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Sample records for conjunctive bayesian networks

  1. Adaptive Dynamic Bayesian Networks

    SciTech Connect

    Ng, B M

    2007-10-26

    A discrete-time Markov process can be compactly modeled as a dynamic Bayesian network (DBN)--a graphical model with nodes representing random variables and directed edges indicating causality between variables. Each node has a probability distribution, conditional on the variables represented by the parent nodes. A DBN's graphical structure encodes fixed conditional dependencies between variables. But in real-world systems, conditional dependencies between variables may be unknown a priori or may vary over time. Model errors can result if the DBN fails to capture all possible interactions between variables. Thus, we explore the representational framework of adaptive DBNs, whose structure and parameters can change from one time step to the next: a distribution's parameters and its set of conditional variables are dynamic. This work builds on recent work in nonparametric Bayesian modeling, such as hierarchical Dirichlet processes, infinite-state hidden Markov networks and structured priors for Bayes net learning. In this paper, we will explain the motivation for our interest in adaptive DBNs, show how popular nonparametric methods are combined to formulate the foundations for adaptive DBNs, and present preliminary results.

  2. Conjunctivitis

    PubMed Central

    Azari, Amir A.; Barney, Neal P.

    2014-01-01

    IMPORTANCE Conjunctivitis is a common problem. OBJECTIVE To examine the diagnosis, management, and treatment of conjunctivitis, including various antibiotics and alternatives to antibiotic use in infectious conjunctivitis and use of antihistamines and mast cell stabilizers in allergic conjunctivitis. EVIDENCE REVIEW A search of the literature published through March 2013, using PubMed, the ISI Web of Knowledge database, and the Cochrane Library was performed. Eligible articles were selected after review of titles, abstracts, and references. FINDINGS Viral conjunctivitis is the most common overall cause of infectious conjunctivitis and usually does not require treatment; the signs and symptoms at presentation are variable. Bacterial conjunctivitis is the second most common cause of infectious conjunctivitis, with most uncomplicated cases resolving in 1 to 2 weeks. Mattering and adherence of the eyelids on waking, lack of itching, and absence of a history of conjunctivitis are the strongest factors associated with bacterial conjunctivitis. Topical antibiotics decrease the duration of bacterial conjunctivitis and allow earlier return to school or work. Conjunctivitis secondary to sexually transmitted diseases such as chlamydia and gonorrhea requires systemic treatment in addition to topical antibiotic therapy. Allergic conjunctivitis is encountered in up to 40% of the population, but only a small proportion of these individuals seek medical help; itching is the most consistent sign in allergic conjunctivitis, and treatment consists of topical antihistamines and mast cell inhibitors. CONCLUSIONS AND RELEVANCE The majority of cases in bacterial conjunctivitis are self-limiting and no treatment is necessary in uncomplicated cases. However, conjunctivitis caused by gonorrhea or chlamydia and conjunctivitis in contact lens wearers should be treated with antibiotics. Treatment for viral conjunctivitis is supportive. Treatment with antihistamines and mast cell stabilizers

  3. Conjunctivitis

    MedlinePlus

    ... this page: //medlineplus.gov/ency/article/001010.htm Conjunctivitis To use the sharing features on this page, please enable JavaScript. Conjunctivitis is swelling (inflammation) or infection of the conjunctiva . ...

  4. Conjunctivitis

    MedlinePlus

    Conjunctivitis is swelling (inflammation) or infection of the conjunctiva . This is the membrane that lines the eyelids ... also contain proteins and antibodies that kill bacteria. Conjunctivitis is most often caused by a virus. Viral ...

  5. Space Shuttle RTOS Bayesian Network

    NASA Technical Reports Server (NTRS)

    Morris, A. Terry; Beling, Peter A.

    2001-01-01

    With shrinking budgets and the requirements to increase reliability and operational life of the existing orbiter fleet, NASA has proposed various upgrades for the Space Shuttle that are consistent with national space policy. The cockpit avionics upgrade (CAU), a high priority item, has been selected as the next major upgrade. The primary functions of cockpit avionics include flight control, guidance and navigation, communication, and orbiter landing support. Secondary functions include the provision of operational services for non-avionics systems such as data handling for the payloads and caution and warning alerts to the crew. Recently, a process to selection the optimal commercial-off-the-shelf (COTS) real-time operating system (RTOS) for the CAU was conducted by United Space Alliance (USA) Corporation, which is a joint venture between Boeing and Lockheed Martin, the prime contractor for space shuttle operations. In order to independently assess the RTOS selection, NASA has used the Bayesian network-based scoring methodology described in this paper. Our two-stage methodology addresses the issue of RTOS acceptability by incorporating functional, performance and non-functional software measures related to reliability, interoperability, certifiability, efficiency, correctness, business, legal, product history, cost and life cycle. The first stage of the methodology involves obtaining scores for the various measures using a Bayesian network. The Bayesian network incorporates the causal relationships between the various and often competing measures of interest while also assisting the inherently complex decision analysis process with its ability to reason under uncertainty. The structure and selection of prior probabilities for the network is extracted from experts in the field of real-time operating systems. Scores for the various measures are computed using Bayesian probability. In the second stage, multi-criteria trade-off analyses are performed between the scores

  6. Quantum Inference on Bayesian Networks

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  7. Optimizing Inequality Constrained Priors in Bayesian Networks

    NASA Astrophysics Data System (ADS)

    Holmes, Dawn E.

    2005-11-01

    Intelligent systems based on Bayesian networks have been successful in medical diagnosis, finance and many other areas. Updating probabilities in Bayesian networks relies on algorithms that require complete causal information. Sensitivity analysis now strongly indicates that probabilities in Bayesian networks are not robust and this reinforces the view that a sound theoretical model for finding a minimally prejudiced estimate of the prior distribution is desirable. In this paper we are concerned with how to find the optimum prior distribution, given all and only the knowledge available. In particular, we show how to integrate prior knowledge expressed in terms of inequality constraints, into a Bayesian network based intelligent system.

  8. 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…

  9. Bayesian Approach to Network Modularity

    PubMed Central

    Hofman, Jake M.; Wiggins, Chris H.

    2009-01-01

    We present an efficient, principled, and interpretable technique for inferring module assignments and for identifying the optimal number of modules in a given network. We show how several existing methods for finding modules can be described as variant, special, or limiting cases of our work, and how the method overcomes the resolution limit problem, accurately recovering the true number of modules. Our approach is based on Bayesian methods for model selection which have been used with success for almost a century, implemented using a variational technique developed only in the past decade. We apply the technique to synthetic and real networks and outline how the method naturally allows selection among competing models. PMID:18643711

  10. An Intuitive Dashboard for Bayesian Network Inference

    NASA Astrophysics Data System (ADS)

    Reddy, Vikas; Charisse Farr, Anna; Wu, Paul; Mengersen, Kerrie; Yarlagadda, Prasad K. D. V.

    2014-03-01

    Current Bayesian network software packages provide good graphical interface for users who design and develop Bayesian networks for various applications. However, the intended end-users of these networks may not necessarily find such an interface appealing and at times it could be overwhelming, particularly when the number of nodes in the network is large. To circumvent this problem, this paper presents an intuitive dashboard, which provides an additional layer of abstraction, enabling the end-users to easily perform inferences over the Bayesian networks. Unlike most software packages, which display the nodes and arcs of the network, the developed tool organises the nodes based on the cause-and-effect relationship, making the user-interaction more intuitive and friendly. In addition to performing various types of inferences, the users can conveniently use the tool to verify the behaviour of the developed Bayesian network. The tool has been developed using QT and SMILE libraries in C++.

  11. 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.

  12. Diagnosis of Subtraction Bugs Using Bayesian Networks

    ERIC Educational Resources Information Center

    Lee, Jihyun; Corter, James E.

    2011-01-01

    Diagnosis of misconceptions or "bugs" in procedural skills is difficult because of their unstable nature. This study addresses this problem by proposing and evaluating a probability-based approach to the diagnosis of bugs in children's multicolumn subtraction performance using Bayesian networks. This approach assumes a causal network relating…

  13. Learning Bayesian Networks from Correlated Data

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  14. Bayesian network structure learning using quantum annealing

    NASA Astrophysics Data System (ADS)

    O'Gorman, B.; Babbush, R.; Perdomo-Ortiz, A.; Aspuru-Guzik, A.; Smelyanskiy, V.

    2015-02-01

    We introduce a method for the problem of learning the structure of a Bayesian network using the quantum adiabatic algorithm. We do so by introducing an efficient reformulation of a standard posterior-probability scoring function on graphs as a pseudo-Boolean function, which is equivalent to a system of 2-body Ising spins, as well as suitable penalty terms for enforcing the constraints necessary for the reformulation; our proposed method requires 𝓞(n2) qubits for n Bayesian network variables. Furthermore, we prove lower bounds on the necessary weighting of these penalty terms. The logical structure resulting from the mapping has the appealing property that it is instance-independent for a given number of Bayesian network variables, as well as being independent of the number of data cases.

  15. Bayesian networks in neuroscience: a survey.

    PubMed

    Bielza, Concha; Larrañaga, Pedro

    2014-01-01

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

  16. Bayesian networks in neuroscience: a survey

    PubMed Central

    Bielza, Concha; Larrañaga, Pedro

    2014-01-01

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

  17. Bayesian network modelling of upper gastrointestinal bleeding

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

  18. BNFinder2: Faster Bayesian network learning and Bayesian classification

    PubMed Central

    Dojer, Norbert; Bednarz, Paweł; Podsiadło, Agnieszka; Wilczyński, Bartek

    2013-01-01

    Summary: Bayesian Networks (BNs) are versatile probabilistic models applicable to many different biological phenomena. In biological applications the structure of the network is usually unknown and needs to be inferred from experimental data. BNFinder is a fast software implementation of an exact algorithm for finding the optimal structure of the network given a number of experimental observations. Its second version, presented in this article, represents a major improvement over the previous version. The improvements include (i) a parallelized learning algorithm leading to an order of magnitude speed-ups in BN structure learning time; (ii) inclusion of an additional scoring function based on mutual information criteria; (iii) possibility of choosing the resulting network specificity based on statistical criteria and (iv) a new module for classification by BNs, including cross-validation scheme and classifier quality measurements with receiver operator characteristic scores. Availability and implementation: BNFinder2 is implemented in python and freely available under the GNU general public license at the project Web site https://launchpad.net/bnfinder, together with a user’s manual, introductory tutorial and supplementary methods. Contact: dojer@mimuw.edu.pl or bartek@mimuw.edu.pl Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23818512

  19. Bayesian network learning for natural hazard assessments

    NASA Astrophysics Data System (ADS)

    Vogel, Kristin

    2016-04-01

    Even though quite different in occurrence and consequences, from a modelling perspective many natural hazards share similar properties and challenges. Their complex nature as well as lacking knowledge about their driving forces and potential effects make their analysis demanding. On top of the uncertainty about the modelling framework, inaccurate or incomplete event observations and the intrinsic randomness of the natural phenomenon add up to different interacting layers of uncertainty, which require a careful handling. Thus, for reliable natural hazard assessments it is crucial not only to capture and quantify involved uncertainties, but also to express and communicate uncertainties in an intuitive way. Decision-makers, who often find it difficult to deal with uncertainties, might otherwise return to familiar (mostly deterministic) proceedings. In the scope of the DFG research training group „NatRiskChange" we apply the probabilistic framework of Bayesian networks for diverse natural hazard and vulnerability studies. The great potential of Bayesian networks was already shown in previous natural hazard assessments. Treating each model component as random variable, Bayesian networks aim at capturing the joint distribution of all considered variables. Hence, each conditional distribution of interest (e.g. the effect of precautionary measures on damage reduction) can be inferred. The (in-)dependencies between the considered variables can be learned purely data driven or be given by experts. Even a combination of both is possible. By translating the (in-)dependences into a graph structure, Bayesian networks provide direct insights into the workings of the system and allow to learn about the underlying processes. Besides numerous studies on the topic, learning Bayesian networks from real-world data remains challenging. In previous studies, e.g. on earthquake induced ground motion and flood damage assessments, we tackled the problems arising with continuous variables

  20. Network Plasticity as Bayesian Inference

    PubMed Central

    Legenstein, Robert; Maass, Wolfgang

    2015-01-01

    General results from statistical learning theory suggest to understand not only brain computations, but also brain plasticity as probabilistic inference. But a model for that has been missing. We propose that inherently stochastic features of synaptic plasticity and spine motility enable cortical networks of neurons to carry out probabilistic inference by sampling from a posterior distribution of network configurations. This model provides a viable alternative to existing models that propose convergence of parameters to maximum likelihood values. It explains how priors on weight distributions and connection probabilities can be merged optimally with learned experience, how cortical networks can generalize learned information so well to novel experiences, and how they can compensate continuously for unforeseen disturbances of the network. The resulting new theory of network plasticity explains from a functional perspective a number of experimental data on stochastic aspects of synaptic plasticity that previously appeared to be quite puzzling. PMID:26545099

  1. Software Health Management with Bayesian Networks

    NASA Technical Reports Server (NTRS)

    Mengshoel, Ole; Schumann, JOhann

    2011-01-01

    Most modern aircraft as well as other complex machinery is equipped with diagnostics systems for its major subsystems. During operation, sensors provide important information about the subsystem (e.g., the engine) and that information is used to detect and diagnose faults. Most of these systems focus on the monitoring of a mechanical, hydraulic, or electromechanical subsystem of the vehicle or machinery. Only recently, health management systems that monitor software have been developed. In this paper, we will discuss our approach of using Bayesian networks for Software Health Management (SWHM). We will discuss SWHM requirements, which make advanced reasoning capabilities for the detection and diagnosis important. Then we will present our approach to using Bayesian networks for the construction of health models that dynamically monitor a software system and is capable of detecting and diagnosing faults.

  2. Learning Bayesian Networks from Correlated Data

    PubMed Central

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

    2016-01-01

    Bayesian networks are probabilistic models that represent complex distributions in a modular way and have become very popular in many fields. There are many methods to build Bayesian networks from a random sample of independent and identically distributed observations. However, many observational studies are designed using some form of clustered sampling that introduces correlations between observations within the same cluster and ignoring this correlation typically inflates the rate of false positive associations. We describe a novel parameterization of Bayesian networks that uses random effects to model the correlation within sample units and can be used for structure and parameter learning from correlated data without inflating the Type I error rate. We compare different learning metrics using simulations and illustrate the method in two real examples: an analysis of genetic and non-genetic factors associated with human longevity from a family-based study, and an example of risk factors for complications of sickle cell anemia from a longitudinal study with repeated measures. PMID:27146517

  3. Learning Bayesian Networks from Correlated Data.

    PubMed

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

    2016-01-01

    Bayesian networks are probabilistic models that represent complex distributions in a modular way and have become very popular in many fields. There are many methods to build Bayesian networks from a random sample of independent and identically distributed observations. However, many observational studies are designed using some form of clustered sampling that introduces correlations between observations within the same cluster and ignoring this correlation typically inflates the rate of false positive associations. We describe a novel parameterization of Bayesian networks that uses random effects to model the correlation within sample units and can be used for structure and parameter learning from correlated data without inflating the Type I error rate. We compare different learning metrics using simulations and illustrate the method in two real examples: an analysis of genetic and non-genetic factors associated with human longevity from a family-based study, and an example of risk factors for complications of sickle cell anemia from a longitudinal study with repeated measures. PMID:27146517

  4. Node Augmentation Technique in Bayesian Network Evidence Analysis and Marshaling

    SciTech Connect

    Keselman, Dmitry; Tompkins, George H; Leishman, Deborah A

    2010-01-01

    Given a Bayesian network, sensitivity analysis is an important activity. This paper begins by describing a network augmentation technique which can simplifY the analysis. Next, we present two techniques which allow the user to determination the probability distribution of a hypothesis node under conditions of uncertain evidence; i.e. the state of an evidence node or nodes is described by a user specified probability distribution. Finally, we conclude with a discussion of three criteria for ranking evidence nodes based on their influence on a hypothesis node. All of these techniques have been used in conjunction with a commercial software package. A Bayesian network based on a directed acyclic graph (DAG) G is a graphical representation of a system of random variables that satisfies the following Markov property: any node (random variable) is independent of its non-descendants given the state of all its parents (Neapolitan, 2004). For simplicities sake, we consider only discrete variables with a finite number of states, though most of the conclusions may be generalized.

  5. Revealing ecological networks using Bayesian network inference algorithms.

    PubMed

    Milns, Isobel; Beale, Colin M; Smith, V Anne

    2010-07-01

    Understanding functional relationships within ecological networks can help reveal keys to ecosystem stability or fragility. Revealing these relationships is complicated by the difficulties of isolating variables or performing experimental manipulations within a natural ecosystem, and thus inferences are often made by matching models to observational data. Such models, however, require assumptions-or detailed measurements-of parameters such as birth and death rate, encounter frequency, territorial exclusion, and predation success. Here, we evaluate the use of a Bayesian network inference algorithm, which can reveal ecological networks based upon species and habitat abundance alone. We test the algorithm's performance and applicability on observational data of avian communities and habitat in the Peak District National Park, United Kingdom. The resulting networks correctly reveal known relationships among habitat types and known interspecific relationships. In addition, the networks produced novel insights into ecosystem structure and identified key species with high connectivity. Thus, Bayesian networks show potential for becoming a valuable tool in ecosystem analysis. PMID:20715607

  6. A Bayesian Networks approach to Operational Risk

    NASA Astrophysics Data System (ADS)

    Aquaro, V.; Bardoscia, M.; Bellotti, R.; Consiglio, A.; De Carlo, F.; Ferri, G.

    2010-04-01

    A system for Operational Risk management based on the computational paradigm of Bayesian Networks is presented. The algorithm allows the construction of a Bayesian Network targeted for each bank and takes into account in a simple and realistic way the correlations among different processes of the bank. The internal losses are averaged over a variable time horizon, so that the correlations at different times are removed, while the correlations at the same time are kept: the averaged losses are thus suitable to perform the learning of the network topology and parameters; since the main aim is to understand the role of the correlations among the losses, the assessments of domain experts are not used. The algorithm has been validated on synthetic time series. It should be stressed that the proposed algorithm has been thought for the practical implementation in a mid or small sized bank, since it has a small impact on the organizational structure of a bank and requires an investment in human resources which is limited to the computational area.

  7. Discovering Alzheimer Genetic Biomarkers Using Bayesian Networks.

    PubMed

    Sherif, Fayroz F; Zayed, Nourhan; Fakhr, Mahmoud

    2015-01-01

    Single nucleotide polymorphisms (SNPs) contribute most of the genetic variation to the human genome. SNPs associate with many complex and common diseases like Alzheimer's disease (AD). Discovering SNP biomarkers at different loci can improve early diagnosis and treatment of these diseases. Bayesian network provides a comprehensible and modular framework for representing interactions between genes or single SNPs. Here, different Bayesian network structure learning algorithms have been applied in whole genome sequencing (WGS) data for detecting the causal AD SNPs and gene-SNP interactions. We focused on polymorphisms in the top ten genes associated with AD and identified by genome-wide association (GWA) studies. New SNP biomarkers were observed to be significantly associated with Alzheimer's disease. These SNPs are rs7530069, rs113464261, rs114506298, rs73504429, rs7929589, rs76306710, and rs668134. The obtained results demonstrated the effectiveness of using BN for identifying AD causal SNPs with acceptable accuracy. The results guarantee that the SNP set detected by Markov blanket based methods has a strong association with AD disease and achieves better performance than both naïve Bayes and tree augmented naïve Bayes. Minimal augmented Markov blanket reaches accuracy of 66.13% and sensitivity of 88.87% versus 61.58% and 59.43% in naïve Bayes, respectively. PMID:26366461

  8. Discovering Alzheimer Genetic Biomarkers Using Bayesian Networks

    PubMed Central

    Sherif, Fayroz F.; Zayed, Nourhan; Fakhr, Mahmoud

    2015-01-01

    Single nucleotide polymorphisms (SNPs) contribute most of the genetic variation to the human genome. SNPs associate with many complex and common diseases like Alzheimer's disease (AD). Discovering SNP biomarkers at different loci can improve early diagnosis and treatment of these diseases. Bayesian network provides a comprehensible and modular framework for representing interactions between genes or single SNPs. Here, different Bayesian network structure learning algorithms have been applied in whole genome sequencing (WGS) data for detecting the causal AD SNPs and gene-SNP interactions. We focused on polymorphisms in the top ten genes associated with AD and identified by genome-wide association (GWA) studies. New SNP biomarkers were observed to be significantly associated with Alzheimer's disease. These SNPs are rs7530069, rs113464261, rs114506298, rs73504429, rs7929589, rs76306710, and rs668134. The obtained results demonstrated the effectiveness of using BN for identifying AD causal SNPs with acceptable accuracy. The results guarantee that the SNP set detected by Markov blanket based methods has a strong association with AD disease and achieves better performance than both naïve Bayes and tree augmented naïve Bayes. Minimal augmented Markov blanket reaches accuracy of 66.13% and sensitivity of 88.87% versus 61.58% and 59.43% in naïve Bayes, respectively. PMID:26366461

  9. Implementing Relevance Feedback in the Bayesian Network Retrieval Model.

    ERIC Educational Resources Information Center

    de Campos, Luis M.; Fernandez-Luna, Juan M.; Huete, Juan F.

    2003-01-01

    Discussion of relevance feedback in information retrieval focuses on a proposal for the Bayesian Network Retrieval Model. Bases the proposal on the propagation of partial evidences in the Bayesian network, representing new information obtained from the user's relevance judgments to compute the posterior relevance probabilities of the documents…

  10. Fuzzy Naive Bayesian for constructing regulated network with weights.

    PubMed

    Zhou, Xi Y; Tian, Xue W; Lim, Joon S

    2015-01-01

    In the data mining field, classification is a very crucial technology, and the Bayesian classifier has been one of the hotspots in classification research area. However, assumptions of Naive Bayesian and Tree Augmented Naive Bayesian (TAN) are unfair to attribute relations. Therefore, this paper proposes a new algorithm named Fuzzy Naive Bayesian (FNB) using neural network with weighted membership function (NEWFM) to extract regulated relations and weights. Then, we can use regulated relations and weights to construct a regulated network. Finally, we will classify the heart and Haberman datasets by the FNB network to compare with experiments of Naive Bayesian and TAN. The experiment results show that the FNB has a higher classification rate than Naive Bayesian and TAN. PMID:26405944

  11. Using consensus bayesian network to model the reactive oxygen species regulatory pathway.

    PubMed

    Hu, Liangdong; Wang, Limin

    2013-01-01

    Bayesian network is one of the most successful graph models for representing the reactive oxygen species regulatory pathway. With the increasing number of microarray measurements, it is possible to construct the bayesian network from microarray data directly. Although large numbers of bayesian network learning algorithms have been developed, when applying them to learn bayesian networks from microarray data, the accuracies are low due to that the databases they used to learn bayesian networks contain too few microarray data. In this paper, we propose a consensus bayesian network which is constructed by combining bayesian networks from relevant literatures and bayesian networks learned from microarray data. It would have a higher accuracy than the bayesian networks learned from one database. In the experiment, we validated the bayesian network combination algorithm on several classic machine learning databases and used the consensus bayesian network to model the Escherichia coli's ROS pathway. PMID:23457624

  12. 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.

  13. Statistical relationship discovery in SNP data using Bayesian networks

    NASA Astrophysics Data System (ADS)

    Szlendak, Pawel; Nowak, Robert M.

    2009-06-01

    The aim of this article is to present an application of Bayesian networks for discovery of affinity relationships based on genetic data. The presented solution uses a search and score algorithm to discover the Bayesian network structure which best fits the data i.e. the alleles of single nucleotide polymorphisms detected by DNA microarrays. The algorithm perceives structure learning as a combinatorial optimization problem. It is a randomized local search algorithm, which uses a Bayesian-Dirichlet scoring function. The algorithm's testing procedure encompasses tests on synthetic data, generated from given Bayesian networks by a forward sampling procedure as well as tests on real-world genetic data. The comparison of Bayesian networks generated by the application and the genetic evidence data confirms the usability of the presented methods.

  14. Inference of Gene Regulatory Network Based on Local Bayesian Networks

    PubMed Central

    Liu, Fei; Zhang, Shao-Wu; Guo, Wei-Feng; Chen, Luonan

    2016-01-01

    The inference of gene regulatory networks (GRNs) from expression data can mine the direct regulations among genes and gain deep insights into biological processes at a network level. During past decades, numerous computational approaches have been introduced for inferring the GRNs. However, many of them still suffer from various problems, e.g., Bayesian network (BN) methods cannot handle large-scale networks due to their high computational complexity, while information theory-based methods cannot identify the directions of regulatory interactions and also suffer from false positive/negative problems. To overcome the limitations, in this work we present a novel algorithm, namely local Bayesian network (LBN), to infer GRNs from gene expression data by using the network decomposition strategy and false-positive edge elimination scheme. Specifically, LBN algorithm first uses conditional mutual information (CMI) to construct an initial network or GRN, which is decomposed into a number of local networks or GRNs. Then, BN method is employed to generate a series of local BNs by selecting the k-nearest neighbors of each gene as its candidate regulatory genes, which significantly reduces the exponential search space from all possible GRN structures. Integrating these local BNs forms a tentative network or GRN by performing CMI, which reduces redundant regulations in the GRN and thus alleviates the false positive problem. The final network or GRN can be obtained by iteratively performing CMI and local BN on the tentative network. In the iterative process, the false or redundant regulations are gradually removed. When tested on the benchmark GRN datasets from DREAM challenge as well as the SOS DNA repair network in E.coli, our results suggest that LBN outperforms other state-of-the-art methods (ARACNE, GENIE3 and NARROMI) significantly, with more accurate and robust performance. In particular, the decomposition strategy with local Bayesian networks not only effectively reduce

  15. Inference of Gene Regulatory Network Based on Local Bayesian Networks.

    PubMed

    Liu, Fei; Zhang, Shao-Wu; Guo, Wei-Feng; Wei, Ze-Gang; Chen, Luonan

    2016-08-01

    The inference of gene regulatory networks (GRNs) from expression data can mine the direct regulations among genes and gain deep insights into biological processes at a network level. During past decades, numerous computational approaches have been introduced for inferring the GRNs. However, many of them still suffer from various problems, e.g., Bayesian network (BN) methods cannot handle large-scale networks due to their high computational complexity, while information theory-based methods cannot identify the directions of regulatory interactions and also suffer from false positive/negative problems. To overcome the limitations, in this work we present a novel algorithm, namely local Bayesian network (LBN), to infer GRNs from gene expression data by using the network decomposition strategy and false-positive edge elimination scheme. Specifically, LBN algorithm first uses conditional mutual information (CMI) to construct an initial network or GRN, which is decomposed into a number of local networks or GRNs. Then, BN method is employed to generate a series of local BNs by selecting the k-nearest neighbors of each gene as its candidate regulatory genes, which significantly reduces the exponential search space from all possible GRN structures. Integrating these local BNs forms a tentative network or GRN by performing CMI, which reduces redundant regulations in the GRN and thus alleviates the false positive problem. The final network or GRN can be obtained by iteratively performing CMI and local BN on the tentative network. In the iterative process, the false or redundant regulations are gradually removed. When tested on the benchmark GRN datasets from DREAM challenge as well as the SOS DNA repair network in E.coli, our results suggest that LBN outperforms other state-of-the-art methods (ARACNE, GENIE3 and NARROMI) significantly, with more accurate and robust performance. In particular, the decomposition strategy with local Bayesian networks not only effectively reduce

  16. Filtering in Hybrid Dynamic Bayesian Networks

    NASA Technical Reports Server (NTRS)

    Andersen, Morten Nonboe; Andersen, Rasmus Orum; Wheeler, Kevin

    2000-01-01

    We implement a 2-time slice dynamic Bayesian network (2T-DBN) framework and make a 1-D state estimation simulation, an extension of the experiment in (v.d. Merwe et al., 2000) and compare different filtering techniques. Furthermore, we demonstrate experimentally that inference in a complex hybrid DBN is possible by simulating fault detection in a watertank system, an extension of the experiment in (Koller & Lerner, 2000) using a hybrid 2T-DBN. In both experiments, we perform approximate inference using standard filtering techniques, Monte Carlo methods and combinations of these. In the watertank simulation, we also demonstrate the use of 'non-strict' Rao-Blackwellisation. We show that the unscented Kalman filter (UKF) and UKF in a particle filtering framework outperform the generic particle filter, the extended Kalman filter (EKF) and EKF in a particle filtering framework with respect to accuracy in terms of estimation RMSE and sensitivity with respect to choice of network structure. Especially we demonstrate the superiority of UKF in a PF framework when our beliefs of how data was generated are wrong. Furthermore, we investigate the influence of data noise in the watertank simulation using UKF and PFUKD and show that the algorithms are more sensitive to changes in the measurement noise level that the process noise level. Theory and implementation is based on (v.d. Merwe et al., 2000).

  17. Filtering in Hybrid Dynamic Bayesian Networks

    NASA Technical Reports Server (NTRS)

    Andersen, Morten Nonboe; Andersen, Rasmus Orum; Wheeler, Kevin

    2004-01-01

    We demonstrate experimentally that inference in a complex hybrid Dynamic Bayesian Network (DBN) is possible using the 2 - T i e Slice DBN (2T-DBN) from [Koller & Lerner, 20001 to model fault detection in a watertank system. In [Koller & Lerner, 20001 a generic Particle Filter (PF) is used for inference. We extend the experiment and perform approximate inference using The Extended Kalman Filter (EKF) and the Unscented Kalman Filter (UKF). Furthermore, we combine these techniques in a 'non-strict' Rao-Blackwellisation framework and apply it to the watertank system. We show that UKF and UKF in a PF framework outperfom the generic PF, EKF and EKF in a PF framework with respect to accuracy and robustness in terms of estimation RMSE. Especially we demonstrate the superiority of UKF in a PF framework when our beliefs of how data was generated are wrong. We also show that the choice of network structure is very important for the performance of the generic PF and the EKF algorithms, but not for the UKF algorithms. Furthermore, we investigate the influence of data noise in the water[ank simulation. Theory and implementation is based on the theory presented.

  18. An empirical evaluation of Bayesian networks derived from fault trees

    NASA Astrophysics Data System (ADS)

    Strasser, Shane; Sheppard, John

    Fault Isolation Manuals (FIMs) are derived from a type of decision tree and play an important role in maintenance troubleshooting of large systems. However, there are some drawbacks to using decision trees for maintenance, such as requiring a static order of tests to reach a conclusion. One method to overcome these limitations is by converting FIMs to Bayesian networks. However, it has been shown that Bayesian networks derived from FIMs will not contain the entire set of fault and alarm relationships present in the system from which the FIM was developed. In this paper we analyze Bayesian networks that have been derived from FIMs and report on several measurements, such as accuracy, relative probability of target diagnoses, diagnosis rank, and KL-divergence. Based on our results, we found that even with incomplete information, the Bayesian networks derived from the FIMs were still able to perform reasonably well.

  19. Using Bayesian Networks to Improve Knowledge Assessment

    ERIC Educational Resources Information Center

    Millan, Eva; Descalco, Luis; Castillo, Gladys; Oliveira, Paula; Diogo, Sandra

    2013-01-01

    In this paper, we describe the integration and evaluation of an existing generic Bayesian student model (GBSM) into an existing computerized testing system within the Mathematics Education Project (PmatE--Projecto Matematica Ensino) of the University of Aveiro. This generic Bayesian student model had been previously evaluated with simulated…

  20. Bayesian Networks for enterprise risk assessment

    NASA Astrophysics Data System (ADS)

    Bonafede, C. E.; Giudici, P.

    2007-08-01

    According to different typologies of activity and priority, risks can assume diverse meanings and it can be assessed in different ways. Risk, in general, is measured in terms of a probability combination of an event (frequency) and its consequence (impact). To estimate the frequency and the impact (severity) historical data or expert opinions (either qualitative or quantitative data) are used. Moreover, qualitative data must be converted in numerical values or bounds to be used in the model. In the case of enterprise risk assessment the considered risks are, for instance, strategic, operational, legal and of image, which many times are difficult to be quantified. So in most cases only expert data, gathered by scorecard approaches, are available for risk analysis. The Bayesian Networks (BNs) are a useful tool to integrate different information and in particular to study the risk's joint distribution by using data collected from experts. In this paper we want to show a possible approach for building a BN in the particular case in which only prior probabilities of node states and marginal correlations between nodes are available, and when the variables have only two states.

  1. Multiple quantitative trait analysis using bayesian networks.

    PubMed

    Scutari, Marco; Howell, Phil; Balding, David J; Mackay, Ian

    2014-09-01

    Models for genome-wide prediction and association studies usually target a single phenotypic trait. However, in animal and plant genetics it is common to record information on multiple phenotypes for each individual that will be genotyped. Modeling traits individually disregards the fact that they are most likely associated due to pleiotropy and shared biological basis, thus providing only a partial, confounded view of genetic effects and phenotypic interactions. In this article we use data from a Multiparent Advanced Generation Inter-Cross (MAGIC) winter wheat population to explore Bayesian networks as a convenient and interpretable framework for the simultaneous modeling of multiple quantitative traits. We show that they are equivalent to multivariate genetic best linear unbiased prediction (GBLUP) and that they are competitive with single-trait elastic net and single-trait GBLUP in predictive performance. Finally, we discuss their relationship with other additive-effects models and their advantages in inference and interpretation. MAGIC populations provide an ideal setting for this kind of investigation because the very low population structure and large sample size result in predictive models with good power and limited confounding due to relatedness. PMID:25236454

  2. Impact assessment of extreme storm events using a Bayesian network

    USGS Publications Warehouse

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

    2012-01-01

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

  3. Semantic segmentation based on neural network and Bayesian network

    NASA Astrophysics Data System (ADS)

    Ge, Wenying; Liu, Guoying

    2013-10-01

    It is rather difficult for low-level visual features to describe the need for specific applications of image understanding, which results in the inconsistency between vision information and application need. In this paper, a new model is proposed to reduce this gap by combining low-level visual features with semantic features. It uses the output of neural network as the semantic feature, which is accompanied with the priori label features to describe the image after making normalization. And then, the proposed method employs Potts to model the distribution of label priori, and utilizes the Bayesian network to classify images. Several experiments on both synthetic and real images have verified that this method can get more accurate segmentation.

  4. Real-time prediction of acute cardiovascular events using hardware-implemented Bayesian networks.

    PubMed

    Tylman, Wojciech; Waszyrowski, Tomasz; Napieralski, Andrzej; Kamiński, Marek; Trafidło, Tamara; Kulesza, Zbigniew; Kotas, Rafał; Marciniak, Paweł; Tomala, Radosław; Wenerski, Maciej

    2016-02-01

    This paper presents a decision support system that aims to estimate a patient׳s general condition and detect situations which pose an immediate danger to the patient׳s health or life. The use of this system might be especially important in places such as accident and emergency departments or admission wards, where a small medical team has to take care of many patients in various general conditions. Particular stress is laid on cardiovascular and pulmonary conditions, including those leading to sudden cardiac arrest. The proposed system is a stand-alone microprocessor-based device that works in conjunction with a standard vital signs monitor, which provides input signals such as temperature, blood pressure, pulseoxymetry, ECG, and ICG. The signals are preprocessed and analysed by a set of artificial intelligence algorithms, the core of which is based on Bayesian networks. The paper focuses on the construction and evaluation of the Bayesian network, both its structure and numerical specification. PMID:26456181

  5. 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.

  6. Bayesian networks as a tool for epidemiological systems analysis

    NASA Astrophysics Data System (ADS)

    Lewis, F. I.

    2012-11-01

    Bayesian network analysis is a form of probabilistic modeling which derives from empirical data a directed acyclic graph (DAG) describing the dependency structure between random variables. Bayesian networks are increasingly finding application in areas such as computational and systems biology, and more recently in epidemiological analyses. The key distinction between standard empirical modeling approaches, such as generalised linear modeling, and Bayesian network analyses is that the latter attempts not only to identify statistically associated variables, but to additionally, and empirically, separate these into those directly and indirectly dependent with one or more outcome variables. Such discrimination is vastly more ambitious but has the potential to reveal far more about key features of complex disease systems. Applying Bayesian network modeling to biological and medical data has considerable computational demands, combined with the need to ensure robust model selection given the vast model space of possible DAGs. These challenges require the use of approximation techniques, such as the Laplace approximation, Markov chain Monte Carlo simulation and parametric bootstrapping, along with computational parallelization. A case study in structure discovery - identification of an optimal DAG for given data - is presented which uses additive Bayesian networks to explore veterinary disease data of industrial and medical relevance.

  7. Exploring the Noisy Threshold Function in Designing Bayesian Networks

    NASA Astrophysics Data System (ADS)

    Jurgelenaite, Rasa; Lucas, Peter; Heskes, Tom

    Causal independence modelling is a well-known method both for reducing the size of probability tables and for explaining the underlying mechanisms in Bayesian networks. Many Bayesian network models incorporate causal independence assumptions; however, only the noisy OR and noisy AND, two examples of causal independence models, are used in practice. Their underlying assumption that either at least one cause, or all causes together, give rise to an effect, however, seems unnecessarily restrictive. In the present paper a new, more flexible, causal independence model is proposed, based on the Boolean threshold function. A connection is established between conditional probability distributions based on the noisy threshold model and Poisson binomial distributions, and the basic properties of this probability distribution are studied in some depth. The successful application of the noisy threshold model in the refinement of a Bayesian network for the diagnosis and treatment of ventilator-associated pneumonia demo nstrates the practical value of the presented theory.

  8. Bayesian approach for neural networks--review and case studies.

    PubMed

    Lampinen, J; Vehtari, A

    2001-04-01

    We give a short review on the Bayesian approach for neural network learning and demonstrate the advantages of the approach in three real applications. We discuss the Bayesian approach with emphasis on the role of prior knowledge in Bayesian models and in classical error minimization approaches. The generalization capability of a statistical model, classical or Bayesian, is ultimately based on the prior assumptions. The Bayesian approach permits propagation of uncertainty in quantities which are unknown to other assumptions in the model, which may be more generally valid or easier to guess in the problem. The case problem studied in this paper include a regression, a classification, and an inverse problem. In the most thoroughly analyzed regression problem, the best models were those with less restrictive priors. This emphasizes the major advantage of the Bayesian approach, that we are not forced to guess attributes that are unknown, such as the number of degrees of freedom in the model, non-linearity of the model with respect to each input variable, or the exact form for the distribution of the model residuals. PMID:11341565

  9. Implementation of an Adaptive Learning System Using a Bayesian Network

    ERIC Educational Resources Information Center

    Yasuda, Keiji; Kawashima, Hiroyuki; Hata, Yoko; Kimura, Hiroaki

    2015-01-01

    An adaptive learning system is proposed that incorporates a Bayesian network to efficiently gauge learners' understanding at the course-unit level. Also, learners receive content that is adapted to their measured level of understanding. The system works on an iPad via the Edmodo platform. A field experiment using the system in an elementary school…

  10. CausalTrail: Testing hypothesis using causal Bayesian networks

    PubMed Central

    Trampert, Patrick; Lenhof, Hans-Peter

    2015-01-01

    Summary Causal Bayesian Networks are a special class of Bayesian networks in which the hierarchy directly encodes the causal relationships between the variables. This allows to compute the effect of interventions, which are external changes to the system, caused by e.g. gene knockouts or an administered drug. Whereas numerous packages for constructing causal Bayesian networks are available, hardly any program targeted at downstream analysis exists. In this paper we present CausalTrail, a tool for performing reasoning on causal Bayesian networks using the do-calculus. CausalTrail's features include multiple data import methods, a flexible query language for formulating hypotheses, as well as an intuitive graphical user interface. The program is able to account for missing data and thus can be readily applied in multi-omics settings where it is common that not all measurements are performed for all samples. Availability and Implementation CausalTrail is implemented in C++ using the Boost and Qt5 libraries. It can be obtained from https://github.com/dstoeckel/causaltrail PMID:26913195

  11. 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…

  12. Model Criticism of Bayesian Networks with Latent Variables.

    ERIC Educational Resources Information Center

    Williamson, David M.; Mislevy, Robert J.; Almond, Russell G.

    This study investigated statistical methods for identifying errors in Bayesian networks (BN) with latent variables, as found in intelligent cognitive assessments. BN, commonly used in artificial intelligence systems, are promising mechanisms for scoring constructed-response examinations. The success of an intelligent assessment or tutoring system…

  13. Nursing Home Care Quality: Insights from a Bayesian Network Approach

    ERIC Educational Resources Information Center

    Goodson, Justin; Jang, Wooseung; Rantz, Marilyn

    2008-01-01

    Purpose: The purpose of this research is twofold. The first purpose is to utilize a new methodology (Bayesian networks) for aggregating various quality indicators to measure the overall quality of care in nursing homes. The second is to provide new insight into the relationships that exist among various measures of quality and how such measures…

  14. Comparison of Lauritzen-Spiegelhalter and successive restrictions algorithms for computing probability distributions in Bayesian networks

    NASA Astrophysics Data System (ADS)

    Smail, Linda

    2016-06-01

    The basic task of any probabilistic inference system in Bayesian networks is computing the posterior probability distribution for a subset or subsets of random variables, given values or evidence for some other variables from the same Bayesian network. Many methods and algorithms have been developed to exact and approximate inference in Bayesian networks. This work compares two exact inference methods in Bayesian networks-Lauritzen-Spiegelhalter and the successive restrictions algorithm-from the perspective of computational efficiency. The two methods were applied for comparison to a Chest Clinic Bayesian Network. Results indicate that the successive restrictions algorithm shows more computational efficiency than the Lauritzen-Spiegelhalter algorithm.

