mean and variance are model parameters. This transdimensional Hierarchical Bayesian approach has been successfully used previously in the inversion of receiver functions in terms of shear and compressional wave speeds of an unknown number of layers [1]. In our method we used a Markov chain Monte Carlo (MCMC) algorithm to find the receiver function that best fits the data while accurately assessing the noise parameters. In order to parameterize the receiver function we model the receiver function as an unknown number of Gaussians of unknown amplitude and width. The algorithm takes multiple steps before calculating the acceptance probability of a new model, in order to avoid getting trapped in local misfit minima. Using both observed and synthetic data, we show that the MCMC deconvolution method can accurately obtain a receiver function as well as an estimate of the noise parameters given the parent and daughter

  9. Hierarchical Models of Attitude.

    ERIC Educational Resources Information Center

    Reddy, Srinivas K.; LaBarbera, Priscilla A.

    1985-01-01

    The application and use of hierarchical models is illustrated, using the example of the structure of attitudes toward a new product and a print advertisement. Subjects were college students who responded to seven-point bipolar scales. Hierarchical models were better than nonhierarchical models in conceptualizing attitude but not intention. (GDC)

  10. A Bayesian, exemplar-based approach to hierarchical shape matching.

    PubMed

    Gavrila, Dariu M

    2007-08-01

    This paper presents a novel probabilistic approach to hierarchical, exemplar-based shape matching. No feature correspondence is needed among exemplars, just a suitable pairwise similarity measure. The approach uses a template tree to efficiently represent and match the variety of shape exemplars. The tree is generated offline by a bottom-up clustering approach using stochastic optimization. Online matching involves a simultaneous coarse-to-fine approach over the template tree and over the transformation parameters. The main contribution of this paper is a Bayesian model to estimate the a posteriori probability of the object class, after a certain match at a node of the tree. This model takes into account object scale and saliency and allows for a principled setting of the matching thresholds such that unpromising paths in the tree traversal process are eliminated early on. The proposed approach was tested in a variety of application domains. Here, results are presented on one of the more challenging domains: real-time pedestrian detection from a moving vehicle. A significant speed-up is obtained when comparing the proposed probabilistic matching approach with a manually tuned nonprobabilistic variant, both utilizing the same template tree structure. PMID:17568144

  11. Bayesian Variable Selection for Hierarchical Gene-Environment and Gene-Gene Interactions

    PubMed Central

    Liu, Changlu; Ma, Jianzhong; Amos, Christopher I.

    2014-01-01

    We propose a Bayesian hierarchical mixture model framework that allows us to investigate the genetic and environmental effects, gene by gene interactions and gene by environment interactions in the same model. Our approach incorporates the natural hierarchical structure between the main effects and interaction effects into a mixture model, such that our methods tend to remove the irrelevant interaction effects more effectively, resulting in more robust and parsimonious models. We consider both strong and weak hierarchical models. For a strong hierarchical model, both of the main effects between interacting factors must be present for the interactions to be considered in the model development, while for a weak hierarchical model, only one of the two main effects is required to be present for the interaction to be evaluated. Our simulation results show that the proposed strong and weak hierarchical mixture models work well in controlling false positive rates and provide a powerful approach for identifying the predisposing effects and interactions in gene-environment interaction studies, in comparison with the naive model that does not impose this hierarchical constraint in most of the scenarios simulated. We illustrated our approach using data for lung cancer and cutaneous melanoma. PMID:25154630

  12. Estimating sources of winter soil respiration in a subalpine forest using a hierarchical Bayesian process-based stable isotope mixing model

    NASA Astrophysics Data System (ADS)

    Tucker, C.; Ogle, K.; Cable, J.

    2011-12-01

    Recent studies show that snow-covered soils in subalpine forest ecosystems may support high levels of biological activity and significant soil respiration. Most winter soil respiration has been attributed to soil microbial activity, but very little work has been conducted to quantify plant root activity during this time period. The lack of such data may reflect common assumptions about over-winter plant dormancy, leading to the expectation that plant roots are inactive during the winter. In this study, we quantify autotrophic (roots and root-associated microbes) and heterotrophic (free-living microbes and soil fauna) respiration, across four (2008-2011) winter seasons in a subalpine forest in Wyoming. We implement a novel hierarchical Bayesian (HB) model that combines a 13C-CO2 stable isotope mixing model with a process-based model of soil heterotrophic and autotrophic temperature responses to facilitate partitioning total respiration between these sources. In particular, the HB approach simultaneously integrates field data on snowpack CO2 concentration and isotope gradients, snowpack and soil physical characteristics (i.e., temperature, moisture, density), root and microbial biomass, soil carbon, and data obtained from laboratory incubations of roots and soils. The process model components include temperature constraints on root and microbial activity, a Michaelis-Menten-type model for microbial respiration in response to substrate limitation, and a diffusion driven model of CO2 transport through the snow. Averaging across years, soil respiration increased from 0.35 μmol CO2 m-2 s-1 in January to 0.6 μmol CO2 m-2 s-1 in May while snow depth increased and soil temperature remained stable over the same period. The increase in respiration appeared to be driven by a two- to four-fold increase in microbial biomass carbon as winter progressed. Carbon limitation of microbial activity during the winter appears to be negligible, and we suggest that high carbon use

  13. Hierarchical Bayesian spatial models for predicting multiple forest variables using waveform LiDAR, hyperspectral imagery, and large inventory datasets

    USGS Publications Warehouse

    Finley, Andrew O.; Banerjee, Sudipto; Cook, Bruce D.; Bradford, John B.

    2013-01-01

    In this paper we detail a multivariate spatial regression model that couples LiDAR, hyperspectral and forest inventory data to predict forest outcome variables at a high spatial resolution. The proposed model is used to analyze forest inventory data collected on the US Forest Service Penobscot Experimental Forest (PEF), ME, USA. In addition to helping meet the regression model's assumptions, results from the PEF analysis suggest that the addition of multivariate spatial random effects improves model fit and predictive ability, compared with two commonly applied modeling approaches. This improvement results from explicitly modeling the covariation among forest outcome variables and spatial dependence among observations through the random effects. Direct application of such multivariate models to even moderately large datasets is often computationally infeasible because of cubic order matrix algorithms involved in estimation. We apply a spatial dimension reduction technique to help overcome this computational hurdle without sacrificing richness in modeling.

  14. A hierarchical Bayesian framework for force field selection in molecular dynamics simulations.

    PubMed

    Wu, S; Angelikopoulos, P; Papadimitriou, C; Moser, R; Koumoutsakos, P

    2016-02-13

    We present a hierarchical Bayesian framework for the selection of force fields in molecular dynamics (MD) simulations. The framework associates the variability of the optimal parameters of the MD potentials under different environmental conditions with the corresponding variability in experimental data. The high computational cost associated with the hierarchical Bayesian framework is reduced by orders of magnitude through a parallelized Transitional Markov Chain Monte Carlo method combined with the Laplace Asymptotic Approximation. The suitability of the hierarchical approach is demonstrated by performing MD simulations with prescribed parameters to obtain data for transport coefficients under different conditions, which are then used to infer and evaluate the parameters of the MD model. We demonstrate the selection of MD models based on experimental data and verify that the hierarchical model can accurately quantify the uncertainty across experiments; improve the posterior probability density function estimation of the parameters, thus, improve predictions on future experiments; identify the most plausible force field to describe the underlying structure of a given dataset. The framework and associated software are applicable to a wide range of nanoscale simulations associated with experimental data with a hierarchical structure. PMID:26712642

  15. Flexible Bayesian Human Fecundity Models

    PubMed Central

    Kim, Sungduk; Sundaram, Rajeshwari; Buck Louis, Germaine M.; Pyper, Cecilia

    2016-01-01

    Human fecundity is an issue of considerable interest for both epidemiological and clinical audiences, and is dependent upon a couple’s biologic capacity for reproduction coupled with behaviors that place a couple at risk for pregnancy. Bayesian hierarchical models have been proposed to better model the conception probabilities by accounting for the acts of intercourse around the day of ovulation, i.e., during the fertile window. These models can be viewed in the framework of a generalized nonlinear model with an exponential link. However, a fixed choice of link function may not always provide the best fit, leading to potentially biased estimates for probability of conception. Motivated by this, we propose a general class of models for fecundity by relaxing the choice of the link function under the generalized nonlinear model framework. We use a sample from the Oxford Conception Study (OCS) to illustrate the utility and fit of this general class of models for estimating human conception. Our findings reinforce the need for attention to be paid to the choice of link function in modeling conception, as it may bias the estimation of conception probabilities. Various properties of the proposed models are examined and a Markov chain Monte Carlo sampling algorithm was developed for implementing the Bayesian computations. The deviance information criterion measure and logarithm of pseudo marginal likelihood are used for guiding the choice of links. The supplemental material section contains technical details of the proof of the theorem stated in the paper, and contains further simulation results and analysis.

  16. Constraint of soil moisture on CO2 efflux from tundra lichen, moss, and tussock in Council, Alaska using a hierarchical Bayesian model

    NASA Astrophysics Data System (ADS)

    Kim, Y.; Nishina, K.; Chae, N.; Park, S.; Yoon, Y.; Lee, B.

    2014-04-01

    The tundra ecosystem is quite vulnerable to drastic climate change in the Arctic, and the quantification of carbon dynamics is of significant importance in response to thawing permafrost, changes in the snow-covered period and snow and shrub community extent, and the decline of sea ice in the Arctic. Here, CO2 efflux measurements using a manual chamber system within a 40 m × 40 m (5 m interval; 81 total points) plot were conducted in dominant tundra vegetation on the Seward Peninsula of Alaska, during the growing seasons of 2011 and 2012, for the assessment of the driving parameters of CO2 efflux. We applied a hierarchical Bayesian (HB) model - which is a function of soil temperature, soil moisture, vegetation type and thaw depth - to quantify the effect of environmental parameters on CO2 efflux, and to estimate growing season CO2 emission. Our results showed that average CO2 efflux in 2011 is 1.4-fold higher than in 2012, resulting from the distinct difference in soil moisture between the two years. Tussock-dominated CO2 efflux is 1.4 to 2.3 times higher than those measured in lichen and moss communities, reflecting tussock as a significant CO2 source in the Arctic, with wide area distribution on a circumpolar scale. CO2 efflux followed soil temperature nearly exponentially from both the observed data and the posterior medians of the HB model. This reveals soil temperature as the most important parameter in regulating CO2 efflux, rather than soil moisture and thaw depth. Obvious changes in soil moisture during the growing seasons of 2011 and 2012 resulted in an explicit difference in CO2 efflux - 742 and 539 g CO2 m-2 period-1 in 2011 and 2012, respectively, suggesting that the 2012 CO2 emission rate was constrained by 27% (95% credible interval: 17-36%) compared to 2011, due to higher soil moisture from severe rain. Estimated growing season CO2 emission rate ranged from 0.86 Mg CO2 period-1 in 2012 to 1.2 Mg CO2 period-1 in 2011 within a 40 m × 40 m plot

  17. Constraint of soil moisture on CO2 efflux from tundra lichen, moss, and tussock in Council, Alaska, using a hierarchical Bayesian model

    NASA Astrophysics Data System (ADS)

    Kim, Y.; Nishina, K.; Chae, N.; Park, S. J.; Yoon, Y. J.; Lee, B. Y.

    2014-10-01

    The tundra ecosystem is quite vulnerable to drastic climate change in the Arctic, and the quantification of carbon dynamics is of significant importance regarding thawing permafrost, changes to the snow-covered period and snow and shrub community extent, and the decline of sea ice in the Arctic. Here, CO2 efflux measurements using a manual chamber system within a 40 m × 40 m (5 m interval; 81 total points) plot were conducted within dominant tundra vegetation on the Seward Peninsula of Alaska, during the growing seasons of 2011 and 2012, for the assessment of driving parameters of CO2 efflux. We applied a hierarchical Bayesian (HB) model - a function of soil temperature, soil moisture, vegetation type, and thaw depth - to quantify the effects of environmental factors on CO2 efflux and to estimate growing season CO2 emissions. Our results showed that average CO2 efflux in 2011 was 1.4 times higher than in 2012, resulting from the distinct difference in soil moisture between the 2 years. Tussock-dominated CO2 efflux is 1.4 to 2.3 times higher than those measured in lichen and moss communities, revealing tussock as a significant CO2 source in the Arctic, with a wide area distribution on the circumpolar scale. CO2 efflux followed soil temperature nearly exponentially from both the observed data and the posterior medians of the HB model. This reveals that soil temperature regulates the seasonal variation of CO2 efflux and that soil moisture contributes to the interannual variation of CO2 efflux for the two growing seasons in question. Obvious changes in soil moisture during the growing seasons of 2011 and 2012 resulted in an explicit difference between CO2 effluxes - 742 and 539 g CO2 m-2 period-1 for 2011 and 2012, respectively, suggesting the 2012 CO2 emission rate was reduced to 27% (95% credible interval: 17-36%) of the 2011 emission, due to higher soil moisture from severe rain. The estimated growing season CO2 emission rate ranged from 0.86 Mg CO2 in 2012 to 1

  18. A Bayesian Alternative to Mutual Information for the Hierarchical Clustering of Dependent Random Variables.

    PubMed

    Marrelec, Guillaume; Messé, Arnaud; Bellec, Pierre

    2015-01-01

    The use of mutual information as a similarity measure in agglomerative hierarchical clustering (AHC) raises an important issue: some correction needs to be applied for the dimensionality of variables. In this work, we formulate the decision of merging dependent multivariate normal variables in an AHC procedure as a Bayesian model comparison. We found that the Bayesian formulation naturally shrinks the empirical covariance matrix towards a matrix set a priori (e.g., the identity), provides an automated stopping rule, and corrects for dimensionality using a term that scales up the measure as a function of the dimensionality of the variables. Also, the resulting log Bayes factor is asymptotically proportional to the plug-in estimate of mutual information, with an additive correction for dimensionality in agreement with the Bayesian information criterion. We investigated the behavior of these Bayesian alternatives (in exact and asymptotic forms) to mutual information on simulated and real data. An encouraging result was first derived on simulations: the hierarchical clustering based on the log Bayes factor outperformed off-the-shelf clustering techniques as well as raw and normalized mutual information in terms of classification accuracy. On a toy example, we found that the Bayesian approaches led to results that were similar to those of mutual information clustering techniques, with the advantage of an automated thresholding. On real functional magnetic resonance imaging (fMRI) datasets measuring brain activity, it identified clusters consistent with the established outcome of standard procedures. On this application, normalized mutual information had a highly atypical behavior, in the sense that it systematically favored very large clusters. These initial experiments suggest that the proposed Bayesian alternatives to mutual information are a useful new tool for hierarchical clustering. PMID:26406245

  19. A Bayesian Alternative to Mutual Information for the Hierarchical Clustering of Dependent Random Variables

    PubMed Central

    Marrelec, Guillaume; Messé, Arnaud; Bellec, Pierre

    2015-01-01

    The use of mutual information as a similarity measure in agglomerative hierarchical clustering (AHC) raises an important issue: some correction needs to be applied for the dimensionality of variables. In this work, we formulate the decision of merging dependent multivariate normal variables in an AHC procedure as a Bayesian model comparison. We found that the Bayesian formulation naturally shrinks the empirical covariance matrix towards a matrix set a priori (e.g., the identity), provides an automated stopping rule, and corrects for dimensionality using a term that scales up the measure as a function of the dimensionality of the variables. Also, the resulting log Bayes factor is asymptotically proportional to the plug-in estimate of mutual information, with an additive correction for dimensionality in agreement with the Bayesian information criterion. We investigated the behavior of these Bayesian alternatives (in exact and asymptotic forms) to mutual information on simulated and real data. An encouraging result was first derived on simulations: the hierarchical clustering based on the log Bayes factor outperformed off-the-shelf clustering techniques as well as raw and normalized mutual information in terms of classification accuracy. On a toy example, we found that the Bayesian approaches led to results that were similar to those of mutual information clustering techniques, with the advantage of an automated thresholding. On real functional magnetic resonance imaging (fMRI) datasets measuring brain activity, it identified clusters consistent with the established outcome of standard procedures. On this application, normalized mutual information had a highly atypical behavior, in the sense that it systematically favored very large clusters. These initial experiments suggest that the proposed Bayesian alternatives to mutual information are a useful new tool for hierarchical clustering. PMID:26406245

  20. Correlation Between Hierarchical Bayesian and Aerosol Optical Depth PM2.5 Data and Respiratory-Cardiovascular Chronic Diseases

    EPA Science Inventory

    Tools to estimate PM2.5 mass have expanded in recent years, and now include: 1) stationary monitor readings, 2) Community Multi-Scale Air Quality (CMAQ) model estimates, 3) Hierarchical Bayesian (HB) estimates from combined stationary monitor readings and CMAQ model output; and, ...

