Science.gov

Sample records for hierarchical bayesian models

  1. Hierarchical Bayesian Models of Subtask Learning

    ERIC Educational Resources Information Center

    Anglim, Jeromy; Wynton, Sarah K. A.

    2015-01-01

    The current study used Bayesian hierarchical methods to challenge and extend previous work on subtask learning consistency. A general model of individual-level subtask learning was proposed focusing on power and exponential functions with constraints to test for inconsistency. To study subtask learning, we developed a novel computer-based booking…

  2. Hierarchical Bayesian models of cognitive development.

    PubMed

    Glassen, Thomas; Nitsch, Verena

    2016-06-01

    This article provides an introductory overview of the state of research on Hierarchical Bayesian Modeling in cognitive development. First, a brief historical summary and a definition of hierarchies in Bayesian modeling are given. Subsequently, some model structures are described based on four examples in the literature. These are models for the development of the shape bias, for learning ontological kinds and causal schemata as well as for the categorization of objects. The Bayesian modeling approach is then compared with the connectionist and nativist modeling paradigms and considered in view of Marr's (1982) three description levels of information-processing mechanisms. In this context, psychologically plausible algorithms and ideas of their neural implementation are presented. In addition to criticism and limitations of the approach, research needs are identified. PMID:27222110

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. Hierarchical Approximate Bayesian Computation

    PubMed Central

    Turner, Brandon M.; Van Zandt, Trisha

    2013-01-01

    Approximate Bayesian computation (ABC) is a powerful technique for estimating the posterior distribution of a model’s parameters. It is especially important when the model to be fit has no explicit likelihood function, which happens for computational (or simulation-based) models such as those that are popular in cognitive neuroscience and other areas in psychology. However, ABC is usually applied only to models with few parameters. Extending ABC to hierarchical models has been difficult because high-dimensional hierarchical models add computational complexity that conventional ABC cannot accommodate. In this paper we summarize some current approaches for performing hierarchical ABC and introduce a new algorithm called Gibbs ABC. This new algorithm incorporates well-known Bayesian techniques to improve the accuracy and efficiency of the ABC approach for estimation of hierarchical models. We then use the Gibbs ABC algorithm to estimate the parameters of two models of signal detection, one with and one without a tractable likelihood function. PMID:24297436

  8. 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.

  9. [A medical image semantic modeling based on hierarchical Bayesian networks].

    PubMed

    Lin, Chunyi; Ma, Lihong; Yin, Junxun; Chen, Jianyu

    2009-04-01

    A semantic modeling approach for medical image semantic retrieval based on hierarchical Bayesian networks was proposed, in allusion to characters of medical images. It used GMM (Gaussian mixture models) to map low-level image features into object semantics with probabilities, then it captured high-level semantics through fusing these object semantics using a Bayesian network, so that it built a multi-layer medical image semantic model, aiming to enable automatic image annotation and semantic retrieval by using various keywords at different semantic levels. As for the validity of this method, we have built a multi-level semantic model from a small set of astrocytoma MRI (magnetic resonance imaging) samples, in order to extract semantics of astrocytoma in malignant degree. Experiment results show that this is a superior approach.

  10. 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.

  11. DISSECTING MAGNETAR VARIABILITY WITH BAYESIAN HIERARCHICAL MODELS

    SciTech Connect

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

  12. Calibrating Subjective Probabilities Using Hierarchical Bayesian Models

    NASA Astrophysics Data System (ADS)

    Merkle, Edgar C.

    A body of psychological research has examined the correspondence between a judge's subjective probability of an event's outcome and the event's actual outcome. The research generally shows that subjective probabilities are noisy and do not match the "true" probabilities. However, subjective probabilities are still useful for forecasting purposes if they bear some relationship to true probabilities. The purpose of the current research is to exploit relationships between subjective probabilities and outcomes to create improved, model-based probabilities for forecasting. Once the model has been trained in situations where the outcome is known, it can then be used in forecasting situations where the outcome is unknown. These concepts are demonstrated using experimental psychology data, and potential applications are discussed.

  13. Bayesian hierarchical modeling for detecting safety signals in clinical trials.

    PubMed

    Xia, H Amy; Ma, Haijun; Carlin, Bradley P

    2011-09-01

    Detection of safety signals from clinical trial adverse event data is critical in drug development, but carries a challenging statistical multiplicity problem. Bayesian hierarchical mixture modeling is appealing for its ability to borrow strength across subgroups in the data, as well as moderate extreme findings most likely due merely to chance. We implement such a model for subject incidence (Berry and Berry, 2004 ) using a binomial likelihood, and extend it to subject-year adjusted incidence rate estimation under a Poisson likelihood. We use simulation to choose a signal detection threshold, and illustrate some effective graphics for displaying the flagged signals.

  14. Using Bayesian Networks to Model Hierarchical Relationships in Epidemiological Studies

    PubMed Central

    2011-01-01

    OBJECTIVES To propose an alternative procedure, based on a Bayesian network (BN), for estimation and prediction, and to discuss its usefulness for taking into account the hierarchical relationships among covariates. METHODS The procedure is illustrated by modeling the risk of diarrhea infection for 2,740 children aged 0 to 59 months in Cameroon. We compare the procedure with a standard logistic regression and with a model based on multi-level logistic regression. RESULTS The standard logistic regression approach is inadequate, or at least incomplete, in that it does not attempt to account for potentially causal relationships between risk factors. The multi-level logistic regression does model the hierarchical structure, but does so in a piecewise manner; the resulting estimates and interpretations differ from those of the BN approach proposed here. An advantage of the BN approach is that it enables one to determine the probability that a risk factor (and/or the outcome) is in any specific state, given the states of the others. The currently available approaches can only predict the outcome (disease), given the states of the covariates. CONCLUSION A major advantage of BNs is that they can deal with more complex interrelationships between variables whereas competing approaches deal at best only with hierarchical ones. We propose that BN be considered as well as a worthwhile method for summarizing the data in epidemiological studies whose aim is understanding the determinants of diseases and quantifying their effects. PMID:21779534

  15. 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

  16. A Bayesian hierarchical model for wind gust prediction

    NASA Astrophysics Data System (ADS)

    Friederichs, Petra; Oesting, Marco; Schlather, Martin

    2014-05-01

    A postprocessing method for ensemble wind gust forecasts given by a mesoscale limited area numerical weather prediction (NWP) model is presented, which is based on extreme value theory. A process layer for the parameters of a generalized extreme value distribution (GEV) is introduced using a Bayesian hierarchical model (BHM). Incorporating the information of the COMSO-DE forecasts, the process parameters model the spatial response surfaces of the GEV parameters as Gaussian random fields. The spatial BHM provides area wide forecasts of wind gusts in terms of a conditional GEV. It models the marginal distribution of the spatial gust process and provides not only forecasts of the conditional GEV at locations without observations, but also uncertainty information about the estimates. A disadvantages of BHM model is that it assumes conditional independent observations. In order to incorporate the dependence between gusts at neighboring locations as well as the spatial random fields of observed and forecasted maximal wind gusts, we propose to model them jointly by a bivariate Brown-Resnick process.

  17. 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

  18. 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

  19. Hierarchical models and Bayesian analysis of bird survey information

    USGS Publications Warehouse

    Sauer, J.R.; Link, W.A.; Royle, J. Andrew; Ralph, C. John; Rich, Terrell D.

    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.

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

    PubMed

    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.

  1. 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

  2. A Hierarchical Bayesian Model to Predict Self-Thinning Line for Chinese Fir in Southern China

    PubMed Central

    Zhang, Xiongqing; Zhang, Jianguo; Duan, Aiguo

    2015-01-01

    Self-thinning is a dynamic equilibrium between forest growth and mortality at full site occupancy. Parameters of the self-thinning lines are often confounded by differences across various stand and site conditions. For overcoming the problem of hierarchical and repeated measures, we used hierarchical Bayesian method to estimate the self-thinning line. The results showed that the self-thinning line for Chinese fir (Cunninghamia lanceolata (Lamb.)Hook.) plantations was not sensitive to the initial planting density. The uncertainty of model predictions was mostly due to within-subject variability. The simulation precision of hierarchical Bayesian method was better than that of stochastic frontier function (SFF). Hierarchical Bayesian method provided a reasonable explanation of the impact of other variables (site quality, soil type, aspect, etc.) on self-thinning line, which gave us the posterior distribution of parameters of self-thinning line. The research of self-thinning relationship could be benefit from the use of hierarchical Bayesian method. PMID:26440942

  3. 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...

  4. 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...

  5. 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 ...

  6. 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 ...

  7. 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 ...

  8. 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 ...

  9. 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 ...

  10. 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...

  11. Model-based hand tracking using a hierarchical Bayesian filter.

    PubMed

    Stenger, Björn; Thayananthan, Arasanathan; Torr, Philip H S; Cipolla, Roberto

    2006-09-01

    This paper sets out a tracking framework, which is applied to the recovery of three-dimensional hand motion from an image sequence. The method handles the issues of initialization, tracking, and recovery in a unified way. In a single input image with no prior information of the hand pose, the algorithm is equivalent to a hierarchical detection scheme, where unlikely pose candidates are rapidly discarded. In image sequences, a dynamic model is used to guide the search and approximate the optimal filtering equations. A dynamic model is given by transition probabilities between regions in parameter space and is learned from training data obtained by capturing articulated motion. The algorithm is evaluated on a number of image sequences, which include hand motion with self-occlusion in front of a cluttered background.

  12. 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.

  13. Phosphorus load estimation in the Saginaw River, MI using a Bayesian hierarchical/multilevel model.

    PubMed

    Cha, YoonKyung; Stow, Craig A; Reckhow, Kenneth H; DeMarchi, Carlo; Johengen, Thomas H

    2010-05-01

    We propose the use of Bayesian hierarchical/multilevel ratio approach to estimate the annual riverine phosphorus loads in the Saginaw River, Michigan, from 1968 to 2008. The ratio estimator is known to be an unbiased, precise approach for differing flow-concentration relationships and sampling schemes. A Bayesian model can explicitly address the uncertainty in prediction by using a posterior predictive distribution, while in comparison, a Bayesian hierarchical technique can overcome the limitation of interpreting the estimated annual loads inferred from small sample sizes by borrowing strength from the underlying population shared by the years of interest. Thus, by combining the ratio estimator with the Bayesian hierarchical modeling framework, long-term loads estimation can be addressed with explicit quantification of uncertainty. Our study results indicate a slight decrease in total phosphorus load early in the series. The estimated ratio parameter, which can be interpreted as flow-weighted concentration, shows a clearer decrease, damping the noise that yearly flow variation adds to the load. Despite the reductions, it is not likely that Saginaw Bay meets with its target phosphorus load, 440 tonnes/yr. Throughout the decades, the probabilities of the Saginaw Bay not complying with the target load are estimated as 1.00, 0.50, 0.57 and 0.36 in 1977, 1987, 1997, and 2007, respectively. We show that the Bayesian hierarchical model results in reasonable goodness-of-fits to the observations whether or not individual loads are aggregated. Also, this modeling approach can substantially reduce uncertainties associated with small sample sizes both in the estimated parameters and loads. PMID:20382406

  14. 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.

  15. Bayesian hierarchical modeling and the integration of heterogeneous information on the effectiveness of cardiovascular therapies.

    PubMed

    Kwok, Heemun; Lewis, Roger J

    2011-11-01

    When making therapeutic decisions for an individual patient or formulating treatment guidelines on a population level, it is often necessary to utilize information arising from different study designs, settings, or treatments. In clinical practice, heterogeneous information is frequently synthesized qualitatively, whereas in comparative effectiveness research and guideline development, it is imperative that heterogeneous data are integrated quantitatively and in a manner that accurately captures the true uncertainty in the results. Bayesian hierarchical modeling is a technique that utilizes all available information from multiple sources and naturally yields a revised estimate of the treatment effect associated with each source. A hierarchical model consists of multiple levels (ie, a hierarchy) of probability distributions that represent relationships between information arising within single populations or trials, as well as relationships between information arising from different populations or trials. We describe the structure of Bayesian hierarchical models and discuss their advantages over simpler models when multiple information sources are relevant. Two examples are presented that illustrate this technique: a meta-analysis of immunosuppressive therapy in idiopathic dilated cardiomyopathy and a subgroup analysis of the National Institute of Neurological Disorders and Stroke Intravenous Tissue Plasminogen Activator Stroke Trial. PMID:22085987

  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. 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.

  18. A hierarchical bayesian model to quantify uncertainty of stream water temperature forecasts.

    PubMed

    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.

  19. 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.

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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

    2015-02-10

    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.

  5. 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.

  6. 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.

  7. 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.

  8. Bayesian hierarchical Poisson models with a hidden Markov structure for the detection of influenza epidemic outbreaks.

    PubMed

    Conesa, D; Martínez-Beneito, M A; Amorós, R; López-Quílez, A

    2015-04-01

    Considerable effort has been devoted to the development of statistical algorithms for the automated monitoring of influenza surveillance data. In this article, we introduce a framework of models for the early detection of the onset of an influenza epidemic which is applicable to different kinds of surveillance data. In particular, the process of the observed cases is modelled via a Bayesian Hierarchical Poisson model in which the intensity parameter is a function of the incidence rate. The key point is to consider this incidence rate as a normal distribution in which both parameters (mean and variance) are modelled differently, depending on whether the system is in an epidemic or non-epidemic phase. To do so, we propose a hidden Markov model in which the transition between both phases is modelled as a function of the epidemic state of the previous week. Different options for modelling the rates are described, including the option of modelling the mean at each phase as autoregressive processes of order 0, 1 or 2. Bayesian inference is carried out to provide the probability of being in an epidemic state at any given moment. The methodology is applied to various influenza data sets. The results indicate that our methods outperform previous approaches in terms of sensitivity, specificity and timeliness.

  9. Assessing convergence of Markov chain Monte Carlo simulations in hierarchical Bayesian models for population pharmacokinetics.

    PubMed

    Dodds, Michael G; Vicini, Paolo

    2004-09-01

    Advances in computer hardware and the associated computer-intensive algorithms made feasible by these advances [like Markov chain Monte Carlo (MCMC) data analysis techniques] have made possible the application of hierarchical full Bayesian methods in analyzing pharmacokinetic and pharmacodynamic (PK-PD) data sets that are multivariate in nature. Pharmacokinetic data analysis in particular has been one area that has seized upon this technology to refine estimates of drug parameters from sparse data gathered in a large, highly variable population of patients. A drawback in this type of analysis is that it is difficult to quantitatively assess convergence of the Markov chains to a target distribution, and thus, it is sometimes difficult to assess the reliability of estimates gained from this procedure. Another complicating factor is that, although the application of MCMC methods to population PK-PD problems has been facilitated by new software designed for the PK-PD domain (specifically PKBUGS), experts in PK-PD may not have the necessary experience with MCMC methods to detect and understand problems with model convergence. The objective of this work is to provide an example of a set of diagnostics useful to investigators, by analyzing in detail three convergence criteria (namely the Raftery and Lewis, Geweke, and Heidelberger and Welch methods) on a simulated problem and with a rule of thumb of 10,000 chain elements in the Markov chain. We used two publicly available software packages to assess convergence of MCMC parameter estimates; the first performs Bayesian parameter estimation (PKBUGS/WinBUGS), and the second is focused on posterior analysis of estimates (BOA). The main message that seems to emerge is that accurately estimating confidence regions for the parameters of interest is more demanding than estimating the parameter means. Together, these tools provide numerical means by which an investigator can establish confidence in convergence and thus in the

  10. Bayesian hierarchical models for smoothing in two-phase studies, with application to small area estimation

    PubMed Central

    Ross, Michelle; Wakefield, Jon

    2015-01-01

    Summary Two-phase study designs are appealing since they allow for the oversampling of rare sub-populations which improves efficiency. In this paper we describe a Bayesian hierarchical model for the analysis of two-phase data. Such a model is particularly appealing in a spatial setting in which random effects are introduced to model between-area variability. In such a situation, one may be interested in estimating regression coefficients or, in the context of small area estimation, in reconstructing the population totals by strata. The efficiency gains of the two-phase sampling scheme are compared to standard approaches using 2011 birth data from the research triangle area of North Carolina. We show that the proposed method can overcome small sample difficulties and improve on existing techniques. We conclude that the two-phase design is an attractive approach for small area estimation. PMID:26705382

  11. 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.

  12. 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

  13. Relationships between anaemia and parasitic infections in Kenyan schoolchildren: a Bayesian hierarchical modelling approach.

    PubMed

    Koukounari, Artemis; Estambale, Benson B A; Njagi, J Kiambo; Cundill, Bonnie; Ajanga, Anthony; Crudder, Christopher; Otido, Julius; Jukes, Matthew C H; Clarke, Siân E; Brooker, Simon

    2008-12-01

    Anaemia is multi-factorial in origin and disentangling its aetiology remains problematic, with surprisingly few studies investigating the relative contribution of different parasitic infections to anaemia amongst schoolchildren. We report cross-sectional data on haemoglobin, malaria parasitaemia, helminth infection and undernutrition among 1523 schoolchildren enrolled in classes 5 and 6 (aged 10-21 years) in 30 primary schools in western Kenya. Bayesian hierarchical modelling was used to investigate putative relationships. Children infected with Plasmodium falciparum or with a heavy Schistosoma mansoni infection, stunted children and girls were found to have lower haemoglobin concentrations. Children heavily infected with S. mansoni were also more likely to be anaemic compared with uninfected children. This study further highlights the importance of malaria and intestinal schistosomiasis as contributors to reduced haemoglobin levels among schoolchildren and helps guide the implementation of integrated school health programmes in areas of differing parasite transmission.

  14. Relationships between anaemia and parasitic infections in Kenyan schoolchildren: A Bayesian hierarchical modelling approach

    PubMed Central

    Koukounari, Artemis; Estambale, Benson B.A.; Kiambo Njagi, J.; Cundill, Bonnie; Ajanga, Anthony; Crudder, Christopher; Otido, Julius; Jukes, Matthew C.H.; Clarke, Siân E.; Brooker, Simon

    2008-01-01

    Anaemia is multi-factorial in origin and disentangling its aetiology remains problematic, with surprisingly few studies investigating the relative contribution of different parasitic infections to anaemia amongst schoolchildren. We report cross-sectional data on haemoglobin, malaria parasitaemia, helminth infection and undernutrition among 1523 schoolchildren enrolled in classes 5 and 6 (aged 10–21 years) in 30 primary schools in western Kenya. Bayesian hierarchical modelling was used to investigate putative relationships. Children infected with Plasmodium falciparum or with a heavy Schistosoma mansoni infection, stunted children and girls were found to have lower haemoglobin concentrations. Children heavily infected with S. mansoni were also more likely to be anaemic compared with uninfected children. This study further highlights the importance of malaria and intestinal schistosomiasis as contributors to reduced haemoglobin levels among schoolchildren and helps guide the implementation of integrated school health programmes in areas of differing parasite transmission. PMID:18621051

  15. 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.

  16. Bayesian Hierarchical Poisson Regression Models: An Application to a Driving Study with Kinematic Events

    PubMed Central

    Kim, Sungduk; Chen, Zhen; Zhang, Zhiwei; Simons-Morton, Bruce G.; Albert, Paul S.

    2013-01-01

    Although there is evidence that teenagers are at a high risk of crashes in the early months after licensure, the driving behavior of these teenagers is not well understood. The Naturalistic Teenage Driving Study (NTDS) is the first U.S. study to document continuous driving performance of newly-licensed teenagers during their first 18 months of licensure. Counts of kinematic events such as the number of rapid accelerations are available for each trip, and their incidence rates represent different aspects of driving behavior. We propose a hierarchical Poisson regression model incorporating over-dispersion, heterogeneity, and serial correlation as well as a semiparametric mean structure. Analysis of the NTDS data is carried out with a hierarchical Bayesian framework using reversible jump Markov chain Monte Carlo algorithms to accommodate the flexible mean structure. We show that driving with a passenger and night driving decrease kinematic events, while having risky friends increases these events. Further the within-subject variation in these events is comparable to the between-subject variation. This methodology will be useful for other intensively collected longitudinal count data, where event rates are low and interest focuses on estimating the mean and variance structure of the process. This article has online supplementary materials. PMID:24076760

  17. 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

  18. 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.

  19. A BAYESIAN HIERARCHICAL SPATIAL MODEL FOR DENTAL CARIES ASSESSMENT USING NON-GAUSSIAN MARKOV RANDOM FIELDS

    PubMed Central

    Jin, Ick Hoon; Yuan, Ying; Bandyopadhyay, Dipankar

    2016-01-01

    Research in dental caries generates data with two levels of hierarchy: that of a tooth overall and that of the different surfaces of the tooth. The outcomes often exhibit spatial referencing among neighboring teeth and surfaces, i.e., the disease status of a tooth or surface might be influenced by the status of a set of proximal teeth/surfaces. Assessments of dental caries (tooth decay) at the tooth level yield binary outcomes indicating the presence/absence of teeth, and trinary outcomes at the surface level indicating healthy, decayed, or filled surfaces. The presence of these mixed discrete responses complicates the data analysis under a unified framework. To mitigate complications, we develop a Bayesian two-level hierarchical model under suitable (spatial) Markov random field assumptions that accommodates the natural hierarchy within the mixed responses. At the first level, we utilize an autologistic model to accommodate the spatial dependence for the tooth-level binary outcomes. For the second level and conditioned on a tooth being non-missing, we utilize a Potts model to accommodate the spatial referencing for the surface-level trinary outcomes. The regression models at both levels were controlled for plausible covariates (risk factors) of caries, and remain connected through shared parameters. To tackle the computational challenges in our Bayesian estimation scheme caused due to the doubly-intractable normalizing constant, we employ a double Metropolis-Hastings sampler. We compare and contrast our model performances to the standard non-spatial (naive) model using a small simulation study, and illustrate via an application to a clinical dataset on dental caries. PMID:27807470

  20. 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

  1. Hierarchical Bayesian Approach to Locating Seismic Events

    SciTech Connect

    Johannesson, G; Myers, S C; Hanley, W G

    2005-11-09

    We propose a hierarchical Bayesian model for conducting inference on the location of multiple seismic events (earthquakes) given data on the arrival of various seismic phases to sensor locations. The model explicitly accounts for the uncertainty associated with a theoretical seismic-wave travel-time model used along with the uncertainty of the arrival data. Posterior inferences is carried out using Markov chain Monte Carlo (MCMC).

  2. 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

  3. A hierarchical Bayesian model to estimate the unobservable predation rate on sawfly cocoons by small mammals

    PubMed Central

    Pinkantayong, Panisara; Suzuki, Satoshi; Kubo, Mamoru; Muramoto, Ken-ichiro; Kamata, Naoto

    2015-01-01

    Predation by small mammals has been reported as an important mortality factor for the cocoons of sawfly species. However, it is difficult to provide an accurate estimate of newly spun cocoons and subsequent predation rates by small mammals for several reasons. First, all larvae do not spin cocoons at the same time. Second, cocoons are exposed to small mammal predation immediately after being spun. Third, the cocoons of the current generation are indistinguishable from those of the previous generation. We developed a hierarchical Bayesian model to estimate these values from annual one-time soil sampling datasets. To apply this model to an actual data set, field surveys were conducted in eight stands of larch plantations in central Hokkaido (Japan) from 2009 to 2012. Ten 0.04-m2 soil samples were annually collected from each site in mid-October. The abundance of unopened cocoons (I), cocoons emptied by small-mammal predation (M), and empty cocoons caused by something other than small-mammal predation (H) were determined. The abundance of newly spun cocoons, the predation rate by small mammals before and after cocoon sampling, and the annual rate of empty cocoons that remained were estimated. A posterior predictive check yielded Bayesian P-values of 0.54, 0.48, and 0.07 for I, M, and H, respectively. Estimated predation rates showed a significant positive correlation with the number of trap captures of small mammals. Estimates of the number of newly spun cocoons had a significant positive correlation with defoliation intensity. These results indicate that our model showed an acceptable fit, with reasonable estimates. Our model is expected to be widely applicable to all hymenopteran and lepidopteran insects that spin cocoons in soil. PMID:25691994

  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 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.

  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. 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

  8. Hierarchical Bayesian modeling of heterogeneous variances in average daily weight gain of commercial feedlot cattle.

    PubMed

    Cernicchiaro, N; Renter, D G; Xiang, S; White, B J; Bello, N M

    2013-06-01

    Variability in ADG of feedlot cattle can affect profits, thus making overall returns more unstable. Hence, knowledge of the factors that contribute to heterogeneity of variances in animal performance can help feedlot managers evaluate risks and minimize profit volatility when making managerial and economic decisions in commercial feedlots. The objectives of the present study were to evaluate heteroskedasticity, defined as heterogeneity of variances, in ADG of cohorts of commercial feedlot cattle, and to identify cattle demographic factors at feedlot arrival as potential sources of variance heterogeneity, accounting for cohort- and feedlot-level information in the data structure. An operational dataset compiled from 24,050 cohorts from 25 U. S. commercial feedlots in 2005 and 2006 was used for this study. Inference was based on a hierarchical Bayesian model implemented with Markov chain Monte Carlo, whereby cohorts were modeled at the residual level and feedlot-year clusters were modeled as random effects. Forward model selection based on deviance information criteria was used to screen potentially important explanatory variables for heteroskedasticity at cohort- and feedlot-year levels. The Bayesian modeling framework was preferred as it naturally accommodates the inherently hierarchical structure of feedlot data whereby cohorts are nested within feedlot-year clusters. Evidence for heterogeneity of variance components of ADG was substantial and primarily concentrated at the cohort level. Feedlot-year specific effects were, by far, the greatest contributors to ADG heteroskedasticity among cohorts, with an estimated ∼12-fold change in dispersion between most and least extreme feedlot-year clusters. In addition, identifiable demographic factors associated with greater heterogeneity of cohort-level variance included smaller cohort sizes, fewer days on feed, and greater arrival BW, as well as feedlot arrival during summer months. These results support that

  9. Modeling hypoxia in the Chesapeake Bay: Ensemble estimation using a Bayesian hierarchical model

    NASA Astrophysics Data System (ADS)

    Stow, Craig A.; Scavia, Donald

    2009-02-01

    Quantifying parameter and prediction uncertainty in a rigorous framework can be an important component of model skill assessment. Generally, models with lower uncertainty will be more useful for prediction and inference than models with higher uncertainty. Ensemble estimation, an idea with deep roots in the Bayesian literature, can be useful to reduce model uncertainty. It is based on the idea that simultaneously estimating common or similar parameters among models can result in more precise estimates. We demonstrate this approach using the Streeter-Phelps dissolved oxygen sag model fit to 29 years of data from Chesapeake Bay. Chesapeake Bay has a long history of bottom water hypoxia and several models are being used to assist management decision-making in this system. The Bayesian framework is particularly useful in a decision context because it can combine both expert-judgment and rigorous parameter estimation to yield model forecasts and a probabilistic estimate of the forecast uncertainty.

  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 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

  12. 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.

  13. 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

  14. Multiple testing on standardized mortality ratios: a Bayesian hierarchical model for FDR estimation.

    PubMed

    Ventrucci, Massimo; Scott, E Marian; Cocchi, Daniela

    2011-01-01

    The analysis of large data sets of standardized mortality ratios (SMRs), obtained by collecting observed and expected disease counts in a map of contiguous regions, is a first step in descriptive epidemiology to detect potential environmental risk factors. A common situation arises when counts are collected in small areas, that is, where the expected count is very low, and disease risks underlying the map are spatially correlated. Traditional p-value-based methods, which control the false discovery rate (FDR) by means of Poisson p-values, might achieve small sensitivity in identifying risk in small areas. This problem is the focus of the present work, where a Bayesian approach which performs a test to evaluate the null hypothesis of no risk over each SMR and controls the posterior FDR is proposed. A Bayesian hierarchical model including spatial random effects to allow for extra-Poisson variability is implemented providing estimates of the posterior probabilities that the null hypothesis of absence of risk is true. By means of such posterior probabilities, an estimate of the posterior FDR conditional on the data can be computed. A conservative estimation is needed to achieve the control which is checked by simulation. The availability of this estimate allows the practitioner to determine nonarbitrary FDR-based selection rules to identify high-risk areas according to a preset FDR level. Sensitivity and specificity of FDR-based rules are studied via simulation and a comparison with p-value-based rules is also shown. A real data set is analyzed using rules based on several FDR levels.

  15. Bayesian Hierarchical Mixture Modelling to Assign Copy Number from a targeted CNV array

    PubMed Central

    Cardin, Niall; Holmes, Chris; Donnelly, Peter; Marchini, Jonathan

    2011-01-01

    Accurate assignment of copy number at known copy number variant (CNV) loci is important for both increasing understanding of the structural evolution of genomes as well as for carrying out association studies of copy number with disease. As with calling SNP genotypes, the task can be framed as a clustering problem but for a number of reasons assigning copy number is much more challenging. CNV-assays have lower signal to noise ratios than SNP assays, often display heavy tailed and asymmetric intensity distributions, contain outlying observations and may exhibit systematic technical differences among different cohorts. In addition, the number of copy-number classes at a CNV in the population may be unknown a priori. Due to these complications automatic and robust assignment of copy number from array data remains a challenging problem. We have developed a copy number assignment algorithm, CNVCALL, for a targeted CNV array, such as that used by the Wellcome Trust Case Control Consortium’s recent CNV association study. We use a Bayesian hierarchical mixture model that robustly identifies both the number of different copy number classes at a specific locus as well as relative copy number for each individual in the sample. This approach is fully automated which is a critical requirement when analysing large numbers of CNVs. We illustrate the methods performance using real data from the WTCCC’s CNV association study and using simulated data. PMID:21769931

  16. Estimation of isoform expression in RNA-seq data using a hierarchical Bayesian model.

    PubMed

    Wang, Zengmiao; Wang, Jun; Wu, Changjing; Deng, Minghua

    2015-12-01

    Estimation of gene or isoform expression is a fundamental step in many transcriptome analysis tasks, such as differential expression analysis, eQTL (or sQTL) studies, and biological network construction. RNA-seq technology enables us to monitor the expression on genome-wide scale at single base pair resolution and offers the possibility of accurately measuring expression at the level of isoform. However, challenges remain because of non-uniform read sampling and the presence of various biases in RNA-seq data. In this paper, we present a novel hierarchical Bayesian method to estimate isoform expression. While most of the existing methods treat gene expression as a by-product, we incorporate it into our model and explicitly describe its relationship with corresponding isoform expression using a Multinomial distribution. In this way, gene and isoform expression are included in a unified framework and it helps us achieve a better performance over other state-of-the-art algorithms for isoform expression estimation. The effectiveness of the proposed method is demonstrated using both simulated data with known ground truth and two real RNA-seq datasets from MAQC project. The codes are available at http://www.math.pku.edu.cn/teachers/dengmh/GIExp/.

  17. A hierarchical Bayesian modeling approach to searching and stopping in multi-attribute judgment.

    PubMed

    van Ravenzwaaij, Don; Moore, Chris P; Lee, Michael D; Newell, Ben R

    2014-01-01

    In most decision-making situations, there is a plethora of information potentially available to people. Deciding what information to gather and what to ignore is no small feat. How do decision makers determine in what sequence to collect information and when to stop? In two experiments, we administered a version of the German cities task developed by Gigerenzer and Goldstein (1996), in which participants had to decide which of two cities had the larger population. Decision makers were not provided with the names of the cities, but they were able to collect different kinds of cues for both response alternatives (e.g., "Does this city have a university?") before making a decision. Our experiments differed in whether participants were free to determine the number of cues they examined. We demonstrate that a novel model, using hierarchical latent mixtures and Bayesian inference (Lee & Newell, ) provides a more complete description of the data from both experiments than simple conventional strategies, such as the take-the-best or the Weighted Additive heuristics. PMID:24646326

  18. The application of a hierarchical Bayesian spatiotemporal model for forecasting the SAA trapped particle flux distribution

    NASA Astrophysics Data System (ADS)

    Suparta, Wayan; Gusrizal

    2014-08-01

    We implement a hierarchical Bayesian spatiotemporal (HBST) model to forecast the daily trapped particle flux distribution over the South Atlantic Anomaly (SAA) region. The National Oceanic and Atmospheric Administration (NOAA)-15 data from 1-30 March 2008 with particle energies as >30 keV (mep0e1) and >300 keV (mep0e3) for electrons and 80-240 keV (mep0p2) and > 6900 keV (mep0p6) for protons were used as the model input to forecast the flux values on 31 March 2008. Data were transformed into logarithmic values and gridded in a 5∘×5∘ longitude and latitude size to fulfill the modelling precondition. A Monte Carlo Markov chain (MCMC) was then performed to solve the HBST Gaussian Process (GP) model by using the Gibbs sampling method. The result for this model was interpolated by a Kriging technique to achieve the whole distribution figure over the SAA region. Statistical results of the root mean square error (RMSE), mean absolute percentage error (MAPE), and bias (BIAS) showed a good indicator of the HBST method. The statistical validation also indicated the high variability of particle flux values in the SAA core area. The visual validation showed a powerful combination of HBST-GP model with Kriging interpolation technique. The Kriging also produced a good quality of the distribution map of particle flux over the SAA region as indicated by its small variance value. This suggests that the model can be applied in the development of a Low Earth Orbit (LEO)-Equatorial satellite for monitoring trapped particle radiation hazard.

  19. Bayesian hierarchical models for soil CO{sub 2} flux and leak detection at geologic sequestration sites

    SciTech Connect

    Yang, Ya-Mei; Small, Mitchell J.; Junker, Brian; Bromhal, Grant S.; Strazisar, Brian; Wells, Arthur

    2011-10-01

    Proper characterizations of background soil CO{sub 2} respiration rates are critical for interpreting CO{sub 2} leakage monitoring results at geologic sequestration sites. In this paper, a method is developed for determining temperature-dependent critical values of soil CO{sub 2} flux for preliminary leak detection inference. The method is illustrated using surface CO{sub 2} flux measurements obtained from the AmeriFlux network fit with alternative models for the soil CO{sub 2} flux versus soil temperature relationship. The models are fit first to determine pooled parameter estimates across the sites, then using a Bayesian hierarchical method to obtain both global and site-specific parameter estimates. Model comparisons are made using the deviance information criterion (DIC), which considers both goodness of fit and model complexity. The hierarchical models consistently outperform the corresponding pooled models, demonstrating the need for site-specific data and estimates when determining relationships for background soil respiration. A hierarchical model that relates the square root of the CO{sub 2} flux to a quadratic function of soil temperature is found to provide the best fit for the AmeriFlux sites among the models tested. This model also yields effective prediction intervals, consistent with the upper envelope of the flux data across the modeled sites and temperature ranges. Calculation of upper prediction intervals using the proposed method can provide a basis for setting critical values in CO{sub 2} leak detection monitoring at sequestration sites.

  20. 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

  1. Development of Hierarchical Bayesian Model Based on Regional Frequency Analysis and Its Application to Estimate Areal Rainfall in South Korea

    NASA Astrophysics Data System (ADS)

    Kim, J.; Kwon, H. H.

    2014-12-01

    The existing regional frequency analysis has disadvantages in that it is difficult to consider geographical characteristics in estimating areal rainfall. In this regard, This study aims to develop a hierarchical Bayesian model based regional frequency analysis in that spatial patterns of the design rainfall with geographical information are explicitly incorporated. This study assumes that the parameters of Gumbel distribution are a function of geographical characteristics (e.g. altitude, latitude and longitude) within a general linear regression framework. Posterior distributions of the regression parameters are estimated by Bayesian Markov Chain Monte Calro (MCMC) method, and the identified functional relationship is used to spatially interpolate the parameters of the Gumbel distribution by using digital elevation models (DEM) as inputs. The proposed model is applied to derive design rainfalls over the entire Han-river watershed. It was found that the proposed Bayesian regional frequency analysis model showed similar results compared to L-moment based regional frequency analysis. In addition, the model showed an advantage in terms of quantifying uncertainty of the design rainfall and estimating the area rainfall considering geographical information. Acknowledgement: This research was supported by a grant (14AWMP-B079364-01) from Water Management Research Program funded by Ministry of Land, Infrastructure and Transport of Korean government.

  2. 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.

  3. Analysis of human mini-exome sequencing data from Genetic Analysis Workshop 17 using a Bayesian hierarchical mixture model

    PubMed Central

    2011-01-01

    Next-generation sequencing technologies are rapidly changing the field of genetic epidemiology and enabling exploration of the full allele frequency spectrum underlying complex diseases. Although sequencing technologies have shifted our focus toward rare genetic variants, statistical methods traditionally used in genetic association studies are inadequate for estimating effects of low minor allele frequency variants. Four our study we use the Genetic Analysis Workshop 17 data from 697 unrelated individuals (genotypes for 24,487 autosomal variants from 3,205 genes). We apply a Bayesian hierarchical mixture model to identify genes associated with a simulated binary phenotype using a transformed genotype design matrix weighted by allele frequencies. A Metropolis Hasting algorithm is used to jointly sample each indicator variable and additive genetic effect pair from its conditional posterior distribution, and remaining parameters are sampled by Gibbs sampling. This method identified 58 genes with a posterior probability greater than 0.8 for being associated with the phenotype. One of these 58 genes, PIK3C2B was correctly identified as being associated with affected status based on the simulation process. This project demonstrates the utility of Bayesian hierarchical mixture models using a transformed genotype matrix to detect genes containing rare and common variants associated with a binary phenotype. PMID:22373180

  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. 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

  6. 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.

  7. 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.

  8. 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

  9. Advances in Parameter and Uncertainty Quantification Using Bayesian Hierarchical Techniques with a Spatially Referenced Watershed Model (Invited)

    NASA Astrophysics Data System (ADS)

    Alexander, R. B.; Boyer, E. W.; Schwarz, G. E.; Smith, R. A.

    2013-12-01

    Estimating water and material stores and fluxes in watershed studies is frequently complicated by uncertainties in quantifying hydrological and biogeochemical effects of factors such as land use, soils, and climate. Although these process-related effects are commonly measured and modeled in separate catchments, researchers are especially challenged by their complexity across catchments and diverse environmental settings, leading to a poor understanding of how model parameters and prediction uncertainties vary spatially. To address these concerns, we illustrate the use of Bayesian hierarchical modeling techniques with a dynamic version of the spatially referenced watershed model SPARROW (SPAtially Referenced Regression On Watershed attributes). The dynamic SPARROW model is designed to predict streamflow and other water cycle components (e.g., evapotranspiration, soil and groundwater storage) for monthly varying hydrological regimes, using mechanistic functions, mass conservation constraints, and statistically estimated parameters. In this application, the model domain includes nearly 30,000 NHD (National Hydrologic Data) stream reaches and their associated catchments in the Susquehanna River Basin. We report the results of our comparisons of alternative models of varying complexity, including models with different explanatory variables as well as hierarchical models that account for spatial and temporal variability in model parameters and variance (error) components. The model errors are evaluated for changes with season and catchment size and correlations in time and space. The hierarchical models consist of a two-tiered structure in which climate forcing parameters are modeled as random variables, conditioned on watershed properties. Quantification of spatial and temporal variations in the hydrological parameters and model uncertainties in this approach leads to more efficient (lower variance) and less biased model predictions throughout the river network

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. Bayesian Hierarchical Model for Multiple Repeated Measures and Survival Data: an application to Parkinson's Disease

    PubMed Central

    Luo, Sheng; Wang, Jue

    2014-01-01

    Multilevel item response theory (MLIRT) 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 MLIRT 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 DATATOP study to investigate the effect of tocopherol in slowing PD progression. PMID:24935619

  16. 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

  17. 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

  18. 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

  19. Bayesian Hierarchical Model for Estimating Gene Expression Intensity Using Multiple Scanned Microarrays

    PubMed Central

    2008-01-01

    We propose a method for improving the quality of signal from DNA microarrays by using several scans at varying scanner sen-sitivities. A Bayesian latent intensity model is introduced for the analysis of such data. The method improves the accuracy at which expressions can be measured in all ranges and extends the dynamic range of measured gene expression at the high end. Our method is generic and can be applied to data from any organism, for imaging with any scanner that allows varying the laser power, and for extraction with any image analysis software. Results from a self-self hybridization data set illustrate an improved precision in the estimation of the expression of genes compared to what can be achieved by applying standard methods and using only a single scan. PMID:18464926

  20. Manual hierarchical clustering of regional geochemical data using a Bayesian finite mixture model

    USGS Publications Warehouse

    Ellefsen, Karl J.; Smith, David

    2016-01-01

    Interpretation of regional scale, multivariate geochemical data is aided by a statistical technique called “clustering.” We investigate a particular clustering procedure by applying it to geochemical data collected in the State of Colorado, United States of America. The clustering procedure partitions the field samples for the entire survey area into two clusters. The field samples in each cluster are partitioned again to create two subclusters, and so on. This manual procedure generates a hierarchy of clusters, and the different levels of the hierarchy show geochemical and geological processes occurring at different spatial scales. Although there are many different clustering methods, we use Bayesian finite mixture modeling with two probability distributions, which yields two clusters. The model parameters are estimated with Hamiltonian Monte Carlo sampling of the posterior probability density function, which usually has multiple modes. Each mode has its own set of model parameters; each set is checked to ensure that it is consistent both with the data and with independent geologic knowledge. The set of model parameters that is most consistent with the independent geologic knowledge is selected for detailed interpretation and partitioning of the field samples.