  15. Theory-independent limits on correlations from generalized Bayesian networks

    NASA Astrophysics Data System (ADS)

    Henson, Joe; Lal, Raymond; Pusey, Matthew F.

    2014-11-01

    Bayesian networks provide a powerful tool for reasoning about probabilistic causation, used in many areas of science. They are, however, intrinsically classical. In particular, Bayesian networks naturally yield the Bell inequalities. Inspired by this connection, we generalize the formalism of classical Bayesian networks in order to investigate non-classical correlations in arbitrary causal structures. Our framework of ‘generalized Bayesian networks’ replaces latent variables with the resources of any generalized probabilistic theory, most importantly quantum theory, but also, for example, Popescu-Rohrlich boxes. We obtain three main sets of results. Firstly, we prove that all of the observable conditional independences required by the classical theory also hold in our generalization; to obtain this, we extend the classical d-separation theorem to our setting. Secondly, we find that the theory-independent constraints on probabilities can go beyond these conditional independences. For example we find that no probabilistic theory predicts perfect correlation between three parties using only bipartite common causes. Finally, we begin a classification of those causal structures, such as the Bell scenario, that may yield a separation between classical, quantum and general-probabilistic correlations.

  16. Using Bayesian networks to support decision-focused information retrieval

    SciTech Connect

    Lehner, P.; Elsaesser, C.; Seligman, L.

    1996-12-31

    This paper has described an approach to controlling the process of pulling data/information from distributed data bases in a way that is specific to a persons specific decision making context. Our prototype implementation of this approach uses a knowledge-based planner to generate a plan, an automatically constructed Bayesian network to evaluate the plan, specialized processing of the network to derive key information items that would substantially impact the evaluation of the plan (e.g., determine that replanning is needed), automated construction of Standing Requests for Information (SRIs) which are automated functions that monitor changes and trends in distributed data base that are relevant to the key information items. This emphasis of this paper is on how Bayesian networks are used.

  17. THREAT ANTICIPATION AND DECEPTIVE REASONING USING BAYESIAN BELIEF NETWORKS

    SciTech Connect

    Allgood, Glenn O; Olama, Mohammed M; Lake, Joe E

    2009-01-01

    Recent events highlight the need for tools to anticipate threats posed by terrorists. Assessing these threats requires combining information from disparate data sources such as analytic models, simulations, historical data, sensor networks, and user judgments. These disparate data can be combined in a coherent, analytically defensible, and understandable manner using a Bayesian belief network (BBN). In this paper, we develop a BBN threat anticipatory model based on a deceptive reasoning algorithm using a network engineering process that treats the probability distributions of the BBN nodes within the broader context of the system development process.

  18. Conjunctive management of multi-reservoir network system and groundwater system

    NASA Astrophysics Data System (ADS)

    Mani, A.; Tsai, F. T. C.

    2015-12-01

    This study develops a successive mixed-integer linear fractional programming (successive MILFP) method to conjunctively manage water resources provided by a multi-reservoir network system and a groundwater system. The conjunctive management objectives are to maximize groundwater withdrawals and maximize reservoir storages while satisfying water demands and raising groundwater level to a target level. The decision variables in the management problem are reservoir releases and spills, network flows and groundwater pumping rates. Using the fractional programming approach, the objective function is defined as a ratio of total groundwater withdraws to total reservoir storage deficits from the maximum storages. Maximizing this ratio function tends to maximizing groundwater use and minimizing surface water use. This study introduces a conditional constraint on groundwater head in order to sustain aquifers from overpumping: if current groundwater level is less than a target level, groundwater head at the next time period has to be raised; otherwise, it is allowed to decrease up to a certain extent. This conditional constraint is formulated into a set of mixed binary nonlinear constraints and results in a mixed-integer nonlinear fractional programming (MINLFP) problem. To solve the MINLFP problem, we first use the response matrix approach to linearize groundwater head with respect to pumping rate and reduce the problem to an MILFP problem. Using the Charnes-Cooper transformation, the MILFP is transformed to an equivalent mixed-integer linear programming (MILP). The solution of the MILP is successively updated by updating the response matrix in every iteration. The study uses IBM CPLEX to solve the MILP problem. The methodology is applied to water resources management in northern Louisiana. This conjunctive management approach aims to recover the declining groundwater level of the stressed Sparta aquifer by using surface water from a network of four reservoirs as an

  19. A system for automated general medical diagnosis using Bayesian networks.

    PubMed

    Zagorecki, Adam; Orzechowski, Piotr; Hołownia, Katarzyna

    2013-01-01

    In this paper we present a computer-assisted diagnostic system for general medical diagnosis developed using Bayesian network methodology and a medical data base created by experts. The system is intended for the general public as a self-diagnostic tool and is available online free of charge (currently only in Polish, with an English version to be released soon). It serves as an educational self-diagnostic tool intended to encourage the user to visit a doctor if the system so suggests, as is most often the case. In this paper we discuss the underlying modeling principles: assumptions behind Bayesian network architecture, solutions to scalability challenges, and computation performance. The distributed software architecture is presented, and finally, initial results based on over 97,000 diagnoses are discussed. The results suggest that the most common health problems for the young generation in Poland (typical user profile) are those resulting from stress and an unhealthy lifestyle. PMID:23920597

  20. Predicting Software Suitability Using a Bayesian Belief Network

    NASA Technical Reports Server (NTRS)

    Beaver, Justin M.; Schiavone, Guy A.; Berrios, Joseph S.

    2005-01-01

    The ability to reliably predict the end quality of software under development presents a significant advantage for a development team. It provides an opportunity to address high risk components earlier in the development life cycle, when their impact is minimized. This research proposes a model that captures the evolution of the quality of a software product, and provides reliable forecasts of the end quality of the software being developed in terms of product suitability. Development team skill, software process maturity, and software problem complexity are hypothesized as driving factors of software product quality. The cause-effect relationships between these factors and the elements of software suitability are modeled using Bayesian Belief Networks, a machine learning method. This research presents a Bayesian Network for software quality, and the techniques used to quantify the factors that influence and represent software quality. The developed model is found to be effective in predicting the end product quality of small-scale software development efforts.

  1. Understanding disease processes by partitioned dynamic Bayesian networks.

    PubMed

    Bueno, Marcos L P; Hommersom, Arjen; Lucas, Peter J F; Lappenschaar, Martijn; Janzing, Joost G E

    2016-06-01

    For many clinical problems in patients the underlying pathophysiological process changes in the course of time as a result of medical interventions. In model building for such problems, the typical scarcity of data in a clinical setting has been often compensated by utilizing time homogeneous models, such as dynamic Bayesian networks. As a consequence, the specificities of the underlying process are lost in the obtained models. In the current work, we propose the new concept of partitioned dynamic Bayesian networks to capture distribution regime changes, i.e. time non-homogeneity, benefiting from an intuitive and compact representation with the solid theoretical foundation of Bayesian network models. In order to balance specificity and simplicity in real-world scenarios, we propose a heuristic algorithm to search and learn these non-homogeneous models taking into account a preference for less complex models. An extensive set of experiments were ran, in which simulating experiments show that the heuristic algorithm was capable of constructing well-suited solutions, in terms of goodness of fit and statistical distance to the original distributions, in consonance with the underlying processes that generated data, whether it was homogeneous or non-homogeneous. Finally, a study case on psychotic depression was conducted using non-homogeneous models learned by the heuristic, leading to insightful answers for clinically relevant questions concerning the dynamics of this mental disorder. PMID:27182055

  2. Bayesian network models for error detection in radiotherapy plans.

    PubMed

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

    2015-04-01

    The purpose of this study is to design and develop a probabilistic network for detecting errors in radiotherapy plans for use at the time of initial plan verification. Our group has initiated a multi-pronged approach to reduce these errors. We report on our development of Bayesian models of radiotherapy plans. Bayesian networks consist of joint probability distributions that define the probability of one event, given some set of other known information. Using the networks, we find the probability of obtaining certain radiotherapy parameters, given a set of initial clinical information. A low probability in a propagated network then corresponds to potential errors to be flagged for investigation. To build our networks we first interviewed medical physicists and other domain experts to identify the relevant radiotherapy concepts and their associated interdependencies and to construct a network topology. Next, to populate the network's conditional probability tables, we used the Hugin Expert software to learn parameter distributions from a subset of de-identified data derived from a radiation oncology based clinical information database system. These data represent 4990 unique prescription cases over a 5 year period. Under test case scenarios with approximately 1.5% introduced error rates, network performance produced areas under the ROC curve of 0.88, 0.98, and 0.89 for the lung, brain and female breast cancer error detection networks, respectively. Comparison of the brain network to human experts performance (AUC of 0.90 ± 0.01) shows the Bayes network model performs better than domain experts under the same test conditions. Our results demonstrate the feasibility and effectiveness of comprehensive probabilistic models as part of decision support systems for improved detection of errors in initial radiotherapy plan verification procedures. PMID:25768885

  3. Markov Chain Monte Carlo Bayesian Learning for Neural Networks

    NASA Technical Reports Server (NTRS)

    Goodrich, Michael S.

    2011-01-01

    Conventional training methods for neural networks involve starting al a random location in the solution space of the network weights, navigating an error hyper surface to reach a minimum, and sometime stochastic based techniques (e.g., genetic algorithms) to avoid entrapment in a local minimum. It is further typically necessary to preprocess the data (e.g., normalization) to keep the training algorithm on course. Conversely, Bayesian based learning is an epistemological approach concerned with formally updating the plausibility of competing candidate hypotheses thereby obtaining a posterior distribution for the network weights conditioned on the available data and a prior distribution. In this paper, we developed a powerful methodology for estimating the full residual uncertainty in network weights and therefore network predictions by using a modified Jeffery's prior combined with a Metropolis Markov Chain Monte Carlo method.

  4. Pinkeye (Conjunctivitis)

    MedlinePlus

    ... How Can I Help a Friend Who Cuts? Pinkeye (Conjunctivitis) KidsHealth > For Teens > Pinkeye (Conjunctivitis) Print A A ... are common with allergic conjunctivitis. How Long Is Conjunctivitis Contagious? Conjunctivitis that's caused by bacteria is contagious ...

  5. Framework for network modularization and Bayesian network analysis to investigate the perturbed metabolic network

    PubMed Central

    2011-01-01

    Background Genome-scale metabolic network models have contributed to elucidating biological phenomena, and predicting gene targets to engineer for biotechnological applications. With their increasing importance, their precise network characterization has also been crucial for better understanding of the cellular physiology. Results We herein introduce a framework for network modularization and Bayesian network analysis (FMB) to investigate organism’s metabolism under perturbation. FMB reveals direction of influences among metabolic modules, in which reactions with similar or positively correlated flux variation patterns are clustered, in response to specific perturbation using metabolic flux data. With metabolic flux data calculated by constraints-based flux analysis under both control and perturbation conditions, FMB, in essence, reveals the effects of specific perturbations on the biological system through network modularization and Bayesian network analysis at metabolic modular level. As a demonstration, this framework was applied to the genetically perturbed Escherichia coli metabolism, which is a lpdA gene knockout mutant, using its genome-scale metabolic network model. Conclusions After all, it provides alternative scenarios of metabolic flux distributions in response to the perturbation, which are complementary to the data obtained from conventionally available genome-wide high-throughput techniques or metabolic flux analysis. PMID:22784571

  6. Bayesian network models for error detection in radiotherapy plans

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  7. Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent

    PubMed Central

    Wen, Dingqiao; Yu, Yun; Nakhleh, Luay

    2016-01-01

    The multispecies coalescent (MSC) is a statistical framework that models how gene genealogies grow within the branches of a species tree. The field of computational phylogenetics has witnessed an explosion in the development of methods for species tree inference under MSC, owing mainly to the accumulating evidence of incomplete lineage sorting in phylogenomic analyses. However, the evolutionary history of a set of genomes, or species, could be reticulate due to the occurrence of evolutionary processes such as hybridization or horizontal gene transfer. We report on a novel method for Bayesian inference of genome and species phylogenies under the multispecies network coalescent (MSNC). This framework models gene evolution within the branches of a phylogenetic network, thus incorporating reticulate evolutionary processes, such as hybridization, in addition to incomplete lineage sorting. As phylogenetic networks with different numbers of reticulation events correspond to points of different dimensions in the space of models, we devise a reversible-jump Markov chain Monte Carlo (RJMCMC) technique for sampling the posterior distribution of phylogenetic networks under MSNC. We implemented the methods in the publicly available, open-source software package PhyloNet and studied their performance on simulated and biological data. The work extends the reach of Bayesian inference to phylogenetic networks and enables new evolutionary analyses that account for reticulation. PMID:27144273

  8. Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent.

    PubMed

    Wen, Dingqiao; Yu, Yun; Nakhleh, Luay

    2016-05-01

    The multispecies coalescent (MSC) is a statistical framework that models how gene genealogies grow within the branches of a species tree. The field of computational phylogenetics has witnessed an explosion in the development of methods for species tree inference under MSC, owing mainly to the accumulating evidence of incomplete lineage sorting in phylogenomic analyses. However, the evolutionary history of a set of genomes, or species, could be reticulate due to the occurrence of evolutionary processes such as hybridization or horizontal gene transfer. We report on a novel method for Bayesian inference of genome and species phylogenies under the multispecies network coalescent (MSNC). This framework models gene evolution within the branches of a phylogenetic network, thus incorporating reticulate evolutionary processes, such as hybridization, in addition to incomplete lineage sorting. As phylogenetic networks with different numbers of reticulation events correspond to points of different dimensions in the space of models, we devise a reversible-jump Markov chain Monte Carlo (RJMCMC) technique for sampling the posterior distribution of phylogenetic networks under MSNC. We implemented the methods in the publicly available, open-source software package PhyloNet and studied their performance on simulated and biological data. The work extends the reach of Bayesian inference to phylogenetic networks and enables new evolutionary analyses that account for reticulation. PMID:27144273

  9. Bayesian approach for network modeling of brain structural features

    NASA Astrophysics Data System (ADS)

    Joshi, Anand A.; Joshi, Shantanu H.; Leahy, Richard M.; Shattuck, David W.; Dinov, Ivo; Toga, Arthur W.

    2010-03-01

    Brain connectivity patterns are useful in understanding brain function and organization. Anatomical brain connectivity is largely determined using the physical synaptic connections between neurons. In contrast statistical brain connectivity in a given brain population refers to the interaction and interdependencies of statistics of multitudes of brain features including cortical area, volume, thickness etc. Traditionally, this dependence has been studied by statistical correlations of cortical features. In this paper, we propose the use of Bayesian network modeling for inferring statistical brain connectivity patterns that relate to causal (directed) as well as non-causal (undirected) relationships between cortical surface areas. We argue that for multivariate cortical data, the Bayesian model provides for a more accurate representation by removing the effect of confounding correlations that get introduced due to canonical dependence between the data. Results are presented for a population of 466 brains, where a SEM (structural equation modeling) approach is used to generate a Bayesian network model, as well as a dependency graph for the joint distribution of cortical areas.

  10. Mobile sensor network noise reduction and recalibration using a Bayesian network

    NASA Astrophysics Data System (ADS)

    Xiang, Y.; Tang, Y.; Zhu, W.

    2016-02-01

    People are becoming increasingly interested in mobile air quality sensor network applications. By eliminating the inaccuracies caused by spatial and temporal heterogeneity of pollutant distributions, this method shows great potential for atmospheric research. However, systems based on low-cost air quality sensors often suffer from sensor noise and drift. For the sensing systems to operate stably and reliably in real-world applications, those problems must be addressed. In this work, we exploit the correlation of different types of sensors caused by cross sensitivity to help identify and correct the outlier readings. By employing a Bayesian network based system, we are able to recover the erroneous readings and recalibrate the drifted sensors simultaneously. Our method improves upon the state-of-art Bayesian belief network techniques by incorporating the virtual evidence and adjusting the sensor calibration functions recursively.Specifically, we have (1) designed a system based on the Bayesian belief network to detect and recover the abnormal readings, (2) developed methods to update the sensor calibration functions infield without requirement of ground truth, and (3) extended the Bayesian network with virtual evidence for infield sensor recalibration. To validate our technique, we have tested our technique with metal oxide sensors measuring NO2, CO, and O3 in a real-world deployment. Compared with the existing Bayesian belief network techniques, results based on our experiment setup demonstrate that our system can reduce error by 34.1 % and recover 4 times more data on average.

  11. Validation of the thermal challenge problem using Bayesian Belief Networks.

    SciTech Connect

    McFarland, John; Swiler, Laura Painton

    2005-11-01

    The thermal challenge problem has been developed at Sandia National Laboratories as a testbed for demonstrating various types of validation approaches and prediction methods. This report discusses one particular methodology to assess the validity of a computational model given experimental data. This methodology is based on Bayesian Belief Networks (BBNs) and can incorporate uncertainty in experimental measurements, in physical quantities, and model uncertainties. The approach uses the prior and posterior distributions of model output to compute a validation metric based on Bayesian hypothesis testing (a Bayes' factor). This report discusses various aspects of the BBN, specifically in the context of the thermal challenge problem. A BBN is developed for a given set of experimental data in a particular experimental configuration. The development of the BBN and the method for ''solving'' the BBN to develop the posterior distribution of model output through Monte Carlo Markov Chain sampling is discussed in detail. The use of the BBN to compute a Bayes' factor is demonstrated.

  12. A Bayesian Network Approach to Modeling Learning Progressions and Task Performance. CRESST Report 776

    ERIC Educational Resources Information Center

    West, Patti; Rutstein, Daisy Wise; Mislevy, Robert J.; Liu, Junhui; Choi, Younyoung; Levy, Roy; Crawford, Aaron; DiCerbo, Kristen E.; Chappel, Kristina; Behrens, John T.

    2010-01-01

    A major issue in the study of learning progressions (LPs) is linking student performance on assessment tasks to the progressions. This report describes the challenges faced in making this linkage using Bayesian networks to model LPs in the field of computer networking. The ideas are illustrated with exemplar Bayesian networks built on Cisco…

  13. A Dynamic Bayesian Network for Mt. Etna Volcano State Assessment

    NASA Astrophysics Data System (ADS)

    Cannavo', Flavio; Cassisi, Carmelo; Aliotta, Marco; Cannata, Andrea; Montalto, Placido; Prestifilippo, Michele

    2015-04-01

    Nowadays, the real-time monitoring of Mt. Etna volcano is mostly delegated to one or more human experts in volcanology, who interpret the data coming from different kind of monitoring networks. Among their duties, the evaluation of the volcano state is one of the most critical task for civil protection purposes. Unfortunately, the coupling of highly non-linear and complex volcanic dynamic processes leads to measurable effects that can show a large variety of different behaviors. Moreover, due to intrinsic uncertainties and possible failures in some recorded data the volcano state needs to be expressed in probabilistic terms, thus making the fast volcano state assessment sometimes impracticable for the personnel on duty at the 24h control room. With the aim of aiding the personnel on duty in volcano monitoring, here we present an expert system approach based on Bayesian networks to estimate automatically the ongoing volcano state from all the available different kind of measurements. A Bayesian network is a static probabilistic graphical model that represents a set of random variables and their conditional dependencies via a directed acyclic graph. We consider model variables both the measurements and the possible states of the volcano. In order to include the time in the model, we use a Dynamic Bayesian Network (DBN) which relates variables to each other over adjacent time steps. The model output consists of an estimation of the probability distribution of the feasible volcano states. We build the model by considering the long record of data from 2011 to 2014 and we cross-validate it by considering 3 years for parameter estimation and 1 year for testing in simulated real-time mode.

  14. Discriminating complex networks through supervised NDR and Bayesian classifier

    NASA Astrophysics Data System (ADS)

    Yan, Ke-Sheng; Rong, Li-Li; Yu, Kai

    2016-12-01

    Discriminating complex networks is a particularly important task for the purpose of the systematic study of networks. In order to discriminate unknown networks exactly, a large set of network measurements are needed to be taken into account for comprehensively considering network properties. However, as we demonstrate in this paper, these measurements are nonlinear correlated with each other in general, resulting in a wide variety of redundant measurements which unintentionally explain the same aspects of network properties. To solve this problem, we adopt supervised nonlinear dimensionality reduction (NDR) to eliminate the nonlinear redundancy and visualize networks in a low-dimensional projection space. Though unsupervised NDR can achieve the same aim, we illustrate that supervised NDR is more appropriate than unsupervised NDR for discrimination task. After that, we perform Bayesian classifier (BC) in the projection space to discriminate the unknown network by considering the projection score vectors as the input of the classifier. We also demonstrate the feasibility and effectivity of this proposed method in six extensive research real networks, ranging from technological to social or biological. Moreover, the effectiveness and advantage of the proposed method is proved by the contrast experiments with the existing method.

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

    PubMed

    Wang, Jie; Huang, Helai

    2016-05-01

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

  16. Multiscale Bayesian neural networks for soil water content estimation

    NASA Astrophysics Data System (ADS)

    Jana, Raghavendra B.; Mohanty, Binayak P.; Springer, Everett P.

    2008-08-01

    Artificial neural networks (ANN) have been used for some time now to estimate soil hydraulic parameters from other available or more easily measurable soil properties. However, most such uses of ANNs as pedotransfer functions (PTFs) have been at matching spatial scales (1:1) of inputs and outputs. This approach assumes that the outputs are only required at the same scale as the input data. Unfortunately, this is rarely true. Different hydrologic, hydroclimatic, and contaminant transport models require soil hydraulic parameter data at different spatial scales, depending upon their grid sizes. While conventional (deterministic) ANNs have been traditionally used in these studies, the use of Bayesian training of ANNs is a more recent development. In this paper, we develop a Bayesian framework to derive soil water retention function including its uncertainty at the point or local scale using PTFs trained with coarser-scale Soil Survey Geographic (SSURGO)-based soil data. The approach includes an ANN trained with Bayesian techniques as a PTF tool with training and validation data collected across spatial extents (scales) in two different regions in the United States. The two study areas include the Las Cruces Trench site in the Rio Grande basin of New Mexico, and the Southern Great Plains 1997 (SGP97) hydrology experimental region in Oklahoma. Each region-specific Bayesian ANN is trained using soil texture and bulk density data from the SSURGO database (scale 1:24,000), and predictions of the soil water contents at different pressure heads with point scale data (1:1) inputs are made. The resulting outputs are corrected for bias using both linear and nonlinear correction techniques. The results show good agreement between the soil water content values measured at the point scale and those predicted by the Bayesian ANN-based PTFs for both the study sites. Overall, Bayesian ANNs coupled with nonlinear bias correction are found to be very suitable tools for deriving soil

  17. Neonatal conjunctivitis

    MedlinePlus

    Newborn conjunctivitis; Conjunctivitis of the newborn; Ophthalmia neonatorum; Eye infection - neonatal conjunctivitis ... diseases spread through sexual contact to prevent newborn conjunctivitis caused by these infections. Putting eye drops into ...

  18. Quantum Bayesian networks with application to games displaying Parrondo's paradox

    NASA Astrophysics Data System (ADS)

    Pejic, Michael

    Bayesian networks and their accompanying graphical models are widely used for prediction and analysis across many disciplines. We will reformulate these in terms of linear maps. This reformulation will suggest a natural extension, which we will show is equivalent to standard textbook quantum mechanics. Therefore, this extension will be termed quantum. However, the term quantum should not be taken to imply this extension is necessarily only of utility in situations traditionally thought of as in the domain of quantum mechanics. In principle, it may be employed in any modelling situation, say forecasting the weather or the stock market---it is up to experiment to determine if this extension is useful in practice. Even restricting to the domain of quantum mechanics, with this new formulation the advantages of Bayesian networks can be maintained for models incorporating quantum and mixed classical-quantum behavior. The use of these will be illustrated by various basic examples. Parrondo's paradox refers to the situation where two, multi-round games with a fixed winning criteria, both with probability greater than one-half for one player to win, are combined. Using a possibly biased coin to determine the rule to employ for each round, paradoxically, the previously losing player now wins the combined game with probabilitygreater than one-half. Using the extended Bayesian networks, we will formulate and analyze classical observed, classical hidden, and quantum versions of a game that displays this paradox, finding bounds for the discrepancy from naive expectations for the occurrence of the paradox. A quantum paradox inspired by Parrondo's paradox will also be analyzed. We will prove a bound for the discrepancy from naive expectations for this paradox as well. Games involving quantum walks that achieve this bound will be presented.

  19. Bayesian Inference of Natural Rankings in Incomplete Competition Networks

    PubMed Central

    Park, Juyong; Yook, Soon-Hyung

    2014-01-01

    Competition between a complex system's constituents and a corresponding reward mechanism based on it have profound influence on the functioning, stability, and evolution of the system. But determining the dominance hierarchy or ranking among the constituent parts from the strongest to the weakest – essential in determining reward and penalty – is frequently an ambiguous task due to the incomplete (partially filled) nature of competition networks. Here we introduce the “Natural Ranking,” an unambiguous ranking method applicable to a round robin tournament, and formulate an analytical model based on the Bayesian formula for inferring the expected mean and error of the natural ranking of nodes from an incomplete network. We investigate its potential and uses in resolving important issues of ranking by applying it to real-world competition networks. PMID:25163528

  20. Bayesian Inference of Epidemics on Networks via Belief Propagation

    NASA Astrophysics Data System (ADS)

    Altarelli, Fabrizio; Braunstein, Alfredo; Dall'Asta, Luca; Lage-Castellanos, Alejandro; Zecchina, Riccardo

    2014-03-01

    We study several Bayesian inference problems for irreversible stochastic epidemic models on networks from a statistical physics viewpoint. We derive equations which allow us to accurately compute the posterior distribution of the time evolution of the state of each node given some observations. At difference with most existing methods, we allow very general observation models, including unobserved nodes, state observations made at different or unknown times, and observations of infection times, possibly mixed together. Our method, which is based on the belief propagation algorithm, is efficient, naturally distributed, and exact on trees. As a particular case, we consider the problem of finding the "zero patient" of a susceptible-infected-recovered or susceptible-infected epidemic given a snapshot of the state of the network at a later unknown time. Numerical simulations show that our method outperforms previous ones on both synthetic and real networks, often by a very large margin.

  1. 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

  2. Diagnosis of breast cancer using Bayesian networks: a case study.

    PubMed

    Cruz-Ramírez, Nicandro; Acosta-Mesa, Héctor Gabriel; Carrillo-Calvet, Humberto; Nava-Fernández, Luis Alonso; Barrientos-Martínez, Rocío Erandi

    2007-11-01

    We evaluate the effectiveness of seven Bayesian network classifiers as potential tools for the diagnosis of breast cancer using two real-world databases containing fine-needle aspiration of the breast lesion cases collected by a single observer and multiple observers, respectively. The results show a certain ingredient of subjectivity implicitly contained in these data: we get an average accuracy of 93.04% for the former and 83.31% for the latter. These findings suggest that observers see different things when looking at the samples in the microscope; a situation that significantly diminishes the performance of these classifiers in diagnosing such a disease. PMID:17434159

  3. Diagnosing Intermittent and Persistent Faults using Static Bayesian Networks

    NASA Technical Reports Server (NTRS)

    Megshoel, Ole Jakob

    2010-01-01

    Both intermittent and persistent faults may occur in a wide range of systems. We present in this paper the introduction of intermittent fault handling techniques into ProDiagnose, an algorithm that previously only handled persistent faults. We discuss novel algorithmic techniques as well as how our static Bayesian networks help diagnose, in an integrated manner, a range of intermittent and persistent faults. Through experiments with data from the ADAPT electrical power system test bed, generated as part of the Second International Diagnostic Competition (DXC-10), we show that this novel variant of ProDiagnose diagnoses intermittent faults accurately and quickly, while maintaining strong performance on persistent faults.

  4. Immune allied genetic algorithm for Bayesian network structure learning

    NASA Astrophysics Data System (ADS)

    Song, Qin; Lin, Feng; Sun, Wei; Chang, KC

    2012-06-01

    Bayesian network (BN) structure learning is a NP-hard problem. In this paper, we present an improved approach to enhance efficiency of BN structure learning. To avoid premature convergence in traditional single-group genetic algorithm (GA), we propose an immune allied genetic algorithm (IAGA) in which the multiple-population and allied strategy are introduced. Moreover, in the algorithm, we apply prior knowledge by injecting immune operator to individuals which can effectively prevent degeneration. To illustrate the effectiveness of the proposed technique, we present some experimental results.

  5. Application of Bayesian Networks to hindcast barrier island morphodynamics

    USGS Publications Warehouse

    Wilson, Kathleen E.; Adams, Peter N.; Hapke, Cheryl J.; Lentz, Erika E.; Brenner, Owen T.

    2015-01-01

    We refine a preliminary Bayesian Network by 1) increasing model experience through additional observations, 2) including anthropogenic modification history, and 3) replacing parameterized wave impact values with maximum run-up elevation. Further, we develop and train a pair of generalized models with an additional dataset encompassing a different storm event, which expands the observations beyond our hindcast objective. We compare the skill of the generalized models against the Nor'Ida specific model formulation, balancing the reduced skill with an expectation of increased transferability. Results of Nor'Ida hindcasts ranged in skill from 0.37 to 0.51 and accuracy of 65.0 to 81.9%.

  6. Simplifying Probability Elicitation and Uncertainty Modeling in Bayesian Networks

    SciTech Connect

    Paulson, Patrick R; Carroll, Thomas E; Sivaraman, Chitra; Neorr, Peter A; Unwin, Stephen D; Hossain, Shamina S

    2011-04-16

    In this paper we contribute two methods that simplify the demands of knowledge elicitation for particular types of Bayesian networks. The first method simplify the task of providing probabilities when the states that a random variable takes can be described by a new, fully ordered state set in which a state implies all the preceding states. The second method leverages Dempster-Shafer theory of evidence to provide a way for the expert to express the degree of ignorance that they feel about the estimates being provided.

  7. A Bayesian Network Implementation of Differential Diagnosis of Oral Soft Tissue Enlargements

    PubMed Central

    Xing, Yan; Wang, Yue; Yang, Lan

    2002-01-01

    Differential diagnosis of oral soft tissue enlargements is complicated due to its large amount of abnormality variations. A Bayesian network (BN) implemented in Hugin Lite® v5.7 is presented to demonstrate how Bayesian inference can be used to assist in differential diagnosis of this field. The Bayesian network presented here is intended for educational use as a quick reference for inexperienced dental school students. Further evaluation and validation are needed for future clinical use.

  8. Learning Bayesian networks from big meteorological spatial datasets. An alternative to complex network analysis

    NASA Astrophysics Data System (ADS)

    Gutiérrez, Jose Manuel; San Martín, Daniel; Herrera, Sixto; Santiago Cofiño, Antonio

    2016-04-01

    The growing availability of spatial datasets (observations, reanalysis, and regional and global climate models) demands efficient multivariate spatial modeling techniques for many problems of interest (e.g. teleconnection analysis, multi-site downscaling, etc.). Complex networks have been recently applied in this context using graphs built from pairwise correlations between the different stations (or grid boxes) forming the dataset. However, this analysis does not take into account the full dependence structure underlying the data, gien by all possible marginal and conditional dependencies among the stations, and does not allow a probabilistic analysis of the dataset. In this talk we introduce Bayesian networks as an alternative multivariate analysis and modeling data-driven technique which allows building a joint probability distribution of the stations including all relevant dependencies in the dataset. Bayesian networks is a sound machine learning technique using a graph to 1) encode the main dependencies among the variables and 2) to obtain a factorization of the joint probability distribution of the stations given by a reduced number of parameters. For a particular problem, the resulting graph provides a qualitative analysis of the spatial relationships in the dataset (alternative to complex network analysis), and the resulting model allows for a probabilistic analysis of the dataset. Bayesian networks have been widely applied in many fields, but their use in climate problems is hampered by the large number of variables (stations) involved in this field, since the complexity of the existing algorithms to learn from data the graphical structure grows nonlinearly with the number of variables. In this contribution we present a modified local learning algorithm for Bayesian networks adapted to this problem, which allows inferring the graphical structure for thousands of stations (from observations) and/or gridboxes (from model simulations) thus providing new

  9. Direct message passing for hybrid Bayesian networks and performance analysis

    NASA Astrophysics Data System (ADS)

    Sun, Wei; Chang, K. C.

    2010-04-01

    Probabilistic inference for hybrid Bayesian networks, which involves both discrete and continuous variables, has been an important research topic over the recent years. This is not only because a number of efficient inference algorithms have been developed and used maturely for simple types of networks such as pure discrete model, but also for the practical needs that continuous variables are inevitable in modeling complex systems. Pearl's message passing algorithm provides a simple framework to compute posterior distribution by propagating messages between nodes and can provides exact answer for polytree models with pure discrete or continuous variables. In addition, applying Pearl's message passing to network with loops usually converges and results in good approximation. However, for hybrid model, there is a need of a general message passing algorithm between different types of variables. In this paper, we develop a method called Direct Message Passing (DMP) for exchanging messages between discrete and continuous variables. Based on Pearl's algorithm, we derive formulae to compute messages for variables in various dependence relationships encoded in conditional probability distributions. Mixture of Gaussian is used to represent continuous messages, with the number of mixture components up to the size of the joint state space of all discrete parents. For polytree Conditional Linear Gaussian (CLG) Bayesian network, DMP has the same computational requirements and can provide exact solution as the one obtained by the Junction Tree (JT) algorithm. However, while JT can only work for the CLG model, DMP can be applied for general nonlinear, non-Gaussian hybrid model to produce approximate solution using unscented transformation and loopy propagation. Furthermore, we can scale the algorithm by restricting the number of mixture components in the messages. Empirically, we found that the approximation errors are relatively small especially for nodes that are far away from

  10. Risk analysis of dust explosion scenarios using Bayesian networks.

    PubMed

    Yuan, Zhi; Khakzad, Nima; Khan, Faisal; Amyotte, Paul

    2015-02-01

    In this study, a methodology has been proposed for risk analysis of dust explosion scenarios based on Bayesian network. Our methodology also benefits from a bow-tie diagram to better represent the logical relationships existing among contributing factors and consequences of dust explosions. In this study, the risks of dust explosion scenarios are evaluated, taking into account common cause failures and dependencies among root events and possible consequences. Using a diagnostic analysis, dust particle properties, oxygen concentration, and safety training of staff are identified as the most critical root events leading to dust explosions. The probability adaptation concept is also used for sequential updating and thus learning from past dust explosion accidents, which is of great importance in dynamic risk assessment and management. We also apply the proposed methodology to a case study to model dust explosion scenarios, to estimate the envisaged risks, and to identify the vulnerable parts of the system that need additional safety measures. PMID:25264172

  11. Development of a Bayesian Belief Network Runway Incursion Model

    NASA Technical Reports Server (NTRS)

    Green, Lawrence L.

    2014-01-01

    In a previous paper, a statistical analysis of runway incursion (RI) events was conducted to ascertain their relevance to the top ten Technical Challenges (TC) of the National Aeronautics and Space Administration (NASA) Aviation Safety Program (AvSP). The study revealed connections to perhaps several of the AvSP top ten TC. That data also identified several primary causes and contributing factors for RI events that served as the basis for developing a system-level Bayesian Belief Network (BBN) model for RI events. The system-level BBN model will allow NASA to generically model the causes of RI events and to assess the effectiveness of technology products being developed under NASA funding. These products are intended to reduce the frequency of RI events in particular, and to improve runway safety in general. The development, structure and assessment of that BBN for RI events by a Subject Matter Expert panel are documented in this paper.

  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. NML computation algorithms for tree-structured multinomial Bayesian networks.

    PubMed

    Kontkanen, Petri; Wettig, Hannes; Myllymäki, Petri

    2007-01-01

    Typical problems in bioinformatics involve large discrete datasets. Therefore, in order to apply statistical methods in such domains, it is important to develop efficient algorithms suitable for discrete data. The minimum description length (MDL) principle is a theoretically well-founded, general framework for performing statistical inference. The mathematical formalization of MDL is based on the normalized maximum likelihood (NML) distribution, which has several desirable theoretical properties. In the case of discrete data, straightforward computation of the NML distribution requires exponential time with respect to the sample size, since the definition involves a sum over all the possible data samples of a fixed size. In this paper, we first review some existing algorithms for efficient NML computation in the case of multinomial and naive Bayes model families. Then we proceed by extending these algorithms to more complex, tree-structured Bayesian networks. PMID:18382603

  14. Dynamic Bayesian Networks for Context-Aware Fall Risk Assessment

    PubMed Central

    Koshmak, Gregory; Linden, Maria; Loutfi, Amy

    2014-01-01

    Fall incidents among the elderly often occur in the home and can cause serious injuries affecting their independent living. This paper presents an approach where data from wearable sensors integrated in a smart home environment is combined using a dynamic Bayesian network. The smart home environment provides contextual data, obtained from environmental sensors, and contributes to assessing a fall risk probability. The evaluation of the developed system is performed through simulation. Each time step is represented by a single user activity and interacts with a fall sensors located on a mobile device. A posterior probability is calculated for each recognized activity or contextual information. The output of the system provides a total risk assessment of falling given a response from the fall sensor. PMID:24859032

  15. Assessing Requirements Volatility and Risk Using Bayesian Networks

    NASA Technical Reports Server (NTRS)

    Russell, Michael S.

    2010-01-01

    There are many factors that affect the level of requirements volatility a system experiences over its lifecycle and the risk that volatility imparts. Improper requirements generation, undocumented user expectations, conflicting design decisions, and anticipated / unanticipated world states are representative of these volatility factors. Combined, these volatility factors can increase programmatic risk and adversely affect successful system development. This paper proposes that a Bayesian Network can be used to support reasonable judgments concerning the most likely sources and types of requirements volatility a developing system will experience prior to starting development and by doing so it is possible to predict the level of requirements volatility the system will experience over its lifecycle. This assessment offers valuable insight to the system's developers, particularly by providing a starting point for risk mitigation planning and execution.

  16. Aggregated Residential Load Modeling Using Dynamic Bayesian Networks

    SciTech Connect

    Vlachopoulou, Maria; Chin, George; Fuller, Jason C.; Lu, Shuai

    2014-09-28

    Abstract—It is already obvious that the future power grid will have to address higher demand for power and energy, and to incorporate renewable resources of different energy generation patterns. Demand response (DR) schemes could successfully be used to manage and balance power supply and demand under operating conditions of the future power grid. To achieve that, more advanced tools for DR management of operations and planning are necessary that can estimate the available capacity from DR resources. In this research, a Dynamic Bayesian Network (DBN) is derived, trained, and tested that can model aggregated load of Heating, Ventilation, and Air Conditioning (HVAC) systems. DBNs can provide flexible and powerful tools for both operations and planing, due to their unique analytical capabilities. The DBN model accuracy and flexibility of use is demonstrated by testing the model under different operational scenarios.

  17. Dynamic Bayesian networks for context-aware fall risk assessment.

    PubMed

    Koshmak, Gregory; Linden, Maria; Loutfi, Amy

    2014-01-01

    Fall incidents among the elderly often occur in the home and can cause serious injuries affecting their independent living. This paper presents an approach where data from wearable sensors integrated in a smart home environment is combined using a dynamic Bayesian network. The smart home environment provides contextual data, obtained from environmental sensors, and contributes to assessing a fall risk probability. The evaluation of the developed system is performed through simulation. Each time step is represented by a single user activity and interacts with a fall sensors located on a mobile device. A posterior probability is calculated for each recognized activity or contextual information. The output of the system provides a total risk assessment of falling given a response from the fall sensor. PMID:24859032

  18. Model for Aggregated Water Heater Load Using Dynamic Bayesian Networks

    SciTech Connect

    Vlachopoulou, Maria; Chin, George; Fuller, Jason C.; Lu, Shuai; Kalsi, Karanjit

    2012-07-19

    The transition to the new generation power grid, or “smart grid”, requires novel ways of using and analyzing data collected from the grid infrastructure. Fundamental functionalities like demand response (DR), that the smart grid needs, rely heavily on the ability of the energy providers and distributors to forecast the load behavior of appliances under different DR strategies. This paper presents a new model of aggregated water heater load, based on dynamic Bayesian networks (DBNs). The model has been validated against simulated data from an open source distribution simulation software (GridLAB-D). The results presented in this paper demonstrate that the DBN model accurately tracks the load profile curves of aggregated water heaters under different testing scenarios.