  1. Characterization of uncertainties in atmospheric trace gas inversions using hierarchical Bayesian methods

    NASA Astrophysics Data System (ADS)

    Ganesan, A. L.; Rigby, M.; Zammit-Mangion, A.; Manning, A. J.; Prinn, R. G.; Fraser, P. J.; Harth, C. M.; Kim, K.-R.; Krummel, P. B.; Li, S.; Mühle, J.; O'Doherty, S. J.; Park, S.; Salameh, P. K.; Steele, L. P.; Weiss, R. F.

    2014-04-01

    We present a hierarchical Bayesian method for atmospheric trace gas inversions. This method is used to estimate emissions of trace gases as well as "hyper-parameters" that characterize the probability density functions (PDFs) of the a priori emissions and model-measurement covariances. By exploring the space of "uncertainties in uncertainties", we show that the hierarchical method results in a more complete estimation of emissions and their uncertainties than traditional Bayesian inversions, which rely heavily on expert judgment. We present an analysis that shows the effect of including hyper-parameters, which are themselves informed by the data, and show that this method can serve to reduce the effect of errors in assumptions made about the a priori emissions and model-measurement uncertainties. We then apply this method to the estimation of sulfur hexafluoride (SF6) emissions over 2012 for the regions surrounding four Advanced Global Atmospheric Gases Experiment (AGAGE) stations. We find that improper accounting of model representation uncertainties, in particular, can lead to the derivation of emissions and associated uncertainties that are unrealistic and show that those derived using the hierarchical method are likely to be more representative of the true uncertainties in the system. We demonstrate through this SF6 case study that this method is less sensitive to outliers in the data and to subjective assumptions about a priori emissions and model-measurement uncertainties than traditional methods.

  2. Characterization of uncertainties in atmospheric trace gas inversions using hierarchical Bayesian methods

    NASA Astrophysics Data System (ADS)

    Ganesan, A. L.; Rigby, M.; Zammit-Mangion, A.; Manning, A. J.; Prinn, R. G.; Fraser, P. J.; Harth, C. M.; Kim, K.-R.; Krummel, P. B.; Li, S.; Mühle, J.; O'Doherty, S. J.; Park, S.; Salameh, P. K.; Steele, L. P.; Weiss, R. F.

    2013-12-01

    We present a hierarchical Bayesian method for atmospheric trace gas inversions. This method is used to estimate emissions of trace gases as well as "hyper-parameters" that characterize the probability density functions (PDF) of the a priori emissions and model-measurement covariances. By exploring the space of "uncertainties in uncertainties", we show that the hierarchical method results in a more complete estimation of emissions and their uncertainties than traditional Bayesian inversions, which rely heavily on expert judgement. We present an analysis that shows the effect of including hyper-parameters, which are themselves informed by the data, and show that this method can serve to reduce the effect of errors in assumptions made about the a priori emissions and model-measurement uncertainties. We then apply this method to the estimation of sulfur hexafluoride (SF6) emissions over 2012 for the regions surrounding four Advanced Global Atmospheric Gases Experiment (AGAGE) stations. We find that improper accounting of model representation uncertainties, in particular, can lead to the derivation of emissions and associated uncertainties that are unrealistic and show that those derived using the hierarchical method are likely to be more representative of the true uncertainties in the system. We demonstrate through this SF6 case study that this method is less sensitive to outliers in the data and to subjective assumptions about a priori emissions and model-measurement uncertainties, than traditional methods.

  3. Risk Assessment for Mobile Systems Through a Multilayered Hierarchical Bayesian Network.

    PubMed

    Li, Shancang; Tryfonas, Theo; Russell, Gordon; Andriotis, Panagiotis

    2016-08-01

    Mobile systems are facing a number of application vulnerabilities that can be combined together and utilized to penetrate systems with devastating impact. When assessing the overall security of a mobile system, it is important to assess the security risks posed by each mobile applications (apps), thus gaining a stronger understanding of any vulnerabilities present. This paper aims at developing a three-layer framework that assesses the potential risks which apps introduce within the Android mobile systems. A Bayesian risk graphical model is proposed to evaluate risk propagation in a layered risk architecture. By integrating static analysis, dynamic analysis, and behavior analysis in a hierarchical framework, the risks and their propagation through each layer are well modeled by the Bayesian risk graph, which can quantitatively analyze risks faced to both apps and mobile systems. The proposed hierarchical Bayesian risk graph model offers a novel way to investigate the security risks in mobile environment and enables users and administrators to evaluate the potential risks. This strategy allows to strengthen both app security as well as the security of the entire system. PMID:27076477

  4. Pitman Yor Diffusion Trees for Bayesian Hierarchical Clustering.

    PubMed

    Knowles, David A; Ghahramani, Zoubin

    2015-02-01

    In this paper we introduce the Pitman Yor Diffusion Tree (PYDT), a Bayesian non-parametric prior over tree structures which generalises the Dirichlet Diffusion Tree [30] and removes the restriction to binary branching structure. The generative process is described and shown to result in an exchangeable distribution over data points. We prove some theoretical properties of the model including showing its construction as the continuum limit of a nested Chinese restaurant process model. We then present two alternative MCMC samplers which allow us to model uncertainty over tree structures, and a computationally efficient greedy Bayesian EM search algorithm. Both algorithms use message passing on the tree structure. The utility of the model and algorithms is demonstrated on synthetic and real world data, both continuous and binary. PMID:26353241

  5. Predicting Hydrologic Response Through a Pooled Watershed Knowledge Base: A Hierarchical Bayesian Approach

    NASA Astrophysics Data System (ADS)

    Smith, T. J.; Marshall, L. A.; Sharma, A.

    2011-12-01

    Hydrologic modelers are confronted with the challenge of producing estimates of the uncertainty associated with model predictions across a wide array of watersheds, often under very limited data conditions. Statistical methods for hydrologic modeling have evolved rapidly over the recent past in response to these challenges, from improved strategies to both estimate optimal parameter values and predictive uncertainty to approaches that aim to link model parameters to watershed characteristics and allow parameters to be transferred to data-poor watersheds. However, despite the advances that have been made in the application of such statistical tools there remains significant work to be done, particularly regarding the quantification/transfer of predictive uncertainty at/to data-limited locations. Here, we present a hierarchical Bayesian modeling technique referred to as Bayes Empirical Bayes (BEB) as a means of addressing the difficulties in making reliable hydrologic predictions under uncertainty in data-limited watersheds. The BEB technique utilizes formal hierarchical Bayesian analysis (specifically the resultant posterior probability distributions for each estimated model parameter) to pool information from auxiliary watersheds to generate informed probability distributions for each parameter at a data-limited watershed of interest. The application of such a method has thus far been untested in hydrologic applications but has been used more extensively in ecological studies. This technique represents a significant departure from earlier attempts to make predictions in data-limited watersheds in both its usage of available data and its ability to simultaneously quantify predictive uncertainty directly. By utilizing the Bayesian toolkit under a hierarchical approach, information available from auxiliary watersheds can be integrated and summarized into the prediction at the site of interest.

  6. Rigorous Approach in Investigation of Seismic Structure and Source Characteristicsin Northeast Asia: Hierarchical and Trans-dimensional Bayesian Inversion

    NASA Astrophysics Data System (ADS)

    Mustac, M.; Kim, S.; Tkalcic, H.; Rhie, J.; Chen, Y.; Ford, S. R.; Sebastian, N.

    2015-12-01

    Conventional approaches to inverse problems suffer from non-linearity and non-uniqueness in estimations of seismic structures and source properties. Estimated results and associated uncertainties are often biased by applied regularizations and additional constraints, which are commonly introduced to solve such problems. Bayesian methods, however, provide statistically meaningful estimations of models and their uncertainties constrained by data information. In addition, hierarchical and trans-dimensional (trans-D) techniques are inherently implemented in the Bayesian framework to account for involved error statistics and model parameterizations, and, in turn, allow more rigorous estimations of the same. Here, we apply Bayesian methods throughout the entire inference process to estimate seismic structures and source properties in Northeast Asia including east China, the Korean peninsula, and the Japanese islands. Ambient noise analysis is first performed to obtain a base three-dimensional (3-D) heterogeneity model using continuous broadband waveforms from more than 300 stations. As for the tomography of surface wave group and phase velocities in the 5-70 s band, we adopt a hierarchical and trans-D Bayesian inversion method using Voronoi partition. The 3-D heterogeneity model is further improved by joint inversions of teleseismic receiver functions and dispersion data using a newly developed high-efficiency Bayesian technique. The obtained model is subsequently used to prepare 3-D structural Green's functions for the source characterization. A hierarchical Bayesian method for point source inversion using regional complete waveform data is applied to selected events from the region. The seismic structure and source characteristics with rigorously estimated uncertainties from the novel Bayesian methods provide enhanced monitoring and discrimination of seismic events in northeast Asia.

  7. A Rasch Hierarchical Measurement Model.

    ERIC Educational Resources Information Center

    Maier, Kimberly S.

    This paper describes a model that integrates an item response theory (IRT) Rasch model and a hierarchical linear model and presents a method of estimating model parameter values that does not rely on large-sample theory and normal approximations. The model resulting from the integration of a hierarchical linear model and the Rasch model allows one…

  8. Determining the Bayesian optimal sampling strategy in a hierarchical system.

    SciTech Connect

    Grace, Matthew D.; Ringland, James T.; Boggs, Paul T.; Pebay, Philippe Pierre

    2010-09-01

    Consider a classic hierarchy tree as a basic model of a 'system-of-systems' network, where each node represents a component system (which may itself consist of a set of sub-systems). For this general composite system, we present a technique for computing the optimal testing strategy, which is based on Bayesian decision analysis. In previous work, we developed a Bayesian approach for computing the distribution of the reliability of a system-of-systems structure that uses test data and prior information. This allows for the determination of both an estimate of the reliability and a quantification of confidence in the estimate. Improving the accuracy of the reliability estimate and increasing the corresponding confidence require the collection of additional data. However, testing all possible sub-systems may not be cost-effective, feasible, or even necessary to achieve an improvement in the reliability estimate. To address this sampling issue, we formulate a Bayesian methodology that systematically determines the optimal sampling strategy under specified constraints and costs that will maximally improve the reliability estimate of the composite system, e.g., by reducing the variance of the reliability distribution. This methodology involves calculating the 'Bayes risk of a decision rule' for each available sampling strategy, where risk quantifies the relative effect that each sampling strategy could have on the reliability estimate. A general numerical algorithm is developed and tested using an example multicomponent system. The results show that the procedure scales linearly with the number of components available for testing.

  9. A hierarchical Bayesian approach to adaptive vision testing: A case study with the contrast sensitivity function

    PubMed Central

    Gu, Hairong; Kim, Woojae; Hou, Fang; Lesmes, Luis Andres; Pitt, Mark A.; Lu, Zhong-Lin; Myung, Jay I.

    2016-01-01

    Measurement efficiency is of concern when a large number of observations are required to obtain reliable estimates for parametric models of vision. The standard entropy-based Bayesian adaptive testing procedures addressed the issue by selecting the most informative stimulus in sequential experimental trials. Noninformative, diffuse priors were commonly used in those tests. Hierarchical adaptive design optimization (HADO; Kim, Pitt, Lu, Steyvers, & Myung, 2014) further improves the efficiency of the standard Bayesian adaptive testing procedures by constructing an informative prior using data from observers who have already participated in the experiment. The present study represents an empirical validation of HADO in estimating the human contrast sensitivity function. The results show that HADO significantly improves the accuracy and precision of parameter estimates, and therefore requires many fewer observations to obtain reliable inference about contrast sensitivity, compared to the method of quick contrast sensitivity function (Lesmes, Lu, Baek, & Albright, 2010), which uses the standard Bayesian procedure. The improvement with HADO was maintained even when the prior was constructed from heterogeneous populations or a relatively small number of observers. These results of this case study support the conclusion that HADO can be used in Bayesian adaptive testing by replacing noninformative, diffuse priors with statistically justified informative priors without introducing unwanted bias. PMID:27105061

  10. Hierarchical models of animal abundance and occurrence

    USGS Publications Warehouse

    Royle, J. Andrew; Dorazio, R.M.

    2006-01-01

    Much of animal ecology is devoted to studies of abundance and occurrence of species, based on surveys of spatially referenced sample units. These surveys frequently yield sparse counts that are contaminated by imperfect detection, making direct inference about abundance or occurrence based on observational data infeasible. This article describes a flexible hierarchical modeling framework for estimation and inference about animal abundance and occurrence from survey data that are subject to imperfect detection. Within this framework, we specify models of abundance and detectability of animals at the level of the local populations defined by the sample units. Information at the level of the local population is aggregated by specifying models that describe variation in abundance and detection among sites. We describe likelihood-based and Bayesian methods for estimation and inference under the resulting hierarchical model. We provide two examples of the application of hierarchical models to animal survey data, the first based on removal counts of stream fish and the second based on avian quadrat counts. For both examples, we provide a Bayesian analysis of the models using the software WinBUGS.

  11. Assimilating irregularly spaced sparsely observed turbulent signals with hierarchical Bayesian reduced stochastic filters

    SciTech Connect

    Brown, Kristen A.; Harlim, John

    2013-02-15

    In this paper, we consider a practical filtering approach for assimilating irregularly spaced, sparsely observed turbulent signals through a hierarchical Bayesian reduced stochastic filtering framework. The proposed hierarchical Bayesian approach consists of two steps, blending a data-driven interpolation scheme and the Mean Stochastic Model (MSM) filter. We examine the potential of using the deterministic piecewise linear interpolation scheme and the ordinary kriging scheme in interpolating irregularly spaced raw data to regularly spaced processed data and the importance of dynamical constraint (through MSM) in filtering the processed data on a numerically stiff state estimation problem. In particular, we test this approach on a two-layer quasi-geostrophic model in a two-dimensional domain with a small radius of deformation to mimic ocean turbulence. Our numerical results suggest that the dynamical constraint becomes important when the observation noise variance is large. Second, we find that the filtered estimates with ordinary kriging are superior to those with linear interpolation when observation networks are not too sparse; such robust results are found from numerical simulations with many randomly simulated irregularly spaced observation networks, various observation time intervals, and observation error variances. Third, when the observation network is very sparse, we find that both the kriging and linear interpolations are comparable.