  1. 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

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

    PubMed

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

    2014-09-01

    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.

  3. 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

  4. Influence of Climate Change on Flood Hazard using Climate Informed Bayesian Hierarchical Model in Johnson Creek River

    NASA Astrophysics Data System (ADS)

    Zarekarizi, M.; Moradkhani, H.

    2015-12-01

    Extreme events are proven to be affected by climate change, influencing hydrologic simulations for which stationarity is usually a main assumption. Studies have discussed that this assumption would lead to large bias in model estimations and higher flood hazard consequently. Getting inspired by the importance of non-stationarity, we determined how the exceedance probabilities have changed over time in Johnson Creek River, Oregon. This could help estimate the probability of failure of a structure that was primarily designed to resist less likely floods according to common practice. Therefore, we built a climate informed Bayesian hierarchical model and non-stationarity was considered in modeling framework. Principle component analysis shows that North Atlantic Oscillation (NAO), Western Pacific Index (WPI) and Eastern Asia (EA) are mostly affecting stream flow in this river. We modeled flood extremes using peaks over threshold (POT) method rather than conventional annual maximum flood (AMF) mainly because it is possible to base the model on more information. We used available threshold selection methods to select a suitable threshold for the study area. Accounting for non-stationarity, model parameters vary through time with climate indices. We developed a couple of model scenarios and chose one which could best explain the variation in data based on performance measures. We also estimated return periods under non-stationarity condition. Results show that ignoring stationarity could increase the flood hazard up to four times which could increase the probability of an in-stream structure being overtopped.

  5. Predicting the probability of abortion in dairy cows: a hierarchical Bayesian logistic-survival model using sequential pregnancy data.

    PubMed

    Thurmond, M C; Branscum, A J; Johnson, W O; Bedrick, E J; Hanson, T E

    2005-05-10

    Although abortion contributes substantially to poor reproductive health of dairy herds, little is known about the predictability of abortion based on age, previous abortion or gravidity (number of previous pregnancies). A poor understanding of effects of maternal factors on abortion risk exists, in part, because of methodological difficulties related to non-independence of multiple pregnancies of the same cow in analysis of fetal survival data. We prospectively examined sequential pregnancies to investigate relationships between fetal survival and putative dam risk factors for 2991 abortions from 24,706 pregnancies of 13,145 cows in nine California dairy herds. Relative risks and predicted probabilities of abortion (PPA) were estimated using a previously described hierarchical Bayesian logistic-survival model generalized to incorporate longitudinal data of multiple pregnancies from a single cow. The PPA increased with increasing dam age at conception, with increasing number of previous abortions, and if the previous pregnancy was aborted >60 days in gestation. The PPA decreased with increasing gravidity and with increasing number of days open. For cows that aborted, the median time to fetal death decreased slightly as gravidity increased. The study considers several methodological issues faced in epidemiologic investigations of fetal health, including multi-modal hazard functions, extensive censoring and non-independence of multiple pregnancies. The model improves our ability to predict bovine abortion and to characterize fetal survival, which have important applications to herd health management.

  6. 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

  7. 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.

  8. A Bayesian hierarchical model of Antarctic fur seal foraging and pup growth related to sea ice and prey abundance.

    PubMed

    Hiruki-Raring, Lisa M; Ver Hoef, Jay M; Boveng, Peter L; Bengtson, John L

    2012-03-01

    We created a Bayesian hierarchical model (BHM) to investigate ecosystem relationships between the physical ecosystem (sea ice extent), a prey measure (krill density), predator behaviors (diving and foraging effort of female Antarctic fur seals, Arctocephalus gazella, with pups) and predator characteristics (mass of maternal fur seals and pups). We collected data on Antarctic fur seals from 1987/1988 to 1994/1995 at Seal Island, Antarctica. The BHM allowed us to link together predators and prey into a model that uses all the data efficiently and accounts for major sources of uncertainty. Based on the literature, we made hypotheses about the relationships in the model, which we compared with the model outcome after fitting the BHM. For each BHM parameter, we calculated the mean of the posterior density and the 95% credible interval. Our model confirmed others' findings that increased sea ice was related to increased krill density. Higher krill density led to reduced dive intensity of maternal fur seals, as measured by dive depth and duration, and to less time spent foraging by maternal fur seals. Heavier maternal fur seals and lower maternal foraging effort resulted in heavier pups at 22 d. No relationship was found between krill density and maternal mass, or between maternal mass and foraging effort on pup growth rates between 22 and 85 days of age. Maternal mass may have reflected environmental conditions prior to the pup provisioning season, rather than summer prey densities. Maternal mass and foraging effort were not related to pup growth rates between 22 and 85 d, possibly indicating that food was not limiting, food sources other than krill were being used, or differences occurred before pups reached age 22 d.

  9. Development of a hierarchical Bayesian model to estimate the growth parameters of Listeria monocytogenes in minimally processed fresh leafy salads.

    PubMed

    Crépet, Amélie; Stahl, Valérie; Carlin, Frédéric

    2009-05-31

    The optimal growth rate mu(opt) of Listeria monocytogenes in minimally processed (MP) fresh leafy salads was estimated with a hierarchical Bayesian model at (mean+/-standard deviation) 0.33+/-0.16 h(-1). This mu(opt) value was much lower on average than that in nutrient broth, liquid dairy, meat and seafood products (0.7-1.3 h(-1)), and of the same order of magnitude as in cheese. Cardinal temperatures T(min), T(opt) and T(max) were determined at -4.5+/-1.3 degrees C, 37.1+/-1.3 degrees C and 45.4+/-1.2 degrees C respectively. These parameters were determined from 206 growth curves of L. monocytogenes in MP fresh leafy salads (lettuce including iceberg lettuce, broad leaf endive, curly leaf endive, lamb's lettuce, and mixtures of them) selected in the scientific literature and in technical reports. The adequacy of the model was evaluated by comparing observed data (bacterial concentrations at each experimental time for the completion of the 206 growth curves, mean log(10) increase at selected times and temperatures, L. monocytogenes concentrations in naturally contaminated MP iceberg lettuce) with the distribution of the predicted data generated by the model. The sensitivity of the model to assumptions about the prior values also was tested. The observed values mostly fell into the 95% credible interval of the distribution of predicted values. The mu(opt) and its uncertainty determined in this work could be used in quantitative microbial risk assessment for L. monocytogenes in minimally processed fresh leafy salads.

  10. 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.

  11. 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

  12. 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

  13. 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

  14. 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.

  15. 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

  16. 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

  17. 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

  18. 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…

  19. 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…

  20. 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...

  1. 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

  2. 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.

  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

    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

  5. 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

  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.

  7. 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

  8. Bayesian hierarchical framework for occupational hygiene decision making.

    PubMed

    Banerjee, Sudipto; Ramachandran, Gurumurthy; Vadali, Monika; Sahmel, Jennifer

    2014-11-01

    A hierarchical Bayesian framework has been developed for exposure assessment that makes use of statistical sampling-based techniques to estimate the posterior probability of the 95th percentile or arithmetic mean of the exposure distribution being located in one of several exposure categories. The framework can synthesize professional judgment and monitoring data to yield an updated posterior exposure assignment for routine exposure management. The framework is versatile enough that it can be modified for use in epidemiological studies for classifying the arithmetic mean instead of the 95th percentile into several exposure categories. Various physico-chemical exposure models have also been incorporated in the hierarchical framework. The use of the framework in three settings has been illustrated. First, subjective judgments about exposure magnitude obtained from industrial hygienists for five tasks were treated as priors in the Bayesian framework. Monitoring data for each task were used to create a likelihood function in the hierarchical framework and the posterior was predicted in terms of the 95th percentile being located in each of the four AIHA exposure categories. The accuracy of the exposure judgments was then evaluated. Second, we illustrate the use of exposure models to develop priors in this framework and compare with monitoring data in an iron foundry. Finally, we illustrate the use of this approach for retrospective exposure assessment in a chemical manufacturing facility, to categorize exposures based on arithmetic mean instead of 95th percentile.

  9. A hierarchical variational Bayesian approximation approach in acoustic imaging

    NASA Astrophysics Data System (ADS)

    Chu, Ning; Mohammad-Djafari, Ali; Gac, Nicolas; Picheral, José

    2015-01-01

    Acoustic imaging is a powerful technique for acoustic source localization and power reconstruction from limited noisy measurements at microphone sensors. But it inevitably confronts a very ill-posed inverse problem which causes unexpected solution uncertainty. Recently, the Bayesian inference methods using sparse priors have been effectively investigated. In this paper, we propose to use a hierarchical variational Bayesian approximation for robust acoustic imaging. And we explore the Student-t priors with heavy tails to enforce source sparsity, and to model non-Gaussian noise respectively. Compared to conventional methods, the proposed approach can achieve the higher spatial resolution and wider dynamic range of source powers for real data from automobile wind tunnel.

  10. 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

  11. 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

  12. The importance of being spatial (and reserved): assessing northern spotted owl habitat relationships with hierarchical Bayesian models.

    PubMed

    Carroll, Carlos; Johnson, Devin S

    2008-08-01

    Regional conservation planning increasingly draws on habitat suitability models to support decisions regarding land allocation and management. Nevertheless, statistical techniques commonly used for developing such models may give misleading results because they fail to account for 3 factors common in data sets of species distribution: spatial autocorrelation, the large number of sites where the species is absent (zero inflation), and uneven survey effort. We used spatial autoregressive models fit with Bayesian Markov Chain Monte Carlo techniques to assess the relationship between older coniferous forest and the abundance of Northern Spotted Owl nest and activity sites throughout the species' range. The spatial random-effect term incorporated in the autoregressive models successfully accounted for zero inflation and reduced the effect of survey bias on estimates of species-habitat associations. Our results support the hypothesis that the relationship between owl distribution and older forest varies with latitude. A quadratic relationship between owl abundance and older forest was evident in the southern portion of the range, and a pseudothreshold relationship was evident in the northern portion of the range. Our results suggest that proposed changes to the network of owl habitat reserves would reduce the proportion of the population protected by up to one-third, and that proposed guidelines for forest management within reserves underestimate the proportion of older forest associated with maximum owl abundance and inappropriately generalize threshold relationships among subregions. Bayesian spatial models can greatly enhance the utility of habitat analysis for conservation planning because they add the statistical flexibility necessary for analyzing regional survey data while retaining the interpretability of simpler models. PMID:18477026

  13. 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.

  14. 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. PMID:27437134

  15. 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

  16. 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.

  17. Bayesian Hierarchical Grouping: perceptual grouping as mixture estimation

    PubMed Central

    Froyen, Vicky; Feldman, Jacob; Singh, Manish

    2015-01-01

    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

  18. Inferring on the intentions of others by hierarchical Bayesian learning.

    PubMed

    Diaconescu, Andreea O; Mathys, Christoph; Weber, Lilian A E; Daunizeau, Jean; Kasper, Lars; Lomakina, Ekaterina I; Fehr, Ernst; Stephan, Klaas E

    2014-09-01

    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

  19. Inferring on the intentions of others by hierarchical Bayesian learning.

    PubMed

    Diaconescu, Andreea O; Mathys, Christoph; Weber, Lilian A E; Daunizeau, Jean; Kasper, Lars; Lomakina, Ekaterina I; Fehr, Ernst; Stephan, Klaas E

    2014-09-01

    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.

  20. 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…

  1. 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.

  2. A hybrid Bayesian hierarchical model combining cohort and case-control studies for meta-analysis of diagnostic tests: Accounting for partial verification bias.

    PubMed

    Ma, Xiaoye; Chen, Yong; Cole, Stephen R; Chu, Haitao

    2014-05-26

    To account for between-study heterogeneity in meta-analysis of diagnostic accuracy studies, bivariate random effects models have been recommended to jointly model the sensitivities and specificities. As study design and population vary, the definition of disease status or severity could differ across studies. Consequently, sensitivity and specificity may be correlated with disease prevalence. To account for this dependence, a trivariate random effects model had been proposed. However, the proposed approach can only include cohort studies with information estimating study-specific disease prevalence. In addition, some diagnostic accuracy studies only select a subset of samples to be verified by the reference test. It is known that ignoring unverified subjects may lead to partial verification bias in the estimation of prevalence, sensitivities, and specificities in a single study. However, the impact of this bias on a meta-analysis has not been investigated. In this paper, we propose a novel hybrid Bayesian hierarchical model combining cohort and case-control studies and correcting partial verification bias at the same time. We investigate the performance of the proposed methods through a set of simulation studies. Two case studies on assessing the diagnostic accuracy of gadolinium-enhanced magnetic resonance imaging in detecting lymph node metastases and of adrenal fluorine-18 fluorodeoxyglucose positron emission tomography in characterizing adrenal masses are presented.

  3. 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

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. Hierarchical Bayesian space-time interpolation versus spatio-temporal BME approach

    NASA Astrophysics Data System (ADS)

    Hussain, I.; Pilz, J.; Spoeck, G.

    2010-03-01

    The restrictions of the analysis of natural processes which are observed at any point in space or time to a purely spatial or purely temporal domain may cause loss of information and larger prediction errors. Moreover, the arbitrary combinations of purely spatial and purely temporal models may not yield valid models for the space-time domain. For such processes the variation can be characterized by sophisticated spatio-temporal modeling. In the present study the composite spatio-temporal Bayesian maximum entropy (BME) method and transformed hierarchical Bayesian space-time interpolation are used in order to predict precipitation in Pakistan during the monsoon period. Monthly average precipitation data whose time domain is the monsoon period for the years 1974-2000 and whose spatial domain are various regions in Pakistan are considered. The prediction of space-time precipitation is applicable in many sectors of industry and economy in Pakistan especially; the agricultural sector. Mean field maps and prediction error maps for both methods are estimated and compared. In this paper it is shown that the transformed hierarchical Bayesian model is providing more accuracy and lower prediction error compared to the spatio-temporal Bayesian maximum entropy method; additionally, the transformed hierarchical Bayesian model also provides predictive distributions.

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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, ...

  16. 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

  17. 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.

  18. 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

  19. Learning emergent behaviours for a hierarchical Bayesian framework for active robotic perception.

    PubMed

    Ferreira, João Filipe; Tsiourti, Christiana; Dias, Jorge

    2012-08-01

    In this research work, we contribute with a behaviour learning process for a hierarchical Bayesian framework for multimodal active perception, devised to be emergent, scalable and adaptive. This framework is composed by models built upon a common spatial configuration for encoding perception and action that is naturally fitting for the integration of readings from multiple sensors, using a Bayesian approach devised in previous work. The proposed learning process is shown to reproduce goal-dependent human-like active perception behaviours by learning model parameters (referred to as "attentional sets") for different free-viewing and active search tasks. Learning was performed by presenting several 3D audiovisual virtual scenarios using a head-mounted display, while logging the spatial distribution of fixations of the subject (in 2D, on left and right images, and in 3D space), data which are consequently used as the training set for the framework. As a consequence, the hierarchical Bayesian framework adequately implements high-level behaviour resulting from low-level interaction of simpler building blocks by using the attentional sets learned for each task, and is able to change these attentional sets "on the fly," allowing the implementation of goal-dependent behaviours (i.e., top-down influences).

  20. 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.

  1. 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.

  2. 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.

  3. 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…

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. Joint Lung CT Image Segmentation: A Hierarchical Bayesian Approach

    PubMed Central

    Cheng, Wenjun; Ma, Luyao; Yang, Tiejun; Liang, Jiali

    2016-01-01

    Accurate lung CT image segmentation is of great clinical value, especially when it comes to delineate pathological regions including lung tumor. In this paper, we present a novel framework that jointly segments multiple lung computed tomography (CT) images via hierarchical Dirichlet process (HDP). In specifics, based on the assumption that lung CT images from different patients share similar image structure (organ sets and relative positioning), we derive a mathematical model to segment them simultaneously so that shared information across patients could be utilized to regularize each individual segmentation. Moreover, compared to many conventional models, the algorithm requires little manual involvement due to the nonparametric nature of Dirichlet process (DP). We validated proposed model upon clinical data consisting of healthy and abnormal (lung cancer) patients. We demonstrate that, because of the joint segmentation fashion, more accurate and consistent segmentations could be obtained. PMID:27611188

  9. Joint Lung CT Image Segmentation: A Hierarchical Bayesian Approach.

    PubMed

    Cheng, Wenjun; Ma, Luyao; Yang, Tiejun; Liang, Jiali; Zhang, Yan

    2016-01-01

    Accurate lung CT image segmentation is of great clinical value, especially when it comes to delineate pathological regions including lung tumor. In this paper, we present a novel framework that jointly segments multiple lung computed tomography (CT) images via hierarchical Dirichlet process (HDP). In specifics, based on the assumption that lung CT images from different patients share similar image structure (organ sets and relative positioning), we derive a mathematical model to segment them simultaneously so that shared information across patients could be utilized to regularize each individual segmentation. Moreover, compared to many conventional models, the algorithm requires little manual involvement due to the nonparametric nature of Dirichlet process (DP). We validated proposed model upon clinical data consisting of healthy and abnormal (lung cancer) patients. We demonstrate that, because of the joint segmentation fashion, more accurate and consistent segmentations could be obtained. PMID:27611188

  10. Trans-dimensional and hierarchical Bayesian approaches toward rigorous estimation of seismic sources and structures in the Northeast Asia

    NASA Astrophysics Data System (ADS)

    Kim, Seongryong; Tkalčić, Hrvoje; Mustać, Marija; Rhie, Junkee; Ford, Sean

    2016-04-01

    A framework is presented within which we provide rigorous estimations for seismic sources and structures in the Northeast Asia. We use Bayesian inversion methods, which enable statistical estimations of models and their uncertainties based on data information. Ambiguities in error statistics and model parameterizations are addressed by hierarchical and trans-dimensional (trans-D) techniques, which can be inherently implemented in the Bayesian inversions. Hence reliable estimation of model parameters and their uncertainties is possible, thus avoiding arbitrary regularizations and parameterizations. Hierarchical and trans-D inversions are performed to develop a three-dimensional velocity model using ambient noise data. To further improve the model, we perform joint inversions with receiver function data using a newly developed Bayesian method. For the source estimation, a novel moment tensor inversion method is presented and applied to regional waveform data of the North Korean nuclear explosion tests. By the combination of new Bayesian techniques and the structural model, coupled with meaningful uncertainties related to each of the processes, more quantitative monitoring and discrimination of seismic events is possible.

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. 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.

    2016-11-01

    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.

  16. Hierarchical Bayesian approach for estimating physical properties in spiral galaxies: Age Maps for M74

    NASA Astrophysics Data System (ADS)

    Sánchez Gil, M. Carmen; Berihuete, Angel; Alfaro, Emilio J.; Pérez, Enrique; Sarro, Luis M.

    2015-09-01

    One of the fundamental goals of modern Astronomy is to estimate the physical parameters of galaxies from images in different spectral bands. We present a hierarchical Bayesian model for obtaining age maps from images in the Ha line (taken with Taurus Tunable Filter (TTF)), ultraviolet band (far UV or FUV, from GALEX) and infrared bands (24, 70 and 160 microns (μm), from Spitzer). As shown in [1], we present the burst ages for young stellar populations in the nearby and nearly face on galaxy M74. As it is shown in the previous work, the Hα to FUV flux ratio gives a good relative indicator of very recent star formation history (SFH). As a nascent star-forming region evolves, the Ha line emission declines earlier than the UV continuum, leading to a decrease in the HαFUV ratio. Through a specific star-forming galaxy model (Starburst 99, SB99), we can obtain the corresponding theoretical ratio Hα / FUV to compare with our observed flux ratios, and thus to estimate the ages of the observed regions. Due to the nature of the problem, it is necessary to propose a model of high complexity to take into account the mean uncertainties, and the interrelationship between parameters when the Hα / FUV flux ratio mentioned above is obtained. To address the complexity of the model, we propose a Bayesian hierarchical model, where a joint probability distribution is defined to determine the parameters (age, metallicity, IMF), from the observed data, in this case the observed flux ratios Hα / FUV. The joint distribution of the parameters is described through an i.i.d. (independent and identically distributed random variables), generated through MCMC (Markov Chain Monte Carlo) techniques.

  17. A Bayesian hierarchical approach for combining case-control and prospective studies.

    PubMed

    Müller, P; Parmigiani, G; Schildkraut, J; Tardella, L

    1999-09-01

    Motivated by the absolute risk predictions required in medical decision making and patient counseling, we propose an approach for the combined analysis of case-control and prospective studies of disease risk factors. The approach is hierarchical to account for parameter heterogeneity among studies and among sampling units of the same study. It is based on modeling the retrospective distribution of the covariates given the disease outcome, a strategy that greatly simplifies both the combination of prospective and retrospective studies and the computation of Bayesian predictions in the hierarchical case-control context. Retrospective modeling differentiates our approach from most current strategies for inference on risk factors, which are based on the assumption of a specific prospective model. To ensure modeling flexibility, we propose using a mixture model for the retrospective distributions of the covariates. This leads to a general nonlinear regression family for the implied prospective likelihood. After introducing and motivating our proposal, we present simple results that highlight its relationship with existing approaches, develop Markov chain Monte Carlo methods for inference and prediction, and present an illustration using ovarian cancer data. PMID:11315018

  18. 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.

  19. Using time-varying asymptotic length and body condition of top piscivores to indicate ecosystem regime shift in the main basin of Lake Huron: a Bayesian hierarchical modeling approach

    USGS Publications Warehouse

    He, Ji X.; Bence, James R.; Roseman, Edward F.; Fielder, David G.; Ebener, Mark P.

    2015-01-01

    We evaluated the ecosystem regime shift in the main basin of Lake Huron that was indicated by the 2003 collapse of alewives, and dramatic declines in Chinook salmon abundance thereafter. We found that the period of 1995-2002 should be considered as the early phase of the final regime shift. We developed two Bayesian hierarchical models to describe time-varying growth based on the von Bertalanffy growth function and the length-mass relationship. We used asymptotic length as an index of growth potential, and predicted body mass at a given length as an index of body condition. Modeling fits to length and body mass at age of lake trout, Chinook salmon, and walleye were excellent. Based on posterior distributions, we evaluated the shifts in among-year geometric means of the growth potential and body condition. For a given top piscivore, one of the two indices responded to the regime shift much earlier than the 2003 collapse of alewives, the other corresponded to the 2003 changes, and which index provided the early signal differed among the three top piscivores.

  20. 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

  1. 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.

  2. What are hierarchical models and how do we analyze them?

    USGS Publications Warehouse

    Royle, Andy

    2016-01-01

    In this chapter we provide a basic definition of hierarchical models and introduce the two canonical hierarchical models in this book: site occupancy and N-mixture models. The former is a hierarchical extension of logistic regression and the latter is a hierarchical extension of Poisson regression. We introduce basic concepts of probability modeling and statistical inference including likelihood and Bayesian perspectives. We go through the mechanics of maximizing the likelihood and characterizing the posterior distribution by Markov chain Monte Carlo (MCMC) methods. We give a general perspective on topics such as model selection and assessment of model fit, although we demonstrate these topics in practice in later chapters (especially Chapters 5, 6, 7, and 10 Chapter 5 Chapter 6 Chapter 7 Chapter 10)

  3. 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…

  4. 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...

  5. 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.

  6. 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

  7. Bayesian modeling of differential gene expression.

    PubMed

    Lewin, Alex; Richardson, Sylvia; Marshall, Clare; Glazier, Anne; Aitman, Tim

    2006-03-01

    We present a Bayesian hierarchical model for detecting differentially expressing genes that includes simultaneous estimation of array effects, and show how to use the output for choosing lists of genes for further investigation. We give empirical evidence that expression-level dependent array effects are needed, and explore different nonlinear functions as part of our model-based approach to normalization. The model includes gene-specific variances but imposes some necessary shrinkage through a hierarchical structure. Model criticism via posterior predictive checks is discussed. Modeling the array effects (normalization) simultaneously with differential expression gives fewer false positive results. To choose a list of genes, we propose to combine various criteria (for instance, fold change and overall expression) into a single indicator variable for each gene. The posterior distribution of these variables is used to pick the list of genes, thereby taking into account uncertainty in parameter estimates. In an application to mouse knockout data, Gene Ontology annotations over- and underrepresented among the genes on the chosen list are consistent with biological expectations.

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. A hierarchical Bayesian approach for estimation of photosynthetic parameters of C(3) plants.

    PubMed

    Patrick, Lisa D; Ogle, Kiona; Tissue, David T

    2009-12-01

    We describe a hierarchical Bayesian (HB) approach to fitting the Farquhar et al.model of photosynthesis to leaf gas exchange data. We illustrate the utility of this approach for estimating photosynthetic parameters using data from desert shrubs. Unique to the HB method is its ability to simultaneously estimate plant- and species-level parameters, adjust for peaked or non-peaked temperature dependence of parameters, explicitly estimate the 'critical' intracellular [CO(2)] marking the transition between ribulose 1.5-bisphosphate carboxylase/oxygenase (Rubisco) and ribulose-1,5-bisphosphate (RuBP) limitations, and use both light response and CO(2) response curve data to better inform parameter estimates. The model successfully predicted observed photosynthesis and yielded estimates of photosynthetic parameters and their uncertainty. The model with peaked temperature responses fit the data best, and inclusion of light response data improved estimates for day respiration (R(d)). Species differed in R(d25) (R(d) at 25 degrees C), maximum rate of electron transport (J(max25)), a Michaelis-Menten constant (K(c25)) and a temperature dependence parameter (DeltaS). Such differences could potentially reflect differential physiological adaptations to environmental variation. Plants differed in R(d25), J(max25), mesophyll conductance (g(m25)) and maximum rate of Rubisco carboxylation (V(cmax25)). These results suggest that plant- and species-level variation should be accounted for when applying the Farquhar et al. model in an inferential or predictive framework.

  14. A method of spherical harmonic analysis in the geosciences via hierarchical Bayesian inference

    NASA Astrophysics Data System (ADS)

    Muir, J. B.; Tkalčić, H.

    2015-11-01

    The problem of decomposing irregular data on the sphere into a set of spherical harmonics is common in many fields of geosciences where it is necessary to build a quantitative understanding of a globally varying field. For example, in global seismology, a compressional or shear wave speed that emerges from tomographic images is used to interpret current state and composition of the mantle, and in geomagnetism, secular variation of magnetic field intensity measured at the surface is studied to better understand the changes in the Earth's core. Optimization methods are widely used for spherical harmonic analysis of irregular data, but they typically do not treat the dependence of the uncertainty estimates on the imposed regularization. This can cause significant difficulties in interpretation, especially when the best-fit model requires more variables as a result of underestimating data noise. Here, with the above limitations in mind, the problem of spherical harmonic expansion of irregular data is treated within the hierarchical Bayesian framework. The hierarchical approach significantly simplifies the problem by removing the need for regularization terms and user-supplied noise estimates. The use of the corrected Akaike Information Criterion for picking the optimal maximum degree of spherical harmonic expansion and the resulting spherical harmonic analyses are first illustrated on a noisy synthetic data set. Subsequently, the method is applied to two global data sets sensitive to the Earth's inner core and lowermost mantle, consisting of PKPab-df and PcP-P differential traveltime residuals relative to a spherically symmetric Earth model. The posterior probability distributions for each spherical harmonic coefficient are calculated via Markov Chain Monte Carlo sampling; the uncertainty obtained for the coefficients thus reflects the noise present in the real data and the imperfections in the spherical harmonic expansion.

  15. 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.

  16. 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.

  17. 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.

  18. Hierarchical model of matching

    NASA Technical Reports Server (NTRS)

    Pedrycz, Witold; Roventa, Eugene

    1992-01-01

    The issue of matching two fuzzy sets becomes an essential design aspect of many algorithms including fuzzy controllers, pattern classifiers, knowledge-based systems, etc. This paper introduces a new model of matching. Its principal features involve the following: (1) matching carried out with respect to the grades of membership of fuzzy sets as well as some functionals defined on them (like energy, entropy,transom); (2) concepts of hierarchies in the matching model leading to a straightforward distinction between 'local' and 'global' levels of matching; and (3) a distributed character of the model realized as a logic-based neural network.

  19. 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…

  20. 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

  1. 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.

  2. 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

  3. Bayesian model updating using incomplete modal data without mode matching

    NASA Astrophysics Data System (ADS)

    Sun, Hao; Büyüköztürk, Oral

    2016-04-01

    This study investigates a new probabilistic strategy for model updating using incomplete modal data. A hierarchical Bayesian inference is employed to model the updating problem. A Markov chain Monte Carlo technique with adaptive random-work steps is used to draw parameter samples for uncertainty quantification. Mode matching between measured and predicted modal quantities is not required through model reduction. We employ an iterated improved reduced system technique for model reduction. The reduced model retains the dynamic features as close as possible to those of the model before reduction. The proposed algorithm is finally validated by an experimental example.

  4. 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.

  5. 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).

  6. Hierarchical structure of the Sicilian goats revealed by Bayesian analyses of microsatellite information.

    PubMed

    Siwek, M; Finocchiaro, R; Curik, I; Portolano, B

    2011-02-01

    Genetic structure and relationship amongst the main goat populations in Sicily (Girgentana, Derivata di Siria, Maltese and Messinese) were analysed using information from 19 microsatellite markers genotyped on 173 individuals. A posterior Bayesian approach implemented in the program STRUCTURE revealed a hierarchical structure with two clusters at the first level (Girgentana vs. Messinese, Derivata di Siria and Maltese), explaining 4.8% of variation (amovaФ(ST) estimate). Seven clusters nested within these first two clusters (further differentiations of Girgentana, Derivata di Siria and Maltese), explaining 8.5% of variation (amovaФ(SC) estimate). The analyses and methods applied in this study indicate their power to detect subtle population structure.

  7. Multicollinearity in hierarchical linear models.

    PubMed

    Yu, Han; Jiang, Shanhe; Land, Kenneth C

    2015-09-01

    This study investigates an ill-posed problem (multicollinearity) in Hierarchical Linear Models from both the data and the model perspectives. We propose an intuitive, effective approach to diagnosing the presence of multicollinearity and its remedies in this class of models. A simulation study demonstrates the impacts of multicollinearity on coefficient estimates, associated standard errors, and variance components at various levels of multicollinearity for finite sample sizes typical in social science studies. We further investigate the role multicollinearity plays at each level for estimation of coefficient parameters in terms of shrinkage. Based on these analyses, we recommend a top-down method for assessing multicollinearity in HLMs that first examines the contextual predictors (Level-2 in a two-level model) and then the individual predictors (Level-1) and uses the results for data collection, research problem redefinition, model re-specification, variable selection and estimation of a final model.

  8. 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.

  9. 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.

  10. Bayesian inference for OPC modeling

    NASA Astrophysics Data System (ADS)

    Burbine, Andrew; Sturtevant, John; Fryer, David; Smith, Bruce W.

    2016-03-01

    The use of optical proximity correction (OPC) demands increasingly accurate models of the photolithographic process. Model building and inference techniques in the data science community have seen great strides in the past two decades which make better use of available information. This paper aims to demonstrate the predictive power of Bayesian inference as a method for parameter selection in lithographic models by quantifying the uncertainty associated with model inputs and wafer data. Specifically, the method combines the model builder's prior information about each modelling assumption with the maximization of each observation's likelihood as a Student's t-distributed random variable. Through the use of a Markov chain Monte Carlo (MCMC) algorithm, a model's parameter space is explored to find the most credible parameter values. During parameter exploration, the parameters' posterior distributions are generated by applying Bayes' rule, using a likelihood function and the a priori knowledge supplied. The MCMC algorithm used, an affine invariant ensemble sampler (AIES), is implemented by initializing many walkers which semiindependently explore the space. The convergence of these walkers to global maxima of the likelihood volume determine the parameter values' highest density intervals (HDI) to reveal champion models. We show that this method of parameter selection provides insights into the data that traditional methods do not and outline continued experiments to vet the method.

  11. 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.

  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. Modeling abundance using hierarchical distance sampling

    USGS Publications Warehouse

    Royle, Andy; Kery, Marc

    2016-01-01

    In this chapter, we provide an introduction to classical distance sampling ideas for point and line transect data, and for continuous and binned distance data. We introduce the conditional and the full likelihood, and we discuss Bayesian analysis of these models in BUGS using the idea of data augmentation, which we discussed in Chapter 7. We then extend the basic ideas to the problem of hierarchical distance sampling (HDS), where we have multiple point or transect sample units in space (or possibly in time). The benefit of HDS in practice is that it allows us to directly model spatial variation in population size among these sample units. This is a preeminent concern of most field studies that use distance sampling methods, but it is not a problem that has received much attention in the literature. We show how to analyze HDS models in both the unmarked package and in the BUGS language for point and line transects, and for continuous and binned distance data. We provide a case study of HDS applied to a survey of the island scrub-jay on Santa Cruz Island, California.

  14. Bayesian Uncertainty Analyses Via Deterministic Model

    NASA Astrophysics Data System (ADS)

    Krzysztofowicz, R.

    2001-05-01

    Rational decision-making requires that the total uncertainty about a variate of interest (a predictand) be quantified in terms of a probability distribution, conditional on all available information and knowledge. Suppose the state-of-knowledge is embodied in a deterministic model, which is imperfect and outputs only an estimate of the predictand. Fundamentals are presented of three Bayesian approaches to producing a probability distribution of the predictand via any deterministic model. The Bayesian Processor of Output (BPO) quantifies the total uncertainty in terms of a posterior distribution, conditional on model output. The Bayesian Processor of Ensemble (BPE) quantifies the total uncertainty in terms of a posterior distribution, conditional on an ensemble of model output. The Bayesian Forecasting System (BFS) decomposes the total uncertainty into input uncertainty and model uncertainty, which are characterized independently and then integrated into a predictive distribution.

  15. Hierarchical Bayesian analysis of outcome- and process-based social preferences and beliefs in Dictator Games and sequential Prisoner's Dilemmas.

    PubMed

    Aksoy, Ozan; Weesie, Jeroen

    2014-05-01

    In this paper, using a within-subjects design, we estimate the utility weights that subjects attach to the outcome of their interaction partners in four decision situations: (1) binary Dictator Games (DG), second player's role in the sequential Prisoner's Dilemma (PD) after the first player (2) cooperated and (3) defected, and (4) first player's role in the sequential Prisoner's Dilemma game. We find that the average weights in these four decision situations have the following order: (1)>(2)>(4)>(3). Moreover, the average weight is positive in (1) but negative in (2), (3), and (4). Our findings indicate the existence of strong negative and small positive reciprocity for the average subject, but there is also high interpersonal variation in the weights in these four nodes. We conclude that the PD frame makes subjects more competitive than the DG frame. Using hierarchical Bayesian modeling, we simultaneously analyze beliefs of subjects about others' utility weights in the same four decision situations. We compare several alternative theoretical models on beliefs, e.g., rational beliefs (Bayesian-Nash equilibrium) and a consensus model. Our results on beliefs strongly support the consensus effect and refute rational beliefs: there is a strong relationship between own preferences and beliefs and this relationship is relatively stable across the four decision situations.

  16. 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

  17. 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

  18. Bayesian Methods for High Dimensional Linear Models

    PubMed Central

    Mallick, Himel; Yi, Nengjun

    2013-01-01

    In this article, we present a selective overview of some recent developments in Bayesian model and variable selection methods for high dimensional linear models. While most of the reviews in literature are based on conventional methods, we focus on recently developed methods, which have proven to be successful in dealing with high dimensional variable selection. First, we give a brief overview of the traditional model selection methods (viz. Mallow’s Cp, AIC, BIC, DIC), followed by a discussion on some recently developed methods (viz. EBIC, regularization), which have occupied the minds of many statisticians. Then, we review high dimensional Bayesian methods with a particular emphasis on Bayesian regularization methods, which have been used extensively in recent years. We conclude by briefly addressing the asymptotic behaviors of Bayesian variable selection methods for high dimensional linear models under different regularity conditions. PMID:24511433

  19. Bayesian Methods for High Dimensional Linear Models.

    PubMed

    Mallick, Himel; Yi, Nengjun

    2013-06-01

    In this article, we present a selective overview of some recent developments in Bayesian model and variable selection methods for high dimensional linear models. While most of the reviews in literature are based on conventional methods, we focus on recently developed methods, which have proven to be successful in dealing with high dimensional variable selection. First, we give a brief overview of the traditional model selection methods (viz. Mallow's Cp, AIC, BIC, DIC), followed by a discussion on some recently developed methods (viz. EBIC, regularization), which have occupied the minds of many statisticians. Then, we review high dimensional Bayesian methods with a particular emphasis on Bayesian regularization methods, which have been used extensively in recent years. We conclude by briefly addressing the asymptotic behaviors of Bayesian variable selection methods for high dimensional linear models under different regularity conditions.

  20. Bayesian Modeling of a Human MMORPG Player

    NASA Astrophysics Data System (ADS)

    Synnaeve, Gabriel; Bessière, Pierre

    2011-03-01

    This paper describes an application of Bayesian programming to the control of an autonomous avatar in a multiplayer role-playing game (the example is based on World of Warcraft). We model a particular task, which consists of choosing what to do and to select which target in a situation where allies and foes are present. We explain the model in Bayesian programming and show how we could learn the conditional probabilities from data gathered during human-played sessions.

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. Bayesian methods for assessing system reliability: models and computation.

    SciTech Connect

    Graves, T. L.; Hamada, Michael,

    2004-01-01

    There are many challenges with assessing the reliability of a system today. These challenges arise because a system may be aging and full system tests may be too expensive or can no longer be performed. Without full system testing, one must integrate (1) all science and engineering knowledge, models and simulations, (2) information and data at various levels of the system, e.g., subsystems and components and (3) information and data from similar systems, subsystems and components. The analyst must work with various data types and how the data are collected, account for measurement bias and uncertainty, deal with model and simulation uncertainty and incorporate expert knowledge. Bayesian hierarchical modeling provides a rigorous way to combine information from multiple sources and different types of information. However, an obstacle to applying Bayesian methods is the need to develop new software to analyze novel statistical models. We discuss a new statistical modeling environment, YADAS, that facilitates the development of Bayesian statistical analyses. It includes classes that help analysts specify new models, as well as classes that support the creation of new analysis algorithms. We illustrate these concepts using several examples.