  19. Learning Predictive Interactions Using Information Gain and Bayesian Network Scoring

    PubMed Central

    Jiang, Xia; Jao, Jeremy; Neapolitan, Richard

    2015-01-01

    Background The problems of correlation and classification are long-standing in the fields of statistics and machine learning, and techniques have been developed to address these problems. We are now in the era of high-dimensional data, which is data that can concern billions of variables. These data present new challenges. In particular, it is difficult to discover predictive variables, when each variable has little marginal effect. An example concerns Genome-wide Association Studies (GWAS) datasets, which involve millions of single nucleotide polymorphism (SNPs), where some of the SNPs interact epistatically to affect disease status. Towards determining these interacting SNPs, researchers developed techniques that addressed this specific problem. However, the problem is more general, and so these techniques are applicable to other problems concerning interactions. A difficulty with many of these techniques is that they do not distinguish whether a learned interaction is actually an interaction or whether it involves several variables with strong marginal effects. Methodology/Findings We address this problem using information gain and Bayesian network scoring. First, we identify candidate interactions by determining whether together variables provide more information than they do separately. Then we use Bayesian network scoring to see if a candidate interaction really is a likely model. Our strategy is called MBS-IGain. Using 100 simulated datasets and a real GWAS Alzheimer’s dataset, we investigated the performance of MBS-IGain. Conclusions/Significance When analyzing the simulated datasets, MBS-IGain substantially out-performed nine previous methods at locating interacting predictors, and at identifying interactions exactly. When analyzing the real Alzheimer’s dataset, we obtained new results and results that substantiated previous findings. We conclude that MBS-IGain is highly effective at finding interactions in high-dimensional datasets. This result is

  20. Discrete Dynamic Bayesian Network Analysis of fMRI Data

    PubMed Central

    Burge, John; Lane, Terran; Link, Hamilton; Qiu, Shibin; Clark, Vincent P.

    2010-01-01

    We examine the efficacy of using discrete Dynamic Bayesian Networks (dDBNs), a data-driven modeling technique employed in machine learning, to identify functional correlations among neuroanatomical regions of interest. Unlike many neuroimaging analysis techniques, this method is not limited by linear and/or Gaussian noise assumptions. It achieves this by modeling the time series of neuroanatomical regions as discrete, as opposed to continuous, random variables with multinomial distributions. We demonstrated this method using an fMRI dataset collected from healthy and demented elderly subjects and identify correlates based on a diagnosis of dementia. The results are validated in three ways. First, the elicited correlates are shown to be robust over leave-one-out cross-validation and, via a Fourier bootstrapping method, that they were not likely due to random chance. Second, the dDBNs identified correlates that would be expected given the experimental paradigm. Third, the dDBN's ability to predict dementia is competitive with two commonly employed machine-learning classifiers: the support vector machine and the Gaussian naïve Bayesian network. We also verify that the dDBN selects correlates based on non-linear criteria. Finally, we provide a brief analysis of the correlates elicited from Buckner et al.'s data that suggests that demented elderly subjects have reduced involvement of entorhinal and occipital cortex and greater involvement of the parietal lobe and amygdala in brain activity compared with healthy elderly (as measured via functional correlations among BOLD measurements). Limitations and extensions to the dDBN method are discussed. PMID:17990301

  1. Mobile sensor network noise reduction and re-calibration using Bayesian network

    NASA Astrophysics Data System (ADS)

    Xiang, Y.; Tang, Y.; Zhu, W.

    2015-08-01

    People are becoming increasingly interested in mobile air quality sensor network applications. By eliminating the inaccuracies caused by spatial and temporal heterogeneity of pollutant distributions, this method shows great potentials in atmosphere researches. However, such system usually suffers from the problem of sensor noises and drift. For the sensing systems to operate stably and reliably in the real-world applications, those problems must be addressed. In this work, we exploit the correlation of different types of sensors caused by cross sensitivity to help identify and correct the outlier readings. By employing a Bayesian network based system, we are able to recover the erroneous readings and re-calibrate the drifted sensors simultaneously. Specifically, we have (1) designed a Bayesian belief network based system to detect and recover the abnormal readings; (2) developed methods to update the sensor calibration functions in-field without requirement of ground truth; and (3) deployed a real-world mobile sensor network using the custom-built M-Pods to verify our assumptions and technique. Compared with the existing Bayesian belief network technique, the experiment results on the real-world data demonstrate that our system can reduce error by 34.1 % and recover 4 times more data on average.

  2. Dynamic Bayesian Network Modeling of Game Based Diagnostic Assessments. CRESST Report 837

    ERIC Educational Resources Information Center

    Levy, Roy

    2014-01-01

    Digital games offer an appealing environment for assessing student proficiencies, including skills and misconceptions in a diagnostic setting. This paper proposes a dynamic Bayesian network modeling approach for observations of student performance from an educational video game. A Bayesian approach to model construction, calibration, and use in…

  3. Construction of gene regulatory networks using biclustering and bayesian networks

    PubMed Central

    2011-01-01

    Background Understanding gene interactions in complex living systems can be seen as the ultimate goal of the systems biology revolution. Hence, to elucidate disease ontology fully and to reduce the cost of drug development, gene regulatory networks (GRNs) have to be constructed. During the last decade, many GRN inference algorithms based on genome-wide data have been developed to unravel the complexity of gene regulation. Time series transcriptomic data measured by genome-wide DNA microarrays are traditionally used for GRN modelling. One of the major problems with microarrays is that a dataset consists of relatively few time points with respect to the large number of genes. Dimensionality is one of the interesting problems in GRN modelling. Results In this paper, we develop a biclustering function enrichment analysis toolbox (BicAT-plus) to study the effect of biclustering in reducing data dimensions. The network generated from our system was validated via available interaction databases and was compared with previous methods. The results revealed the performance of our proposed method. Conclusions Because of the sparse nature of GRNs, the results of biclustering techniques differ significantly from those of previous methods. PMID:22018164

  4. Making Supply Chains Resilient to Floods Using a Bayesian Network

    NASA Astrophysics Data System (ADS)

    Haraguchi, M.

    2015-12-01

    Natural hazards distress the global economy by disrupting the interconnected supply chain networks. Manufacturing companies have created cost-efficient supply chains by reducing inventories, streamlining logistics and limiting the number of suppliers. As a result, today's supply chains are profoundly susceptible to systemic risks. In Thailand, for example, the GDP growth rate declined by 76 % in 2011 due to prolonged flooding. Thailand incurred economic damage including the loss of USD 46.5 billion, approximately 70% of which was caused by major supply chain disruptions in the manufacturing sector. Similar problems occurred after the Great East Japan Earthquake and Tsunami in 2011, the Mississippi River floods and droughts during 2011 - 2013, and Hurricane Sandy in 2012. This study proposes a methodology for modeling supply chain disruptions using a Bayesian network analysis (BNA) to estimate expected values of countermeasures of floods, such as inventory management, supplier management and hard infrastructure management. We first performed a spatio-temporal correlation analysis between floods and extreme precipitation data for the last 100 years at a global scale. Then we used a BNA to create synthetic networks that include variables associated with the magnitude and duration of floods, major components of supply chains and market demands. We also included decision variables of countermeasures that would mitigate potential losses caused by supply chain disruptions. Finally, we conducted a cost-benefit analysis by estimating the expected values of these potential countermeasures while conducting a sensitivity analysis. The methodology was applied to supply chain disruptions caused by the 2011 Thailand floods. Our study demonstrates desirable typical data requirements for the analysis, such as anonymized supplier network data (i.e. critical dependencies, vulnerability information of suppliers) and sourcing data(i.e. locations of suppliers, and production rates and

  5. A Bayesian belief network of threat anticipation and terrorist motivations

    NASA Astrophysics Data System (ADS)

    Olama, Mohammed M.; Allgood, Glenn O.; Davenport, Kristen M.; Schryver, Jack C.

    2010-04-01

    Recent events highlight the need for efficient tools for anticipating the threat posed by terrorists, whether individual or groups. Antiterrorism includes fostering awareness of potential threats, deterring aggressors, developing security measures, planning for future events, halting an event in process, and ultimately mitigating and managing the consequences of an event. To analyze such components, one must understand various aspects of threat elements like physical assets and their economic and social impacts. To this aim, we developed a three-layer Bayesian belief network (BBN) model that takes into consideration the relative threat of an attack against a particular asset (physical layer) as well as the individual psychology and motivations that would induce a person to either act alone or join a terrorist group and commit terrorist acts (social and economic layers). After researching the many possible motivations to become a terrorist, the main factors are compiled and sorted into categories such as initial and personal indicators, exclusion factors, and predictive behaviors. Assessing such threats requires combining information from disparate data sources most of which involve uncertainties. BBN combines these data in a coherent, analytically defensible, and understandable manner. The developed BBN model takes into consideration the likelihood and consequence of a threat in order to draw inferences about the risk of a terrorist attack so that mitigation efforts can be optimally deployed. The model is constructed using a network engineering process that treats the probability distributions of all the BBN nodes within the broader context of the system development process.

  6. Bayesian Networks for Clinical Decision Support in Lung Cancer Care

    PubMed Central

    Sesen, M. Berkan; Nicholson, Ann E.; Banares-Alcantara, Rene; Kadir, Timor; Brady, Michael

    2013-01-01

    Survival prediction and treatment selection in lung cancer care are characterised by high levels of uncertainty. Bayesian Networks (BNs), which naturally reason with uncertain domain knowledge, can be applied to aid lung cancer experts by providing personalised survival estimates and treatment selection recommendations. Based on the English Lung Cancer Database (LUCADA), we evaluate the feasibility of BNs for these two tasks, while comparing the performances of various causal discovery approaches to uncover the most feasible network structure from expert knowledge and data. We show first that the BN structure elicited from clinicians achieves a disappointing area under the ROC curve of 0.75 (± 0.03), whereas a structure learned by the CAMML hybrid causal discovery algorithm, which adheres with the temporal restrictions, achieves 0.81 (± 0.03). Second, our causal intervention results reveal that BN treatment recommendations, based on prescribing the treatment plan that maximises survival, can only predict the recorded treatment plan 29% of the time. However, this percentage rises to 76% when partial matches are included. PMID:24324773

  7. A Bayesian Belief Network of Threat Anticipation and Terrorist Motivations

    SciTech Connect

    Olama, Mohammed M; Allgood, Glenn O; Davenport, Kristen M; Schryver, Jack C

    2010-01-01

    Recent events highlight the need for efficient tools for anticipating the threat posed by terrorists, whether individual or groups. Antiterrorism includes fostering awareness of potential threats, deterring aggressors, developing security measures, planning for future events, halting an event in process, and ultimately mitigating and managing the consequences of an event. To analyze such components, one must understand various aspects of threat elements like physical assets and their economic and social impacts. To this aim, we developed a three-layer Bayesian belief network (BBN) model that takes into consideration the relative threat of an attack against a particular asset (physical layer) as well as the individual psychology and motivations that would induce a person to either act alone or join a terrorist group and commit terrorist acts (social and economic layers). After researching the many possible motivations to become a terrorist, the main factors are compiled and sorted into categories such as initial and personal indicators, exclusion factors, and predictive behaviors. Assessing such threats requires combining information from disparate data sources most of which involve uncertainties. BBN combines these data in a coherent, analytically defensible, and understandable manner. The developed BBN model takes into consideration the likelihood and consequence of a threat in order to draw inferences about the risk of a terrorist attack so that mitigation efforts can be optimally deployed. The model is constructed using a network engineering process that treats the probability distributions of all the BBN nodes within the broader context of the system development process.

  8. Estimating uncertainty of streamflow simulation using Bayesian neural networks

    NASA Astrophysics Data System (ADS)

    Zhang, Xuesong; Liang, Faming; Srinivasan, Raghavan; van Liew, Michael

    2009-02-01

    Recent studies have shown that Bayesian neural networks (BNNs) are powerful tools for providing reliable hydrologic prediction and quantifying the prediction uncertainty. The reasonable estimation of the prediction uncertainty, a valuable tool for decision making to address water resources management and design problems, is influenced by the techniques used to deal with different uncertainty sources. In this study, four types of BNNs with different treatments of the uncertainties related to parameters (neural network's weights) and model structures were applied for uncertainty estimation of streamflow simulation in two U.S. Department of Agriculture Agricultural Research Service watersheds (Little River Experimental Watershed in Georgia and Reynolds Creek Experimental Watershed in Idaho). An advanced Markov chain Monte Carlo algorithm, evolutionary Monte Carlo, was used to train the BNNs and to estimate uncertainty limits of streamflow simulation. The results obtained in these two case study watersheds show that the 95% uncertainty limits estimated by different types of BNNs are different from each other. The BNNs that only consider the parameter uncertainty with noninformative prior knowledge contain the least number of observed streamflow data in their 95% uncertainty bound. By considering variable model structure and informative prior knowledge, the BNNs can provide more reasonable quantification of the uncertainty of streamflow simulation. This study stresses the need for improving understanding and quantifying methods of different uncertainty sources for effective estimation of uncertainty of hydrologic simulation using BNNs.

  9. On Bayesian Network Classifiers with Reduced Precision Parameters.

    PubMed

    Tschiatschek, Sebastian; Pernkopf, Franz

    2015-04-01

    Bayesian network classifier (BNCs) are typically implemented on nowadays desktop computers. However, many real world applications require classifier implementation on embedded or low power systems. Aspects for this purpose have not been studied rigorously. We partly close this gap by analyzing reduced precision implementations of BNCs. In detail, we investigate the quantization of the parameters of BNCs with discrete valued nodes including the implications on the classification rate (CR). We derive worst-case and probabilistic bounds on the CR for different bit-widths. These bounds are evaluated on several benchmark datasets. Furthermore, we compare the classification performance and the robustness of BNCs with generatively and discriminatively optimized parameters, i.e. parameters optimized for high data likelihood and parameters optimized for classification, with respect to parameter quantization. Generatively optimized parameters are more robust for very low bit-widths, i.e. less classifications change because of quantization. However, classification performance is better for discriminatively optimized parameters for all but very low bit-widths. Additionally, we perform analysis for margin-optimized tree augmented network (TAN) structures which outperform generatively optimized TAN structures in terms of CR and robustness. PMID:26353293

  10. Knowledge Discovery Using Bayesian Network Framework for Intelligent Telecommunication Network Management

    NASA Astrophysics Data System (ADS)

    Bashar, Abul; Parr, Gerard; McClean, Sally; Scotney, Bryan; Nauck, Detlef

    The ever-evolving nature of telecommunication networks has put enormous pressure on contemporary Network Management Systems (NMSs) to come up with improved functionalities for efficient monitoring, control and management. In such a context, the rapid deployments of Next Generation Networks (NGN) and their management requires intelligent, autonomic and resilient mechanisms to guarantee Quality of Service (QoS) to the end users and at the same time to maximize revenue for the service/network providers. We present a framework for evaluating a Bayesian Networks (BN) based Decision Support System (DSS) for assisting and improving the performance of a Simple Network Management Protocol (SNMP) based NMS. More specifically, we describe our methodology through a case study which implements the function of Call Admission Control (CAC) in a multi-class video conferencing service scenario. Simulation results are presented for a proof of concept, followed by a critical analysis of our proposed approach and its application.

  11. Vernal conjunctivitis

    MedlinePlus

    Vernal conjunctivitis is long-term (chronic) swelling (inflammation) of the outer lining of the eyes. It is due to ... Vernal conjunctivitis often occurs in people with a strong family history of allergies. These may include allergic rhinitis , asthma , ...

  12. Allergic Conjunctivitis

    MedlinePlus

    ... water. This is called conjunctivitis, also known as “pink eye.” Causes & Risk Factors What causes allergic conjunctivitis? ... example, if you are allergic to pollen or mold, stay indoors when pollen and mold levels are ...

  13. Learning Dynamic Bayesian Networks for Analyzing Causal Relationship Between o-Economic Index

    NASA Astrophysics Data System (ADS)

    Wang, Hui; Li, Yu-Jie; Wang, Shuang-Cheng

    Dynamic Bayesian networks is a powerful tool in modeling multivariate stochastic processes. At present, the methods of learning dynamic Bayesian network structure have low efficiency and reliability and can not make certain the causal direction of all edges. In this paper, an high effective and reliable and practical method of learning dynamic Bayesian network structure is presented to find dynamic causal knowledge from data. Firstly, a maximal likelihood tree is built from data. Then a causal tree is obtained by orienting the edges of the maximal likelihood tree and the variables can be sorted in the light of the causal tree. Finally, a dynamic Bayesian network structure can be established based on the causal order of variables and local search & scoring method by finding father nodes of a node.

  14. Integrated Bayesian network framework for modeling complex ecological issues.

    PubMed

    Johnson, Sandra; Mengersen, Kerrie

    2012-07-01

    The management of environmental problems is multifaceted, requiring varied and sometimes conflicting objectives and perspectives to be considered. Bayesian network (BN) modeling facilitates the integration of information from diverse sources and is well suited to tackling the management challenges of complex environmental problems. However, combining several perspectives in one model can lead to large, unwieldy BNs that are difficult to maintain and understand. Conversely, an oversimplified model may lead to an unrealistic representation of the environmental problem. Environmental managers require the current research and available knowledge about an environmental problem of interest to be consolidated in a meaningful way, thereby enabling the assessment of potential impacts and different courses of action. Previous investigations of the environmental problem of interest may have already resulted in the construction of several disparate ecological models. On the other hand, the opportunity may exist to initiate this modeling. In the first instance, the challenge is to integrate existing models and to merge the information and perspectives from these models. In the second instance, the challenge is to include different aspects of the environmental problem incorporating both the scientific and management requirements. Although the paths leading to the combined model may differ for these 2 situations, the common objective is to design an integrated model that captures the available information and research, yet is simple to maintain, expand, and refine. BN modeling is typically an iterative process, and we describe a heuristic method, the iterative Bayesian network development cycle (IBNDC), for the development of integrated BN models that are suitable for both situations outlined above. The IBNDC approach facilitates object-oriented BN (OOBN) modeling, arguably viewed as the next logical step in adaptive management modeling, and that embraces iterative development

  15. Advanced obstacle avoidance for a laser based wheelchair using optimised Bayesian neural networks.

    PubMed

    Trieu, Hoang T; Nguyen, Hung T; Willey, Keith

    2008-01-01

    In this paper we present an advanced method of obstacle avoidance for a laser based intelligent wheelchair using optimized Bayesian neural networks. Three neural networks are designed for three separate sub-tasks: passing through a door way, corridor and wall following and general obstacle avoidance. The accurate usable accessible space is determined by including the actual wheelchair dimensions in a real-time map used as inputs to each networks. Data acquisitions are performed separately to collect the patterns required for specified sub-tasks. Bayesian frame work is used to determine the optimal neural network structure in each case. Then these networks are trained under the supervision of Bayesian rule. Experiment results showed that compare to the VFH algorithm our neural networks navigated a smoother path following a near optimum trajectory. PMID:19163454

  16. Bayesian Model Selection with Network Based Diffusion Analysis.

    PubMed

    Whalen, Andrew; Hoppitt, William J E

    2016-01-01

    A number of recent studies have used Network Based Diffusion Analysis (NBDA) to detect the role of social transmission in the spread of a novel behavior through a population. In this paper we present a unified framework for performing NBDA in a Bayesian setting, and demonstrate how the Watanabe Akaike Information Criteria (WAIC) can be used for model selection. We present a specific example of applying this method to Time to Acquisition Diffusion Analysis (TADA). To examine the robustness of this technique, we performed a large scale simulation study and found that NBDA using WAIC could recover the correct model of social transmission under a wide range of cases, including under the presence of random effects, individual level variables, and alternative models of social transmission. This work suggests that NBDA is an effective and widely applicable tool for uncovering whether social transmission underpins the spread of a novel behavior, and may still provide accurate results even when key model assumptions are relaxed. PMID:27092089

  17. Classification of Maize and Weeds by Bayesian Networks

    NASA Astrophysics Data System (ADS)

    Chapron, Michel; Oprea, Alina; Sultana, Bogdan; Assemat, Louis

    2007-11-01

    Precision Agriculture is concerned with all sorts of within-field variability, spatially and temporally, that reduces the efficacy of agronomic practices applied in a uniform way all over the field. Because of these sources of heterogeneity, uniform management actions strongly reduce the efficiency of the resource input to the crop (i.e. fertilization, water) or for the agrochemicals use for pest control (i.e. herbicide). Moreover, this low efficacy means high environmental cost (pollution) and reduced economic return for the farmer. Weed plants are one of these sources of variability for the crop, as they occur in patches in the field. Detecting the location, size and internal density of these patches, along with identification of main weed species involved, open the way to a site-specific weed control strategy, where only patches of weeds would receive the appropriate herbicide (type and dose). Herein, an automatic recognition method of vegetal species is described. First, the pixels of soil and vegetation are classified in two classes, then the vegetation part of the input image is segmented from the distance image by using the watershed method and finally the leaves of the vegetation are partitioned in two parts maize and weeds thanks to the two Bayesian networks.

  18. Bridging groundwater models and decision support with a Bayesian network

    USGS Publications Warehouse

    Fienen, Michael N.; Masterson, John P.; Plant, Nathaniel G.; Gutierrez, Benjamin T.; Thieler, E. Robert

    2013-01-01

    Resource managers need to make decisions to plan for future environmental conditions, particularly sea level rise, in the face of substantial uncertainty. Many interacting processes factor in to the decisions they face. Advances in process models and the quantification of uncertainty have made models a valuable tool for this purpose. Long-simulation runtimes and, often, numerical instability make linking process models impractical in many cases. A method for emulating the important connections between model input and forecasts, while propagating uncertainty, has the potential to provide a bridge between complicated numerical process models and the efficiency and stability needed for decision making. We explore this using a Bayesian network (BN) to emulate a groundwater flow model. We expand on previous approaches to validating a BN by calculating forecasting skill using cross validation of a groundwater model of Assateague Island in Virginia and Maryland, USA. This BN emulation was shown to capture the important groundwater-flow characteristics and uncertainty of the groundwater system because of its connection to island morphology and sea level. Forecast power metrics associated with the validation of multiple alternative BN designs guided the selection of an optimal level of BN complexity. Assateague island is an ideal test case for exploring a forecasting tool based on current conditions because the unique hydrogeomorphological variability of the island includes a range of settings indicative of past, current, and future conditions. The resulting BN is a valuable tool for exploring the response of groundwater conditions to sea level rise in decision support.

  19. CRAFFT: An Activity Prediction Model based on Bayesian Networks

    PubMed Central

    Nazerfard, Ehsan; Cook, Diane J.

    2014-01-01

    Recent advances in the areas of pervasive computing, data mining, and machine learning offer unique opportunities to provide health monitoring and assistance for individuals facing difficulties to live independently in their homes. Several components have to work together to provide health monitoring for smart home residents including, but not limited to, activity recognition, activity discovery, activity prediction, and prompting system. Compared to the significant research done to discover and recognize activities, less attention has been given to predict the future activities that the resident is likely to perform. Activity prediction components can play a major role in design of a smart home. For instance, by taking advantage of an activity prediction module, a smart home can learn context-aware rules to prompt individuals to initiate important activities. In this paper, we propose an activity prediction model using Bayesian networks together with a novel two-step inference process to predict both the next activity features and the next activity label. We also propose an approach to predict the start time of the next activity which is based on modeling the relative start time of the predicted activity using the continuous normal distribution and outlier detection. To validate our proposed models, we used real data collected from physical smart environments. PMID:25937847

  20. Evidence for single top quark production using Bayesian neural networks

    SciTech Connect

    Kau, Daekwang; /Florida State U.

    2007-08-01

    We present results of a search for single top quark production in p{bar p} collisions using a dataset of approximately 1 fb{sup -1} collected with the D0 detector. This analysis considers the muon+jets and electron+jets final states and makes use of Bayesian neural networks to separate the expected signals from backgrounds. The observed excess is associated with a p-value of 0.081%, assuming the background-only hypothesis, which corresponds to an excess over background of 3.2 standard deviations for a Gaussian density. The p-value computed using the SM signal cross section of 2.9 pb is 1.6%, corresponding to an expected significance of 2.2 standard deviations. Assuming the observed excess is due to single top production, we measure a single top quark production cross section of {sigma}(p{bar p} {yields} tb + X, tqb + X) = 4.4 {+-} 1.5 pb.

  1. Bayesian network model of crowd emotion and negative behavior

    NASA Astrophysics Data System (ADS)

    Ramli, Nurulhuda; Ghani, Noraida Abdul; Hatta, Zulkarnain Ahmad; Hashim, Intan Hashimah Mohd; Sulong, Jasni; Mahudin, Nor Diana Mohd; Rahman, Shukran Abd; Saad, Zarina Mat

    2014-12-01

    The effects of overcrowding have become a major concern for event organizers. One aspect of this concern has been the idea that overcrowding can enhance the occurrence of serious incidents during events. As one of the largest Muslim religious gathering attended by pilgrims from all over the world, Hajj has become extremely overcrowded with many incidents being reported. The purpose of this study is to analyze the nature of human emotion and negative behavior resulting from overcrowding during Hajj events from data gathered in Malaysian Hajj Experience Survey in 2013. The sample comprised of 147 Malaysian pilgrims (70 males and 77 females). Utilizing a probabilistic model called Bayesian network, this paper models the dependence structure between different emotions and negative behaviors of pilgrims in the crowd. The model included the following variables of emotion: negative, negative comfortable, positive, positive comfortable and positive spiritual and variables of negative behaviors; aggressive and hazardous acts. The study demonstrated that emotions of negative, negative comfortable, positive spiritual and positive emotion have a direct influence on aggressive behavior whereas emotion of negative comfortable, positive spiritual and positive have a direct influence on hazardous acts behavior. The sensitivity analysis showed that a low level of negative and negative comfortable emotions leads to a lower level of aggressive and hazardous behavior. Findings of the study can be further improved to identify the exact cause and risk factors of crowd-related incidents in preventing crowd disasters during the mass gathering events.

  2. Using a Bayesian network to predict barrier island geomorphologic characteristics

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    Quantifying geomorphic variability of coastal environments is important for understanding and describing the vulnerability of coastal topography, infrastructure, and ecosystems to future storms and sea level rise. Here we use a Bayesian network (BN) to test the importance of multiple interactions between barrier island geomorphic variables. This approach models complex interactions and handles uncertainty, which is intrinsic to future sea level rise, storminess, or anthropogenic processes (e.g., beach nourishment and other forms of coastal management). The BN was developed and tested at Assateague Island, Maryland/Virginia, USA, a barrier island with sufficient geomorphic and temporal variability to evaluate our approach. We tested the ability to predict dune height, beach width, and beach height variables using inputs that included longer-term, larger-scale, or external variables (historical shoreline change rates, distances to inlets, barrier width, mean barrier elevation, and anthropogenic modification). Data sets from three different years spanning nearly a decade sampled substantial temporal variability and serve as a proxy for analysis of future conditions. We show that distinct geomorphic conditions are associated with different long-term shoreline change rates and that the most skillful predictions of dune height, beach width, and beach height depend on including multiple input variables simultaneously. The predictive relationships are robust to variations in the amount of input data and to variations in model complexity. The resulting model can be used to evaluate scenarios related to coastal management plans and/or future scenarios where shoreline change rates may differ from those observed historically.

  3. Utilization of extended bayesian networks in decision making under uncertainty

    SciTech Connect

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

    2009-01-01

    Bayesian network tool (called IKE for Integrated Knowledge Engine) has been developed to assess the probability of undesirable events. The tool allows indications and observables from sensors and/or intelligence to feed directly into hypotheses of interest, thus allowing one to quantify the probability and uncertainty of these events resulting from very disparate evidence. For example, the probability that a facility is processing nuclear fuel or assembling a weapon can be assessed by examining the processes required, establishing the observables that should be present, then assembling information from intelligence, sensors and other information sources related to the observables. IKE also has the capability to determine tasking plans, that is, prioritize which observable should be collected next to most quickly ascertain the 'true' state and drive the probability toward 'zero' or 'one.' This optimization capability is called 'evidence marshaling.' One example to be discussed is a denied facility monitoring situation; there is concern that certain process(es) are being executed at the site (due to some intelligence or other data). We will show how additional pieces of evidence will then ascertain with some degree of certainty the likelihood of this process(es) as each piece of evidence is obtained. This example shows how both intelligence and sensor data can be incorporated into the analysis. A second example involves real-time perimeter security. For this demonstration we used seismic, acoustic, and optical sensors linked back to IKE. We show how these sensors identified and assessed the likelihood of 'intruder' versus friendly vehicles.

  4. Bayesian Model Selection with Network Based Diffusion Analysis

    PubMed Central

    Whalen, Andrew; Hoppitt, William J. E.

    2016-01-01

    A number of recent studies have used Network Based Diffusion Analysis (NBDA) to detect the role of social transmission in the spread of a novel behavior through a population. In this paper we present a unified framework for performing NBDA in a Bayesian setting, and demonstrate how the Watanabe Akaike Information Criteria (WAIC) can be used for model selection. We present a specific example of applying this method to Time to Acquisition Diffusion Analysis (TADA). To examine the robustness of this technique, we performed a large scale simulation study and found that NBDA using WAIC could recover the correct model of social transmission under a wide range of cases, including under the presence of random effects, individual level variables, and alternative models of social transmission. This work suggests that NBDA is an effective and widely applicable tool for uncovering whether social transmission underpins the spread of a novel behavior, and may still provide accurate results even when key model assumptions are relaxed. PMID:27092089

  5. A Bayesian Network to Predict Barrier Island Geomorphologic Characteristics

    NASA Astrophysics Data System (ADS)

    Gutierrez, B.; Plant, N. G.; Thieler, E. R.; Turecek, A.; Stippa, S.

    2014-12-01

    Understanding how barrier islands along the Atlantic and Gulf coasts of the United States respond to storms and sea-level rise is an important management concern. Although these threats are well recognized, quantifying the integrated vulnerability is challenging due to the range of time and space scalesover which these processes act. Developing datasets and methods to identify the physical vulnerabilities of coastal environments due to storms and sea-level rise thus is an important scientific focus that supports land management decision making. Here we employ a Bayesian Network (BN) to model the interactions between geomorphic variables sampled from existing datasets that capture both storm-and sea-level rise related coastal evolution. The BN provides a means of estimating probabilities of changes in specific geomorphic characteristics such as foredune crest height, beach width, beach height, given knowledge of barrier island width, maximum barrier island elevation, distance from an inlet, the presence of anthropogenic modifications, and long-term shoreline change rates, which we assume to be directly related to sea-level rise. We evaluate BN skill and explore how different constraints, such as shoreline change characteristics (eroding, stable, accreting), distance to nearby inlets and island width, affect the probability distributions of future morphological characteristics. Our work demonstrates that a skillful BN can be constructed and that factors such as distance to inlet, shoreline change rate, and the presence of human alterations have the strongest influences on network performance. For Assateague Island, Maryland/Virginia, USA, we find that different shoreline change behaviors affect the probabilities of specific geomorphic characteristics, such as dune height, which allows us to identify vulnerable locations on the barrier island where habitat or infrastructure may be vulnerable to storms and sea-level rise.

  6. Bayesian Belief Networks Approach for Modeling Irrigation Behavior

    NASA Astrophysics Data System (ADS)

    Andriyas, S.; McKee, M.

    2012-12-01

    Canal operators need information to manage water deliveries to irrigators. Short-term irrigation demand forecasts can potentially valuable information for a canal operator who must manage an on-demand system. Such forecasts could be generated by using information about the decision-making processes of irrigators. Bayesian models of irrigation behavior can provide insight into the likely criteria which farmers use to make irrigation decisions. This paper develops a Bayesian belief network (BBN) to learn irrigation decision-making behavior of farmers and utilizes the resulting model to make forecasts of future irrigation decisions based on factor interaction and posterior probabilities. Models for studying irrigation behavior have been rarely explored in the past. The model discussed here was built from a combination of data about biotic, climatic, and edaphic conditions under which observed irrigation decisions were made. The paper includes a case study using data collected from the Canal B region of the Sevier River, near Delta, Utah. Alfalfa, barley and corn are the main crops of the location. The model has been tested with a portion of the data to affirm the model predictive capabilities. Irrigation rules were deduced in the process of learning and verified in the testing phase. It was found that most of the farmers used consistent rules throughout all years and across different types of crops. Soil moisture stress, which indicates the level of water available to the plant in the soil profile, was found to be one of the most significant likely driving forces for irrigation. Irrigations appeared to be triggered by a farmer's perception of soil stress, or by a perception of combined factors such as information about a neighbor irrigating or an apparent preference to irrigate on a weekend. Soil stress resulted in irrigation probabilities of 94.4% for alfalfa. With additional factors like weekend and irrigating when a neighbor irrigates, alfalfa irrigation

  7. An Anticipatory and Deceptive AI Utilizing Bayesian Belief Networks

    SciTech Connect

    Lake, Joe E; Allgood, Glenn O; Olama, Mohammed M; Saffold, JAy

    2009-01-01

    The U.S. military defines antiterrorism as the defensive posture taken against terrorist threats. Antiterrorism includes fostering awareness of potential threats, deterring aggressors, developing security measures, planning for future events, interdicting an event in progress, and ultimately mitigating and managing the consequences of an event. Recent events highlight the need for efficient tools for training our military and homeland security officers for anticipating threats posed by terrorists. These tools need to be easy enough so that they are readily usable without substantial training, but still maintain the complexity to allow for a level of deceptive reasoning on the part of the opponent. To meet this need, we propose to integrate a Bayesian Belief Network (BBN) model for threat anticipation and deceptive reasoning into training simulation environments currently utilized by several organizations within the Department of Defense (DoD). BBNs have the ability to deal with various types of uncertainties; such as identities, capabilities, target attractiveness, and the combinations of the previous. They also allow for disparate types of data to be fused in a coherent, analytically defensible, and understandable manner. A BBN has been developed by ORNL uses a network engineering process that treats the probability distributions of each node with in the broader context of the system development effort as a whole, and not in isolation. The network will be integrated into the Research Network Inc,(RNI) developed Game Distributed Interactive Simulation (GDIS) as a smart artificial intelligence module. GDIS is utilized by several DoD and civilian organizations as a distributed training tool for a multiplicity of reasons. It has garnered several awards for its realism, ease of use, and popularity. One area that it still has room to excel in, as most video training tools do, is in the area of artificial intelligence of opponent combatants. It is believed that by

  8. Bayesian network representing system dynamics in risk analysis of nuclear systems

    NASA Astrophysics Data System (ADS)

    Varuttamaseni, Athi

    2011-12-01

    A dynamic Bayesian network (DBN) model is used in conjunction with the alternating conditional expectation (ACE) regression method to analyze the risk associated with the loss of feedwater accident coupled with a subsequent initiation of the feed and bleed operation in the Zion-1 nuclear power plant. The use of the DBN allows the joint probability distribution to be factorized, enabling the analysis to be done on many simpler network structures rather than on one complicated structure. The construction of the DBN model assumes conditional independence relations among certain key reactor parameters. The choice of parameter to model is based on considerations of the macroscopic balance statements governing the behavior of the reactor under a quasi-static assumption. The DBN is used to relate the peak clad temperature to a set of independent variables that are known to be important in determining the success of the feed and bleed operation. A simple linear relationship is then used to relate the clad temperature to the core damage probability. To obtain a quantitative relationship among different nodes in the DBN, surrogates of the RELAP5 reactor transient analysis code are used. These surrogates are generated by applying the ACE algorithm to output data obtained from about 50 RELAP5 cases covering a wide range of the selected independent variables. These surrogates allow important safety parameters such as the fuel clad temperature to be expressed as a function of key reactor parameters such as the coolant temperature and pressure together with important independent variables such as the scram delay time. The time-dependent core damage probability is calculated by sampling the independent variables from their probability distributions and propagate the information up through the Bayesian network to give the clad temperature. With the knowledge of the clad temperature and the assumption that the core damage probability has a one-to-one relationship to it, we have

  9. Characterizing structural association alterations within brain networks in normal aging using Gaussian Bayesian networks

    PubMed Central

    Guo, Xiaojuan; Wang, Yan; Chen, Kewei; Wu, Xia; Zhang, Jiacai; Li, Ke; Jin, Zhen; Yao, Li

    2014-01-01

    Recent multivariate neuroimaging studies have revealed aging-related alterations in brain structural networks. However, the sensory/motor networks such as the auditory, visual and motor networks, have obtained much less attention in normal aging research. In this study, we used Gaussian Bayesian networks (BN), an approach investigating possible inter-regional directed relationship, to characterize aging effects on structural associations between core brain regions within each of these structural sensory/motor networks using volumetric MRI data. We then further examined the discriminability of BN models for the young (N = 109; mean age =22.73 years, range 20–28) and old (N = 82; mean age =74.37 years, range 60–90) groups. The results of the BN modeling demonstrated that structural associations exist between two homotopic brain regions from the left and right hemispheres in each of the three networks. In particular, compared with the young group, the old group had significant connection reductions in each of the three networks and lesser connection numbers in the visual network. Moreover, it was found that the aging-related BN models could distinguish the young and old individuals with 90.05, 73.82, and 88.48% accuracy for the auditory, visual, and motor networks, respectively. Our findings suggest that BN models can be used to investigate the normal aging process with reliable statistical power. Moreover, these differences in structural inter-regional interactions may help elucidate the neuronal mechanism of anatomical changes in normal aging. PMID:25324771

  10. A Fault Diagnosis Methodology for Gear Pump Based on EEMD and Bayesian Network

    PubMed Central

    Liu, Zengkai; Liu, Yonghong; Shan, Hongkai; Cai, Baoping; Huang, Qing

    2015-01-01

    This paper proposes a fault diagnosis methodology for a gear pump based on the ensemble empirical mode decomposition (EEMD) method and the Bayesian network. Essentially, the presented scheme is a multi-source information fusion based methodology. Compared with the conventional fault diagnosis with only EEMD, the proposed method is able to take advantage of all useful information besides sensor signals. The presented diagnostic Bayesian network consists of a fault layer, a fault feature layer and a multi-source information layer. Vibration signals from sensor measurement are decomposed by the EEMD method and the energy of intrinsic mode functions (IMFs) are calculated as fault features. These features are added into the fault feature layer in the Bayesian network. The other sources of useful information are added to the information layer. The generalized three-layer Bayesian network can be developed by fully incorporating faults and fault symptoms as well as other useful information such as naked eye inspection and maintenance records. Therefore, diagnostic accuracy and capacity can be improved. The proposed methodology is applied to the fault diagnosis of a gear pump and the structure and parameters of the Bayesian network is established. Compared with artificial neural network and support vector machine classification algorithms, the proposed model has the best diagnostic performance when sensor data is used only. A case study has demonstrated that some information from human observation or system repair records is very helpful to the fault diagnosis. It is effective and efficient in diagnosing faults based on uncertain, incomplete information. PMID:25938760

  11. A Fault Diagnosis Methodology for Gear Pump Based on EEMD and Bayesian Network.

    PubMed

    Liu, Zengkai; Liu, Yonghong; Shan, Hongkai; Cai, Baoping; Huang, Qing

    2015-01-01

    This paper proposes a fault diagnosis methodology for a gear pump based on the ensemble empirical mode decomposition (EEMD) method and the Bayesian network. Essentially, the presented scheme is a multi-source information fusion based methodology. Compared with the conventional fault diagnosis with only EEMD, the proposed method is able to take advantage of all useful information besides sensor signals. The presented diagnostic Bayesian network consists of a fault layer, a fault feature layer and a multi-source information layer. Vibration signals from sensor measurement are decomposed by the EEMD method and the energy of intrinsic mode functions (IMFs) are calculated as fault features. These features are added into the fault feature layer in the Bayesian network. The other sources of useful information are added to the information layer. The generalized three-layer Bayesian network can be developed by fully incorporating faults and fault symptoms as well as other useful information such as naked eye inspection and maintenance records. Therefore, diagnostic accuracy and capacity can be improved. The proposed methodology is applied to the fault diagnosis of a gear pump and the structure and parameters of the Bayesian network is established. Compared with artificial neural network and support vector machine classification algorithms, the proposed model has the best diagnostic performance when sensor data is used only. A case study has demonstrated that some information from human observation or system repair records is very helpful to the fault diagnosis. It is effective and efficient in diagnosing faults based on uncertain, incomplete information. PMID:25938760

  12. Bayesian network classifiers for categorizing cortical GABAergic interneurons.

    PubMed

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

    2015-04-01

    An accepted classification of GABAergic interneurons of the cerebral cortex is a major goal in neuroscience. A recently proposed taxonomy based on patterns of axonal arborization promises to be a pragmatic method for achieving this goal. It involves characterizing interneurons according to five axonal arborization features, called F1-F5, and classifying them into a set of predefined types, most of which are established in the literature. Unfortunately, there is little consensus among expert neuroscientists regarding the morphological definitions of some of the proposed types. While supervised classifiers were able to categorize the interneurons in accordance with experts' assignments, their accuracy was limited because they were trained with disputed labels. Thus, here we automatically classify interneuron subsets with different label reliability thresholds (i.e., such that every cell's label is backed by at least a certain (threshold) number of experts). We quantify the cells with parameters of axonal and dendritic morphologies and, in order to predict the type, also with axonal features F1-F4 provided by the experts. Using Bayesian network classifiers, we accurately characterize and classify the interneurons and identify useful predictor variables. In particular, we discriminate among reliable examples of common basket, horse-tail, large basket, and Martinotti cells with up to 89.52% accuracy, and single out the number of branches at 180 μm from the soma, the convex hull 2D area, and the axonal features F1-F4 as especially useful predictors for distinguishing among these types. These results open up new possibilities for an objective and pragmatic classification of interneurons. PMID:25420745

  13. Emulation Modeling with Bayesian Networks for Efficient Decision Support

    NASA Astrophysics Data System (ADS)

    Fienen, M. N.; Masterson, J.; Plant, N. G.; Gutierrez, B. T.; Thieler, E. R.