  12. Assimilating irregularly spaced sparsely observed turbulent signals with hierarchical Bayesian reduced stochastic filters

    NASA Astrophysics Data System (ADS)

    Brown, Kristen A.; Harlim, John

    2013-02-01

    In this paper, we consider a practical filtering approach for assimilating irregularly spaced, sparsely observed turbulent signals through a hierarchical Bayesian reduced stochastic filtering framework. The proposed hierarchical Bayesian approach consists of two steps, blending a data-driven interpolation scheme and the Mean Stochastic Model (MSM) filter. We examine the potential of using the deterministic piecewise linear interpolation scheme and the ordinary kriging scheme in interpolating irregularly spaced raw data to regularly spaced processed data and the importance of dynamical constraint (through MSM) in filtering the processed data on a numerically stiff state estimation problem. In particular, we test this approach on a two-layer quasi-geostrophic model in a two-dimensional domain with a small radius of deformation to mimic ocean turbulence. Our numerical results suggest that the dynamical constraint becomes important when the observation noise variance is large. Second, we find that the filtered estimates with ordinary kriging are superior to those with linear interpolation when observation networks are not too sparse; such robust results are found from numerical simulations with many randomly simulated irregularly spaced observation networks, various observation time intervals, and observation error variances. Third, when the observation network is very sparse, we find that both the kriging and linear interpolations are comparable.

  13. Receiver function deconvolution using transdimensional hierarchical Bayesian inference

    NASA Astrophysics Data System (ADS)

    Kolb, J. M.; Lekić, V.

    2014-06-01

    Teleseismic waves can convert from shear to compressional (Sp) or compressional to shear (Ps) across impedance contrasts in the subsurface. Deconvolving the parent waveforms (P for Ps or S for Sp) from the daughter waveforms (S for Ps or P for Sp) generates receiver functions which can be used to analyse velocity structure beneath the receiver. Though a variety of deconvolution techniques have been developed, they are all adversely affected by background and signal-generated noise. In order to take into account the unknown noise characteristics, we propose a method based on transdimensional hierarchical Bayesian inference in which both the noise magnitude and noise spectral character are parameters in calculating the likelihood probability distribution. We use a reversible-jump implementation of a Markov chain Monte Carlo algorithm to find an ensemble of receiver functions whose relative fits to the data have been calculated while simultaneously inferring the values of the noise parameters. Our noise parametrization is determined from pre-event noise so that it approximates observed noise characteristics. We test the algorithm on synthetic waveforms contaminated with noise generated from a covariance matrix obtained from observed noise. We show that the method retrieves easily interpretable receiver functions even in the presence of high noise levels. We also show that we can obtain useful estimates of noise amplitude and frequency content. Analysis of the ensemble solutions produced by our method can be used to quantify the uncertainties associated with individual receiver functions as well as with individual features within them, providing an objective way for deciding which features warrant geological interpretation. This method should make possible more robust inferences on subsurface structure using receiver function analysis, especially in areas of poor data coverage or under noisy station conditions.

  14. A hierarchical Bayesian-MAP approach to inverse problems in imaging

    NASA Astrophysics Data System (ADS)

    Raj, Raghu G.

    2016-07-01

    We present a novel approach to inverse problems in imaging based on a hierarchical Bayesian-MAP (HB-MAP) formulation. In this paper we specifically focus on the difficult and basic inverse problem of multi-sensor (tomographic) imaging wherein the source object of interest is viewed from multiple directions by independent sensors. Given the measurements recorded by these sensors, the problem is to reconstruct the image (of the object) with a high degree of fidelity. We employ a probabilistic graphical modeling extension of the compound Gaussian distribution as a global image prior into a hierarchical Bayesian inference procedure. Since the prior employed by our HB-MAP algorithm is general enough to subsume a wide class of priors including those typically employed in compressive sensing (CS) algorithms, HB-MAP algorithm offers a vehicle to extend the capabilities of current CS algorithms to include truly global priors. After rigorously deriving the regression algorithm for solving our inverse problem from first principles, we demonstrate the performance of the HB-MAP algorithm on Monte Carlo trials and on real empirical data (natural scenes). In all cases we find that our algorithm outperforms previous approaches in the literature including filtered back-projection and a variety of state-of-the-art CS algorithms. We conclude with directions of future research emanating from this work.

  15. A Hierarchical Bayesian Approach to Ecological Count Data: A Flexible Tool for Ecologists

    PubMed Central

    Fordyce, James A.; Gompert, Zachariah; Forister, Matthew L.; Nice, Chris C.

    2011-01-01

    Many ecological studies use the analysis of count data to arrive at biologically meaningful inferences. Here, we introduce a hierarchical Bayesian approach to count data. This approach has the advantage over traditional approaches in that it directly estimates the parameters of interest at both the individual-level and population-level, appropriately models uncertainty, and allows for comparisons among models, including those that exceed the complexity of many traditional approaches, such as ANOVA or non-parametric analogs. As an example, we apply this method to oviposition preference data for butterflies in the genus Lycaeides. Using this method, we estimate the parameters that describe preference for each population, compare the preference hierarchies among populations, and explore various models that group populations that share the same preference hierarchy. PMID:22132077

  16. A Hierarchical Bayesian Approach for Learning Sparse Spatio-Temporal Decomposition of Multichannel EEG

    PubMed Central

    Wu, Wei; Chen, Zhe; Gao, Shangkai; Brown, Emery N.

    2011-01-01

    Multichannel electroencephalography (EEG) offers a non-invasive tool to explore spatio-temporal dynamics of brain activity. With EEG recordings consisting of multiple trials, traditional signal processing approaches that ignore inter-trial variability in the data may fail to accurately estimate the underlying spatio-temporal brain patterns. Moreover, precise characterization of such inter-trial variability per se can be of high scientific value in establishing the relationship between brain activity and behavior. In this paper, a statistical modeling framework is introduced for learning spatiotemporal decomposition of multiple-trial EEG data recorded under two contrasting experimental conditions. By modeling the variance of source signals as random variables varying across trials, the proposed two-stage hierarchical Bayesian model is able to capture inter-trial amplitude variability in the data in a sparse way where a parsimonious representation of the data can be obtained. A variational Bayesian (VB) algorithm is developed for statistical inference of the hierarchical model. The efficacy of the proposed modeling framework is validated with the analysis of both synthetic and real EEG data. In the simulation study we show that even at low signal-to-noise ratios our approach is able to recover with high precision the underlying spatiotemporal patterns and the evolution of source amplitude across trials; on two brain-computer interface (BCI) data sets we show that our VB algorithm can extract physiologically meaningful spatio-temporal patterns and make more accurate predictions than other two widely used algorithms: the common spatial patterns (CSP) algorithm and the Infomax algorithm for independent component analysis (ICA). The results demonstrate that our statistical modeling framework can serve as a powerful tool for extracting brain patterns, characterizing trial-to-trial brain dynamics, and decoding brain states by exploiting useful structures in the data. PMID

  17. A hierarchical Bayesian approach for reconstructing the Initial Mass Function of Single Stellar Populations

    NASA Astrophysics Data System (ADS)

    Dries, M.; Trager, S. C.; Koopmans, L. V. E.

    2016-08-01

    Recent studies based on the integrated light of distant galaxies suggest that the initial mass function (IMF) might not be universal. Variations of the IMF with galaxy type and/or formation time may have important consequences for our understanding of galaxy evolution. We have developed a new stellar population synthesis (SPS) code specifically designed to reconstruct the IMF. We implement a novel approach combining regularization with hierarchical Bayesian inference. Within this approach we use a parametrized IMF prior to regulate a direct inference of the IMF. This direct inference gives more freedom to the IMF and allows the model to deviate from parametrized models when demanded by the data. We use Markov Chain Monte Carlo sampling techniques to reconstruct the best parameters for the IMF prior, the age, and the metallicity of a single stellar population. We present our code and apply our model to a number of mock single stellar populations with different ages, metallicities, and IMFs. When systematic uncertainties are not significant, we are able to reconstruct the input parameters that were used to create the mock populations. Our results show that if systematic uncertainties do play a role, this may introduce a bias on the results. Therefore, it is important to objectively compare different ingredients of SPS models. Through its Bayesian framework, our model is well-suited for this.

  18. Delaware River Streamflow Reconstruction using Tree Rings: Exploration of Hierarchical Bayesian Regression

    NASA Astrophysics Data System (ADS)

    Devineni, N.; Lall, U.; Cook, E.; Pederson, N.

    2011-12-01

    We present the application of a linear model in a Hierarchical Bayesian Regression (HBR) framework for reconstructing the summer seasonal averaged streamflow at five stations in the Delaware River Basin using eight newly developed regional tree ring chronologies. This technique directly provides estimates of the posterior probability distribution of each reconstructed streamflow value, considering model parameter uncertainty. The methodology also allows us to shrink the model parameters towards a common mean to incorporate the predictive ability of each tree chronology on multiple stations. We present the results from HBR analysis along with the results from traditional Point by Point Regression (PPR) analysis to demonstrate the benefits of developing the reconstructions under a Bayesian modeling framework. Further, we also present the comparative results of the model validation using various performance evaluation metrics such as reduction in error (RE) and coefficient of efficiency (CE). The reconstructed streamflow at various stations can be utilized to examine the frequency and recurrence attributes of extreme droughts in the region and their potential connections to known low frequency climate modes.

  19. Bayesian Model Selection for Group Studies

    PubMed Central

    Stephan, Klaas Enno; Penny, Will D.; Daunizeau, Jean; Moran, Rosalyn J.; Friston, Karl J.

    2009-01-01

    Bayesian model selection (BMS) is a powerful method for determining the most likely among a set of competing hypotheses about the mechanisms that generated observed data. BMS has recently found widespread application in neuroimaging, particularly in the context of dynamic causal modelling (DCM). However, so far, combining BMS results from several subjects has relied on simple (fixed effects) metrics, e.g. the group Bayes factor (GBF), that do not account for group heterogeneity or outliers. In this paper, we compare the GBF with two random effects methods for BMS at the between-subject or group level. These methods provide inference on model-space using a classical and Bayesian perspective respectively. First, a classical (frequentist) approach uses the log model evidence as a subject-specific summary statistic. This enables one to use analysis of variance to test for differences in log-evidences over models, relative to inter-subject differences. We then consider the same problem in Bayesian terms and describe a novel hierarchical model, which is optimised to furnish a probability density on the models themselves. This new variational Bayes method rests on treating the model as a random variable and estimating the parameters of a Dirichlet distribution which describes the probabilities for all models considered. These probabilities then define a multinomial distribution over model space, allowing one to compute how likely it is that a specific model generated the data of a randomly chosen subject as well as the exceedance probability of one model being more likely than any other model. Using empirical and synthetic data, we show that optimising a conditional density of the model probabilities, given the log-evidences for each model over subjects, is more informative and appropriate than both the GBF and frequentist tests of the log-evidences. In particular, we found that the hierarchical Bayesian approach is considerably more robust than either of the other

  20. Exploring a Bayesian hierarchical approach for developing safety performance functions for a mountainous freeway.

    PubMed

    Ahmed, Mohamed; Huang, Helai; Abdel-Aty, Mohamed; Guevara, Bernardo

    2011-07-01

    While rural freeways generally have lower crash rates, interactions between driver behavior, traffic and geometric characteristics, and adverse weather conditions may increase the crash risk along some freeway sections. This paper examines the safety effects of roadway geometrics on crash occurrence along a freeway section that features mountainous terrain and adverse weather. Starting from preliminary exploration using Poisson models, Bayesian hierarchical models with spatial and random effects were developed to efficiently model the crash frequencies on road segments on the 20-mile freeway section of study. Crash data for 6 years (2000-2005), roadway geometry, traffic characteristics and weather information in addition to the effect of steep slopes and adverse weather of snow and dry seasons, were used in the investigation. Estimation of the model coefficients indicates that roadway geometry is significantly associated with crash risk; segments with steep downgrades were found to drastically increase the crash risk. Moreover, this crash risk could be significantly increased during snow season compared to dry season as a confounding effect between grades and pavement condition. Moreover, sites with higher degree of curvature, wider medians and an increase of the number of lanes appear to be associated with lower crash rate. Finally, a Bayesian ranking technique was implemented to rank the hazard levels of the roadway segments; the results confirmed that segments with steep downgrades are more crash prone along the study section. PMID:21545893

  1. TYPE Ia SUPERNOVA LIGHT-CURVE INFERENCE: HIERARCHICAL BAYESIAN ANALYSIS IN THE NEAR-INFRARED

    SciTech Connect

    Mandel, Kaisey S.; Friedman, Andrew S.; Kirshner, Robert P.; Wood-Vasey, W. Michael

    2009-10-10

    We present a comprehensive statistical analysis of the properties of Type Ia supernova (SN Ia) light curves in the near-infrared using recent data from Peters Automated InfraRed Imaging TELescope and the literature. We construct a hierarchical Bayesian framework, incorporating several uncertainties including photometric error, peculiar velocities, dust extinction, and intrinsic variations, for principled and coherent statistical inference. SN Ia light-curve inferences are drawn from the global posterior probability of parameters describing both individual supernovae and the population conditioned on the entire SN Ia NIR data set. The logical structure of the hierarchical model is represented by a directed acyclic graph. Fully Bayesian analysis of the model and data is enabled by an efficient Markov Chain Monte Carlo algorithm exploiting the conditional probabilistic structure using Gibbs sampling. We apply this framework to the JHK{sub s} SN Ia light-curve data. A new light-curve model captures the observed J-band light-curve shape variations. The marginal intrinsic variances in peak absolute magnitudes are sigma(M{sub J}) = 0.17 +- 0.03, sigma(M{sub H}) = 0.11 +- 0.03, and sigma(M{sub Ks}) = 0.19 +- 0.04. We describe the first quantitative evidence for correlations between the NIR absolute magnitudes and J-band light-curve shapes, and demonstrate their utility for distance estimation. The average residual in the Hubble diagram for the training set SNe at cz > 2000kms{sup -1} is 0.10 mag. The new application of bootstrap cross-validation to SN Ia light-curve inference tests the sensitivity of the statistical model fit to the finite sample and estimates the prediction error at 0.15 mag. These results demonstrate that SN Ia NIR light curves are as effective as corrected optical light curves, and, because they are less vulnerable to dust absorption, they have great potential as precise and accurate cosmological distance indicators.

  2. Hierarchical Bayesian method for mapping biogeochemical hot spots using induced polarization imaging

    NASA Astrophysics Data System (ADS)

    Wainwright, Haruko M.; Flores Orozco, Adrian; Bücker, Matthias; Dafflon, Baptiste; Chen, Jinsong; Hubbard, Susan S.; Williams, Kenneth H.

    2016-01-01

    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 study, 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 and 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.

  3. Hierarchical Bayesian inference of galaxy redshift distributions from photometric surveys

    NASA Astrophysics Data System (ADS)

    Leistedt, Boris; Mortlock, Daniel J.; Peiris, Hiranya V.