  6. 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

  7. A Bayesian hierarchical method to account for random effects in cytogenetic dosimetry based on calibration curves.

    PubMed

    Mano, Shuhei; Suto, Yumiko

    2014-11-01

    The dicentric chromosome assay (DCA) is one of the most sensitive and reliable methods of inferring doses of radiation exposure in patients. In DCA, one calibration curve is prepared in advance by in vitro irradiation to blood samples from one or sometimes multiple healthy donors in considering possible inter-individual variability. Although the standard method has been demonstrated to be quite accurate for actual dose estimates, it cannot account for random effects, which come from such as the blood donor used to prepare the calibration curve, the radiation-exposed patient, and the examiners. To date, it is unknown how these random effects impact on the standard method of dose estimation. We propose a novel Bayesian hierarchical method that incorporates random effects into the dose estimation. To demonstrate dose estimation by the proposed method and to assess the impact of inter-individual variability in samples from multiple donors on the estimation, peripheral blood samples from 13 occupationally non-exposed, non-smoking, healthy individuals were collected and irradiated with gamma rays. The results clearly showed significant inter-individual variability and the standard method using a sample from a single donor gave anti-conservative confidence interval of the irradiated dose. In contrast, the Bayesian credible interval for irradiated dose calculated by the proposed method using samples from multiple donors properly covered the actual doses. Although the classical confidence interval of calibration curve with accounting inter-individual variability in samples from multiple donors was roughly coincident with the Bayesian credible interval, the proposed method has better reasoning and potential for extensions.

  8. What’s in a Name: A Bayesian Hierarchical Analysis of the Name-Letter Effect

    PubMed Central

    Dyjas, Oliver; Grasman, Raoul P. P. P.; Wetzels, Ruud; van der Maas, Han L. J.; Wagenmakers, Eric-Jan

    2012-01-01

    People generally prefer their initials to the other letters of the alphabet, a phenomenon known as the name-letter effect. This effect, researchers have argued, makes people move to certain cities, buy particular brands of consumer products, and choose particular professions (e.g., Angela moves to Los Angeles, Phil buys a Philips TV, and Dennis becomes a dentist). In order to establish such associations between people’s initials and their behavior, researchers typically carry out statistical analyses of large databases. Current methods of analysis ignore the hierarchical structure of the data, do not naturally handle order-restrictions, and are fundamentally incapable of confirming the null hypothesis. Here we outline a Bayesian hierarchical analysis that avoids these limitations and allows coherent inference both on the level of the individual and on the level of the group. To illustrate our method, we re-analyze two data sets that address the question of whether people are disproportionately likely to live in cities that resemble their name. PMID:23055989

  9. 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…

  10. 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…

  11. 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…

  12. Testing Bayesian models of human coincidence timing.

    PubMed

    Miyazaki, Makoto; Nozaki, Daichi; Nakajima, Yasoichi

    2005-07-01

    A sensorimotor control task often requires an accurate estimation of the timing of the arrival of an external target (e.g., when hitting a pitched ball). Conventional studies of human timing processes have ignored the stochastic features of target timing: e.g., the speed of the pitched ball is not generally constant, but is variable. Interestingly, based on Bayesian theory, it has been recently shown that the human sensorimotor system achieves the optimal estimation by integrating sensory information with prior knowledge of the probabilistic structure of the target variation. In this study, we tested whether Bayesian integration is also implemented while performing a coincidence-timing type of sensorimotor task by manipulating the trial-by-trial variability (i.e., the prior distribution) of the target timing. As a result, within several hundred trials of learning, subjects were able to generate systematic timing behavior according to the width of the prior distribution, as predicted by the optimal Bayesian model. Considering the previous studies showing that the human sensorimotor system uses Bayesian integration in spacing and force-grading tasks, our result indicates that Bayesian integration is fundamental to all aspects of human sensorimotor control. Moreover, it was noteworthy that the subjects could adjust their behavior both when the prior distribution was switched from wide to narrow and vice versa, although the adjustment was slower in the former case. Based on a comparison with observations in a previous study, we discuss the flexibility and adaptability of Bayesian sensorimotor learning.

  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. 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…

  15. Bayesian modeling of flexible cognitive control

    PubMed Central

    Jiang, Jiefeng; Heller, Katherine; Egner, Tobias

    2014-01-01

    “Cognitive control” describes endogenous guidance of behavior in situations where routine stimulus-response associations are suboptimal for achieving a desired goal. The computational and neural mechanisms underlying this capacity remain poorly understood. We examine recent advances stemming from the application of a Bayesian learner perspective that provides optimal prediction for control processes. In reviewing the application of Bayesian models to cognitive control, we note that an important limitation in current models is a lack of a plausible mechanism for the flexible adjustment of control over conflict levels changing at varying temporal scales. We then show that flexible cognitive control can be achieved by a Bayesian model with a volatility-driven learning mechanism that modulates dynamically the relative dependence on recent and remote experiences in its prediction of future control demand. We conclude that the emergent Bayesian perspective on computational mechanisms of cognitive control holds considerable promise, especially if future studies can identify neural substrates of the variables encoded by these models, and determine the nature (Bayesian or otherwise) of their neural implementation. PMID:24929218

  16. 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…

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. 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.

  2. A Bayesian nonparametric meta-analysis model.

    PubMed

    Karabatsos, George; Talbott, Elizabeth; Walker, Stephen G

    2015-03-01

    In a meta-analysis, it is important to specify a model that adequately describes the effect-size distribution of the underlying population of studies. The conventional normal fixed-effect and normal random-effects models assume a normal effect-size population distribution, conditionally on parameters and covariates. For estimating the mean overall effect size, such models may be adequate, but for prediction, they surely are not if the effect-size distribution exhibits non-normal behavior. To address this issue, we propose a Bayesian nonparametric meta-analysis model, which can describe a wider range of effect-size distributions, including unimodal symmetric distributions, as well as skewed and more multimodal distributions. We demonstrate our model through the analysis of real meta-analytic data arising from behavioral-genetic research. We compare the predictive performance of the Bayesian nonparametric model against various conventional and more modern normal fixed-effects and random-effects models.

  3. Bayesian hierarchical regression analysis of variations in sea surface temperature change over the past million years

    NASA Astrophysics Data System (ADS)

    Snyder, Carolyn W.

    2016-09-01

    Statistical challenges often preclude comparisons among different sea surface temperature (SST) reconstructions over the past million years. Inadequate consideration of uncertainty can result in misinterpretation, overconfidence, and biased conclusions. Here I apply Bayesian hierarchical regressions to analyze local SST responsiveness to climate changes for 54 SST reconstructions from across the globe over the past million years. I develop methods to account for multiple sources of uncertainty, including the quantification of uncertainty introduced from absolute dating into interrecord comparisons. The estimates of local SST responsiveness explain 64% (62% to 77%, 95% interval) of the total variation within each SST reconstruction with a single number. There is remarkable agreement between SST proxy methods, with the exception of Mg/Ca proxy methods estimating muted responses at high latitudes. The Indian Ocean exhibits a muted response in comparison to other oceans. I find a stable estimate of the proposed "universal curve" of change in local SST responsiveness to climate changes as a function of sin2(latitude) over the past 400,000 years: SST change at 45°N/S is larger than the average tropical response by a factor of 1.9 (1.5 to 2.6, 95% interval) and explains 50% (35% to 58%, 95% interval) of the total variation between each SST reconstruction. These uncertainty and statistical methods are well suited for application across paleoclimate and environmental data series intercomparisons.

  4. A Bayesian approach for the multiplicative binomial regression model

    NASA Astrophysics Data System (ADS)

    Paraíba, Carolina C. M.; Diniz, Carlos A. R.; Pires, Rubiane M.

    2012-10-01

    In the present paper, we focus our attention on Altham's multiplicative binomial model under the Bayesian perspective, modeling both the probability of success and the dispersion parameters. We present results based on a simulated data set to access the quality of Bayesian estimates and Bayesian diagnostic for model assessment.

  5. 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…

  6. 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

  7. 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

  8. 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.

  9. Posterior Predictive Bayesian Phylogenetic Model Selection

    PubMed Central

    Lewis, Paul O.; Xie, Wangang; Chen, Ming-Hui; Fan, Yu; Kuo, Lynn

    2014-01-01

    We present two distinctly different posterior predictive approaches to Bayesian phylogenetic model selection and illustrate these methods using examples from green algal protein-coding cpDNA sequences and flowering plant rDNA sequences. The Gelfand–Ghosh (GG) approach allows dissection of an overall measure of model fit into components due to posterior predictive variance (GGp) and goodness-of-fit (GGg), which distinguishes this method from the posterior predictive P-value approach. The conditional predictive ordinate (CPO) method provides a site-specific measure of model fit useful for exploratory analyses and can be combined over sites yielding the log pseudomarginal likelihood (LPML) which is useful as an overall measure of model fit. CPO provides a useful cross-validation approach that is computationally efficient, requiring only a sample from the posterior distribution (no additional simulation is required). Both GG and CPO add new perspectives to Bayesian phylogenetic model selection based on the predictive abilities of models and complement the perspective provided by the marginal likelihood (including Bayes Factor comparisons) based solely on the fit of competing models to observed data. [Bayesian; conditional predictive ordinate; CPO; L-measure; LPML; model selection; phylogenetics; posterior predictive.] PMID:24193892

  10. Bayesian cross-validation for model evaluation and selection with application to the North American breeding survey

    USGS Publications Warehouse

    Link, William; Sauer, John

    2016-01-01

    The analysis of ecological data has changed in two important ways over the last fifteen years. The development and easy availability of Bayesian computational methods has allowed and encouraged the fitting of complex hierarchical models. At the same time, there has been increasing emphasis on acknowledging and accounting for model uncertainty. Unfortunately, the ability to fit complex models has outstripped the development of tools for model selection and model evaluation: familiar model selection tools such as Akaike's information criterion and the deviance information criterion are widely known to be inadequate for hierarchical models. In addition, little attention has been paid to the evaluation of model adequacy in context of hierarchical modeling, i.e., to the evaluation of fit for a single model. In this paper we describe Bayesian cross-validation, which provides tools for model selection and evaluation. We describe the Bayesian predictive information criterion (BPIC) and a Bayesian approximation to the BPIC known as the Watanabe-Akaike information criterion (WAIC). We illustrate the use of these tools for model selection, and the use of Bayesian cross-validation as a tool for model evaluation, using 3 large data sets from the North American Breeding Bird Survey.

  11. Bayesian cross-validation for model evaluation and selection, with application to the North American Breeding Bird Survey

    USGS Publications Warehouse

    Link, William; Sauer, John R.

    2016-01-01

    The analysis of ecological data has changed in two important ways over the last 15 years. The development and easy availability of Bayesian computational methods has allowed and encouraged the fitting of complex hierarchical models. At the same time, there has been increasing emphasis on acknowledging and accounting for model uncertainty. Unfortunately, the ability to fit complex models has outstripped the development of tools for model selection and model evaluation: familiar model selection tools such as Akaike's information criterion and the deviance information criterion are widely known to be inadequate for hierarchical models. In addition, little attention has been paid to the evaluation of model adequacy in context of hierarchical modeling, i.e., to the evaluation of fit for a single model. In this paper, we describe Bayesian cross-validation, which provides tools for model selection and evaluation. We describe the Bayesian predictive information criterion and a Bayesian approximation to the BPIC known as the Watanabe-Akaike information criterion. We illustrate the use of these tools for model selection, and the use of Bayesian cross-validation as a tool for model evaluation, using three large data sets from the North American Breeding Bird Survey.

  12. Modeling the Climatology of Tornado Occurrence with Bayesian Inference

    NASA Astrophysics Data System (ADS)

    Cheng, Vincent Y. S.

    -related variables are more uniform across seasons. The residual variability of the same modeling framework (a reflection of the fidelity of the statistical formulation considered) is subsequently used to delineate distinct geographical patterns of tornado activity. This piece of information provides the foundation for the Bayesian hierarchical prognostic model presented in the third chapter of my dissertation. The results of the latter approach reinforce my earlier finding that the spatial variability of the annual and warm seasonal tornado occurrence is well explained by convective available potential energy and storm relative helicity alone, while vertical wind shear is better at reproducing the cool season tornado activity. The Bayesian hierarchical modeling framework offers a promising methodological tool for understanding regional tornado environments and obtaining reliable predictions in North America.

  13. Bayesian Recurrent Neural Network for Language Modeling.

    PubMed

    Chien, Jen-Tzung; Ku, Yuan-Chu

    2016-02-01

    A language model (LM) is calculated as the probability of a word sequence that provides the solution to word prediction for a variety of information systems. A recurrent neural network (RNN) is powerful to learn the large-span dynamics of a word sequence in the continuous space. However, the training of the RNN-LM is an ill-posed problem because of too many parameters from a large dictionary size and a high-dimensional hidden layer. This paper presents a Bayesian approach to regularize the RNN-LM and apply it for continuous speech recognition. We aim to penalize the too complicated RNN-LM by compensating for the uncertainty of the estimated model parameters, which is represented by a Gaussian prior. The objective function in a Bayesian classification network is formed as the regularized cross-entropy error function. The regularized model is constructed not only by calculating the regularized parameters according to the maximum a posteriori criterion but also by estimating the Gaussian hyperparameter by maximizing the marginal likelihood. A rapid approximation to a Hessian matrix is developed to implement the Bayesian RNN-LM (BRNN-LM) by selecting a small set of salient outer-products. The proposed BRNN-LM achieves a sparser model than the RNN-LM. Experiments on different corpora show the robustness of system performance by applying the rapid BRNN-LM under different conditions.

  14. Bayesian population modeling of drug dosing adherence.

    PubMed

    Fellows, Kelly; Stoneking, Colin J; Ramanathan, Murali

    2015-10-01

    Adherence is a frequent contributing factor to variations in drug concentrations and efficacy. The purpose of this work was to develop an integrated population model to describe variation in adherence, dose-timing deviations, overdosing and persistence to dosing regimens. The hybrid Markov chain-von Mises method for modeling adherence in individual subjects was extended to the population setting using a Bayesian approach. Four integrated population models for overall adherence, the two-state Markov chain transition parameters, dose-timing deviations, overdosing and persistence were formulated and critically compared. The Markov chain-Monte Carlo algorithm was used for identifying distribution parameters and for simulations. The model was challenged with medication event monitoring system data for 207 hypertension patients. The four Bayesian models demonstrated good mixing and convergence characteristics. The distributions of adherence, dose-timing deviations, overdosing and persistence were markedly non-normal and diverse. The models varied in complexity and the method used to incorporate inter-dependence with the preceding dose in the two-state Markov chain. The model that incorporated a cooperativity term for inter-dependence and a hyperbolic parameterization of the transition matrix probabilities was identified as the preferred model over the alternatives. The simulated probability densities from the model satisfactorily fit the observed probability distributions of adherence, dose-timing deviations, overdosing and persistence parameters in the sample patients. The model also adequately described the median and observed quartiles for these parameters. The Bayesian model for adherence provides a parsimonious, yet integrated, description of adherence in populations. It may find potential applications in clinical trial simulations and pharmacokinetic-pharmacodynamic modeling. PMID:26319548

  15. Bayesian model selection analysis of WMAP3

    SciTech Connect

    Parkinson, David; Mukherjee, Pia; Liddle, Andrew R.

    2006-06-15

    We present a Bayesian model selection analysis of WMAP3 data using our code CosmoNest. We focus on the density perturbation spectral index n{sub S} and the tensor-to-scalar ratio r, which define the plane of slow-roll inflationary models. We find that while the Bayesian evidence supports the conclusion that n{sub S}{ne}1, the data are not yet powerful enough to do so at a strong or decisive level. If tensors are assumed absent, the current odds are approximately 8 to 1 in favor of n{sub S}{ne}1 under our assumptions, when WMAP3 data is used together with external data sets. WMAP3 data on its own is unable to distinguish between the two models. Further, inclusion of r as a parameter weakens the conclusion against the Harrison-Zel'dovich case (n{sub S}=1, r=0), albeit in a prior-dependent way. In appendices we describe the CosmoNest code in detail, noting its ability to supply posterior samples as well as to accurately compute the Bayesian evidence. We make a first public release of CosmoNest, now available at www.cosmonest.org.

  16. Managing Clustered Data Using Hierarchical Linear Modeling

    ERIC Educational Resources Information Center

    Warne, Russell T.; Li, Yan; McKyer, E. Lisako J.; Condie, Rachel; Diep, Cassandra S.; Murano, Peter S.

    2012-01-01

    Researchers in nutrition research often use cluster or multistage sampling to gather participants for their studies. These sampling methods often produce violations of the assumption of data independence that most traditional statistics share. Hierarchical linear modeling is a statistical method that can overcome violations of the independence…

  17. A Bayesian Model of Biases in Artificial Language Learning: The Case of a Word-Order Universal

    ERIC Educational Resources Information Center

    Culbertson, Jennifer; Smolensky, Paul

    2012-01-01

    In this article, we develop a hierarchical Bayesian model of learning in a general type of artificial language-learning experiment in which learners are exposed to a mixture of grammars representing the variation present in real learners' input, particularly at times of language change. The modeling goal is to formalize and quantify hypothesized…

  18. A Bayesian model of context-sensitive value attribution

    PubMed Central

    Rigoli, Francesco; Friston, Karl J; Martinelli, Cristina; Selaković, Mirjana; Shergill, Sukhwinder S; Dolan, Raymond J

    2016-01-01

    Substantial evidence indicates that incentive value depends on an anticipation of rewards within a given context. However, the computations underlying this context sensitivity remain unknown. To address this question, we introduce a normative (Bayesian) account of how rewards map to incentive values. This assumes that the brain inverts a model of how rewards are generated. Key features of our account include (i) an influence of prior beliefs about the context in which rewards are delivered (weighted by their reliability in a Bayes-optimal fashion), (ii) the notion that incentive values correspond to precision-weighted prediction errors, (iii) and contextual information unfolding at different hierarchical levels. This formulation implies that incentive value is intrinsically context-dependent. We provide empirical support for this model by showing that incentive value is influenced by context variability and by hierarchically nested contexts. The perspective we introduce generates new empirical predictions that might help explaining psychopathologies, such as addiction. DOI: http://dx.doi.org/10.7554/eLife.16127.001 PMID:27328323

  19. Bayesian structural equation modeling in sport and exercise psychology.

    PubMed

    Stenling, Andreas; Ivarsson, Andreas; Johnson, Urban; Lindwall, Magnus

    2015-08-01

    Bayesian statistics is on the rise in mainstream psychology, but applications in sport and exercise psychology research are scarce. In this article, the foundations of Bayesian analysis are introduced, and we will illustrate how to apply Bayesian structural equation modeling in a sport and exercise psychology setting. More specifically, we contrasted a confirmatory factor analysis on the Sport Motivation Scale II estimated with the most commonly used estimator, maximum likelihood, and a Bayesian approach with weakly informative priors for cross-loadings and correlated residuals. The results indicated that the model with Bayesian estimation and weakly informative priors provided a good fit to the data, whereas the model estimated with a maximum likelihood estimator did not produce a well-fitting model. The reasons for this discrepancy between maximum likelihood and Bayesian estimation are discussed as well as potential advantages and caveats with the Bayesian approach.

  20. Bayesian structural equation modeling in sport and exercise psychology.

    PubMed

    Stenling, Andreas; Ivarsson, Andreas; Johnson, Urban; Lindwall, Magnus

    2015-08-01

    Bayesian statistics is on the rise in mainstream psychology, but applications in sport and exercise psychology research are scarce. In this article, the foundations of Bayesian analysis are introduced, and we will illustrate how to apply Bayesian structural equation modeling in a sport and exercise psychology setting. More specifically, we contrasted a confirmatory factor analysis on the Sport Motivation Scale II estimated with the most commonly used estimator, maximum likelihood, and a Bayesian approach with weakly informative priors for cross-loadings and correlated residuals. The results indicated that the model with Bayesian estimation and weakly informative priors provided a good fit to the data, whereas the model estimated with a maximum likelihood estimator did not produce a well-fitting model. The reasons for this discrepancy between maximum likelihood and Bayesian estimation are discussed as well as potential advantages and caveats with the Bayesian approach. PMID:26442771

  1. Assessing global vegetation activity using spatio-temporal Bayesian modelling

    NASA Astrophysics Data System (ADS)

    Mulder, Vera L.; van Eck, Christel M.; Friedlingstein, Pierre; Regnier, Pierre A. G.

    2016-04-01

    This work demonstrates the potential of modelling vegetation activity using a hierarchical Bayesian spatio-temporal model. This approach allows modelling changes in vegetation and climate simultaneous in space and time. Changes of vegetation activity such as phenology are modelled as a dynamic process depending on climate variability in both space and time. Additionally, differences in observed vegetation status can be contributed to other abiotic ecosystem properties, e.g. soil and terrain properties. Although these properties do not change in time, they do change in space and may provide valuable information in addition to the climate dynamics. The spatio-temporal Bayesian models were calibrated at a regional scale because the local trends in space and time can be better captured by the model. The regional subsets were defined according to the SREX segmentation, as defined by the IPCC. Each region is considered being relatively homogeneous in terms of large-scale climate and biomes, still capturing small-scale (grid-cell level) variability. Modelling within these regions is hence expected to be less uncertain due to the absence of these large-scale patterns, compared to a global approach. This overall modelling approach allows the comparison of model behavior for the different regions and may provide insights on the main dynamic processes driving the interaction between vegetation and climate within different regions. The data employed in this study encompasses the global datasets for soil properties (SoilGrids), terrain properties (Global Relief Model based on SRTM DEM and ETOPO), monthly time series of satellite-derived vegetation indices (GIMMS NDVI3g) and climate variables (Princeton Meteorological Forcing Dataset). The findings proved the potential of a spatio-temporal Bayesian modelling approach for assessing vegetation dynamics, at a regional scale. The observed interrelationships of the employed data and the different spatial and temporal trends support

  2. Bayesian residual analysis for beta-binomial regression models

    NASA Astrophysics Data System (ADS)

    Pires, Rubiane Maria; Diniz, Carlos Alberto Ribeiro

    2012-10-01

    The beta-binomial regression model is an alternative model to the sum of any sequence of equicorrelated binary variables with common probability of success p. In this work a Bayesian perspective of this model is presented considering different link functions and different correlation structures. A general Bayesian residual analysis for this model, a issue which is often neglected in Bayesian analysis, using the residuals based on the predicted values obtained by the conditional predictive ordinate [1], the residuals based on the posterior distribution of the model parameters [2] and the Bayesian deviance residual [3] are presented in order to check the assumptions in the model.

  3. Bayesian Kinematic Finite Fault Source Models (Invited)

    NASA Astrophysics Data System (ADS)

    Minson, S. E.; Simons, M.; Beck, J. L.

    2010-12-01

    Finite fault earthquake source models are inherently under-determined: there is no unique solution to the inverse problem of determining the rupture history at depth as a function of time and space when our data are only limited observations at the Earth's surface. Traditional inverse techniques rely on model constraints and regularization to generate one model from the possibly broad space of all possible solutions. However, Bayesian methods allow us to determine the ensemble of all possible source models which are consistent with the data and our a priori assumptions about the physics of the earthquake source. Until now, Bayesian techniques have been of limited utility because they are computationally intractable for problems with as many free parameters as kinematic finite fault models. We have developed a methodology called Cascading Adaptive Tempered Metropolis In Parallel (CATMIP) which allows us to sample very high-dimensional problems in a parallel computing framework. The CATMIP algorithm combines elements of simulated annealing and genetic algorithms with the Metropolis algorithm to dynamically optimize the algorithm's efficiency as it runs. We will present synthetic performance tests of finite fault models made with this methodology as well as a kinematic source model for the 2007 Mw 7.7 Tocopilla, Chile earthquake. This earthquake was well recorded by multiple ascending and descending interferograms and a network of high-rate GPS stations whose records can be used as near-field seismograms.

  4. Posterior predictive Bayesian phylogenetic model selection.

    PubMed

    Lewis, Paul O; Xie, Wangang; Chen, Ming-Hui; Fan, Yu; Kuo, Lynn

    2014-05-01

    We present two distinctly different posterior predictive approaches to Bayesian phylogenetic model selection and illustrate these methods using examples from green algal protein-coding cpDNA sequences and flowering plant rDNA sequences. The Gelfand-Ghosh (GG) approach allows dissection of an overall measure of model fit into components due to posterior predictive variance (GGp) and goodness-of-fit (GGg), which distinguishes this method from the posterior predictive P-value approach. The conditional predictive ordinate (CPO) method provides a site-specific measure of model fit useful for exploratory analyses and can be combined over sites yielding the log pseudomarginal likelihood (LPML) which is useful as an overall measure of model fit. CPO provides a useful cross-validation approach that is computationally efficient, requiring only a sample from the posterior distribution (no additional simulation is required). Both GG and CPO add new perspectives to Bayesian phylogenetic model selection based on the predictive abilities of models and complement the perspective provided by the marginal likelihood (including Bayes Factor comparisons) based solely on the fit of competing models to observed data. PMID:24193892

  5. Inferring cetacean population densities from the absolute dynamic topography of the ocean in a hierarchical Bayesian framework.

    PubMed

    Pardo, Mario A; Gerrodette, Tim; Beier, Emilio; Gendron, Diane; Forney, Karin A; Chivers, Susan J; Barlow, Jay; Palacios, Daniel M

    2015-01-01

    We inferred the population densities of blue whales (Balaenoptera musculus) and short-beaked common dolphins (Delphinus delphis) in the Northeast Pacific Ocean as functions of the water-column's physical structure by implementing hierarchical models in a Bayesian framework. This approach allowed us to propagate the uncertainty of the field observations into the inference of species-habitat relationships and to generate spatially explicit population density predictions with reduced effects of sampling heterogeneity. Our hypothesis was that the large-scale spatial distributions of these two cetacean species respond primarily to ecological processes resulting from shoaling and outcropping of the pycnocline in regions of wind-forced upwelling and eddy-like circulation. Physically, these processes affect the thermodynamic balance of the water column, decreasing its volume and thus the height of the absolute dynamic topography (ADT). Biologically, they lead to elevated primary productivity and persistent aggregation of low-trophic-level prey. Unlike other remotely sensed variables, ADT provides information about the structure of the entire water column and it is also routinely measured at high spatial-temporal resolution by satellite altimeters with uniform global coverage. Our models provide spatially explicit population density predictions for both species, even in areas where the pycnocline shoals but does not outcrop (e.g. the Costa Rica Dome and the North Equatorial Countercurrent thermocline ridge). Interannual variations in distribution during El Niño anomalies suggest that the population density of both species decreases dramatically in the Equatorial Cold Tongue and the Costa Rica Dome, and that their distributions retract to particular areas that remain productive, such as the more oceanic waters in the central California Current System, the northern Gulf of California, the North Equatorial Countercurrent thermocline ridge, and the more southern portion of the

  6. Inferring cetacean population densities from the absolute dynamic topography of the ocean in a hierarchical Bayesian framework.

    PubMed

    Pardo, Mario A; Gerrodette, Tim; Beier, Emilio; Gendron, Diane; Forney, Karin A; Chivers, Susan J; Barlow, Jay; Palacios, Daniel M

    2015-01-01

    We inferred the population densities of blue whales (Balaenoptera musculus) and short-beaked common dolphins (Delphinus delphis) in the Northeast Pacific Ocean as functions of the water-column's physical structure by implementing hierarchical models in a Bayesian framework. This approach allowed us to propagate the uncertainty of the field observations into the inference of species-habitat relationships and to generate spatially explicit population density predictions with reduced effects of sampling heterogeneity. Our hypothesis was that the large-scale spatial distributions of these two cetacean species respond primarily to ecological processes resulting from shoaling and outcropping of the pycnocline in regions of wind-forced upwelling and eddy-like circulation. Physically, these processes affect the thermodynamic balance of the water column, decreasing its volume and thus the height of the absolute dynamic topography (ADT). Biologically, they lead to elevated primary productivity and persistent aggregation of low-trophic-level prey. Unlike other remotely sensed variables, ADT provides information about the structure of the entire water column and it is also routinely measured at high spatial-temporal resolution by satellite altimeters with uniform global coverage. Our models provide spatially explicit population density predictions for both species, even in areas where the pycnocline shoals but does not outcrop (e.g. the Costa Rica Dome and the North Equatorial Countercurrent thermocline ridge). Interannual variations in distribution during El Niño anomalies suggest that the population density of both species decreases dramatically in the Equatorial Cold Tongue and the Costa Rica Dome, and that their distributions retract to particular areas that remain productive, such as the more oceanic waters in the central California Current System, the northern Gulf of California, the North Equatorial Countercurrent thermocline ridge, and the more southern portion of the

  7. Estimating methane and nitrous oxide emissions in California using multi-tower observations and hierarchical Bayesian inversion

    NASA Astrophysics Data System (ADS)

    Jeong, S.; Hsu, Y.; Newman, S.; Zhang, J.; Andrews, A. E.; Bianco, L.; Bagley, J.; Cui, X.; Graven, H. D.; Kim, J.; Salameh, P.; LaFranchi, B. W.; Priest, C.; Campos-Pineda, M.; Novakovskaia, E.; Sloop, C.; Michelsen, H. A.; Bambha, R.; Weiss, R. F.; Keeling, R. F.; Fischer, M. L.

    2015-12-01

    We present an analysis of annual state total methane (CH4) and nitrous oxide (N2O) emissions from California using atmospheric observations from thirteen sites (six sites for N2O) in California during June 2013 - May 2014. A hierarchical Bayesian inversion (HBI) method is used to estimate CH4 and N2O emissions for spatial regions (0.3 degree pixels) by comparing measured mixing ratios with transport model (WRF-STILT) predictions. Using the multi-site measurements across California, the HBI analysis constrains a significant portion of expected emissions for both CH4 and N2O in the Central Valley and southern California. Based on the HBI analysis, we estimate a likely range of the state's annual CH4 emissions is 2.4 - 2.7 Tg CH4/yr (at 68% confidence), which is 1.4 - 1.6 times the total estimated by the California Air Resources Board (CARB). Similarly, we estimate the state's annual N2O emissions to be 77 - 95 Gg N2O/yr (at 68% confidence), which are 1.6 - 2.0 times CARB's state total. These results suggest that the combined total of CH4 and N2O emissions from the HBI analysis would comprise 18 - 21% of state total greenhouse gas (GHG) emissions, higher than 12% estimated in the current state inventory. Additionally, we expand previous evaluations of possible systematic bias in annual emission estimates due to transport model error by comparing measured and predicted carbon monoxide (CO) for four of the sites. These results highlight the need for multiple independent methods to estimate non-CO2 GHG emissions, and offer insight into opportunities for non-CO2 GHG emission mitigation efforts towards achieving California's GHG emission goals.

  8. Inferring Cetacean Population Densities from the Absolute Dynamic Topography of the Ocean in a Hierarchical Bayesian Framework

    PubMed Central

    Pardo, Mario A.; Gerrodette, Tim; Beier, Emilio; Gendron, Diane; Forney, Karin A.; Chivers, Susan J.; Barlow, Jay; Palacios, Daniel M.

    2015-01-01

    We inferred the population densities of blue whales (Balaenoptera musculus) and short-beaked common dolphins (Delphinus delphis) in the Northeast Pacific Ocean as functions of the water-column’s physical structure by implementing hierarchical models in a Bayesian framework. This approach allowed us to propagate the uncertainty of the field observations into the inference of species-habitat relationships and to generate spatially explicit population density predictions with reduced effects of sampling heterogeneity. Our hypothesis was that the large-scale spatial distributions of these two cetacean species respond primarily to ecological processes resulting from shoaling and outcropping of the pycnocline in regions of wind-forced upwelling and eddy-like circulation. Physically, these processes affect the thermodynamic balance of the water column, decreasing its volume and thus the height of the absolute dynamic topography (ADT). Biologically, they lead to elevated primary productivity and persistent aggregation of low-trophic-level prey. Unlike other remotely sensed variables, ADT provides information about the structure of the entire water column and it is also routinely measured at high spatial-temporal resolution by satellite altimeters with uniform global coverage. Our models provide spatially explicit population density predictions for both species, even in areas where the pycnocline shoals but does not outcrop (e.g. the Costa Rica Dome and the North Equatorial Countercurrent thermocline ridge). Interannual variations in distribution during El Niño anomalies suggest that the population density of both species decreases dramatically in the Equatorial Cold Tongue and the Costa Rica Dome, and that their distributions retract to particular areas that remain productive, such as the more oceanic waters in the central California Current System, the northern Gulf of California, the North Equatorial Countercurrent thermocline ridge, and the more southern portion of

  9. Hierarchical Climate Modeling for Cosmoclimatology

    NASA Astrophysics Data System (ADS)

    Ohfuchi, Wataru

    2010-05-01

    It has been reported that there are correlations among solar activity, amount of galactic cosmic ray, amount of low clouds and surface air temperature (Svensmark and Friis-Chistensen, 1997). These correlations seem to exist for current climate change, Little Ice Age, and geological time scale climate changes. Some hypothetic mechanisms have been argued for the correlations but it still needs quantitative studies to understand the mechanism. In order to decrease uncertainties, only first principles or laws very close to first principles should be used. Our group at Japan Agency for Marine-Earth Science and Technology has started modeling effort to tackle this problem. We are constructing models from galactic cosmic ray inducing ionization, to aerosol formation, to cloud formation, to global climate. In this talk, we introduce our modeling activities. For aerosol formation, we use molecular dynamics. For cloud formation, we use a new cloud microphysics model called "super droplet method". We also try to couple a nonhydrostatic atmospheric regional cloud resolving model and a hydrostatic atmospheric general circulation model.

  10. Moving beyond qualitative evaluations of Bayesian models of cognition.

    PubMed

    Hemmer, Pernille; Tauber, Sean; Steyvers, Mark

    2015-06-01

    Bayesian models of cognition provide a powerful way to understand the behavior and goals of individuals from a computational point of view. Much of the focus in the Bayesian cognitive modeling approach has been on qualitative model evaluations, where predictions from the models are compared to data that is often averaged over individuals. In many cognitive tasks, however, there are pervasive individual differences. We introduce an approach to directly infer individual differences related to subjective mental representations within the framework of Bayesian models of cognition. In this approach, Bayesian data analysis methods are used to estimate cognitive parameters and motivate the inference process within a Bayesian cognitive model. We illustrate this integrative Bayesian approach on a model of memory. We apply the model to behavioral data from a memory experiment involving the recall of heights of people. A cross-validation analysis shows that the Bayesian memory model with inferred subjective priors predicts withheld data better than a Bayesian model where the priors are based on environmental statistics. In addition, the model with inferred priors at the individual subject level led to the best overall generalization performance, suggesting that individual differences are important to consider in Bayesian models of cognition.

  11. Inference and Hierarchical Modeling in the Social Sciences.

    ERIC Educational Resources Information Center

    Draper, David

    1995-01-01

    The use of hierarchical models in social science research is discussed, with emphasis on causal inference and consideration of the limitations of hierarchical models. The increased use of Gibbs sampling and other Markov-chain Monte Carlo methods in the application of hierarchical models is recommended. (SLD)

  12. A Bayesian Shrinkage Approach for AMMI Models

    PubMed Central

    de Oliveira, Luciano Antonio; Nuvunga, Joel Jorge; Pamplona, Andrezza Kéllen Alves

    2015-01-01

    Linear-bilinear models, especially the additive main effects and multiplicative interaction (AMMI) model, are widely applicable to genotype-by-environment interaction (GEI) studies in plant breeding programs. These models allow a parsimonious modeling of GE interactions, retaining a small number of principal components in the analysis. However, one aspect of the AMMI model that is still debated is the selection criteria for determining the number of multiplicative terms required to describe the GE interaction pattern. Shrinkage estimators have been proposed as selection criteria for the GE interaction components. In this study, a Bayesian approach was combined with the AMMI model with shrinkage estimators for the principal components. A total of 55 maize genotypes were evaluated in nine different environments using a complete blocks design with three replicates. The results show that the traditional Bayesian AMMI model produces low shrinkage of singular values but avoids the usual pitfalls in determining the credible intervals in the biplot. On the other hand, Bayesian shrinkage AMMI models have difficulty with the credible interval for model parameters, but produce stronger shrinkage of the principal components, converging to GE matrices that have more shrinkage than those obtained using mixed models. This characteristic allowed more parsimonious models to be chosen, and resulted in models being selected that were similar to those obtained by the Cornelius F-test (α = 0.05) in traditional AMMI models and cross validation based on leave-one-out. This characteristic allowed more parsimonious models to be chosen and more GEI pattern retained on the first two components. The resulting model chosen by posterior distribution of singular value was also similar to those produced by the cross-validation approach in traditional AMMI models. Our method enables the estimation of credible interval for AMMI biplot plus the choice of AMMI model based on direct posterior

  13. A Bayesian Shrinkage Approach for AMMI Models.

    PubMed

    da Silva, Carlos Pereira; de Oliveira, Luciano Antonio; Nuvunga, Joel Jorge; Pamplona, Andrezza Kéllen Alves; Balestre, Marcio

    2015-01-01

    Linear-bilinear models, especially the additive main effects and multiplicative interaction (AMMI) model, are widely applicable to genotype-by-environment interaction (GEI) studies in plant breeding programs. These models allow a parsimonious modeling of GE interactions, retaining a small number of principal components in the analysis. However, one aspect of the AMMI model that is still debated is the selection criteria for determining the number of multiplicative terms required to describe the GE interaction pattern. Shrinkage estimators have been proposed as selection criteria for the GE interaction components. In this study, a Bayesian approach was combined with the AMMI model with shrinkage estimators for the principal components. A total of 55 maize genotypes were evaluated in nine different environments using a complete blocks design with three replicates. The results show that the traditional Bayesian AMMI model produces low shrinkage of singular values but avoids the usual pitfalls in determining the credible intervals in the biplot. On the other hand, Bayesian shrinkage AMMI models have difficulty with the credible interval for model parameters, but produce stronger shrinkage of the principal components, converging to GE matrices that have more shrinkage than those obtained using mixed models. This characteristic allowed more parsimonious models to be chosen, and resulted in models being selected that were similar to those obtained by the Cornelius F-test (α = 0.05) in traditional AMMI models and cross validation based on leave-one-out. This characteristic allowed more parsimonious models to be chosen and more GEI pattern retained on the first two components. The resulting model chosen by posterior distribution of singular value was also similar to those produced by the cross-validation approach in traditional AMMI models. Our method enables the estimation of credible interval for AMMI biplot plus the choice of AMMI model based on direct posterior

  14. Model Comparison of Bayesian Semiparametric and Parametric Structural Equation Models

    ERIC Educational Resources Information Center

    Song, Xin-Yuan; Xia, Ye-Mao; Pan, Jun-Hao; Lee, Sik-Yum

    2011-01-01

    Structural equation models have wide applications. One of the most important issues in analyzing structural equation models is model comparison. This article proposes a Bayesian model comparison statistic, namely the "L[subscript nu]"-measure for both semiparametric and parametric structural equation models. For illustration purposes, we consider…

  15. A Nonparametric Bayesian Model for Nested Clustering.

    PubMed

    Lee, Juhee; Müller, Peter; Zhu, Yitan; Ji, Yuan

    2016-01-01

    We propose a nonparametric Bayesian model for clustering where clusters of experimental units are determined by a shared pattern of clustering another set of experimental units. The proposed model is motivated by the analysis of protein activation data, where we cluster proteins such that all proteins in one cluster give rise to the same clustering of patients. That is, we define clusters of proteins by the way that patients group with respect to the corresponding protein activations. This is in contrast to (almost) all currently available models that use shared parameters in the sampling model to define clusters. This includes in particular model based clustering, Dirichlet process mixtures, product partition models, and more. We show results for two typical biostatistical inference problems that give rise to clustering. PMID:26519174

  16. Global Trends and Factors Associated with the Illegal Killing of Elephants: A Hierarchical Bayesian Analysis of Carcass Encounter Data

    PubMed Central

    Burn, Robert W.; Underwood, Fiona M.; Blanc, Julian

    2011-01-01

    Elephant poaching and the ivory trade remain high on the agenda at meetings of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Well-informed debates require robust estimates of trends, the spatial distribution of poaching, and drivers of poaching. We present an analysis of trends and drivers of an indicator of elephant poaching of all elephant species. The site-based monitoring system known as Monitoring the Illegal Killing of Elephants (MIKE), set up by the 10th Conference of the Parties of CITES in 1997, produces carcass encounter data reported mainly by anti-poaching patrols. Data analyzed were site by year totals of 6,337 carcasses from 66 sites in Africa and Asia from 2002–2009. Analysis of these observational data is a serious challenge to traditional statistical methods because of the opportunistic and non-random nature of patrols, and the heterogeneity across sites. Adopting a Bayesian hierarchical modeling approach, we used the proportion of carcasses that were illegally killed (PIKE) as a poaching index, to estimate the trend and the effects of site- and country-level factors associated with poaching. Important drivers of illegal killing that emerged at country level were poor governance and low levels of human development, and at site level, forest cover and area of the site in regions where human population density is low. After a drop from 2002, PIKE remained fairly constant from 2003 until 2006, after which it increased until 2008. The results for 2009 indicate a decline. Sites with PIKE ranging from the lowest to the highest were identified. The results of the analysis provide a sound information base for scientific evidence-based decision making in the CITES process. PMID:21912670

  17. Global trends and factors associated with the illegal killing of elephants: A hierarchical bayesian analysis of carcass encounter data.