    2012-12-01

    Bayesian decision networks (BDN) have long been used to provide decision support in systems that require explicit consideration of uncertainty; applications range from ecology to medical diagnostics and terrorism threat assessments. Until recently, however, few studies have applied BDNs to the study of groundwater systems. BDNs are particularly useful for representing real-world system variability by synthesizing a range of hydrogeologic situations within a single simulation. Because BDN output is cast in terms of probability—an output desired by decision makers—they explicitly incorporate the uncertainty of a system. BDNs can thus serve as a more efficient alternative to other uncertainty characterization methods such as computationally demanding Monte Carlo analyses and others methods restricted to linear model analyses. We present a unique application of a BDN to a groundwater modeling analysis of the hydrologic response of Assateague Island, Maryland to sea-level rise. Using both input and output variables of the modeled groundwater response to different sea-level (SLR) rise scenarios, the BDN predicts the probability of changes in the depth to fresh water, which exerts an important influence on physical and biological island evolution. Input variables included barrier-island width, maximum island elevation, and aquifer recharge. The variability of these inputs and their corresponding outputs are sampled along cross sections in a single model run to form an ensemble of input/output pairs. The BDN outputs, which are the posterior distributions of water table conditions for the sea-level rise scenarios, are evaluated through error analysis and cross-validation to assess both fit to training data and predictive power. The key benefit for using BDNs in groundwater modeling analyses is that they provide a method for distilling complex model results into predictions with associated uncertainty, which is useful to decision makers. Future efforts incorporate

  14. Evaluation of a Partial Genome Screening of Two Asthma Susceptibility Regions Using Bayesian Network Based Bayesian Multilevel Analysis of Relevance

    PubMed Central

    Antal, Péter; Kiszel, Petra Sz.; Gézsi, András; Hadadi, Éva; Virág, Viktor; Hajós, Gergely; Millinghoffer, András; Nagy, Adrienne; Kiss, András; Semsei, Ágnes F.; Temesi, Gergely; Melegh, Béla; Kisfali, Péter; Széll, Márta; Bikov, András; Gálffy, Gabriella; Tamási, Lilla; Falus, András; Szalai, Csaba

    2012-01-01

    Genetic studies indicate high number of potential factors related to asthma. Based on earlier linkage analyses we selected the 11q13 and 14q22 asthma susceptibility regions, for which we designed a partial genome screening study using 145 SNPs in 1201 individuals (436 asthmatic children and 765 controls). The results were evaluated with traditional frequentist methods and we applied a new statistical method, called Bayesian network based Bayesian multilevel analysis of relevance (BN-BMLA). This method uses Bayesian network representation to provide detailed characterization of the relevance of factors, such as joint significance, the type of dependency, and multi-target aspects. We estimated posteriors for these relations within the Bayesian statistical framework, in order to estimate the posteriors whether a variable is directly relevant or its association is only mediated. With frequentist methods one SNP (rs3751464 in the FRMD6 gene) provided evidence for an association with asthma (OR = 1.43(1.2–1.8); p = 3×10−4). The possible role of the FRMD6 gene in asthma was also confirmed in an animal model and human asthmatics. In the BN-BMLA analysis altogether 5 SNPs in 4 genes were found relevant in connection with asthma phenotype: PRPF19 on chromosome 11, and FRMD6, PTGER2 and PTGDR on chromosome 14. In a subsequent step a partial dataset containing rhinitis and further clinical parameters was used, which allowed the analysis of relevance of SNPs for asthma and multiple targets. These analyses suggested that SNPs in the AHNAK and MS4A2 genes were indirectly associated with asthma. This paper indicates that BN-BMLA explores the relevant factors more comprehensively than traditional statistical methods and extends the scope of strong relevance based methods to include partial relevance, global characterization of relevance and multi-target relevance. PMID:22432035

  15. Method for Building a Medical Training Simulator with Bayesian Networks: SimDeCS.

    PubMed

    Flores, Cecilia Dias; Fonseca, João Marcelo; Bez, Marta Rosecler; Respício, Ana; Coelho, Helder

    2014-01-01

    Distance education has grown in importance with the advent of the internet. An adequate evaluation of students in this mode is still difficult. Distance tests or occasional on-site exams do not meet the needs of evaluation of the learning process for distance education. Bayesian networks are adequate for simulating several aspects of clinical reasoning. The possibility of integrating them in distance education student evaluation has not yet been explored much. The present work describes a Simulator based on probabilistic networks built to represent knowledge of clinical practice guidelines in Family and Community Medicine. The Bayesian Network, the basis of the simulator, was modeled to playable by the student, to give immediate feedback according to pedagogical strategies adapted to the student according to past performance, and to give a broad evaluation of performance at the end of the game. Simulators structured by Bayesian Networks may become alternatives in the evaluation of students of Medical Distance Education. PMID:25488216

  16. A Dynamic Bayesian Network Model for the Production and Inventory Control

    NASA Astrophysics Data System (ADS)

    Shin, Ji-Sun; Takazaki, Noriyuki; Lee, Tae-Hong; Kim, Jin-Il; Lee, Hee-Hyol

    In general, the production quantities and delivered goods are changed randomly and then the total stock is also changed randomly. This paper deals with the production and inventory control using the Dynamic Bayesian Network. Bayesian Network is a probabilistic model which represents the qualitative dependence between two or more random variables by the graph structure, and indicates the quantitative relations between individual variables by the conditional probability. The probabilistic distribution of the total stock is calculated through the propagation of the probability on the network. Moreover, an adjusting rule of the production quantities to maintain the probability of a lower limit and a ceiling of the total stock to certain values is shown.

  17. Explaining Inference on a Population of Independent Agents Using Bayesian Networks

    ERIC Educational Resources Information Center

    Sutovsky, Peter

    2013-01-01

    The main goal of this research is to design, implement, and evaluate a novel explanation method, the hierarchical explanation method (HEM), for explaining Bayesian network (BN) inference when the network is modeling a population of conditionally independent agents, each of which is modeled as a subnetwork. For example, consider disease-outbreak…

  18. Diagnosis and Reconfiguration using Bayesian Networks: An Electrical Power System Case Study

    NASA Technical Reports Server (NTRS)

    Knox, W. Bradley; Mengshoel, Ole

    2009-01-01

    Automated diagnosis and reconfiguration are important computational techniques that aim to minimize human intervention in autonomous systems. In this paper, we develop novel techniques and models in the context of diagnosis and reconfiguration reasoning using causal Bayesian networks (BNs). We take as starting point a successful diagnostic approach, using a static BN developed for a real-world electrical power system. We discuss in this paper the extension of this diagnostic approach along two dimensions, namely: (i) from a static BN to a dynamic BN; and (ii) from a diagnostic task to a reconfiguration task. More specifically, we discuss the auto-generation of a dynamic Bayesian network from a static Bayesian network. In addition, we discuss subtle, but important, differences between Bayesian networks when used for diagnosis versus reconfiguration. We discuss a novel reconfiguration agent, which models a system causally, including effects of actions through time, using a dynamic Bayesian network. Though the techniques we discuss are general, we demonstrate them in the context of electrical power systems (EPSs) for aircraft and spacecraft. EPSs are vital subsystems on-board aircraft and spacecraft, and many incidents and accidents of these vehicles have been attributed to EPS failures. We discuss a case study that provides initial but promising results for our approach in the setting of electrical power systems.

  19. A new research tool for hybrid Bayesian networks using script language

    NASA Astrophysics Data System (ADS)

    Sun, Wei; Park, Cheol Young; Carvalho, Rommel

    2011-06-01

    While continuous variables become more and more inevitable in Bayesian networks for modeling real-life applications in complex systems, there are not much software tools to support it. Popular commercial Bayesian network tools such as Hugin, and Netica etc., are either expensive or have to discretize continuous variables. In addition, some free programs existing in the literature, commonly known as BNT, GeNie/SMILE, etc, have their own advantages and disadvantages respectively. In this paper, we introduce a newly developed Java tool for model construction and inference for hybrid Bayesian networks. Via the representation power of the script language, this tool can build the hybrid model automatically based on a well defined string that follows the specific grammars. Furthermore, it implements several inference algorithms capable to accommodate hybrid Bayesian networks, including Junction Tree algorithm (JT) for conditional linear Gaussian model (CLG), and Direct Message Passing (DMP) for general hybrid Bayesian networks with CLG structure. We believe this tool will be useful for researchers in the field.

  20. Bayesian networks for evaluating forensic DNA profiling evidence: a review and guide to literature.

    PubMed

    Biedermann, A; Taroni, F

    2012-03-01

    Almost 30 years ago, Bayesian networks (BNs) were developed in the field of artificial intelligence as a framework that should assist researchers and practitioners in applying the theory of probability to inference problems of more substantive size and, thus, to more realistic and practical problems. Since the late 1980s, Bayesian networks have also attracted researchers in forensic science and this tendency has considerably intensified throughout the last decade. This review article provides an overview of the scientific literature that describes research on Bayesian networks as a tool that can be used to study, develop and implement probabilistic procedures for evaluating the probative value of particular items of scientific evidence in forensic science. Primary attention is drawn here to evaluative issues that pertain to forensic DNA profiling evidence because this is one of the main categories of evidence whose assessment has been studied through Bayesian networks. The scope of topics is large and includes almost any aspect that relates to forensic DNA profiling. Typical examples are inference of source (or, 'criminal identification'), relatedness testing, database searching and special trace evidence evaluation (such as mixed DNA stains or stains with low quantities of DNA). The perspective of the review presented here is not exclusively restricted to DNA evidence, but also includes relevant references and discussion on both, the concept of Bayesian networks as well as its general usage in legal sciences as one among several different graphical approaches to evidence evaluation. PMID:21775236

  1. Hidden Markov induced Dynamic Bayesian Network for recovering time evolving gene regulatory networks

    PubMed Central

    Zhu, Shijia; Wang, Yadong

    2015-01-01

    Dynamic Bayesian Networks (DBN) have been widely used to recover gene regulatory relationships from time-series data in computational systems biology. Its standard assumption is ‘stationarity’, and therefore, several research efforts have been recently proposed to relax this restriction. However, those methods suffer from three challenges: long running time, low accuracy and reliance on parameter settings. To address these problems, we propose a novel non-stationary DBN model by extending each hidden node of Hidden Markov Model into a DBN (called HMDBN), which properly handles the underlying time-evolving networks. Correspondingly, an improved structural EM algorithm is proposed to learn the HMDBN. It dramatically reduces searching space, thereby substantially improving computational efficiency. Additionally, we derived a novel generalized Bayesian Information Criterion under the non-stationary assumption (called BWBIC), which can help significantly improve the reconstruction accuracy and largely reduce over-fitting. Moreover, the re-estimation formulas for all parameters of our model are derived, enabling us to avoid reliance on parameter settings. Compared to the state-of-the-art methods, the experimental evaluation of our proposed method on both synthetic and real biological data demonstrates more stably high prediction accuracy and significantly improved computation efficiency, even with no prior knowledge and parameter settings. PMID:26680653

  2. Hidden Markov induced Dynamic Bayesian Network for recovering time evolving gene regulatory networks

    NASA Astrophysics Data System (ADS)

    Zhu, Shijia; Wang, Yadong

    2015-12-01

    Dynamic Bayesian Networks (DBN) have been widely used to recover gene regulatory relationships from time-series data in computational systems biology. Its standard assumption is ‘stationarity’, and therefore, several research efforts have been recently proposed to relax this restriction. However, those methods suffer from three challenges: long running time, low accuracy and reliance on parameter settings. To address these problems, we propose a novel non-stationary DBN model by extending each hidden node of Hidden Markov Model into a DBN (called HMDBN), which properly handles the underlying time-evolving networks. Correspondingly, an improved structural EM algorithm is proposed to learn the HMDBN. It dramatically reduces searching space, thereby substantially improving computational efficiency. Additionally, we derived a novel generalized Bayesian Information Criterion under the non-stationary assumption (called BWBIC), which can help significantly improve the reconstruction accuracy and largely reduce over-fitting. Moreover, the re-estimation formulas for all parameters of our model are derived, enabling us to avoid reliance on parameter settings. Compared to the state-of-the-art methods, the experimental evaluation of our proposed method on both synthetic and real biological data demonstrates more stably high prediction accuracy and significantly improved computation efficiency, even with no prior knowledge and parameter settings.

  3. Hidden Markov induced Dynamic Bayesian Network for recovering time evolving gene regulatory networks.

    PubMed

    Zhu, Shijia; Wang, Yadong

    2015-01-01

    Dynamic Bayesian Networks (DBN) have been widely used to recover gene regulatory relationships from time-series data in computational systems biology. Its standard assumption is 'stationarity', and therefore, several research efforts have been recently proposed to relax this restriction. However, those methods suffer from three challenges: long running time, low accuracy and reliance on parameter settings. To address these problems, we propose a novel non-stationary DBN model by extending each hidden node of Hidden Markov Model into a DBN (called HMDBN), which properly handles the underlying time-evolving networks. Correspondingly, an improved structural EM algorithm is proposed to learn the HMDBN. It dramatically reduces searching space, thereby substantially improving computational efficiency. Additionally, we derived a novel generalized Bayesian Information Criterion under the non-stationary assumption (called BWBIC), which can help significantly improve the reconstruction accuracy and largely reduce over-fitting. Moreover, the re-estimation formulas for all parameters of our model are derived, enabling us to avoid reliance on parameter settings. Compared to the state-of-the-art methods, the experimental evaluation of our proposed method on both synthetic and real biological data demonstrates more stably high prediction accuracy and significantly improved computation efficiency, even with no prior knowledge and parameter settings. PMID:26680653

  4. Using Bayesian Networks for Candidate Generation in Consistency-based Diagnosis

    NASA Technical Reports Server (NTRS)

    Narasimhan, Sriram; Mengshoel, Ole

    2008-01-01

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

  5. Parameterizing Bayesian network Representations of Social-Behavioral Models by Expert Elicitation

    SciTech Connect

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

    2010-05-23

    Bayesian networks provide a general framework with which to model many natural phenomena. The mathematical nature of Bayesian networks enables a plethora of model validation and calibration techniques: e.g parameter estimation, goodness of fit tests, and diagnostic checking of the model assumptions. However, they are not free of shortcomings. Parameter estimation from relevant extant data is a common approach to calibrating the model parameters. In practice it is not uncommon to find oneself lacking adequate data to reliably estimate all model parameters. In this paper we present the early development of a novel application of conjoint analysis as a method for eliciting and modeling expert opinions and using the results in a methodology for calibrating the parameters of a Bayesian network.

  6. Multi-entity Bayesian network for the handling of uncertainties in SATCOM links

    NASA Astrophysics Data System (ADS)

    Tian, Xin; Chen, Genshe; Chang, K. C.; Martin, Todd; Nguyen, Tien; Pham, Khanh; Blasch, Erik

    2015-05-01

    Accurate prediction of satellite communications (SATCOM) data link loss is critical for SATCOM systems to effectively achieve required Quality of Service (QoS) and link availability. A major challenge is to account for various sources of uncertainties (such as atmospheric loss, rain loss, depolarization loss, pointing offset loss, etc.,) and their impacts on the aggregated link loss. This paper investigates the use of Bayesian Network (BN) for acquiring accurate SATCOM link loss estimation and link budget analysis over various modulation and coding schemes. Based on the proposed BN models, a SATCOM Bayesian Network Analysis toolbox has been developed to support link budget analysis and decision making for robust SATCOM applications.

  7. Conjunction Functions

    ERIC Educational Resources Information Center

    Riddle, Bob

    2007-01-01

    This spring, as the school year starts to wind down, there will be many opportunities for students to observe bright planets and to wrap up the year with some great conjunctions and close occultation with the Moon, planets, bright stars, and star clusters). These observations can be coordinated with student observations of the Moon's phase cycle…

  8. Applying Bayesian belief networks in rapid response situations

    SciTech Connect

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

    2008-01-01

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

  9. On The Use of Dynamic Bayesian Networks in Reconstructing Functional Neuronal Networks from Spike Train Ensembles

    PubMed Central

    Eldawlatly, Seif; Zhou, Yang; Jin, Rong; Oweiss, Karim G.

    2009-01-01

    Coordination among cortical neurons is believed to be key element in mediating many high level cortical processes such as perception, attention, learning and memory formation. Inferring the topology of the neural circuitry underlying this coordination is important to characterize the highly non-linear, time-varying interactions between cortical neurons in the presence of complex stimuli. In this work, we investigate the applicability of Dynamic Bayesian Networks (DBNs) in inferring the effective connectivity between spiking cortical neurons from their observed spike trains. We demonstrate that DBNs can infer the underlying non-linear and time-varying causal interactions between these neurons and can discriminate between mono and polysynaptic links between them under certain constraints governing their putative connectivity. We analyzed conditionally-Poisson spike train data mimicking spiking activity of cortical networks of small and moderately-large sizes. The performance was assessed and compared to other methods under systematic variations of the network structure to mimic a wide range of responses typically observed in the cortex. Results demonstrate the utility of DBN in inferring the effective connectivity in cortical networks. PMID:19852619

  10. Bayesian networks for evaluation of evidence from forensic entomology.

    PubMed

    Andersson, M Gunnar; Sundström, Anders; Lindström, Anders

    2013-09-01

    In the aftermath of a CBRN incident, there is an urgent need to reconstruct events in order to bring the perpetrators to court and to take preventive actions for the future. The challenge is to discriminate, based on available information, between alternative scenarios. Forensic interpretation is used to evaluate to what extent results from the forensic investigation favor the prosecutors' or the defendants' arguments, using the framework of Bayesian hypothesis testing. Recently, several new scientific disciplines have been used in a forensic context. In the AniBioThreat project, the framework was applied to veterinary forensic pathology, tracing of pathogenic microorganisms, and forensic entomology. Forensic entomology is an important tool for estimating the postmortem interval in, for example, homicide investigations as a complement to more traditional methods. In this article we demonstrate the applicability of the Bayesian framework for evaluating entomological evidence in a forensic investigation through the analysis of a hypothetical scenario involving suspect movement of carcasses from a clandestine laboratory. Probabilities of different findings under the alternative hypotheses were estimated using a combination of statistical analysis of data, expert knowledge, and simulation, and entomological findings are used to update the beliefs about the prosecutors' and defendants' hypotheses and to calculate the value of evidence. The Bayesian framework proved useful for evaluating complex hypotheses using findings from several insect species, accounting for uncertainty about development rate, temperature, and precolonization. The applicability of the forensic statistic approach to evaluating forensic results from a CBRN incident is discussed. PMID:23971824

  11. Synaptic depression in conjunction with A-current channels promote phase constancy in a rhythmic network.

    PubMed

    Greenberg, Idan; Manor, Yair

    2005-02-01

    In many central pattern generators, pairs of neurons maintain an approximately fixed phase despite large changes in the frequency. The mechanisms underlying phase maintenance are not clear. Previous theoretical work suggested that inhibitory synapses that show short-term depression could play a critical role in this respect. In this work we examine how the interaction between synaptic depression and the kinetics of a transient potassium (A-like) current could be advantageous for phase constancy in a rhythmic network. To demonstrate the mechanism in the context of a realistic central pattern generator, we constructed a detailed model of the crustacean pyloric circuit. The frequency of the rhythm was modified by changing the level of a ligand-activated current in one of the pyloric neurons. We examined how the time difference of firing activities between two selected neurons in this circuit is affected by synaptic depression, A-current, and a combination of the two. We tuned the parameters of the model such that with synaptic depression alone, or A-current alone, phase was not maintained between these two neurons. However, when these two components came together, they acted synergistically to maintain the phase across a wide range of cycle periods. This suggests that synaptic depression may be necessary to allow an A-current to delay a postsynaptic neuron in a frequency-dependent manner, such that phase invariance is ensured. PMID:15356180

  12. Comparison of a Bayesian Network with a Logistic Regression Model to Forecast IgA Nephropathy

    PubMed Central

    Ducher, Michel; Kalbacher, Emilie; Combarnous, François; Finaz de Vilaine, Jérome; McGregor, Brigitte; Fouque, Denis; Fauvel, Jean Pierre

    2013-01-01

    Models are increasingly used in clinical practice to improve the accuracy of diagnosis. The aim of our work was to compare a Bayesian network to logistic regression to forecast IgA nephropathy (IgAN) from simple clinical and biological criteria. Retrospectively, we pooled the results of all biopsies (n = 155) performed by nephrologists in a specialist clinical facility between 2002 and 2009. Two groups were constituted at random. The first subgroup was used to determine the parameters of the models adjusted to data by logistic regression or Bayesian network, and the second was used to compare the performances of the models using receiver operating characteristics (ROC) curves. IgAN was found (on pathology) in 44 patients. Areas under the ROC curves provided by both methods were highly significant but not different from each other. Based on the highest Youden indices, sensitivity reached (100% versus 67%) and specificity (73% versus 95%) using the Bayesian network and logistic regression, respectively. A Bayesian network is at least as efficient as logistic regression to estimate the probability of a patient suffering IgAN, using simple clinical and biological data obtained during consultation. PMID:24328031

  13. A Bayesian network approach for causal inferences in pesticide risk assessment and management

    EPA Science Inventory

    Pesticide risk assessment and management must balance societal benefits and ecosystem protection, based on quantified risks and the strength of the causal linkages between uses of the pesticide and socioeconomic and ecological endpoints of concern. A Bayesian network (BN) is a gr...

  14. A General Structure for Legal Arguments about Evidence Using Bayesian Networks

    ERIC Educational Resources Information Center

    Fenton, Norman; Neil, Martin; Lagnado, David A.

    2013-01-01

    A Bayesian network (BN) is a graphical model of uncertainty that is especially well suited to legal arguments. It enables us to visualize and model dependencies between different hypotheses and pieces of evidence and to calculate the revised probability beliefs about all uncertain factors when any piece of new evidence is presented. Although BNs…

  15. Using Discrete Loss Functions and Weighted Kappa for Classification: An Illustration Based on Bayesian Network Analysis

    ERIC Educational Resources Information Center

    Zwick, Rebecca; Lenaburg, Lubella

    2009-01-01

    In certain data analyses (e.g., multiple discriminant analysis and multinomial log-linear modeling), classification decisions are made based on the estimated posterior probabilities that individuals belong to each of several distinct categories. In the Bayesian network literature, this type of classification is often accomplished by assigning…

  16. Use of limited data to construct Bayesian networks for probabilistic risk assessment.

    SciTech Connect

    Groth, Katrina M.; Swiler, Laura Painton

    2013-03-01

    Probabilistic Risk Assessment (PRA) is a fundamental part of safety/quality assurance for nuclear power and nuclear weapons. Traditional PRA very effectively models complex hardware system risks using binary probabilistic models. However, traditional PRA models are not flexible enough to accommodate non-binary soft-causal factors, such as digital instrumentation&control, passive components, aging, common cause failure, and human errors. Bayesian Networks offer the opportunity to incorporate these risks into the PRA framework. This report describes the results of an early career LDRD project titled %E2%80%9CUse of Limited Data to Construct Bayesian Networks for Probabilistic Risk Assessment%E2%80%9D. The goal of the work was to establish the capability to develop Bayesian Networks from sparse data, and to demonstrate this capability by producing a data-informed Bayesian Network for use in Human Reliability Analysis (HRA) as part of nuclear power plant Probabilistic Risk Assessment (PRA). This report summarizes the research goal and major products of the research.

  17. Bayesian estimation inherent in a Mexican-hat-type neural network

    NASA Astrophysics Data System (ADS)

    Takiyama, Ken

    2016-05-01

    Brain functions, such as perception, motor control and learning, and decision making, have been explained based on a Bayesian framework, i.e., to decrease the effects of noise inherent in the human nervous system or external environment, our brain integrates sensory and a priori information in a Bayesian optimal manner. However, it remains unclear how Bayesian computations are implemented in the brain. Herein, I address this issue by analyzing a Mexican-hat-type neural network, which was used as a model of the visual cortex, motor cortex, and prefrontal cortex. I analytically demonstrate that the dynamics of an order parameter in the model corresponds exactly to a variational inference of a linear Gaussian state-space model, a Bayesian estimation, when the strength of recurrent synaptic connectivity is appropriately stronger than that of an external stimulus, a plausible condition in the brain. This exact correspondence can reveal the relationship between the parameters in the Bayesian estimation and those in the neural network, providing insight for understanding brain functions.

  18. Spatiotemporal Bayesian Networks for Malaria Prediction: Case Study of Northern Thailand.

    PubMed

    Haddawy, Peter; Kasantikul, Rangwan; Hasan, A H M Imrul; Rattanabumrung, Chunyanuch; Rungrun, Pichamon; Suksopee, Natwipa; Tantiwaranpant, Saran; Niruntasuk, Natcha

    2016-01-01

    While a diversity of modeling technique have been used to create predictive models of malaria, no work has made use of Bayesian networks. Bayes nets are attractive due to their ability to represent uncertainty, model time lagged and nonlinear relations, and provide explanations of inferences. This paper explores the use of Bayesian networks to model malaria, demonstrating the approach by creating a village level model with weekly temporal resolution for Tha Song Yang district in northern Thailand. The network is learned using data on cases and environmental covariates. The network models incidence over time as well as evolution of the environmental variables, and captures time lagged and nonlinear effects. Out of sample evaluation shows the model to have high accuracy for one and two week predictions. PMID:27577491

  19. Chain Graph Models to Elicit the Structure of a Bayesian Network

    PubMed Central

    Stefanini, Federico M.

    2014-01-01

    Bayesian networks are possibly the most successful graphical models to build decision support systems. Building the structure of large networks is still a challenging task, but Bayesian methods are particularly suited to exploit experts' degree of belief in a quantitative way while learning the network structure from data. In this paper details are provided about how to build a prior distribution on the space of network structures by eliciting a chain graph model on structural reference features. Several structural features expected to be often useful during the elicitation are described. The statistical background needed to effectively use this approach is summarized, and some potential pitfalls are illustrated. Finally, a few seminal contributions from the literature are reformulated in terms of structural features. PMID:24688427

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

    PubMed Central

    2012-01-01

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

  1. 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.

  2. A Graphical Approach to Diagnosing the Validity of the Conditional Independence Assumptions of a Bayesian Network Given Data

    SciTech Connect

    Walsh, Stephen J.; Whitney, Paul D.

    2012-12-14

    Bayesian networks have attained widespread use in data analysis and decision making. Well studied topics include: efficient inference, evidence propagation, parameter learning from data for complete and incomplete data scenarios, expert elicitation for calibrating Bayesian network probabilities, and structure learning. It is not uncommon for the researcher to assume the structure of the Bayesian network or to glean the structure from expert elicitation or domain knowledge. In this scenario, the model may be calibrated through learning the parameters from relevant data. There is a lack of work on model diagnostics for fitted Bayesian networks; this is the contribution of this paper. We key on the definition of (conditional) independence to develop a graphical diagnostic method which indicates if the conditional independence assumptions imposed when one assumes the structure of the Bayesian network are supported by the data. We develop the approach theoretically and describe a Monte Carlo method to generate uncertainty measures for the consistency of the data with conditional independence assumptions under the model structure. We describe how this theoretical information and the data are presented in a graphical diagnostic tool. We demonstrate the approach through data simulated from Bayesian networks under different conditional independence assumptions. We also apply the diagnostic to a real world data set. The results indicate that our approach is a reasonable way of visualizing and inspecting the conditional independence assumption of a Bayesian network given data.

  3. Application of a data-mining method based on Bayesian networks to lesion-deficit analysis

    NASA Technical Reports Server (NTRS)

    Herskovits, Edward H.; Gerring, Joan P.

    2003-01-01

    Although lesion-deficit analysis (LDA) has provided extensive information about structure-function associations in the human brain, LDA has suffered from the difficulties inherent to the analysis of spatial data, i.e., there are many more variables than subjects, and data may be difficult to model using standard distributions, such as the normal distribution. We herein describe a Bayesian method for LDA; this method is based on data-mining techniques that employ Bayesian networks to represent structure-function associations. These methods are computationally tractable, and can represent complex, nonlinear structure-function associations. When applied to the evaluation of data obtained from a study of the psychiatric sequelae of traumatic brain injury in children, this method generates a Bayesian network that demonstrates complex, nonlinear associations among lesions in the left caudate, right globus pallidus, right side of the corpus callosum, right caudate, and left thalamus, and subsequent development of attention-deficit hyperactivity disorder, confirming and extending our previous statistical analysis of these data. Furthermore, analysis of simulated data indicates that methods based on Bayesian networks may be more sensitive and specific for detecting associations among categorical variables than methods based on chi-square and Fisher exact statistics.

  4. Regularized variational Bayesian learning of echo state networks with delay&sum readout.

    PubMed

    Shutin, Dmitriy; Zechner, Christoph; Kulkarni, Sanjeev R; Poor, H Vincent

    2012-04-01

    In this work, a variational Bayesian framework for efficient training of echo state networks (ESNs) with automatic regularization and delay&sum (D&S) readout adaptation is proposed. The algorithm uses a classical batch learning of ESNs. By treating the network echo states as fixed basis functions parameterized with delay parameters, we propose a variational Bayesian ESN training scheme. The variational approach allows for a seamless combination of sparse Bayesian learning ideas and a variational Bayesian space-alternating generalized expectation-maximization (VB-SAGE) algorithm for estimating parameters of superimposed signals. While the former method realizes automatic regularization of ESNs, which also determines which echo states and input signals are relevant for "explaining" the desired signal, the latter method provides a basis for joint estimation of D&S readout parameters. The proposed training algorithm can naturally be extended to ESNs with fixed filter neurons. It also generalizes the recently proposed expectation-maximization-based D&S readout adaptation method. The proposed algorithm was tested on synthetic data prediction tasks as well as on dynamic handwritten character recognition. PMID:22168555

  5. 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

  6. Inferring metabolic networks using the Bayesian adaptive graphical lasso with informative priors

    PubMed Central

    PETERSON, CHRISTINE; VANNUCCI, MARINA; KARAKAS, CEMAL; CHOI, WILLIAM; MA, LIHUA; MALETIĆ-SAVATIĆ, MIRJANA

    2014-01-01

    Metabolic processes are essential for cellular function and survival. We are interested in inferring a metabolic network in activated microglia, a major neuroimmune cell in the brain responsible for the neuroinflammation associated with neurological diseases, based on a set of quantified metabolites. To achieve this, we apply the Bayesian adaptive graphical lasso with informative priors that incorporate known relationships between covariates. To encourage sparsity, the Bayesian graphical lasso places double exponential priors on the off-diagonal entries of the precision matrix. The Bayesian adaptive graphical lasso allows each double exponential prior to have a unique shrinkage parameter. These shrinkage parameters share a common gamma hyperprior. We extend this model to create an informative prior structure by formulating tailored hyperpriors on the shrinkage parameters. By choosing parameter values for each hyperprior that shift probability mass toward zero for nodes that are close together in a reference network, we encourage edges between covariates with known relationships. This approach can improve the reliability of network inference when the sample size is small relative to the number of parameters to be estimated. When applied to the data on activated microglia, the inferred network includes both known relationships and associations of potential interest for further investigation. PMID:24533172

  7. Parameter estimation of brain tumors using intraoperative thermal imaging based on artificial tactile sensing in conjunction with artificial neural network

    NASA Astrophysics Data System (ADS)

    Sadeghi-Goughari, M.; Mojra, A.; Sadeghi, S.

    2016-02-01

    Intraoperative Thermal Imaging (ITI) is a new minimally invasive diagnosis technique that can potentially locate margins of brain tumor in order to achieve maximum tumor resection with least morbidity. This study introduces a new approach to ITI based on artificial tactile sensing (ATS) technology in conjunction with artificial neural networks (ANN) and feasibility and applicability of this method in diagnosis and localization of brain tumors is investigated. In order to analyze validity and reliability of the proposed method, two simulations were performed. (i) An in vitro experimental setup was designed and fabricated using a resistance heater embedded in agar tissue phantom in order to simulate heat generation by a tumor in the brain tissue; and (ii) A case report patient with parafalcine meningioma was presented to simulate ITI in the neurosurgical procedure. In the case report, both brain and tumor geometries were constructed from MRI data and tumor temperature and depth of location were estimated. For experimental tests, a novel assisted surgery robot was developed to palpate the tissue phantom surface to measure temperature variations and ANN was trained to estimate the simulated tumor’s power and depth. Results affirm that ITI based ATS is a non-invasive method which can be useful to detect, localize and characterize brain tumors.

  8. SU-E-T-51: Bayesian Network Models for Radiotherapy Error Detection

    SciTech Connect

    Kalet, A; Phillips, M; Gennari, J

    2014-06-01

    Purpose: To develop a probabilistic model of radiotherapy plans using Bayesian networks that will detect potential errors in radiation delivery. Methods: Semi-structured interviews with medical physicists and other domain experts were employed to generate a set of layered nodes and arcs forming a Bayesian Network (BN) which encapsulates relevant radiotherapy concepts and their associated interdependencies. Concepts in the final network were limited to those whose parameters are represented in the institutional database at a level significant enough to develop mathematical distributions. The concept-relation knowledge base was constructed using the Web Ontology Language (OWL) and translated into Hugin Expert Bayes Network files via the the RHugin package in the R statistical programming language. A subset of de-identified data derived from a Mosaiq relational database representing 1937 unique prescription cases was processed and pre-screened for errors and then used by the Hugin implementation of the Estimation-Maximization (EM) algorithm for machine learning all parameter distributions. Individual networks were generated for each of several commonly treated anatomic regions identified by ICD-9 neoplasm categories including lung, brain, lymphoma, and female breast. Results: The resulting Bayesian networks represent a large part of the probabilistic knowledge inherent in treatment planning. By populating the networks entirely with data captured from a clinical oncology information management system over the course of several years of normal practice, we were able to create accurate probability tables with no additional time spent by experts or clinicians. These probabilistic descriptions of the treatment planning allow one to check if a treatment plan is within the normal scope of practice, given some initial set of clinical evidence and thereby detect for potential outliers to be flagged for further investigation. Conclusion: The networks developed here support the

  9. From complex questionnaire and interviewing data to intelligent Bayesian Network models for medical decision support

    PubMed Central

    Constantinou, Anthony Costa; Fenton, Norman; Marsh, William; Radlinski, Lukasz

    2016-01-01

    Objectives 1) To develop a rigorous and repeatable method for building effective Bayesian network (BN) models for medical decision support from complex, unstructured and incomplete patient questionnaires and interviews that inevitably contain examples of repetitive, redundant and contradictory responses; 2) To exploit expert knowledge in the BN development since further data acquisition is usually not possible; 3) To ensure the BN model can be used for interventional analysis; 4) To demonstrate why using data alone to learn the model structure and parameters is often unsatisfactory even when extensive data is available. Method The method is based on applying a range of recent BN developments targeted at helping experts build BNs given limited data. While most of the components of the method are based on established work, its novelty is that it provides a rigorous consolidated and generalised framework that addresses the whole life-cycle of BN model development. The method is based on two original and recent validated BN models in forensic psychiatry, known as DSVM-MSS and DSVM-P. Results When employed with the same datasets, the DSVM-MSS demonstrated competitive to superior predictive performance (AUC scores 0.708 and 0.797) against the state-of-the-art (AUC scores ranging from 0.527 to 0.705), and the DSVM-P demonstrated superior predictive performance (cross-validated AUC score of 0.78) against the state-of-the-art (AUC scores ranging from 0.665 to 0.717). More importantly, the resulting models go beyond improving predictive accuracy and into usefulness for risk management purposes through intervention, and enhanced decision support in terms of answering complex clinical questions that are based on unobserved evidence. Conclusions This development process is applicable to any application domain which involves large-scale decision analysis based on such complex information, rather than based on data with hard facts, and in conjunction with the incorporation of

  10. A Bayesian network approach to knowledge integration and representation of farm irrigation: 3. Spatial application

    NASA Astrophysics Data System (ADS)

    Robertson, D. E.; Wang, Q. J.; McAllister, A. T.; Abuzar, M.; Malano, H. M.; Etchells, T.

    2009-02-01

    Catchment managers are interested in understanding impacts of the management options they promote at both farm and regional scales. In this third paper of this series, we use Inteca-Farm, a Bayesian network model of farm irrigation in the Shepparton Irrigation Region of northern Victoria, Australia, to assess the current condition of management outcome measures and the impact of historical and future management intervention. To help overcome difficulties in comprehending modeling results that are expressed as probability distributions, to capture uncertainties, we introduce methods to spatially display and compare the output from Bayesian network models and to use these methods to compare model predictions for three management scenarios. Model predictions suggest that management intervention has made a substantial improvement to the condition of management outcome measures and that further improvements are possible. The results highlight that the management impacts are spatially variable, which demonstrates that farm modeling can provide valuable evidence in substantiating the impact of catchment management intervention.

  11. A Bayesian network approach to knowledge integration and representation of farm irrigation: 2. Model validation

    NASA Astrophysics Data System (ADS)

    Robertson, D. E.; Wang, Q. J.; Malano, H.; Etchells, T.

    2009-02-01

    For models to be useful, they need to adequately describe the systems they represent. The probabilistic nature of Bayesian network models has traditionally meant that model validation is difficult. In this paper we present a process to validate Inteca-Farm, a Bayesian network model of farm irrigation that we described in the first paper of this series. We assessed three aspects of the quality of model predictions, namely, bias, accuracy, and skill, for the two variables for which validation data are available directly or indirectly. We also examined model predictions for any systematic errors. The validation results show that the bias and accuracy of the two validated variables are within acceptable tolerances and that systematic errors are minimal. This suggests that Inteca-Farm is a plausible representation of farm irrigation system in the Shepparton Irrigation Region of northern Victoria, Australia.

  12. Prediction of Sybil attack on WSN using Bayesian network and swarm intelligence

    NASA Astrophysics Data System (ADS)

    Muraleedharan, Rajani; Ye, Xiang; Osadciw, Lisa Ann

    2008-04-01

    Security in wireless sensor networks is typically sacrificed or kept minimal due to limited resources such as memory and battery power. Hence, the sensor nodes are prone to Denial-of-service attacks and detecting the threats is crucial in any application. In this paper, the Sybil attack is analyzed and a novel prediction method, combining Bayesian algorithm and Swarm Intelligence (SI) is proposed. Bayesian Networks (BN) is used in representing and reasoning problems, by modeling the elements of uncertainty. The decision from the BN is applied to SI forming an Hybrid Intelligence Scheme (HIS) to re-route the information and disconnecting the malicious nodes in future routes. A performance comparison based on the prediction using HIS vs. Ant System (AS) helps in prioritizing applications where decisions are time-critical.

  13. Developing Large-Scale Bayesian Networks by Composition: Fault Diagnosis of Electrical Power Systems in Aircraft and Spacecraft

    NASA Technical Reports Server (NTRS)

    Mengshoel, Ole Jakob; Poll, Scott; Kurtoglu, Tolga

    2009-01-01

    This CD contains files that support the talk (see CASI ID 20100021404). There are 24 models that relate to the ADAPT system and 1 Excel worksheet. In the paper an investigation into the use of Bayesian networks to construct large-scale diagnostic systems is described. The high-level specifications, Bayesian networks, clique trees, and arithmetic circuits representing 24 different electrical power systems are described in the talk. The data in the CD are the models of the 24 different power systems.

  14. Understanding the Scalability of Bayesian Network Inference Using Clique Tree Growth Curves

    NASA Technical Reports Server (NTRS)

    Mengshoel, Ole J.