    2016-08-01

    Accurately characterizing the redshift distributions of galaxies is essential for analysing deep photometric surveys and testing cosmological models. We present a technique to simultaneously infer redshift distributions and individual redshifts from photometric galaxy catalogues. Our model constructs a piecewise constant representation (effectively a histogram) of the distribution of galaxy types and redshifts, the parameters of which are efficiently inferred from noisy photometric flux measurements. This approach can be seen as a generalization of template-fitting photometric redshift methods and relies on a library of spectral templates to relate the photometric fluxes of individual galaxies to their redshifts. We illustrate this technique on simulated galaxy survey data, and demonstrate that it delivers correct posterior distributions on the underlying type and redshift distributions, as well as on the individual types and redshifts of galaxies. We show that even with uninformative priors, large photometric errors and parameter degeneracies, the redshift and type distributions can be recovered robustly thanks to the hierarchical nature of the model, which is not possible with common photometric redshift estimation techniques. As a result, redshift uncertainties can be fully propagated in cosmological analyses for the first time, fulfilling an essential requirement for the current and future generations of surveys.

  4. A Transdimensional, Hierarchical Bayesian Inversion Framework for Estimating Regional Trace Gas Emissions

    NASA Astrophysics Data System (ADS)

    Lunt, M. F.; Rigby, M. L.; Ganesan, A.; Grant, A.; Stavert, A.; Young, D.; O'Doherty, S.

    2015-12-01

    Bayesian inverse modelling is very widely used for estimating trace gas flux fields using atmospheric observations. For reasons of computational expense, and to avoid under-determination, these high-dimensional fields are usually partitioned into a set of basis functions, or are estimated subject to some choice of correlation between grid cells. This partitioning or smoothing of the space is typically based on some set of subjective decisions made by the investigator. However, both the derived flux estimates, and their uncertainties, can be strongly dependent on these choices. Furthermore, traditional approaches do not allow for the uncertainty surrounding these choices to be propagated through to the derived fluxes. We outline a method whereby the number of basis functions, and therefore resolution at which fluxes are estimated, are determined using the data. A priori, we consider the number of flux basis functions and their configuration in the inversion domain to be unknown. In such a framework, the dimensionality of the inverse problem can change, and is therefore referred to as a "transdimensional" inversion. Reversible-jump Markov Chain-Monte Carlo tools to perform such dimension changing were first devised over two decades ago, but their uptake within atmospheric science has been limited. We present a novel application of this method for regional emissions estimation, also incorporating hierarchical Bayesian methods for the quantification of model-related and prior uncertainties. We show that, since the arrangement and geometry of the flux basis functions is no longer fixed, a relatively sparse, and therefore computationally efficient, partitioning can achieve a high effective spatial resolution of fluxes, where permitted by the data. We present an example of this new system for estimating fluxes in the UK, using data from the Deriving Emissions Related to Climate Change (DECC) network. This transdimensional, hierarchical approach is of particular relevance

  5. Application of Bayesian inference to the study of hierarchical organization in self-organized complex adaptive systems

    NASA Astrophysics Data System (ADS)

    Knuth, K. H.

    2001-05-01

    We consider the application of Bayesian inference to the study of self-organized structures in complex adaptive systems. In particular, we examine the distribution of elements, agents, or processes in systems dominated by hierarchical structure. We demonstrate that results obtained by Caianiello [1] on Hierarchical Modular Systems (HMS) can be found by applying Jaynes' Principle of Group Invariance [2] to a few key assumptions about our knowledge of hierarchical organization. Subsequent application of the Principle of Maximum Entropy allows inferences to be made about specific systems. The utility of the Bayesian method is considered by examining both successes and failures of the hierarchical model. We discuss how Caianiello's original statements suffer from the Mind Projection Fallacy [3] and we restate his assumptions thus widening the applicability of the HMS model. The relationship between inference and statistical physics, described by Jaynes [4], is reiterated with the expectation that this realization will aid the field of complex systems research by moving away from often inappropriate direct application of statistical mechanics to a more encompassing inferential methodology.

  6. Two waves of diversification in mammals and reptiles of Baja California revealed by hierarchical Bayesian analysis.

    PubMed

    Leaché, Adam D; Crews, Sarah C; Hickerson, Michael J

    2007-12-22

    Many species inhabiting the Peninsular Desert of Baja California demonstrate a phylogeographic break at the mid-peninsula, and previous researchers have attributed this shared pattern to a single vicariant event, a mid-peninsular seaway. However, previous studies have not explicitly considered the inherent stochasticity associated with the gene-tree coalescence for species preceding the time of the putative mid-peninsular divergence. We use a Bayesian analysis of a hierarchical model to test for simultaneous vicariance across co-distributed sister lineages sharing a genealogical break at the mid-peninsula. This Bayesian method is advantageous over traditional phylogenetic interpretations of biogeography because it considers the genetic variance associated with the coalescent and mutational processes, as well as the among-lineage demographic differences that affect gene-tree coalescent patterns. Mitochondrial DNA data from six small mammals and six squamate reptiles do not support the perception of a shared vicariant history among lineages exhibiting a north-south divergence at the mid-peninsula, and instead support two events differentially structuring genetic diversity in this region. PMID:17698443

  7. A Hierarchical Bayesian Procedure for Two-Mode Cluster Analysis

    ERIC Educational Resources Information Center

    DeSarbo, Wayne S.; Fong, Duncan K. H.; Liechty, John; Saxton, M. Kim

    2004-01-01

    This manuscript introduces a new Bayesian finite mixture methodology for the joint clustering of row and column stimuli/objects associated with two-mode asymmetric proximity, dominance, or profile data. That is, common clusters are derived which partition both the row and column stimuli/objects simultaneously into the same derived set of clusters.…

  8. Bayesian Model Averaging for Propensity Score Analysis

    ERIC Educational Resources Information Center

    Kaplan, David; Chen, Jianshen

    2013-01-01

    The purpose of this study is to explore Bayesian model averaging in the propensity score context. Previous research on Bayesian propensity score analysis does not take into account model uncertainty. In this regard, an internally consistent Bayesian framework for model building and estimation must also account for model uncertainty. The…

  9. Bayesian stable isotope mixing models

    EPA Science Inventory

    In this paper we review recent advances in Stable Isotope Mixing Models (SIMMs) and place them into an over-arching Bayesian statistical framework which allows for several useful extensions. SIMMs are used to quantify the proportional contributions of various sources to a mixtur...

  10. Bayesian model reduction and empirical Bayes for group (DCM) studies.

    PubMed

    Friston, Karl J; Litvak, Vladimir; Oswal, Ashwini; Razi, Adeel; Stephan, Klaas E; van Wijk, Bernadette C M; Ziegler, Gabriel; Zeidman, Peter

    2016-03-01

    This technical note describes some Bayesian procedures for the analysis of group studies that use nonlinear models at the first (within-subject) level - e.g., dynamic causal models - and linear models at subsequent (between-subject) levels. Its focus is on using Bayesian model reduction to finesse the inversion of multiple models of a single dataset or a single (hierarchical or empirical Bayes) model of multiple datasets. These applications of Bayesian model reduction allow one to consider parametric random effects and make inferences about group effects very efficiently (in a few seconds). We provide the relatively straightforward theoretical background to these procedures and illustrate their application using a worked example. This example uses a simulated mismatch negativity study of schizophrenia. We illustrate the robustness of Bayesian model reduction to violations of the (commonly used) Laplace assumption in dynamic causal modelling and show how its recursive application can facilitate both classical and Bayesian inference about group differences. Finally, we consider the application of these empirical Bayesian procedures to classification and prediction. PMID:26569570

  11. Bayesian model reduction and empirical Bayes for group (DCM) studies

    PubMed Central

    Friston, Karl J.; Litvak, Vladimir; Oswal, Ashwini; Razi, Adeel; Stephan, Klaas E.; van Wijk, Bernadette C.M.; Ziegler, Gabriel; Zeidman, Peter

    2016-01-01

    This technical note describes some Bayesian procedures for the analysis of group studies that use nonlinear models at the first (within-subject) level – e.g., dynamic causal models – and linear models at subsequent (between-subject) levels. Its focus is on using Bayesian model reduction to finesse the inversion of multiple models of a single dataset or a single (hierarchical or empirical Bayes) model of multiple datasets. These applications of Bayesian model reduction allow one to consider parametric random effects and make inferences about group effects very efficiently (in a few seconds). We provide the relatively straightforward theoretical background to these procedures and illustrate their application using a worked example. This example uses a simulated mismatch negativity study of schizophrenia. We illustrate the robustness of Bayesian model reduction to violations of the (commonly used) Laplace assumption in dynamic causal modelling and show how its recursive application can facilitate both classical and Bayesian inference about group differences. Finally, we consider the application of these empirical Bayesian procedures to classification and prediction. PMID:26569570

  12. 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.

  13. Bayesian methods for estimating the reliability in complex hierarchical networks (interim report).

    SciTech Connect

    Marzouk, Youssef M.; Zurn, Rena M.; Boggs, Paul T.; Diegert, Kathleen V.; Red-Horse, John Robert; Pebay, Philippe Pierre

    2007-05-01

    Current work on the Integrated Stockpile Evaluation (ISE) project is evidence of Sandia's commitment to maintaining the integrity of the nuclear weapons stockpile. In this report, we undertake a key element in that process: development of an analytical framework for determining the reliability of the stockpile in a realistic environment of time-variance, inherent uncertainty, and sparse available information. This framework is probabilistic in nature and is founded on a novel combination of classical and computational Bayesian analysis, Bayesian networks, and polynomial chaos expansions. We note that, while the focus of the effort is stockpile-related, it is applicable to any reasonably-structured hierarchical system, including systems with feedback.

  14. Bayesian kinematic earthquake source models

    NASA Astrophysics Data System (ADS)

    Minson, S. E.; Simons, M.; Beck, J. L.; Genrich, J. F.; Galetzka, J. E.; Chowdhury, F.; Owen, S. E.; Webb, F.; Comte, D.; Glass, B.; Leiva, C.; Ortega, F. H.

    2009-12-01

    Most coseismic, postseismic, and interseismic slip models are based on highly regularized optimizations which yield one solution which satisfies the data given a particular set of regularizing constraints. This regularization hampers our ability to answer basic questions such as whether seismic and aseismic slip overlap or instead rupture separate portions of the fault zone. We present a Bayesian methodology for generating kinematic earthquake source models with a focus on large subduction zone earthquakes. Unlike classical optimization approaches, Bayesian techniques sample the ensemble of all acceptable models presented as an a posteriori probability density function (PDF), and thus we can explore the entire solution space to determine, for example, which model parameters are well determined and which are not, or what is the likelihood that two slip distributions overlap in space. Bayesian sampling also has the advantage that all a priori knowledge of the source process can be used to mold the a posteriori ensemble of models. Although very powerful, Bayesian methods have up to now been of limited use in geophysical modeling because they are only computationally feasible for problems with a small number of free parameters due to what is called the "curse of dimensionality." However, our methodology can successfully sample solution spaces of many hundreds of parameters, which is sufficient to produce finite fault kinematic earthquake models. Our algorithm is a modification of the tempered Markov chain Monte Carlo (tempered MCMC or TMCMC) method. In our algorithm, we sample a "tempered" a posteriori PDF using many MCMC simulations running in parallel and evolutionary computation in which models which fit the data poorly are preferentially eliminated in favor of models which better predict the data. We present results for both synthetic test problems as well as for the 2007 Mw 7.8 Tocopilla, Chile earthquake, the latter of which is constrained by InSAR, local high

  15. Bridging Inter- and Intraspecific Trait Evolution with a Hierarchical Bayesian Approach.

    PubMed

    Kostikova, Anna; Silvestro, Daniele; Pearman, Peter B; Salamin, Nicolas

    2016-05-01

    The evolution of organisms is crucially dependent on the evolution of intraspecific variation. Its interactions with selective agents in the biotic and abiotic environments underlie many processes, such as intraspecific competition, resource partitioning and, eventually, species formation. Nevertheless, comparative models of trait evolution neither allow explicit testing of hypotheses related to the evolution of intraspecific variation nor do they simultaneously estimate rates of trait evolution by accounting for both trait mean and variance. Here, we present a model of phenotypic trait evolution using a hierarchical Bayesian approach that simultaneously incorporates interspecific and intraspecific variation. We assume that species-specific trait means evolve under a simple Brownian motion process, whereas species-specific trait variances are modeled with Brownian or Ornstein-Uhlenbeck processes. After evaluating the power of the method through simulations, we examine whether life-history traits impact evolution of intraspecific variation in the Eriogonoideae (buckwheat family, Polygonaceae). Our model is readily extendible to more complex scenarios of the evolution of inter- and intraspecific variation and presents a step toward more comprehensive comparative models for macroevolutionary studies. PMID:26911152

  16. Composite behavior analysis for video surveillance using hierarchical dynamic Bayesian networks

    NASA Astrophysics Data System (ADS)

    Cheng, Huanhuan; Shan, Yong; Wang, Runsheng

    2011-03-01

    Analyzing composite behaviors involving objects from multiple categories in surveillance videos is a challenging task due to the complicated relationships among human and objects. This paper presents a novel behavior analysis framework using a hierarchical dynamic Bayesian network (DBN) for video surveillance systems. The model is built for extracting objects' behaviors and their relationships by representing behaviors using spatial-temporal characteristics. The recognition of object behaviors is processed by the DBN at multiple levels: features of objects at low level, objects and their relationships at middle level, and event at high level, where event refers to behaviors of a single type object as well as behaviors consisting of several types of objects such as ``a person getting in a car.'' Furthermore, to reduce the complexity, a simple model selection criterion is addressed, by which the appropriated model is picked out from a pool of candidate models. Experiments are shown to demonstrate that the proposed framework could efficiently recognize and semantically describe composite object and human activities in surveillance videos.

  17. Frequentist tests for Bayesian models

    NASA Astrophysics Data System (ADS)

    Lucy, L. B.

    2016-04-01

    Analogues of the frequentist chi-square and F tests are proposed for testing goodness-of-fit and consistency for Bayesian models. Simple examples exhibit these tests' detection of inconsistency between consecutive experiments with identical parameters, when the first experiment provides the prior for the second. In a related analysis, a quantitative measure is derived for judging the degree of tension between two different experiments with partially overlapping parameter vectors.

  18. A Hierarchical Bayesian Approcah for Earthquake Location and Data Uncertainty Estimation in 3D Heterogeneous Media

    NASA Astrophysics Data System (ADS)

    Arroucau, P.; Custodio, S.

    2014-12-01

    Solving inverse problems requires an estimate of data uncertainties. This usually takes the form of a data covariance matrix, which determines the shape of the model posterior distribution. Those uncertainties are yet not always known precisely and it is common practice to simply set them to a fixed, reasonable value. In the case of earthquake location, the hypocentral parameters (longitude, latitude, depth and origin time) are typically inverted for using seismic phase arrival times. But quantitative data variance estimates are rarely provided. Instead, arrival time catalogs usually associate phase picks with a quality factor, which is subsequently interpreted more or less arbitrarily in terms of data uncertainty in the location procedure. Here, we present a hierarchical Bayesian algorithm for earthquake location in 3D heterogeneous media, in which not only the earthquake hypocentral parameters, but also the P- and S-wave arrival time uncertainties, are inverted for, hence allowing more realistic posterior model covariance estimates. Forward modeling is achieved by means of the Fast Marching Method (FMM), an eikonal solver which has the ability to take interfaces into account, so direct, reflected and refracted phases can be used in the inversion. We illustrate the ability of our algorithm to retrieve earthquake hypocentral parameters as well as data uncertainties through synthetic examples and using a subset of arrival time catalogs for mainland Portugal and its Atlantic margin.