    PubMed

    Burn, Robert W; Underwood, Fiona M; Blanc, Julian

    2011-01-01

    Elephant poaching and the ivory trade remain high on the agenda at meetings of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Well-informed debates require robust estimates of trends, the spatial distribution of poaching, and drivers of poaching. We present an analysis of trends and drivers of an indicator of elephant poaching of all elephant species. The site-based monitoring system known as Monitoring the Illegal Killing of Elephants (MIKE), set up by the 10(th) Conference of the Parties of CITES in 1997, produces carcass encounter data reported mainly by anti-poaching patrols. Data analyzed were site by year totals of 6,337 carcasses from 66 sites in Africa and Asia from 2002-2009. Analysis of these observational data is a serious challenge to traditional statistical methods because of the opportunistic and non-random nature of patrols, and the heterogeneity across sites. Adopting a bayesian hierarchical modeling approach, we used the proportion of carcasses that were illegally killed (PIKE) as a poaching index, to estimate the trend and the effects of site- and country-level factors associated with poaching. Important drivers of illegal killing that emerged at country level were poor governance and low levels of human development, and at site level, forest cover and area of the site in regions where human population density is low. After a drop from 2002, PIKE remained fairly constant from 2003 until 2006, after which it increased until 2008. The results for 2009 indicate a decline. Sites with PIKE ranging from the lowest to the highest were identified. The results of the analysis provide a sound information base for scientific evidence-based decision making in the CITES process. PMID:21912670

  18. Global trends and factors associated with the illegal killing of elephants: A hierarchical bayesian analysis of carcass encounter data.

    PubMed

    Burn, Robert W; Underwood, Fiona M; Blanc, Julian

    2011-01-01

    Elephant poaching and the ivory trade remain high on the agenda at meetings of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Well-informed debates require robust estimates of trends, the spatial distribution of poaching, and drivers of poaching. We present an analysis of trends and drivers of an indicator of elephant poaching of all elephant species. The site-based monitoring system known as Monitoring the Illegal Killing of Elephants (MIKE), set up by the 10(th) Conference of the Parties of CITES in 1997, produces carcass encounter data reported mainly by anti-poaching patrols. Data analyzed were site by year totals of 6,337 carcasses from 66 sites in Africa and Asia from 2002-2009. Analysis of these observational data is a serious challenge to traditional statistical methods because of the opportunistic and non-random nature of patrols, and the heterogeneity across sites. Adopting a bayesian hierarchical modeling approach, we used the proportion of carcasses that were illegally killed (PIKE) as a poaching index, to estimate the trend and the effects of site- and country-level factors associated with poaching. Important drivers of illegal killing that emerged at country level were poor governance and low levels of human development, and at site level, forest cover and area of the site in regions where human population density is low. After a drop from 2002, PIKE remained fairly constant from 2003 until 2006, after which it increased until 2008. The results for 2009 indicate a decline. Sites with PIKE ranging from the lowest to the highest were identified. The results of the analysis provide a sound information base for scientific evidence-based decision making in the CITES process.

  19. A hierarchical nest survival model integrating incomplete temporally varying covariates.

    PubMed

    Converse, Sarah J; Royle, J Andrew; Adler, Peter H; Urbanek, Richard P; Barzen, Jeb A

    2013-11-01

    Nest success is a critical determinant of the dynamics of avian populations, and nest survival modeling has played a key role in advancing avian ecology and management. Beginning with the development of daily nest survival models, and proceeding through subsequent extensions, the capacity for modeling the effects of hypothesized factors on nest survival has expanded greatly. We extend nest survival models further by introducing an approach to deal with incompletely observed, temporally varying covariates using a hierarchical model. Hierarchical modeling offers a way to separate process and observational components of demographic models to obtain estimates of the parameters of primary interest, and to evaluate structural effects of ecological and management interest. We built a hierarchical model for daily nest survival to analyze nest data from reintroduced whooping cranes (Grus americana) in the Eastern Migratory Population. This reintroduction effort has been beset by poor reproduction, apparently due primarily to nest abandonment by breeding birds. We used the model to assess support for the hypothesis that nest abandonment is caused by harassment from biting insects. We obtained indices of blood-feeding insect populations based on the spatially interpolated counts of insects captured in carbon dioxide traps. However, insect trapping was not conducted daily, and so we had incomplete information on a temporally variable covariate of interest. We therefore supplemented our nest survival model with a parallel model for estimating the values of the missing insect covariates. We used Bayesian model selection to identify the best predictors of daily nest survival. Our results suggest that the black fly Simulium annulus may be negatively affecting nest survival of reintroduced whooping cranes, with decreasing nest survival as abundance of S. annulus increases. The modeling framework we have developed will be applied in the future to a larger data set to evaluate the

  20. A hierarchical nest survival model integrating incomplete temporally varying covariates

    USGS Publications Warehouse

    Converse, Sarah J.; Royle, J. Andrew; Adler, Peter H.; Urbanek, Richard P.; Barzan, Jeb A.

    2013-01-01

    Nest success is a critical determinant of the dynamics of avian populations, and nest survival modeling has played a key role in advancing avian ecology and management. Beginning with the development of daily nest survival models, and proceeding through subsequent extensions, the capacity for modeling the effects of hypothesized factors on nest survival has expanded greatly. We extend nest survival models further by introducing an approach to deal with incompletely observed, temporally varying covariates using a hierarchical model. Hierarchical modeling offers a way to separate process and observational components of demographic models to obtain estimates of the parameters of primary interest, and to evaluate structural effects of ecological and management interest. We built a hierarchical model for daily nest survival to analyze nest data from reintroduced whooping cranes (Grus americana) in the Eastern Migratory Population. This reintroduction effort has been beset by poor reproduction, apparently due primarily to nest abandonment by breeding birds. We used the model to assess support for the hypothesis that nest abandonment is caused by harassment from biting insects. We obtained indices of blood-feeding insect populations based on the spatially interpolated counts of insects captured in carbon dioxide traps. However, insect trapping was not conducted daily, and so we had incomplete information on a temporally variable covariate of interest. We therefore supplemented our nest survival model with a parallel model for estimating the values of the missing insect covariates. We used Bayesian model selection to identify the best predictors of daily nest survival. Our results suggest that the black fly Simulium annulus may be negatively affecting nest survival of reintroduced whooping cranes, with decreasing nest survival as abundance of S. annulus increases. The modeling framework we have developed will be applied in the future to a larger data set to evaluate the

  1. A hierarchical nest survival model integrating incomplete temporally varying covariates.

    PubMed

    Converse, Sarah J; Royle, J Andrew; Adler, Peter H; Urbanek, Richard P; Barzen, Jeb A

    2013-11-01

    Nest success is a critical determinant of the dynamics of avian populations, and nest survival modeling has played a key role in advancing avian ecology and management. Beginning with the development of daily nest survival models, and proceeding through subsequent extensions, the capacity for modeling the effects of hypothesized factors on nest survival has expanded greatly. We extend nest survival models further by introducing an approach to deal with incompletely observed, temporally varying covariates using a hierarchical model. Hierarchical modeling offers a way to separate process and observational components of demographic models to obtain estimates of the parameters of primary interest, and to evaluate structural effects of ecological and management interest. We built a hierarchical model for daily nest survival to analyze nest data from reintroduced whooping cranes (Grus americana) in the Eastern Migratory Population. This reintroduction effort has been beset by poor reproduction, apparently due primarily to nest abandonment by breeding birds. We used the model to assess support for the hypothesis that nest abandonment is caused by harassment from biting insects. We obtained indices of blood-feeding insect populations based on the spatially interpolated counts of insects captured in carbon dioxide traps. However, insect trapping was not conducted daily, and so we had incomplete information on a temporally variable covariate of interest. We therefore supplemented our nest survival model with a parallel model for estimating the values of the missing insect covariates. We used Bayesian model selection to identify the best predictors of daily nest survival. Our results suggest that the black fly Simulium annulus may be negatively affecting nest survival of reintroduced whooping cranes, with decreasing nest survival as abundance of S. annulus increases. The modeling framework we have developed will be applied in the future to a larger data set to evaluate the

  2. Model feedback in Bayesian propensity score estimation.

    PubMed

    Zigler, Corwin M; Watts, Krista; Yeh, Robert W; Wang, Yun; Coull, Brent A; Dominici, Francesca

    2013-03-01

    Methods based on the propensity score comprise one set of valuable tools for comparative effectiveness research and for estimating causal effects more generally. These methods typically consist of two distinct stages: (1) a propensity score stage where a model is fit to predict the propensity to receive treatment (the propensity score), and (2) an outcome stage where responses are compared in treated and untreated units having similar values of the estimated propensity score. Traditional techniques conduct estimation in these two stages separately; estimates from the first stage are treated as fixed and known for use in the second stage. Bayesian methods have natural appeal in these settings because separate likelihoods for the two stages can be combined into a single joint likelihood, with estimation of the two stages carried out simultaneously. One key feature of joint estimation in this context is "feedback" between the outcome stage and the propensity score stage, meaning that quantities in a model for the outcome contribute information to posterior distributions of quantities in the model for the propensity score. We provide a rigorous assessment of Bayesian propensity score estimation to show that model feedback can produce poor estimates of causal effects absent strategies that augment propensity score adjustment with adjustment for individual covariates. We illustrate this phenomenon with a simulation study and with a comparative effectiveness investigation of carotid artery stenting versus carotid endarterectomy among 123,286 Medicare beneficiaries hospitlized for stroke in 2006 and 2007. PMID:23379793

  3. Bayesian model comparison of solar flare spectra

    NASA Astrophysics Data System (ADS)

    Ireland, J.; Holman, G.

    2012-12-01

    The detailed understanding of solar flares requires an understanding of the physics of accelerated electrons, since electrons carry a large fraction of the total energy released in a flare. Hard X-ray energy flux spectral observations of solar flares can be fit with different parameterized models of the interaction of the flare-accelerated electrons with the solar plasma. Each model describes different possible physical effects that may occur in solar flares. Bayesian model comparison provides a technique for assessing which model best describes the data. The advantage of this technique over others is that it can fully account for the different number and type of parameters in each model. We demonstrate this using Ramaty High Energy Solar Spectroscopic Imager (RHESSI) spectral data from the GOES (Geostationary Operational Environmental Satellite) X4.8 flare of 23-July-2002. We suggest that the observed spectrum can be reproduced using two different parameterized models of the flare electron content. The first model assumes that the flare-accelerated electron spectrum consisting of a single power law with a fixed low energy cutoff assumed to be below the range of fitted X-ray energies, interacting with a non-uniformly ionized target. The second model assumes that the flare-accelerated electron spectrum has a broken power law and a low energy cutoff, which interacts with a fully ionized target plasma. The low energy cutoff in this model is a parameter used in fitting the data. We will introduce and use Bayesian model comparison techniques to decide which model best explains the observed data. This work is funded by the NASA Solar and Heliospheric Physics program.

  4. Experience With Bayesian Image Based Surface Modeling

    NASA Technical Reports Server (NTRS)

    Stutz, John C.

    2005-01-01

    Bayesian surface modeling from images requires modeling both the surface and the image generation process, in order to optimize the models by comparing actual and generated images. Thus it differs greatly, both conceptually and in computational difficulty, from conventional stereo surface recovery techniques. But it offers the possibility of using any number of images, taken under quite different conditions, and by different instruments that provide independent and often complementary information, to generate a single surface model that fuses all available information. I describe an implemented system, with a brief introduction to the underlying mathematical models and the compromises made for computational efficiency. I describe successes and failures achieved on actual imagery, where we went wrong and what we did right, and how our approach could be improved. Lastly I discuss how the same approach can be extended to distinct types of instruments, to achieve true sensor fusion.

  5. Bayesian Lasso for Semiparametric Structural Equation Models

    PubMed Central

    Guo, Ruixin; Zhu, Hongtu; Chow, Sy-Miin; Ibrahim, Joseph G.

    2011-01-01

    Summary There has been great interest in developing nonlinear structural equation models and associated statistical inference procedures, including estimation and model selection methods. In this paper a general semiparametric structural equation model (SSEM) is developed in which the structural equation is composed of nonparametric functions of exogenous latent variables and fixed covariates on a set of latent endogenous variables. A basis representation is used to approximate these nonparametric functions in the structural equation and the Bayesian Lasso method coupled with a Markov Chain Monte Carlo (MCMC) algorithm is used for simultaneous estimation and model selection. The proposed method is illustrated using a simulation study and data from the Affective Dynamics and Individual Differences (ADID) study. Results demonstrate that our method can accurately estimate the unknown parameters and correctly identify the true underlying model. PMID:22376150

  6. An Accessible Method for Implementing Hierarchical Models with Spatio-Temporal Abundance Data

    PubMed Central

    Ross, Beth E.; Hooten, Mevin B.; Koons, David N.

    2012-01-01

    A common goal in ecology and wildlife management is to determine the causes of variation in population dynamics over long periods of time and across large spatial scales. Many assumptions must nevertheless be overcome to make appropriate inference about spatio-temporal variation in population dynamics, such as autocorrelation among data points, excess zeros, and observation error in count data. To address these issues, many scientists and statisticians have recommended the use of Bayesian hierarchical models. Unfortunately, hierarchical statistical models remain somewhat difficult to use because of the necessary quantitative background needed to implement them, or because of the computational demands of using Markov Chain Monte Carlo algorithms to estimate parameters. Fortunately, new tools have recently been developed that make it more feasible for wildlife biologists to fit sophisticated hierarchical Bayesian models (i.e., Integrated Nested Laplace Approximation, ‘INLA’). We present a case study using two important game species in North America, the lesser and greater scaup, to demonstrate how INLA can be used to estimate the parameters in a hierarchical model that decouples observation error from process variation, and accounts for unknown sources of excess zeros as well as spatial and temporal dependence in the data. Ultimately, our goal was to make unbiased inference about spatial variation in population trends over time. PMID:23166658

  7. An Accessible Method for Implementing Hierarchical Models with Spatio-Temporal Abundance Data

    USGS Publications Warehouse

    Ross, Beth E.; Hooten, Melvin B.; Koons, David N.

    2012-01-01

    A common goal in ecology and wildlife management is to determine the causes of variation in population dynamics over long periods of time and across large spatial scales. Many assumptions must nevertheless be overcome to make appropriate inference about spatio-temporal variation in population dynamics, such as autocorrelation among data points, excess zeros, and observation error in count data. To address these issues, many scientists and statisticians have recommended the use of Bayesian hierarchical models. Unfortunately, hierarchical statistical models remain somewhat difficult to use because of the necessary quantitative background needed to implement them, or because of the computational demands of using Markov Chain Monte Carlo algorithms to estimate parameters. Fortunately, new tools have recently been developed that make it more feasible for wildlife biologists to fit sophisticated hierarchical Bayesian models (i.e., Integrated Nested Laplace Approximation, ‘INLA’). We present a case study using two important game species in North America, the lesser and greater scaup, to demonstrate how INLA can be used to estimate the parameters in a hierarchical model that decouples observation error from process variation, and accounts for unknown sources of excess zeros as well as spatial and temporal dependence in the data. Ultimately, our goal was to make unbiased inference about spatial variation in population trends over time.

  8. The effect of suspended sediment on fertilization success in the urchin Evechinus chloroticus: analysis of experimental data using hierarchical Bayesian methods.

    PubMed

    Miller, S L; Richardson, K; Edwards, P A

    2014-11-15

    Terrestrial sediments are a significant stressor on coastal ecosystems, with both suspended and deposited sediment having adverse effects on aquatic organisms. However, information on the effect of suspended sediments on fertilization success for urchin species is lacking. Using sediment levels similar to those encountered in situ, a controlled experiment was conducted to test whether suspended sediment affects fertilization success in the urchin Evechinus chloroticus. Analyses used generalized linear mixed models (GLMMs) and hierarchical Bayesian (HB) regression. Both approaches showed a significant decrease in fertilization success with increased suspended sediment levels. Uncertainties in estimates were narrower for HB models, suggesting that this approach has advantages over GLMMs for sparse data problems sometimes encountered in laboratory experiments. Given future global change scenarios, this work is important for predicting the effects of stressors such as sedimentation that may ultimately impact marine populations.

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

    PubMed

    Jones, Matt; Love, Bradley C

    2011-08-01

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

  10. Hopes and Cautions in Implementing Bayesian Structural Equation Modeling

    ERIC Educational Resources Information Center

    MacCallum, Robert C.; Edwards, Michael C.; Cai, Li

    2012-01-01

    Muthen and Asparouhov (2012) have proposed and demonstrated an approach to model specification and estimation in structural equation modeling (SEM) using Bayesian methods. Their contribution builds on previous work in this area by (a) focusing on the translation of conventional SEM models into a Bayesian framework wherein parameters fixed at zero…

  11. A Bayesian Model of Category-Specific Emotional Brain Responses

    PubMed Central

    Wager, Tor D.; Kang, Jian; Johnson, Timothy D.; Nichols, Thomas E.; Satpute, Ajay B.; Barrett, Lisa Feldman

    2015-01-01

    Understanding emotion is critical for a science of healthy and disordered brain function, but the neurophysiological basis of emotional experience is still poorly understood. We analyzed human brain activity patterns from 148 studies of emotion categories (2159 total participants) using a novel hierarchical Bayesian model. The model allowed us to classify which of five categories—fear, anger, disgust, sadness, or happiness—is engaged by a study with 66% accuracy (43-86% across categories). Analyses of the activity patterns encoded in the model revealed that each emotion category is associated with unique, prototypical patterns of activity across multiple brain systems including the cortex, thalamus, amygdala, and other structures. The results indicate that emotion categories are not contained within any one region or system, but are represented as configurations across multiple brain networks. The model provides a precise summary of the prototypical patterns for each emotion category, and demonstrates that a sufficient characterization of emotion categories relies on (a) differential patterns of involvement in neocortical systems that differ between humans and other species, and (b) distinctive patterns of cortical-subcortical interactions. Thus, these findings are incompatible with several contemporary theories of emotion, including those that emphasize emotion-dedicated brain systems and those that propose emotion is localized primarily in subcortical activity. They are consistent with componential and constructionist views, which propose that emotions are differentiated by a combination of perceptual, mnemonic, prospective, and motivational elements. Such brain-based models of emotion provide a foundation for new translational and clinical approaches. PMID:25853490

  12. Hierarchical modeling and inference in ecology: The analysis of data from populations, metapopulations and communities

    USGS Publications Warehouse

    Royle, J. Andrew; Dorazio, Robert M.

    2008-01-01

    A guide to data collection, modeling and inference strategies for biological survey data using Bayesian and classical statistical methods. This book describes a general and flexible framework for modeling and inference in ecological systems based on hierarchical models, with a strict focus on the use of probability models and parametric inference. Hierarchical models represent a paradigm shift in the application of statistics to ecological inference problems because they combine explicit models of ecological system structure or dynamics with models of how ecological systems are observed. The principles of hierarchical modeling are developed and applied to problems in population, metapopulation, community, and metacommunity systems. The book provides the first synthetic treatment of many recent methodological advances in ecological modeling and unifies disparate methods and procedures. The authors apply principles of hierarchical modeling to ecological problems, including * occurrence or occupancy models for estimating species distribution * abundance models based on many sampling protocols, including distance sampling * capture-recapture models with individual effects * spatial capture-recapture models based on camera trapping and related methods * population and metapopulation dynamic models * models of biodiversity, community structure and dynamics.

  13. Merging Digital Surface Models Implementing Bayesian Approaches

    NASA Astrophysics Data System (ADS)

    Sadeq, H.; Drummond, J.; Li, Z.

    2016-06-01

    In this research different DSMs from different sources have been merged. The merging is based on a probabilistic model using a Bayesian Approach. The implemented data have been sourced from very high resolution satellite imagery sensors (e.g. WorldView-1 and Pleiades). It is deemed preferable to use a Bayesian Approach when the data obtained from the sensors are limited and it is difficult to obtain many measurements or it would be very costly, thus the problem of the lack of data can be solved by introducing a priori estimations of data. To infer the prior data, it is assumed that the roofs of the buildings are specified as smooth, and for that purpose local entropy has been implemented. In addition to the a priori estimations, GNSS RTK measurements have been collected in the field which are used as check points to assess the quality of the DSMs and to validate the merging result. The model has been applied in the West-End of Glasgow containing different kinds of buildings, such as flat roofed and hipped roofed buildings. Both quantitative and qualitative methods have been employed to validate the merged DSM. The validation results have shown that the model was successfully able to improve the quality of the DSMs and improving some characteristics such as the roof surfaces, which consequently led to better representations. In addition to that, the developed model has been compared with the well established Maximum Likelihood model and showed similar quantitative statistical results and better qualitative results. Although the proposed model has been applied on DSMs that were derived from satellite imagery, it can be applied to any other sourced DSMs.

  14. Effect on Prediction when Modeling Covariates in Bayesian Nonparametric Models.

    PubMed

    Cruz-Marcelo, Alejandro; Rosner, Gary L; Müller, Peter; Stewart, Clinton F

    2013-04-01

    In biomedical research, it is often of interest to characterize biologic processes giving rise to observations and to make predictions of future observations. Bayesian nonparametric methods provide a means for carrying out Bayesian inference making as few assumptions about restrictive parametric models as possible. There are several proposals in the literature for extending Bayesian nonparametric models to include dependence on covariates. Limited attention, however, has been directed to the following two aspects. In this article, we examine the effect on fitting and predictive performance of incorporating covariates in a class of Bayesian nonparametric models by one of two primary ways: either in the weights or in the locations of a discrete random probability measure. We show that different strategies for incorporating continuous covariates in Bayesian nonparametric models can result in big differences when used for prediction, even though they lead to otherwise similar posterior inferences. When one needs the predictive density, as in optimal design, and this density is a mixture, it is better to make the weights depend on the covariates. We demonstrate these points via a simulated data example and in an application in which one wants to determine the optimal dose of an anticancer drug used in pediatric oncology. PMID:23687472

  15. Bayesian spatio-temporal modeling of particulate matter concentrations in Peninsular Malaysia

    NASA Astrophysics Data System (ADS)

    Manga, Edna; Awang, Norhashidah

    2016-06-01

    This article presents an application of a Bayesian spatio-temporal Gaussian process (GP) model on particulate matter concentrations from Peninsular Malaysia. We analyze daily PM10 concentration levels from 35 monitoring sites in June and July 2011. The spatiotemporal model set in a Bayesian hierarchical framework allows for inclusion of informative covariates, meteorological variables and spatiotemporal interactions. Posterior density estimates of the model parameters are obtained by Markov chain Monte Carlo methods. Preliminary data analysis indicate information on PM10 levels at sites classified as industrial locations could explain part of the space time variations. We include the site-type indicator in our modeling efforts. Results of the parameter estimates for the fitted GP model show significant spatio-temporal structure and positive effect of the location-type explanatory variable. We also compute some validation criteria for the out of sample sites that show the adequacy of the model for predicting PM10 at unmonitored sites.

  16. Bayesian Models of Graphs, Arrays and Other Exchangeable Random Structures.

    PubMed

    Orbanz, Peter; Roy, Daniel M

    2015-02-01

    The natural habitat of most Bayesian methods is data represented by exchangeable sequences of observations, for which de Finetti's theorem provides the theoretical foundation. Dirichlet process clustering, Gaussian process regression, and many other parametric and nonparametric Bayesian models fall within the remit of this framework; many problems arising in modern data analysis do not. This article provides an introduction to Bayesian models of graphs, matrices, and other data that can be modeled by random structures. We describe results in probability theory that generalize de Finetti's theorem to such data and discuss their relevance to nonparametric Bayesian modeling. With the basic ideas in place, we survey example models available in the literature; applications of such models include collaborative filtering, link prediction, and graph and network analysis. We also highlight connections to recent developments in graph theory and probability, and sketch the more general mathematical foundation of Bayesian methods for other types of data beyond sequences and arrays. PMID:26353253

  17. A Bayesian Analysis of Finite Mixtures in the LISREL Model.

    ERIC Educational Resources Information Center

    Zhu, Hong-Tu; Lee, Sik-Yum

    2001-01-01

    Proposes a Bayesian framework for estimating finite mixtures of the LISREL model. The model augments the observed data of the manifest variables with the latent variables and allocation variables and uses the Gibbs sampler to obtain the Bayesian solution. Discusses other associated statistical inferences. (SLD)

  18. CP violation in hierarchical Yukawa models

    SciTech Connect

    Peccei, R. D.

    2011-04-01

    Because 4-dimensional CP is a good symmetry of many higher-dimensional theories, this suggests the possible existence of an universal CP-violating phase originating from the process of compactification. Such a phase, if it existed, would not be easy to uncover since the phases in Yukawa matrices are not simply related to the observed Cabibbo-Kobayashi-Maskawa phase {delta}. Hierarchical Yukawa models, of the type arising in F-theory GUT models provide an interesting exception. Recently, Heckman and Vafa studied a particular F-theory GUT model with hierarchical Yukawa matrices with complex phases of O(1) and showed, by examining the Jarlskog invariant, that this model leads to sin{delta}{approx}O(1). A more detailed examination of the model, although confirming their results, is seen to be also compatible with having a phase {delta}{sub o}={pi}/3 imprinted on the Hermitian Yukawa matrices, leading to sin{delta}{approx_equal}sin{delta}{sub o}.

  19. A sensorimotor paradigm for Bayesian model selection.

    PubMed

    Genewein, Tim; Braun, Daniel A

    2012-01-01

    Sensorimotor control is thought to rely on predictive internal models in order to cope efficiently with uncertain environments. Recently, it has been shown that humans not only learn different internal models for different tasks, but that they also extract common structure between tasks. This raises the question of how the motor system selects between different structures or models, when each model can be associated with a range of different task-specific parameters. Here we design a sensorimotor task that requires subjects to compensate visuomotor shifts in a three-dimensional virtual reality setup, where one of the dimensions can be mapped to a model variable and the other dimension to the parameter variable. By introducing probe trials that are neutral in the parameter dimension, we can directly test for model selection. We found that model selection procedures based on Bayesian statistics provided a better explanation for subjects' choice behavior than simple non-probabilistic heuristics. Our experimental design lends itself to the general study of model selection in a sensorimotor context as it allows to separately query model and parameter variables from subjects. PMID:23125827

  20. Model parameter updating using Bayesian networks

    SciTech Connect

    Treml, C. A.; Ross, Timothy J.

    2004-01-01

    This paper outlines a model parameter updating technique for a new method of model validation using a modified model reference adaptive control (MRAC) framework with Bayesian Networks (BNs). The model parameter updating within this method is generic in the sense that the model/simulation to be validated is treated as a black box. It must have updateable parameters to which its outputs are sensitive, and those outputs must have metrics that can be compared to that of the model reference, i.e., experimental data. Furthermore, no assumptions are made about the statistics of the model parameter uncertainty, only upper and lower bounds need to be specified. This method is designed for situations where a model is not intended to predict a complete point-by-point time domain description of the item/system behavior; rather, there are specific points, features, or events of interest that need to be predicted. These specific points are compared to the model reference derived from actual experimental data. The logic for updating the model parameters to match the model reference is formed via a BN. The nodes of this BN consist of updateable model input parameters and the specific output values or features of interest. Each time the model is executed, the input/output pairs are used to adapt the conditional probabilities of the BN. Each iteration further refines the inferred model parameters to produce the desired model output. After parameter updating is complete and model inputs are inferred, reliabilities for the model output are supplied. Finally, this method is applied to a simulation of a resonance control cooling system for a prototype coupled cavity linac. The results are compared to experimental data.

  1. Universality: Accurate Checks in Dyson's Hierarchical Model

    NASA Astrophysics Data System (ADS)

    Godina, J. J.; Meurice, Y.; Oktay, M. B.

    2003-06-01

    In this talk we present high-accuracy calculations of the susceptibility near βc for Dyson's hierarchical model in D = 3. Using linear fitting, we estimate the leading (γ) and subleading (Δ) exponents. Independent estimates are obtained by calculating the first two eigenvalues of the linearized renormalization group transformation. We found γ = 1.29914073 ± 10 -8 and, Δ = 0.4259469 ± 10-7 independently of the choice of local integration measure (Ising or Landau-Ginzburg). After a suitable rescaling, the approximate fixed points for a large class of local measure coincide accurately with a fixed point constructed by Koch and Wittwer.

  2. Hierarchical decomposition model for reconfigurable architecture

    NASA Astrophysics Data System (ADS)

    Erdogan, Simsek; Wahab, Abdul

    1996-10-01

    This paper introduces a systematic approach for abstract modeling of VLSI digital systems using a hierarchical decomposition process and HDL. In particular, the modeling of the back propagation neural network on a massively parallel reconfigurable hardware is used to illustrate the design process rather than toy examples. Based on the design specification of the algorithm, a functional model is developed through successive refinement and decomposition for execution on the reconfiguration machine. First, a top- level block diagram of the system is derived. Then, a schematic sheet of the corresponding structural model is developed to show the interconnections of the main functional building blocks. Next, the functional blocks are decomposed iteratively as required. Finally, the blocks are modeled using HDL and verified against the block specifications.

  3. Bayesian Local Contamination Models for Multivariate Outliers

    PubMed Central

    Page, Garritt L.; Dunson, David B.

    2013-01-01

    In studies where data are generated from multiple locations or sources it is common for there to exist observations that are quite unlike the majority. Motivated by the application of establishing a reference value in an inter-laboratory setting when outlying labs are present, we propose a local contamination model that is able to accommodate unusual multivariate realizations in a flexible way. The proposed method models the process level of a hierarchical model using a mixture with a parametric component and a possibly nonparametric contamination. Much of the flexibility in the methodology is achieved by allowing varying random subsets of the elements in the lab-specific mean vectors to be allocated to the contamination component. Computational methods are developed and the methodology is compared to three other possible approaches using a simulation study. We apply the proposed method to a NIST/NOAA sponsored inter-laboratory study which motivated the methodological development. PMID:24363465

  4. Bayesian model selection for LISA pathfinder

    NASA Astrophysics Data System (ADS)

    Karnesis, Nikolaos; Nofrarias, Miquel; Sopuerta, Carlos F.; Gibert, Ferran; Armano, Michele; Audley, Heather; Congedo, Giuseppe; Diepholz, Ingo; Ferraioli, Luigi; Hewitson, Martin; Hueller, Mauro; Korsakova, Natalia; McNamara, Paul W.; Plagnol, Eric; Vitale, Stefano

    2014-03-01

    The main goal of the LISA Pathfinder (LPF) mission is to fully characterize the acceleration noise models and to test key technologies for future space-based gravitational-wave observatories similar to the eLISA concept. The data analysis team has developed complex three-dimensional models of the LISA Technology Package (LTP) experiment onboard the LPF. These models are used for simulations, but, more importantly, they will be used for parameter estimation purposes during flight operations. One of the tasks of the data analysis team is to identify the physical effects that contribute significantly to the properties of the instrument noise. A way of approaching this problem is to recover the essential parameters of a LTP model fitting the data. Thus, we want to define the simplest model that efficiently explains the observations. To do so, adopting a Bayesian framework, one has to estimate the so-called Bayes factor between two competing models. In our analysis, we use three main different methods to estimate it: the reversible jump Markov chain Monte Carlo method, the Schwarz criterion, and the Laplace approximation. They are applied to simulated LPF experiments in which the most probable LTP model that explains the observations is recovered. The same type of analysis presented in this paper is expected to be followed during flight operations. Moreover, the correlation of the output of the aforementioned methods with the design of the experiment is explored.

  5. Newton, Einstein, Jeffreys and Bayesian model selection

    NASA Astrophysics Data System (ADS)

    Chettri, Samir; Batchelor, David; Campbell, William; Balakrishnan, Karthik

    2005-11-01

    In Jefferys and Berger apply Bayesian model selection to the problem of choosing between rival theories, in particular between Einstein's theory of general relativity (GR) and Newtonian gravity (NG). [1] presents a debate between Harold Jeffreys and Charles Poor regarding the observed 43''/century anomalous perhelion precession of Mercury. GR made a precise prediction of 42.98''/century while proponents of NG suggested several physical mechanisms that were eventually refuted, with the exception of a modified inverse square law. Using Bayes Factors (BF) and data available in 1921, shows that GR is preferable to NG by a factor of about 25 to 1. A scale for BF used by Jeffreys, suggests that this is positive to strong evidence for GR over modified NG but it is not very strong or even overwhelming. In this work we calculate the BF from the period 1921 till 1993. By 1960 we see that the BF, due to better data gathering techniques and advances in technology, had reached a factor of greater than 100 to 1, making GR strongly preferable to NG and by 1990 the BF reached 1000:1. Ironically while BF had reached a state of near certainty even in 1960 rival theories of gravitation were on the rise - notably the Brans-Dicke (BD) scalar-tensor theory of gravity. The BD theory is postulated in such a way that for small positive values of a scalar parameter ω, the BF would favor GR while the BF would approach unity with certainty as ω grows larger, at which point either theory would be prefered, i.e., it is a theory that cannot lose. Does this mean Bayesian model selection needs to be overthrown? This points to the need for cogent prior information guided by physics and physical experiment.

  6. Online Dectection and Modeling of Safety Boundaries for Aerospace Application Using Bayesian Statistics

    NASA Technical Reports Server (NTRS)

    He, Yuning

    2015-01-01

    The behavior of complex aerospace systems is governed by numerous parameters. For safety analysis it is important to understand how the system behaves with respect to these parameter values. In particular, understanding the boundaries between safe and unsafe regions is of major importance. In this paper, we describe a hierarchical Bayesian statistical modeling approach for the online detection and characterization of such boundaries. Our method for classification with active learning uses a particle filter-based model and a boundary-aware metric for best performance. From a library of candidate shapes incorporated with domain expert knowledge, the location and parameters of the boundaries are estimated using advanced Bayesian modeling techniques. The results of our boundary analysis are then provided in a form understandable by the domain expert. We illustrate our approach using a simulation model of a NASA neuro-adaptive flight control system, as well as a system for the detection of separation violations in the terminal airspace.

  7. Loss Function Based Ranking in Two-Stage, Hierarchical Models

    PubMed Central

    Lin, Rongheng; Louis, Thomas A.; Paddock, Susan M.; Ridgeway, Greg

    2009-01-01

    Performance evaluations of health services providers burgeons. Similarly, analyzing spatially related health information, ranking teachers and schools, and identification of differentially expressed genes are increasing in prevalence and importance. Goals include valid and efficient ranking of units for profiling and league tables, identification of excellent and poor performers, the most differentially expressed genes, and determining “exceedances” (how many and which unit-specific true parameters exceed a threshold). These data and inferential goals require a hierarchical, Bayesian model that accounts for nesting relations and identifies both population values and random effects for unit-specific parameters. Furthermore, the Bayesian approach coupled with optimizing a loss function provides a framework for computing non-standard inferences such as ranks and histograms. Estimated ranks that minimize Squared Error Loss (SEL) between the true and estimated ranks have been investigated. The posterior mean ranks minimize SEL and are “general purpose,” relevant to a broad spectrum of ranking goals. However, other loss functions and optimizing ranks that are tuned to application-specific goals require identification and evaluation. For example, when the goal is to identify the relatively good (e.g., in the upper 10%) or relatively poor performers, a loss function that penalizes classification errors produces estimates that minimize the error rate. We construct loss functions that address this and other goals, developing a unified framework that facilitates generating candidate estimates, comparing approaches and producing data analytic performance summaries. We compare performance for a fully parametric, hierarchical model with Gaussian sampling distribution under Gaussian and a mixture of Gaussians prior distributions. We illustrate approaches via analysis of standardized mortality ratio data from the United States Renal Data System. Results show that SEL

  8. Advances in Bayesian Modeling in Educational Research

    ERIC Educational Resources Information Center

    Levy, Roy

    2016-01-01

    In this article, I provide a conceptually oriented overview of Bayesian approaches to statistical inference and contrast them with frequentist approaches that currently dominate conventional practice in educational research. The features and advantages of Bayesian approaches are illustrated with examples spanning several statistical modeling…

  9. Bayesian Student Modeling and the Problem of Parameter Specification.

    ERIC Educational Resources Information Center

    Millan, Eva; Agosta, John Mark; Perez de la Cruz, Jose Luis

    2001-01-01

    Discusses intelligent tutoring systems and the application of Bayesian networks to student modeling. Considers reasons for not using Bayesian networks, including the computational complexity of the algorithms and the difficulty of knowledge acquisition, and proposes an approach to simplify knowledge acquisition that applies causal independence to…

  10. A Tutorial Introduction to Bayesian Models of Cognitive Development

    ERIC Educational Resources Information Center

    Perfors, Amy; Tenenbaum, Joshua B.; Griffiths, Thomas L.; Xu, Fei

    2011-01-01

    We present an introduction to Bayesian inference as it is used in probabilistic models of cognitive development. Our goal is to provide an intuitive and accessible guide to the "what", the "how", and the "why" of the Bayesian approach: what sorts of problems and data the framework is most relevant for, and how and why it may be useful for…

  11. A SEMIPARAMETRIC BAYESIAN MODEL FOR CIRCULAR-LINEAR REGRESSION

    EPA Science Inventory

    We present a Bayesian approach to regress a circular variable on a linear predictor. The regression coefficients are assumed to have a nonparametric distribution with a Dirichlet process prior. The semiparametric Bayesian approach gives added flexibility to the model and is usefu...