    2010-01-01

    One of the main approaches to performing computation in Bayesian networks (BNs) is clique tree clustering and propagation. The clique tree approach consists of propagation in a clique tree compiled from a Bayesian network, and while it was introduced in the 1980s, there is still a lack of understanding of how clique tree computation time depends on variations in BN size and structure. In this article, we improve this understanding by developing an approach to characterizing clique tree growth as a function of parameters that can be computed in polynomial time from BNs, specifically: (i) the ratio of the number of a BN s non-root nodes to the number of root nodes, and (ii) the expected number of moral edges in their moral graphs. Analytically, we partition the set of cliques in a clique tree into different sets, and introduce a growth curve for the total size of each set. For the special case of bipartite BNs, there are two sets and two growth curves, a mixed clique growth curve and a root clique growth curve. In experiments, where random bipartite BNs generated using the BPART algorithm are studied, we systematically increase the out-degree of the root nodes in bipartite Bayesian networks, by increasing the number of leaf nodes. Surprisingly, root clique growth is well-approximated by Gompertz growth curves, an S-shaped family of curves that has previously been used to describe growth processes in biology, medicine, and neuroscience. We believe that this research improves the understanding of the scaling behavior of clique tree clustering for a certain class of Bayesian networks; presents an aid for trade-off studies of clique tree clustering using growth curves; and ultimately provides a foundation for benchmarking and developing improved BN inference and machine learning algorithms.

  15. Study on uncertainty of geospatial semantic Web services composition based on broker approach and Bayesian networks

    NASA Astrophysics Data System (ADS)

    Yang, Xiaodong; Cui, Weihong; Liu, Zhen; Ouyang, Fucheng

    2008-10-01

    The Semantic Web has a major weakness which is lacking of a principled means to represent and reason about uncertainty. This is also located in the services composition approaches such as BPEL4WS and Semantic Description Model. We analyze the uncertainty of Geospatial Web Service composition through mining the knowledge in historical records of composition based on Broker approach and Bayesian Networks. We proved this approach is effective and efficient through a sample scenario in this paper.

  16. Online Variational Bayesian Filtering-Based Mobile Target Tracking in Wireless Sensor Networks

    PubMed Central

    Zhou, Bingpeng; Chen, Qingchun; Li, Tiffany Jing; Xiao, Pei

    2014-01-01

    The received signal strength (RSS)-based online tracking for a mobile node in wireless sensor networks (WSNs) is investigated in this paper. Firstly, a multi-layer dynamic Bayesian network (MDBN) is introduced to characterize the target mobility with either directional or undirected movement. In particular, it is proposed to employ the Wishart distribution to approximate the time-varying RSS measurement precision's randomness due to the target movement. It is shown that the proposed MDBN offers a more general analysis model via incorporating the underlying statistical information of both the target movement and observations, which can be utilized to improve the online tracking capability by exploiting the Bayesian statistics. Secondly, based on the MDBN model, a mean-field variational Bayesian filtering (VBF) algorithm is developed to realize the online tracking of a mobile target in the presence of nonlinear observations and time-varying RSS precision, wherein the traditional Bayesian filtering scheme cannot be directly employed. Thirdly, a joint optimization between the real-time velocity and its prior expectation is proposed to enable online velocity tracking in the proposed online tacking scheme. Finally, the associated Bayesian Cramer–Rao Lower Bound (BCRLB) analysis and numerical simulations are conducted. Our analysis unveils that, by exploiting the potential state information via the general MDBN model, the proposed VBF algorithm provides a promising solution to the online tracking of a mobile node in WSNs. In addition, it is shown that the final tracking accuracy linearly scales with its expectation when the RSS measurement precision is time-varying. PMID:25393784

  17. Online variational Bayesian filtering-based mobile target tracking in wireless sensor networks.

    PubMed

    Zhou, Bingpeng; Chen, Qingchun; Li, Tiffany Jing; Xiao, Pei

    2014-01-01

    The received signal strength (RSS)-based online tracking for a mobile node in wireless sensor networks (WSNs) is investigated in this paper. Firstly, a multi-layer dynamic Bayesian network (MDBN) is introduced to characterize the target mobility with either directional or undirected movement. In particular, it is proposed to employ the Wishart distribution to approximate the time-varying RSS measurement precision's randomness due to the target movement. It is shown that the proposed MDBN offers a more general analysis model via incorporating the underlying statistical information of both the target movement and observations, which can be utilized to improve the online tracking capability by exploiting the Bayesian statistics. Secondly, based on the MDBN model, a mean-field variational Bayesian filtering (VBF) algorithm is developed to realize the online tracking of a mobile target in the presence of nonlinear observations and time-varying RSS precision, wherein the traditional Bayesian filtering scheme cannot be directly employed. Thirdly, a joint optimization between the real-time velocity and its prior expectation is proposed to enable online velocity tracking in the proposed online tacking scheme. Finally, the associated Bayesian Cramer-Rao Lower Bound (BCRLB) analysis and numerical simulations are conducted. Our analysis unveils that, by exploiting the potential state information via the general MDBN model, the proposed VBF algorithm provides a promising solution to the online tracking of a mobile node in WSNs. In addition, it is shown that the final tracking accuracy linearly scales with its expectation when the RSS measurement precision is time-varying. PMID:25393784

  18. Construction of monitoring model and algorithm design on passenger security during shipping based on improved Bayesian network.

    PubMed

    Wang, Jiali; Zhang, Qingnian; Ji, Wenfeng

    2014-01-01

    A large number of data is needed by the computation of the objective Bayesian network, but the data is hard to get in actual computation. The calculation method of Bayesian network was improved in this paper, and the fuzzy-precise Bayesian network was obtained. Then, the fuzzy-precise Bayesian network was used to reason Bayesian network model when the data is limited. The security of passengers during shipping is affected by various factors, and it is hard to predict and control. The index system that has the impact on the passenger safety during shipping was established on basis of the multifield coupling theory in this paper. Meanwhile, the fuzzy-precise Bayesian network was applied to monitor the security of passengers in the shipping process. The model was applied to monitor the passenger safety during shipping of a shipping company in Hainan, and the effectiveness of this model was examined. This research work provides guidance for guaranteeing security of passengers during shipping. PMID:25254227

  19. Construction of Monitoring Model and Algorithm Design on Passenger Security during Shipping Based on Improved Bayesian Network

    PubMed Central

    Wang, Jiali; Zhang, Qingnian; Ji, Wenfeng

    2014-01-01

    A large number of data is needed by the computation of the objective Bayesian network, but the data is hard to get in actual computation. The calculation method of Bayesian network was improved in this paper, and the fuzzy-precise Bayesian network was obtained. Then, the fuzzy-precise Bayesian network was used to reason Bayesian network model when the data is limited. The security of passengers during shipping is affected by various factors, and it is hard to predict and control. The index system that has the impact on the passenger safety during shipping was established on basis of the multifield coupling theory in this paper. Meanwhile, the fuzzy-precise Bayesian network was applied to monitor the security of passengers in the shipping process. The model was applied to monitor the passenger safety during shipping of a shipping company in Hainan, and the effectiveness of this model was examined. This research work provides guidance for guaranteeing security of passengers during shipping. PMID:25254227

  20. Bayesian Nonlinear Model Selection for Gene Regulatory Networks

    PubMed Central

    Ni, Yang; Stingo, Francesco C.; Baladandayuthapani, Veerabhadran

    2015-01-01

    Summary Gene regulatory networks represent the regulatory relationships between genes and their products and are important for exploring and defining the underlying biological processes of cellular systems. We develop a novel framework to recover the structure of nonlinear gene regulatory networks using semiparametric spline-based directed acyclic graphical models. Our use of splines allows the model to have both flexibility in capturing nonlinear dependencies as well as control of overfitting via shrinkage, using mixed model representations of penalized splines. We propose a novel discrete mixture prior on the smoothing parameter of the splines that allows for simultaneous selection of both linear and nonlinear functional relationships as well as inducing sparsity in the edge selection. Using simulation studies, we demonstrate the superior performance of our methods in comparison with several existing approaches in terms of network reconstruction and functional selection. We apply our methods to a gene expression dataset in glioblastoma multiforme, which reveals several interesting and biologically relevant nonlinear relationships. PMID:25854759

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

    PubMed

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

    2011-12-01

    Neuron morphology is crucial for neuronal connectivity and brain information processing. Computational models are important tools for studying dendritic morphology and its role in brain function. We applied a class of probabilistic graphical models called Bayesian networks to generate virtual dendrites from layer III pyramidal neurons from three different regions of the neocortex of the mouse. A set of 41 morphological variables were measured from the 3D reconstructions of real dendrites and their probability distributions used in a machine learning algorithm to induce the model from the data. A simulation algorithm is also proposed to obtain new dendrites by sampling values from Bayesian networks. The main advantage of this approach is that it takes into account and automatically locates the relationships between variables in the data instead of using predefined dependencies. Therefore, the methodology can be applied to any neuronal class while at the same time exploiting class-specific properties. Also, a Bayesian network was defined for each part of the dendrite, allowing the relationships to change in the different sections and to model heterogeneous developmental factors or spatial influences. Several univariate statistical tests and a novel multivariate test based on Kullback-Leibler divergence estimation confirmed that virtual dendrites were similar to real ones. The analyses of the models showed relationships that conform to current neuroanatomical knowledge and support model correctness. At the same time, studying the relationships in the models can help to identify new interactions between variables related to dendritic morphology. PMID:21305364

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

    USGS Publications Warehouse

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

    2011-01-01

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

  3. Maritime Transportation Risk Assessment of Tianjin Port with Bayesian Belief Networks.

    PubMed

    Zhang, Jinfen; Teixeira, Ângelo P; Guedes Soares, C; Yan, Xinping; Liu, Kezhong

    2016-06-01

    This article develops a Bayesian belief network model for the prediction of accident consequences in the Tianjin port. The study starts with a statistical analysis of historical accident data of six years from 2008 to 2013. Then a Bayesian belief network is constructed to express the dependencies between the indicator variables and accident consequences. The statistics and expert knowledge are synthesized in the Bayesian belief network model to obtain the probability distribution of the consequences. By a sensitivity analysis, several indicator variables that have influence on the consequences are identified, including navigational area, ship type and time of the day. The results indicate that the consequences are most sensitive to the position where the accidents occurred, followed by time of day and ship length. The results also reflect that the navigational risk of the Tianjin port is at the acceptable level, despite that there is more room of improvement. These results can be used by the Maritime Safety Administration to take effective measures to enhance maritime safety in the Tianjin port. PMID:26895225

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

    PubMed Central

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

    2014-01-01

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

  5. Discrimination of acidic and alkaline enzyme using Chou's pseudo amino acid composition in conjunction with probabilistic neural network model.

    PubMed

    Khan, Zaheer Ullah; Hayat, Maqsood; Khan, Muazzam Ali

    2015-01-21

    Enzyme catalysis is one of the most essential and striking processes among of all the complex processes that have evolved in living organisms. Enzymes are biological catalysts, which play a significant role in industrial applications as well as in medical areas, due to profound specificity, selectivity and catalytic efficiency. Refining catalytic efficiency of enzymes has become the most challenging job of enzyme engineering, into acidic and alkaline. Discrimination of acidic and alkaline enzymes through experimental approaches is difficult, sometimes impossible due to lack of established structures. Therefore, it is highly desirable to develop a computational model for discriminating acidic and alkaline enzymes from primary sequences. In this study, we have developed a robust, accurate and high throughput computational model using two discrete sample representation methods Pseudo amino acid composition (PseAAC) and split amino acid composition. Various classification algorithms including probabilistic neural network (PNN), K-nearest neighbor, decision tree, multi-layer perceptron and support vector machine are applied to predict acidic and alkaline with high accuracy. 10-fold cross validation test and several statistical measures namely, accuracy, F-measure, and area under ROC are used to evaluate the performance of the proposed model. The performance of the model is examined using two benchmark datasets to demonstrate the effectiveness of the model. The empirical results show that the performance of PNN in conjunction with PseAAC is quite promising compared to existing approaches in the literature so for. It has achieved 96.3% accuracy on dataset1 and 99.2% on dataset2. It is ascertained that the proposed model might be useful for basic research and drug related application areas. PMID:25452135

  6. Prediction and assimilation of surf-zone processes using a Bayesian network: Part I: Forward models

    USGS Publications Warehouse

    Plant, Nathaniel G.; Holland, K. Todd

    2011-01-01

    Prediction of coastal processes, including waves, currents, and sediment transport, can be obtained from a variety of detailed geophysical-process models with many simulations showing significant skill. This capability supports a wide range of research and applied efforts that can benefit from accurate numerical predictions. However, the predictions are only as accurate as the data used to drive the models and, given the large temporal and spatial variability of the surf zone, inaccuracies in data are unavoidable such that useful predictions require corresponding estimates of uncertainty. We demonstrate how a Bayesian-network model can be used to provide accurate predictions of wave-height evolution in the surf zone given very sparse and/or inaccurate boundary-condition data. The approach is based on a formal treatment of a data-assimilation problem that takes advantage of significant reduction of the dimensionality of the model system. We demonstrate that predictions of a detailed geophysical model of the wave evolution are reproduced accurately using a Bayesian approach. In this surf-zone application, forward prediction skill was 83%, and uncertainties in the model inputs were accurately transferred to uncertainty in output variables. We also demonstrate that if modeling uncertainties were not conveyed to the Bayesian network (i.e., perfect data or model were assumed), then overly optimistic prediction uncertainties were computed. More consistent predictions and uncertainties were obtained by including model-parameter errors as a source of input uncertainty. Improved predictions (skill of 90%) were achieved because the Bayesian network simultaneously estimated optimal parameters while predicting wave heights.

  7. Parameter inference in small world network disease models with approximate Bayesian Computational methods

    NASA Astrophysics Data System (ADS)

    Walker, David M.; Allingham, David; Lee, Heung Wing Joseph; Small, Michael

    2010-02-01

    Small world network models have been effective in capturing the variable behaviour of reported case data of the SARS coronavirus outbreak in Hong Kong during 2003. Simulations of these models have previously been realized using informed “guesses” of the proposed model parameters and tested for consistency with the reported data by surrogate analysis. In this paper we attempt to provide statistically rigorous parameter distributions using Approximate Bayesian Computation sampling methods. We find that such sampling schemes are a useful framework for fitting parameters of stochastic small world network models where simulation of the system is straightforward but expressing a likelihood is cumbersome.

  8. Bayesian neural networks for bivariate binary data: an application to prostate cancer study.

    PubMed

    Chakraborty, Sounak; Ghosh, Malay; Maiti, Tapabrata; Tewari, Ashutosh

    2005-12-15

    Prostate cancer is one of the most common cancers in American men. The cancer could either be locally confined, or it could spread outside the organ. When locally confined, there are several options for treating and curing this disease. Otherwise, surgery is the only option, and in extreme cases of outside spread, it could very easily recur within a short time even after surgery and subsequent radiation therapy. Hence, it is important to know, based on pre-surgery biopsy results how likely the cancer is organ-confined or not. The paper considers a hierarchical Bayesian neural network approach for posterior prediction probabilities of certain features indicative of non-organ confined prostate cancer. In particular, we find such probabilities for margin positivity (MP) and seminal vesicle (SV) positivity jointly. The available training set consists of bivariate binary outcomes indicating the presence or absence of the two. In addition, we have certain covariates such as prostate specific antigen (PSA), gleason score and the indicator for the cancer to be unilateral or bilateral (i.e. spread on one or both sides) in one data set and gene expression microarrays in another data set. We take a hierarchical Bayesian neural network approach to find the posterior prediction probabilities for a test and validation set, and compare these with the actual outcomes for the first data set. In case of the microarray data we use leave one out cross-validation to access the accuracy of our method. We also demonstrate the superiority of our method to the other competing methods through a simulation study. The Bayesian procedure is implemented by an application of the Markov chain Monte Carlo numerical integration technique. For the problem at hand, our Bayesian bivariate neural network procedure is shown to be superior to the classical neural network, Radford Neal's Bayesian neural network as well as bivariate logistic models to predict jointly the MP and SV in a patient in both the

  9. Investigating the Effects of Imputation Methods for Modelling Gene Networks Using a Dynamic Bayesian Network from Gene Expression Data

    PubMed Central

    CHAI, Lian En; LAW, Chow Kuan; MOHAMAD, Mohd Saberi; CHONG, Chuii Khim; CHOON, Yee Wen; DERIS, Safaai; ILLIAS, Rosli Md

    2014-01-01

    Background: Gene expression data often contain missing expression values. Therefore, several imputation methods have been applied to solve the missing values, which include k-nearest neighbour (kNN), local least squares (LLS), and Bayesian principal component analysis (BPCA). However, the effects of these imputation methods on the modelling of gene regulatory networks from gene expression data have rarely been investigated and analysed using a dynamic Bayesian network (DBN). Methods: In the present study, we separately imputed datasets of the Escherichia coli S.O.S. DNA repair pathway and the Saccharomyces cerevisiae cell cycle pathway with kNN, LLS, and BPCA, and subsequently used these to generate gene regulatory networks (GRNs) using a discrete DBN. We made comparisons on the basis of previous studies in order to select the gene network with the least error. Results: We found that BPCA and LLS performed better on larger networks (based on the S. cerevisiae dataset), whereas kNN performed better on smaller networks (based on the E. coli dataset). Conclusion: The results suggest that the performance of each imputation method is dependent on the size of the dataset, and this subsequently affects the modelling of the resultant GRNs using a DBN. In addition, on the basis of these results, a DBN has the capacity to discover potential edges, as well as display interactions, between genes. PMID:24876803

  10. Candidate gene association study in pediatric acute lymphoblastic leukemia evaluated by Bayesian network based Bayesian multilevel analysis of relevance

    PubMed Central

    2012-01-01

    Background We carried out a candidate gene association study in pediatric acute lymphoblastic leukemia (ALL) to identify possible genetic risk factors in a Hungarian population. Methods The results were evaluated with traditional statistical methods and with our newly developed Bayesian network based Bayesian multilevel analysis of relevance (BN-BMLA) method. We collected genomic DNA and clinical data from 543 children, who underwent chemotherapy due to ALL, and 529 healthy controls. Altogether 66 single nucleotide polymorphisms (SNPs) in 19 candidate genes were genotyped. Results With logistic regression, we identified 6 SNPs in the ARID5B and IKZF1 genes associated with increased risk to B-cell ALL, and two SNPs in the STAT3 gene, which decreased the risk to hyperdiploid ALL. Because the associated SNPs were in linkage in each gene, these associations corresponded to one signal per gene. The odds ratio (OR) associated with the tag SNPs were: OR = 1.69, P = 2.22x10-7 for rs4132601 (IKZF1), OR = 1.53, P = 1.95x10-5 for rs10821936 (ARID5B) and OR = 0.64, P = 2.32x10-4 for rs12949918 (STAT3). With the BN-BMLA we confirmed the findings of the frequentist-based method and received additional information about the nature of the relations between the SNPs and the disease. E.g. the rs10821936 in ARID5B and rs17405722 in STAT3 showed a weak interaction, and in case of T-cell lineage sample group, the gender showed a weak interaction with three SNPs in three genes. In the hyperdiploid patient group the BN-BMLA detected a strong interaction among SNPs in the NOTCH1, STAT1, STAT3 and BCL2 genes. Evaluating the survival rate of the patients with ALL, the BN-BMLA showed that besides risk groups and subtypes, genetic variations in the BAX and CEBPA genes might also influence the probability of survival of the patients. Conclusions In the present study we confirmed the roles of genetic variations in ARID5B and IKZF1 in the susceptibility to B-cell ALL

  11. Nonlinear inversion of electrical resistivity imaging using pruning Bayesian neural networks

    NASA Astrophysics Data System (ADS)

    Jiang, Fei-Bo; Dai, Qian-Wei; Dong, Li

    2016-06-01

    Conventional artificial neural networks used to solve electrical resistivity imaging (ERI) inversion problem suffer from overfitting and local minima. To solve these problems, we propose to use a pruning Bayesian neural network (PBNN) nonlinear inversion method and a sample design method based on the K-medoids clustering algorithm. In the sample design method, the training samples of the neural network are designed according to the prior information provided by the K-medoids clustering results; thus, the training process of the neural network is well guided. The proposed PBNN, based on Bayesian regularization, is used to select the hidden layer structure by assessing the effect of each hidden neuron to the inversion results. Then, the hyperparameter α k , which is based on the generalized mean, is chosen to guide the pruning process according to the prior distribution of the training samples under the small-sample condition. The proposed algorithm is more efficient than other common adaptive regularization methods in geophysics. The inversion of synthetic data and field data suggests that the proposed method suppresses the noise in the neural network training stage and enhances the generalization. The inversion results with the proposed method are better than those of the BPNN, RBFNN, and RRBFNN inversion methods as well as the conventional least squares inversion.

  12. Reconstruction of large-scale gene regulatory networks using Bayesian model averaging.

    PubMed

    Kim, Haseong; Gelenbe, Erol

    2012-09-01

    Gene regulatory networks provide the systematic view of molecular interactions in a complex living system. However, constructing large-scale gene regulatory networks is one of the most challenging problems in systems biology. Also large burst sets of biological data require a proper integration technique for reliable gene regulatory network construction. Here we present a new reverse engineering approach based on Bayesian model averaging which attempts to combine all the appropriate models describing interactions among genes. This Bayesian approach with a prior based on the Gibbs distribution provides an efficient means to integrate multiple sources of biological data. In a simulation study with maximum of 2000 genes, our method shows better sensitivity than previous elastic-net and Gaussian graphical models, with a fixed specificity of 0.99. The study also shows that the proposed method outperforms the other standard methods for a DREAM dataset generated by nonlinear stochastic models. In brain tumor data analysis, three large-scale networks consisting of 4422 genes were built using the gene expression of non-tumor, low and high grade tumor mRNA expression samples, along with DNA-protein binding affinity information. We found that genes having a large variation of degree distribution among the three tumor networks are the ones that see most involved in regulatory and developmental processes, which possibly gives a novel insight concerning conventional differentially expressed gene analysis. PMID:22987132

  13. Using mechanistic Bayesian networks to identify downstream targets of the Sonic Hedgehog pathway

    PubMed Central

    2009-01-01

    Background The topology of a biological pathway provides clues as to how a pathway operates, but rationally using this topology information with observed gene expression data remains a challenge. Results We introduce a new general-purpose analytic method called Mechanistic Bayesian Networks (MBNs) that allows for the integration of gene expression data and known constraints within a signal or regulatory pathway to predict new downstream pathway targets. The MBN framework is implemented in an open-source Bayesian network learning package, the Python Environment for Bayesian Learning (PEBL). We demonstrate how MBNs can be used by modeling the early steps of the sonic hedgehog pathway using gene expression data from different developmental stages and genetic backgrounds in mouse. Using the MBN approach we are able to automatically identify many of the known downstream targets of the hedgehog pathway such as Gas1 and Gli1, along with a short list of likely targets such as Mig12. Conclusions The MBN approach shown here can easily be extended to other pathways and data types to yield a more mechanistic framework for learning genetic regulatory models. PMID:20021670

  14. Experimental design and Bayesian networks for enhancement of delta-endotoxin production by Bacillus thuringiensis.

    PubMed

    Ennouri, Karim; Ayed, Rayda Ben; Hassen, Hanen Ben; Mazzarello, Maura; Ottaviani, Ennio

    2015-12-01

    Bacillus thuringiensis (Bt) is a Gram-positive bacterium. The entomopathogenic activity of Bt is related to the existence of the crystal consisting of protoxins, also called delta-endotoxins. In order to optimize and explain the production of delta-endotoxins of Bacillus thuringiensis kurstaki, we studied seven medium components: soybean meal, starch, KH₂PO₄, K₂HPO₄, FeSO₄, MnSO₄, and MgSO₄and their relationships with the concentration of delta-endotoxins using an experimental design (Plackett-Burman design) and Bayesian networks modelling. The effects of the ingredients of the culture medium on delta-endotoxins production were estimated. The developed model showed that different medium components are important for the Bacillus thuringiensis fermentation. The most important factors influenced the production of delta-endotoxins are FeSO₄, K2HPO₄, starch and soybean meal. Indeed, it was found that soybean meal, K₂HPO₄, KH₂PO₄and starch also showed positive effect on the delta-endotoxins production. However, FeSO4 and MnSO4 expressed opposite effect. The developed model, based on Bayesian techniques, can automatically learn emerging models in data to serve in the prediction of delta-endotoxins concentrations. The constructed model in the present study implies that experimental design (Plackett-Burman design) joined with Bayesian networks method could be used for identification of effect variables on delta-endotoxins variation. PMID:26689874

  15. Bayesian Belief Networks for Astronomical Object Recognition and Classification in CTI-II

    NASA Astrophysics Data System (ADS)

    Ritthaler, M.; Luger, G.; Young, R. Mcgraw, J.; Zimmer, P.

    2007-10-01

    The University of New Mexico (UNM) is currently designing and building the CCD Transit Instrument II (CTI-II: McGraw et al. 2006), a 1.8-m transit survey telescope. The stationary CTI-II uses the time delay and integrate readout mode with a mosaic of CCDs to generate over 100 gigapixels per night which are required to be analyzed within a day of observation. We are attempting to develop robust machine learning techniques that use multiple scientific and engineering data streams to classify objects within an image frame and the image frame itself. We propose the use of Bayesian belief nets as both classifiers and as tools to integrate and explore the data streams. This initial report explores the use of Bayesian networks as source/noise separators.

  16. Learning an L1-regularized Gaussian Bayesian network in the equivalence class space.

    PubMed

    Vidaurre, Diego; Bielza, Concha; Larrañaga, Pedro

    2010-10-01

    Learning the structure of a graphical model from data is a common task in a wide range of practical applications. In this paper, we focus on Gaussian Bayesian networks, i.e., on continuous data and directed acyclic graphs with a joint probability density of all variables given by a Gaussian. We propose to work in an equivalence class search space, specifically using the k-greedy equivalence search algorithm. This, combined with regularization techniques to guide the structure search, can learn sparse networks close to the one that generated the data. We provide results on some synthetic networks and on modeling the gene network of the two biological pathways regulating the biosynthesis of isoprenoids for the Arabidopsis thaliana plant. PMID:20083459

  17. Prediction and assimilation of surf-zone processes using a Bayesian network: Part II: Inverse models

    USGS Publications Warehouse

    Plant, Nathaniel G.; Holland, K. Todd

    2011-01-01

    A Bayesian network model has been developed to simulate a relatively simple problem of wave propagation in the surf zone (detailed in Part I). Here, we demonstrate that this Bayesian model can provide both inverse modeling and data-assimilation solutions for predicting offshore wave heights and depth estimates given limited wave-height and depth information from an onshore location. The inverse method is extended to allow data assimilation using observational inputs that are not compatible with deterministic solutions of the problem. These inputs include sand bar positions (instead of bathymetry) and estimates of the intensity of wave breaking (instead of wave-height observations). Our results indicate that wave breaking information is essential to reduce prediction errors. In many practical situations, this information could be provided from a shore-based observer or from remote-sensing systems. We show that various combinations of the assimilated inputs significantly reduce the uncertainty in the estimates of water depths and wave heights in the model domain. Application of the Bayesian network model to new field data demonstrated significant predictive skill (R2 = 0.7) for the inverse estimate of a month-long time series of offshore wave heights. The Bayesian inverse results include uncertainty estimates that were shown to be most accurate when given uncertainty in the inputs (e.g., depth and tuning parameters). Furthermore, the inverse modeling was extended to directly estimate tuning parameters associated with the underlying wave-process model. The inverse estimates of the model parameters not only showed an offshore wave height dependence consistent with results of previous studies but the uncertainty estimates of the tuning parameters also explain previously reported variations in the model parameters.

  18. Analysis of molecular expression patterns and integration with other knowledge bases using probabilistic Bayesian network models

    SciTech Connect

    Moler, Edward J.; Mian, I.S.

    2000-03-01

    How can molecular expression experiments be interpreted with greater than ten to the fourth measurements per chip? How can one get the most quantitative information possible from the experimental data with good confidence? These are important questions whose solutions require an interdisciplinary combination of molecular and cellular biology, computer science, statistics, and complex systems analysis. The explosion of data from microarray techniques present the problem of interpreting the experiments. The availability of large-scale knowledge bases provide the opportunity to maximize the information extracted from these experiments. We have developed new methods of discovering biological function, metabolic pathways, and regulatory networks from these data and knowledge bases. These techniques are applicable to analyses for biomedical engineering, clinical, and fundamental cell and molecular biology studies. Our approach uses probabilistic, computational methods that give quantitative interpretations of data in a biological context. We have selected Bayesian statistical models with graphical network representations as a framework for our methods. As a first step, we use a nave Bayesian classifier to identify statistically significant patterns in gene expression data. We have developed methods which allow us to (a) characterize which genes or experiments distinguish each class from the others, (b) cross-index the resulting classes with other databases to assess biological meaning of the classes, and (c) display a gross overview of cellular dynamics. We have developed a number of visualization tools to convey the results. We report here our methods of classification and our first attempts at integrating the data and other knowledge bases together with new visualization tools. We demonstrate the utility of these methods and tools by analysis of a series of yeast cDNA microarray data and to a set of cancerous/normal sample data from colon cancer patients. We discuss

  19. Bayesian network reconstruction using systems genetics data: comparison of MCMC methods.

    PubMed

    Tasaki, Shinya; Sauerwine, Ben; Hoff, Bruce; Toyoshiba, Hiroyoshi; Gaiteri, Chris; Chaibub Neto, Elias

    2015-04-01

    Reconstructing biological networks using high-throughput technologies has the potential to produce condition-specific interactomes. But are these reconstructed networks a reliable source of biological interactions? Do some network inference methods offer dramatically improved performance on certain types of networks? To facilitate the use of network inference methods in systems biology, we report a large-scale simulation study comparing the ability of Markov chain Monte Carlo (MCMC) samplers to reverse engineer Bayesian networks. The MCMC samplers we investigated included foundational and state-of-the-art Metropolis-Hastings and Gibbs sampling approaches, as well as novel samplers we have designed. To enable a comprehensive comparison, we simulated gene expression and genetics data from known network structures under a range of biologically plausible scenarios. We examine the overall quality of network inference via different methods, as well as how their performance is affected by network characteristics. Our simulations reveal that network size, edge density, and strength of gene-to-gene signaling are major parameters that differentiate the performance of various samplers. Specifically, more recent samplers including our novel methods outperform traditional samplers for highly interconnected large networks with strong gene-to-gene signaling. Our newly developed samplers show comparable or superior performance to the top existing methods. Moreover, this performance gain is strongest in networks with biologically oriented topology, which indicates that our novel samplers are suitable for inferring biological networks. The performance of MCMC samplers in this simulation framework can guide the choice of methods for network reconstruction using systems genetics data. PMID:25631319

  20. Bayesian Network Reconstruction Using Systems Genetics Data: Comparison of MCMC Methods

    PubMed Central

    Tasaki, Shinya; Sauerwine, Ben; Hoff, Bruce; Toyoshiba, Hiroyoshi; Gaiteri, Chris; Chaibub Neto, Elias

    2015-01-01

    Reconstructing biological networks using high-throughput technologies has the potential to produce condition-specific interactomes. But are these reconstructed networks a reliable source of biological interactions? Do some network inference methods offer dramatically improved performance on certain types of networks? To facilitate the use of network inference methods in systems biology, we report a large-scale simulation study comparing the ability of Markov chain Monte Carlo (MCMC) samplers to reverse engineer Bayesian networks. The MCMC samplers we investigated included foundational and state-of-the-art Metropolis–Hastings and Gibbs sampling approaches, as well as novel samplers we have designed. To enable a comprehensive comparison, we simulated gene expression and genetics data from known network structures under a range of biologically plausible scenarios. We examine the overall quality of network inference via different methods, as well as how their performance is affected by network characteristics. Our simulations reveal that network size, edge density, and strength of gene-to-gene signaling are major parameters that differentiate the performance of various samplers. Specifically, more recent samplers including our novel methods outperform traditional samplers for highly interconnected large networks with strong gene-to-gene signaling. Our newly developed samplers show comparable or superior performance to the top existing methods. Moreover, this performance gain is strongest in networks with biologically oriented topology, which indicates that our novel samplers are suitable for inferring biological networks. The performance of MCMC samplers in this simulation framework can guide the choice of methods for network reconstruction using systems genetics data. PMID:25631319

  1. Bayesian WLS/GLS regression for regional skewness analysis for regions with large crest stage gage networks

    USGS Publications Warehouse

    Veilleux, Andrea G.; Stedinger, Jery R.; Eash, David A.

    2012-01-01

    This paper summarizes methodological advances in regional log-space skewness analyses that support flood-frequency analysis with the log Pearson Type III (LP3) distribution. A Bayesian Weighted Least Squares/Generalized Least Squares (B-WLS/B-GLS) methodology that relates observed skewness coefficient estimators to basin characteristics in conjunction with diagnostic statistics represents an extension of the previously developed B-GLS methodology. B-WLS/B-GLS has been shown to be effective in two California studies. B-WLS/B-GLS uses B-WLS to generate stable estimators of model parameters and B-GLS to estimate the precision of those B-WLS regression parameters, as well as the precision of the model. The study described here employs this methodology to develop a regional skewness model for the State of Iowa. To provide cost effective peak-flow data for smaller drainage basins in Iowa, the U.S. Geological Survey operates a large network of crest stage gages (CSGs) that only record flow values above an identified recording threshold (thus producing a censored data record). CSGs are different from continuous-record gages, which record almost all flow values and have been used in previous B-GLS and B-WLS/B-GLS regional skewness studies. The complexity of analyzing a large CSG network is addressed by using the B-WLS/B-GLS framework along with the Expected Moments Algorithm (EMA). Because EMA allows for the censoring of low outliers, as well as the use of estimated interval discharges for missing, censored, and historic data, it complicates the calculations of effective record length (and effective concurrent record length) used to describe the precision of sample estimators because the peak discharges are no longer solely represented by single values. Thus new record length calculations were developed. The regional skewness analysis for the State of Iowa illustrates the value of the new B-WLS/BGLS methodology with these new extensions.

  2. A program for the Bayesian Neural Network in the ROOT framework

    NASA Astrophysics Data System (ADS)

    Zhong, Jiahang; Huang, Run-Sheng; Lee, Shih-Chang

    2011-12-01

    We present a Bayesian Neural Network algorithm implemented in the TMVA package (Hoecker et al., 2007 [1]), within the ROOT framework (Brun and Rademakers, 1997 [2]). Comparing to the conventional utilization of Neural Network as discriminator, this new implementation has more advantages as a non-parametric regression tool, particularly for fitting probabilities. It provides functionalities including cost function selection, complexity control and uncertainty estimation. An example of such application in High Energy Physics is shown. The algorithm is available with ROOT release later than 5.29. Program summaryProgram title: TMVA-BNN Catalogue identifier: AEJX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: BSD license No. of lines in distributed program, including test data, etc.: 5094 No. of bytes in distributed program, including test data, etc.: 1,320,987 Distribution format: tar.gz Programming language: C++ Computer: Any computer system or cluster with C++ compiler and UNIX-like operating system Operating system: Most UNIX/Linux systems. The application programs were thoroughly tested under Fedora and Scientific Linux CERN. Classification: 11.9 External routines: ROOT package version 5.29 or higher ( http://root.cern.ch) Nature of problem: Non-parametric fitting of multivariate distributions Solution method: An implementation of Neural Network following the Bayesian statistical interpretation. Uses Laplace approximation for the Bayesian marginalizations. Provides the functionalities of automatic complexity control and uncertainty estimation. Running time: Time consumption for the training depends substantially on the size of input sample, the NN topology, the number of training iterations, etc. For the example in this manuscript, about 7 min was used on a PC/Linux with 2.0 GHz processors.

  3. 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.

  4. Discovering complex interrelationships between socioeconomic status and health in Europe: A case study applying Bayesian Networks.

    PubMed

    Alvarez-Galvez, Javier

    2016-03-01

    Studies assume that socioeconomic status determines individuals' states of health, but how does health determine socioeconomic status? And how does this association vary depending on contextual differences? To answer this question, our study uses an additive Bayesian Networks model to explain the interrelationships between health and socioeconomic determinants using complex and messy data. This model has been used to find the most probable structure in a network to describe the interdependence of these factors in five European welfare state regimes. The advantage of this study is that it offers a specific picture to describe the complex interrelationship between socioeconomic determinants and health, producing a network that is controlled by socio-demographic factors such as gender and age. The present work provides a general framework to describe and understand the complex association between socioeconomic determinants and health. PMID:26857177

  5. Object-oriented Bayesian networks for paternity cases with allelic dependencies

    PubMed Central

    Hepler, Amanda B.; Weir, Bruce S.

    2008-01-01

    This study extends the current use of Bayesian networks by incorporating the effects of allelic dependencies in paternity calculations. The use of object-oriented networks greatly simplify the process of building and interpreting forensic identification models, allowing researchers to solve new, more complex problems. We explore two paternity examples: the most common scenario where DNA evidence is available from the alleged father, the mother and the child; a more complex casewhere DNA is not available from the alleged father, but is available from the alleged father’s brother. Object-oriented networks are built, using HUGIN, for each example which incorporate the effects of allelic dependence caused by evolutionary relatedness. PMID:19079769

  6. Cerebral Glioma Grading Using Bayesian Network with Features Extracted from Multiple Modalities of Magnetic Resonance Imaging

    PubMed Central

    Wang, Huiting; Liu, Renyuan; Zhang, Xin; Li, Ming; Yang, Yongbo; Yan, Jing; Niu, Fengnan; Tian, Chuanshuai; Wang, Kun; Yu, Haiping; Chen, Weibo; Wan, Suiren; Sun, Yu; Zhang, Bing

    2016-01-01

    Many modalities of magnetic resonance imaging (MRI) have been confirmed to be of great diagnostic value in glioma grading. Contrast enhanced T1-weighted imaging allows the recognition of blood-brain barrier breakdown. Perfusion weighted imaging and MR spectroscopic imaging enable the quantitative measurement of perfusion parameters and metabolic alterations respectively. These modalities can potentially improve the grading process in glioma if combined properly. In this study, Bayesian Network, which is a powerful and flexible method for probabilistic analysis under uncertainty, is used to combine features extracted from contrast enhanced T1-weighted imaging, perfusion weighted imaging and MR spectroscopic imaging. The networks were constructed using K2 algorithm along with manual determination and distribution parameters learned using maximum likelihood estimation. The grading performance was evaluated in a leave-one-out analysis, achieving an overall grading accuracy of 92.86% and an area under the curve of 0.9577 in the receiver operating characteristic analysis given all available features observed in the total 56 patients. Results and discussions show that Bayesian Network is promising in combining features from multiple modalities of MRI for improved grading performance. PMID:27077923

  7. Forensic Signature Detection of Yersinia Pestis Culturing Practices Across Institutions Using a Bayesian Network

    SciTech Connect

    Webb-Robertson, Bobbie-Jo M.; Corley, Courtney D.; McCue, Lee Ann; Clowers, Brian H.; Dowling, Chase P.; Wahl, Karen L.; Wunschel, David S.; Kreuzer, Helen W.

    2014-03-21

    The field of bioforensics is focused on the analysis of evidence from a biocrime. Existing laboratory analyses can identify the specific strain of an organism in the evidence, as well signatures of the specific culture batch of organisms, such as low-frequency contaminants or indicators of growth and processing methods. To link these disparate types of physical data to potential suspects, investigators may need to identify institutions or individuals whose access to strains and culturing practices match those identified from the evidence. In this work we present a Bayesian statistical network to fuse different types of analytical measurements that predict the production environment of a Yersinia pestis sample under investigation with automated test processing of scientific publications to identify institutions with a history of growing Y. pestis under similar conditions. Furthermore, the textual and experimental signatures were evaluated recursively to determine the overall sensitivity of the network across all levels of false positives. We illustrate that institutions associated with several specific culturing practices can be accurately selected based on the experimental signature from only a few analytical measurements. These findings demonstrate that similar Bayesian networks can be generated generically for many organisms of interest and their deployment is not prohibitive due to either computational or experimental factors.

  8. Bayesian Neural Networks for Uncertainty Analysis of Hydrologic Modeling: A Comparison of Two Schemes

    SciTech Connect

    Zhang, Xuesong; Zhao, Kaiguang

    2012-06-01

    Bayesian Neural Networks (BNNs) have been shown as useful tools to analyze modeling uncertainty of Neural Networks (NNs). This research focuses on the comparison of two BNNs. The first BNNs (BNN-I) use statistical methods to describe the characteristics of different uncertainty sources (input, parameter, and model structure) and integrate these uncertainties into a Markov Chain Monte Carlo (MCMC) framework to estimate total uncertainty. The second BNNs (BNN-II) lump all uncertainties into a single error term (i.e. the residual between model prediction and measurement). In this study, we propose a simple BNN-II, which use Genetic Algorithms (GA) and Bayesian Model Averaging (BMA) to calibrate Neural Networks with different structures (number of hidden units) and combine the predictions from different NNs to derive predictions and uncertainty analysis. We tested these two BNNs in two watersheds for daily and monthly hydrologic simulation. The BMA based BNNs developed in this study outperforms BNN-I in the two watersheds in terms of both accurate prediction and uncertainty estimation. These results show that, given incomplete understanding of the characteristics associated with each uncertainty source, the simple lumped error approach may yield better prediction and uncertainty estimation.