  19. A hierarchical Bayesian approach for earthquake location and data uncertainty estimation in 3D heterogeneous media

    NASA Astrophysics Data System (ADS)

    Arroucau, Pierre; Custódio, Susana

    2015-04-01

    Solving inverse problems requires an estimate of data uncertainties. This usually takes the form of a data covariance matrix, which determines the shape of the model posterior distribution. Those uncertainties are yet not always known precisely and it is common practice to simply set them to a fixed, reasonable value. In the case of earthquake location, the hypocentral parameters (longitude, latitude, depth and origin time) are typically inverted for using seismic phase arrival times. But quantitative data variance estimates are rarely provided. Instead, arrival time catalogs usually associate phase picks with a quality factor, which is subsequently interpreted more or less arbitrarily in terms of data uncertainty in the location procedure. Here, we present a hierarchical Bayesian algorithm for earthquake location in 3D heterogeneous media, in which not only the earthquake hypocentral parameters, but also the P- and S-wave arrival time uncertainties, are inverted for, hence allowing more realistic posterior model covariance estimates. Forward modeling is achieved by means of the Fast Marching Method (FMM), an eikonal solver which has the ability to take interfaces into account, so direct, reflected and refracted phases can be used in the inversion. We illustrate the ability of our algorithm to retrieve earthquake hypocentral parameters as well as data uncertainties through synthetic examples and using a subset of arrival time catalogs for mainland Portugal and its Atlantic margin.

  20. Hierarchical Bass model

    NASA Astrophysics Data System (ADS)

    Tashiro, Tohru

    2014-03-01

    We propose a new model about diffusion of a product which includes a memory of how many adopters or advertisements a non-adopter met, where (non-)adopters mean people (not) possessing the product. This effect is lacking in the Bass model. As an application, we utilize the model to fit the iPod sales data, and so the better agreement is obtained than the Bass model.

  1. Bayesian Networks for Social Modeling

    SciTech Connect

    Whitney, Paul D.; White, Amanda M.; Walsh, Stephen J.; Dalton, Angela C.; Brothers, Alan J.

    2011-03-28

    This paper describes a body of work developed over the past five years. The work addresses the use of Bayesian network (BN) models for representing and predicting social/organizational behaviors. The topics covered include model construction, validation, and use. These topics show the bulk of the lifetime of such model, beginning with construction, moving to validation and other aspects of model ‘critiquing’, and finally demonstrating how the modeling approach might be used to inform policy analysis. To conclude, we discuss limitations of using BN for this activity and suggest remedies to address those limitations. The primary benefits of using a well-developed computational, mathematical, and statistical modeling structure, such as BN, are 1) there are significant computational, theoretical and capability bases on which to build 2) ability to empirically critique the model, and potentially evaluate competing models for a social/behavioral phenomena.

  2. A new hierarchical Bayesian approach to analyse environmental and climatic influences on debris flow occurrence

    NASA Astrophysics Data System (ADS)

    Jomelli, Vincent; Pavlova, Irina; Eckert, Nicolas; Grancher, Delphine; Brunstein, Daniel

    2015-12-01

    How can debris flow occurrences be modelled at regional scale and take both environmental and climatic conditions into account? And, of the two, which has the most influence on debris flow activity? In this paper, we try to answer these questions with an innovative Bayesian hierarchical probabilistic model that simultaneously accounts for how debris flows respond to environmental and climatic variables. In it, full decomposition of space and time effects in occurrence probabilities is assumed, revealing an environmental and a climatic trend shared by all years/catchments, respectively, clearly distinguished from residual "random" effects. The resulting regional and annual occurrence probabilities evaluated as functions of the covariates make it possible to weight the respective contribution of the different terms and, more generally, to check the model performances at different spatio-temporal scales. After suitable validation, the model can be used to make predictions at undocumented sites and could be used in further studies for predictions under future climate conditions. Also, the Bayesian paradigm easily copes with missing data, thus making it possible to account for events that may have been missed during surveys. As a case study, we extract 124 debris flow event triggered between 1970 and 2005 in 27 catchments located in the French Alps from the French national natural hazard survey and model their variability of occurrence considering environmental and climatic predictors at the same time. We document the environmental characteristics of each debris flow catchment (morphometry, lithology, land cover, and the presence of permafrost). We also compute 15 climate variables including mean temperature and precipitation between May and October and the number of rainy days with daily cumulative rainfall greater than 10/15/20/25/30/40 mm day- 1. Application of our model shows that the combination of environmental and climatic predictors explained 77% of the overall

  3. Hierarchical Molecular Modelling with Ellipsoids

    SciTech Connect

    Max, N

    2004-03-29

    Protein and DNA structures are represented at varying levels of details using ellipsoidal RGBA textured splats. The splat texture at each level is generated by rendering its children in a hierarchical model, from a distribution of viewing directions, and averaging the result. For rendering, the ellipsoids to be used are chosen adaptively, depending on the distance to the viewpoint. This technique is applied to visualize DNA coiling around nucleosomes in chromosomes.

  4. Modeling Diagnostic Assessments with Bayesian Networks

    ERIC Educational Resources Information Center

    Almond, Russell G.; DiBello, Louis V.; Moulder, Brad; Zapata-Rivera, Juan-Diego

    2007-01-01

    This paper defines Bayesian network models and examines their applications to IRT-based cognitive diagnostic modeling. These models are especially suited to building inference engines designed to be synchronous with the finer grained student models that arise in skills diagnostic assessment. Aspects of the theory and use of Bayesian network models…

  5. Japanese Encephalitis Risk and Contextual Risk Factors in Southwest China: A Bayesian Hierarchical Spatial and Spatiotemporal Analysis

    PubMed Central

    Zhao, Xing; Cao, Mingqin; Feng, Hai-Huan; Fan, Heng; Chen, Fei; Feng, Zijian; Li, Xiaosong; Zhou, Xiao-Hua

    2014-01-01

    It is valuable to study the spatiotemporal pattern of Japanese encephalitis (JE) and its association with the contextual risk factors in southwest China, which is the most endemic area in China. Using data from 2004 to 2009, we applied GISmapping and spatial autocorrelation analysis to analyze reported incidence data of JE in 438 counties in southwest China, finding that JE cases were not randomly distributed, and a Bayesian hierarchical spatiotemporal model identified the east part of southwest China as a high risk area. Meanwhile, the Bayesian hierarchical spatial model in 2006 demonstrated a statistically significant association between JE and the agricultural and climatic variables, including the proportion of rural population, the pig-to-human ratio, the monthly precipitation and the monthly mean minimum and maximum temperatures. Particular emphasis was placed on the time-lagged effect for climatic factors. The regression method and the Spearman correlation analysis both identified a two-month lag for the precipitation, while the regression method found a one-month lag for temperature. The results show that the high risk area in the east part of southwest China may be connected to the agricultural and climatic factors. The routine surveillance and the allocation of health resources should be given more attention in this area. Moreover, the meteorological variables might be considered as possible predictors of JE in southwest China. PMID:24739769

  6. Multivariate Bayesian Models of Extreme Rainfall

    NASA Astrophysics Data System (ADS)

    Rahill-Marier, B.; Devineni, N.; Lall, U.; Farnham, D.

    2013-12-01

    Accounting for spatial heterogeneity in extreme rainfall has important ramifications in hydrological design and climate models alike. Traditional methods, including areal reduction factors and kriging, are sensitive to catchment shape assumptions and return periods, and do not explicitly model spatial dependence between between data points. More recent spatially dense rainfall simulators depend on newer data sources such as radar and may struggle to reproduce extremes because of physical assumptions in the model and short historical records. Rain gauges offer the longest historical record, key when considering rainfall extremes and changes over time, and particularly relevant in today's environment of designing for climate change. In this paper we propose a probabilistic approach of accounting for spatial dependence using the lengthy but spatially disparate hourly rainfall network in the greater New York City area. We build a hierarchical Bayesian model allowing extremes at one station to co-vary with concurrent rainfall fields occurring at other stations. Subsequently we pool across the extreme rainfall fields of all stations, and demonstrate that the expected catchment-wide events are significantly lower when considering spatial fields instead of maxima-only fields. We additionally demonstrate the importance of using concurrent spatial fields, rather than annual maxima, in producing covariance matrices that describe true storm dynamics. This approach is also unique in that it considers short duration storms - from one hour to twenty-four hours - rather than the daily values typically derived from rainfall gauges. The same methodology can be extended to include the radar fields available in the past decade. The hierarchical multilevel approach lends itself easily to integration of long-record parameters and short-record parameters at a station or regional level. In addition climate covariates can be introduced to support the relationship of spatial covariance with

  7. ESTIMATION OF FAILURE RATES OF DIGITAL COMPONENTS USING A HIERARCHICAL BAYESIAN METHOD.

    SciTech Connect

    YUE, M.; CHU, T.L.

    2006-01-30

    One of the greatest challenges in evaluating reliability of digital I&C systems is how to obtain better failure rate estimates of digital components. A common practice of the digital component failure rate estimation is attempting to use empirical formulae to capture the impacts of various factors on the failure rates. The applicability of an empirical formula is questionable because it is not based on laws of physics and requires good data, which is scarce in general. In this study, the concept of population variability of the Hierarchical Bayesian Method (HBM) is applied to estimating the failure rate of a digital component using available data. Markov Chain Monte Carlo (MCMC) simulation is used to implement the HBM. Results are analyzed and compared by selecting different distribution types and priors distributions. Inspired by the sensitivity calculations and based on review of analytic derivations, it seems reasonable to suggest avoiding the use of gamma distribution in two-stage Bayesian analysis and HBM analysis.

  8. Bayesian hierarchical approach and geophysical data sets for estimation of reactive facies over plume scales

    NASA Astrophysics Data System (ADS)

    Wainwright, Haruko M.; Chen, Jinsong; Sassen, Douglas S.; Hubbard, Susan S.

    2014-06-01

    A stochastic model is developed to integrate multiscale geophysical and point data sets for characterizing coupled subsurface physiochemical properties over plume-relevant scales, which is desired for parameterizing reactive transport models. We utilize the concept of reactive facies, which is based on the hypothesis that subsurface units can be identified that have distinct reactive-transport-property distributions. To estimate and spatially distribute reactive facies and their associated properties over plume-relevant scales, we need to (1) document the physiochemical controls on plume behavior and the correspondence between geochemical, hydrogeological, and geophysical measurements; and (2) integrate multisource, multiscale data sets in a consistent manner. To tackle these cross-scale challenges, we develop a hierarchical Bayesian model to jointly invert various wellbore and geophysical data sets that have different resolutions and spatial coverage. We use Markov-chain Monte-Carlo sampling methods to draw many samples from the joint posterior distribution and subsequently estimate the marginal posterior distribution of reactive-facies field and their associated reactive transport properties. Synthetic studies demonstrate that our method can successfully integrate different types of data sets. We tested the framework using the data sets collected at the uranium-contaminated Savannah River Site F-Area, including wellbore lithology, cone penetrometer testing, and crosshole and surface seismic data. Results show that the method can estimate the spatial distribution of reactive facies and their associated reactive-transport properties along a 300 m plume centerline traverse with high resolution (1.2 m by 0.305 m).

  9. Optimizing an estuarine water quality monitoring program through an entropy-based hierarchical spatiotemporal Bayesian framework

    NASA Astrophysics Data System (ADS)

    Alameddine, Ibrahim; Karmakar, Subhankar; Qian, Song S.; Paerl, Hans W.; Reckhow, Kenneth H.

    2013-10-01

    The total maximum daily load program aims to monitor more than 40,000 standard violations in around 20,000 impaired water bodies across the United States. Given resource limitations, future monitoring efforts have to be hedged against the uncertainties in the monitored system, while taking into account existing knowledge. In that respect, we have developed a hierarchical spatiotemporal Bayesian model that can be used to optimize an existing monitoring network by retaining stations that provide the maximum amount of information, while identifying locations that would benefit from the addition of new stations. The model assumes the water quality parameters are adequately described by a joint matrix normal distribution. The adopted approach allows for a reduction in redundancies, while emphasizing information richness rather than data richness. The developed approach incorporates the concept of entropy to account for the associated uncertainties. Three different entropy-based criteria are adopted: total system entropy, chlorophyll-a standard violation entropy, and dissolved oxygen standard violation entropy. A multiple attribute decision making framework is adopted to integrate the competing design criteria and to generate a single optimal design. The approach is implemented on the water quality monitoring system of the Neuse River Estuary in North Carolina, USA. The model results indicate that the high priority monitoring areas identified by the total system entropy and the dissolved oxygen violation entropy criteria are largely coincident. The monitoring design based on the chlorophyll-a standard violation entropy proved to be less informative, given the low probabilities of violating the water quality standard in the estuary.

  10. Hierarchical spatiotemporal matrix models for characterizing invasions

    USGS Publications Warehouse

    Hooten, M.B.; Wikle, C.K.; Dorazio, R.M.; Royle, J. Andrew

    2007-01-01

    The growth and dispersal of biotic organisms is an important subject in ecology. Ecologists are able to accurately describe survival and fecundity in plant and animal populations and have developed quantitative approaches to study the dynamics of dispersal and population size. Of particular interest are the dynamics of invasive species. Such nonindigenous animals and plants can levy significant impacts on native biotic communities. Effective models for relative abundance have been developed; however, a better understanding of the dynamics of actual population size (as opposed to relative abundance) in an invasion would be beneficial to all branches of ecology. In this article, we adopt a hierarchical Bayesian framework for modeling the invasion of such species while addressing the discrete nature of the data and uncertainty associated with the probability of detection. The nonlinear dynamics between discrete time points are intuitively modeled through an embedded deterministic population model with density-dependent growth and dispersal components. Additionally, we illustrate the importance of accommodating spatially varying dispersal rates. The method is applied to the specific case of the Eurasian Collared-Dove, an invasive species at mid-invasion in the United States at the time of this writing. ?? 2006, The International Biometric Society.

  11. Hierarchical spatiotemporal matrix models for characterizing invasions

    USGS Publications Warehouse

    Hooten, Mevin B.; Wikle, Christopher K.; Dorazio, Robert M.; Royle, J. Andrew

    2007-01-01

    The growth and dispersal of biotic organisms is an important subject in ecology. Ecologists are able to accurately describe survival and fecundity in plant and animal populations and have developed quantitative approaches to study the dynamics of dispersal and population size. Of particular interest are the dynamics of invasive species. Such nonindigenous animals and plants can levy significant impacts on native biotic communities. Effective models for relative abundance have been developed; however, a better understanding of the dynamics of actual population size (as opposed to relative abundance) in an invasion would be beneficial to all branches of ecology. In this article, we adopt a hierarchical Bayesian framework for modeling the invasion of such species while addressing the discrete nature of the data and uncertainty associated with the probability of detection. The nonlinear dynamics between discrete time points are intuitively modeled through an embedded deterministic population model with density-dependent growth and dispersal components. Additionally, we illustrate the importance of accommodating spatially varying dispersal rates. The method is applied to the specific case of the Eurasian Collared-Dove, an invasive species at mid-invasion in the United States at the time of this writing.

  12. A hierarchical model for spatial capture-recapture data

    USGS Publications Warehouse

    Royle, J. Andrew; Young, K.V.

    2008-01-01

    Estimating density is a fundamental objective of many animal population studies. Application of methods for estimating population size from ostensibly closed populations is widespread, but ineffective for estimating absolute density because most populations are subject to short-term movements or so-called temporary emigration. This phenomenon invalidates the resulting estimates because the effective sample area is unknown. A number of methods involving the adjustment of estimates based on heuristic considerations are in widespread use. In this paper, a hierarchical model of spatially indexed capture recapture data is proposed for sampling based on area searches of spatial sample units subject to uniform sampling intensity. The hierarchical model contains explicit models for the distribution of individuals and their movements, in addition to an observation model that is conditional on the location of individuals during sampling. Bayesian analysis of the hierarchical model is achieved by the use of data augmentation, which allows for a straightforward implementation in the freely available software WinBUGS. We present results of a simulation study that was carried out to evaluate the operating characteristics of the Bayesian estimator under variable densities and movement patterns of individuals. An application of the model is presented for survey data on the flat-tailed horned lizard (Phrynosoma mcallii) in Arizona, USA.