  12. Bayesian analysis of the backreaction models

    SciTech Connect

    Kurek, Aleksandra; Bolejko, Krzysztof; Szydlowski, Marek

    2010-03-15

    We present a Bayesian analysis of four different types of backreaction models, which are based on the Buchert equations. In this approach, one considers a solution to the Einstein equations for a general matter distribution and then an average of various observable quantities is taken. Such an approach became of considerable interest when it was shown that it could lead to agreement with observations without resorting to dark energy. In this paper we compare the {Lambda}CDM model and the backreaction models with type Ia supernovae, baryon acoustic oscillations, and cosmic microwave background data, and find that the former is favored. However, the tested models were based on some particular assumptions about the relation between the average spatial curvature and the backreaction, as well as the relation between the curvature and curvature index. In this paper we modified the latter assumption, leaving the former unchanged. We find that, by varying the relation between the curvature and curvature index, we can obtain a better fit. Therefore, some further work is still needed--in particular, the relation between the backreaction and the curvature should be revisited in order to fully determine the feasibility of the backreaction models to mimic dark energy.

  13. Medical Inpatient Journey Modeling and Clustering: A Bayesian Hidden Markov Model Based Approach

    PubMed Central

    Huang, Zhengxing; Dong, Wei; Wang, Fei; Duan, Huilong

    2015-01-01

    Modeling and clustering medical inpatient journeys is useful to healthcare organizations for a number of reasons including inpatient journey reorganization in a more convenient way for understanding and browsing, etc. In this study, we present a probabilistic model-based approach to model and cluster medical inpatient journeys. Specifically, we exploit a Bayesian Hidden Markov Model based approach to transform medical inpatient journeys into a probabilistic space, which can be seen as a richer representation of inpatient journeys to be clustered. Then, using hierarchical clustering on the matrix of similarities, inpatient journeys can be clustered into different categories w.r.t their clinical and temporal characteristics. We evaluated the proposed approach on a real clinical data set pertaining to the unstable angina treatment process. The experimental results reveal that our method can identify and model latent treatment topics underlying in personalized inpatient journeys, and yield impressive clustering quality. PMID:26958200

  14. Scale Mixture Models with Applications to Bayesian Inference

    NASA Astrophysics Data System (ADS)

    Qin, Zhaohui S.; Damien, Paul; Walker, Stephen

    2003-11-01

    Scale mixtures of uniform distributions are used to model non-normal data in time series and econometrics in a Bayesian framework. Heteroscedastic and skewed data models are also tackled using scale mixture of uniform distributions.

  15. Stochastic model updating utilizing Bayesian approach and Gaussian process model

    NASA Astrophysics Data System (ADS)

    Wan, Hua-Ping; Ren, Wei-Xin

    2016-03-01

    Stochastic model updating (SMU) has been increasingly applied in quantifying structural parameter uncertainty from responses variability. SMU for parameter uncertainty quantification refers to the problem of inverse uncertainty quantification (IUQ), which is a nontrivial task. Inverse problem solved with optimization usually brings about the issues of gradient computation, ill-conditionedness, and non-uniqueness. Moreover, the uncertainty present in response makes the inverse problem more complicated. In this study, Bayesian approach is adopted in SMU for parameter uncertainty quantification. The prominent strength of Bayesian approach for IUQ problem is that it solves IUQ problem in a straightforward manner, which enables it to avoid the previous issues. However, when applied to engineering structures that are modeled with a high-resolution finite element model (FEM), Bayesian approach is still computationally expensive since the commonly used Markov chain Monte Carlo (MCMC) method for Bayesian inference requires a large number of model runs to guarantee the convergence. Herein we reduce computational cost in two aspects. On the one hand, the fast-running Gaussian process model (GPM) is utilized to approximate the time-consuming high-resolution FEM. On the other hand, the advanced MCMC method using delayed rejection adaptive Metropolis (DRAM) algorithm that incorporates local adaptive strategy with global adaptive strategy is employed for Bayesian inference. In addition, we propose the use of the powerful variance-based global sensitivity analysis (GSA) in parameter selection to exclude non-influential parameters from calibration parameters, which yields a reduced-order model and thus further alleviates the computational burden. A simulated aluminum plate and a real-world complex cable-stayed pedestrian bridge are presented to illustrate the proposed framework and verify its feasibility.

  16. Modeling Heterogeneity in Relationships between Initial Status and Rates of Change: Treating Latent Variable Regression Coefficients as Random Coefficients in a Three-Level Hierarchical Model

    ERIC Educational Resources Information Center

    Choi, Kilchan; Seltzer, Michael

    2010-01-01

    In studies of change in education and numerous other fields, interest often centers on how differences in the status of individuals at the start of a period of substantive interest relate to differences in subsequent change. In this article, the authors present a fully Bayesian approach to estimating three-level Hierarchical Models in which latent…

  17. A guide to Bayesian model selection for ecologists

    USGS Publications Warehouse

    Hooten, Mevin B.; Hobbs, N.T.

    2015-01-01

    The steady upward trend in the use of model selection and Bayesian methods in ecological research has made it clear that both approaches to inference are important for modern analysis of models and data. However, in teaching Bayesian methods and in working with our research colleagues, we have noticed a general dissatisfaction with the available literature on Bayesian model selection and multimodel inference. Students and researchers new to Bayesian methods quickly find that the published advice on model selection is often preferential in its treatment of options for analysis, frequently advocating one particular method above others. The recent appearance of many articles and textbooks on Bayesian modeling has provided welcome background on relevant approaches to model selection in the Bayesian framework, but most of these are either very narrowly focused in scope or inaccessible to ecologists. Moreover, the methodological details of Bayesian model selection approaches are spread thinly throughout the literature, appearing in journals from many different fields. Our aim with this guide is to condense the large body of literature on Bayesian approaches to model selection and multimodel inference and present it specifically for quantitative ecologists as neutrally as possible. We also bring to light a few important and fundamental concepts relating directly to model selection that seem to have gone unnoticed in the ecological literature. Throughout, we provide only a minimal discussion of philosophy, preferring instead to examine the breadth of approaches as well as their practical advantages and disadvantages. This guide serves as a reference for ecologists using Bayesian methods, so that they can better understand their options and can make an informed choice that is best aligned with their goals for inference.

  18. Hierarchical spatial capture-recapture models: modeling population density from stratified populations

    USGS Publications Warehouse

    Royle, J. Andrew; Converse, Sarah J.

    2013-01-01

    1. Capture–recapture studies are often conducted on populations that are stratified by space, time or other factors. In this paper, we develop a Bayesian spatial capture–recapture (SCR) modelling framework for stratified populations – when sampling occurs within multiple distinct spatial and temporal strata. 2. We describe a hierarchical model that integrates distinct models for both the spatial encounter history data from capture–recapture sampling, and also for modelling variation in density among strata. We use an implementation of data augmentation to parameterize the model in terms of a latent categorical stratum or group membership variable, which provides a convenient implementation in popular BUGS software packages. 3. We provide an example application to an experimental study involving small-mammal sampling on multiple trapping grids over multiple years, where the main interest is in modelling a treatment effect on population density among the trapping grids. 4. Many capture–recapture studies involve some aspect of spatial or temporal replication that requires some attention to modelling variation among groups or strata. We propose a hierarchical model that allows explicit modelling of group or strata effects. Because the model is formulated for individual encounter histories and is easily implemented in the BUGS language and other free software, it also provides a general framework for modelling individual effects, such as are present in SCR models.

  19. A continuum model for hierarchical fibril assembly

    NASA Astrophysics Data System (ADS)

    van Lith, B. S.; Muntean, A.; Storm, C.

    2014-06-01

    Most of the biological polymers that make up our cells and tissues are hierarchically structured. For biopolymers ranging from collagen, to actin, to fibrin and amyloid fibrils this hierarchy provides vitally important versatility. The structural hierarchy must be encoded in the self-assembly process, from the earliest stages onward, in order to produce the appropriate substructures. In this letter, we explore the kinetics of multistage self-assembly processes in a model system which allows comparison to bulk probes such as light scattering. We apply our model to recent turbidimetry data on the self-assembly of collagen fibrils. Our analysis suggests a connection between diffusion-limited aggregation kinetics and fibril growth, supported by slow, power-law growth at very long time scales.

  20. Bayesian Case-deletion Model Complexity and Information Criterion

    PubMed Central

    Zhu, Hongtu; Ibrahim, Joseph G.; Chen, Qingxia

    2015-01-01

    We establish a connection between Bayesian case influence measures for assessing the influence of individual observations and Bayesian predictive methods for evaluating the predictive performance of a model and comparing different models fitted to the same dataset. Based on such a connection, we formally propose a new set of Bayesian case-deletion model complexity (BCMC) measures for quantifying the effective number of parameters in a given statistical model. Its properties in linear models are explored. Adding some functions of BCMC to a conditional deviance function leads to a Bayesian case-deletion information criterion (BCIC) for comparing models. We systematically investigate some properties of BCIC and its connection with other information criteria, such as the Deviance Information Criterion (DIC). We illustrate the proposed methodology on linear mixed models with simulations and a real data example. PMID:26180578

  1. Entropic Priors and Bayesian Model Selection

    NASA Astrophysics Data System (ADS)

    Brewer, Brendon J.; Francis, Matthew J.

    2009-12-01

    We demonstrate that the principle of maximum relative entropy (ME), used judiciously, can ease the specification of priors in model selection problems. The resulting effect is that models that make sharp predictions are disfavoured, weakening the usual Bayesian ``Occam's Razor.'' This is illustrated with a simple example involving what Jaynes called a ``sure thing'' hypothesis. Jaynes' resolution of the situation involved introducing a large number of alternative ``sure thing'' hypotheses that were possible before we observed the data. However, in more complex situations, it may not be possible to explicitly enumerate large numbers of alternatives. The entropic priors formalism produces the desired result without modifying the hypothesis space or requiring explicit enumeration of alternatives; all that is required is a good model for the prior predictive distribution for the data. This idea is illustrated with a simple rigged-lottery example, and we outline how this idea may help to resolve a recent debate amongst cosmologists: is dark energy a cosmological constant, or has it evolved with time in some way? And how shall we decide, when the data are in?

  2. Bayesian analysis of a disability model for lung cancer survival.

    PubMed

    Armero, C; Cabras, S; Castellanos, M E; Perra, S; Quirós, A; Oruezábal, M J; Sánchez-Rubio, J

    2016-02-01

    Bayesian reasoning, survival analysis and multi-state models are used to assess survival times for Stage IV non-small-cell lung cancer patients and the evolution of the disease over time. Bayesian estimation is done using minimum informative priors for the Weibull regression survival model, leading to an automatic inferential procedure. Markov chain Monte Carlo methods have been used for approximating posterior distributions and the Bayesian information criterion has been considered for covariate selection. In particular, the posterior distribution of the transition probabilities, resulting from the multi-state model, constitutes a very interesting tool which could be useful to help oncologists and patients make efficient and effective decisions.

  3. Hierarchical Data Structures, Institutional Research, and Multilevel Modeling

    ERIC Educational Resources Information Center

    O'Connell, Ann A.; Reed, Sandra J.

    2012-01-01

    Multilevel modeling (MLM), also referred to as hierarchical linear modeling (HLM) or mixed models, provides a powerful analytical framework through which to study colleges and universities and their impact on students. Due to the natural hierarchical structure of data obtained from students or faculty in colleges and universities, MLM offers many…

  4. Hierarchical Multinomial Processing Tree Models: A Latent-Trait Approach

    ERIC Educational Resources Information Center

    Klauer, Karl Christoph

    2010-01-01

    Multinomial processing tree models are widely used in many areas of psychology. A hierarchical extension of the model class is proposed, using a multivariate normal distribution of person-level parameters with the mean and covariance matrix to be estimated from the data. The hierarchical model allows one to take variability between persons into…

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

    NASA Astrophysics Data System (ADS)

    Loredo, Thomas J.

    2016-01-01

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

  6. Two-Stage Bayesian Model Averaging in Endogenous Variable Models.

    PubMed

    Lenkoski, Alex; Eicher, Theo S; Raftery, Adrian E

    2014-01-01

    Economic modeling in the presence of endogeneity is subject to model uncertainty at both the instrument and covariate level. We propose a Two-Stage Bayesian Model Averaging (2SBMA) methodology that extends the Two-Stage Least Squares (2SLS) estimator. By constructing a Two-Stage Unit Information Prior in the endogenous variable model, we are able to efficiently combine established methods for addressing model uncertainty in regression models with the classic technique of 2SLS. To assess the validity of instruments in the 2SBMA context, we develop Bayesian tests of the identification restriction that are based on model averaged posterior predictive p-values. A simulation study showed that 2SBMA has the ability to recover structure in both the instrument and covariate set, and substantially improves the sharpness of resulting coefficient estimates in comparison to 2SLS using the full specification in an automatic fashion. Due to the increased parsimony of the 2SBMA estimate, the Bayesian Sargan test had a power of 50 percent in detecting a violation of the exogeneity assumption, while the method based on 2SLS using the full specification had negligible power. We apply our approach to the problem of development accounting, and find support not only for institutions, but also for geography and integration as development determinants, once both model uncertainty and endogeneity have been jointly addressed.

  7. Two-Stage Bayesian Model Averaging in Endogenous Variable Models.

    PubMed

    Lenkoski, Alex; Eicher, Theo S; Raftery, Adrian E

    2014-01-01

    Economic modeling in the presence of endogeneity is subject to model uncertainty at both the instrument and covariate level. We propose a Two-Stage Bayesian Model Averaging (2SBMA) methodology that extends the Two-Stage Least Squares (2SLS) estimator. By constructing a Two-Stage Unit Information Prior in the endogenous variable model, we are able to efficiently combine established methods for addressing model uncertainty in regression models with the classic technique of 2SLS. To assess the validity of instruments in the 2SBMA context, we develop Bayesian tests of the identification restriction that are based on model averaged posterior predictive p-values. A simulation study showed that 2SBMA has the ability to recover structure in both the instrument and covariate set, and substantially improves the sharpness of resulting coefficient estimates in comparison to 2SLS using the full specification in an automatic fashion. Due to the increased parsimony of the 2SBMA estimate, the Bayesian Sargan test had a power of 50 percent in detecting a violation of the exogeneity assumption, while the method based on 2SLS using the full specification had negligible power. We apply our approach to the problem of development accounting, and find support not only for institutions, but also for geography and integration as development determinants, once both model uncertainty and endogeneity have been jointly addressed. PMID:24223471

  8. Nonparametric Bayesian Modeling for Automated Database Schema Matching

    SciTech Connect

    Ferragut, Erik M; Laska, Jason A

    2015-01-01

    The problem of merging databases arises in many government and commercial applications. Schema matching, a common first step, identifies equivalent fields between databases. We introduce a schema matching framework that builds nonparametric Bayesian models for each field and compares them by computing the probability that a single model could have generated both fields. Our experiments show that our method is more accurate and faster than the existing instance-based matching algorithms in part because of the use of nonparametric Bayesian models.

  9. Calibrating Bayesian Network Representations of Social-Behavioral Models

    SciTech Connect

    Whitney, Paul D.; Walsh, Stephen J.

    2010-04-08

    While human behavior has long been studied, recent and ongoing advances in computational modeling present opportunities for recasting research outcomes in human behavior. In this paper we describe how Bayesian networks can represent outcomes of human behavior research. We demonstrate a Bayesian network that represents political radicalization research – and show a corresponding visual representation of aspects of this research outcome. Since Bayesian networks can be quantitatively compared with external observations, the representation can also be used for empirical assessments of the research which the network summarizes. For a political radicalization model based on published research, we show this empirical comparison with data taken from the Minorities at Risk Organizational Behaviors database.

  10. Maximum likelihood Bayesian model averaging and its predictive analysis for groundwater reactive transport models

    USGS Publications Warehouse

    Curtis, Gary P.; Lu, Dan; Ye, Ming

    2015-01-01

    While Bayesian model averaging (BMA) has been widely used in groundwater modeling, it is infrequently applied to groundwater reactive transport modeling because of multiple sources of uncertainty in the coupled hydrogeochemical processes and because of the long execution time of each model run. To resolve these problems, this study analyzed different levels of uncertainty in a hierarchical way, and used the maximum likelihood version of BMA, i.e., MLBMA, to improve the computational efficiency. This study demonstrates the applicability of MLBMA to groundwater reactive transport modeling in a synthetic case in which twenty-seven reactive transport models were designed to predict the reactive transport of hexavalent uranium (U(VI)) based on observations at a former uranium mill site near Naturita, CO. These reactive transport models contain three uncertain model components, i.e., parameterization of hydraulic conductivity, configuration of model boundary, and surface complexation reactions that simulate U(VI) adsorption. These uncertain model components were aggregated into the alternative models by integrating a hierarchical structure into MLBMA. The modeling results of the individual models and MLBMA were analyzed to investigate their predictive performance. The predictive logscore results show that MLBMA generally outperforms the best model, suggesting that using MLBMA is a sound strategy to achieve more robust model predictions relative to a single model. MLBMA works best when the alternative models are structurally distinct and have diverse model predictions. When correlation in model structure exists, two strategies were used to improve predictive performance by retaining structurally distinct models or assigning smaller prior model probabilities to correlated models. Since the synthetic models were designed using data from the Naturita site, the results of this study are expected to provide guidance for real-world modeling. Limitations of applying MLBMA to the

  11. Maximum likelihood Bayesian model averaging and its predictive analysis for groundwater reactive transport models

    DOE PAGES

    Lu, Dan; Ye, Ming; Curtis, Gary P.

    2015-08-01

    While Bayesian model averaging (BMA) has been widely used in groundwater modeling, it is infrequently applied to groundwater reactive transport modeling because of multiple sources of uncertainty in the coupled hydrogeochemical processes and because of the long execution time of each model run. To resolve these problems, this study analyzed different levels of uncertainty in a hierarchical way, and used the maximum likelihood version of BMA, i.e., MLBMA, to improve the computational efficiency. Our study demonstrates the applicability of MLBMA to groundwater reactive transport modeling in a synthetic case in which twenty-seven reactive transport models were designed to predict themore » reactive transport of hexavalent uranium (U(VI)) based on observations at a former uranium mill site near Naturita, CO. Moreover, these reactive transport models contain three uncertain model components, i.e., parameterization of hydraulic conductivity, configuration of model boundary, and surface complexation reactions that simulate U(VI) adsorption. These uncertain model components were aggregated into the alternative models by integrating a hierarchical structure into MLBMA. The modeling results of the individual models and MLBMA were analyzed to investigate their predictive performance. The predictive logscore results show that MLBMA generally outperforms the best model, suggesting that using MLBMA is a sound strategy to achieve more robust model predictions relative to a single model. MLBMA works best when the alternative models are structurally distinct and have diverse model predictions. When correlation in model structure exists, two strategies were used to improve predictive performance by retaining structurally distinct models or assigning smaller prior model probabilities to correlated models. Since the synthetic models were designed using data from the Naturita site, the results of this study are expected to provide guidance for real-world modeling. Finally

  12. Maximum likelihood Bayesian model averaging and its predictive analysis for groundwater reactive transport models

    SciTech Connect

    Lu, Dan; Ye, Ming; Curtis, Gary P.

    2015-08-01

    While Bayesian model averaging (BMA) has been widely used in groundwater modeling, it is infrequently applied to groundwater reactive transport modeling because of multiple sources of uncertainty in the coupled hydrogeochemical processes and because of the long execution time of each model run. To resolve these problems, this study analyzed different levels of uncertainty in a hierarchical way, and used the maximum likelihood version of BMA, i.e., MLBMA, to improve the computational efficiency. Our study demonstrates the applicability of MLBMA to groundwater reactive transport modeling in a synthetic case in which twenty-seven reactive transport models were designed to predict the reactive transport of hexavalent uranium (U(VI)) based on observations at a former uranium mill site near Naturita, CO. Moreover, these reactive transport models contain three uncertain model components, i.e., parameterization of hydraulic conductivity, configuration of model boundary, and surface complexation reactions that simulate U(VI) adsorption. These uncertain model components were aggregated into the alternative models by integrating a hierarchical structure into MLBMA. The modeling results of the individual models and MLBMA were analyzed to investigate their predictive performance. The predictive logscore results show that MLBMA generally outperforms the best model, suggesting that using MLBMA is a sound strategy to achieve more robust model predictions relative to a single model. MLBMA works best when the alternative models are structurally distinct and have diverse model predictions. When correlation in model structure exists, two strategies were used to improve predictive performance by retaining structurally distinct models or assigning smaller prior model probabilities to correlated models. Since the synthetic models were designed using data from the Naturita site, the results of this study are expected to provide guidance for real-world modeling. Finally, limitations of

  13. Social Influence on Information Technology Adoption and Sustained Use in Healthcare: A Hierarchical Bayesian Learning Method Analysis

    ERIC Educational Resources Information Center

    Hao, Haijing

    2013-01-01

    Information technology adoption and diffusion is currently a significant challenge in the healthcare delivery setting. This thesis includes three papers that explore social influence on information technology adoption and sustained use in the healthcare delivery environment using conventional regression models and novel hierarchical Bayesian…

  14. Variational Bayesian identification and prediction of stochastic nonlinear dynamic causal models

    PubMed Central

    Daunizeau, J.; Friston, K.J.; Kiebel, S.J.

    2009-01-01

    In this paper, we describe a general variational Bayesian approach for approximate inference on nonlinear stochastic dynamic models. This scheme extends established approximate inference on hidden-states to cover: (i) nonlinear evolution and observation functions, (ii) unknown parameters and (precision) hyperparameters and (iii) model comparison and prediction under uncertainty. Model identification or inversion entails the estimation of the marginal likelihood or evidence of a model. This difficult integration problem can be finessed by optimising a free-energy bound on the evidence using results from variational calculus. This yields a deterministic update scheme that optimises an approximation to the posterior density on the unknown model variables. We derive such a variational Bayesian scheme in the context of nonlinear stochastic dynamic hierarchical models, for both model identification and time-series prediction. The computational complexity of the scheme is comparable to that of an extended Kalman filter, which is critical when inverting high dimensional models or long time-series. Using Monte-Carlo simulations, we assess the estimation efficiency of this variational Bayesian approach using three stochastic variants of chaotic dynamic systems. We also demonstrate the model comparison capabilities of the method, its self-consistency and its predictive power. PMID:19862351

  15. A Bayesian approach for inducing sparsity in generalized linear models with multi-category response

    PubMed Central

    2015-01-01

    Background The dimension and complexity of high-throughput gene expression data create many challenges for downstream analysis. Several approaches exist to reduce the number of variables with respect to small sample sizes. In this study, we utilized the Generalized Double Pareto (GDP) prior to induce sparsity in a Bayesian Generalized Linear Model (GLM) setting. The approach was evaluated using a publicly available microarray dataset containing 99 samples corresponding to four different prostate cancer subtypes. Results A hierarchical Sparse Bayesian GLM using GDP prior (SBGG) was developed to take into account the progressive nature of the response variable. We obtained an average overall classification accuracy between 82.5% and 94%, which was higher than Support Vector Machine, Random Forest or a Sparse Bayesian GLM using double exponential priors. Additionally, SBGG outperforms the other 3 methods in correctly identifying pre-metastatic stages of cancer progression, which can prove extremely valuable for therapeutic and diagnostic purposes. Importantly, using Geneset Cohesion Analysis Tool, we found that the top 100 genes produced by SBGG had an average functional cohesion p-value of 2.0E-4 compared to 0.007 to 0.131 produced by the other methods. Conclusions Using GDP in a Bayesian GLM model applied to cancer progression data results in better subclass prediction. In particular, the method identifies pre-metastatic stages of prostate cancer with substantially better accuracy and produces more functionally relevant gene sets. PMID:26423345

  16. Prospective evaluation of a Bayesian model to predict organizational change.

    PubMed

    Molfenter, Todd; Gustafson, Dave; Kilo, Chuck; Bhattacharya, Abhik; Olsson, Jesper

    2005-01-01

    This research examines a subjective Bayesian model's ability to predict organizational change outcomes and sustainability of those outcomes for project teams participating in a multi-organizational improvement collaborative. PMID:16093893

  17. BAYESIAN METHODS FOR REGIONAL-SCALE EUTROPHICATION MODELS. (R830887)

    EPA Science Inventory

    We demonstrate a Bayesian classification and regression tree (CART) approach to link multiple environmental stressors to biological responses and quantify uncertainty in model predictions. Such an approach can: (1) report prediction uncertainty, (2) be consistent with the amou...

  18. BAYESIAN HIERARCHICAL MODELING OF PERSONAL EXPOSURE TO PARTICULATE MATTER

    EPA Science Inventory

    In the US EPA's 1998 Baltimore Epidemiology-Exposure Panel Study, a group of 21 residents of a single building retirement community wore personal monitors recording personal fine particulate air pollution concentrations (PM2.5) for 27 days, while other monitors recorde...

  19. Testing Adaptive Toolbox Models: A Bayesian Hierarchical Approach

    ERIC Educational Resources Information Center

    Scheibehenne, Benjamin; Rieskamp, Jorg; Wagenmakers, Eric-Jan

    2013-01-01

    Many theories of human cognition postulate that people are equipped with a repertoire of strategies to solve the tasks they face. This theoretical framework of a cognitive toolbox provides a plausible account of intra- and interindividual differences in human behavior. Unfortunately, it is often unclear how to rigorously test the toolbox…

  20. Bayesian Hierarchical Modeling of Cardiac Response to Particulate Matter Exposure

    EPA Science Inventory

    Studies have linked increased levels of particulate air pollution to decreased autonomic control, as measured by heart rate variability (HRV), particularly in populations such as the elderly. In this study, we use data obtained from the 1998 USEPA epidemiology-exposure longitudin...

  1. INACTIVATION OF BACILLUS GLOBIGII BY CHLORINATION: A HIERARCHICAL BAYESIAN MODEL

    EPA Science Inventory

    Recent events where spores of Bacillus anthracis have been used as a bioterrorist weapon have prompted interest in determining the resistance of this organism to commonly used disinfectants, such as chlorine, chlorine dioxide and ozone. This work was undertaken to study ...

  2. Fully Bayesian mixture model for differential gene expression: simulations and model checks.

    PubMed

    Lewin, Alex; Bochkina, Natalia; Richardson, Sylvia

    2007-01-01

    We present a Bayesian hierarchical model for detecting differentially expressed genes using a mixture prior on the parameters representing differential effects. We formulate an easily interpretable 3-component mixture to classify genes as over-expressed, under-expressed and non-differentially expressed, and model gene variances as exchangeable to allow for variability between genes. We show how the proportion of differentially expressed genes, and the mixture parameters, can be estimated in a fully Bayesian way, extending previous approaches where this proportion was fixed and empirically estimated. Good estimates of the false discovery rates are also obtained. Different parametric families for the mixture components can lead to quite different classifications of genes for a given data set. Using Affymetrix data from a knock out and wildtype mice experiment, we show how predictive model checks can be used to guide the choice between possible mixture priors. These checks show that extending the mixture model to allow extra variability around zero instead of the usual point mass null fits the data better. A software package for R is available.

  3. Classifying hospitals as mortality outliers: logistic versus hierarchical logistic models.

    PubMed

    Alexandrescu, Roxana; Bottle, Alex; Jarman, Brian; Aylin, Paul

    2014-05-01

    The use of hierarchical logistic regression for provider profiling has been recommended due to the clustering of patients within hospitals, but has some associated difficulties. We assess changes in hospital outlier status based on standard logistic versus hierarchical logistic modelling of mortality. The study population consisted of all patients admitted to acute, non-specialist hospitals in England between 2007 and 2011 with a primary diagnosis of acute myocardial infarction, acute cerebrovascular disease or fracture of neck of femur or a primary procedure of coronary artery bypass graft or repair of abdominal aortic aneurysm. We compared standardised mortality ratios (SMRs) from non-hierarchical models with SMRs from hierarchical models, without and with shrinkage estimates of the predicted probabilities (Model 1 and Model 2). The SMRs from standard logistic and hierarchical models were highly statistically significantly correlated (r > 0.91, p = 0.01). More outliers were recorded in the standard logistic regression than hierarchical modelling only when using shrinkage estimates (Model 2): 21 hospitals (out of a cumulative number of 565 pairs of hospitals under study) changed from a low outlier and 8 hospitals changed from a high outlier based on the logistic regression to a not-an-outlier based on shrinkage estimates. Both standard logistic and hierarchical modelling have identified nearly the same hospitals as mortality outliers. The choice of methodological approach should, however, also consider whether the modelling aim is judgment or improvement, as shrinkage may be more appropriate for the former than the latter. PMID:24711175

  4. Modelling modal gating of ion channels with hierarchical Markov models

    PubMed Central

    Fackrell, Mark; Crampin, Edmund J.; Taylor, Peter

    2016-01-01

    Many ion channels spontaneously switch between different levels of activity. Although this behaviour known as modal gating has been observed for a long time it is currently not well understood. Despite the fact that appropriately representing activity changes is essential for accurately capturing time course data from ion channels, systematic approaches for modelling modal gating are currently not available. In this paper, we develop a modular approach for building such a model in an iterative process. First, stochastic switching between modes and stochastic opening and closing within modes are represented in separate aggregated Markov models. Second, the continuous-time hierarchical Markov model, a new modelling framework proposed here, then enables us to combine these components so that in the integrated model both mode switching as well as the kinetics within modes are appropriately represented. A mathematical analysis reveals that the behaviour of the hierarchical Markov model naturally depends on the properties of its components. We also demonstrate how a hierarchical Markov model can be parametrized using experimental data and show that it provides a better representation than a previous model of the same dataset. Because evidence is increasing that modal gating reflects underlying molecular properties of the channel protein, it is likely that biophysical processes are better captured by our new approach than in earlier models.

  5. Modelling modal gating of ion channels with hierarchical Markov models

    PubMed Central

    Fackrell, Mark; Crampin, Edmund J.; Taylor, Peter

    2016-01-01

    Many ion channels spontaneously switch between different levels of activity. Although this behaviour known as modal gating has been observed for a long time it is currently not well understood. Despite the fact that appropriately representing activity changes is essential for accurately capturing time course data from ion channels, systematic approaches for modelling modal gating are currently not available. In this paper, we develop a modular approach for building such a model in an iterative process. First, stochastic switching between modes and stochastic opening and closing within modes are represented in separate aggregated Markov models. Second, the continuous-time hierarchical Markov model, a new modelling framework proposed here, then enables us to combine these components so that in the integrated model both mode switching as well as the kinetics within modes are appropriately represented. A mathematical analysis reveals that the behaviour of the hierarchical Markov model naturally depends on the properties of its components. We also demonstrate how a hierarchical Markov model can be parametrized using experimental data and show that it provides a better representation than a previous model of the same dataset. Because evidence is increasing that modal gating reflects underlying molecular properties of the channel protein, it is likely that biophysical processes are better captured by our new approach than in earlier models. PMID:27616917

  6. Higher-Order Item Response Models for Hierarchical Latent Traits

    ERIC Educational Resources Information Center

    Huang, Hung-Yu; Wang, Wen-Chung; Chen, Po-Hsi; Su, Chi-Ming

    2013-01-01

    Many latent traits in the human sciences have a hierarchical structure. This study aimed to develop a new class of higher order item response theory models for hierarchical latent traits that are flexible in accommodating both dichotomous and polytomous items, to estimate both item and person parameters jointly, to allow users to specify…

  7. Evaluating Individualized Reading Programs: A Bayesian Model.

    ERIC Educational Resources Information Center

    Maxwell, Martha

    Simple Bayesian approaches can be applied to answer specific questions in evaluating an individualized reading program. A small reading and study skills program located in the counseling center of a major research university collected and compiled data on student characteristics such as class, number of sessions attended, grade point average, and…

  8. Technical note: Bayesian calibration of dynamic ruminant nutrition models.

    PubMed

    Reed, K F; Arhonditsis, G B; France, J; Kebreab, E

    2016-08-01

    Mechanistic models of ruminant digestion and metabolism have advanced our understanding of the processes underlying ruminant animal physiology. Deterministic modeling practices ignore the inherent variation within and among individual animals and thus have no way to assess how sources of error influence model outputs. We introduce Bayesian calibration of mathematical models to address the need for robust mechanistic modeling tools that can accommodate error analysis by remaining within the bounds of data-based parameter estimation. For the purpose of prediction, the Bayesian approach generates a posterior predictive distribution that represents the current estimate of the value of the response variable, taking into account both the uncertainty about the parameters and model residual variability. Predictions are expressed as probability distributions, thereby conveying significantly more information than point estimates in regard to uncertainty. Our study illustrates some of the technical advantages of Bayesian calibration and discusses the future perspectives in the context of animal nutrition modeling.

  9. A hierarchical modeling approach for estimating national distributions of chemicals in public drinking water systems.

    PubMed

    Qian, Song S; Schulman, Andrew; Koplos, Jonathan; Kotros, Alison; Kellar, Penny

    2004-02-15

    Water quality studies often include the analytical challenge of incorporating censored data and quantifying error of estimation. Many analytical methods exist for estimating distribution parameters when censored data are present. This paper presents a Bayesian-based hierarchical model for estimating the national distribution of the mean concentrations of chemicals occurring in U.S. public drinking water systems using fluoride and thallium as examples. The data used are Safe Drinking Water Act compliance monitoring data (with a significant proportion of left-censored data). The model, which assumes log-normality, was evaluated using simulated data sets generated from a series of Weibull distributions to illustrate the robustness of the model. The hierarchical model is easily implemented using the Markov chain Monte Carlo simulation method. In addition, the Bayesian method is able to quantify the uncertainty in the estimated cumulative density function. The estimated fluoride and thallium national distributions are presented. Results from this study can be used to develop prior distributions for future U.S. drinking water regulatory studies of contaminant occurrence. PMID:14998034

  10. Bayesian experimental design for identification of model propositions and conceptual model uncertainty reduction

    NASA Astrophysics Data System (ADS)

    Pham, Hai V.; Tsai, Frank T.-C.

    2015-09-01

    The lack of hydrogeological data and knowledge often results in different propositions (or alternatives) to represent uncertain model components and creates many candidate groundwater models using the same data. Uncertainty of groundwater head prediction may become unnecessarily high. This study introduces an experimental design to identify propositions in each uncertain model component and decrease the prediction uncertainty by reducing conceptual model uncertainty. A discrimination criterion is developed based on posterior model probability that directly uses data to evaluate model importance. Bayesian model averaging (BMA) is used to predict future observation data. The experimental design aims to find the optimal number and location of future observations and the number of sampling rounds such that the desired discrimination criterion is met. Hierarchical Bayesian model averaging (HBMA) is adopted to assess if highly probable propositions can be identified and the conceptual model uncertainty can be reduced by the experimental design. The experimental design is implemented to a groundwater study in the Baton Rouge area, Louisiana. We design a new groundwater head observation network based on existing USGS observation wells. The sources of uncertainty that create multiple groundwater models are geological architecture, boundary condition, and fault permeability architecture. All possible design solutions are enumerated using a multi-core supercomputer. Several design solutions are found to achieve an 80%-identifiable groundwater model in 5 years by using six or more existing USGS wells. The HBMA result shows that each highly probable proposition can be identified for each uncertain model component once the discrimination criterion is achieved. The variances of groundwater head predictions are significantly decreased by reducing posterior model probabilities of unimportant propositions.

  11. Bayesian Estimation of the Logistic Positive Exponent IRT Model

    ERIC Educational Resources Information Center

    Bolfarine, Heleno; Bazan, Jorge Luis

    2010-01-01

    A Bayesian inference approach using Markov Chain Monte Carlo (MCMC) is developed for the logistic positive exponent (LPE) model proposed by Samejima and for a new skewed Logistic Item Response Theory (IRT) model, named Reflection LPE model. Both models lead to asymmetric item characteristic curves (ICC) and can be appropriate because a symmetric…

  12. Estimating tree height-diameter models with the Bayesian method.

    PubMed

    Zhang, Xiongqing; Duan, Aiguo; Zhang, Jianguo; Xiang, Congwei

    2014-01-01

    Six candidate height-diameter models were used to analyze the height-diameter relationships. The common methods for estimating the height-diameter models have taken the classical (frequentist) approach based on the frequency interpretation of probability, for example, the nonlinear least squares method (NLS) and the maximum likelihood method (ML). The Bayesian method has an exclusive advantage compared with classical method that the parameters to be estimated are regarded as random variables. In this study, the classical and Bayesian methods were used to estimate six height-diameter models, respectively. Both the classical method and Bayesian method showed that the Weibull model was the "best" model using data1. In addition, based on the Weibull model, data2 was used for comparing Bayesian method with informative priors with uninformative priors and classical method. The results showed that the improvement in prediction accuracy with Bayesian method led to narrower confidence bands of predicted value in comparison to that for the classical method, and the credible bands of parameters with informative priors were also narrower than uninformative priors and classical method. The estimated posterior distributions for parameters can be set as new priors in estimating the parameters using data2.

  13. Bayesian 3D X-ray computed tomography image reconstruction with a scaled Gaussian mixture prior model

    SciTech Connect

    Wang, Li; Gac, Nicolas; Mohammad-Djafari, Ali

    2015-01-13

    In order to improve quality of 3D X-ray tomography reconstruction for Non Destructive Testing (NDT), we investigate in this paper hierarchical Bayesian methods. In NDT, useful prior information on the volume like the limited number of materials or the presence of homogeneous area can be included in the iterative reconstruction algorithms. In hierarchical Bayesian methods, not only the volume is estimated thanks to the prior model of the volume but also the hyper parameters of this prior. This additional complexity in the reconstruction methods when applied to large volumes (from 512{sup 3} to 8192{sup 3} voxels) results in an increasing computational cost. To reduce it, the hierarchical Bayesian methods investigated in this paper lead to an algorithm acceleration by Variational Bayesian Approximation (VBA) [1] and hardware acceleration thanks to projection and back-projection operators paralleled on many core processors like GPU [2]. In this paper, we will consider a Student-t prior on the gradient of the image implemented in a hierarchical way [3, 4, 1]. Operators H (forward or projection) and H{sup t} (adjoint or back-projection) implanted in multi-GPU [2] have been used in this study. Different methods will be evalued on synthetic volume 'Shepp and Logan' in terms of quality and time of reconstruction. We used several simple regularizations of order 1 and order 2. Other prior models also exists [5]. Sometimes for a discrete image, we can do the segmentation and reconstruction at the same time, then the reconstruction can be done with less projections.

  14. Comparing models for perfluorooctanoic acid pharmacokinetics using Bayesian analysis.

    PubMed

    Wambaugh, John F; Barton, Hugh A; Setzer, R Woodrow

    2008-12-01

    Selecting the appropriate pharmacokinetic (PK) model given the available data is investigated for perfluorooctanoic acid (PFOA), which has been widely analyzed with an empirical, one-compartment model. This research examined the results of experiments [Kemper R. A., DuPont Haskell Laboratories, USEPA Administrative Record AR-226.1499 (2003)] that administered single oral or iv doses of PFOA to adult male and female rats. PFOA concentration was observed over time; in plasma for some animals and in fecal and urinary excretion for others. There were four rats per dose group, for a total of 36 males and 36 females. Assuming that the PK parameters for each individual within a gender were drawn from the same, biologically varying population, plasma and excretion data were jointly analyzed using a hierarchical framework to separate uncertainty due to measurement error from actual biological variability. Bayesian analysis using Markov Chain Monte Carlo (MCMC) provides tools to perform such an analysis as well as quantitative diagnostics to evaluate and discriminate between models. Starting from a one-compartment PK model with separate clearances to urine and feces, the model was incrementally expanded using Bayesian measures to assess if the expansion was supported by the data. PFOA excretion is sexually dimorphic in rats; male rats have bi-phasic elimination that is roughly 40 times slower than that of the females, which appear to have a single elimination phase. The male and female data were analyzed separately, keeping only the parameters describing the measurement process in common. For male rats, including excretion data initially decreased certainty in the one-compartment parameter estimates compared to an analysis using plasma data only. Allowing a third, unspecified clearance improved agreement and increased certainty when all the data was used, however a significant amount of eliminated PFOA was estimated to be missing from the excretion data. Adding an additional

  15. Modelling blood-brain barrier partitioning using Bayesian neural nets.

    PubMed

    Winkler, David A; Burden, Frank R

    2004-07-01

    We have employed three families of molecular molecular descriptors, together with Bayesian regularized neural nets, to model the partitioning of a diverse range of drugs and other small molecules across the blood-brain barrier (BBB). The relative efficacy of each descriptors class is compared, and the advantages of flexible, parsimonious, model free mapping methods, like Bayesian neural nets, illustrated. The relative importance of the molecular descriptors for the most predictive BBB model were determined by use of automatic relevance determination (ARD), and compared with the important descriptors from other literature models of BBB partitioning.