  9. A Bayesian network model for integrative river rehabilitation planning and management.

    PubMed

    Borsuk, Mark E; Schweizer, Steffen; Reichert, Peter

    2012-07-01

    As rehabilitation of previously channelized rivers becomes more common worldwide, flexible integrative modeling tools are needed to help predict the morphological, hydraulic, economic, and ecological consequences of the rehabilitation activities. Such predictions can provide the basis for planning and long-term management efforts that attempt to balance the diverse interests of river system stakeholders. We have previously reported on a variety of modeling methods and decision support concepts that can assist with various aspects of the river rehabilitation process. Here, we bring all of these tools together into a probability network model that links management actions, through morphological and hydraulic changes, to the ultimate ecological and economic consequences. Although our model uses a causal graph representation common to Bayesian networks, we do not limit ourselves to discrete-valued nodes or conditional Gaussian distributions as required by most Bayesian network implementations. This precludes us from carrying out easy probabilistic inference but gives us the advantages of functional and distributional flexibility and enhanced predictive accuracy, which we believe to be more important in most environmental management applications. We exemplify model application to a large, recently completed rehabilitation project in Switzerland. PMID:21608112

  10. Spatial component analysis of MRI data for Alzheimer's disease diagnosis: a Bayesian network approach

    PubMed Central

    Illan, Ignacio A.; Górriz, Juan M.; Ramírez, Javier; Meyer-Base, Anke

    2014-01-01

    This work presents a spatial-component (SC) based approach to aid the diagnosis of Alzheimer's disease (AD) using magnetic resonance images. In this approach, the whole brain image is subdivided in regions or spatial components, and a Bayesian network is used to model the dependencies between affected regions of AD. The structure of relations between affected regions allows to detect neurodegeneration with an estimated performance of 88% on more than 400 subjects and predict neurodegeneration with 80% accuracy, supporting the conclusion that modeling the dependencies between components increases the recognition of different patterns of brain degeneration in AD. PMID:25505408

  11. Gene regulatory network reconstruction by Bayesian integration of prior knowledge and/or different experimental conditions.

    PubMed

    Werhli, Adriano V; Husmeier, Dirk

    2008-06-01

    There have been various attempts to improve the reconstruction of gene regulatory networks from microarray data by the systematic integration of biological prior knowledge. Our approach is based on pioneering work by Imoto et al. where the prior knowledge is expressed in terms of energy functions, from which a prior distribution over network structures is obtained in the form of a Gibbs distribution. The hyperparameters of this distribution represent the weights associated with the prior knowledge relative to the data. We have derived and tested a Markov chain Monte Carlo (MCMC) scheme for sampling networks and hyperparameters simultaneously from the posterior distribution, thereby automatically learning how to trade off information from the prior knowledge and the data. We have extended this approach to a Bayesian coupling scheme for learning gene regulatory networks from a combination of related data sets, which were obtained under different experimental conditions and are therefore potentially associated with different active subpathways. The proposed coupling scheme is a compromise between (1) learning networks from the different subsets separately, whereby no information between the different experiments is shared; and (2) learning networks from a monolithic fusion of the individual data sets, which does not provide any mechanism for uncovering differences between the network structures associated with the different experimental conditions. We have assessed the viability of all proposed methods on data related to the Raf signaling pathway, generated both synthetically and in cytometry experiments. PMID:18574862

  12. Context Specific and Differential Gene Co-expression Networks via Bayesian Biclustering.

    PubMed

    Gao, Chuan; McDowell, Ian C; Zhao, Shiwen; Brown, Christopher D; Engelhardt, Barbara E

    2016-07-01

    Identifying latent structure in high-dimensional genomic data is essential for exploring biological processes. Here, we consider recovering gene co-expression networks from gene expression data, where each network encodes relationships between genes that are co-regulated by shared biological mechanisms. To do this, we develop a Bayesian statistical model for biclustering to infer subsets of co-regulated genes that covary in all of the samples or in only a subset of the samples. Our biclustering method, BicMix, allows overcomplete representations of the data, computational tractability, and joint modeling of unknown confounders and biological signals. Compared with related biclustering methods, BicMix recovers latent structure with higher precision across diverse simulation scenarios as compared to state-of-the-art biclustering methods. Further, we develop a principled method to recover context specific gene co-expression networks from the estimated sparse biclustering matrices. We apply BicMix to breast cancer gene expression data and to gene expression data from a cardiovascular study cohort, and we recover gene co-expression networks that are differential across ER+ and ER- samples and across male and female samples. We apply BicMix to the Genotype-Tissue Expression (GTEx) pilot data, and we find tissue specific gene networks. We validate these findings by using our tissue specific networks to identify trans-eQTLs specific to one of four primary tissues. PMID:27467526

  13. Context Specific and Differential Gene Co-expression Networks via Bayesian Biclustering

    PubMed Central

    McDowell, Ian C.; Zhao, Shiwen; Brown, Christopher D.; Engelhardt, Barbara E.

    2016-01-01

    Identifying latent structure in high-dimensional genomic data is essential for exploring biological processes. Here, we consider recovering gene co-expression networks from gene expression data, where each network encodes relationships between genes that are co-regulated by shared biological mechanisms. To do this, we develop a Bayesian statistical model for biclustering to infer subsets of co-regulated genes that covary in all of the samples or in only a subset of the samples. Our biclustering method, BicMix, allows overcomplete representations of the data, computational tractability, and joint modeling of unknown confounders and biological signals. Compared with related biclustering methods, BicMix recovers latent structure with higher precision across diverse simulation scenarios as compared to state-of-the-art biclustering methods. Further, we develop a principled method to recover context specific gene co-expression networks from the estimated sparse biclustering matrices. We apply BicMix to breast cancer gene expression data and to gene expression data from a cardiovascular study cohort, and we recover gene co-expression networks that are differential across ER+ and ER- samples and across male and female samples. We apply BicMix to the Genotype-Tissue Expression (GTEx) pilot data, and we find tissue specific gene networks. We validate these findings by using our tissue specific networks to identify trans-eQTLs specific to one of four primary tissues. PMID:27467526

  14. Quantification of biophysical adaptation benefits from Climate-Smart Agriculture using a Bayesian Belief Network

    NASA Astrophysics Data System (ADS)

    de Nijs, Patrick J.; Berry, Nicholas J.; Wells, Geoff J.; Reay, Dave S.

    2014-10-01

    The need for smallholder farmers to adapt their practices to a changing climate is well recognised, particularly in Africa. The cost of adapting to climate change in Africa is estimated to be $20 to $30 billion per year, but the total amount pledged to finance adaptation falls significantly short of this requirement. The difficulty of assessing and monitoring when adaptation is achieved is one of the key barriers to the disbursement of performance-based adaptation finance. To demonstrate the potential of Bayesian Belief Networks for describing the impacts of specific activities on climate change resilience, we developed a simple model that incorporates climate projections, local environmental data, information from peer-reviewed literature and expert opinion to account for the adaptation benefits derived from Climate-Smart Agriculture activities in Malawi. This novel approach allows assessment of vulnerability to climate change under different land use activities and can be used to identify appropriate adaptation strategies and to quantify biophysical adaptation benefits from activities that are implemented. We suggest that multiple-indicator Bayesian Belief Network approaches can provide insights into adaptation planning for a wide range of applications and, if further explored, could be part of a set of important catalysts for the expansion of adaptation finance.

  15. A Bayesian network approach to knowledge integration and representation of farm irrigation: 1. Model development

    NASA Astrophysics Data System (ADS)

    Wang, Q. J.; Robertson, D. E.; Haines, C. L.

    2009-02-01

    Irrigation is important to many agricultural businesses but also has implications for catchment health. A considerable body of knowledge exists on how irrigation management affects farm business and catchment health. However, this knowledge is fragmentary; is available in many forms such as qualitative and quantitative; is dispersed in scientific literature, technical reports, and the minds of individuals; and is of varying degrees of certainty. Bayesian networks allow the integration of dispersed knowledge into quantitative systems models. This study describes the development, validation, and application of a Bayesian network model of farm irrigation in the Shepparton Irrigation Region of northern Victoria, Australia. In this first paper we describe the process used to integrate a range of sources of knowledge to develop a model of farm irrigation. We describe the principal model components and summarize the reaction to the model and its development process by local stakeholders. Subsequent papers in this series describe model validation and the application of the model to assess the regional impact of historical and future management intervention.

  16. Intelligent Condition Diagnosis Method Based on Adaptive Statistic Test Filter and Diagnostic Bayesian Network

    PubMed Central

    Li, Ke; Zhang, Qiuju; Wang, Kun; Chen, Peng; Wang, Huaqing

    2016-01-01

    A new fault diagnosis method for rotating machinery based on adaptive statistic test filter (ASTF) and Diagnostic Bayesian Network (DBN) is presented in this paper. ASTF is proposed to obtain weak fault features under background noise, ASTF is based on statistic hypothesis testing in the frequency domain to evaluate similarity between reference signal (noise signal) and original signal, and remove the component of high similarity. The optimal level of significance α is obtained using particle swarm optimization (PSO). To evaluate the performance of the ASTF, evaluation factor Ipq is also defined. In addition, a simulation experiment is designed to verify the effectiveness and robustness of ASTF. A sensitive evaluation method using principal component analysis (PCA) is proposed to evaluate the sensitiveness of symptom parameters (SPs) for condition diagnosis. By this way, the good SPs that have high sensitiveness for condition diagnosis can be selected. A three-layer DBN is developed to identify condition of rotation machinery based on the Bayesian Belief Network (BBN) theory. Condition diagnosis experiment for rolling element bearings demonstrates the effectiveness of the proposed method. PMID:26761006

  17. Developing a Validation Methodology for Expert-Informed Bayesian Network Models Supporting Nuclear Nonproliferation Analysis

    SciTech Connect

    White, Amanda M.; Gastelum, Zoe N.; Whitney, Paul D.

    2014-05-13

    Under the auspices of Pacific Northwest National Laboratory’s Signature Discovery Initiative (SDI), the research team developed a series of Bayesian Network models to assess multi-source signatures of nuclear programs. A Bayesian network is a mathematical model that can be used to marshal evidence to assess competing hypotheses. The purpose of the models was to allow non-expert analysts to benefit from the use of expert-informed mathematical models to assess nuclear programs, because such assessments require significant technical expertise ranging from the nuclear fuel cycle, construction and engineering, imagery analysis, and so forth. One such model developed under this research was aimed at assessing the consistency of open-source information about a nuclear facility with the facility’s declared use. The model incorporates factors such as location, security and safety features among others identified by subject matter experts as crucial to their assessments. The model includes key features, observables and their relationships. The model also provides documentation, which serves as training materials for the non-experts.

  18. Fuzzy Bayesian Network-Bow-Tie Analysis of Gas Leakage during Biomass Gasification.

    PubMed

    Yan, Fang; Xu, Kaili; Yao, Xiwen; Li, Yang

    2016-01-01

    Biomass gasification technology has been rapidly developed recently. But fire and poisoning accidents caused by gas leakage restrict the development and promotion of biomass gasification. Therefore, probabilistic safety assessment (PSA) is necessary for biomass gasification system. Subsequently, Bayesian network-bow-tie (BN-bow-tie) analysis was proposed by mapping bow-tie analysis into Bayesian network (BN). Causes of gas leakage and the accidents triggered by gas leakage can be obtained by bow-tie analysis, and BN was used to confirm the critical nodes of accidents by introducing corresponding three importance measures. Meanwhile, certain occurrence probability of failure was needed in PSA. In view of the insufficient failure data of biomass gasification, the occurrence probability of failure which cannot be obtained from standard reliability data sources was confirmed by fuzzy methods based on expert judgment. An improved approach considered expert weighting to aggregate fuzzy numbers included triangular and trapezoidal numbers was proposed, and the occurrence probability of failure was obtained. Finally, safety measures were indicated based on the obtained critical nodes. The theoretical occurrence probabilities in one year of gas leakage and the accidents caused by it were reduced to 1/10.3 of the original values by these safety measures. PMID:27463975

  19. Predicting Mycobacterium tuberculosis Complex Clades Using Knowledge-Based Bayesian Networks

    PubMed Central

    Bennett, Kristin P.

    2014-01-01

    We develop a novel approach for incorporating expert rules into Bayesian networks for classification of Mycobacterium tuberculosis complex (MTBC) clades. The proposed knowledge-based Bayesian network (KBBN) treats sets of expert rules as prior distributions on the classes. Unlike prior knowledge-based support vector machine approaches which require rules expressed as polyhedral sets, KBBN directly incorporates the rules without any modification. KBBN uses data to refine rule-based classifiers when the rule set is incomplete or ambiguous. We develop a predictive KBBN model for 69 MTBC clades found in the SITVIT international collection. We validate the approach using two testbeds that model knowledge of the MTBC obtained from two different experts and large DNA fingerprint databases to predict MTBC genetic clades and sublineages. These models represent strains of MTBC using high-throughput biomarkers called spacer oligonucleotide types (spoligotypes), since these are routinely gathered from MTBC isolates of tuberculosis (TB) patients. Results show that incorporating rules into problems can drastically increase classification accuracy if data alone are insufficient. The SITVIT KBBN is publicly available for use on the World Wide Web. PMID:24864238

  20. Nuclear mass predictions for the crustal composition of neutron stars: A Bayesian neural network approach

    NASA Astrophysics Data System (ADS)

    Utama, R.; Piekarewicz, J.; Prosper, H. B.

    2016-01-01

    Background: Besides their intrinsic nuclear-structure value, nuclear mass models are essential for astrophysical applications, such as r -process nucleosynthesis and neutron-star structure. Purpose: To overcome the intrinsic limitations of existing "state-of-the-art" mass models through a refinement based on a Bayesian neural network (BNN) formalism. Methods: A novel BNN approach is implemented with the goal of optimizing mass residuals between theory and experiment. Results: A significant improvement (of about 40%) in the mass predictions of existing models is obtained after BNN refinement. Moreover, these improved results are now accompanied by proper statistical errors. Finally, by constructing a "world average" of these predictions, a mass model is obtained that is used to predict the composition of the outer crust of a neutron star. Conclusions: The power of the Bayesian neural network method has been successfully demonstrated by a systematic improvement in the accuracy of the predictions of nuclear masses. Extension to other nuclear observables is a natural next step that is currently under investigation.

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  2. Intelligent Condition Diagnosis Method Based on Adaptive Statistic Test Filter and Diagnostic Bayesian Network.

    PubMed

    Li, Ke; Zhang, Qiuju; Wang, Kun; Chen, Peng; Wang, Huaqing

    2016-01-01

    A new fault diagnosis method for rotating machinery based on adaptive statistic test filter (ASTF) and Diagnostic Bayesian Network (DBN) is presented in this paper. ASTF is proposed to obtain weak fault features under background noise, ASTF is based on statistic hypothesis testing in the frequency domain to evaluate similarity between reference signal (noise signal) and original signal, and remove the component of high similarity. The optimal level of significance α is obtained using particle swarm optimization (PSO). To evaluate the performance of the ASTF, evaluation factor Ipq is also defined. In addition, a simulation experiment is designed to verify the effectiveness and robustness of ASTF. A sensitive evaluation method using principal component analysis (PCA) is proposed to evaluate the sensitiveness of symptom parameters (SPs) for condition diagnosis. By this way, the good SPs that have high sensitiveness for condition diagnosis can be selected. A three-layer DBN is developed to identify condition of rotation machinery based on the Bayesian Belief Network (BBN) theory. Condition diagnosis experiment for rolling element bearings demonstrates the effectiveness of the proposed method. PMID:26761006

  3. Automated high resolution mapping of coffee in Rwanda using an expert Bayesian network

    NASA Astrophysics Data System (ADS)

    Mukashema, A.; Veldkamp, A.; Vrieling, A.

    2014-12-01

    African highland agro-ecosystems are dominated by small-scale agricultural fields that often contain a mix of annual and perennial crops. This makes such systems difficult to map by remote sensing. We developed an expert Bayesian network model to extract the small-scale coffee fields of Rwanda from very high resolution data. The model was subsequently applied to aerial orthophotos covering more than 99% of Rwanda and on one QuickBird image for the remaining part. The method consists of a stepwise adjustment of pixel probabilities, which incorporates expert knowledge on size of coffee trees and fields, and on their location. The initial naive Bayesian network, which is a spectral-based classification, yielded a coffee map with an overall accuracy of around 50%. This confirms that standard spectral variables alone cannot accurately identify coffee fields from high resolution images. The combination of spectral and ancillary data (DEM and a forest map) allowed mapping of coffee fields and associated uncertainties with an overall accuracy of 87%. Aggregated to district units, the mapped coffee areas demonstrated a high correlation with the coffee areas reported in the detailed national coffee census of 2009 (R2 = 0.92). Unlike the census data our map provides high spatial resolution of coffee area patterns of Rwanda. The proposed method has potential for mapping other perennial small scale cropping systems in the East African Highlands and elsewhere.

  4. Risk analysis of emergent water pollution accidents based on a Bayesian Network.

    PubMed

    Tang, Caihong; Yi, Yujun; Yang, Zhifeng; Sun, Jie

    2016-01-01

    To guarantee the security of water quality in water transfer channels, especially in open channels, analysis of potential emergent pollution sources in the water transfer process is critical. It is also indispensable for forewarnings and protection from emergent pollution accidents. Bridges above open channels with large amounts of truck traffic are the main locations where emergent accidents could occur. A Bayesian Network model, which consists of six root nodes and three middle layer nodes, was developed in this paper, and was employed to identify the possibility of potential pollution risk. Dianbei Bridge is reviewed as a typical bridge on an open channel of the Middle Route of the South to North Water Transfer Project where emergent traffic accidents could occur. Risk of water pollutions caused by leakage of pollutants into water is focused in this study. The risk for potential traffic accidents at the Dianbei Bridge implies a risk for water pollution in the canal. Based on survey data, statistical analysis, and domain specialist knowledge, a Bayesian Network model was established. The human factor of emergent accidents has been considered in this model. Additionally, this model has been employed to describe the probability of accidents and the risk level. The sensitive reasons for pollution accidents have been deduced. The case has also been simulated that sensitive factors are in a state of most likely to lead to accidents. PMID:26433361

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

    SciTech Connect

    Coles, Garill A.; Brothers, Alan J.; Olson, Jarrod; Whitney, Paul D.

    2010-04-16

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

  6. In-Hospital Death Caused by Pancreatic Cancer in Spain: Application with a Bayesian Network

    PubMed Central

    Álvaro-Meca, A.; Gil-Prieto, R.; Gil de Miguel, A.

    2011-01-01

    Pancreatic cancer is one of the least common tumors (2.1%), but it remains one of the most lethal. This lethality is primarily due to late stage diagnosis in the vast majority of patients. Here we demonstrate, using a Bayesian network, that we can determine a posteriori, with a high probability of success, the probability of in-hospital death of pancreatic cancer in hospitals across Spain with information related to the type of admission, the type of procedure, the primary diagnosis or the Charlson co-morbidity index. The advantages of using a Bayesian network are that it allows us to examine multiple hypotheses and to measure the effect of the introduction of variables on our hypotheses. Being able to determine deceases in the probability of survival based on hospital admission data, such as the diagnosis resulting in the present admission or the presence of co-morbidities, could facilitate the detection of deficiencies in the patient treatment and improve hospital management. Moreover, the control of related co-morbidities may have an impact on the in-hospital deaths of these patients. PMID:23675228

  7. Predicting Mycobacterium tuberculosis complex clades using knowledge-based Bayesian networks.

    PubMed

    Aminian, Minoo; Couvin, David; Shabbeer, Amina; Hadley, Kane; Vandenberg, Scott; Rastogi, Nalin; Bennett, Kristin P

    2014-01-01

    We develop a novel approach for incorporating expert rules into Bayesian networks for classification of Mycobacterium tuberculosis complex (MTBC) clades. The proposed knowledge-based Bayesian network (KBBN) treats sets of expert rules as prior distributions on the classes. Unlike prior knowledge-based support vector machine approaches which require rules expressed as polyhedral sets, KBBN directly incorporates the rules without any modification. KBBN uses data to refine rule-based classifiers when the rule set is incomplete or ambiguous. We develop a predictive KBBN model for 69 MTBC clades found in the SITVIT international collection. We validate the approach using two testbeds that model knowledge of the MTBC obtained from two different experts and large DNA fingerprint databases to predict MTBC genetic clades and sublineages. These models represent strains of MTBC using high-throughput biomarkers called spacer oligonucleotide types (spoligotypes), since these are routinely gathered from MTBC isolates of tuberculosis (TB) patients. Results show that incorporating rules into problems can drastically increase classification accuracy if data alone are insufficient. The SITVIT KBBN is publicly available for use on the World Wide Web. PMID:24864238

  8. Assessment of successful smoking cessation by psychological factors using the Bayesian network approach.

    PubMed

    Yang, Xiaorong; Li, Suyun; Pan, Lulu; Wang, Qiang; Li, Huijie; Han, Mingkui; Zhang, Nan; Jiang, Fan; Jia, Chongqi

    2016-07-01

    The association between psychological factors and smoking cessation is complicated and inconsistent in published researches, and the joint effect of psychological factors on smoking cessation is unclear. This study explored how psychological factors jointly affect the success of smoking cessation using a Bayesian network approach. A community-based case control study was designed with 642 adult male successful smoking quitters as the cases, and 700 adult male failed smoking quitters as the controls. General self-efficacy (GSE), trait coping style (positive-trait coping style (PTCS) and negative-trait coping style (NTCS)) and self-rating anxiety (SA) were evaluated by GSE Scale, Trait Coping Style Questionnaire and SA Scale, respectively. Bayesian network was applied to evaluate the relationship between psychological factors and successful smoking cessation. The local conditional probability table of smoking cessation indicated that different joint conditions of psychological factors led to different outcomes for smoking cessation. Among smokers with high PTCS, high NTCS and low SA, only 36.40% successfully quitted smoking. However, among smokers with low pack-years of smoking, high GSE, high PTCS and high SA, 63.64% successfully quitted smoking. Our study indicates psychological factors jointly influence smoking cessation outcome. According to different joint situations, different solutions should be developed to control tobacco in practical intervention. PMID:26264661

  9. Using robust Bayesian network to estimate the residuals of fluoroquinolone antibiotic in soil.

    PubMed

    Li, Xuewen; Xie, Yunfeng; Li, Lianfa; Yang, Xunfeng; Wang, Ning; Wang, Jinfeng

    2015-11-01

    Prediction of antibiotic pollution and its consequences is difficult, due to the uncertainties and complexities associated with multiple related factors. This article employed domain knowledge and spatial data to construct a Bayesian network (BN) model to assess fluoroquinolone antibiotic (FQs) pollution in the soil of an intensive vegetable cultivation area. The results show: (1) The relationships between FQs pollution and contributory factors: Three factors (cultivation methods, crop rotations, and chicken manure types) were consistently identified as predictors in the topological structures of three FQs, indicating their importance in FQs pollution; deduced with domain knowledge, the cultivation methods are determined by the crop rotations, which require different nutrients (derived from the manure) according to different plant biomass. (2) The performance of BN model: The integrative robust Bayesian network model achieved the highest detection probability (pd) of high-risk and receiver operating characteristic (ROC) area, since it incorporates domain knowledge and model uncertainty. Our encouraging findings have implications for the use of BN as a robust approach to assessment of FQs pollution and for informing decisions on appropriate remedial measures. PMID:26141975

  10. Fuzzy Bayesian Network-Bow-Tie Analysis of Gas Leakage during Biomass Gasification

    PubMed Central

    Yan, Fang; Xu, Kaili; Yao, Xiwen; Li, Yang

    2016-01-01

    Biomass gasification technology has been rapidly developed recently. But fire and poisoning accidents caused by gas leakage restrict the development and promotion of biomass gasification. Therefore, probabilistic safety assessment (PSA) is necessary for biomass gasification system. Subsequently, Bayesian network-bow-tie (BN-bow-tie) analysis was proposed by mapping bow-tie analysis into Bayesian network (BN). Causes of gas leakage and the accidents triggered by gas leakage can be obtained by bow-tie analysis, and BN was used to confirm the critical nodes of accidents by introducing corresponding three importance measures. Meanwhile, certain occurrence probability of failure was needed in PSA. In view of the insufficient failure data of biomass gasification, the occurrence probability of failure which cannot be obtained from standard reliability data sources was confirmed by fuzzy methods based on expert judgment. An improved approach considered expert weighting to aggregate fuzzy numbers included triangular and trapezoidal numbers was proposed, and the occurrence probability of failure was obtained. Finally, safety measures were indicated based on the obtained critical nodes. The theoretical occurrence probabilities in one year of gas leakage and the accidents caused by it were reduced to 1/10.3 of the original values by these safety measures. PMID:27463975

  11. Bayesian network meta-analysis for unordered categorical outcomes with incomplete data.

    PubMed

    Schmid, Christopher H; Trikalinos, Thomas A; Olkin, Ingram

    2014-06-01

    We develop a Bayesian multinomial network meta-analysis model for unordered (nominal) categorical outcomes that allows for partially observed data in which exact event counts may not be known for each category. This model properly accounts for correlations of counts in mutually exclusive categories and enables proper comparison and ranking of treatment effects across multiple treatments and multiple outcome categories. We apply the model to analyze 17 trials, each of which compares two of three treatments (high and low dose statins and standard care/control) for three outcomes for which data are complete: cardiovascular death, non-cardiovascular death and no death. We also analyze the cardiovascular death category divided into the three subcategories (coronary heart disease, stroke and other cardiovascular diseases) that are not completely observed. The multinomial and network representations show that high dose statins are effective in reducing the risk of cardiovascular disease. PMID:26052655

  12. An assessment of linkage disequilibrium in Holstein cattle using a Bayesian network.

    PubMed

    Morota, G; Valente, B D; Rosa, G J M; Weigel, K A; Gianola, D

    2012-12-01

    Linkage disequilibrium (LD) is defined as a non-random association of the distributions of alleles at different loci within a population. This association between loci is valuable in prediction of quantitative traits in animals and plants and in genome-wide association studies. A question that arises is whether standard metrics such as D' and r(2) reflect complex associations in a genetic system properly. It seems reasonable to take the view that loci associate and interact together as a system or network, as opposed to in a simple pairwise manner. We used a Bayesian network (BN) as a representation of choice for an LD network. A BN is a graphical depiction of a probability distribution and can represent sets of conditional independencies. Moreover, it provides a visual display of the joint distribution of the set of random variables in question. The usefulness of BN for linkage disequilibrium was explored and illustrated using genetic marker loci found to have the strongest effects on milk protein in Holstein cattle based on three strategies for ranking marker effect estimates: posterior means, standardized posterior means and additive genetic variance. Two different algorithms, Tabu search (a local score-based algorithm) and incremental association Markov blanket (a constraint-based algorithm), coupled with the chi-square test, were used for learning the structure of the BN and were compared with the reference r(2) metric represented as an LD heat map. The BN captured several genetic markers associated as clusters, implying that markers are inter-related in a complicated manner. Further, the BN detected conditionally dependent markers. The results confirm that LD relationships are of a multivariate nature and that r(2) gives an incomplete description and understanding of LD. Use of an LD Bayesian network enables inferring associations between loci in a systems framework and provides a more accurate picture of LD than that resulting from the use of pairwise

  13. Probabilistic age classification with Bayesian networks: A study on the ossification status of the medial clavicular epiphysis.

    PubMed

    Sironi, Emanuele; Pinchi, Vilma; Taroni, Franco

    2016-01-01

    In the past few decades, the rise of criminal, civil and asylum cases involving young people lacking valid identification documents has generated an increase in the demand of age estimation. The chronological age or the probability that an individual is older or younger than a given age threshold are generally estimated by means of some statistical methods based on observations performed on specific physical attributes. Among these statistical methods, those developed in the Bayesian framework allow users to provide coherent and transparent assignments which fulfill forensic and medico-legal purposes. The application of the Bayesian approach is facilitated by using probabilistic graphical tools, such as Bayesian networks. The aim of this work is to test the performances of the Bayesian network for age estimation recently presented in scientific literature in classifying individuals as older or younger than 18 years of age. For these exploratory analyses, a sample related to the ossification status of the medial clavicular epiphysis available in scientific literature was used. Results obtained in the classification are promising: in the criminal context, the Bayesian network achieved, on the average, a rate of correct classifications of approximatively 97%, whilst in the civil context, the rate is, on the average, close to the 88%. These results encourage the continuation of the development and the testing of the method in order to support its practical application in casework. PMID:26699731

  14. Bayesian non-negative factor analysis for reconstructing transcription factor mediated regulatory networks

    PubMed Central

    2011-01-01

    Background Transcriptional regulation by transcription factor (TF) controls the time and abundance of mRNA transcription. Due to the limitation of current proteomics technologies, large scale measurements of protein level activities of TFs is usually infeasible, making computational reconstruction of transcriptional regulatory network a difficult task. Results We proposed here a novel Bayesian non-negative factor model for TF mediated regulatory networks. Particularly, the non-negative TF activities and sample clustering effect are modeled as the factors from a Dirichlet process mixture of rectified Gaussian distributions, and the sparse regulatory coefficients are modeled as the loadings from a sparse distribution that constrains its sparsity using knowledge from database; meantime, a Gibbs sampling solution was developed to infer the underlying network structure and the unknown TF activities simultaneously. The developed approach has been applied to simulated system and breast cancer gene expression data. Result shows that, the proposed method was able to systematically uncover TF mediated transcriptional regulatory network structure, the regulatory coefficients, the TF protein level activities and the sample clustering effect. The regulation target prediction result is highly coordinated with the prior knowledge, and sample clustering result shows superior performance over previous molecular based clustering method. Conclusions The results demonstrated the validity and effectiveness of the proposed approach in reconstructing transcriptional networks mediated by TFs through simulated systems and real data. PMID:22166063

  15. Applications of Bayesian filtering in wireless networks: Clock synchronization, localization, and RF tomography

    NASA Astrophysics Data System (ADS)

    Hamilton, Benjamin Russell

    In this work, we investigate the application of Bayesian filtering techniques such as Kalman Filtering and Particle filtering to the problems of network time synchronization, self-localization and radio-frequency (RF) tomography in wireless networks. Networks of large numbers of small, cheap, mobile wireless devices have shown enormous potential in applications ranging from intrusion detection to environmental monitoring. These applications require the devices to have accurate time and position estimates, however traditional techniques may not be available. Additionally RF tomography offers a new paradigm to sense the network environment and could greatly enhance existing network capabilities. While there are some existing works addressing these problems, they all suffer from limitations. Current time synchronization methods are not energy efficient on small wireless devices with low quality oscillators. Existing localization methods do not consider additional sources of information available to nodes in the network such as measurements from accelerometers or models of the shadowing environment in the network. RF tomography has only been examined briefly in such networks, and current algorithms can not handle node mobility and rely on shadowing models that have not been experimentally verified. We address the time synchronization problem by analyzing the characteristics of the clocks in small wireless devices, developing a model for it, and then applying a Kalman filter to track both clock offset and skew. In our investigation into RF tomography, we present a method using a Kalman filter which jointly estimates and tracks static and dynamic objects in the environment. We also use channel measurements collected from a field test of our RF tomography testbed to compare RF shadowing models. For the localization problem, we present two algorithms incorporating additional information for improved localization: one based on a distributed extended Kalman filter that

  16. Pinkeye (Conjunctivitis) (For Parents)

    MedlinePlus

    ... Story" 5 Things to Know About Zika & Pregnancy Pinkeye (Conjunctivitis) KidsHealth > For Parents > Pinkeye (Conjunctivitis) Print A A ... to Call the Doctor en español Conjuntivitis About Pinkeye Conjunctivitis, commonly called pinkeye, is an inflammation of ...

  17. Bayesian model selection applied to artificial neural networks used for water resources modeling

    NASA Astrophysics Data System (ADS)

    Kingston, Greer B.; Maier, Holger R.; Lambert, Martin F.

    2008-04-01

    Artificial neural networks (ANNs) have proven to be extremely valuable tools in the field of water resources engineering. However, one of the most difficult tasks in developing an ANN is determining the optimum level of complexity required to model a given problem, as there is no formal systematic model selection method. This paper presents a Bayesian model selection (BMS) method for ANNs that provides an objective approach for comparing models of varying complexity in order to select the most appropriate ANN structure. The approach uses Markov Chain Monte Carlo posterior simulations to estimate the evidence in favor of competing models and, in this study, three known methods for doing this are compared in terms of their suitability for being incorporated into the proposed BMS framework for ANNs. However, it is acknowledged that it can be particularly difficult to accurately estimate the evidence of ANN models. Therefore, the proposed BMS approach for ANNs incorporates a further check of the evidence results by inspecting the marginal posterior distributions of the hidden-to-output layer weights, which unambiguously indicate any redundancies in the hidden layer nodes. The fact that this check is available is one of the greatest advantages of the proposed approach over conventional model selection methods, which do not provide such a test and instead rely on the modeler's subjective choice of selection criterion. The advantages of a total Bayesian approach to ANN development, including training and model selection, are demonstrated on two synthetic and one real world water resources case study.

  18. A Bayesian framework for cell-level protein network analysis for multivariate proteomics image data

    NASA Astrophysics Data System (ADS)

    Kovacheva, Violet N.; Sirinukunwattana, Korsuk; Rajpoot, Nasir M.

    2014-03-01

    The recent development of multivariate imaging techniques, such as the Toponome Imaging System (TIS), has facilitated the analysis of multiple co-localisation of proteins. This could hold the key to understanding complex phenomena such as protein-protein interaction in cancer. In this paper, we propose a Bayesian framework for cell level network analysis allowing the identification of several protein pairs having significantly higher co-expression levels in cancerous tissue samples when compared to normal colon tissue. It involves segmenting the DAPI-labeled image into cells and determining the cell phenotypes according to their protein-protein dependence profile. The cells are phenotyped using Gaussian Bayesian hierarchical clustering (GBHC) after feature selection is performed. The phenotypes are then analysed using Difference in Sums of Weighted cO-dependence Profiles (DiSWOP), which detects differences in the co-expression patterns of protein pairs. We demonstrate that the pairs highlighted by the proposed framework have high concordance with recent results using a different phenotyping method. This demonstrates that the results are independent of the clustering method used. In addition, the highlighted protein pairs are further analysed via protein interaction pathway databases and by considering the localization of high protein-protein dependence within individual samples. This suggests that the proposed approach could identify potentially functional protein complexes active in cancer progression and cell differentiation.

  19. Response Surfaces of Neural Networks Learned Using Bayesian Framework and Its Application to Optimization Problem

    NASA Astrophysics Data System (ADS)

    Takeda, Norio

    We verified the generalization ability of the response surfaces of artificial neural networks (NNs), and that the surfaces could be applied to an engineering-design problem. A Bayesian framework to regularize NNs, which was proposed by Gull and Skilling, can be used to generate NN response surfaces with excellent generalization ability, i.e., to determine the regularizing constants in an objective function minimized during NN learning. This well-generalized NN might be useful to find an optimal solution in the process of response surface methodology (RSM). We, therefore, describe three rules based on the Bayesian framework to update the regularizing constants, utilizing these rules to generate NN response surfaces with noisy teacher data drawn from a typical unimodal or multimodal function. Good generalization ability was achieved with regularized NN response surfaces, even though an update rule including trace evaluation failed to determine the regularizing constants regardless of the response function. We, next, selected the most appropriate update rule, which included eigenvalue evaluation, and then the NN response surface regularized using the update rule was applied to finding the optimal solution to an illustrative engineering-design problem. The NN response surface did not fit the noise in the teacher data, and consequently, it could effectively be used to achieve a satisfactory solution. This may increase the opportunities for using NN in the process of RSM.

  20. Pricing and hedging derivative securities with neural networks: Bayesian regularization, early stopping, and bagging.

    PubMed

    Gençay, R; Qi, M

    2001-01-01

    We study the effectiveness of cross validation, Bayesian regularization, early stopping, and bagging to mitigate overfitting and improving generalization for pricing and hedging derivative securities with daily S&P 500 index daily call options from January 1988 to December 1993. Our results indicate that Bayesian regularization can generate significantly smaller pricing and delta-hedging errors than the baseline neural-network (NN) model and the Black-Scholes model for some years. While early stopping does not affect the pricing errors, it significantly reduces the hedging error (HE) in four of the six years we investigated. Although computationally most demanding, bagging seems to provide the most accurate pricing and delta hedging. Furthermore, the standard deviation of the MSPE of bagging is far less than that of the baseline model in all six years, and the standard deviation of the average HE of bagging is far less than that of the baseline model in five out of six years. We conclude that they be used at least in cases when no appropriate hints are available. PMID:18249908

  1. A Measure of Systems Engineering Effectiveness in Government Acquisition of Complex Information Systems: A Bayesian Belief Network-Based Approach

    ERIC Educational Resources Information Center

    Doskey, Steven Craig

    2014-01-01

    This research presents an innovative means of gauging Systems Engineering effectiveness through a Systems Engineering Relative Effectiveness Index (SE REI) model. The SE REI model uses a Bayesian Belief Network to map causal relationships in government acquisitions of Complex Information Systems (CIS), enabling practitioners to identify and…

  2. A multinomial logit model-Bayesian network hybrid approach for driver injury severity analyses in rear-end crashes.

    PubMed

    Chen, Cong; Zhang, Guohui; Tarefder, Rafiqul; Ma, Jianming; Wei, Heng; Guan, Hongzhi

    2015-07-01

    Rear-end crash is one of the most common types of traffic crashes in the U.S. A good understanding of its characteristics and contributing factors is of practical importance. Previously, both multinomial Logit models and Bayesian network methods have been used in crash modeling and analysis, respectively, although each of them has its own application restrictions and limitations. In this study, a hybrid approach is developed to combine multinomial logit models and Bayesian network methods for comprehensively analyzing driver injury severities in rear-end crashes based on state-wide crash data collected in New Mexico from 2010 to 2011. A multinomial logit model is developed to investigate and identify significant contributing factors for rear-end crash driver injury severities classified into three categories: no injury, injury, and fatality. Then, the identified significant factors are utilized to establish a Bayesian network to explicitly formulate statistical associations between injury severity outcomes and explanatory attributes, including driver behavior, demographic features, vehicle factors, geometric and environmental characteristics, etc. The test results demonstrate that the proposed hybrid approach performs reasonably well. The Bayesian network reference analyses indicate that the factors including truck-involvement, inferior lighting conditions, windy weather conditions, the number of vehicles involved, etc. could significantly increase driver injury severities in rear-end crashes. The developed methodology and estimation results provide insights for developing effective countermeasures to reduce rear-end crash injury severities and improve traffic system safety performance. PMID:25888994

  3. Developing Large-Scale Bayesian Networks by Composition: Fault Diagnosis of Electrical Power Systems in Aircraft and Spacecraft

    NASA Technical Reports Server (NTRS)

    Mengshoel, Ole Jakob; Poll, Scott; Kurtoglu, Tolga

    2009-01-01

    In this paper, we investigate the use of Bayesian networks to construct large-scale diagnostic systems. In particular, we consider the development of large-scale Bayesian networks by composition. This compositional approach reflects how (often redundant) subsystems are architected to form systems such as electrical power systems. We develop high-level specifications, Bayesian networks, clique trees, and arithmetic circuits representing 24 different electrical power systems. The largest among these 24 Bayesian networks contains over 1,000 random variables. Another BN represents the real-world electrical power system ADAPT, which is representative of electrical power systems deployed in aerospace vehicles. In addition to demonstrating the scalability of the compositional approach, we briefly report on experimental results from the diagnostic competition DXC, where the ProADAPT team, using techniques discussed here, obtained the highest scores in both Tier 1 (among 9 international competitors) and Tier 2 (among 6 international competitors) of the industrial track. While we consider diagnosis of power systems specifically, we believe this work is relevant to other system health management problems, in particular in dependable systems such as aircraft and spacecraft. (See CASI ID 20100021910 for supplemental data disk.)