  13. Bayesian hierarchical multi-subject multiscale analysis of functional MRI data.

    PubMed

    Sanyal, Nilotpal; Ferreira, Marco A R

    2012-11-15

    We develop a methodology for Bayesian hierarchical multi-subject multiscale analysis of functional Magnetic Resonance Imaging (fMRI) data. We begin by modeling the brain images temporally with a standard general linear model. After that, we transform the resulting estimated standardized regression coefficient maps through a discrete wavelet transformation to obtain a sparse representation in the wavelet space. Subsequently, we assign to the wavelet coefficients a prior that is a mixture of a point mass at zero and a Gaussian white noise. In this mixture prior for the wavelet coefficients, the mixture probabilities are related to the pattern of brain activity across different resolutions. To incorporate this information, we assume that the mixture probabilities for wavelet coefficients at the same location and level are common across subjects. Furthermore, we assign for the mixture probabilities a prior that depends on a few hyperparameters. We develop an empirical Bayes methodology to estimate the hyperparameters and, as these hyperparameters are shared by all subjects, we obtain precise estimated values. Then we carry out inference in the wavelet space and obtain smoothed images of the regression coefficients by applying the inverse wavelet transform to the posterior means of the wavelet coefficients. An application to computer simulated synthetic data has shown that, when compared to single-subject analysis, our multi-subject methodology performs better in terms of mean squared error. Finally, we illustrate the utility and flexibility of our multi-subject methodology with an application to an event-related fMRI dataset generated by Postle (2005) through a multi-subject fMRI study of working memory related brain activation. PMID:22951257

  14. TYPE Ia SUPERNOVA COLORS AND EJECTA VELOCITIES: HIERARCHICAL BAYESIAN REGRESSION WITH NON-GAUSSIAN DISTRIBUTIONS

    SciTech Connect

    Mandel, Kaisey S.; Kirshner, Robert P.; Foley, Ryan J.

    2014-12-20

    We investigate the statistical dependence of the peak intrinsic colors of Type Ia supernovae (SNe Ia) on their expansion velocities at maximum light, measured from the Si II λ6355 spectral feature. We construct a new hierarchical Bayesian regression model, accounting for the random effects of intrinsic scatter, measurement error, and reddening by host galaxy dust, and implement a Gibbs sampler and deviance information criteria to estimate the correlation. The method is applied to the apparent colors from BVRI light curves and Si II velocity data for 79 nearby SNe Ia. The apparent color distributions of high-velocity (HV) and normal velocity (NV) supernovae exhibit significant discrepancies for B – V and B – R, but not other colors. Hence, they are likely due to intrinsic color differences originating in the B band, rather than dust reddening. The mean intrinsic B – V and B – R color differences between HV and NV groups are 0.06 ± 0.02 and 0.09 ± 0.02 mag, respectively. A linear model finds significant slopes of –0.021 ± 0.006 and –0.030 ± 0.009 mag (10{sup 3} km s{sup –1}){sup –1} for intrinsic B – V and B – R colors versus velocity, respectively. Because the ejecta velocity distribution is skewed toward high velocities, these effects imply non-Gaussian intrinsic color distributions with skewness up to +0.3. Accounting for the intrinsic-color-velocity correlation results in corrections to A{sub V} extinction estimates as large as –0.12 mag for HV SNe Ia and +0.06 mag for NV events. Velocity measurements from SN Ia spectra have the potential to diminish systematic errors from the confounding of intrinsic colors and dust reddening affecting supernova distances.

  15. A Bayesian Hierarchical framework for identifying regional hydroclimate trends or climate effects from continental or global data

    NASA Astrophysics Data System (ADS)

    Sun, X.; Lall, U.

    2014-12-01

    Hierarchical Bayesian models are useful for modeling hydroclimatic trends and teleconnections with a formal approach to characterizing and reducing estimation uncertainties. A challenge to the application of these models to large areas is that the response can be spatially heterogeneous, and the choice of a local spatial covariance model and a large scale spatial trend model in the parameters of the Bayesian regression may not be intuitively obvious. We consider a multilevel modeling structure for exploring homogeneity of response in such data sets, through a multi-component mixture model. The approach allows the reduction of uncertainties through partial pooling of parameters across automatically chosen subsets of the data. Applications to a synthetic data set and to extreme precipitation data for the continental USA from the HADEX2 data set is presented considering trends and selected climate indices as potential predictors. The effect of changing the number of components in the mixture is demonstrated through the changing spatial membership and trends in the data.

  16. Bayesian Calibration of Microsimulation Models.

    PubMed

    Rutter, Carolyn M; Miglioretti, Diana L; Savarino, James E

    2009-12-01

    Microsimulation models that describe disease processes synthesize information from multiple sources and can be used to estimate the effects of screening and treatment on cancer incidence and mortality at a population level. These models are characterized by simulation of individual event histories for an idealized population of interest. Microsimulation models are complex and invariably include parameters that are not well informed by existing data. Therefore, a key component of model development is the choice of parameter values. Microsimulation model parameter values are selected to reproduce expected or known results though the process of model calibration. Calibration may be done by perturbing model parameters one at a time or by using a search algorithm. As an alternative, we propose a Bayesian method to calibrate microsimulation models that uses Markov chain Monte Carlo. We show that this approach converges to the target distribution and use a simulation study to demonstrate its finite-sample performance. Although computationally intensive, this approach has several advantages over previously proposed methods, including the use of statistical criteria to select parameter values, simultaneous calibration of multiple parameters to multiple data sources, incorporation of information via prior distributions, description of parameter identifiability, and the ability to obtain interval estimates of model parameters. We develop a microsimulation model for colorectal cancer and use our proposed method to calibrate model parameters. The microsimulation model provides a good fit to the calibration data. We find evidence that some parameters are identified primarily through prior distributions. Our results underscore the need to incorporate multiple sources of variability (i.e., due to calibration data, unknown parameters, and estimated parameters and predicted values) when calibrating and applying microsimulation models. PMID:20076767

  17. Bayesian Calibration of Microsimulation Models

    PubMed Central

    Rutter, Carolyn M.; Miglioretti, Diana L.; Savarino, James E.

    2009-01-01

    Microsimulation models that describe disease processes synthesize information from multiple sources and can be used to estimate the effects of screening and treatment on cancer incidence and mortality at a population level. These models are characterized by simulation of individual event histories for an idealized population of interest. Microsimulation models are complex and invariably include parameters that are not well informed by existing data. Therefore, a key component of model development is the choice of parameter values. Microsimulation model parameter values are selected to reproduce expected or known results though the process of model calibration. Calibration may be done by perturbing model parameters one at a time or by using a search algorithm. As an alternative, we propose a Bayesian method to calibrate microsimulation models that uses Markov chain Monte Carlo. We show that this approach converges to the target distribution and use a simulation study to demonstrate its finite-sample performance. Although computationally intensive, this approach has several advantages over previously proposed methods, including the use of statistical criteria to select parameter values, simultaneous calibration of multiple parameters to multiple data sources, incorporation of information via prior distributions, description of parameter identifiability, and the ability to obtain interval estimates of model parameters. We develop a microsimulation model for colorectal cancer and use our proposed method to calibrate model parameters. The microsimulation model provides a good fit to the calibration data. We find evidence that some parameters are identified primarily through prior distributions. Our results underscore the need to incorporate multiple sources of variability (i.e., due to calibration data, unknown parameters, and estimated parameters and predicted values) when calibrating and applying microsimulation models. PMID:20076767

  18. Type Ia Supernova Colors and Si II Velocities: Hierarchical Bayesian Regression with Non-Gaussian Distributions

    NASA Astrophysics Data System (ADS)

    Mandel, Kaisey; Foley, R. J.; Kirshner, R. P.

    2014-01-01

    Determining supernova distances with high precision and small systematic error is essential to modern constraints on the cosmic expansion history and the properties of dark energy. An interesting correlation between the expansion velocity of the SN Ia explosion and its intrinsic color has been suggested by earlier work. Since this effect is not incorporated into current schemes for SN Ia light curve analysis, there is potential for improving inferences of host galaxy dust, and thus, distance estimates. We investigate the correlations between the intrinsic colors of SN Ia and the expansion velocities measured from spectral lines. We build a hierarchical Bayesian regression model to estimate the dependence of the intrinsic colors of a SN Ia on its measured Si II line velocity. We model the deviations of apparent colors from a mean intrinsic colors-velocity relation as a combination of random intrinsic scatter, measurement error, and reddening by dust. This statistical model allows for non-Gaussian distributions of the intrinsic colors and velocities. We construct a new, fast Gibbs sampler to compute the posterior inferences of the model using observed data. The method is applied to the apparent color data from BVRI light curves and Si II velocity data for nearby SN Ia. For intrinsic B-V colors, we find a significant slope of 0.021 ± 0.008 mag / (1000 km/s) under a linear model, and a mean color difference of 0.06 ± 0.02 mag between high velocity and normal velocity groups under a step function model. The impact of accounting for the peak intrinsic color-velocity correlation can result in extinction corrections as large as -0.10 mag for high velocity SN Ia and +0.05 mag for normal velocity events. We compute the deviance information criterion (DIC) to gauge whether the more complex hypotheses are justified by their improved representation of the data. The DIC favors the simple linear and step functions of intrinsic color versus velocity over no trend, while higher

  19. Hierarchical Classes Modeling of Rating Data

    ERIC Educational Resources Information Center

    Van Mechelen, Iven; Lombardi, Luigi; Ceulemans, Eva

    2007-01-01

    Hierarchical classes (HICLAS) models constitute a distinct family of structural models for N-way N-mode data. All members of the family include N simultaneous and linked classifications of the elements of the N modes implied by the data; those classifications are organized in terms of hierarchical, if-then-type relations. Moreover, the models are…

  20. Sparse Bayesian infinite factor models

    PubMed Central

    Bhattacharya, A.; Dunson, D. B.

    2011-01-01

    We focus on sparse modelling of high-dimensional covariance matrices using Bayesian latent factor models. We propose a multiplicative gamma process shrinkage prior on the factor loadings which allows introduction of infinitely many factors, with the loadings increasingly shrunk towards zero as the column index increases. We use our prior on a parameter-expanded loading matrix to avoid the order dependence typical in factor analysis models and develop an efficient Gibbs sampler that scales well as data dimensionality increases. The gain in efficiency is achieved by the joint conjugacy property of the proposed prior, which allows block updating of the loadings matrix. We propose an adaptive Gibbs sampler for automatically truncating the infinite loading matrix through selection of the number of important factors. Theoretical results are provided on the support of the prior and truncation approximation bounds. A fast algorithm is proposed to produce approximate Bayes estimates. Latent factor regression methods are developed for prediction and variable selection in applications with high-dimensional correlated predictors. Operating characteristics are assessed through simulation studies, and the approach is applied to predict survival times from gene expression data. PMID:23049129

  1. Linking bovine tuberculosis on cattle farms to white-tailed deer and environmental variables using Bayesian hierarchical analysis.

    PubMed

    Walter, W David; Smith, Rick; Vanderklok, Mike; VerCauteren, Kurt C

    2014-01-01

    Bovine tuberculosis is a bacterial disease caused by Mycobacterium bovis in livestock and wildlife with hosts that include Eurasian badgers (Meles meles), brushtail possum (Trichosurus vulpecula), and white-tailed deer (Odocoileus virginianus). Risk-assessment efforts in Michigan have been initiated on farms to minimize interactions of cattle with wildlife hosts but research on M. bovis on cattle farms has not investigated the spatial context of disease epidemiology. To incorporate spatially explicit data, initial likelihood of infection probabilities for cattle farms tested for M. bovis, prevalence of M. bovis in white-tailed deer, deer density, and environmental variables for each farm were modeled in a Bayesian hierarchical framework. We used geo-referenced locations of 762 cattle farms that have been tested for M. bovis, white-tailed deer prevalence, and several environmental variables that may lead to long-term survival and viability of M. bovis on farms and surrounding habitats (i.e., soil type, habitat type). Bayesian hierarchical analyses identified deer prevalence and proportion of sandy soil within our sampling grid as the most supported model. Analysis of cattle farms tested for M. bovis identified that for every 1% increase in sandy soil resulted in an increase in odds of infection by 4%. Our analysis revealed that the influence of prevalence of M. bovis in white-tailed deer was still a concern even after considerable efforts to prevent cattle interactions with white-tailed deer through on-farm mitigation and reduction in the deer population. Cattle farms test positive for M. bovis annually in our study area suggesting that the potential for an environmental source either on farms or in the surrounding landscape may contributing to new or re-infections with M. bovis. Our research provides an initial assessment of potential environmental factors that could be incorporated into additional modeling efforts as more knowledge of deer herd factors and cattle

  2. Linking Bovine Tuberculosis on Cattle Farms to White-Tailed Deer and Environmental Variables Using Bayesian Hierarchical Analysis

    PubMed Central

    Walter, W. David; Smith, Rick; Vanderklok, Mike; VerCauteren, Kurt C.