  16. Bayesian failure probability model sensitivity study. Final report

    SciTech Connect

    Not Available

    1986-05-30

    The Office of the Manager, National Communications System (OMNCS) has developed a system-level approach for estimating the effects of High-Altitude Electromagnetic Pulse (HEMP) on the connectivity of telecommunications networks. This approach incorporates a Bayesian statistical model which estimates the HEMP-induced failure probabilities of telecommunications switches and transmission facilities. The purpose of this analysis is to address the sensitivity of the Bayesian model. This is done by systematically varying two model input parameters--the number of observations, and the equipment failure rates. Throughout the study, a non-informative prior distribution is used. The sensitivity of the Bayesian model to the noninformative prior distribution is investigated from a theoretical mathematical perspective.

  17. On the Bayesian Nonparametric Generalization of IRT-Type Models

    ERIC Educational Resources Information Center

    San Martin, Ernesto; Jara, Alejandro; Rolin, Jean-Marie; Mouchart, Michel

    2011-01-01

    We study the identification and consistency of Bayesian semiparametric IRT-type models, where the uncertainty on the abilities' distribution is modeled using a prior distribution on the space of probability measures. We show that for the semiparametric Rasch Poisson counts model, simple restrictions ensure the identification of a general…

  18. Bayesian non-parametrics and the probabilistic approach to modelling

    PubMed Central

    Ghahramani, Zoubin

    2013-01-01

    Modelling is fundamental to many fields of science and engineering. A model can be thought of as a representation of possible data one could predict from a system. The probabilistic approach to modelling uses probability theory to express all aspects of uncertainty in the model. The probabilistic approach is synonymous with Bayesian modelling, which simply uses the rules of probability theory in order to make predictions, compare alternative models, and learn model parameters and structure from data. This simple and elegant framework is most powerful when coupled with flexible probabilistic models. Flexibility is achieved through the use of Bayesian non-parametrics. This article provides an overview of probabilistic modelling and an accessible survey of some of the main tools in Bayesian non-parametrics. The survey covers the use of Bayesian non-parametrics for modelling unknown functions, density estimation, clustering, time-series modelling, and representing sparsity, hierarchies, and covariance structure. More specifically, it gives brief non-technical overviews of Gaussian processes, Dirichlet processes, infinite hidden Markov models, Indian buffet processes, Kingman’s coalescent, Dirichlet diffusion trees and Wishart processes. PMID:23277609

  19. Bayesian Network Models for Local Dependence among Observable Outcome Variables

    ERIC Educational Resources Information Center

    Almond, Russell G.; Mulder, Joris; Hemat, Lisa A.; Yan, Duanli

    2009-01-01

    Bayesian network models offer a large degree of flexibility for modeling dependence among observables (item outcome variables) from the same task, which may be dependent. This article explores four design patterns for modeling locally dependent observations: (a) no context--ignores dependence among observables; (b) compensatory context--introduces…

  20. Semiparametric Thurstonian Models for Recurrent Choices: A Bayesian Analysis

    ERIC Educational Resources Information Center

    Ansari, Asim; Iyengar, Raghuram

    2006-01-01

    We develop semiparametric Bayesian Thurstonian models for analyzing repeated choice decisions involving multinomial, multivariate binary or multivariate ordinal data. Our modeling framework has multiple components that together yield considerable flexibility in modeling preference utilities, cross-sectional heterogeneity and parameter-driven…

  1. On the Adequacy of Bayesian Evaluations of Categorization Models: Reply to Vanpaemel and Lee (2012)

    ERIC Educational Resources Information Center

    Wills, Andy J.; Pothos, Emmanuel M.

    2012-01-01

    Vanpaemel and Lee (2012) argued, and we agree, that the comparison of formal models can be facilitated by Bayesian methods. However, Bayesian methods neither precede nor supplant our proposals (Wills & Pothos, 2012), as Bayesian methods can be applied both to our proposals and to their polar opposites. Furthermore, the use of Bayesian methods to…

  2. A Hierarchical Model for Distributed Seismicity

    NASA Astrophysics Data System (ADS)

    Tejedor, A.; Gomez, J. B.; Pacheco, A. F.

    2009-04-01

    A cellular automaton model for the interaction between seismic faults in an extended region is presented. The model, which is called HBM, consists of a hierarchical tree structure of levels; each level has a different number of boxes. Faults are represented by boxes, and faults of different area are boxes with different number of sites. With respect to the organization of the model, boxes of equal size are in the same level, and the more sites they have, the higher they are placed in the hierarchy. Interaction between faults is also assumed to be hierarchical. Stress particles are randomly added to the system -simulating the action of the external tectonic forces, in such a manner than the probability of receiving a stress particle by a box is directly proportional to the area of that box. The particles fill progressively the sites of the boxes. When a box is full it topples and the particles are in part redistributed and in part lost. This process is called relaxation. A box relaxation simulates the occurrence of an earthquake in the region. The redistribution of particles occurs mostly in the vertical direction (upwards and downwards); however, a small fraction of the load is transferred to the nearest neighbors in the same level of the relaxing box to simulate long-range interactions. If particles transferred to a box fill it, it also topples producing new relaxations. The largest box relaxed between the external addition of two stress particles defines the magnitude of the resulting main-shock. 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 responsible for earthquakes with a magnitude m - 1, which are placed in the immediate lower level of the hierarchy. It is assumed that the bottom level of the model contains the boxes whose relaxation corresponds to earthquakes of magnitude m = 1. So, the number of levels of the system is directly related to the

  3. Bayesian Inference: with ecological applications

    USGS Publications Warehouse

    Link, William A.; Barker, Richard J.

    2010-01-01

    This text provides a mathematically rigorous yet accessible and engaging introduction to Bayesian inference with relevant examples that will be of interest to biologists working in the fields of ecology, wildlife management and environmental studies as well as students in advanced undergraduate statistics.. This text opens the door to Bayesian inference, taking advantage of modern computational efficiencies and easily accessible software to evaluate complex hierarchical models.

  4. A hierarchical model for estimating change in American Woodcock populations

    USGS Publications Warehouse

    Sauer, J.R.; Link, W.A.; Kendall, W.L.; Kelley, J.R.; Niven, D.K.

    2008-01-01

    The Singing-Ground Survey (SGS) is a primary source of information on population change for American woodcock (Scolopax minor). We analyzed the SGS using a hierarchical log-linear model and compared the estimates of change and annual indices of abundance to a route regression analysis of SGS data. We also grouped SGS routes into Bird Conservation Regions (BCRs) and estimated population change and annual indices using BCRs within states and provinces as strata. Based on the hierarchical model?based estimates, we concluded that woodcock populations were declining in North America between 1968 and 2006 (trend = -0.9%/yr, 95% credible interval: -1.2, -0.5). Singing-Ground Survey results are generally similar between analytical approaches, but the hierarchical model has several important advantages over the route regression. Hierarchical models better accommodate changes in survey efficiency over time and space by treating strata, years, and observers as random effects in the context of a log-linear model, providing trend estimates that are derived directly from the annual indices. We also conducted a hierarchical model analysis of woodcock data from the Christmas Bird Count and the North American Breeding Bird Survey. All surveys showed general consistency in patterns of population change, but the SGS had the shortest credible intervals. We suggest that population management and conservation planning for woodcock involving interpretation of the SGS use estimates provided by the hierarchical model.

  5. Lifting a veil on diversity: a Bayesian approach to fitting relative-abundance models.

    PubMed

    Golicher, Duncan J; O'Hara, Robert B; Ruíz-Montoya, Lorena; Cayuela, Luis

    2006-02-01

    Bayesian methods incorporate prior knowledge into a statistical analysis. This prior knowledge is usually restricted to assumptions regarding the form of probability distributions of the parameters of interest, leaving their values to be determined mainly through the data. Here we show how a Bayesian approach can be applied to the problem of drawing inference regarding species abundance distributions and comparing diversity indices between sites. The classic log series and the lognormal models of relative- abundance distribution are apparently quite different in form. The first is a sampling distribution while the other is a model of abundance of the underlying population. Bayesian methods help unite these two models in a common framework. Markov chain Monte Carlo simulation can be used to fit both distributions as small hierarchical models with shared common assumptions. Sampling error can be assumed to follow a Poisson distribution. Species not found in a sample, but suspected to be present in the region or community of interest, can be given zero abundance. This not only simplifies the process of model fitting, but also provides a convenient way of calculating confidence intervals for diversity indices. The method is especially useful when a comparison of species diversity between sites with different sample sizes is the key motivation behind the research. We illustrate the potential of the approach using data on fruit-feeding butterflies in southern Mexico. We conclude that, once all assumptions have been made transparent, a single data set may provide support for the belief that diversity is negatively affected by anthropogenic forest disturbance. Bayesian methods help to apply theory regarding the distribution of abundance in ecological communities to applied conservation. PMID:16705973

  6. Involving Stakeholders in Building Integrated Fisheries Models Using Bayesian Methods

    NASA Astrophysics Data System (ADS)

    Haapasaari, Päivi; Mäntyniemi, Samu; Kuikka, Sakari

    2013-06-01

    A participatory Bayesian approach was used to investigate how the views of stakeholders could be utilized to develop models to help understand the Central Baltic herring fishery. In task one, we applied the Bayesian belief network methodology to elicit the causal assumptions of six stakeholders on factors that influence natural mortality, growth, and egg survival of the herring stock in probabilistic terms. We also integrated the expressed views into a meta-model using the Bayesian model averaging (BMA) method. In task two, we used influence diagrams to study qualitatively how the stakeholders frame the management problem of the herring fishery and elucidate what kind of causalities the different views involve. The paper combines these two tasks to assess the suitability of the methodological choices to participatory modeling in terms of both a modeling tool and participation mode. The paper also assesses the potential of the study to contribute to the development of participatory modeling practices. It is concluded that the subjective perspective to knowledge, that is fundamental in Bayesian theory, suits participatory modeling better than a positivist paradigm that seeks the objective truth. The methodology provides a flexible tool that can be adapted to different kinds of needs and challenges of participatory modeling. The ability of the approach to deal with small data sets makes it cost-effective in participatory contexts. However, the BMA methodology used in modeling the biological uncertainties is so complex that it needs further development before it can be introduced to wider use in participatory contexts.

  7. Super-Resolution Using Hidden Markov Model and Bayesian Detection Estimation Framework

    NASA Astrophysics Data System (ADS)

    Humblot, Fabrice; Mohammad-Djafari, Ali

    2006-12-01

    This paper presents a new method for super-resolution (SR) reconstruction of a high-resolution (HR) image from several low-resolution (LR) images. The HR image is assumed to be composed of homogeneous regions. Thus, the a priori distribution of the pixels is modeled by a finite mixture model (FMM) and a Potts Markov model (PMM) for the labels. The whole a priori model is then a hierarchical Markov model. The LR images are assumed to be obtained from the HR image by lowpass filtering, arbitrarily translation, decimation, and finally corruption by a random noise. The problem is then put in a Bayesian detection and estimation framework, and appropriate algorithms are developed based on Markov chain Monte Carlo (MCMC) Gibbs sampling. At the end, we have not only an estimate of the HR image but also an estimate of the classification labels which leads to a segmentation result.

  8. Hierarchical Model Validation of Symbolic Performance Models of Scientific Kernels

    SciTech Connect

    Alam, Sadaf R; Vetter, Jeffrey S

    2006-08-01

    Multi-resolution validation of hierarchical performance models of scientific applications is critical primarily for two reasons. First, the step-by-step validation determines the correctness of all essential components or phases in a science simulation. Second, a model that is validated at multiple resolution levels is the very first step to generate predictive performance models, for not only existing systems but also for emerging systems and future problem sizes. We present the design and validation of hierarchical performance models of two scientific benchmarks using a new technique called the modeling assertions (MA). Our MA prototype framework generates symbolic performance models that can be evaluated efficiently by generating the equivalent model representations in Octave and MATLAB. The multi-resolution modeling and validation is conducted on two contemporary, massively-parallel systems, XT3 and Blue Gene/L system. The workload distribution and the growth rates predictions generated by the MA models are confirmed by the experimental data collected on the MPP platforms. In addition, the physical memory requirements that are generated by the MA models are verified by the runtime values on the Blue Gene/L system, which has 512 MBytes and 256 MBytes physical memory capacity in its two unique execution modes.

  9. Bayesian Analysis of Order-Statistics Models for Ranking Data.

    ERIC Educational Resources Information Center

    Yu, Philip L. H.

    2000-01-01

    Studied the order-statistics models, extending the usual normal order-statistics model into one in which the underlying random variables followed a multivariate normal distribution. Used a Bayesian approach and the Gibbs sampling technique. Applied the proposed method to analyze presidential election data from the American Psychological…

  10. Bayesian Estimation of the DINA Model with Gibbs Sampling

    ERIC Educational Resources Information Center

    Culpepper, Steven Andrew

    2015-01-01

    A Bayesian model formulation of the deterministic inputs, noisy "and" gate (DINA) model is presented. Gibbs sampling is employed to simulate from the joint posterior distribution of item guessing and slipping parameters, subject attribute parameters, and latent class probabilities. The procedure extends concepts in Béguin and Glas,…

  11. Small Sample Properties of Bayesian Multivariate Autoregressive Time Series Models

    ERIC Educational Resources Information Center

    Price, Larry R.

    2012-01-01

    The aim of this study was to compare the small sample (N = 1, 3, 5, 10, 15) performance of a Bayesian multivariate vector autoregressive (BVAR-SEM) time series model relative to frequentist power and parameter estimation bias. A multivariate autoregressive model was developed based on correlated autoregressive time series vectors of varying…

  12. A Bayesian Approach for Analyzing Longitudinal Structural Equation Models

    ERIC Educational Resources Information Center

    Song, Xin-Yuan; Lu, Zhao-Hua; Hser, Yih-Ing; Lee, Sik-Yum

    2011-01-01

    This article considers a Bayesian approach for analyzing a longitudinal 2-level nonlinear structural equation model with covariates, and mixed continuous and ordered categorical variables. The first-level model is formulated for measures taken at each time point nested within individuals for investigating their characteristics that are dynamically…

  13. Bayesian Semiparametric Structural Equation Models with Latent Variables

    ERIC Educational Resources Information Center

    Yang, Mingan; Dunson, David B.

    2010-01-01

    Structural equation models (SEMs) with latent variables are widely useful for sparse covariance structure modeling and for inferring relationships among latent variables. Bayesian SEMs are appealing in allowing for the incorporation of prior information and in providing exact posterior distributions of unknowns, including the latent variables. In…

  14. Bayesian Finite Mixtures for Nonlinear Modeling of Educational Data.

    ERIC Educational Resources Information Center

    Tirri, Henry; And Others

    A Bayesian approach for finding latent classes in data is discussed. The approach uses finite mixture models to describe the underlying structure in the data and demonstrate that the possibility of using full joint probability models raises interesting new prospects for exploratory data analysis. The concepts and methods discussed are illustrated…

  15. Bayesian methods for characterizing unknown parameters of material models

    DOE PAGES

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

    2016-02-04

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

  16. Hierarchical abstract semantic model for image classification

    NASA Astrophysics Data System (ADS)

    Ye, Zhipeng; Liu, Peng; Zhao, Wei; Tang, Xianglong

    2015-09-01

    Semantic gap limits the performance of bag-of-visual-words. To deal with this problem, a hierarchical abstract semantics method that builds abstract semantic layers, generates semantic visual vocabularies, measures semantic gap, and constructs classifiers using the Adaboost strategy is proposed. First, abstract semantic layers are proposed to narrow the semantic gap between visual features and their interpretation. Then semantic visual words are extracted as features to train semantic classifiers. One popular form of measurement is used to quantify the semantic gap. The Adaboost training strategy is used to combine weak classifiers into strong ones to further improve performance. For a testing image, the category is estimated layer-by-layer. Corresponding abstract hierarchical structures for popular datasets, including Caltech-101 and MSRC, are proposed for evaluation. The experimental results show that the proposed method is capable of narrowing semantic gaps effectively and performs better than other categorization methods.

  17. Object-Oriented Bayesian Networks (OOBN) for Aviation Accident Modeling and Technology Portfolio Impact Assessment

    NASA Technical Reports Server (NTRS)

    Shih, Ann T.; Ancel, Ersin; Jones, Sharon M.

    2012-01-01

    The concern for reducing aviation safety risk is rising as the National Airspace System in the United States transforms to the Next Generation Air Transportation System (NextGen). The NASA Aviation Safety Program is committed to developing an effective aviation safety technology portfolio to meet the challenges of this transformation and to mitigate relevant safety risks. The paper focuses on the reasoning of selecting Object-Oriented Bayesian Networks (OOBN) as the technique and commercial software for the accident modeling and portfolio assessment. To illustrate the benefits of OOBN in a large and complex aviation accident model, the in-flight Loss-of-Control Accident Framework (LOCAF) constructed as an influence diagram is presented. An OOBN approach not only simplifies construction and maintenance of complex causal networks for the modelers, but also offers a well-organized hierarchical network that is easier for decision makers to exploit the model examining the effectiveness of risk mitigation strategies through technology insertions.

  18. Hiereachical Bayesian Model for Combining Geochemical and Geophysical Data for Environmental Applications Software

    SciTech Connect

    Chen, Jinsong

    2013-05-01

    Development of 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. The SIP data are 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 sub-models: 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 are estimated using Markov chain Monte Carlo methods. By combining the temporally distributed geochemical data with the spatially distributed geophysical data, we obtain the spatio-temporal distribution of ferrous iron, sulfate and sulfide, and their associated uncertainity 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.

  19. Hiereachical Bayesian Model for Combining Geochemical and Geophysical Data for Environmental Applications Software

    2013-05-01

    Development of 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. The SIP data are 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.more » 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 sub-models: 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 are estimated using Markov chain Monte Carlo methods. By combining the temporally distributed geochemical data with the spatially distributed geophysical data, we obtain the spatio-temporal distribution of ferrous iron, sulfate and sulfide, and their associated uncertainity 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.« less

  20. Hierarchical model analysis of the Atlantic Flyway Breeding Waterfowl Survey

    USGS Publications Warehouse

    Sauer, John R.; Zimmerman, Guthrie; Klimstra, Jon D.; Link, William A.

    2014-01-01

    We used log-linear hierarchical models to analyze data from the Atlantic Flyway Breeding Waterfowl Survey. The survey has been conducted by state biologists each year since 1989 in the northeastern United States from Virginia north to New Hampshire and Vermont. Although yearly population estimates from the survey are used by the United States Fish and Wildlife Service for estimating regional waterfowl population status for mallards (Anas platyrhynchos), black ducks (Anas rubripes), wood ducks (Aix sponsa), and Canada geese (Branta canadensis), they are not routinely adjusted to control for time of day effects and other survey design issues. The hierarchical model analysis permits estimation of year effects and population change while accommodating the repeated sampling of plots and controlling for time of day effects in counting. We compared population estimates from the current stratified random sample analysis to population estimates from hierarchical models with alternative model structures that describe year to year changes as random year effects, a trend with random year effects, or year effects modeled as 1-year differences. Patterns of population change from the hierarchical model results generally were similar to the patterns described by stratified random sample estimates, but significant visibility differences occurred between twilight to midday counts in all species. Controlling for the effects of time of day resulted in larger population estimates for all species in the hierarchical model analysis relative to the stratified random sample analysis. The hierarchical models also provided a convenient means of estimating population trend as derived statistics from the analysis. We detected significant declines in mallard and American black ducks and significant increases in wood ducks and Canada geese, a trend that had not been significant for 3 of these 4 species in the prior analysis. We recommend using hierarchical models for analysis of the Atlantic

  1. Bayesian Joint Modelling for Object Localisation in Weakly Labelled Images.

    PubMed

    Shi, Zhiyuan; Hospedales, Timothy M; Xiang, Tao

    2015-10-01

    We address the problem of localisation of objects as bounding boxes in images and videos with weak labels. This weakly supervised object localisation problem has been tackled in the past using discriminative models where each object class is localised independently from other classes. In this paper, a novel framework based on Bayesian joint topic modelling is proposed, which differs significantly from the existing ones in that: (1) All foreground object classes are modelled jointly in a single generative model that encodes multiple object co-existence so that "explaining away" inference can resolve ambiguity and lead to better learning and localisation. (2) Image backgrounds are shared across classes to better learn varying surroundings and "push out" objects of interest. (3) Our model can be learned with a mixture of weakly labelled and unlabelled data, allowing the large volume of unlabelled images on the Internet to be exploited for learning. Moreover, the Bayesian formulation enables the exploitation of various types of prior knowledge to compensate for the limited supervision offered by weakly labelled data, as well as Bayesian domain adaptation for transfer learning. Extensive experiments on the PASCAL VOC, ImageNet and YouTube-Object videos datasets demonstrate the effectiveness of our Bayesian joint model for weakly supervised object localisation. PMID:26340253

  2. Modeling Menstrual Cycle Length and Variability at the Approach of Menopause Using Hierarchical Change Point Models.

    PubMed

    Huang, Xiaobi; Elliott, Michael R; Harlow, Siobán D

    2014-04-01

    As women approach menopause, the patterns of their menstrual cycle lengths change. To study these changes, we need to jointly model both the mean and variability of cycle length. Our proposed model incorporates separate mean and variance change points for each woman and a hierarchical model to link them together, along with regression components to include predictors of menopausal onset such as age at menarche and parity. Additional complexity arises from the fact that the calendar data have substantial missingness due to hormone use, surgery, and failure to report. We integrate multiple imputation and time-to event modeling in a Bayesian estimation framework to deal with different forms of the missingness. Posterior predictive model checks are applied to evaluate the model fit. Our method successfully models patterns of women's menstrual cycle trajectories throughout their late reproductive life and identifies change points for mean and variability of segment length, providing insight into the menopausal process. More generally, our model points the way toward increasing use of joint mean-variance models to predict health outcomes and better understand disease processes.

  3. Modeling Menstrual Cycle Length and Variability at the Approach of Menopause Using Hierarchical Change Point Models

    PubMed Central

    Huang, Xiaobi; Elliott, Michael R.; Harlow, Siobán D.

    2013-01-01

    SUMMARY As women approach menopause, the patterns of their menstrual cycle lengths change. To study these changes, we need to jointly model both the mean and variability of cycle length. Our proposed model incorporates separate mean and variance change points for each woman and a hierarchical model to link them together, along with regression components to include predictors of menopausal onset such as age at menarche and parity. Additional complexity arises from the fact that the calendar data have substantial missingness due to hormone use, surgery, and failure to report. We integrate multiple imputation and time-to event modeling in a Bayesian estimation framework to deal with different forms of the missingness. Posterior predictive model checks are applied to evaluate the model fit. Our method successfully models patterns of women’s menstrual cycle trajectories throughout their late reproductive life and identifies change points for mean and variability of segment length, providing insight into the menopausal process. More generally, our model points the way toward increasing use of joint mean-variance models to predict health outcomes and better understand disease processes. PMID:24729638

  4. An exactly solvable model of hierarchical self-assembly.

    PubMed

    Dudowicz, Jacek; Douglas, Jack F; Freed, Karl F

    2009-06-14

    Many living and nonliving structures in the natural world form by hierarchical organization, but physical theories that describe this type of organization are scarce. To address this problem, a model of equilibrium self-assembly is formulated in which dynamically associating species organize into hierarchical structures that preserve their shape at each stage of assembly. In particular, we consider symmetric m-gons that associate at their vertices into Sierpinski gasket structures involving the hierarchical association of triangles, squares, hexagons, etc., at their corner vertices, thereby leading to fractal structures after many generations of assembly. This rather idealized model of hierarchical assembly yields an infinite sequence of self-assembly transitions as the morphology progressively organizes to higher levels of the hierarchy, and these structures coexists at dynamic equilibrium, as found in real hierarchically self-assembling systems such as amyloid fiber forming proteins. Moreover, the transition sharpness progressively grows with increasing m, corresponding to larger and larger loops in the assembled structures. Calculations are provided for several basic thermodynamic properties (including the order parameters for assembly for each stage of the hierarchy, average mass of clusters, specific heat, transition sharpness, etc.) that are required for characterizing the interaction parameters governing this type of self-assembly and for elucidating other basic qualitative aspects of these systems. Our idealized model of hierarchical assembly gives many insights into this ubiquitous type of self-organization process. PMID:19530788

  5. An exactly solvable model of hierarchical self-assembly

    NASA Astrophysics Data System (ADS)

    Dudowicz, Jacek; Douglas, Jack F.; Freed, Karl F.

    2009-06-01

    Many living and nonliving structures in the natural world form by hierarchical organization, but physical theories that describe this type of organization are scarce. To address this problem, a model of equilibrium self-assembly is formulated in which dynamically associating species organize into hierarchical structures that preserve their shape at each stage of assembly. In particular, we consider symmetric m-gons that associate at their vertices into Sierpinski gasket structures involving the hierarchical association of triangles, squares, hexagons, etc., at their corner vertices, thereby leading to fractal structures after many generations of assembly. This rather idealized model of hierarchical assembly yields an infinite sequence of self-assembly transitions as the morphology progressively organizes to higher levels of the hierarchy, and these structures coexists at dynamic equilibrium, as found in real hierarchically self-assembling systems such as amyloid fiber forming proteins. Moreover, the transition sharpness progressively grows with increasing m, corresponding to larger and larger loops in the assembled structures. Calculations are provided for several basic thermodynamic properties (including the order parameters for assembly for each stage of the hierarchy, average mass of clusters, specific heat, transition sharpness, etc.) that are required for characterizing the interaction parameters governing this type of self-assembly and for elucidating other basic qualitative aspects of these systems. Our idealized model of hierarchical assembly gives many insights into this ubiquitous type of self-organization process.

  6. Bayesian approach to neural-network modeling with input uncertainty.

    PubMed

    Wright, W A

    1999-01-01

    It is generally assumed when using Bayesian inference methods for neural networks that the input data contains no noise or corruption. For real-world (errors in variable) problems this is clearly an unsafe assumption. This paper presents a Bayesian neural-network framework which allows for input noise provided that some model of the noise process exists. In the limit where the noise process is small and symmetric it is shown, using the Laplace approximation, that this method gives an additional term to the usual Bayesian error bar which depends on the variance of the input noise process. Further by treating the true (noiseless) input as a hidden variable and sampling this jointly with the network's weights, using a Markov chain Monte Carlo method, it is demonstrated that it is possible to infer the regression over the noiseless input.

  7. Hierarchical modeling of bycatch rates of sea turtles in the western North Atlantic

    USGS Publications Warehouse

    Gardner, B.; Sullivan, P.J.; Epperly, S.; Morreale, S.J.

    2008-01-01

    Previous studies indicate that the locations of the endangered loggerhead Caretta caretta and critically endangered leatherback Dermochelys coriacea sea turtles are influenced by water temperatures, and that incidental catch rates in the pelagic longline fishery vary by region. We present a Bayesian hierarchical model to examine the effects of environmental variables, including water temperature, on the number of sea turtles captured in the US pelagic longline fishery in the western North Atlantic. The modeling structure is highly flexible, utilizes a Bayesian model selection technique, and is fully implemented in the software program WinBUGS. The number of sea turtles captured is modeled as a zero-inflated Poisson distribution and the model incorporates fixed effects to examine region-specific differences in the parameter estimates. Results indicate that water temperature, region, bottom depth, and target species are all significant predictors of the number of loggerhead sea turtles captured. For leatherback sea turtles, the model with only target species had the most posterior model weight, though a re-parameterization of the model indicates that temperature influences the zero-inflation parameter. The relationship between the number of sea turtles captured and the variables of interest all varied by region. This suggests that management decisions aimed at reducing sea turtle bycatch may be more effective if they are spatially explicit. ?? Inter-Research 2008.

  8. Free-Energy Bounds for Hierarchical Spin Models

    NASA Astrophysics Data System (ADS)

    Castellana, Michele; Barra, Adriano; Guerra, Francesco

    2014-04-01

    In this paper we study two non-mean-field (NMF) spin models built on a hierarchical lattice: the hierarchical Edward-Anderson model (HEA) of a spin glass, and Dyson's hierarchical model (DHM) of a ferromagnet. For the HEA, we prove the existence of the thermodynamic limit of the free energy and the replica-symmetry-breaking (RSB) free-energy bounds previously derived for the Sherrington-Kirkpatrick model of a spin glass. These RSB mean-field bounds are exact only if the order-parameter fluctuations (OPF) vanish: given that such fluctuations are not negligible in NMF models, we develop a novel strategy to tackle part of OPF in hierarchical models. The method is based on absorbing part of OPF of a block of spins into an effective Hamiltonian of the underlying spin blocks. We illustrate this method for DHM and show that, compared to the mean-field bound for the free energy, it provides a tighter NMF bound, with a critical temperature closer to the exact one. To extend this method to the HEA model, a suitable generalization of Griffith's correlation inequalities for Ising ferromagnets is needed: since correlation inequalities for spin glasses are still an open topic, we leave the extension of this method to hierarchical spin glasses as a future perspective.

  9. Bayesian IRT Guessing Models for Partial Guessing Behaviors

    ERIC Educational Resources Information Center

    Cao, Jing; Stokes, S. Lynne

    2008-01-01

    According to the recent Nation's Report Card, 12th-graders failed to produce gains on the 2005 National Assessment of Educational Progress (NAEP) despite earning better grades on average. One possible explanation is that 12th-graders were not motivated taking the NAEP, which is a low-stakes test. We develop three Bayesian IRT mixture models to…

  10. Shortlist B: A Bayesian Model of Continuous Speech Recognition

    ERIC Educational Resources Information Center

    Norris, Dennis; McQueen, James M.

    2008-01-01

    A Bayesian model of continuous speech recognition is presented. It is based on Shortlist (D. Norris, 1994; D. Norris, J. M. McQueen, A. Cutler, & S. Butterfield, 1997) and shares many of its key assumptions: parallel competitive evaluation of multiple lexical hypotheses, phonologically abstract prelexical and lexical representations, a feedforward…

  11. Space-time Bayesian survival modeling of chronic wasting disease in deer.

    PubMed

    Song, Hae-Ryoung; Lawson, Andrew

    2009-09-01

    The primary objectives of this study are to describe the spatial and temporal variation in disease prevalence of chronic wasting disease (CWD), to assess the effect of demographic factors such as age and sex on disease prevalence and to model the disease clustering effects over space and time. We propose a Bayesian hierarchical survival model where latent parameters capture temporal and spatial trends in disease incidence, incorporating several individual covariates and random effects. The model is applied to a data set which consists of 65085 harvested deer in Wisconsin from 2002 to 2006. We found significant sex effects, spatial effects, temporal effects and spatio-temporal interacted effects in CWD infection in deer in Wisconsin. The risk of infection for male deer was significantly higher than that of female deer, and CWD has been significantly different over space, time, and space and time based on the harvest samples.

  12. Hierarchical modelling of mobile, seeing robots

    NASA Technical Reports Server (NTRS)

    Luh, Cheng-Jye; Zeigler, Bernard P.

    1990-01-01

    This paper describes the implementation of a hierarchical robot simulation which supports the design of robots with vision and mobility. A seeing robot applies a classification expert system for visual identification of laboratory objects. The visual data acquisition algorithm used by the robot vision system has been developed to exploit multiple viewing distances and perspectives. Several different simulations have been run testing the visual logic in a laboratory environment. Much work remains to integrate the vision system with the rest of the robot system.

  13. Hierarchical Bayesian regularization of reconstructions for diffuse optical tomography using multiple priors

    PubMed Central

    Abdelnour, Farras; Genovese, Christopher; Huppert, Theodore

    2010-01-01

    Diffuse optical tomography (DOT) is a non-invasive brain imaging technique that uses low-levels of near-infrared light to measure optical absorption changes due to regional blood flow and blood oxygen saturation in the brain. By arranging light sources and detectors in a grid over the surface of the scalp, DOT studies attempt to spatially localize changes in oxy- and deoxy-hemoglobin in the brain that result from evoked brain activity during functional experiments. However, the reconstruction of accurate spatial images of hemoglobin changes from DOT data is an ill-posed linearized inverse problem, which requires model regularization to yield appropriate solutions. In this work, we describe and demonstrate the application of a parametric restricted maximum likelihood method (ReML) to incorporate multiple statistical priors into the recovery of optical images. This work is based on similar methods that have been applied to the inverse problem for magnetoencephalography (MEG). Herein, we discuss the adaptation of this model to DOT and demonstrate that this approach provides a means to objectively incorporate reconstruction constraints and demonstrate this approach through a series of simulated numerical examples. PMID:21258532

  14. Hierarchic plate and shell models based on p-extension

    NASA Technical Reports Server (NTRS)

    Szabo, Barna A.; Sahrmann, Glenn J.

    1988-01-01

    Formulations of finite element models for beams, arches, plates and shells based on the principle of virtual work was studied. The focus is on computer implementation of hierarchic sequences of finite element models suitable for numerical solution of a large variety of practical problems which may concurrently contain thin and thick plates and shells, stiffeners, and regions where three dimensional representation is required. The approximate solutions corresponding to the hierarchic sequence of models converge to the exact solution of the fully three dimensional model. The stopping criterion is based on: (1) estimation of the relative error in energy norm; (2) equilibrium tests, and (3) observation of the convergence of quantities of interest.

  15. A Bayesian A-optimal and model robust design criterion.

    PubMed

    Zhou, Xiaojie; Joseph, Lawrence; Wolfson, David B; Bélisle, Patrick

    2003-12-01

    Suppose that the true model underlying a set of data is one of a finite set of candidate models, and that parameter estimation for this model is of primary interest. With this goal, optimal design must depend on a loss function across all possible models. A common method that accounts for model uncertainty is to average the loss over all models; this is the basis of what is known as Läuter's criterion. We generalize Läuter's criterion and show that it can be placed in a Bayesian decision theoretic framework, by extending the definition of Bayesian A-optimality. We use this generalized A-optimality to find optimal design points in an environmental safety setting. In estimating the smallest detectable trace limit in a water contamination problem, we obtain optimal designs that are quite different from those suggested by standard A-optimality.

  16. Determining Predictor Importance in Hierarchical Linear Models Using Dominance Analysis

    ERIC Educational Resources Information Center

    Luo, Wen; Azen, Razia

    2013-01-01

    Dominance analysis (DA) is a method used to evaluate the relative importance of predictors that was originally proposed for linear regression models. This article proposes an extension of DA that allows researchers to determine the relative importance of predictors in hierarchical linear models (HLM). Commonly used measures of model adequacy in…

  17. Modelling hierarchical and modular complex networks: division and independence

    NASA Astrophysics Data System (ADS)

    Kim, D.-H.; Rodgers, G. J.; Kahng, B.; Kim, D.

    2005-06-01

    We introduce a growing network model which generates both modular and hierarchical structure in a self-organized way. To this end, we modify the Barabási-Albert model into the one evolving under the principles of division and independence as well as growth and preferential attachment (PA). A newly added vertex chooses one of the modules composed of existing vertices, and attaches edges to vertices belonging to that module following the PA rule. When the module size reaches a proper size, the module is divided into two, and a new module is created. The karate club network studied by Zachary is a simple version of the current model. We find that the model can reproduce both modular and hierarchical properties, characterized by the hierarchical clustering function of a vertex with degree k, C(k), being in good agreement with empirical measurements for real-world networks.

  18. A Bayesian Alternative for Multi-objective Ecohydrological Model Specification

    NASA Astrophysics Data System (ADS)

    Tang, Y.; Marshall, L. A.; Sharma, A.; Ajami, H.

    2015-12-01

    Process-based ecohydrological models combine the study of hydrological, physical, biogeochemical and ecological processes of the catchments, which are usually more complex and parametric than conceptual hydrological models. Thus, appropriate calibration objectives and model uncertainty analysis are essential for ecohydrological modeling. In recent years, Bayesian inference has become one of the most popular tools for quantifying the uncertainties in hydrological modeling with the development of Markov Chain Monte Carlo (MCMC) techniques. Our study aims to develop appropriate prior distributions and likelihood functions that minimize the model uncertainties and bias within a Bayesian ecohydrological framework. In our study, a formal Bayesian approach is implemented in an ecohydrological model which combines a hydrological model (HyMOD) and a dynamic vegetation model (DVM). Simulations focused on one objective likelihood (Streamflow/LAI) and multi-objective likelihoods (Streamflow and LAI) with different weights are compared. Uniform, weakly informative and strongly informative prior distributions are used in different simulations. The Kullback-leibler divergence (KLD) is used to measure the dis(similarity) between different priors and corresponding posterior distributions to examine the parameter sensitivity. Results show that different prior distributions can strongly influence posterior distributions for parameters, especially when the available data is limited or parameters are insensitive to the available data. We demonstrate differences in optimized parameters and uncertainty limits in different cases based on multi-objective likelihoods vs. single objective likelihoods. We also demonstrate the importance of appropriately defining the weights of objectives in multi-objective calibration according to different data types.

  19. An examination of disparities in cancer incidence in Texas using Bayesian random coefficient models

    PubMed Central

    2015-01-01

    Disparities in cancer risk exist between ethnic groups in the United States. These disparities often result from differential access to healthcare, differences in socioeconomic status and differential exposure to carcinogens. This study uses cancer incidence data from the population based Texas Cancer Registry to investigate the disparities in digestive and respiratory cancers from 2000 to 2008. A Bayesian hierarchical regression approach is used. All models are fit using the INLA method of Bayesian model estimation. Specifically, a spatially varying coefficient model of the disparity between Hispanic and Non-Hispanic incidence is used. Results suggest that a spatio-temporal heterogeneity model best accounts for the observed Hispanic disparity in cancer risk. Overall, there is a significant disadvantage for the Hispanic population of Texas with respect to both of these cancers, and this disparity varies significantly over space. The greatest disparities between Hispanics and Non-Hispanics in digestive and respiratory cancers occur in eastern Texas, with patterns emerging as early as 2000 and continuing until 2008. PMID:26421245

  20. Hierarchical Chain Model of Spider Capture Silk Elasticity

    NASA Astrophysics Data System (ADS)

    Zhou, Haijun; Zhang, Yang

    2005-01-01

    Spider capture silk is a biomaterial with both high strength and high elasticity, but the structural design principle underlying these remarkable properties is still unknown. It was revealed recently by atomic force microscopy that an exponential force-extension relationship holds both for capture silk mesostructures and for intact capture silk fibers [N. Becker et al.,

    Nat. Mater. 2, 278 (2003)1476-1122
    ]. In this Letter a simple hierarchical chain model was proposed to understand and reproduce this striking observation. In the hierarchical chain model, a polymer is composed of many structural motifs which organize into structural modules and supramodules in a hierarchical manner. Each module in this hierarchy has its own characteristic force. The repetitive patterns in the amino-acid sequence of the major flagelliform protein of spider capture silk is in support of this model.