  4. Elucidation of Genetic Interactions in the Yeast GATA-Factor Network Using Bayesian Model Selection

    PubMed Central

    Milias-Argeitis, Andreas; Oliveira, Ana Paula; Gerosa, Luca; Falter, Laura; Sauer, Uwe; Lygeros, John

    2016-01-01

    Understanding the structure and function of complex gene regulatory networks using classical genetic assays is an error-prone procedure that frequently generates ambiguous outcomes. Even some of the best-characterized gene networks contain interactions whose validity is not conclusively proven. Founded on dynamic experimental data, mechanistic mathematical models are able to offer detailed insights that would otherwise require prohibitively large numbers of genetic experiments. Here we attempt mechanistic modeling of the transcriptional network formed by the four GATA-factor proteins, a well-studied system of central importance for nitrogen-source regulation of transcription in the yeast Saccharomyces cerevisiae. To resolve ambiguities in the network organization, we encoded a set of five interactions hypothesized in the literature into a set of 32 mathematical models, and employed Bayesian model selection to identify the most plausible set of interactions based on dynamic gene expression data. The top-ranking model was validated on newly generated GFP reporter dynamic data and was subsequently used to gain a better understanding of how yeast cells organize their transcriptional response to dynamic changes of nitrogen sources. Our work constitutes a necessary and important step towards obtaining a holistic view of the yeast nitrogen regulation mechanisms; on the computational side, it provides a demonstration of how powerful Monte Carlo techniques can be creatively combined and used to address the great challenges of large-scale dynamical system inference. PMID:26967983

  5. Explicitly integrating parameter, input, and structure uncertainties into Bayesian Neural Networks for probabilistic hydrologic forecasting

    SciTech Connect

    Zhang, Xuesong; Liang, Faming; Yu, Beibei; Zong, Ziliang

    2011-11-09

    Estimating uncertainty of hydrologic forecasting is valuable to water resources and other relevant decision making processes. Recently, Bayesian Neural Networks (BNNs) have been proved powerful tools for quantifying uncertainty of streamflow forecasting. In this study, we propose a Markov Chain Monte Carlo (MCMC) framework to incorporate the uncertainties associated with input, model structure, and parameter into BNNs. This framework allows the structure of the neural networks to change by removing or adding connections between neurons and enables scaling of input data by using rainfall multipliers. The results show that the new BNNs outperform the BNNs that only consider uncertainties associated with parameter and model structure. Critical evaluation of posterior distribution of neural network weights, number of effective connections, rainfall multipliers, and hyper-parameters show that the assumptions held in our BNNs are not well supported. Further understanding of characteristics of different uncertainty sources and including output error into the MCMC framework are expected to enhance the application of neural networks for uncertainty analysis of hydrologic forecasting.

  6. Bayesian network structure learning based on the chaotic particle swarm optimization algorithm.

    PubMed

    Zhang, Q; Li, Z; Zhou, C J; Wei, X P

    2013-01-01

    The Bayesian network (BN) is a knowledge representation form, which has been proven to be valuable in the gene regulatory network reconstruction because of its capability of capturing causal relationships between genes. Learning BN structures from a database is a nondeterministic polynomial time (NP)-hard problem that remains one of the most exciting challenges in machine learning. Several heuristic searching techniques have been used to find better network structures. Among these algorithms, the classical K2 algorithm is the most successful. Nonetheless, the performance of the K2 algorithm is greatly affected by a prior ordering of input nodes. The proposed method in this paper is based on the chaotic particle swarm optimization (CPSO) and the K2 algorithm. Because the PSO algorithm completely entraps the local minimum in later evolutions, we combined the PSO algorithm with the chaos theory, which has the properties of ergodicity, randomness, and regularity. Experimental results show that the proposed method can improve the convergence rate of particles and identify networks more efficiently and accurately. PMID:24222226

  7. Using Bayesian Networks and Rule-Based Trending to Predict Patient Status in the Intensive Care Unit

    PubMed Central

    Crump, Cindy; Saxena, Sunil; Wilson, Bruce; Farrell, Patrick; Rafiq, Azhar; Silvers, Christine Tsien

    2009-01-01

    Multivariate Bayesian models trained with machine learning, in conjunction with rule-based time-series statistical techniques, are explored for the purpose of improving patient monitoring. Three vital sign data streams and known outcomes for 36 intensive care unit (ICU) patients were captured retrospectively and used to train a set of Bayesian net models and to construct time-series models. Models were validated on a reserved dataset from 16 additional patients. Receiver operating characteristic (ROC) curves were calculated. Area under the curve (AUC) was 91% for predicting improving outcome. The model’s AUC for predicting declining outcome increased from 70% to 85% when the model was indexed to personalized baselines for each patient. The rule-based trending and alerting system was accurate 100% of the time in alerting a subsequent decline in condition. These techniques promise to improve the monitoring of ICU patients with high-sensitivity alerts, fewer false alarms, and earlier intervention. PMID:20351835

  8. Online state-of-health estimation of lithium-ion batteries using Dynamic Bayesian Networks

    NASA Astrophysics Data System (ADS)

    He, Zhiwei; Gao, Mingyu; Ma, Guojin; Liu, Yuanyuan; Chen, Sanxin

    2014-12-01

    Li-ion batteries are widely used in energy storage systems, electric vehicles, communication systems, etc. The State of Health (SOH) of batteries is of great importance to the safety of these systems. This paper presents a novel online method for the estimation of the SOH of Lithium (Li)-ion batteries based on Dynamic Bayesian Networks (DBNs). The structure of the DBN model is built according to the experience of experts, with the state of charges used as hidden states and the terminal voltages used as observations in the DBN. Parameters of the DBN model are learned based on training data collected through Li-ion battery aging experiments. A forward algorithm is applied for the inference of the DBN model in order to estimate the SOH in real-time. Experimental results show that the proposed method is effective and efficient in estimating the SOH of Li-ion batteries.

  9. Team performance and collective efficacy in the dynamic psychology of competitive team: a Bayesian network analysis.

    PubMed

    Fuster-Parra, P; García-Mas, A; Ponseti, F J; Leo, F M

    2015-04-01

    The purpose of this paper was to discover the relationships among 22 relevant psychological features in semi-professional football players in order to study team's performance and collective efficacy via a Bayesian network (BN). The paper includes optimization of team's performance and collective efficacy using intercausal reasoning pattern which constitutes a very common pattern in human reasoning. The BN is used to make inferences regarding our problem, and therefore we obtain some conclusions; among them: maximizing the team's performance causes a decrease in collective efficacy and when team's performance achieves the minimum value it causes an increase in moderate/high values of collective efficacy. Similarly, we may reason optimizing team collective efficacy instead. It also allows us to determine the features that have the strongest influence on performance and which on collective efficacy. From the BN two different coaching styles were differentiated taking into account the local Markov property: training leadership and autocratic leadership. PMID:25546263

  10. Evaluation of the diagnostic power of thermography in breast cancer using Bayesian network classifiers.

    PubMed

    Nicandro, Cruz-Ramírez; Efrén, Mezura-Montes; María Yaneli, Ameca-Alducin; Enrique, Martín-Del-Campo-Mena; Héctor Gabriel, Acosta-Mesa; Nancy, Pérez-Castro; Alejandro, Guerra-Hernández; Guillermo de Jesús, Hoyos-Rivera; Rocío Erandi, Barrientos-Martínez

    2013-01-01

    Breast cancer is one of the leading causes of death among women worldwide. There are a number of techniques used for diagnosing this disease: mammography, ultrasound, and biopsy, among others. Each of these has well-known advantages and disadvantages. A relatively new method, based on the temperature a tumor may produce, has recently been explored: thermography. In this paper, we will evaluate the diagnostic power of thermography in breast cancer using Bayesian network classifiers. We will show how the information provided by the thermal image can be used in order to characterize patients suspected of having cancer. Our main contribution is the proposal of a score, based on the aforementioned information, that could help distinguish sick patients from healthy ones. Our main results suggest the potential of this technique in such a goal but also show its main limitations that have to be overcome to consider it as an effective diagnosis complementary tool. PMID:23762182

  11. Evaluation of the Diagnostic Power of Thermography in Breast Cancer Using Bayesian Network Classifiers

    PubMed Central

    Nicandro, Cruz-Ramírez; Efrén, Mezura-Montes; María Yaneli, Ameca-Alducin; Enrique, Martín-Del-Campo-Mena; Héctor Gabriel, Acosta-Mesa; Nancy, Pérez-Castro; Alejandro, Guerra-Hernández; Guillermo de Jesús, Hoyos-Rivera; Rocío Erandi, Barrientos-Martínez

    2013-01-01

    Breast cancer is one of the leading causes of death among women worldwide. There are a number of techniques used for diagnosing this disease: mammography, ultrasound, and biopsy, among others. Each of these has well-known advantages and disadvantages. A relatively new method, based on the temperature a tumor may produce, has recently been explored: thermography. In this paper, we will evaluate the diagnostic power of thermography in breast cancer using Bayesian network classifiers. We will show how the information provided by the thermal image can be used in order to characterize patients suspected of having cancer. Our main contribution is the proposal of a score, based on the aforementioned information, that could help distinguish sick patients from healthy ones. Our main results suggest the potential of this technique in such a goal but also show its main limitations that have to be overcome to consider it as an effective diagnosis complementary tool. PMID:23762182

  12. Technical note: An R package for fitting Bayesian regularized neural networks with applications in animal breeding.

    PubMed

    Pérez-Rodríguez, P; Gianola, D; Weigel, K A; Rosa, G J M; Crossa, J

    2013-08-01

    In recent years, several statistical models have been developed for predicting genetic values for complex traits using information on dense molecular markers, pedigrees, or both. These models include, among others, the Bayesian regularized neural networks (BRNN) that have been widely used in prediction problems in other fields of application and, more recently, for genome-enabled prediction. The R package described here (brnn) implements BRNN models and extends these to include both additive and dominance effects. The implementation takes advantage of multicore architectures via a parallel computing approach using openMP (Open Multiprocessing) for the computations. This note briefly describes the classes of models that can be fitted using the brnn package, and it also illustrates its use through several real examples. PMID:23658327

  13. Assessing land-use impacts on viability of intermountain trouts using Bayesian belief networks

    SciTech Connect

    Lee, D.C.

    1994-12-31

    Many salmonid populations of the intermountain region of North America are threatened by habitat degradation resulting from changing land-use practices. Public lands managed by the USDA Forest Service and USDI Bureau of Land Management comprise a significant portion of the remaining suitable habitat. Public land-use decisions must consider the potential effects on sensitive species. A computer-aided viability assessment model is presented which can help anticipate impacts of management actions on resident trout populations. Central to this system is a Bayesian belief network that links physical habitat characteristics directly to reproduction and survival parameters of a population viability model. Recognizing that such linkages are imprecise and knowledge is uncertain, this system provides probabilistic risk assessments of land-use impacts. Preliminary results suggest that the principal threats to population viability arise from a combination of chronic habitat degradation and increased risks of major or catastrophic disturbances.

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  16. Bayesian belief network analysis applied to determine the progression of temporomandibular disorders using MRI

    PubMed Central

    2015-01-01

    Objectives: This study investigated the applicability of a Bayesian belief network (BBN) to MR images to diagnose temporomandibular disorders (TMDs). Our aim was to determine the progression of TMDs, focusing on how each finding affects the other. Methods: We selected 1.5-T MRI findings (33 variables) and diagnoses (bone changes and disc displacement) of patients with TMD from 2007 to 2008. There were a total of 295 cases with 590 sides of temporomandibular joints (TMJs). The data were modified according to the research diagnostic criteria of TMD. We compared the accuracy of the BBN using 11 algorithms (necessary path condition, path condition, greedy search-and-score with Bayesian information criterion, Chow–Liu tree, Rebane–Pearl poly tree, tree augmented naïve Bayes model, maximum log likelihood, Akaike information criterion, minimum description length, K2 and C4.5), a multiple regression analysis and an artificial neural network using resubstitution validation and 10-fold cross-validation. Results: There were 191 TMJs (32.4%) with bone changes and 340 (57.6%) with articular disc displacement. The BBN path condition algorithm using resubstitution validation and 10-fold cross-validation was >99% accurate. However, the main advantage of a BBN is that it can represent the causal relationships between different findings and assign conditional probabilities, which can then be used to interpret the progression of TMD. Conclusions: Osteoarthritic bone changes progressed from condyle to articular fossa and finally to mandibular bone contours. Disc displacement was directly related to severe bone changes. Early bone changes were not directly related to disc displacement. TMJ functional factors (condylar translation, bony space and disc form) and age mediated between bone changes and disc displacement. PMID:25472616

  17. Dynamic Bayesian Network Modeling of the Interplay between EGFR and Hedgehog Signaling

    PubMed Central

    Fröhlich, Holger; Bahamondez, Gloria; Götschel, Frank; Korf, Ulrike

    2015-01-01

    Aberrant activation of sonic Hegdehog (SHH) signaling has been found to disrupt cellular differentiation in many human cancers and to increase proliferation. The SHH pathway is known to cross-talk with EGFR dependent signaling. Recent studies experimentally addressed this interplay in Daoy cells, which are presumable a model system for medulloblastoma, a highly malignant brain tumor that predominately occurs in children. Currently ongoing are several clinical trials for different solid cancers, which are designed to validate the clinical benefits of targeting the SHH in combination with other pathways. This has motivated us to investigate interactions between EGFR and SHH dependent signaling in greater depth. To our knowledge, there is no mathematical model describing the interplay between EGFR and SHH dependent signaling in medulloblastoma so far. Here we come up with a fully probabilistic approach using Dynamic Bayesian Networks (DBNs). To build our model, we made use of literature based knowledge describing SHH and EGFR signaling and integrated gene expression (Illumina) and cellular location dependent time series protein expression data (Reverse Phase Protein Arrays). We validated our model by sub-sampling training data and making Bayesian predictions on the left out test data. Our predictions focusing on key transcription factors and p70S6K, showed a high level of concordance with experimental data. Furthermore, the stability of our model was tested by a parametric bootstrap approach. Stable network features were in agreement with published data. Altogether we believe that our model improved our understanding of the interplay between two highly oncogenic signaling pathways in Daoy cells. This may open new perspectives for the future therapy of Hedghog/EGF-dependent solid tumors. PMID:26571415

  18. Dynamic Bayesian Network Modeling of the Interplay between EGFR and Hedgehog Signaling.

    PubMed

    Fröhlich, Holger; Bahamondez, Gloria; Götschel, Frank; Korf, Ulrike

    2015-01-01

    Aberrant activation of sonic Hegdehog (SHH) signaling has been found to disrupt cellular differentiation in many human cancers and to increase proliferation. The SHH pathway is known to cross-talk with EGFR dependent signaling. Recent studies experimentally addressed this interplay in Daoy cells, which are presumable a model system for medulloblastoma, a highly malignant brain tumor that predominately occurs in children. Currently ongoing are several clinical trials for different solid cancers, which are designed to validate the clinical benefits of targeting the SHH in combination with other pathways. This has motivated us to investigate interactions between EGFR and SHH dependent signaling in greater depth. To our knowledge, there is no mathematical model describing the interplay between EGFR and SHH dependent signaling in medulloblastoma so far. Here we come up with a fully probabilistic approach using Dynamic Bayesian Networks (DBNs). To build our model, we made use of literature based knowledge describing SHH and EGFR signaling and integrated gene expression (Illumina) and cellular location dependent time series protein expression data (Reverse Phase Protein Arrays). We validated our model by sub-sampling training data and making Bayesian predictions on the left out test data. Our predictions focusing on key transcription factors and p70S6K, showed a high level of concordance with experimental data. Furthermore, the stability of our model was tested by a parametric bootstrap approach. Stable network features were in agreement with published data. Altogether we believe that our model improved our understanding of the interplay between two highly oncogenic signaling pathways in Daoy cells. This may open new perspectives for the future therapy of Hedghog/EGF-dependent solid tumors. PMID:26571415

  19. Bayesian prediction of earthquake network based on space-time influence domain

    NASA Astrophysics Data System (ADS)

    Zhang, Ya; Zhao, Hai; He, Xuan; Pei, Fan-Dong; Li, Guang-Guang

    2016-03-01

    Bayesian networks (BNs) are used to analyze the conditional dependencies among different events, which are expressed by conditional probability. Scientists have already investigated the seismic activities by using BNs. Recently, earthquake network is used as a novel methodology to analyze the relationships among the earthquake events. In this paper, we propose a way to predict earthquake from a new perspective. The BN is constructed after processing, which is derived from the earthquake network based on space-time influence domain. And then, the BN parameters are learnt by using the cases which are designed from the seismic data in the period between 00:00:00 on January 1, 1992 and 00:00:00 on January 1, 2012. At last, predictions are done for the data in the period between 00:00:00 on January 1, 2012 and 00:00:00 on January 1, 2015 combining the BN with the parameters. The results show that the success rate of the prediction including delayed prediction is about 65%. It is also discovered that the predictions for some nodes have high rate of accuracy under investigation.

  20. Development of a Bayesian Belief Network Runway Incursion and Excursion Model

    NASA Technical Reports Server (NTRS)

    Green, Lawrence L.

    2014-01-01

    In a previous work, a statistical analysis of runway incursion (RI) event data was conducted to ascertain the relevance of this data to the top ten Technical Challenges (TC) of the National Aeronautics and Space Administration (NASA) Aviation Safety Program (AvSP). The study revealed connections to several of the AvSP top ten TC and identified numerous primary causes and contributing factors of RI events. The statistical analysis served as the basis for developing a system-level Bayesian Belief Network (BBN) model for RI events, also previously reported. Through literature searches and data analysis, this RI event network has now been extended to also model runway excursion (RE) events. These RI and RE event networks have been further modified and vetted by a Subject Matter Expert (SME) panel. The combined system-level BBN model will allow NASA to generically model the causes of RI and RE events and to assess the effectiveness of technology products being developed under NASA funding. These products are intended to reduce the frequency of runway safety incidents/accidents, and to improve runway safety in general. The development and structure of the BBN for both RI and RE events are documented in this paper.

  1. A Bayesian Framework That Integrates Heterogeneous Data for Inferring Gene Regulatory Networks

    PubMed Central

    Santra, Tapesh

    2014-01-01

    Reconstruction of gene regulatory networks (GRNs) from experimental data is a fundamental challenge in systems biology. A number of computational approaches have been developed to infer GRNs from mRNA expression profiles. However, expression profiles alone are proving to be insufficient for inferring GRN topologies with reasonable accuracy. Recently, it has been shown that integration of external data sources (such as gene and protein sequence information, gene ontology data, protein–protein interactions) with mRNA expression profiles may increase the reliability of the inference process. Here, I propose a new approach that incorporates transcription factor binding sites (TFBS) and physical protein interactions (PPI) among transcription factors (TFs) in a Bayesian variable selection (BVS) algorithm which can infer GRNs from mRNA expression profiles subjected to genetic perturbations. Using real experimental data, I show that the integration of TFBS and PPI data with mRNA expression profiles leads to significantly more accurate networks than those inferred from expression profiles alone. Additionally, the performance of the proposed algorithm is compared with a series of least absolute shrinkage and selection operator (LASSO) regression-based network inference methods that can also incorporate prior knowledge in the inference framework. The results of this comparison suggest that BVS can outperform LASSO regression-based method in some circumstances. PMID:25152886

  2. Portfolios in Stochastic Local Search: Efficiently Computing Most Probable Explanations in Bayesian Networks

    NASA Technical Reports Server (NTRS)

    Mengshoel, Ole J.; Roth, Dan; Wilkins, David C.

    2001-01-01

    Portfolio methods support the combination of different algorithms and heuristics, including stochastic local search (SLS) heuristics, and have been identified as a promising approach to solve computationally hard problems. While successful in experiments, theoretical foundations and analytical results for portfolio-based SLS heuristics are less developed. This article aims to improve the understanding of the role of portfolios of heuristics in SLS. We emphasize the problem of computing most probable explanations (MPEs) in Bayesian networks (BNs). Algorithmically, we discuss a portfolio-based SLS algorithm for MPE computation, Stochastic Greedy Search (SGS). SGS supports the integration of different initialization operators (or initialization heuristics) and different search operators (greedy and noisy heuristics), thereby enabling new analytical and experimental results. Analytically, we introduce a novel Markov chain model tailored to portfolio-based SLS algorithms including SGS, thereby enabling us to analytically form expected hitting time results that explain empirical run time results. For a specific BN, we show the benefit of using a homogenous initialization portfolio. To further illustrate the portfolio approach, we consider novel additive search heuristics for handling determinism in the form of zero entries in conditional probability tables in BNs. Our additive approach adds rather than multiplies probabilities when computing the utility of an explanation. We motivate the additive measure by studying the dramatic impact of zero entries in conditional probability tables on the number of zero-probability explanations, which again complicates the search process. We consider the relationship between MAXSAT and MPE, and show that additive utility (or gain) is a generalization, to the probabilistic setting, of MAXSAT utility (or gain) used in the celebrated GSAT and WalkSAT algorithms and their descendants. Utilizing our Markov chain framework, we show that

  3. Bayesian Inference for Time Trends in Parameter Values: Case Study for the Ageing PSA Network of the European Commission

    SciTech Connect

    Dana L. Kelly; Albert Malkhasyan

    2010-06-01

    There is a nearly ubiquitous assumption in PSA that parameter values are at least piecewise-constant in time. As a result, Bayesian inference tends to incorporate many years of plant operation, over which there have been significant changes in plant operational and maintenance practices, plant management, etc. These changes can cause significant changes in parameter values over time; however, failure to perform Bayesian inference in the proper time-dependent framework can mask these changes. Failure to question the assumption of constant parameter values, and failure to perform Bayesian inference in the proper time-dependent framework were noted as important issues in NUREG/CR-6813, performed for the U. S. Nuclear Regulatory Commission’s Advisory Committee on Reactor Safeguards in 2003. That report noted that “industry lacks tools to perform time-trend analysis with Bayesian updating.” This paper describes an application of time-dependent Bayesian inference methods developed for the European Commission Ageing PSA Network. These methods utilize open-source software, implementing Markov chain Monte Carlo sampling. The paper also illustrates the development of a generic prior distribution, which incorporates multiple sources of generic data via weighting factors that address differences in key influences, such as vendor, component boundaries, conditions of the operating environment, etc.

  4. Assessing Vermont's stream health and biological integrity using artificial neural networks and Bayesian methods

    NASA Astrophysics Data System (ADS)

    Rizzo, D. M.; Fytilis, N.; Stevens, L.

    2012-12-01

    Environmental managers are increasingly required to monitor and forecast long-term effects and vulnerability of biophysical systems to human-generated stresses. Ideally, a study involving both physical and biological assessments conducted concurrently (in space and time) could provide a better understanding of the mechanisms and complex relationships. However, costs and resources associated with monitoring the complex linkages between the physical, geomorphic and habitat conditions and the biological integrity of stream reaches are prohibitive. Researchers have used classification techniques to place individual streams and rivers into a broader spatial context (hydrologic or health condition). Such efforts require environmental managers to gather multiple forms of information - quantitative, qualitative and subjective. We research and develop a novel classification tool that combines self-organizing maps with a Naïve Bayesian classifier to direct resources to stream reaches most in need. The Vermont Agency of Natural Resources has developed and adopted protocols for physical stream geomorphic and habitat assessments throughout the state of Vermont. Separate from these assessments, the Vermont Department of Environmental Conservation monitors the biological communities and the water quality in streams. Our initial hypothesis is that the geomorphic reach assessments and water quality data may be leveraged to reduce error and uncertainty associated with predictions of biological integrity and stream health. We test our hypothesis using over 2500 Vermont stream reaches (~1371 stream miles) assessed by the two agencies. In the development of this work, we combine a Naïve Bayesian classifier with a modified Kohonen Self-Organizing Map (SOM). The SOM is an unsupervised artificial neural network that autonomously analyzes inherent dataset properties using input data only. It is typically used to cluster data into similar categories when a priori classes do not exist. The

  5. A Bayesian network approach for modeling local failure in lung cancer

    NASA Astrophysics Data System (ADS)

    Oh, Jung Hun; Craft, Jeffrey; Lozi, Rawan Al; Vaidya, Manushka; Meng, Yifan; Deasy, Joseph O.; Bradley, Jeffrey D.; El Naqa, Issam

    2011-03-01

    Locally advanced non-small cell lung cancer (NSCLC) patients suffer from a high local failure rate following radiotherapy. Despite many efforts to develop new dose-volume models for early detection of tumor local failure, there was no reported significant improvement in their application prospectively. Based on recent studies of biomarker proteins' role in hypoxia and inflammation in predicting tumor response to radiotherapy, we hypothesize that combining physical and biological factors with a suitable framework could improve the overall prediction. To test this hypothesis, we propose a graphical Bayesian network framework for predicting local failure in lung cancer. The proposed approach was tested using two different datasets of locally advanced NSCLC patients treated with radiotherapy. The first dataset was collected retrospectively, which comprises clinical and dosimetric variables only. The second dataset was collected prospectively in which in addition to clinical and dosimetric information, blood was drawn from the patients at various time points to extract candidate biomarkers as well. Our preliminary results show that the proposed method can be used as an efficient method to develop predictive models of local failure in these patients and to interpret relationships among the different variables in the models. We also demonstrate the potential use of heterogeneous physical and biological variables to improve the model prediction. With the first dataset, we achieved better performance compared with competing Bayesian-based classifiers. With the second dataset, the combined model had a slightly higher performance compared to individual physical and biological models, with the biological variables making the largest contribution. Our preliminary results highlight the potential of the proposed integrated approach for predicting post-radiotherapy local failure in NSCLC patients.

  6. Identification of Functional Modules by Integration of Multiple Data Sources Using a Bayesian Network Classifier

    PubMed Central

    Wang, Jinlian; Zuo, Yiming; Liu, Lun; Man, Yangao; Tadesse, Mahlet G.; Ressom, Habtom W

    2014-01-01

    Background Prediction of functional modules is indispensable for detecting protein deregulation in human complex diseases such as cancer. Bayesian network (BN) is one of the most commonly used models to integrate heterogeneous data from multiple sources such as protein domain, interactome, functional annotation, genome-wide gene expression, and the literature. Methods and Results In this paper, we present a BN classifier that is customized to: 1) increase the ability to integrate diverse information from different sources, 2) effectively predict protein-protein interactions, 3) infer aberrant networks with scale-free and small world properties, and 4) group molecules into functional modules or pathways based on the primary function and biological features. Application of this model on discovering protein biomarkers of hepatocelluar carcinoma (HCC) leads to the identification of functional modules that provide insights into the mechanism of the development and progression of HCC. These functional modules include cell cycle deregulation, increased angiogenesis (e.g., vascular endothelial growth factor, blood vessel morphogenesis), oxidative metabolic alterations, and aberrant activation of signaling pathways involved in cellular proliferation, survival, and differentiation. Conclusion The discoveries and conclusions derived from our customized BN classifier are consistent with previously published results. The proposed approach for determining BN structure facilitates the integration of heterogeneous data from multiple sources to elucidate the mechanisms of complex diseases. PMID:24736851

  7. Longitudinal Prediction of the Infant Gut Microbiome with Dynamic Bayesian Networks

    PubMed Central

    McGeachie, Michael J.; Sordillo, Joanne E.; Gibson, Travis; Weinstock, George M.; Liu, Yang-Yu; Gold, Diane R.; Weiss, Scott T.; Litonjua, Augusto

    2016-01-01

    Sequencing of the 16S rRNA gene allows comprehensive assessment of bacterial community composition from human body sites. Previously published and publicly accessible data on 58 preterm infants in the Neonatal Intensive Care Unit who underwent frequent stool collection was used. We constructed Dynamic Bayesian Networks from the data and analyzed predictive performance and network characteristics. We constructed a DBN model of the infant gut microbial ecosystem, which explicitly captured specific relationships and general trends in the data: increasing amounts of Clostridia, residual amounts of Bacilli, and increasing amounts of Gammaproteobacteria that then give way to Clostridia. Prediction performance of DBNs with fewer edges were overall more accurate, although less so on harder-to-predict subjects (p = 0.045). DBNs provided quantitative likelihood estimates for rare abruptions events. Iterative prediction was less accurate (p < 0.001), but showed remarkable insensitivity to initial conditions and predicted convergence to a mix of Clostridia, Gammaproteobacteria, and Bacilli. DBNs were able to identify important relationships between microbiome taxa and predict future changes in microbiome composition from measured or synthetic initial conditions. DBNs also provided likelihood estimates for sudden, dramatic shifts in microbiome composition, which may be useful in guiding further analysis of those samples. PMID:26853461

  8. Longitudinal Prediction of the Infant Gut Microbiome with Dynamic Bayesian Networks.

    PubMed

    McGeachie, Michael J; Sordillo, Joanne E; Gibson, Travis; Weinstock, George M; Liu, Yang-Yu; Gold, Diane R; Weiss, Scott T; Litonjua, Augusto

    2016-01-01

    Sequencing of the 16S rRNA gene allows comprehensive assessment of bacterial community composition from human body sites. Previously published and publicly accessible data on 58 preterm infants in the Neonatal Intensive Care Unit who underwent frequent stool collection was used. We constructed Dynamic Bayesian Networks from the data and analyzed predictive performance and network characteristics. We constructed a DBN model of the infant gut microbial ecosystem, which explicitly captured specific relationships and general trends in the data: increasing amounts of Clostridia, residual amounts of Bacilli, and increasing amounts of Gammaproteobacteria that then give way to Clostridia. Prediction performance of DBNs with fewer edges were overall more accurate, although less so on harder-to-predict subjects (p = 0.045). DBNs provided quantitative likelihood estimates for rare abruptions events. Iterative prediction was less accurate (p < 0.001), but showed remarkable insensitivity to initial conditions and predicted convergence to a mix of Clostridia, Gammaproteobacteria, and Bacilli. DBNs were able to identify important relationships between microbiome taxa and predict future changes in microbiome composition from measured or synthetic initial conditions. DBNs also provided likelihood estimates for sudden, dramatic shifts in microbiome composition, which may be useful in guiding further analysis of those samples. PMID:26853461

  9. Exploring the utility of Bayesian Networks for modelling cultural ecosystem services: A canoeing case study.

    PubMed

    Shaw, Edward; Kumar, Vikas; Lange, Eckart; Lerner, David N

    2016-01-01

    Modelling cultural ecosystem services is challenging as they often involve subjective and intangible concepts. As a consequence they have been neglected in ecosystem service studies, something that needs remedying if environmental decision making is to be truly holistic. We suggest Bayesian Networks (BNs) have a number of qualities that may make them well-suited for dealing with cultural services. For example, they define relationships between variables probabilistically, enabling conceptual and physical variables to be linked, and therefore the numerical representation of stakeholder opinions. We assess whether BNs are a good method for modelling cultural services by building one collaboratively with canoeists to predict how the subjective concepts of fun and danger are impacted on by weir modification. The BN successfully captured the relationships between the variables, with model output being broadly consistent with verbal descriptions by the canoeists. There were however a number of discrepancies indicating imperfect knowledge capture. This is likely due to the structure of the network and the abstract and laborious nature of the probability elicitation stage. New techniques should be developed to increase the intuitiveness and efficiency of probability elicitation. The limitations we identified with BNs are avoided if their structure can be kept simple, and it is in such circumstances that BNs can offer a good method for modelling cultural ecosystem services. PMID:26345252

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  11. On the Relevance of Using Bayesian Belief Networks in Wireless Sensor Networks Situation Recognition

    PubMed Central

    Bagula, Antoine B.; Osunmakinde, Isaac; Zennaro, Marco

    2010-01-01

    Achieving situation recognition in ubiquitous sensor networks (USNs) is an important issue that has been poorly addressed by both the research and practitioner communities. This paper describes some steps taken to address this issue by effecting USN middleware intelligence using an emerging situation awareness (ESA) technology. We propose a situation recognition framework where temporal probabilistic reasoning is used to derive and emerge situation awareness in ubiquitous sensor networks. Using data collected from an outdoor environment monitoring in the city of Cape Town, we illustrate the use of the ESA technology in terms of sensor system operating conditions and environmental situation recognition. PMID:22163509

  12. Modelling Inter-relationships among water, governance, human development variables in developing countries with Bayesian networks.

    NASA Astrophysics Data System (ADS)

    Dondeynaz, C.; Lopez-Puga, J.; Carmona-Moreno, C.

    2012-04-01

    Improving Water and Sanitation Services (WSS), being a complex and interdisciplinary issue, passes through collaboration and coordination of different sectors (environment, health, economic activities, governance, and international cooperation). This inter-dependency has been recognised with the adoption of the "Integrated Water Resources Management" principles that push for the integration of these various dimensions involved in WSS delivery to ensure an efficient and sustainable management. The understanding of these interrelations appears as crucial for decision makers in the water sector in particular in developing countries where WSS still represent an important leverage for livelihood improvement. In this framework, the Joint Research Centre of the European Commission has developed a coherent database (WatSan4Dev database) containing 29 indicators from environmental, socio-economic, governance and financial aid flows data focusing on developing countries (Celine et al, 2011 under publication). The aim of this work is to model the WatSan4Dev dataset using probabilistic models to identify the key variables influencing or being influenced by the water supply and sanitation access levels. Bayesian Network Models are suitable to map the conditional dependencies between variables and also allows ordering variables by level of influence on the dependent variable. Separated models have been built for water supply and for sanitation because of different behaviour. The models are validated if complying with statistical criteria but either with scientific knowledge and literature. A two steps approach has been adopted to build the structure of the model; Bayesian network is first built for each thematic cluster of variables (e.g governance, agricultural pressure, or human development) keeping a detailed level for interpretation later one. A global model is then built based on significant indicators of each cluster being previously modelled. The structure of the

  13. Using Bayesian Belief Networks to Explore the Effects of Nitrogen Inputs on Wetland Ecosystem Services

    NASA Astrophysics Data System (ADS)

    Spence, P. L.; Jordan, S. J.

    2011-12-01

    Increased reactive nitrogen (Nr) inputs to freshwater wetlands resulting from infrastructure development due to population growth along with intensive agricultural practices associated with food production can threaten regulating (i.e. climate change, water purification, and waste treatment) and supporting (i.e. nutrient cycling) ecosystem services. Wetlands generally respond both by sequestering Nr (i.e. soil accumulation and biomass assimilation) and converting Nr into inert gaseous forms via biogeochemical processes. It is important for wetlands to be efficient in removing excessive Nr inputs from polluted waters to reduce eutrophication in downstream receiving water bodies while producing negligible amounts of nitrous oxide (N2O), a potent greenhouse gas, which results from incomplete denitrification. Wetlands receiving excessive Nr lose their ability to provide a constant balance between regulating water quality and mitigating climate change. The purpose of this study is to explore the effects of Nr inputs on ecosystem services provided by wetlands using a Bayesian Belief Network (BBN). The network was developed from established relationships between a variety of wetland function indicators and biogeochemical process associated with Nr removal. Empirical data for 34 freshwater wetlands were gathered from a comprehensive review of published peer-reviewed and gray literature. The BBN was trained using 30 wetlands (88% of the freshwater wetland case file) and tested using 4 wetlands (12% of the freshwater wetland case file). Sensitivity analysis suggested that Nr removal, water quality, soil Nr accumulation and N2O emissions had the greatest influence on ecosystem service tradeoffs. The magnitude of Nr inputs did not affect ecosystem services. The network implies that Nr removal efficiency has a greater influence on final ecosystem services associated with water quality impairment and atmospheric pollution. A very low error rate, which was based on 4 wetland

  14. A Bayesian network to predict coastal vulnerability to sea level rise

    USGS Publications Warehouse

    Gutierrez, B.T.; Plant, N.G.; Thieler, E.R.

    2011-01-01

    Sea level rise during the 21st century will have a wide range of effects on coastal environments, human development, and infrastructure in coastal areas. The broad range of complex factors influencing coastal systems contributes to large uncertainties in predicting long-term sea level rise impacts. Here we explore and demonstrate the capabilities of a Bayesian network (BN) to predict long-term shoreline change associated with sea level rise and make quantitative assessments of prediction uncertainty. A BN is used to define relationships between driving forces, geologic constraints, and coastal response for the U.S. Atlantic coast that include observations of local rates of relative sea level rise, wave height, tide range, geomorphic classification, coastal slope, and shoreline change rate. The BN is used to make probabilistic predictions of shoreline retreat in response to different future sea level rise rates. Results demonstrate that the probability of shoreline retreat increases with higher rates of sea level rise. Where more specific information is included, the probability of shoreline change increases in a number of cases, indicating more confident predictions. A hindcast evaluation of the BN indicates that the network correctly predicts 71% of the cases. Evaluation of the results using Brier skill and log likelihood ratio scores indicates that the network provides shoreline change predictions that are better than the prior probability. Shoreline change outcomes indicating stability (-1 1 m/yr) was not well predicted. We find that BNs can assimilate important factors contributing to coastal change in response to sea level rise and can make quantitative, probabilistic predictions that can be applied to coastal management decisions. Copyright ?? 2011 by the American Geophysical Union.

  15. Probabilistic Subset Conjunction

    ERIC Educational Resources Information Center

    Kohli, Rajeev; Jedidi, Kamel

    2005-01-01

    The authors introduce subset conjunction as a classification rule by which an acceptable alternative must satisfy some minimum number of criteria. The rule subsumes conjunctive and disjunctive decision strategies as special cases. Subset conjunction can be represented in a binary-response model, for example, in a logistic regression, using only…

  16. An application of GIS and Bayesian network in studying spatial-causal relations between enterprises and environmental factors

    NASA Astrophysics Data System (ADS)

    Shen, Tiyan; Li, Xi; Li, Maiqing

    2009-10-01

    The paper intends to employ Geographic Information System (GIS) and Bayesian Network to discover the spatial causality between enterprises and environmental factors in Beijing Metropolis. The census data of Beijing was spatialized by means of GIS in the beginning, and then the training data was made using density mapping technique. Base on the training data, the structure of a Bayesian Network was learnt with the help of Maximum Weight Spanning Tree. Eight direct relations were discussed in the end, of which, the most exciting discovery, "Enterprise-Run Society", as the symbol of the former planned economy, was emphasized in the spatial relations between heavy industry and schools. Though the final result is not so creative in economic perspective, it is of significance in technique view due to all discoveries were drawn from data, therefore leading to the realization of the importance of GIS and data mining to economic geography research.

  17. A Bayesian network approach to the study of historical epidemiological databases: modelling meningitis outbreaks in the Niger

    PubMed Central

    Bertherat, E; Perea, W; Soga, G; Souley, R; Dupont, D; Hugonnet, S

    2012-01-01

    Abstract Objective To develop a tool for evaluating the risk that an outbreak of meningitis will occur in a particular district of the Niger after outbreaks have been reported in other, specified districts of the country. Methods A Bayesian network was represented by a graph composed of 38 nodes (one for each district in the Niger) connected by arrows. In the graph, each node directly influenced each of the “child” nodes that lay at the ends of the arrows arising from that node, according to conditional probabilities. The probabilities between “influencing” and “influenced” districts were estimated by analysis of databases that held weekly records of meningitis outbreaks in the Niger between 1986 and 2005. For each week of interest, each district was given a Boolean-variable score of 1 (if meningitis incidence in the district reached an epidemic threshold in that week) or 0. Findings The Bayesian network approach provided important and original information, allowing the identification of the districts that influence meningitis risk in other districts (and the districts that are influenced by any particular district) and the evaluation of the level of influence between each pair of districts. Conclusion Bayesian networks offer a promising approach to understanding the dynamics of epidemics, estimating the risk of outbreaks in particular areas and allowing control interventions to be targeted at high-risk areas. PMID:22690030

  18. A Bayesian network modeling approach to forecasting the 21st century worldwide status of polar bears

    NASA Astrophysics Data System (ADS)

    Amstrup, Steven C.; Marcot, Bruce G.; Douglas, David C.

    To inform the U.S. Fish and Wildlife Service decision, whether or not to list polar bears as threatened under the Endangered Species Act (ESA), we projected the status of the world's polar bears (Ursus maritimus) for decades centered on future years 2025, 2050, 2075, and 2095. We defined four ecoregions based on current and projected sea ice conditions: seasonal ice, Canadian Archipelago, polar basin divergent, and polar basin convergent ecoregions. We incorporated general circulation model projections of future sea ice into a Bayesian network (BN) model structured around the factors considered in ESA decisions. This first-generation BN model combined empirical data, interpretations of data, and professional judgments of one polar bear expert into a probabilistic framework that identifies causal links between environmental stressors and polar bear responses. We provide guidance regarding steps necessary to refine the model, including adding inputs from other experts. The BN model projected extirpation of polar bears from the seasonal ice and polar basin divergent ecoregions, where ≈2/3 of the world's polar bears currently occur, by mid century. Projections were less dire in other ecoregions. Decline in ice habitat was the overriding factor driving the model outcomes. Although this is a first-generation model, the dependence of polar bears on sea ice is universally accepted, and the observed sea ice decline is faster than models suggest. Therefore, incorporating judgments of multiple experts in a final model is not expected to fundamentally alter the outlook for polar bears described here.

  19. Dynamic Bayesian Network for Accurate Detection of Peptides from Tandem Mass Spectra.

    PubMed

    Halloran, John T; Bilmes, Jeff A; Noble, William S

    2016-08-01

    A central problem in mass spectrometry analysis involves identifying, for each observed tandem mass spectrum, the corresponding generating peptide. We present a dynamic Bayesian network (DBN) toolkit that addresses this problem by using a machine learning approach. At the heart of this toolkit is a DBN for Rapid Identification (DRIP), which can be trained from collections of high-confidence peptide-spectrum matches (PSMs). DRIP's score function considers fragment ion matches using Gaussians rather than fixed fragment-ion tolerances and also finds the optimal alignment between the theoretical and observed spectrum by considering all possible alignments, up to a threshold that is controlled using a beam-pruning algorithm. This function not only yields state-of-the art database search accuracy but also can be used to generate features that significantly boost the performance of the Percolator postprocessor. The DRIP software is built upon a general purpose DBN toolkit (GMTK), thereby allowing a wide variety of options for user-specific inference tasks as well as facilitating easy modifications to the DRIP model in future work. DRIP is implemented in Python and C++ and is available under Apache license at http://melodi-lab.github.io/dripToolkit . PMID:27397138

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

    NASA Astrophysics Data System (ADS)

    Gosangi, Rakesh; Gutierrez-Osuna, Ricardo

    2011-09-01

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

  1. Spatially implemented Bayesian network model to assess environmental impacts of water management

    NASA Astrophysics Data System (ADS)

    Morrison, Ryan R.; Stone, Mark C.