    2014-01-01

    Bovine tuberculosis is a bacterial disease caused by Mycobacterium bovis in livestock and wildlife with hosts that include Eurasian badgers (Meles meles), brushtail possum (Trichosurus vulpecula), and white-tailed deer (Odocoileus virginianus). Risk-assessment efforts in Michigan have been initiated on farms to minimize interactions of cattle with wildlife hosts but research on M. bovis on cattle farms has not investigated the spatial context of disease epidemiology. To incorporate spatially explicit data, initial likelihood of infection probabilities for cattle farms tested for M. bovis, prevalence of M. bovis in white-tailed deer, deer density, and environmental variables for each farm were modeled in a Bayesian hierarchical framework. We used geo-referenced locations of 762 cattle farms that have been tested for M. bovis, white-tailed deer prevalence, and several environmental variables that may lead to long-term survival and viability of M. bovis on farms and surrounding habitats (i.e., soil type, habitat type). Bayesian hierarchical analyses identified deer prevalence and proportion of sandy soil within our sampling grid as the most supported model. Analysis of cattle farms tested for M. bovis identified that for every 1% increase in sandy soil resulted in an increase in odds of infection by 4%. Our analysis revealed that the influence of prevalence of M. bovis in white-tailed deer was still a concern even after considerable efforts to prevent cattle interactions with white-tailed deer through on-farm mitigation and reduction in the deer population. Cattle farms test positive for M. bovis annually in our study area suggesting that the potential for an environmental source either on farms or in the surrounding landscape may contributing to new or re-infections with M. bovis. Our research provides an initial assessment of potential environmental factors that could be incorporated into additional modeling efforts as more knowledge of deer herd factors and cattle

  3. Bayesian modeling of ChIP-chip data using latent variables

    PubMed Central

    2009-01-01

    Background The ChIP-chip technology has been used in a wide range of biomedical studies, such as identification of human transcription factor binding sites, investigation of DNA methylation, and investigation of histone modifications in animals and plants. Various methods have been proposed in the literature for analyzing the ChIP-chip data, such as the sliding window methods, the hidden Markov model-based methods, and Bayesian methods. Although, due to the integrated consideration of uncertainty of the models and model parameters, Bayesian methods can potentially work better than the other two classes of methods, the existing Bayesian methods do not perform satisfactorily. They usually require multiple replicates or some extra experimental information to parametrize the model, and long CPU time due to involving of MCMC simulations. Results In this paper, we propose a Bayesian latent model for the ChIP-chip data. The new model mainly differs from the existing Bayesian models, such as the joint deconvolution model, the hierarchical gamma mixture model, and the Bayesian hierarchical model, in two respects. Firstly, it works on the difference between the averaged treatment and control samples. This enables the use of a simple model for the data, which avoids the probe-specific effect and the sample (control/treatment) effect. As a consequence, this enables an efficient MCMC simulation of the posterior distribution of the model, and also makes the model more robust to the outliers. Secondly, it models the neighboring dependence of probes by introducing a latent indicator vector. A truncated Poisson prior distribution is assumed for the latent indicator variable, with the rationale being justified at length. Conclusion The Bayesian latent method is successfully applied to real and ten simulated datasets, with comparisons with some of the existing Bayesian methods, hidden Markov model methods, and sliding window methods. The numerical results indicate that the Bayesian

  4. Spatial Intensity Duration Frequency Relationships Using Hierarchical Bayesian Analysis for Urban Areas

    NASA Astrophysics Data System (ADS)

    Rupa, Chandra; Mujumdar, Pradeep

    2016-04-01

    In urban areas, quantification of extreme precipitation is important in the design of storm water drains and other infrastructure. Intensity Duration Frequency (IDF) relationships are generally used to obtain design return level for a given duration and return period. Due to lack of availability of extreme precipitation data for sufficiently large number of years, estimating the probability of extreme events is difficult. Typically, a single station data is used to obtain the design return levels for various durations and return periods, which are used in the design of urban infrastructure for the entire city. In an urban setting, the spatial variation of precipitation can be high; the precipitation amounts and patterns often vary within short distances of less than 5 km. Therefore it is crucial to study the uncertainties in the spatial variation of return levels for various durations. In this work, the extreme precipitation is modeled spatially using the Bayesian hierarchical analysis and the spatial variation of return levels is studied. The analysis is carried out with Block Maxima approach for defining the extreme precipitation, using Generalized Extreme Value (GEV) distribution for Bangalore city, Karnataka state, India. Daily data for nineteen stations in and around Bangalore city is considered in the study. The analysis is carried out for summer maxima (March - May), monsoon maxima (June - September) and the annual maxima rainfall. In the hierarchical analysis, the statistical model is specified in three layers. The data layer models the block maxima, pooling the extreme precipitation from all the stations. In the process layer, the latent spatial process characterized by geographical and climatological covariates (lat-lon, elevation, mean temperature etc.) which drives the extreme precipitation is modeled and in the prior level, the prior distributions that govern the latent process are modeled. Markov Chain Monte Carlo (MCMC) algorithm (Metropolis Hastings

  5. Hierarchical Bayesian Spatio-Temporal Analysis of Climatic and Socio-Economic Determinants of Rocky Mountain Spotted Fever.

    PubMed

    Raghavan, Ram K; Goodin, Douglas G; Neises, Daniel; Anderson, Gary A; Ganta, Roman R

    2016-01-01

    This study aims to examine the spatio-temporal dynamics of Rocky Mountain spotted fever (RMSF) prevalence in four contiguous states of Midwestern United States, and to determine the impact of environmental and socio-economic factors associated with this disease. Bayesian hierarchical models were used to quantify space and time only trends and spatio-temporal interaction effect in the case reports submitted to the state health departments in the region. Various socio-economic, environmental and climatic covariates screened a priori in a bivariate procedure were added to a main-effects Bayesian model in progressive steps to evaluate important drivers of RMSF space-time patterns in the region. Our results show a steady increase in RMSF incidence over the study period to newer geographic areas, and the posterior probabilities of county-specific trends indicate clustering of high risk counties in the central and southern parts of the study region. At the spatial scale of a county, the prevalence levels of RMSF is influenced by poverty status, average relative humidity, and average land surface temperature (>35°C) in the region, and the relevance of these factors in the context of climate-change impacts on tick-borne diseases are discussed. PMID:26942604

  6. Hierarchical Bayesian Spatio–Temporal Analysis of Climatic and Socio–Economic Determinants of Rocky Mountain Spotted Fever

    PubMed Central

    Raghavan, Ram K.; Goodin, Douglas G.; Neises, Daniel; Anderson, Gary A.; Ganta, Roman R.

    2016-01-01

    This study aims to examine the spatio-temporal dynamics of Rocky Mountain spotted fever (RMSF) prevalence in four contiguous states of Midwestern United States, and to determine the impact of environmental and socio–economic factors associated with this disease. Bayesian hierarchical models were used to quantify space and time only trends and spatio–temporal interaction effect in the case reports submitted to the state health departments in the region. Various socio–economic, environmental and climatic covariates screened a priori in a bivariate procedure were added to a main–effects Bayesian model in progressive steps to evaluate important drivers of RMSF space-time patterns in the region. Our results show a steady increase in RMSF incidence over the study period to newer geographic areas, and the posterior probabilities of county-specific trends indicate clustering of high risk counties in the central and southern parts of the study region. At the spatial scale of a county, the prevalence levels of RMSF is influenced by poverty status, average relative humidity, and average land surface temperature (>35°C) in the region, and the relevance of these factors in the context of climate–change impacts on tick–borne diseases are discussed. PMID:26942604

  7. Hierarchical model for distributed seismicity

    SciTech Connect

    Tejedor, Alejandro; Gomez, Javier B.; Pacheco, Amalio F.

    2010-07-15

    A cellular automata model for the interaction between seismic faults in an extended region is presented. Faults are represented by boxes formed by a different number of sites and located in the nodes of a fractal tree. Both the distribution of box sizes and the interaction between them is assumed to be hierarchical. Load particles are randomly added to the system, simulating the action of external tectonic forces. These particles fill the sites of the boxes progressively. When a box is full it topples, some of the particles are redistributed to other boxes and some of them are lost. A box relaxation simulates the occurrence of an earthquake in the region. The particle redistributions mostly occur upwards (to larger faults) and downwards (to smaller faults) in the hierarchy producing new relaxations. A simple and efficient bookkeeping of the information allows the running of systems with more than fifty million faults. This model is consistent with the definition of magnitude, i.e., earthquakes of magnitude m take place in boxes with a number of sites ten times bigger than those boxes responsible for earthquakes with a magnitude m-1 which are placed in the immediate lower level of the hierarchy. The three parameters of the model have a geometrical nature: the height or number of levels of the fractal tree, the coordination of the tree and the ratio of areas between boxes in two consecutive levels. Besides reproducing several seismicity properties and regularities, this model is used to test the performance of some precursory patterns.

  8. A Bayesian population PBPK model for multiroute chloroform exposure

    PubMed Central

    Yang, Yuching; Xu, Xu; Georgopoulos, Panos G.

    2011-01-01

    A Bayesian hierarchical model was developed to estimate the parameters in a physiologically based pharmacokinetic (PBPK) model for chloroform using prior information and biomarker data from different exposure pathways. In particular, the model provides a quantitative description of the changes in physiological parameters associated with hot-water bath and showering scenarios. Through Bayesian inference, uncertainties in the PBPK parameters were reduced from the prior distributions. Prediction of biomarker data with the calibrated PBPK model was improved by the calibration. The posterior results indicate that blood flow rates varied under two different exposure scenarios, with a two-fold increase of the skin's blood flow rate predicted in the hot-bath scenario. This result highlights the importance of considering scenario-specific parameters in PBPK modeling. To demonstrate the application of a probability approach in toxicological assessment, results from the posterior distributions from this calibrated model were used to predict target tissue dose based on the rate of chloroform metabolized in liver. This study demonstrates the use of the Bayesian approach to optimize PBPK model parameters for typical household exposure scenarios. PMID:19471319

  9. Source Mechanisms of Earthquakes at the Geysers Geothermal Region Using a Hierarchical Bayesian Approach

    NASA Astrophysics Data System (ADS)

    Burky, A.; Mustac, M.; Tkalcic, H.; Dreger, D. S.

    2015-12-01

    The Geysers geothermal region in northern California is a valuable resource for the production of geothermal electric power. Injection of water into the reservoir is necessary to maintain pressure and causes an increase in the number of earthquakes per day, but their source mechanisms are not well understood (Johnson, 2015). Previous studies of source mechanisms for events in the Geysers have identified a large number of events with significant isotropic and compensated linear vector dipole components. These source complexities most likely arise from the presence of pressurized liquids and gases, as well as temperature changes, at depth. The existence of non-double couple components in volcanic and geothermal environments has been extensively documented by previous studies, but it has also been shown that spurious components might occur due to a range of factors such as an inadequate knowledge of Earth structure and earthquake location, or noisy waveform data. Therefore, it is not entirely surprising that non-double-couple components from different source studies, each following a different experimental method and using different data types, do not agree well (e.g. Guilhem et al., 2014). The assessment of the solution robustness is critical for the physical interpretation of source mechanisms.Here, we apply a hierarchical Bayesian approach (Mustac and Tkalcic, 2015) to waveform data from M>4.5 events in the Geysers in order to produce moment tensor "solutions" and simultaneously estimate their robustness. By using a Bayesian inversion, we quantify the uncertainties from an ensemble of probable solutions instead of a single optimized solution and sample solutions at a range of centroid locations. Moreover, the hierarchical approach allows noise in the data to be sampled as a free parameter in the inversion. A rigorous approach in accounting for the data correlated noise covariance matrix prevents "over-interpretation" of noise, thus avoiding erroneous solutions. We

  10. Hierarchical model for distributed seismicity.

    PubMed

    Tejedor, Alejandro; Gómez, Javier B; Pacheco, Amalio F

    2010-07-01

    A cellular automata model for the interaction between seismic faults in an extended region is presented. Faults are represented by boxes formed by a different number of sites and located in the nodes of a fractal tree. Both the distribution of box sizes and the interaction between them is assumed to be hierarchical. Load particles are randomly added to the system, simulating the action of external tectonic forces. These particles fill the sites of the boxes progressively. When a box is full it topples, some of the particles are redistributed to other boxes and some of them are lost. A box relaxation simulates the occurrence of an earthquake in the region. The particle redistributions mostly occur upwards (to larger faults) and downwards (to smaller faults) in the hierarchy producing new relaxations. A simple and efficient bookkeeping of the information allows the running of systems with more than fifty million faults. This model is consistent with the definition of magnitude, i.e., earthquakes of magnitude m take place in boxes with a number of sites ten times bigger than those boxes responsible for earthquakes with a magnitude m-1 which are placed in the immediate lower level of the hierarchy. The three parameters of the model have a geometrical nature: the height or number of levels of the fractal tree, the coordination of the tree and the ratio of areas between boxes in two consecutive levels. Besides reproducing several seismicity properties and regularities, this model is used to test the performance of some precursory patterns. PMID:20866700

  11. Modeling Associations among Multivariate Longitudinal Categorical Variables in Survey Data: A Semiparametric Bayesian Approach

    ERIC Educational Resources Information Center

    Tchumtchoua, Sylvie; Dey, Dipak K.

    2012-01-01

    This paper proposes a semiparametric Bayesian framework for the analysis of associations among multivariate longitudinal categorical variables in high-dimensional data settings. This type of data is frequent, especially in the social and behavioral sciences. A semiparametric hierarchical factor analysis model is developed in which the…

  12. Applying Bayesian Modeling and Receiver Operating Characteristic Methodologies for Test Utility Analysis

    ERIC Educational Resources Information Center

    Wang, Qiu; Diemer, Matthew A.; Maier, Kimberly S.

    2013-01-01

    This study integrated Bayesian hierarchical modeling and receiver operating characteristic analysis (BROCA) to evaluate how interest strength (IS) and interest differentiation (ID) predicted low–socioeconomic status (SES) youth's interest-major congruence (IMC). Using large-scale Kuder Career Search online-assessment data, this study fit three…

  13. Weakly Informative Prior for Point Estimation of Covariance Matrices in Hierarchical Models

    ERIC Educational Resources Information Center

    Chung, Yeojin; Gelman, Andrew; Rabe-Hesketh, Sophia; Liu, Jingchen; Dorie, Vincent

    2015-01-01

    When fitting hierarchical regression models, maximum likelihood (ML) estimation has computational (and, for some users, philosophical) advantages compared to full Bayesian inference, but when the number of groups is small, estimates of the covariance matrix (S) of group-level varying coefficients are often degenerate. One can do better, even from…

  14. Exploring the light and darkness: Hierarchical Bayesian analyses on early-type galaxies and dark matter

    NASA Astrophysics Data System (ADS)

    Shu, Yiping

    Being the end-product of the hierarchical merging scenario, early-type (elliptical and lenticular) galaxies (ETGs) are the "live" fossil records that permit compelling tests of galaxy formation theories within a cosmological context. Also, ETGs can be extremely luminous and serve as the ideal cosmological tracers in the Universe. Additionally, the mysterious dark matter (DM), which is believed to constitute almost 85% of the observed mass portion, acts as the host of galaxies and hence plays a pivotal role in shaping the observed Universe. A thorough understanding of DM, including its nature, properties, and structures provides crucial insights into the fundamental laws of physics and cosmology. On the luminous side, a hierarchical Bayesian determination of the velocity-dispersion function of approximately 430000 massive luminous red galaxies observed by the Baryon Oscillation Spectroscopic Survey (BOSS) is performed. We use the full velocity-dispersion likelihood function for each galaxy to make a self-consistent determination of the velocity-dispersion distribution parameters as a function of absolute magnitude and redshift. Parameterizing the distribution at each point in the luminosity-redshift plane with a log-normal form, we detect significant evolution in the width of the distribution toward higher intrinsic scatter at higher redshifts, which indicates a more diverse heterogeneity in ETGs at earlier cosmic time. On the dark side, I report the discovery of 40 strong gravitational lenses in the SLACS for the Masses (S4TM) Survey and 33 additional systems with single-lensed images in S4TM and SLACS Surveys, for which upper limits of the Einstein radii are determined. A hierarchical Bayesian analysis reveals strong evidence (4sigma) of variations of the total mass-density structure toward shallower profiles at larger velocity dispersion when upper limits are incorporated. Estimating the stellar masses based on the HST I-band photometry, we find a significant

  15. Bayesian Data-Model Fit Assessment for Structural Equation Modeling

    ERIC Educational Resources Information Center

    Levy, Roy

    2011-01-01

    Bayesian approaches to modeling are receiving an increasing amount of attention in the areas of model construction and estimation in factor analysis, structural equation modeling (SEM), and related latent variable models. However, model diagnostics and model criticism remain relatively understudied aspects of Bayesian SEM. This article describes…

  16. An Integrated Bayesian Model for DIF Analysis

    ERIC Educational Resources Information Center

    Soares, Tufi M.; Goncalves, Flavio B.; Gamerman, Dani

    2009-01-01

    In this article, an integrated Bayesian model for differential item functioning (DIF) analysis is proposed. The model is integrated in the sense of modeling the responses along with the DIF analysis. This approach allows DIF detection and explanation in a simultaneous setup. Previous empirical studies and/or subjective beliefs about the item…

  17. Heterogeneous Factor Analysis Models: A Bayesian Approach.

    ERIC Educational Resources Information Center

    Ansari, Asim; Jedidi, Kamel; Dube, Laurette

    2002-01-01

    Developed Markov Chain Monte Carlo procedures to perform Bayesian inference, model checking, and model comparison in heterogeneous factor analysis. Tested the approach with synthetic data and data from a consumption emotion study involving 54 consumers. Results show that traditional psychometric methods cannot fully capture the heterogeneity in…

  18. A hierarchical, ontology-driven Bayesian concept for ubiquitous medical environments--a case study for pulmonary diseases.