  1. Model-based hierarchical reinforcement learning and human action control.

    PubMed

    Botvinick, Matthew; Weinstein, Ari

    2014-11-01

    Recent work has reawakened interest in goal-directed or 'model-based' choice, where decisions are based on prospective evaluation of potential action outcomes. Concurrently, there has been growing attention to the role of hierarchy in decision-making and action control. We focus here on the intersection between these two areas of interest, considering the topic of hierarchical model-based control. To characterize this form of action control, we draw on the computational framework of hierarchical reinforcement learning, using this to interpret recent empirical findings. The resulting picture reveals how hierarchical model-based mechanisms might play a special and pivotal role in human decision-making, dramatically extending the scope and complexity of human behaviour.

  2. Model-based hierarchical reinforcement learning and human action control

    PubMed Central

    Botvinick, Matthew; Weinstein, Ari

    2014-01-01

    Recent work has reawakened interest in goal-directed or ‘model-based’ choice, where decisions are based on prospective evaluation of potential action outcomes. Concurrently, there has been growing attention to the role of hierarchy in decision-making and action control. We focus here on the intersection between these two areas of interest, considering the topic of hierarchical model-based control. To characterize this form of action control, we draw on the computational framework of hierarchical reinforcement learning, using this to interpret recent empirical findings. The resulting picture reveals how hierarchical model-based mechanisms might play a special and pivotal role in human decision-making, dramatically extending the scope and complexity of human behaviour. PMID:25267822

  3. Revised assessment of cancer risk to dichloromethane: part I Bayesian PBPK and dose-response modeling in mice.

    PubMed

    Marino, Dale J; Clewell, Harvey J; Gentry, P Robinan; Covington, Tammie R; Hack, C Eric; David, Raymond M; Morgott, David A

    2006-06-01

    The current USEPA cancer risk assessment for dichloromethane (DCM) is based on deterministic physiologically based pharmacokinetic (PBPK) modeling involving comparative metabolism of DCM by the GST pathway in the lung and liver of humans and mice. Recent advances in PBPK modeling include probabilistic methods and, in particular, Bayesian inference to quantitatively address variability and uncertainty separately. Although Bayesian analysis of human PBPK models has been published, no such efforts have been reported specifically addressing the mouse, apart from results included in the OSHA final rule on DCM. Certain aspects of the OSHA model, however, are not consistent with current approaches or with the USEPA's current DCM cancer risk assessment. Therefore, Bayesian analysis of the mouse PBPK model and dose-response modeling was undertaken to support development of an improved cancer risk assessment for DCM. A hierarchical population model was developed and prior parameter distributions were selected to reflect parameter values that were considered the most appropriate and best available. Bayesian modeling was conducted using MCSim, a publicly available software program for Markov Chain Monte Carlo analysis. Mean posterior values from the calibrated model were used to develop internal dose metrics, i.e., mg DCM metabolized by the GST pathway/L tissue/day in the lung and liver using exposure concentrations and results from the NTP mouse bioassay, consistent with the approach used by the USEPA for its current DCM cancer risk assessment. Internal dose metrics were 3- to 4-fold higher than those that support the current USEPA IRIS assessment. A decrease of similar magnitude was also noted in dose-response modeling results. These results show that the Bayesian PBPK model in the mouse provides an improved basis for a cancer risk assessment of DCM.

  4. APPLICATION OF BAYESIAN MONTE CARLO ANALYSIS TO A LAGRANGIAN PHOTOCHEMICAL AIR QUALITY MODEL. (R824792)

    EPA Science Inventory

    Uncertainties in ozone concentrations predicted with a Lagrangian photochemical air quality model have been estimated using Bayesian Monte Carlo (BMC) analysis. Bayesian Monte Carlo analysis provides a means of combining subjective "prior" uncertainty estimates developed ...

  5. Flexible distributions for triple-goal estimates in two-stage hierarchical models

    PubMed Central

    Paddock, Susan M.; Ridgeway, Greg; Lin, Rongheng; Louis, Thomas A.

    2009-01-01

    Performance evaluations often aim to achieve goals such as obtaining estimates of unit-specific means, ranks, and the distribution of unit-specific parameters. The Bayesian approach provides a powerful way to structure models for achieving these goals. While no single estimate can be optimal for achieving all three inferential goals, the communication and credibility of results will be enhanced by reporting a single estimate that performs well for all three. Triple goal estimates [Shen and Louis, 1998. Triple-goal estimates in two-stage hierarchical models. J. Roy. Statist. Soc. Ser. B 60, 455–471] have this performance and are appealing for performance evaluations. Because triple-goal estimates rely more heavily on the entire distribution than do posterior means, they are more sensitive to misspecification of the population distribution and we present various strategies to robustify triple-goal estimates by using nonparametric distributions. We evaluate performance based on the correctness and efficiency of the robustified estimates under several scenarios and compare empirical Bayes and fully Bayesian approaches to model the population distribution. We find that when data are quite informative, conclusions are robust to model misspecification. However, with less information in the data, conclusions can be quite sensitive to the choice of population distribution. Generally, use of a nonparametric distribution pays very little in efficiency when a parametric population distribution is valid, but successfully protects against model misspecification. PMID:19603088

  6. Polygenic Modeling with Bayesian Sparse Linear Mixed Models

    PubMed Central

    Zhou, Xiang; Carbonetto, Peter; Stephens, Matthew

    2013-01-01

    Both linear mixed models (LMMs) and sparse regression models are widely used in genetics applications, including, recently, polygenic modeling in genome-wide association studies. These two approaches make very different assumptions, so are expected to perform well in different situations. However, in practice, for a given dataset one typically does not know which assumptions will be more accurate. Motivated by this, we consider a hybrid of the two, which we refer to as a “Bayesian sparse linear mixed model” (BSLMM) that includes both these models as special cases. We address several key computational and statistical issues that arise when applying BSLMM, including appropriate prior specification for the hyper-parameters and a novel Markov chain Monte Carlo algorithm for posterior inference. We apply BSLMM and compare it with other methods for two polygenic modeling applications: estimating the proportion of variance in phenotypes explained (PVE) by available genotypes, and phenotype (or breeding value) prediction. For PVE estimation, we demonstrate that BSLMM combines the advantages of both standard LMMs and sparse regression modeling. For phenotype prediction it considerably outperforms either of the other two methods, as well as several other large-scale regression methods previously suggested for this problem. Software implementing our method is freely available from http://stephenslab.uchicago.edu/software.html. PMID:23408905

  7. A Bayesian nonlinear mixed-effects disease progression model

    PubMed Central

    Kim, Seongho; Jang, Hyejeong; Wu, Dongfeng; Abrams, Judith

    2016-01-01

    A nonlinear mixed-effects approach is developed for disease progression models that incorporate variation in age in a Bayesian framework. We further generalize the probability model for sensitivity to depend on age at diagnosis, time spent in the preclinical state and sojourn time. The developed models are then applied to the Johns Hopkins Lung Project data and the Health Insurance Plan for Greater New York data using Bayesian Markov chain Monte Carlo and are compared with the estimation method that does not consider random-effects from age. Using the developed models, we obtain not only age-specific individual-level distributions, but also population-level distributions of sensitivity, sojourn time and transition probability. PMID:26798562

  8. Exemplar models as a mechanism for performing Bayesian inference.

    PubMed

    Shi, Lei; Griffiths, Thomas L; Feldman, Naomi H; Sanborn, Adam N

    2010-08-01

    Probabilistic models have recently received much attention as accounts of human cognition. However, most research in which probabilistic models have been used has been focused on formulating the abstract problems behind cognitive tasks and their optimal solutions, rather than on mechanisms that could implement these solutions. Exemplar models are a successful class of psychological process models in which an inventory of stored examples is used to solve problems such as identification, categorization, and function learning. We show that exemplar models can be used to perform a sophisticated form of Monte Carlo approximation known as importance sampling and thus provide a way to perform approximate Bayesian inference. Simulations of Bayesian inference in speech perception, generalization along a single dimension, making predictions about everyday events, concept learning, and reconstruction from memory show that exemplar models can often account for human performance with only a few exemplars, for both simple and relatively complex prior distributions. These results suggest that exemplar models provide a possible mechanism for implementing at least some forms of Bayesian inference. PMID:20702863

  9. The Revised Hierarchical Model: A Critical Review and Assessment

    ERIC Educational Resources Information Center

    Kroll, Judith F.; van Hell, Janet G.; Tokowicz, Natasha; Green, David W.

    2010-01-01

    Brysbaert and Duyck (this issue) suggest that it is time to abandon the Revised Hierarchical Model (Kroll and Stewart, 1994) in favor of connectionist models such as BIA+ (Dijkstra and Van Heuven, 2002) that more accurately account for the recent evidence on non-selective access in bilingual word recognition. In this brief response, we first…

  10. Testing Crites' Model of Career Maturity: A Hierarchical Strategy.

    ERIC Educational Resources Information Center

    Wallbrown, Fred H.; And Others

    1986-01-01

    Investigated the construct validity of Crites' model of career maturity and the Career Maturity Inventory (CMI). Results from a nationwide sample of adolescents, using hierarchical factor analytic methodology, indicated confirmatory support for the multidimensionality of Crites' model of career maturity, and the construct validity of the CMI as a…

  11. HIBAYES: Global 21-cm Bayesian Monte-Carlo Model Fitting

    NASA Astrophysics Data System (ADS)

    Zwart, Jonathan T. L.; Price, Daniel; Bernardi, Gianni

    2016-06-01

    HIBAYES implements fully-Bayesian extraction of the sky-averaged (global) 21-cm signal from the Cosmic Dawn and Epoch of Reionization in the presence of foreground emission. User-defined likelihood and prior functions are called by the sampler PyMultiNest (ascl:1606.005) in order to jointly explore the full (signal plus foreground) posterior probability distribution and evaluate the Bayesian evidence for a given model. Implemented models, for simulation and fitting, include gaussians (HI signal) and polynomials (foregrounds). Some simple plotting and analysis tools are supplied. The code can be extended to other models (physical or empirical), to incorporate data from other experiments, or to use alternative Monte-Carlo sampling engines as required.

  12. Bayesian point event modeling in spatial and environmental epidemiology.

    PubMed

    Lawson, Andrew B

    2012-10-01

    This paper reviews the current state of point event modeling in spatial epidemiology from a Bayesian perspective. Point event (or case event) data arise when geo-coded addresses of disease events are available. Often, this level of spatial resolution would not be accessible due to medical confidentiality constraints. However, for the examination of small spatial scales, it is important to be capable of examining point process data directly. Models for such data are usually formulated based on point process theory. In addition, special conditioning arguments can lead to simpler Bernoulli likelihoods and logistic spatial models. Goodness-of-fit diagnostics and Bayesian residuals are also considered. Applications within putative health hazard risk assessment, cluster detection, and linkage to environmental risk fields (misalignment) are considered.

  13. An evaluation of the Bayesian approach to fitting the N-mixture model for use with pseudo-replicated count data

    USGS Publications Warehouse

    Toribo, S.G.; Gray, B.R.; Liang, S.

    2011-01-01

    The N-mixture model proposed by Royle in 2004 may be used to approximate the abundance and detection probability of animal species in a given region. In 2006, Royle and Dorazio discussed the advantages of using a Bayesian approach in modelling animal abundance and occurrence using a hierarchical N-mixture model. N-mixture models assume replication on sampling sites, an assumption that may be violated when the site is not closed to changes in abundance during the survey period or when nominal replicates are defined spatially. In this paper, we studied the robustness of a Bayesian approach to fitting the N-mixture model for pseudo-replicated count data. Our simulation results showed that the Bayesian estimates for abundance and detection probability are slightly biased when the actual detection probability is small and are sensitive to the presence of extra variability within local sites.

  14. Application of the Bayesian dynamic survival model in medicine.

    PubMed

    He, Jianghua; McGee, Daniel L; Niu, Xufeng

    2010-02-10

    The Bayesian dynamic survival model (BDSM), a time-varying coefficient survival model from the Bayesian prospective, was proposed in early 1990s but has not been widely used or discussed. In this paper, we describe the model structure of the BDSM and introduce two estimation approaches for BDSMs: the Markov Chain Monte Carlo (MCMC) approach and the linear Bayesian (LB) method. The MCMC approach estimates model parameters through sampling and is computationally intensive. With the newly developed geoadditive survival models and software BayesX, the BDSM is available for general applications. The LB approach is easier in terms of computations but it requires the prespecification of some unknown smoothing parameters. In a simulation study, we use the LB approach to show the effects of smoothing parameters on the performance of the BDSM and propose an ad hoc method for identifying appropriate values for those parameters. We also demonstrate the performance of the MCMC approach compared with the LB approach and a penalized partial likelihood method available in software R packages. A gastric cancer trial is utilized to illustrate the application of the BDSM. PMID:20014356

  15. Application of the Bayesian dynamic survival model in medicine.

    PubMed

    He, Jianghua; McGee, Daniel L; Niu, Xufeng

    2010-02-10

    The Bayesian dynamic survival model (BDSM), a time-varying coefficient survival model from the Bayesian prospective, was proposed in early 1990s but has not been widely used or discussed. In this paper, we describe the model structure of the BDSM and introduce two estimation approaches for BDSMs: the Markov Chain Monte Carlo (MCMC) approach and the linear Bayesian (LB) method. The MCMC approach estimates model parameters through sampling and is computationally intensive. With the newly developed geoadditive survival models and software BayesX, the BDSM is available for general applications. The LB approach is easier in terms of computations but it requires the prespecification of some unknown smoothing parameters. In a simulation study, we use the LB approach to show the effects of smoothing parameters on the performance of the BDSM and propose an ad hoc method for identifying appropriate values for those parameters. We also demonstrate the performance of the MCMC approach compared with the LB approach and a penalized partial likelihood method available in software R packages. A gastric cancer trial is utilized to illustrate the application of the BDSM.

  16. Bayesian analysis of botanical epidemics using stochastic compartmental models.

    PubMed

    Gibson, G J; Kleczkowski, A; Gilligan, C A

    2004-08-17

    A stochastic model for an epidemic, incorporating susceptible, latent, and infectious states, is developed. The model represents primary and secondary infection rates and a time-varying host susceptibility with applications to a wide range of epidemiological systems. A Markov chain Monte Carlo algorithm is presented that allows the model to be fitted to experimental observations within a Bayesian framework. The approach allows the uncertainty in unobserved aspects of the process to be represented in the parameter posterior densities. The methods are applied to experimental observations of damping-off of radish (Raphanus sativus) caused by the fungal pathogen Rhizoctonia solani, in the presence and absence of the antagonistic fungus Trichoderma viride, a biological control agent that has previously been shown to affect the rate of primary infection by using a maximum-likelihood estimate for a simpler model with no allowance for a latent period. Using the Bayesian analysis, we are able to estimate the latent period from population data, even when there is uncertainty in discriminating infectious from latently infected individuals in data collection. We also show that the inference that T. viride can control primary, but not secondary, infection is robust to inclusion of the latent period in the model, although the absolute values of the parameters change. Some refinements and potential difficulties with the Bayesian approach in this context, when prior information on parameters is lacking, are discussed along with broader applications of the methods to a wide range of epidemiological systems.

  17. Assessment of substitution model adequacy using frequentist and Bayesian methods.

    PubMed

    Ripplinger, Jennifer; Sullivan, Jack

    2010-12-01

    In order to have confidence in model-based phylogenetic methods, such as maximum likelihood (ML) and Bayesian analyses, one must use an appropriate model of molecular evolution identified using statistically rigorous criteria. Although model selection methods such as the likelihood ratio test and Akaike information criterion are widely used in the phylogenetic literature, model selection methods lack the ability to reject all models if they provide an inadequate fit to the data. There are two methods, however, that assess absolute model adequacy, the frequentist Goldman-Cox (GC) test and Bayesian posterior predictive simulations (PPSs), which are commonly used in conjunction with the multinomial log likelihood test statistic. In this study, we use empirical and simulated data to evaluate the adequacy of common substitution models using both frequentist and Bayesian methods and compare the results with those obtained with model selection methods. In addition, we investigate the relationship between model adequacy and performance in ML and Bayesian analyses in terms of topology, branch lengths, and bipartition support. We show that tests of model adequacy based on the multinomial likelihood often fail to reject simple substitution models, especially when the models incorporate among-site rate variation (ASRV), and normally fail to reject less complex models than those chosen by model selection methods. In addition, we find that PPSs often fail to reject simpler models than the GC test. Use of the simplest substitution models not rejected based on fit normally results in similar but divergent estimates of tree topology and branch lengths. In addition, use of the simplest adequate substitution models can affect estimates of bipartition support, although these differences are often small with the largest differences confined to poorly supported nodes. We also find that alternative assumptions about ASRV can affect tree topology, tree length, and bipartition support. Our

  18. Conceptual hierarchical modeling to describe wetland plant community organization

    USGS Publications Warehouse

    Little, A.M.; Guntenspergen, G.R.; Allen, T.F.H.

    2010-01-01

    Using multivariate analysis, we created a hierarchical modeling process that describes how differently-scaled environmental factors interact to affect wetland-scale plant community organization in a system of small, isolated wetlands on Mount Desert Island, Maine. We followed the procedure: 1) delineate wetland groups using cluster analysis, 2) identify differently scaled environmental gradients using non-metric multidimensional scaling, 3) order gradient hierarchical levels according to spatiotem-poral scale of fluctuation, and 4) assemble hierarchical model using group relationships with ordination axes and post-hoc tests of environmental differences. Using this process, we determined 1) large wetland size and poor surface water chemistry led to the development of shrub fen wetland vegetation, 2) Sphagnum and water chemistry differences affected fen vs. marsh / sedge meadows status within small wetlands, and 3) small-scale hydrologic differences explained transitions between forested vs. non-forested and marsh vs. sedge meadow vegetation. This hierarchical modeling process can help explain how upper level contextual processes constrain biotic community response to lower-level environmental changes. It creates models with more nuanced spatiotemporal complexity than classification and regression tree procedures. Using this process, wetland scientists will be able to generate more generalizable theories of plant community organization, and useful management models. ?? Society of Wetland Scientists 2009.

  19. Bayesian Inference of High-Dimensional Dynamical Ocean Models

    NASA Astrophysics Data System (ADS)

    Lin, J.; Lermusiaux, P. F. J.; Lolla, S. V. T.; Gupta, A.; Haley, P. J., Jr.

    2015-12-01

    This presentation addresses a holistic set of challenges in high-dimension ocean Bayesian nonlinear estimation: i) predict the probability distribution functions (pdfs) of large nonlinear dynamical systems using stochastic partial differential equations (PDEs); ii) assimilate data using Bayes' law with these pdfs; iii) predict the future data that optimally reduce uncertainties; and (iv) rank the known and learn the new model formulations themselves. Overall, we allow the joint inference of the state, equations, geometry, boundary conditions and initial conditions of dynamical models. Examples are provided for time-dependent fluid and ocean flows, including cavity, double-gyre and Strait flows with jets and eddies. The Bayesian model inference, based on limited observations, is illustrated first by the estimation of obstacle shapes and positions in fluid flows. Next, the Bayesian inference of biogeochemical reaction equations and of their states and parameters is presented, illustrating how PDE-based machine learning can rigorously guide the selection and discovery of complex ecosystem models. Finally, the inference of multiscale bottom gravity current dynamics is illustrated, motivated in part by classic overflows and dense water formation sites and their relevance to climate monitoring and dynamics. This is joint work with our MSEAS group at MIT.

  20. Bayesian models with dominance effects for genomic evaluation of quantitative traits.

    PubMed

    Wellmann, Robin; Bennewitz, Jörn

    2012-02-01

    Genomic selection refers to the use of dense, genome-wide markers for the prediction of breeding values (BV) and subsequent selection of breeding individuals. It has become a standard tool in livestock and plant breeding for accelerating genetic gain. The core of genomic selection is the prediction of a large number of marker effects from a limited number of observations. Various Bayesian methods that successfully cope with this challenge are known. Until now, the main research emphasis has been on additive genetic effects. Dominance coefficients of quantitative trait loci (QTLs), however, can also be large, even if dominance variance and inbreeding depression are relatively small. Considering dominance might contribute to the accuracy of genomic selection and serve as a guide for choosing mating pairs with good combining abilities. A general hierarchical Bayesian model for genomic selection that can realistically account for dominance is introduced. Several submodels are proposed and compared with respect to their ability to predict genomic BV, dominance deviations and genotypic values (GV) by stochastic simulation. These submodels differ in the way the dependency between additive and dominance effects is modelled. Depending on the marker panel, the inclusion of dominance effects increased the accuracy of GV by about 17% and the accuracy of genomic BV by 2% in the offspring. Furthermore, it slowed down the decrease of the accuracies in subsequent generations. It was possible to obtain accurate estimates of GV, which enables mate selection programmes.

  1. Control of discrete event systems modeled as hierarchical state machines

    NASA Technical Reports Server (NTRS)

    Brave, Y.; Heymann, M.

    1991-01-01

    The authors examine a class of discrete event systems (DESs) modeled as asynchronous hierarchical state machines (AHSMs). For this class of DESs, they provide an efficient method for testing reachability, which is an essential step in many control synthesis procedures. This method utilizes the asynchronous nature and hierarchical structure of AHSMs, thereby illustrating the advantage of the AHSM representation as compared with its equivalent (flat) state machine representation. An application of the method is presented where an online minimally restrictive solution is proposed for the problem of maintaining a controlled AHSM within prescribed legal bounds.

  2. Toward a hierarchical goal theory model of school motivation.

    PubMed

    McInerney, Dennis M; Marsh, Herbert W; Yeung, Alexander Seeshing

    2003-01-01

    Instead of concentrating on mastery and performance goal orientations, recent research on school motivation has suggested a multidimensional structure of achievement goal orientations. Students in Australian high schools (N =774) responded to 35 survey items on 10 goal orientation constructs (effort, task, sense of purpose, praise, competition, power, token, social concern, social dependence, and affiliation) and 14 items on general mastery, general performance, general social, and global motivation constructs. Confirmatory factor analysis results supported a hierarchical, multidimensional school motivation construct. The hierarchical, multidimensional model has provided a strong theoretical structure for further school motivation research.

  3. Johnson-Neyman Type Technique in Hierarchical Linear Models

    ERIC Educational Resources Information Center

    Miyazaki, Yasuo; Maier, Kimberly S.

    2005-01-01

    In hierarchical linear models we often find that group indicator variables at the cluster level are significant predictors for the regression slopes. When this is the case, the average relationship between the outcome and a key independent variable are different from group to group. In these settings, a question such as "what range of the…

  4. Sensitivity Analysis for Hierarchical Models Employing "t" Level-1 Assumptions.

    ERIC Educational Resources Information Center

    Seltzer, Michael; Novak, John; Choi, Kilchan; Lim, Nelson

    2002-01-01

    Examines the ways in which level-1 outliers can impact the estimation of fixed effects and random effects in hierarchical models (HMs). Also outlines and illustrates the use of Markov Chain Monte Carlo algorithms for conducting sensitivity analyses under "t" level-1 assumptions, including algorithms for settings in which the degrees of freedom at…

  5. Sonar image segmentation using an unsupervised hierarchical MRF model.

    PubMed

    Mignotte, M; Collet, C; Perez, P; Bouthemy, P

    2000-01-01

    This paper is concerned with hierarchical Markov random field (MRP) models and their application to sonar image segmentation. We present an original hierarchical segmentation procedure devoted to images given by a high-resolution sonar. The sonar image is segmented into two kinds of regions: shadow (corresponding to a lack of acoustic reverberation behind each object lying on the sea-bed) and sea-bottom reverberation. The proposed unsupervised scheme takes into account the variety of the laws in the distribution mixture of a sonar image, and it estimates both the parameters of noise distributions and the parameters of the Markovian prior. For the estimation step, we use an iterative technique which combines a maximum likelihood approach (for noise model parameters) with a least-squares method (for MRF-based prior). In order to model more precisely the local and global characteristics of image content at different scales, we introduce a hierarchical model involving a pyramidal label field. It combines coarse-to-fine causal interactions with a spatial neighborhood structure. This new method of segmentation, called the scale causal multigrid (SCM) algorithm, has been successfully applied to real sonar images and seems to be well suited to the segmentation of very noisy images. The experiments reported in this paper demonstrate that the discussed method performs better than other hierarchical schemes for sonar image segmentation.

  6. Testing forecasts of a new Bayesian time-predictable model of eruption occurrence

    NASA Astrophysics Data System (ADS)

    Passarelli, L.; Sansò, B.; Sandri, L.; Marzocchi, W.

    2010-12-01

    In this paper we propose a model to forecast eruptions in a real forward perspective. Specifically, the model provides a forecast of the next eruption after the end of the last one, using only the data available up to that time. We focus our attention on volcanoes with open conduit regime and high eruption frequency. We assume a generalization of the classical time predictable model to describe the eruptive behavior of open conduit volcanoes and we use a Bayesian hierarchical model to make probabilistic forecasts. We apply the model to Kilauea volcano eruptive data and Mount Etna volcano flank eruption data. The aims of the proposed model are: (1) to test whether or not the Kilauea and Mount Etna volcanoes follow a time predictable behavior; (2) to discuss the volcanological implications of the time predictable model parameters inferred; (3) to compare the forecast capabilities of this model with other models present in literature. The results obtained using the MCMC sampling algorithm show that both volcanoes follow a time predictable behavior. The numerical values inferred for the parameters of the time predictable model suggest that the amount of the erupted volume could change the dynamics of the magma chamber refilling process during the repose period. The probability gain of this model compared with other models already present in literature is appreciably greater than zero. This means that our model provides better forecast than previous models and it could be used in a probabilistic volcanic hazard assessment scheme.

  7. Bayesian regression model for seasonal forecast of precipitation over Korea

    NASA Astrophysics Data System (ADS)

    Jo, Seongil; Lim, Yaeji; Lee, Jaeyong; Kang, Hyun-Suk; Oh, Hee-Seok

    2012-08-01

    In this paper, we apply three different Bayesian methods to the seasonal forecasting of the precipitation in a region around Korea (32.5°N-42.5°N, 122.5°E-132.5°E). We focus on the precipitation of summer season (June-July-August; JJA) for the period of 1979-2007 using the precipitation produced by the Global Data Assimilation and Prediction System (GDAPS) as predictors. Through cross-validation, we demonstrate improvement for seasonal forecast of precipitation in terms of root mean squared error (RMSE) and linear error in probability space score (LEPS). The proposed methods yield RMSE of 1.09 and LEPS of 0.31 between the predicted and observed precipitations, while the prediction using GDAPS output only produces RMSE of 1.20 and LEPS of 0.33 for CPC Merged Analyzed Precipitation (CMAP) data. For station-measured precipitation data, the RMSE and LEPS of the proposed Bayesian methods are 0.53 and 0.29, while GDAPS output is 0.66 and 0.33, respectively. The methods seem to capture the spatial pattern of the observed precipitation. The Bayesian paradigm incorporates the model uncertainty as an integral part of modeling in a natural way. We provide a probabilistic forecast integrating model uncertainty.

  8. Utilizing Gaussian Markov random field properties of Bayesian animal models.

    PubMed

    Steinsland, Ingelin; Jensen, Henrik

    2010-09-01

    In this article, we demonstrate how Gaussian Markov random field properties give large computational benefits and new opportunities for the Bayesian animal model. We make inference by computing the posteriors for important quantitative genetic variables. For the single-trait animal model, a nonsampling-based approximation is presented. For the multitrait model, we set up a robust and fast Markov chain Monte Carlo algorithm. The proposed methodology was used to analyze quantitative genetic properties of morphological traits of a wild house sparrow population. Results for single- and multitrait models were compared.

  9. Modeling urban air pollution with optimized hierarchical fuzzy inference system.

    PubMed

    Tashayo, Behnam; Alimohammadi, Abbas

    2016-10-01

    Environmental exposure assessments (EEA) and epidemiological studies require urban air pollution models with appropriate spatial and temporal resolutions. Uncertain available data and inflexible models can limit air pollution modeling techniques, particularly in under developing countries. This paper develops a hierarchical fuzzy inference system (HFIS) to model air pollution under different land use, transportation, and meteorological conditions. To improve performance, the system treats the issue as a large-scale and high-dimensional problem and develops the proposed model using a three-step approach. In the first step, a geospatial information system (GIS) and probabilistic methods are used to preprocess the data. In the second step, a hierarchical structure is generated based on the problem. In the third step, the accuracy and complexity of the model are simultaneously optimized with a multiple objective particle swarm optimization (MOPSO) algorithm. We examine the capabilities of the proposed model for predicting daily and annual mean PM2.5 and NO2 and compare the accuracy of the results with representative models from existing literature. The benefits provided by the model features, including probabilistic preprocessing, multi-objective optimization, and hierarchical structure, are precisely evaluated by comparing five different consecutive models in terms of accuracy and complexity criteria. Fivefold cross validation is used to assess the performance of the generated models. The respective average RMSEs and coefficients of determination (R (2)) for the test datasets using proposed model are as follows: daily PM2.5 = (8.13, 0.78), annual mean PM2.5 = (4.96, 0.80), daily NO2 = (5.63, 0.79), and annual mean NO2 = (2.89, 0.83). The obtained results demonstrate that the developed hierarchical fuzzy inference system can be utilized for modeling air pollution in EEA and epidemiological studies.

  10. A Bayesian Nonparametric Meta-Analysis Model

    ERIC Educational Resources Information Center

    Karabatsos, George; Talbott, Elizabeth; Walker, Stephen G.

    2015-01-01

    In a meta-analysis, it is important to specify a model that adequately describes the effect-size distribution of the underlying population of studies. The conventional normal fixed-effect and normal random-effects models assume a normal effect-size population distribution, conditionally on parameters and covariates. For estimating the mean overall…

  11. Bayesian Geostatistical Modeling of Leishmaniasis Incidence in Brazil

    PubMed Central

    Karagiannis-Voules, Dimitrios-Alexios; Scholte, Ronaldo G. C.; Guimarães, Luiz H.; Utzinger, Jürg; Vounatsou, Penelope

    2013-01-01

    Background Leishmaniasis is endemic in 98 countries with an estimated 350 million people at risk and approximately 2 million cases annually. Brazil is one of the most severely affected countries. Methodology We applied Bayesian geostatistical negative binomial models to analyze reported incidence data of cutaneous and visceral leishmaniasis in Brazil covering a 10-year period (2001–2010). Particular emphasis was placed on spatial and temporal patterns. The models were fitted using integrated nested Laplace approximations to perform fast approximate Bayesian inference. Bayesian variable selection was employed to determine the most important climatic, environmental, and socioeconomic predictors of cutaneous and visceral leishmaniasis. Principal Findings For both types of leishmaniasis, precipitation and socioeconomic proxies were identified as important risk factors. The predicted number of cases in 2010 were 30,189 (standard deviation [SD]: 7,676) for cutaneous leishmaniasis and 4,889 (SD: 288) for visceral leishmaniasis. Our risk maps predicted the highest numbers of infected people in the states of Minas Gerais and Pará for visceral and cutaneous leishmaniasis, respectively. Conclusions/Significance Our spatially explicit, high-resolution incidence maps identified priority areas where leishmaniasis control efforts should be targeted with the ultimate goal to reduce disease incidence. PMID:23675545

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

    NASA Astrophysics Data System (ADS)

    Morris, David; Macko, Stephen

    2016-04-01

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

  13. A Hierarchical Systems Approach to Model Validation

    NASA Astrophysics Data System (ADS)

    Easterbrook, S. M.

    2011-12-01

    Existing approaches to the question of how climate models should be evaluated tend to rely on either philosophical arguments about the status of models as scientific tools, or on empirical arguments about how well runs from a given model match observational data. These have led to quantitative approaches expressed in terms of model bias or forecast skill, and ensemble approaches where models are assessed according to the extent to which the ensemble brackets the observational data. Unfortunately, such approaches focus the evaluation on models per se (or more specifically, on the simulation runs they produce) as though the models can be isolated from their context. Such approach may overlook a number of important aspects of the use of climate models: - the process by which models are selected and configured for a given scientific question. - the process by which model outputs are selected, aggregated and interpreted by a community of expertise in climatology. - the software fidelity of the models (i.e. whether the running code is actually doing what the modellers think it's doing). - the (often convoluted) history that begat a given model, along with the modelling choices long embedded in the code. - variability in the scientific maturity of different model components within a coupled system. These omissions mean that quantitative approaches cannot assess whether a model produces the right results for the wrong reasons, or conversely, the wrong results for the right reasons (where, say the observational data is problematic, or the model is configured to be unlike the earth system for a specific reason). Hence, we argue that it is a mistake to think that validation is a post-hoc process to be applied to an individual "finished" model, to ensure it meets some criteria for fidelity to the real world. We are therefore developing a framework for model validation that extends current approaches down into the detailed codebase and the processes by which the code is built

  14. Bayesian sensitivity analysis of bifurcating nonlinear models

    NASA Astrophysics Data System (ADS)

    Becker, W.; Worden, K.; Rowson, J.

    2013-01-01

    Sensitivity analysis allows one to investigate how changes in input parameters to a system affect the output. When computational expense is a concern, metamodels such as Gaussian processes can offer considerable computational savings over Monte Carlo methods, albeit at the expense of introducing a data modelling problem. In particular, Gaussian processes assume a smooth, non-bifurcating response surface. This work highlights a recent extension to Gaussian processes which uses a decision tree to partition the input space into homogeneous regions, and then fits separate Gaussian processes to each region. In this way, bifurcations can be modelled at region boundaries and different regions can have different covariance properties. To test this method, both the treed and standard methods were applied to the bifurcating response of a Duffing oscillator and a bifurcating FE model of a heart valve. It was found that the treed Gaussian process provides a practical way of performing uncertainty and sensitivity analysis on large, potentially-bifurcating models, which cannot be dealt with by using a single GP, although an open problem remains how to manage bifurcation boundaries that are not parallel to coordinate axes.

  15. Bayesian inference and model comparison for metallic fatigue data

    NASA Astrophysics Data System (ADS)

    Babuška, Ivo; Sawlan, Zaid; Scavino, Marco; Szabó, Barna; Tempone, Raúl

    2016-06-01

    In this work, we present a statistical treatment of stress-life (S-N) data drawn from a collection of records of fatigue experiments that were performed on 75S-T6 aluminum alloys. Our main objective is to predict the fatigue life of materials by providing a systematic approach to model calibration, model selection and model ranking with reference to S-N data. To this purpose, we consider fatigue-limit models and random fatigue-limit models that are specially designed to allow the treatment of the run-outs (right-censored data). We first fit the models to the data by maximum likelihood methods and estimate the quantiles of the life distribution of the alloy specimen. To assess the robustness of the estimation of the quantile functions, we obtain bootstrap confidence bands by stratified resampling with respect to the cycle ratio. We then compare and rank the models by classical measures of fit based on information criteria. We also consider a Bayesian approach that provides, under the prior distribution of the model parameters selected by the user, their simulation-based posterior distributions. We implement and apply Bayesian model comparison methods, such as Bayes factor ranking and predictive information criteria based on cross-validation techniques under various a priori scenarios.

  16. Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics

    PubMed Central

    Baele, Guy; Li, Wai Lok Sibon; Drummond, Alexei J.; Suchard, Marc A.; Lemey, Philippe

    2013-01-01

    Recent implementations of path sampling (PS) and stepping-stone sampling (SS) have been shown to outperform the harmonic mean estimator (HME) and a posterior simulation-based analog of Akaike’s information criterion through Markov chain Monte Carlo (AICM), in Bayesian model selection of demographic and molecular clock models. Almost simultaneously, a Bayesian model averaging approach was developed that avoids conditioning on a single model but averages over a set of relaxed clock models. This approach returns estimates of the posterior probability of each clock model through which one can estimate the Bayes factor in favor of the maximum a posteriori (MAP) clock model; however, this Bayes factor estimate may suffer when the posterior probability of the MAP model approaches 1. Here, we compare these two recent developments with the HME, stabilized/smoothed HME (sHME), and AICM, using both synthetic and empirical data. Our comparison shows reassuringly that MAP identification and its Bayes factor provide similar performance to PS and SS and that these approaches considerably outperform HME, sHME, and AICM in selecting the correct underlying clock model. We also illustrate the importance of using proper priors on a large set of empirical data sets. PMID:23090976

  17. Bayesian Thurstonian models for ranking data using JAGS.

    PubMed

    Johnson, Timothy R; Kuhn, Kristine M

    2013-09-01

    A Thurstonian model for ranking data assumes that observed rankings are consistent with those of a set of underlying continuous variables. This model is appealing since it renders ranking data amenable to familiar models for continuous response variables-namely, linear regression models. To date, however, the use of Thurstonian models for ranking data has been very rare in practice. One reason for this may be that inferences based on these models require specialized technical methods. These methods have been developed to address computational challenges involved in these models but are not easy to implement without considerable technical expertise and are not widely available in software packages. To address this limitation, we show that Bayesian Thurstonian models for ranking data can be very easily implemented with the JAGS software package. We provide JAGS model files for Thurstonian ranking models for general use, discuss their implementation, and illustrate their use in analyses. PMID:23539504

  18. Predicting coastal cliff erosion using a Bayesian probabilistic model

    USGS Publications Warehouse

    Hapke, C.; Plant, N.

    2010-01-01

    Regional coastal cliff retreat is difficult to model due to the episodic nature of failures and the along-shore variability of retreat events. There is a growing demand, however, for predictive models that can be used to forecast areas vulnerable to coastal erosion hazards. Increasingly, probabilistic models are being employed that require data sets of high temporal density to define the joint probability density function that relates forcing variables (e.g. wave conditions) and initial conditions (e.g. cliff geometry) to erosion events. In this study we use a multi-parameter Bayesian network to investigate correlations between key variables that control and influence variations in cliff retreat processes. The network uses Bayesian statistical methods to estimate event probabilities using existing observations. Within this framework, we forecast the spatial distribution of cliff retreat along two stretches of cliffed coast in Southern California. The input parameters are the height and slope of the cliff, a descriptor of material strength based on the dominant cliff-forming lithology, and the long-term cliff erosion rate that represents prior behavior. The model is forced using predicted wave impact hours. Results demonstrate that the Bayesian approach is well-suited to the forward modeling of coastal cliff retreat, with the correct outcomes forecast in 70-90% of the modeled transects. The model also performs well in identifying specific locations of high cliff erosion, thus providing a foundation for hazard mapping. This approach can be employed to predict cliff erosion at time-scales ranging from storm events to the impacts of sea-level rise at the century-scale. ?? 2010.

  19. LiDAR based prediction of forest biomass using hierarchical models with spatially varying coefficients

    USGS Publications Warehouse

    Babcock, Chad; Finley, Andrew O.; Bradford, John B.; Kolka, Randall K.; Birdsey, Richard A.; Ryan, Michael G.

    2015-01-01

    Many studies and production inventory systems have shown the utility of coupling covariates derived from Light Detection and Ranging (LiDAR) data with forest variables measured on georeferenced inventory plots through regression models. The objective of this study was to propose and assess the use of a Bayesian hierarchical modeling framework that accommodates both residual spatial dependence and non-stationarity of model covariates through the introduction of spatial random effects. We explored this objective using four forest inventory datasets that are part of the North American Carbon Program, each comprising point-referenced measures of above-ground forest biomass and discrete LiDAR. For each dataset, we considered at least five regression model specifications of varying complexity. Models were assessed based on goodness of fit criteria and predictive performance using a 10-fold cross-validation procedure. Results showed that the addition of spatial random effects to the regression model intercept improved fit and predictive performance in the presence of substantial residual spatial dependence. Additionally, in some cases, allowing either some or all regression slope parameters to vary spatially, via the addition of spatial random effects, further improved model fit and predictive performance. In other instances, models showed improved fit but decreased predictive performance—indicating over-fitting and underscoring the need for cross-validation to assess predictive ability. The proposed Bayesian modeling framework provided access to pixel-level posterior predictive distributions that were useful for uncertainty mapping, diagnosing spatial extrapolation issues, revealing missing model covariates, and discovering locally significant parameters.

  20. Hierarchical Item Response Models for Cognitive Diagnosis

    ERIC Educational Resources Information Center

    Hansen, Mark Patrick

    2013-01-01

    Cognitive diagnosis models (see, e.g., Rupp, Templin, & Henson, 2010) have received increasing attention within educational and psychological measurement. The popularity of these models may be largely due to their perceived ability to provide useful information concerning both examinees (classifying them according to their attribute profiles)…

  1. DPpackage: Bayesian Semi- and Nonparametric Modeling in R

    PubMed Central

    Jara, Alejandro; Hanson, Timothy E.; Quintana, Fernando A.; Müller, Peter; Rosner, Gary L.

    2011-01-01

    Data analysis sometimes requires the relaxation of parametric assumptions in order to gain modeling flexibility and robustness against mis-specification of the probability model. In the Bayesian context, this is accomplished by placing a prior distribution on a function space, such as the space of all probability distributions or the space of all regression functions. Unfortunately, posterior distributions ranging over function spaces are highly complex and hence sampling methods play a key role. This paper provides an introduction to a simple, yet comprehensive, set of programs for the implementation of some Bayesian non- and semi-parametric models in R, DPpackage. Currently DPpackage includes models for marginal and conditional density estimation, ROC curve analysis, interval-censored data, binary regression data, item response data, longitudinal and clustered data using generalized linear mixed models, and regression data using generalized additive models. The package also contains functions to compute pseudo-Bayes factors for model comparison, and for eliciting the precision parameter of the Dirichlet process prior. To maximize computational efficiency, the actual sampling for each model is carried out using compiled FORTRAN. PMID:21796263

  2. DPpackage: Bayesian Non- and Semi-parametric Modelling in R.

    PubMed

    Jara, Alejandro; Hanson, Timothy E; Quintana, Fernando A; Müller, Peter; Rosner, Gary L

    2011-04-01

    Data analysis sometimes requires the relaxation of parametric assumptions in order to gain modeling flexibility and robustness against mis-specification of the probability model. In the Bayesian context, this is accomplished by placing a prior distribution on a function space, such as the space of all probability distributions or the space of all regression functions. Unfortunately, posterior distributions ranging over function spaces are highly complex and hence sampling methods play a key role. This paper provides an introduction to a simple, yet comprehensive, set of programs for the implementation of some Bayesian non- and semi-parametric models in R, DPpackage. Currently DPpackage includes models for marginal and conditional density estimation, ROC curve analysis, interval-censored data, binary regression data, item response data, longitudinal and clustered data using generalized linear mixed models, and regression data using generalized additive models. The package also contains functions to compute pseudo-Bayes factors for model comparison, and for eliciting the precision parameter of the Dirichlet process prior. To maximize computational efficiency, the actual sampling for each model is carried out using compiled FORTRAN. PMID:21796263

  3. Bayesian inference in camera trapping studies for a class of spatial capture-recapture models

    USGS Publications Warehouse

    Royle, J. Andrew; Karanth, K. Ullas; Gopalaswamy, Arjun M.; Kumar, N. Samba

    2009-01-01

    We develop a class of models for inference about abundance or density using spatial capture-recapture data from studies based on camera trapping and related methods. The model is a hierarchical model composed of two components: a point process model describing the distribution of individuals in space (or their home range centers) and a model describing the observation of individuals in traps. We suppose that trap- and individual-specific capture probabilities are a function of distance between individual home range centers and trap locations. We show that the models can be regarded as generalized linear mixed models, where the individual home range centers are random effects. We adopt a Bayesian framework for inference under these models using a formulation based on data augmentation. We apply the models to camera trapping data on tigers from the Nagarahole Reserve, India, collected over 48 nights in 2006. For this study, 120 camera locations were used, but cameras were only operational at 30 locations during any given sample occasion. Movement of traps is common in many camera-trapping studies and represents an important feature of the observation model that we address explicitly in our application.

  4. An adaptive sparse-grid high-order stochastic collocation method for Bayesian inference in groundwater reactive transport modeling

    SciTech Connect

    Zhang, Guannan; Webster, Clayton G; Gunzburger, Max D

    2012-09-01

    Although Bayesian analysis has become vital to the quantification of prediction uncertainty in groundwater modeling, its application has been hindered due to the computational cost associated with numerous model executions needed for exploring the posterior probability density function (PPDF) of model parameters. This is particularly the case when the PPDF is estimated using Markov Chain Monte Carlo (MCMC) sampling. In this study, we develop a new approach that improves computational efficiency of Bayesian inference by constructing a surrogate system based on an adaptive sparse-grid high-order stochastic collocation (aSG-hSC) method. Unlike previous works using first-order hierarchical basis, we utilize a compactly supported higher-order hierar- chical basis to construct the surrogate system, resulting in a significant reduction in the number of computational simulations required. In addition, we use hierarchical surplus as an error indi- cator to determine adaptive sparse grids. This allows local refinement in the uncertain domain and/or anisotropic detection with respect to the random model parameters, which further improves computational efficiency. Finally, we incorporate a global optimization technique and propose an iterative algorithm for building the surrogate system for the PPDF with multiple significant modes. Once the surrogate system is determined, the PPDF can be evaluated by sampling the surrogate system directly with very little computational cost. The developed method is evaluated first using a simple analytical density function with multiple modes and then using two synthetic groundwater reactive transport models. The groundwater models represent different levels of complexity; the first example involves coupled linear reactions and the second example simulates nonlinear ura- nium surface complexation. The results show that the aSG-hSC is an effective and efficient tool for Bayesian inference in groundwater modeling in comparison with conventional

  5. Hierarchical spatial models for predicting pygmy rabbit distribution and relative abundance

    USGS Publications Warehouse

    Wilson, T.L.; Odei, J.B.; Hooten, M.B.; Edwards, T.C.

    2010-01-01

    Conservationists routinely use species distribution models to plan conservation, restoration and development actions, while ecologists use them to infer process from pattern. These models tend to work well for common or easily observable species, but are of limited utility for rare and cryptic species. This may be because honest accounting of known observation bias and spatial autocorrelation are rarely included, thereby limiting statistical inference of resulting distribution maps. We specified and implemented a spatially explicit Bayesian hierarchical model for a cryptic mammal species (pygmy rabbit Brachylagus idahoensis). Our approach used two levels of indirect sign that are naturally hierarchical (burrows and faecal pellets) to build a model that allows for inference on regression coefficients as well as spatially explicit model parameters. We also produced maps of rabbit distribution (occupied burrows) and relative abundance (number of burrows expected to be occupied by pygmy rabbits). The model demonstrated statistically rigorous spatial prediction by including spatial autocorrelation and measurement uncertainty. We demonstrated flexibility of our modelling framework by depicting probabilistic distribution predictions using different assumptions of pygmy rabbit habitat requirements. Spatial representations of the variance of posterior predictive distributions were obtained to evaluate heterogeneity in model fit across the spatial domain. Leave-one-out cross-validation was conducted to evaluate the overall model fit. Synthesis and applications. Our method draws on the strengths of previous work, thereby bridging and extending two active areas of ecological research: species distribution models and multi-state occupancy modelling. Our framework can be extended to encompass both larger extents and other species for which direct estimation of abundance is difficult. ?? 2010 The Authors. Journal compilation ?? 2010 British Ecological Society.

  6. Estimating anatomical trajectories with Bayesian mixed-effects modeling

    PubMed Central

    Ziegler, G.; Penny, W.D.; Ridgway, G.R.; Ourselin, S.; Friston, K.J.

    2015-01-01

    We introduce a mass-univariate framework for the analysis of whole-brain structural trajectories using longitudinal Voxel-Based Morphometry data and Bayesian inference. Our approach to developmental and aging longitudinal studies characterizes heterogeneous structural growth/decline between and within groups. In particular, we propose a probabilistic generative model that parameterizes individual and ensemble average changes in brain structure using linear mixed-effects models of age and subject-specific covariates. Model inversion uses Expectation Maximization (EM), while voxelwise (empirical) priors on the size of individual differences are estimated from the data. Bayesian inference on individual and group trajectories is realized using Posterior Probability Maps (PPM). In addition to parameter inference, the framework affords comparisons of models with varying combinations of model order for fixed and random effects using model evidence. We validate the model in simulations and real MRI data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) project. We further demonstrate how subject specific characteristics contribute to individual differences in longitudinal volume changes in healthy subjects, Mild Cognitive Impairment (MCI), and Alzheimer's Disease (AD). PMID:26190405

  7. Estimating anatomical trajectories with Bayesian mixed-effects modeling.

    PubMed

    Ziegler, G; Penny, W D; Ridgway, G R; Ourselin, S; Friston, K J

    2015-11-01

    We introduce a mass-univariate framework for the analysis of whole-brain structural trajectories using longitudinal Voxel-Based Morphometry data and Bayesian inference. Our approach to developmental and aging longitudinal studies characterizes heterogeneous structural growth/decline between and within groups. In particular, we propose a probabilistic generative model that parameterizes individual and ensemble average changes in brain structure using linear mixed-effects models of age and subject-specific covariates. Model inversion uses Expectation Maximization (EM), while voxelwise (empirical) priors on the size of individual differences are estimated from the data. Bayesian inference on individual and group trajectories is realized using Posterior Probability Maps (PPM). In addition to parameter inference, the framework affords comparisons of models with varying combinations of model order for fixed and random effects using model evidence. We validate the model in simulations and real MRI data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) project. We further demonstrate how subject specific characteristics contribute to individual differences in longitudinal volume changes in healthy subjects, Mild Cognitive Impairment (MCI), and Alzheimer's Disease (AD).

  8. Estimating anatomical trajectories with Bayesian mixed-effects modeling.

    PubMed

    Ziegler, G; Penny, W D; Ridgway, G R; Ourselin, S; Friston, K J

    2015-11-01

    We introduce a mass-univariate framework for the analysis of whole-brain structural trajectories using longitudinal Voxel-Based Morphometry data and Bayesian inference. Our approach to developmental and aging longitudinal studies characterizes heterogeneous structural growth/decline between and within groups. In particular, we propose a probabilistic generative model that parameterizes individual and ensemble average changes in brain structure using linear mixed-effects models of age and subject-specific covariates. Model inversion uses Expectation Maximization (EM), while voxelwise (empirical) priors on the size of individual differences are estimated from the data. Bayesian inference on individual and group trajectories is realized using Posterior Probability Maps (PPM). In addition to parameter inference, the framework affords comparisons of models with varying combinations of model order for fixed and random effects using model evidence. We validate the model in simulations and real MRI data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) project. We further demonstrate how subject specific characteristics contribute to individual differences in longitudinal volume changes in healthy subjects, Mild Cognitive Impairment (MCI), and Alzheimer's Disease (AD). PMID:26190405

  9. Bayesian analysis of physiologically based toxicokinetic and toxicodynamic models.

    PubMed

    Hack, C Eric

    2006-04-17

    Physiologically based toxicokinetic (PBTK) and toxicodynamic (TD) models of bromate in animals and humans would improve our ability to accurately estimate the toxic doses in humans based on available animal studies. These mathematical models are often highly parameterized and must be calibrated in order for the model predictions of internal dose to adequately fit the experimentally measured doses. Highly parameterized models are difficult to calibrate and it is difficult to obtain accurate estimates of uncertainty or variability in model parameters with commonly used frequentist calibration methods, such as maximum likelihood estimation (MLE) or least squared error approaches. The Bayesian approach called Markov chain Monte Carlo (MCMC) analysis can be used to successfully calibrate these complex models. Prior knowledge about the biological system and associated model parameters is easily incorporated in this approach in the form of prior parameter distributions, and the distributions are refined or updated using experimental data to generate posterior distributions of parameter estimates. The goal of this paper is to give the non-mathematician a brief description of the Bayesian approach and Markov chain Monte Carlo analysis, how this technique is used in risk assessment, and the issues associated with this approach.

  10. A hierarchical modeling framework for multiple observer transect surveys.

    PubMed

    Conn, Paul B; Laake, Jeffrey L; Johnson, Devin S

    2012-01-01

    Ecologists often use multiple observer transect surveys to census animal populations. In addition to animal counts, these surveys produce sequences of detections and non-detections for each observer. When combined with additional data (i.e. covariates such as distance from the transect line), these sequences provide the additional information to estimate absolute abundance when detectability on the transect line is less than one. Although existing analysis approaches for such data have proven extremely useful, they have some limitations. For instance, it is difficult to extrapolate from observed areas to unobserved areas unless a rigorous sampling design is adhered to; it is also difficult to share information across spatial and temporal domains or to accommodate habitat-abundance relationships. In this paper, we introduce a hierarchical modeling framework for multiple observer line transects that removes these limitations. In particular, abundance intensities can be modeled as a function of habitat covariates, making it easier to extrapolate to unsampled areas. Our approach relies on a complete data representation of the state space, where unobserved animals and their covariates are modeled using a reversible jump Markov chain Monte Carlo algorithm. Observer detections are modeled via a bivariate normal distribution on the probit scale, with dependence induced by a distance-dependent correlation parameter. We illustrate performance of our approach with simulated data and on a known population of golf tees. In both cases, we show that our hierarchical modeling approach yields accurate inference about abundance and related parameters. In addition, we obtain accurate inference about population-level covariates (e.g. group size). We recommend that ecologists consider using hierarchical models when analyzing multiple-observer transect data, especially when it is difficult to rigorously follow pre-specified sampling designs. We provide a new R package, hierarchical

  11. Bayesian partial linear model for skewed longitudinal data.

    PubMed

    Tang, Yuanyuan; Sinha, Debajyoti; Pati, Debdeep; Lipsitz, Stuart; Lipshultz, Steven

    2015-07-01

    Unlike majority of current statistical models and methods focusing on mean response for highly skewed longitudinal data, we present a novel model for such data accommodating a partially linear median regression function, a skewed error distribution and within subject association structures. We provide theoretical justifications for our methods including asymptotic properties of the posterior and associated semiparametric Bayesian estimators. We also provide simulation studies to investigate the finite sample properties of our methods. Several advantages of our method compared with existing methods are demonstrated via analysis of a cardiotoxicity study of children of HIV-infected mothers.

  12. Star formation in a hierarchical model for Cloud Complexes

    NASA Astrophysics Data System (ADS)

    Sanchez, N.; Parravano, A.

    The effects of the external and initial conditions on the star formation processes in Molecular Cloud Complexes are examined in the context of a schematic model. The model considers a hierarchical system with five predefined phases: warm gas, neutral gas, low density molecular gas, high density molecular gas and protostars. The model follows the mass evolution of each substructure by computing its mass exchange with their parent and children. The parent-child mass exchange depends on the radiation density at the interphase, which is produced by the radiation coming from the stars that form at the end of the hierarchical structure, and by the external radiation field. The system is chaotic in the sense that its temporal evolution is very sensitive to small changes in the initial or external conditions. However, global features such as the star formation efficience and the Initial Mass Function are less affected by those variations.

  13. Petascale Hierarchical Modeling VIA Parallel Execution

    SciTech Connect

    Gelman, Andrew

    2014-04-14

    The research allows more effective model building. By allowing researchers to fit complex models to large datasets in a scalable manner, our algorithms and software enable more effective scientific research. In the new area of “big data,” it is often necessary to fit “big models” to adjust for systematic differences between sample and population. For this task, scalable and efficient model-fitting tools are needed, and these have been achieved with our new Hamiltonian Monte Carlo algorithm, the no-U-turn sampler, and our new C++ program, Stan. In layman’s terms, our research enables researchers to create improved mathematical modes for large and complex systems.

  14. A study of finite mixture model: Bayesian approach on financial time series data

    NASA Astrophysics Data System (ADS)

    Phoong, Seuk-Yen; Ismail, Mohd Tahir

    2014-07-01

    Recently, statistician have emphasized on the fitting finite mixture model by using Bayesian method. Finite mixture model is a mixture of distributions in modeling a statistical distribution meanwhile Bayesian method is a statistical method that use to fit the mixture model. Bayesian method is being used widely because it has asymptotic properties which provide remarkable result. In addition, Bayesian method also shows consistency characteristic which means the parameter estimates are close to the predictive distributions. In the present paper, the number of components for mixture model is studied by using Bayesian Information Criterion. Identify the number of component is important because it may lead to an invalid result. Later, the Bayesian method is utilized to fit the k-component mixture model in order to explore the relationship between rubber price and stock market price for Malaysia, Thailand, Philippines and Indonesia. Lastly, the results showed that there is a negative effect among rubber price and stock market price for all selected countries.

  15. Trans-dimensional inversion of microtremor array dispersion data with hierarchical autoregressive error models

    NASA Astrophysics Data System (ADS)

    Dettmer, Jan; Molnar, Sheri; Steininger, Gavin; Dosso, Stan E.; Cassidy, John F.

    2012-02-01

    This paper applies a general trans-dimensional Bayesian inference methodology and hierarchical autoregressive data-error models to the inversion of microtremor array dispersion data for shear wave velocity (vs) structure. This approach accounts for the limited knowledge of the optimal earth model parametrization (e.g. the number of layers in the vs profile) and of the data-error statistics 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 indexing parameter) are considered in the results. The earth model is parametrized in terms of a partition model with interfaces given over a depth-range of interest. In this work, the number of interfaces (layers) in the partition model represents the trans-dimensional model indexing. In addition, serial data-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 data-error statistics, and have no requirement for computing the inverse or determinant of a data-error covariance matrix. This approach is particularly useful for trans-dimensional inverse problems, as point estimates may not be representative of the

  16. Predictive RANS simulations via Bayesian Model-Scenario Averaging

    SciTech Connect

    Edeling, W.N.; Cinnella, P.; Dwight, R.P.

    2014-10-15

    The turbulence closure model is the dominant source of error in most Reynolds-Averaged Navier–Stokes simulations, yet no reliable estimators for this error component currently exist. Here we develop a stochastic, a posteriori error estimate, calibrated to specific classes of flow. It is based on variability in model closure coefficients across multiple flow scenarios, for multiple closure models. The variability is estimated using Bayesian calibration against experimental data for each scenario, and Bayesian Model-Scenario Averaging (BMSA) is used to collate the resulting posteriors, to obtain a stochastic estimate of a Quantity of Interest (QoI) in an unmeasured (prediction) scenario. The scenario probabilities in BMSA are chosen using a sensor which automatically weights those scenarios in the calibration set which are similar to the prediction scenario. The methodology is applied to the class of turbulent boundary-layers subject to various pressure gradients. For all considered prediction scenarios the standard-deviation of the stochastic estimate is consistent with the measurement ground truth. Furthermore, the mean of the estimate is more consistently accurate than the individual model predictions.

  17. Quantum-Like Bayesian Networks for Modeling Decision Making

    PubMed Central

    Moreira, Catarina; Wichert, Andreas

    2016-01-01

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

  18. Quantum-Like Bayesian Networks for Modeling Decision Making.

    PubMed

    Moreira, Catarina; Wichert, Andreas

    2016-01-01

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

  19. Continuum damage modeling and simulation of hierarchical dental enamel

    NASA Astrophysics Data System (ADS)

    Ma, Songyun; Scheider, Ingo; Bargmann, Swantje

    2016-05-01

    Dental enamel exhibits high fracture toughness and stiffness due to a complex hierarchical and graded microstructure, optimally organized from nano- to macro-scale. In this study, a 3D representative volume element (RVE) model is adopted to study the deformation and damage behavior of the fibrous microstructure. A continuum damage mechanics model coupled to hyperelasticity is developed for modeling the initiation and evolution of damage in the mineral fibers as well as protein matrix. Moreover, debonding of the interface between mineral fiber and protein is captured by employing a cohesive zone model. The dependence of the failure mechanism on the aspect ratio of the mineral fibers is investigated. In addition, the effect of the interface strength on the damage behavior is studied with respect to geometric features of enamel. Further, the effect of an initial flaw on the overall mechanical properties is analyzed to understand the superior damage tolerance of dental enamel. The simulation results are validated by comparison to experimental data from micro-cantilever beam testing at two hierarchical levels. The transition of the failure mechanism at different hierarchical levels is also well reproduced in the simulations.

  20. Assessing uncertainty in a stand growth model by Bayesian synthesis

    SciTech Connect

    Green, E.J.; MacFarlane, D.W.; Valentine, H.T.; Strawderman, W.E.

    1999-11-01

    The Bayesian synthesis method (BSYN) was used to bound the uncertainty in projections calculated with PIPESTEM, a mechanistic model of forest growth. The application furnished posterior distributions of (a) the values of the model's parameters, and (b) the values of three of the model's output variables--basal area per unit land area, average tree height, and tree density--at different points in time. Confidence or credible intervals for the output variables were obtained directly from the posterior distributions. The application also provides estimates of correlation among the parameters and output variables. BSYN, which originally was applied to a population dynamics model for bowhead whales, is generally applicable to deterministic models. Extension to two or more linked models is discussed. A simple worked example is included in an appendix.

  1. BiomeNet: A Bayesian Model for Inference of Metabolic Divergence among Microbial Communities

    PubMed Central

    Chipman, Hugh; Gu, Hong; Bielawski, Joseph P.

    2014-01-01

    Metagenomics yields enormous numbers of microbial sequences that can be assigned a metabolic function. Using such data to infer community-level metabolic divergence is hindered by the lack of a suitable statistical framework. Here, we describe a novel hierarchical Bayesian model, called BiomeNet (Bayesian inference of metabolic networks), for inferring differential prevalence of metabolic subnetworks among microbial communities. To infer the structure of community-level metabolic interactions, BiomeNet applies a mixed-membership modelling framework to enzyme abundance information. The basic idea is that the mixture components of the model (metabolic reactions, subnetworks, and networks) are shared across all groups (microbiome samples), but the mixture proportions vary from group to group. Through this framework, the model can capture nested structures within the data. BiomeNet is unique in modeling each metagenome sample as a mixture of complex metabolic systems (metabosystems). The metabosystems are composed of mixtures of tightly connected metabolic subnetworks. BiomeNet differs from other unsupervised methods by allowing researchers to discriminate groups of samples through the metabolic patterns it discovers in the data, and by providing a framework for interpreting them. We describe a collapsed Gibbs sampler for inference of the mixture weights under BiomeNet, and we use simulation to validate the inference algorithm. Application of BiomeNet to human gut metagenomes revealed a metabosystem with greater prevalence among inflammatory bowel disease (IBD) patients. Based on the discriminatory subnetworks for this metabosystem, we inferred that the community is likely to be closely associated with the human gut epithelium, resistant to dietary interventions, and interfere with human uptake of an antioxidant connected to IBD. Because this metabosystem has a greater capacity to exploit host-associated glycans, we speculate that IBD-associated communities might arise

  2. A Bayesian approach to biokinetic models of internally- deposited radionuclides

    NASA Astrophysics Data System (ADS)

    Amer, Mamun F.

    Bayesian methods were developed and applied to estimate parameters of biokinetic models of internally deposited radionuclides for the first time. Marginal posterior densities for the parameters, given the available data, were obtained and graphed. These densities contain all the information available about the parameters and fully describe their uncertainties. Two different numerical integration methods were employed to approximate the multi-dimensional integrals needed to obtain these densities and to verify our results. One numerical method was based on Gaussian quadrature. The other method was a lattice rule that was developed by Conroy. The lattice rule method is applied here for the first time in conjunction with Bayesian analysis. Computer codes were developed in Mathematica's own programming language to perform the integrals. Several biokinetic models were studied. The first model was a single power function, a/ t-b that was used to describe 226Ra whole body retention data for long periods of time in many patients. The posterior odds criterion for model identification was applied to select, from among some competing models, the best model to represent 226Ra retention in man. The highest model posterior was attained by the single power function. Posterior densities for the model parameters were obtained for each patient. Also, predictive densities for retention, given the available retention values and some selected times, were obtained. These predictive densities characterize the uncertainties in the unobservable retention values taking into consideration the uncertainties of other parameters in the model. The second model was a single exponential function, α e-/beta t, that was used to represent one patient's whole body retention as well as total excretion of 137Cs. Missing observations (censored data) in the two responses were replaced by unknown parameters and were handled in the same way other model parameters are treated. By applying the Bayesian

  3. Approximate Bayesian computation for forward modeling in cosmology

    NASA Astrophysics Data System (ADS)

    Akeret, Joël; Refregier, Alexandre; Amara, Adam; Seehars, Sebastian; Hasner, Caspar

    2015-08-01

    Bayesian inference is often used in cosmology and astrophysics to derive constraints on model parameters from observations. This approach relies on the ability to compute the likelihood of the data given a choice of model parameters. In many practical situations, the likelihood function may however be unavailable or intractable due to non-gaussian errors, non-linear measurements processes, or complex data formats such as catalogs and maps. In these cases, the simulation of mock data sets can often be made through forward modeling. We discuss how Approximate Bayesian Computation (ABC) can be used in these cases to derive an approximation to the posterior constraints using simulated data sets. This technique relies on the sampling of the parameter set, a distance metric to quantify the difference between the observation and the simulations and summary statistics to compress the information in the data. We first review the principles of ABC and discuss its implementation using a Population Monte-Carlo (PMC) algorithm and the Mahalanobis distance metric. We test the performance of the implementation using a Gaussian toy model. We then apply the ABC technique to the practical case of the calibration of image simulations for wide field cosmological surveys. We find that the ABC analysis is able to provide reliable parameter constraints for this problem and is therefore a promising technique for other applications in cosmology and astrophysics. Our implementation of the ABC PMC method is made available via a public code release.

  4. Bayesian Gaussian Copula Factor Models for Mixed Data

    PubMed Central

    Murray, Jared S.; Dunson, David B.; Carin, Lawrence; Lucas, Joseph E.

    2013-01-01

    Gaussian factor models have proven widely useful for parsimoniously characterizing dependence in multivariate data. There is a rich literature on their extension to mixed categorical and continuous variables, using latent Gaussian variables or through generalized latent trait models acommodating measurements in the exponential family. However, when generalizing to non-Gaussian measured variables the latent variables typically influence both the dependence structure and the form of the marginal distributions, complicating interpretation and introducing artifacts. To address this problem we propose a novel class of Bayesian Gaussian copula factor models which decouple the latent factors from the marginal distributions. A semiparametric specification for the marginals based on the extended rank likelihood yields straightforward implementation and substantial computational gains. We provide new theoretical and empirical justifications for using this likelihood in Bayesian inference. We propose new default priors for the factor loadings and develop efficient parameter-expanded Gibbs sampling for posterior computation. The methods are evaluated through simulations and applied to a dataset in political science. The models in this paper are implemented in the R package bfa.1 PMID:23990691

  5. Bayesian Gaussian Copula Factor Models for Mixed Data.

    PubMed

    Murray, Jared S; Dunson, David B; Carin, Lawrence; Lucas, Joseph E

    2013-06-01

    Gaussian factor models have proven widely useful for parsimoniously characterizing dependence in multivariate data. There is a rich literature on their extension to mixed categorical and continuous variables, using latent Gaussian variables or through generalized latent trait models acommodating measurements in the exponential family. However, when generalizing to non-Gaussian measured variables the latent variables typically influence both the dependence structure and the form of the marginal distributions, complicating interpretation and introducing artifacts. To address this problem we propose a novel class of Bayesian Gaussian copula factor models which decouple the latent factors from the marginal distributions. A semiparametric specification for the marginals based on the extended rank likelihood yields straightforward implementation and substantial computational gains. We provide new theoretical and empirical justifications for using this likelihood in Bayesian inference. We propose new default priors for the factor loadings and develop efficient parameter-expanded Gibbs sampling for posterior computation. The methods are evaluated through simulations and applied to a dataset in political science. The models in this paper are implemented in the R package bfa.

  6. Bayesian Models for fMRI Data Analysis

    PubMed Central

    Zhang, Linlin; Guindani, Michele; Vannucci, Marina

    2015-01-01

    Functional magnetic resonance imaging (fMRI), a noninvasive neuroimaging method that provides an indirect measure of neuronal activity by detecting blood flow changes, has experienced an explosive growth in the past years. Statistical methods play a crucial role in understanding and analyzing fMRI data. Bayesian approaches, in particular, have shown great promise in applications. A remarkable feature of fully Bayesian approaches is that they allow a flexible modeling of spatial and temporal correlations in the data. This paper provides a review of the most relevant models developed in recent years. We divide methods according to the objective of the analysis. We start from spatio-temporal models for fMRI data that detect task-related activation patterns. We then address the very important problem of estimating brain connectivity. We also touch upon methods that focus on making predictions of an individual's brain activity or a clinical or behavioral response. We conclude with a discussion of recent integrative models that aim at combining fMRI data with other imaging modalities, such as EEG/MEG and DTI data, measured on the same subjects. We also briefly discuss the emerging field of imaging genetics. PMID:25750690

  7. Bayesian Sensitivity Analysis of Statistical Models with Missing Data

    PubMed Central

    ZHU, HONGTU; IBRAHIM, JOSEPH G.; TANG, NIANSHENG

    2013-01-01

    Methods for handling missing data depend strongly on the mechanism that generated the missing values, such as missing completely at random (MCAR) or missing at random (MAR), as well as other distributional and modeling assumptions at various stages. It is well known that the resulting estimates and tests may be sensitive to these assumptions as well as to outlying observations. In this paper, we introduce various perturbations to modeling assumptions and individual observations, and then develop a formal sensitivity analysis to assess these perturbations in the Bayesian analysis of statistical models with missing data. We develop a geometric framework, called the Bayesian perturbation manifold, to characterize the intrinsic structure of these perturbations. We propose several intrinsic influence measures to perform sensitivity analysis and quantify the effect of various perturbations to statistical models. We use the proposed sensitivity analysis procedure to systematically investigate the tenability of the non-ignorable missing at random (NMAR) assumption. Simulation studies are conducted to evaluate our methods, and a dataset is analyzed to illustrate the use of our diagnostic measures. PMID:24753718

  8. A Comparison of General Diagnostic Models (GDM) and Bayesian Networks Using a Middle School Mathematics Test

    ERIC Educational Resources Information Center

    Wu, Haiyan

    2013-01-01

    General diagnostic models (GDMs) and Bayesian networks are mathematical frameworks that cover a wide variety of psychometric models. Both extend latent class models, and while GDMs also extend item response theory (IRT) models, Bayesian networks can be parameterized using discretized IRT. The purpose of this study is to examine similarities and…

  9. Hierarchical models and the analysis of bird survey information

    USGS Publications Warehouse

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

    2003-01-01

    Management of birds often requires analysis of collections of estimates. We describe a hierarchical modeling approach to the analysis of these data, in which parameters associated with the individual species estimates are treated as random variables, and probability statements are made about the species parameters conditioned on the data. A Markov-Chain Monte Carlo (MCMC) procedure is used to fit the hierarchical model. This approach is computer intensive, and is based upon simulation. MCMC allows for estimation both of parameters and of derived statistics. To illustrate the application of this method, we use the case in which we are interested in attributes of a collection of estimates of population change. Using data for 28 species of grassland-breeding birds from the North American Breeding Bird Survey, we estimate the number of species with increasing populations, provide precision-adjusted rankings of species trends, and describe a measure of population stability as the probability that the trend for a species is within a certain interval. Hierarchical models can be applied to a variety of bird survey applications, and we are investigating their use in estimation of population change from survey data.

  10. A Bayesian random effects discrete-choice model for resource selection: Population-level selection inference

    USGS Publications Warehouse

    Thomas, D.L.; Johnson, D.; Griffith, B.

    2006-01-01

    Bayesian hierarchical discrete-choice model for resource selection can provide managers with 2 components of population-level inference: average population selection and variability of selection. Both components are necessary to make sound management decisions based on animal selection.

  11. Model Selection in Historical Research Using Approximate Bayesian Computation

    PubMed Central

    Rubio-Campillo, Xavier

    2016-01-01

    Formal Models and History Computational models are increasingly being used to study historical dynamics. This new trend, which could be named Model-Based History, makes use of recently published datasets and innovative quantitative methods to improve our understanding of past societies based on their written sources. The extensive use of formal models allows historians to re-evaluate hypotheses formulated decades ago and still subject to debate due to the lack of an adequate quantitative framework. The initiative has the potential to transform the discipline if it solves the challenges posed by the study of historical dynamics. These difficulties are based on the complexities of modelling social interaction, and the methodological issues raised by the evaluation of formal models against data with low sample size, high variance and strong fragmentation. Case Study This work examines an alternate approach to this evaluation based on a Bayesian-inspired model selection method. The validity of the classical Lanchester’s laws of combat is examined against a dataset comprising over a thousand battles spanning 300 years. Four variations of the basic equations are discussed, including the three most common formulations (linear, squared, and logarithmic) and a new variant introducing fatigue. Approximate Bayesian Computation is then used to infer both parameter values and model selection via Bayes Factors. Impact Results indicate decisive evidence favouring the new fatigue model. The interpretation of both parameter estimations and model selection provides new insights into the factors guiding the evolution of warfare. At a methodological level, the case study shows how model selection methods can be used to guide historical research through the comparison between existing hypotheses and empirical evidence. PMID:26730953

  12. Uncovering Transcriptional Regulatory Networks by Sparse Bayesian Factor Model

    NASA Astrophysics Data System (ADS)

    Meng, Jia; Zhang, Jianqiu(Michelle); Qi, Yuan(Alan); Chen, Yidong; Huang, Yufei

    2010-12-01

    The problem of uncovering transcriptional regulation by transcription factors (TFs) based on microarray data is considered. A novel Bayesian sparse correlated rectified factor model (BSCRFM) is proposed that models the unknown TF protein level activity, the correlated regulations between TFs, and the sparse nature of TF-regulated genes. The model admits prior knowledge from existing database regarding TF-regulated target genes based on a sparse prior and through a developed Gibbs sampling algorithm, a context-specific transcriptional regulatory network specific to the experimental condition of the microarray data can be obtained. The proposed model and the Gibbs sampling algorithm were evaluated on the simulated systems, and results demonstrated the validity and effectiveness of the proposed approach. The proposed model was then applied to the breast cancer microarray data of patients with Estrogen Receptor positive ([InlineEquation not available: see fulltext.]) status and Estrogen Receptor negative ([InlineEquation not available: see fulltext.]) status, respectively.

  13. Preferential sampling and Bayesian geostatistics: Statistical modeling and examples.

    PubMed

    Cecconi, Lorenzo; Grisotto, Laura; Catelan, Dolores; Lagazio, Corrado; Berrocal, Veronica; Biggeri, Annibale

    2016-08-01

    Preferential sampling refers to any situation in which the spatial process and the sampling locations are not stochastically independent. In this paper, we present two examples of geostatistical analysis in which the usual assumption of stochastic independence between the point process and the measurement process is violated. To account for preferential sampling, we specify a flexible and general Bayesian geostatistical model that includes a shared spatial random component. We apply the proposed model to two different case studies that allow us to highlight three different modeling and inferential aspects of geostatistical modeling under preferential sampling: (1) continuous or finite spatial sampling frame; (2) underlying causal model and relevant covariates; and (3) inferential goals related to mean prediction surface or prediction uncertainty.

  14. Preferential sampling and Bayesian geostatistics: Statistical modeling and examples.

    PubMed

    Cecconi, Lorenzo; Grisotto, Laura; Catelan, Dolores; Lagazio, Corrado; Berrocal, Veronica; Biggeri, Annibale

    2016-08-01

    Preferential sampling refers to any situation in which the spatial process and the sampling locations are not stochastically independent. In this paper, we present two examples of geostatistical analysis in which the usual assumption of stochastic independence between the point process and the measurement process is violated. To account for preferential sampling, we specify a flexible and general Bayesian geostatistical model that includes a shared spatial random component. We apply the proposed model to two different case studies that allow us to highlight three different modeling and inferential aspects of geostatistical modeling under preferential sampling: (1) continuous or finite spatial sampling frame; (2) underlying causal model and relevant covariates; and (3) inferential goals related to mean prediction surface or prediction uncertainty. PMID:27566774

  15. Bayesian Inference for Generalized Linear Models for Spiking Neurons

    PubMed Central

    Gerwinn, Sebastian; Macke, Jakob H.; Bethge, Matthias

    2010-01-01

    Generalized Linear Models (GLMs) are commonly used statistical methods for modelling the relationship between neural population activity and presented stimuli. When the dimension of the parameter space is large, strong regularization has to be used in order to fit GLMs to datasets of realistic size without overfitting. By imposing properly chosen priors over parameters, Bayesian inference provides an effective and principled approach for achieving regularization. Here we show how the posterior distribution over model parameters of GLMs can be approximated by a Gaussian using the Expectation Propagation algorithm. In this way, we obtain an estimate of the posterior mean and posterior covariance, allowing us to calculate Bayesian confidence intervals that characterize the uncertainty about the optimal solution. From the posterior we also obtain a different point estimate, namely the posterior mean as opposed to the commonly used maximum a posteriori estimate. We systematically compare the different inference techniques on simulated as well as on multi-electrode recordings of retinal ganglion cells, and explore the effects of the chosen prior and the performance measure used. We find that good performance can be achieved by choosing an Laplace prior together with the posterior mean estimate. PMID:20577627

  16. A bayesian integrative model for genetical genomics with spatially informed variable selection.

    PubMed

    Cassese, Alberto; Guindani, Michele; Vannucci, Marina

    2014-01-01

    We consider a Bayesian hierarchical model for the integration of gene expression levels with comparative genomic hybridization (CGH) array measurements collected on the same subjects. The approach defines a measurement error model that relates the gene expression levels to latent copy number states. In turn, the latent states are related to the observed surrogate CGH measurements via a hidden Markov model. The model further incorporates variable selection with a spatial prior based on a probit link that exploits dependencies across adjacent DNA segments. Posterior inference is carried out via Markov chain Monte Carlo stochastic search techniques. We study the performance of the model in simulations and show better results than those achieved with recently proposed alternative priors. We also show an application to data from a genomic study on lung squamous cell carcinoma, where we identify potential candidates of associations between copy number variants and the transcriptional activity of target genes. Gene ontology (GO) analyses of our findings reveal enrichments in genes that code for proteins involved in cancer. Our model also identifies a number of potential candidate biomarkers for further experimental validation. PMID:25288877

  17. Hierarchical Heteroclinics in Dynamical Model of Cognitive Processes: Chunking

    NASA Astrophysics Data System (ADS)

    Afraimovich, Valentin S.; Young, Todd R.; Rabinovich, Mikhail I.

    Combining the results of brain imaging and nonlinear dynamics provides a new hierarchical vision of brain network functionality that is helpful in understanding the relationship of the network to different mental tasks. Using these ideas it is possible to build adequate models for the description and prediction of different cognitive activities in which the number of variables is usually small enough for analysis. The dynamical images of different mental processes depend on their temporal organization and, as a rule, cannot be just simple attractors since cognition is characterized by transient dynamics. The mathematical image for a robust transient is a stable heteroclinic channel consisting of a chain of saddles connected by unstable separatrices. We focus here on hierarchical chunking dynamics that can represent several cognitive activiti