    PubMed

    Maragoudakis, Manolis; Lymberopoulos, Dimitrios; Fakotakis, Nikos; Spiropoulos, Kostas

    2008-01-01

    The present paper extends work on an existing computer-based Decision Support System (DSS) that aims to provide assistance to physicians as regards to pulmonary diseases. The extension deals with allowing for a hierarchical decomposition of the task, at different levels of domain granularity, using a novel approach, i.e. Hierarchical Bayesian Networks. The proposed framework uses data from various networking appliances such as mobile phones and wireless medical sensors to establish a ubiquitous environment for medical treatment of pulmonary diseases. Domain knowledge is encoded at the upper levels of the hierarchy, thus making the process of generalization easier to accomplish. The experimental results were carried out under the Pulmonary Department, University Regional Hospital Patras, Patras, Greece. They have supported our initial beliefs about the ability of Bayesian networks to provide an effective, yet semantically-oriented, means of prognosis and reasoning under conditions of uncertainty. PMID:19163541

  19. Linking bovine tuberculosis on cattle farms to white-tailed deer and environmental variables using Bayesian hierarchical analysis

    USGS Publications Warehouse

    Walter, William D.; Smith, Rick; Vanderklok, Mike; VerCauterren, Kurt C.

    2014-01-01

    Bovine tuberculosis is a bacterial disease caused by Mycobacterium bovis in livestock and wildlife with hosts that include Eurasian badgers (Meles meles), brushtail possum (Trichosurus vulpecula), and white-tailed deer (Odocoileus virginianus). Risk-assessment efforts in Michigan have been initiated on farms to minimize interactions of cattle with wildlife hosts but research onM. bovis on cattle farms has not investigated the spatial context of disease epidemiology. To incorporate spatially explicit data, initial likelihood of infection probabilities for cattle farms tested for M. bovis, prevalence of M. bovis in white-tailed deer, deer density, and environmental variables for each farm were modeled in a Bayesian hierarchical framework. We used geo-referenced locations of 762 cattle farms that have been tested for M. bovis, white-tailed deer prevalence, and several environmental variables that may lead to long-term survival and viability of M. bovis on farms and surrounding habitats (i.e., soil type, habitat type). Bayesian hierarchical analyses identified deer prevalence and proportion of sandy soil within our sampling grid as the most supported model. Analysis of cattle farms tested for M. bovisidentified that for every 1% increase in sandy soil resulted in an increase in odds of infection by 4%. Our analysis revealed that the influence of prevalence of M. bovis in white-tailed deer was still a concern even after considerable efforts to prevent cattle interactions with white-tailed deer through on-farm mitigation and reduction in the deer population. Cattle farms test positive for M. bovis annually in our study area suggesting that the potential for an environmental source either on farms or in the surrounding landscape may contributing to new or re-infections with M. bovis. Our research provides an initial assessment of potential environmental factors that could be incorporated into additional modeling efforts as more knowledge of deer herd

  20. Analysis hierarchical model for discrete event systems

    NASA Astrophysics Data System (ADS)

    Ciortea, E. M.

    2015-11-01

    The This paper presents the hierarchical model based on discrete event network for robotic systems. Based on the hierarchical approach, Petri network is analysed as a network of the highest conceptual level and the lowest level of local control. For modelling and control of complex robotic systems using extended Petri nets. Such a system is structured, controlled and analysed in this paper by using Visual Object Net ++ package that is relatively simple and easy to use, and the results are shown as representations easy to interpret. The hierarchical structure of the robotic system is implemented on computers analysed using specialized programs. Implementation of hierarchical model discrete event systems, as a real-time operating system on a computer network connected via a serial bus is possible, where each computer is dedicated to local and Petri model of a subsystem global robotic system. Since Petri models are simplified to apply general computers, analysis, modelling, complex manufacturing systems control can be achieved using Petri nets. Discrete event systems is a pragmatic tool for modelling industrial systems. For system modelling using Petri nets because we have our system where discrete event. To highlight the auxiliary time Petri model using transport stream divided into hierarchical levels and sections are analysed successively. Proposed robotic system simulation using timed Petri, offers the opportunity to view the robotic time. Application of goods or robotic and transmission times obtained by measuring spot is obtained graphics showing the average time for transport activity, using the parameters sets of finished products. individually.

  1. Survey of Bayesian Models for Modelling of Stochastic Temporal Processes

    SciTech Connect

    Ng, B

    2006-10-12

    This survey gives an overview of popular generative models used in the modeling of stochastic temporal systems. In particular, this survey is organized into two parts. The first part discusses the discrete-time representations of dynamic Bayesian networks and dynamic relational probabilistic models, while the second part discusses the continuous-time representation of continuous-time Bayesian networks.

  2. Bayesian state space models for dynamic genetic network construction across multiple tissues.

    PubMed

    Liang, Yulan; Kelemen, Arpad

    2016-08-01

    Construction of gene-gene interaction networks and potential pathways is a challenging and important problem in genomic research for complex diseases while estimating the dynamic changes of the temporal correlations and non-stationarity are the keys in this process. In this paper, we develop dynamic state space models with hierarchical Bayesian settings to tackle this challenge for inferring the dynamic profiles and genetic networks associated with disease treatments. We treat both the stochastic transition matrix and the observation matrix time-variant and include temporal correlation structures in the covariance matrix estimations in the multivariate Bayesian state space models. The unevenly spaced short time courses with unseen time points are treated as hidden state variables. Hierarchical Bayesian approaches with various prior and hyper-prior models with Monte Carlo Markov Chain and Gibbs sampling algorithms are used to estimate the model parameters and the hidden state variables. We apply the proposed Hierarchical Bayesian state space models to multiple tissues (liver, skeletal muscle, and kidney) Affymetrix time course data sets following corticosteroid (CS) drug administration. Both simulation and real data analysis results show that the genomic changes over time and gene-gene interaction in response to CS treatment can be well captured by the proposed models. The proposed dynamic Hierarchical Bayesian state space modeling approaches could be expanded and applied to other large scale genomic data, such as next generation sequence (NGS) combined with real time and time varying electronic health record (EHR) for more comprehensive and robust systematic and network based analysis in order to transform big biomedical data into predictions and diagnostics for precision medicine and personalized healthcare with better decision making and patient outcomes. PMID:27343475

  3. Hierarchical Bayesian clustering for nonstationary flood frequency analysis: Application to trends of annual maximum flow in Germany

    NASA Astrophysics Data System (ADS)

    Sun, Xun; Lall, Upmanu; Merz, Bruno; Dung, Nguyen Viet

    2015-08-01

    Especially for extreme precipitation or floods, there is considerable spatial and temporal variability in long term trends or in the response of station time series to large-scale climate indices. Consequently, identifying trends or sensitivity of these extremes to climate parameters can be marked by high uncertainty. When one develops a nonstationary frequency analysis model, a key step is the identification of potential trends or effects of climate indices on the station series. An automatic clustering procedure that effectively pools stations where there are similar responses is desirable to reduce the estimation variance, thus improving the identification of trends or responses, and accounting for spatial dependence. This paper presents a new hierarchical Bayesian approach for exploring homogeneity of response in large area data sets, through a multicomponent mixture model. The approach allows the reduction of uncertainties through both full pooling and partial pooling of stations across automatically chosen subsets of the data. We apply the model to study the trends in annual maximum daily stream flow at 68 gauges over Germany. The effects of changing the number of clusters and the parameters used for clustering are demonstrated. The results show that there are large, mainly upward trends in the gauges of the River Rhine Basin in Western Germany and along the main stream of the Danube River in the south, while there are also some small upward trends at gauges in Central and Northern Germany.

  4. An agglomerative hierarchical clustering approach to visualisation in Bayesian clustering problems

    PubMed Central

    Dawson, Kevin J.; Belkhir, Khalid

    2009-01-01

    Clustering problems (including the clustering of individuals into outcrossing populations, hybrid generations, full-sib families and selfing lines) have recently received much attention in population genetics. In these clustering problems, the parameter of interest is a partition of the set of sampled individuals, - the sample partition. In a fully Bayesian approach to clustering problems of this type, our knowledge about the sample partition is represented by a probability distribution on the space of possible sample partitions. Since the number of possible partitions grows very rapidly with the sample size, we can not visualise this probability distribution in its entirety, unless the sample is very small. As a solution to this visualisation problem, we recommend using an agglomerative hierarchical clustering algorithm, which we call the exact linkage algorithm. This algorithm is a special case of the maximin clustering algorithm that we introduced previously. The exact linkage algorithm is now implemented in our software package Partition View. The exact linkage algorithm takes the posterior co-assignment probabilities as input, and yields as output a rooted binary tree, - or more generally, a forest of such trees. Each node of this forest defines a set of individuals, and the node height is the posterior co-assignment probability of this set. This provides a useful visual representation of the uncertainty associated with the assignment of individuals to categories. It is also a useful starting point for a more detailed exploration of the posterior distribution in terms of the co-assignment probabilities. PMID:19337306

  5. Bayesian joint modeling of longitudinal and spatial survival AIDS data.

    PubMed

    Martins, Rui; Silva, Giovani L; Andreozzi, Valeska

    2016-08-30

    Joint analysis of longitudinal and survival data has received increasing attention in the recent years, especially for analyzing cancer and AIDS data. As both repeated measurements (longitudinal) and time-to-event (survival) outcomes are observed in an individual, a joint modeling is more appropriate because it takes into account the dependence between the two types of responses, which are often analyzed separately. We propose a Bayesian hierarchical model for jointly modeling longitudinal and survival data considering functional time and spatial frailty effects, respectively. That is, the proposed model deals with non-linear longitudinal effects and spatial survival effects accounting for the unobserved heterogeneity among individuals living in the same region. This joint approach is applied to a cohort study of patients with HIV/AIDS in Brazil during the years 2002-2006. Our Bayesian joint model presents considerable improvements in the estimation of survival times of the Brazilian HIV/AIDS patients when compared with those obtained through a separate survival model and shows that the spatial risk of death is the same across the different Brazilian states. Copyright © 2016 John Wiley & Sons, Ltd. PMID:26990773

  6. A Hierarchical Process-Dissociation Model

    ERIC Educational Resources Information Center

    Rouder, Jeffrey N.; Lu, Jun; Morey, Richard D.; Sun, Dongchu; Speckman, Paul L.

    2008-01-01

    In fitting the process-dissociation model (L. L. Jacoby, 1991) to observed data, researchers aggregate outcomes across participant, items, or both. T. Curran and D. L. Hintzman (1995) demonstrated how biases from aggregation may lead to artifactual support for the model. The authors develop a hierarchical process-dissociation model that does not…

  7. A hierarchical community occurrence model for North Carolina stream fish

    USGS Publications Warehouse

    Midway, S.R.; Wagner, Tyler; Tracy, B.H.

    2016-01-01

    The southeastern USA is home to one of the richest—and most imperiled and threatened—freshwater fish assemblages in North America. For many of these rare and threatened species, conservation efforts are often limited by a lack of data. Drawing on a unique and extensive data set spanning over 20 years, we modeled occurrence probabilities of 126 stream fish species sampled throughout North Carolina, many of which occur more broadly in the southeastern USA. Specifically, we developed species-specific occurrence probabilities from hierarchical Bayesian multispecies models that were based on common land use and land cover covariates. We also used index of biotic integrity tolerance classifications as a second level in the model hierarchy; we identify this level as informative for our work, but it is flexible for future model applications. Based on the partial-pooling property of the models, we were able to generate occurrence probabilities for many imperiled and data-poor species in addition to highlighting a considerable amount of occurrence heterogeneity that supports species-specific investigations whenever possible. Our results provide critical species-level information on many threatened and imperiled species as well as information that may assist with re-evaluation of existing management strategies, such as the use of surrogate species. Finally, we highlight the use of a relatively simple hierarchical model that can easily be generalized for similar situations in which conventional models fail to provide reliable estimates for data-poor groups.

  8. Statistical label fusion with hierarchical performance models

    PubMed Central

    Asman, Andrew J.; Dagley, Alexander S.; Landman, Bennett A.

    2014-01-01

    Label fusion is a critical step in many image segmentation frameworks (e.g., multi-atlas segmentation) as it provides a mechanism for generalizing a collection of labeled examples into a single estimate of the underlying segmentation. In the multi-label case, typical label fusion algorithms treat all labels equally – fully neglecting the known, yet complex, anatomical relationships exhibited in the data. To address this problem, we propose a generalized statistical fusion framework using hierarchical models of rater performance. Building on the seminal work in statistical fusion, we reformulate the traditional rater performance model from a multi-tiered hierarchical perspective. This new approach provides a natural framework for leveraging known anatomical relationships and accurately modeling the types of errors that raters (or atlases) make within a hierarchically consistent formulation. Herein, we describe several contributions. First, we derive a theoretical advancement to the statistical fusion framework that enables the simultaneous estimation of multiple (hierarchical) performance models within the statistical fusion context. Second, we demonstrate that the proposed hierarchical formulation is highly amenable to the state-of-the-art advancements that have been made to the statistical fusion framework. Lastly, in an empirical whole-brain segmentation task we demonstrate substantial qualitative and significant quantitative improvement in overall segmentation accuracy. PMID:24817809

  9. Bayesian Multiscale Modeling of Closed Curves in Point Clouds

    PubMed Central

    Gu, Kelvin; Pati, Debdeep; Dunson, David B.

    2014-01-01

    Modeling object boundaries based on image or point cloud data is frequently necessary in medical and scientific applications ranging from detecting tumor contours for targeted radiation therapy, to the classification of organisms based on their structural information. In low-contrast images or sparse and noisy point clouds, there is often insufficient data to recover local segments of the boundary in isolation. Thus, it becomes critical to model the entire boundary in the form of a closed curve. To achieve this, we develop a Bayesian hierarchical model that expresses highly diverse 2D objects in the form of closed curves. The model is based on a novel multiscale deformation process. By relating multiple objects through a hierarchical formulation, we can successfully recover missing boundaries by borrowing structural information from similar objects at the appropriate scale. Furthermore, the model’s latent parameters help interpret the population, indicating dimensions of significant structural variability and also specifying a ‘central curve’ that summarizes the collection. Theoretical properties of our prior are studied in specific cases and efficient Markov chain Monte Carlo methods are developed, evaluated through simulation examples and applied to panorex teeth images for modeling teeth contours and also to a brain tumor contour detection problem. PMID:25544786

  10. Normativity, interpretation, and Bayesian models

    PubMed Central

    Oaksford, Mike

    2014-01-01

    It has been suggested that evaluative normativity should be expunged from the psychology of reasoning. A broadly Davidsonian response to these arguments is presented. It is suggested that two distinctions, between different types of rationality, are more permeable than this argument requires and that the fundamental objection is to selecting theories that make the most rational sense of the data. It is argued that this is inevitable consequence of radical interpretation where understanding others requires assuming they share our own norms of reasoning. This requires evaluative normativity and it is shown that when asked to evaluate others’ arguments participants conform to rational Bayesian norms. It is suggested that logic and probability are not in competition and that the variety of norms is more limited than the arguments against evaluative normativity suppose. Moreover, the universality of belief ascription suggests that many of our norms are universal and hence evaluative. It is concluded that the union of evaluative normativity and descriptive psychology implicit in Davidson and apparent in the psychology of reasoning is a good thing. PMID:24860519