    2014-10-01

    Bayesian networks (BNs) have become a popular method of assessing environmental impacts of water management. However, spatial attributes that influence ecological processes are rarely included in BN models. We demonstrate the benefits of combining two-dimensional hydrodynamic and BN modeling frameworks to explicitly incorporate the spatial variability within a system. The impacts of two diversion scenarios on riparian vegetation recruitment at the Gila River, New Mexico, USA, were evaluated using a coupled modeling framework. We focused on five individual sites in the Upper Gila basin. Our BN model incorporated key ecological drivers based on the "recruitment box" conceptual model, including the timing of seed availability, floodplain inundation, river recession rate, and groundwater depths. Results indicated that recruitment potential decreased by >20% at some locations within each study site, relative to existing conditions. The largest impacts occurring along dynamic fluvial landforms, such as side channels and sand bars. Reductions in recruitment potential varied depending on the diversion scenario. Our unique approach allowed us to evaluate recruitment consequences of water management scenarios at a fine spatial scale, which not only helped differentiate impacts at distinct channel locations but also was useful for informing stakeholders of possible ecological impacts. Our findings also demonstrate that minor changes to river flow may have large ecological implications.

  2. Hierarchical Bayesian approaches for detecting inconsistency in network meta-analysis.

    PubMed

    Zhao, Hong; Hodges, James S; Ma, Haijun; Jiang, Qi; Carlin, Bradley P

    2016-09-10

    Network meta-analysis (NMA), also known as multiple treatment comparisons, is commonly used to incorporate direct and indirect evidence comparing treatments. With recent advances in methods and software, Bayesian approaches to NMA have become quite popular and allow models of previously unanticipated complexity. However, when direct and indirect evidence differ in an NMA, the model is said to suffer from inconsistency. Current inconsistency detection in NMA is usually based on contrast-based (CB) models; however, this approach has certain limitations. In this work, we propose an arm-based random effects model, where we detect discrepancy of direct and indirect evidence for comparing two treatments using the fixed effects in the model while flagging extreme trials using the random effects. We define discrepancy factors to characterize evidence of inconsistency for particular treatment comparisons, which is novel in NMA research. Our approaches permit users to address issues previously tackled via CB models. We compare sources of inconsistency identified by our approach and existing loop-based CB methods using real and simulated datasets and demonstrate that our methods can offer powerful inconsistency detection. Copyright © 2016 John Wiley & Sons, Ltd. PMID:27037506

  3. Assessing Flood Risk from Hurricane-induced Precipitation and Storm Surge: A Bayesian Network Approach

    NASA Astrophysics Data System (ADS)

    Sebastian, A.; Dupuits, E. J. C.; Morales-Napoles, O.

    2015-12-01

    Hurricanes pose a major flood hazard to communities on the U.S. Atlantic and Gulf Coasts. Over the past decade, the economic costs associated with hurricane flood damages have escalated and recent studies indicate that a large percentage of flood damages are occurring outside of FEMA-designated flood hazard areas. While FEMA recently upgraded coastal flood hazard maps using the Advanced CIRCulation (ADCIRC) Model, these maps do not consider the flood hazard resulting from the joint occurrence of precipitation over the watershed and storm surge at the coast. Instead, the two individual hazards are mapped separately, ignoring the floodplain resulting from their interaction.In this study, a risk assessment methodology was developed to predict the damages associated with hurricane-induced flooding in the Houston Galveston Bay Area. Historical hurricanes were analyzed to derive probability distributions for storm surge height, cumulative precipitation, hurricane landfall, wind speed, angle of approach, radius to maximum winds, and forward speed. A Bayesian Network was built and used to simulate a large number of synthetic storms. The resulting 1% combinations of storm surge and precipitation were applied as boundary conditions to a hydraulic modeled and the maximum extent of flooding was compared to the FEMA-designated flood hazard areas. A high resolution GIS-based model was used to predict damages.

  4. A Bayesian network for modelling blood glucose concentration and exercise in type 1 diabetes.

    PubMed

    Ewings, Sean M; Sahu, Sujit K; Valletta, John J; Byrne, Christopher D; Chipperfield, Andrew J

    2015-06-01

    This article presents a new statistical approach to analysing the effects of everyday physical activity on blood glucose concentration in people with type 1 diabetes. A physiologically based model of blood glucose dynamics is developed to cope with frequently sampled data on food, insulin and habitual physical activity; the model is then converted to a Bayesian network to account for measurement error and variability in the physiological processes. A simulation study is conducted to determine the feasibility of using Markov chain Monte Carlo methods for simultaneous estimation of all model parameters and prediction of blood glucose concentration. Although there are problems with parameter identification in a minority of cases, most parameters can be estimated without bias. Predictive performance is unaffected by parameter misspecification and is insensitive to misleading prior distributions. This article highlights important practical and theoretical issues not previously addressed in the quest for an artificial pancreas as treatment for type 1 diabetes. The proposed methods represent a new paradigm for analysis of deterministic mathematical models of blood glucose concentration. PMID:24492795

  5. Novel dynamic Bayesian networks for facial action element recognition and understanding

    NASA Astrophysics Data System (ADS)

    Zhao, Wei; Park, Jeong-Seon; Choi, Dong-You; Lee, Sang-Woong

    2011-12-01

    In daily life, language is an important tool of communication between people. Besides language, facial action can also provide a great amount of information. Therefore, facial action recognition has become a popular research topic in the field of human-computer interaction (HCI). However, facial action recognition is quite a challenging task due to its complexity. In a literal sense, there are thousands of facial muscular movements, many of which have very subtle differences. Moreover, muscular movements always occur simultaneously when the pose is changed. To address this problem, we first build a fully automatic facial points detection system based on a local Gabor filter bank and principal component analysis. Then, novel dynamic Bayesian networks are proposed to perform facial action recognition using the junction tree algorithm over a limited number of feature points. In order to evaluate the proposed method, we have used the Korean face database for model training. For testing, we used the CUbiC FacePix, facial expressions and emotion database, Japanese female facial expression database, and our own database. Our experimental results clearly demonstrate the feasibility of the proposed approach.

  6. Unusual behavior detection in the entry gate scenes of subway station using Bayesian networks and inference

    NASA Astrophysics Data System (ADS)

    Kwak, Sooyeong; Bae, Guntae; Kim, Manbae; Byun, Hyeran

    2008-02-01

    In this paper, we propose a method for detecting unusual human behavior using monocular camera which is not moving. Our system composed of three modules which are moving object detection, tracking, and event recognition. The key part is event recognition module. We define unusual events which are composed of two simple events (drop off luggage, unattended luggage) and two complex events (abandoned luggage and steal luggage). In order to detect the simple event, we construct Bayesian network in each unusual event. We extract evidences using bounding box properties which are the location of moving objects, speed, distance between the person and the other moving object (such as bag), existing time. And then, we use finite state automaton which shows the temporal relation of two simple events to detect complex events. To evaluate the performance, we compare the frame number when an even is triggered with our results and the ground truth. The proposed algorithm showed good results on the real world environment and also worked at real time speed.

  7. Integrating System Dynamics and Bayesian Networks with Application to Counter-IED Scenarios

    SciTech Connect

    Jarman, Kenneth D.; Brothers, Alan J.; Whitney, Paul D.; Young, Jonathan; Niesen, David A.

    2010-06-06

    The practice of choosing a single modeling paradigm for predictive analysis can limit the scope and relevance of predictions and their utility to decision-making processes. Considering multiple modeling methods simultaneously may improve this situation, but a better solution provides a framework for directly integrating different, potentially complementary modeling paradigms to enable more comprehensive modeling and predictions, and thus better-informed decisions. The primary challenges of this kind of model integration are to bridge language and conceptual gaps between modeling paradigms, and to determine whether natural and useful linkages can be made in a formal mathematical manner. To address these challenges in the context of two specific modeling paradigms, we explore mathematical and computational options for linking System Dynamics (SD) and Bayesian network (BN) models and incorporating data into the integrated models. We demonstrate that integrated SD/BN models can naturally be described as either state space equations or Dynamic Bayes Nets, which enables the use of many existing computational methods for simulation and data integration. To demonstrate, we apply our model integration approach to techno-social models of insurgent-led attacks and security force counter-measures centered on improvised explosive devices.

  8. Bayesian-network-based safety risk assessment for steel construction projects.

    PubMed

    Leu, Sou-Sen; Chang, Ching-Miao

    2013-05-01

    There are four primary accident types at steel building construction (SC) projects: falls (tumbles), object falls, object collapse, and electrocution. Several systematic safety risk assessment approaches, such as fault tree analysis (FTA) and failure mode and effect criticality analysis (FMECA), have been used to evaluate safety risks at SC projects. However, these traditional methods ineffectively address dependencies among safety factors at various levels that fail to provide early warnings to prevent occupational accidents. To overcome the limitations of traditional approaches, this study addresses the development of a safety risk-assessment model for SC projects by establishing the Bayesian networks (BN) based on fault tree (FT) transformation. The BN-based safety risk-assessment model was validated against the safety inspection records of six SC building projects and nine projects in which site accidents occurred. The ranks of posterior probabilities from the BN model were highly consistent with the accidents that occurred at each project site. The model accurately provides site safety-management abilities by calculating the probabilities of safety risks and further analyzing the causes of accidents based on their relationships in BNs. In practice, based on the analysis of accident risks and significant safety factors, proper preventive safety management strategies can be established to reduce the occurrence of accidents on SC sites. PMID:23499984

  9. A fuzzy Bayesian network approach to quantify the human behaviour during an evacuation

    NASA Astrophysics Data System (ADS)

    Ramli, Nurulhuda; Ghani, Noraida Abdul; Ahmad, Nazihah

    2016-06-01

    Bayesian Network (BN) has been regarded as a successful representation of inter-relationship of factors affecting human behavior during an emergency. This paper is an extension of earlier work of quantifying the variables involved in the BN model of human behavior during an evacuation using a well-known direct probability elicitation technique. To overcome judgment bias and reduce the expert's burden in providing precise probability values, a new approach for the elicitation technique is required. This study proposes a new fuzzy BN approach for quantifying human behavior during an evacuation. Three major phases of methodology are involved, namely 1) development of qualitative model representing human factors during an evacuation, 2) quantification of BN model using fuzzy probability and 3) inferencing and interpreting the BN result. A case study of three inter-dependencies of human evacuation factors such as danger assessment ability, information about the threat and stressful conditions are used to illustrate the application of the proposed method. This approach will serve as an alternative to the conventional probability elicitation technique in understanding the human behavior during an evacuation.

  10. Bayesian decision-network modeling of multiple stakeholders for reef ecosystem restoration in the coral triangle.

    PubMed

    Varkey, Divya A; Pitcher, Tony J; McAllister, Murdoch K; Sumaila, Rashid S

    2013-06-01

    Proposals for marine conservation measures have proliferated in the last 2 decades due to increased reports of fishery declines and interest in conservation. Fishers and fisheries managers have often disagreed strongly when discussing controls on fisheries. In such situations, ecosystem-based models and fisheries-stock assessment models can help resolve disagreements by highlighting the trade-offs that would be made under alternative management scenarios. We extended the analytical framework for modeling such trade-offs by including additional stakeholders whose livelihoods and the value they place on conservation depend on the condition of the marine ecosystem. To do so, we used Bayesian decision-network models (BDNs) in a case study of an Indonesian coral reef fishery. Our model included interests of the fishers and fishery managers; individuals in the tourism industry; conservation interests of the state, nongovernmental organizations, and the local public; and uncertainties in ecosystem status, projections of fisheries revenues, tourism growth, and levels of interest in conservation. We calculated the total utility (i.e., value) of a range of restoration scenarios. Restricting net fisheries and live-fish fisheries appeared to be the best compromise solutions under several combinations of settings of modeled variables. Results of our case study highlight the implications of alternate formulations for coral reef stakeholder utility functions and discount rates for the calculation of the net benefits of alternative fisheries management options. This case study may also serve as a useful example for other decision analyses with multiple stakeholders. PMID:23530881

  11. 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.

  12. Initialization and Restart in Stochastic Local Search: Computing a Most Probable Explanation in Bayesian Networks

    NASA Technical Reports Server (NTRS)

    Mengshoel, Ole J.; Wilkins, David C.; Roth, Dan

    2010-01-01

    For hard computational problems, stochastic local search has proven to be a competitive approach to finding optimal or approximately optimal problem solutions. Two key research questions for stochastic local search algorithms are: Which algorithms are effective for initialization? When should the search process be restarted? In the present work we investigate these research questions in the context of approximate computation of most probable explanations (MPEs) in Bayesian networks (BNs). We introduce a novel approach, based on the Viterbi algorithm, to explanation initialization in BNs. While the Viterbi algorithm works on sequences and trees, our approach works on BNs with arbitrary topologies. We also give a novel formalization of stochastic local search, with focus on initialization and restart, using probability theory and mixture models. Experimentally, we apply our methods to the problem of MPE computation, using a stochastic local search algorithm known as Stochastic Greedy Search. By carefully optimizing both initialization and restart, we reduce the MPE search time for application BNs by several orders of magnitude compared to using uniform at random initialization without restart. On several BNs from applications, the performance of Stochastic Greedy Search is competitive with clique tree clustering, a state-of-the-art exact algorithm used for MPE computation in BNs.

  13. Alternative method of highway traffic safety analysis for developing countries using delphi technique and Bayesian network.

    PubMed

    Mbakwe, Anthony C; Saka, Anthony A; Choi, Keechoo; Lee, Young-Jae

    2016-08-01

    Highway traffic accidents all over the world result in more than 1.3 million fatalities annually. An alarming number of these fatalities occurs in developing countries. There are many risk factors that are associated with frequent accidents, heavy loss of lives, and property damage in developing countries. Unfortunately, poor record keeping practices are very difficult obstacle to overcome in striving to obtain a near accurate casualty and safety data. In light of the fact that there are numerous accident causes, any attempts to curb the escalating death and injury rates in developing countries must include the identification of the primary accident causes. This paper, therefore, seeks to show that the Delphi Technique is a suitable alternative method that can be exploited in generating highway traffic accident data through which the major accident causes can be identified. In order to authenticate the technique used, Korea, a country that underwent similar problems when it was in its early stages of development in addition to the availability of excellent highway safety records in its database, is chosen and utilized for this purpose. Validation of the methodology confirms the technique is suitable for application in developing countries. Furthermore, the Delphi Technique, in combination with the Bayesian Network Model, is utilized in modeling highway traffic accidents and forecasting accident rates in the countries of research. PMID:27183516

  14. Bayesian network for estimating the interaction between ecological health and waterfowl abundance

    NASA Astrophysics Data System (ADS)

    Teng, Te Hui; Fang, Wei Ta; Yu, Hwa Lung

    2013-04-01

    The serious decrease of biodiversity which is mainly induced by Habitat disappear is important issue of species field and in the world. The study area chooses Tauyuan County at subtropical area because of the most artificial farm ponds in Taiwan where the total area includes 27 km2. The effectiveness of these ponds is storage and irrigation and also supplies all kinds of environment like refuges for migratory birds, especially for water birds. Due to human development, farm ponds in this city not only suffer from largely disappear recent year, but also lead to the habitat and bird species reduce. Biological research usually contains incomplete and uncertain information, therefore, this study adopts Bayesian Network model to analyze interaction between land use and water birds. The habitat parameters include elevation, urbanization, building area, farm area, reconsolidation, forest area, irrigation area, farm pond area and lawn area; the biological factors have reproductive capacity, habitat condition, hydrological condition and food source. Using this structure can estimate the interaction of spatiotemporal abundance distribution between habitat parameter and biological parameter. In addition, the former results can define all the reasonable relationship of all hidden states and provide decision-makers with reasonable evaluation.

  15. A Parallel and Incremental Approach for Data-Intensive Learning of Bayesian Networks.

    PubMed

    Yue, Kun; Fang, Qiyu; Wang, Xiaoling; Li, Jin; Liu, Weiyi

    2015-12-01

    Bayesian network (BN) has been adopted as the underlying model for representing and inferring uncertain knowledge. As the basis of realistic applications centered on probabilistic inferences, learning a BN from data is a critical subject of machine learning, artificial intelligence, and big data paradigms. Currently, it is necessary to extend the classical methods for learning BNs with respect to data-intensive computing or in cloud environments. In this paper, we propose a parallel and incremental approach for data-intensive learning of BNs from massive, distributed, and dynamically changing data by extending the classical scoring and search algorithm and using MapReduce. First, we adopt the minimum description length as the scoring metric and give the two-pass MapReduce-based algorithms for computing the required marginal probabilities and scoring the candidate graphical model from sample data. Then, we give the corresponding strategy for extending the classical hill-climbing algorithm to obtain the optimal structure, as well as that for storing a BN by pairs. Further, in view of the dynamic characteristics of the changing data, we give the concept of influence degree to measure the coincidence of the current BN with new data, and then propose the corresponding two-pass MapReduce-based algorithms for BNs incremental learning. Experimental results show the efficiency, scalability, and effectiveness of our methods. PMID:25622335

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  17. Statistical-Dynamical Drought Forecast within Bayesian Networks and Data Assimilation: How to Quantify Drought Recovery

    NASA Astrophysics Data System (ADS)

    Moradkhani, Hamid

    2015-04-01

    Drought forecasting is vital for resource management and planning. Both societal and agricultural requirements for water weigh heavily on the natural environment, which may become scarce in the event of drought. Although drought forecasts are an important tool for managing water in hydrologic systems, these forecasts are plagued by uncertainties, owing to the complexities of water dynamics and the spatial heterogeneities of pertinent variables. Due to these uncertainties, it is necessary to frame forecasts in a probabilistic manner. Here we present a statistical-dynamical probabilistic drought forecast framework within Bayesian networks. The statistical forecast model applies a family of multivariate distribution functions to forecast future drought conditions given the drought status in the past. The advantage of the statistical forecast model is that it develops conditional probabilities of a given forecast variable, and returns the highest probable forecast along with an assessment of the uncertainty around that value. The dynamical model relies on data assimilation to characterize the initial land surface condition uncertainty which correspondingly reflect on drought forecast. In addition, the recovery of drought will be examined. From these forecasts, it is found that drought recovery is a longer process than suggested in recent literature. Drought in land surface variables (snow, soil moisture) is shown to be persistent up to a year in certain locations, depending on the intensity of the drought. Location within the basin appears to be a driving factor in the ability of the land surface to recover from drought, allowing for differentiation between drought prone and drought resistant regions.

  18. Development and validation of a Bayesian network for the differential diagnosis of anterior uveitis.

    PubMed

    González-López, J J; García-Aparicio, Á M; Sánchez-Ponce, D; Muñoz-Sanz, N; Fernandez-Ledo, N; Beneyto, P; Westcott, M C

    2016-06-01

    PurposeTo develop and validate a Bayesian belief network algorithm for the differential diagnosis of anterior uveitis.Patients and methodsThe 11 most common etiologies were included (idiopathic, ankylosing spondylitis, psoriasic arthritis, reactive arthritis, inflammatory bowel diseases, sarcoidosis, tuberculosis, Behçet, Posner-Schlossman syndrome, juvenile idiopathic arthritis (JIA), and Fuchs' heterochromic cyclitis). Frequencies of association between factors and etiologies were retrieved from a systematic review of the literature. Prevalences were calculated using a random sample of 200 patients receiving a diagnosis of anterior uveitis in Moorfields Eye Hospital in 2012. The network was validated in a random sample of 200 patients receiving a diagnosis of anterior uveitis in the same hospital in 2013 plus 10 extra cases of the most rare etiologies (JIA, Behçet, and psoriasic arthritis).ResultsIn 63.8% of patients the most probable etiology by the algorithm matched the senior clinician diagnosis. In 80.5% of patients the clinician diagnosis matched the first or second most probable results by the algorithm. Taking into account only the most probable diagnosis by the algorithm, sensitivities for each etiology ranged from 100% (7 of 7 patients with reactive arthritis and 5 of 5 with Behçet correctly classified) to 46.7% (7 of 15 patients with tuberculosis-related uveitis). Specificities ranged from 88.8% for sarcoidosis to 99.5% in Posner.ConclusionsThis algorithm could help clinicians with the differential diagnosis of anterior uveitis. In addition, it could help with the selection of the diagnostic tests performed. PMID:27055672

  19. User-Adapted Recommendation of Content on Mobile Devices Using Bayesian Networks

    NASA Astrophysics Data System (ADS)

    Iwasaki, Hirotoshi; Mizuno, Nobuhiro; Hara, Kousuke; Motomura, Yoichi

    Mobile devices, such as cellular phones and car navigation systems, are essential to daily life. People acquire necessary information and preferred content over communication networks anywhere, anytime. However, usability issues arise from the simplicity of user interfaces themselves. Thus, a recommendation of content that is adapted to a user's preference and situation will help the user select content. In this paper, we describe a method to realize such a system using Bayesian networks. This user-adapted mobile system is based on a user model that provides recommendation of content (i.e., restaurants, shops, and music that are suitable to the user and situation) and that learns incrementally based on accumulated usage history data. However, sufficient samples are not always guaranteed, since a user model would require combined dependency among users, situations, and contents. Therefore, we propose the LK method for modeling, which complements incomplete and insufficient samples using knowledge data, and CPT incremental learning for adaptation based on a small number of samples. In order to evaluate the methods proposed, we applied them to restaurant recommendations made on car navigation systems. The evaluation results confirmed that our model based on the LK method can be expected to provide better generalization performance than that of the conventional method. Furthermore, our system would require much less operation than current car navigation systems from the beginning of use. Our evaluation results also indicate that learning a user's individual preference through CPT incremental learning would be beneficial to many users, even with only a few samples. As a result, we have developed the technology of a system that becomes more adapted to a user the more it is used.

  20. Assessment of groundwater quality: a fusion of geochemical and geophysical information via Bayesian neural networks.

    PubMed

    Maiti, Saumen; Erram, V C; Gupta, Gautam; Tiwari, Ram Krishna; Kulkarni, U D; Sangpal, R R

    2013-04-01

    Deplorable quality of groundwater arising from saltwater intrusion, natural leaching and anthropogenic activities is one of the major concerns for the society. Assessment of groundwater quality is, therefore, a primary objective of scientific research. Here, we propose an artificial neural network-based method set in a Bayesian neural network (BNN) framework and employ it to assess groundwater quality. The approach is based on analyzing 36 water samples and inverting up to 85 Schlumberger vertical electrical sounding data. We constructed a priori model by suitably parameterizing geochemical and geophysical data collected from the western part of India. The posterior model (post-inversion) was estimated using the BNN learning procedure and global hybrid Monte Carlo/Markov Chain Monte Carlo optimization scheme. By suitable parameterization of geochemical and geophysical parameters, we simulated 1,500 training samples, out of which 50 % samples were used for training and remaining 50 % were used for validation and testing. We show that the trained model is able to classify validation and test samples with 85 % and 80 % accuracy respectively. Based on cross-correlation analysis and Gibb's diagram of geochemical attributes, the groundwater qualities of the study area were classified into following three categories: "Very good", "Good", and "Unsuitable". The BNN model-based results suggest that groundwater quality falls mostly in the range of "Good" to "Very good" except for some places near the Arabian Sea. The new modeling results powered by uncertainty and statistical analyses would provide useful constrain, which could be utilized in monitoring and assessment of the groundwater quality. PMID:22899457

  1. Neural network uncertainty assessment using Bayesian statistics: a remote sensing application

    NASA Technical Reports Server (NTRS)

    Aires, F.; Prigent, C.; Rossow, W. B.

    2004-01-01

    Neural network (NN) techniques have proved successful for many regression problems, in particular for remote sensing; however, uncertainty estimates are rarely provided. In this article, a Bayesian technique to evaluate uncertainties of the NN parameters (i.e., synaptic weights) is first presented. In contrast to more traditional approaches based on point estimation of the NN weights, we assess uncertainties on such estimates to monitor the robustness of the NN model. These theoretical developments are illustrated by applying them to the problem of retrieving surface skin temperature, microwave surface emissivities, and integrated water vapor content from a combined analysis of satellite microwave and infrared observations over land. The weight uncertainty estimates are then used to compute analytically the uncertainties in the network outputs (i.e., error bars and correlation structure of these errors). Such quantities are very important for evaluating any application of an NN model. The uncertainties on the NN Jacobians are then considered in the third part of this article. Used for regression fitting, NN models can be used effectively to represent highly nonlinear, multivariate functions. In this situation, most emphasis is put on estimating the output errors, but almost no attention has been given to errors associated with the internal structure of the regression model. The complex structure of dependency inside the NN is the essence of the model, and assessing its quality, coherency, and physical character makes all the difference between a blackbox model with small output errors and a reliable, robust, and physically coherent model. Such dependency structures are described to the first order by the NN Jacobians: they indicate the sensitivity of one output with respect to the inputs of the model for given input data. We use a Monte Carlo integration procedure to estimate the robustness of the NN Jacobians. A regularization strategy based on principal component

  2. Combining Volcano Monitoring Timeseries Analyses with Bayesian Belief Networks to Update Hazard Forecast Estimates

    NASA Astrophysics Data System (ADS)

    Odbert, Henry; Hincks, Thea; Aspinall, Willy

    2015-04-01

    Volcanic hazard assessments must combine information about the physical processes of hazardous phenomena with observations that indicate the current state of a volcano. Incorporating both these lines of evidence can inform our belief about the likelihood (probability) and consequences (impact) of possible hazardous scenarios, forming a basis for formal quantitative hazard assessment. However, such evidence is often uncertain, indirect or incomplete. Approaches to volcano monitoring have advanced substantially in recent decades, increasing the variety and resolution of multi-parameter timeseries data recorded at volcanoes. Interpreting these multiple strands of parallel, partial evidence thus becomes increasingly complex. In practice, interpreting many timeseries requires an individual to be familiar with the idiosyncrasies of the volcano, monitoring techniques, configuration of recording instruments, observations from other datasets, and so on. In making such interpretations, an individual must consider how different volcanic processes may manifest as measureable observations, and then infer from the available data what can or cannot be deduced about those processes. We examine how parts of this process may be synthesised algorithmically using Bayesian inference. Bayesian Belief Networks (BBNs) use probability theory to treat and evaluate uncertainties in a rational and auditable scientific manner, but only to the extent warranted by the strength of the available evidence. The concept is a suitable framework for marshalling multiple strands of evidence (e.g. observations, model results and interpretations) and their associated uncertainties in a methodical manner. BBNs are usually implemented in graphical form and could be developed as a tool for near real-time, ongoing use in a volcano observatory, for example. We explore the application of BBNs in analysing volcanic data from the long-lived eruption at Soufriere Hills Volcano, Montserrat. We show how our method

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

    NASA Astrophysics Data System (ADS)

    Maiti, Saumen; Tiwari, Ram Krishna

    2010-10-01

    A new probabilistic approach based on the concept of Bayesian neural network (BNN) learning theory is proposed for decoding litho-facies boundaries from well-log data. We show that how a multi-layer-perceptron neural network model can be employed in Bayesian framework to classify changes in litho-log successions. The method is then applied to the German Continental Deep Drilling Program (KTB) well-log data for classification and uncertainty estimation in the litho-facies boundaries. In this framework, a posteriori distribution of network parameter is estimated via the principle of Bayesian probabilistic theory, and an objective function is minimized following the scaled conjugate gradient optimization scheme. For the model development, we inflict a suitable criterion, which provides probabilistic information by emulating different combinations of synthetic data. Uncertainty in the relationship between the data and the model space is appropriately taken care by assuming a Gaussian a priori distribution of networks parameters (e.g., synaptic weights and biases). Prior to applying the new method to the real KTB data, we tested the proposed method on synthetic examples to examine the sensitivity of neural network hyperparameters in prediction. Within this framework, we examine stability and efficiency of this new probabilistic approach using different kinds of synthetic data assorted with different level of correlated noise. Our data analysis suggests that the designed network topology based on the Bayesian paradigm is steady up to nearly 40% correlated noise; however, adding more noise (˜50% or more) degrades the results. We perform uncertainty analyses on training, validation, and test data sets with and devoid of intrinsic noise by making the Gaussian approximation of the a posteriori distribution about the peak model. We present a standard deviation error-map at the network output corresponding to the three types of the litho-facies present over the entire litho

  4. Continuous time Bayesian networks identify Prdm1 as a negative regulator of TH17 cell differentiation in humans

    PubMed Central

    Acerbi, Enzo; Viganò, Elena; Poidinger, Michael; Mortellaro, Alessandra; Zelante, Teresa; Stella, Fabio

    2016-01-01

    T helper 17 (TH17) cells represent a pivotal adaptive cell subset involved in multiple immune disorders in mammalian species. Deciphering the molecular interactions regulating TH17 cell differentiation is particularly critical for novel drug target discovery designed to control maladaptive inflammatory conditions. Using continuous time Bayesian networks over a time-course gene expression dataset, we inferred the global regulatory network controlling TH17 differentiation. From the network, we identified the Prdm1 gene encoding the B lymphocyte-induced maturation protein 1 as a crucial negative regulator of human TH17 cell differentiation. The results have been validated by perturbing Prdm1 expression on freshly isolated CD4+ naïve T cells: reduction of Prdm1 expression leads to augmentation of IL-17 release. These data unravel a possible novel target to control TH17 polarization in inflammatory disorders. Furthermore, this study represents the first in vitro validation of continuous time Bayesian networks as gene network reconstruction method and as hypothesis generation tool for wet-lab biological experiments. PMID:26976045

  5. Inference of nonlinear gene regulatory networks through optimized ensemble of support vector regression and dynamic Bayesian networks.

    PubMed

    Akutekwe, Arinze; Seker, Huseyin

    2015-08-01

    Comprehensive understanding of gene regulatory networks (GRNs) is a major challenge in systems biology. Most methods for modeling and inferring the dynamics of GRNs, such as those based on state space models, vector autoregressive models and G1DBN algorithm, assume linear dependencies among genes. However, this strong assumption does not make for true representation of time-course relationships across the genes, which are inherently nonlinear. Nonlinear modeling methods such as the S-systems and causal structure identification (CSI) have been proposed, but are known to be statistically inefficient and analytically intractable in high dimensions. To overcome these limitations, we propose an optimized ensemble approach based on support vector regression (SVR) and dynamic Bayesian networks (DBNs). The method called SVR-DBN, uses nonlinear kernels of the SVR to infer the temporal relationships among genes within the DBN framework. The two-stage ensemble is further improved by SVR parameter optimization using Particle Swarm Optimization. Results on eight insilico-generated datasets, and two real world datasets of Drosophila Melanogaster and Escherichia Coli, show that our method outperformed the G1DBN algorithm by a total average accuracy of 12%. We further applied our method to model the time-course relationships of ovarian carcinoma. From our results, four hub genes were discovered. Stratified analysis further showed that the expression levels Prostrate differentiation factor and BTG family member 2 genes, were significantly increased by the cisplatin and oxaliplatin platinum drugs; while expression levels of Polo-like kinase and Cyclin B1 genes, were both decreased by the platinum drugs. These hub genes might be potential biomarkers for ovarian carcinoma. PMID:26738192

  6. Optimal Observation Network Design for Model Discrimination using Information Theory and Bayesian Model Averaging

    NASA Astrophysics Data System (ADS)

    Pham, H. V.; Tsai, F. T. C.

    2014-12-01

    Groundwater systems are complex and subject to multiple interpretations and conceptualizations due to a lack of sufficient information. As a result, multiple conceptual models are often developed and their mean predictions are preferably used to avoid biased predictions from using a single conceptual model. Yet considering too many conceptual models may lead to high prediction uncertainty and may lose the purpose of model development. In order to reduce the number of models, an optimal observation network design is proposed based on maximizing the Kullback-Leibler (KL) information to discriminate competing models. The KL discrimination function derived by Box and Hill [1967] for one additional observation datum at a time is expanded to account for multiple independent spatiotemporal observations. The Bayesian model averaging (BMA) method is used to incorporate existing data and quantify future observation uncertainty arising from conceptual and parametric uncertainties in the discrimination function. To consider the future observation uncertainty, the Monte Carlo realizations of BMA predicted future observations are used to calculate the mean and variance of posterior model probabilities of the competing models. The goal of the optimal observation network design is to find the number and location of observation wells and sampling rounds such that the highest posterior model probability of a model is larger than a desired probability criterion (e.g., 95%). The optimal observation network design is implemented to a groundwater study in the Baton Rouge area, Louisiana to collect new groundwater heads from USGS wells. The considered sources of uncertainty that create multiple groundwater models are the geological architecture, the boundary condition, and the fault permeability architecture. All possible design solutions are enumerated using high performance computing systems. Results show that total model variance (the sum of within-model variance and between

  7. Long-Lead Quantitative Flood Forecasts in Ungauged Basins Using Bayesian Neural Networks

    NASA Astrophysics Data System (ADS)

    Barros, A. P.; Yoo, J.

    2004-05-01

    Previously, Kim and Barros (2001) demonstrated the use of a hierarchy of neural network models to forecast flood peaks in four small and medium size ungauged basins (750 to about 9,000 km-sq) in the Northern Appalachian Mountains in Pennsylvania. Using regional rainfall, radiosonde and mesoscale infrared (IR) satellite imagery, their approach consisted of identifying the presence and type of convective activity from the IR imagery, information which was subsequently used to characterize the dominant synoptic scale weather patters and predict storm path and evolution using rainfall and radiosonde data far away from the forecast location. In this regard, the organizational skeleton of the inputs is built to mimic our understanding of physical processes associated with rainstorms. The approach was very successful with skill scores on the order of 80-90 per cent for 18-hour lead-time forecasts of winter and spring floods in response to heavy rainfall (i.e. not associated with snowmelt alone). One weakness of this work was however the lack of a measure of forecast uncertainty, or alternatively a measure of forecast reliability that could be used in hydrometeorological operations. To address this question, we have modified and adapted the existing neural network models according to the principles of Bayesian statistics. In this context, forecasts are issued along with an error bar and are associated with a known probability distribution. One additional advantage of this methodology is that it provides an objective basis for selecting the best model during learning based on the posterior distribution of the parameters. In this context, forecasts are issued along with an error bar and are associated with a known probability distribution. An intercomparison study against Kim and Barros (2001) shows that the 18- and 24-hour lead time BNN forecasts are statistically more robust than those generated by the standard backward-learning NNs. We submit that given the consistently

  8. Epistemic-based investigation of the probability of hazard scenarios using Bayesian network for the lifting operation of floating objects

    NASA Astrophysics Data System (ADS)

    Toroody, Ahmad Bahoo; Abaiee, Mohammad Mahdi; Gholamnia, Reza; Ketabdari, Mohammad Javad

    2016-07-01

    Owing to the increase in unprecedented accidents with new root causes in almost all operational areas, the importance of risk management has dramatically risen. Risk assessment, one of the most significant aspects of risk management, has a substantial impact on the system-safety level of organizations, industries, and operations. If the causes of all kinds of failure and the interactions between them are considered, effective risk assessment can be highly accurate. A combination of traditional risk assessment approaches and modern scientific probability methods can help in realizing better quantitative risk assessment methods. Most researchers face the problem of minimal field data with respect to the probability and frequency of each failure. Because of this limitation in the availability of epistemic knowledge, it is important to conduct epistemic estimations by applying the Bayesian theory for identifying plausible outcomes. In this paper, we propose an algorithm and demonstrate its application in a case study for a light-weight lifting operation in the Persian Gulf of Iran. First, we identify potential accident scenarios and present them in an event tree format. Next, excluding human error, we use the event tree to roughly estimate the prior probability of other hazard-promoting factors using a minimal amount of field data. We then use the Success Likelihood Index Method (SLIM) to calculate the probability of human error. On the basis of the proposed event tree, we use the Bayesian network of the provided scenarios to compensate for the lack of data. Finally, we determine the resulting probability of each event based on its evidence in the epistemic estimation format by building on two Bayesian network types: the probability of hazard promotion factors and the Bayesian theory. The study results indicate that despite the lack of available information on the operation of floating objects, a satisfactory result can be achieved using epistemic data.

  9. Using Bayesian networks to guide the assessment of new evidence in an appeal case

    PubMed Central

    Smit, Nadine M.; Lagnado, David A.; Morgan, Ruth M.; Fenton, Norman E.

    2016-01-01

    When new forensic evidence becomes available after a conviction there is no systematic framework to help lawyers to determine whether it raises sufficient questions about the verdict in order to launch an appeal. This paper presents such a framework driven by a recent case, in which a defendant was convicted primarily on the basis of audio evidence, but where subsequent analysis of the evidence revealed additional sounds that were not considered during the trial. The framework is intended to overcome the gap between what is generally known from scientific analyses and what is hypothesized in a legal setting. It is based on Bayesian networks (BNs) which have the potential to be a structured and understandable way to evaluate the evidence in a specific case context. However, BN methods suffered a setback with regards to the use in court due to the confusing way they have been used in some legal cases in the past. To address this concern, we show the extent to which the reasoning and decisions within the particular case can be made explicit and transparent. The BN approach enables us to clearly define the relevant propositions and evidence, and uses sensitivity analysis to assess the impact of the evidence under different assumptions. The results show that such a framework is suitable to identify information that is currently missing, yet clearly crucial for a valid and complete reasoning process. Furthermore, a method is provided whereby BNs can serve as a guide to not only reason with incomplete evidence in forensic cases, but also identify very specific research questions that should be addressed to extend the evidence base and solve similar issues in the future. PMID:27376015

  10. Bayesian Belief Network to support conflict analysis for groundwater protection: the case of the Apulia region.

    PubMed

    Giordano, Raffaele; D'Agostino, Daniela; Apollonio, Ciro; Lamaddalena, Nicola; Vurro, Michele

    2013-01-30

    Water resource management is often characterized by conflicts, as a result of the heterogeneity of interests associated with a shared resource. Many water conflicts arise on a global scale and, in particular, an increasing level of conflicts can be observed in the Mediterranean basin, characterized by water scarcity. In the present work, in order to assist the conflict analysis process, and thus outline a proper groundwater management, stakeholders were involved in the process and suitable tools were used in a Mediterranean area (the Apulia region, in Italy). In particular, this paper seeks to elicit and structure farmers' mental models influencing their decision over the main water source for irrigation. The more crucial groundwater is for farmers' objectives, the more controversial is the groundwater protection strategy. Bayesian Belief Networks were developed to simulate farmers' behavior with regard to groundwater management and to assess the impacts of protection strategy. These results have been used to calculate the conflict degree in the study area, derived from the introduction of policies for the reduction of groundwater exploitation for irrigation purposes. The less acceptable the policy is, the more likely it is that conflict will develop between farmers and the Regional Authority. The results of conflict analysis were also used to contribute to the debate concerning potential conflict mitigation measures. The approach adopted in this work has been discussed with a number of experts in groundwater management policies and irrigation management, and its main strengths and weaknesses have been identified. Increasing awareness of the existence of potential conflicts and the need to deal with them can be seen as an interesting initial shift in the Apulia region's water management regime, which is still grounded in merely technical approaches. PMID:23246906

  11. An Investigation Into Bayesian Networks for Modeling National Ignition Facility Capsule Implosions

    SciTech Connect

    Mitrani, J

    2008-08-18

    Bayesian networks (BN) are an excellent tool for modeling uncertainties in systems with several interdependent variables. A BN is a directed acyclic graph, and consists of a structure, or the set of directional links between variables that depend on other variables, and conditional probabilities (CP) for each variable. In this project, we apply BN's to understand uncertainties in NIF ignition experiments. One can represent various physical properties of National Ignition Facility (NIF) capsule implosions as variables in a BN. A dataset containing simulations of NIF capsule implosions was provided. The dataset was generated from a radiation hydrodynamics code, and it contained 120 simulations of 16 variables. Relevant knowledge about the physics of NIF capsule implosions and greedy search algorithms were used to search for hypothetical structures for a BN. Our preliminary results found 6 links between variables in the dataset. However, we thought there should have been more links between the dataset variables based on the physics of NIF capsule implosions. Important reasons for the paucity of links are the relatively small size of the dataset, and the sampling of the values for dataset variables. Another factor that might have caused the paucity of links is the fact that in the dataset, 20% of the simulations represented successful fusion, and 80% didn't, (simulations of unsuccessful fusion are useful for measuring certain diagnostics) which skewed the distributions of several variables, and possibly reduced the number of links. Nevertheless, by illustrating the interdependencies and conditional probabilities of several parameters and diagnostics, an accurate and complete BN built from an appropriate simulation set would provide uncertainty quantification for NIF capsule implosions.

  12. Bayesian network modeling: A case study of an epidemiologic system analysis of cardiovascular risk.

    PubMed

    Fuster-Parra, P; Tauler, P; Bennasar-Veny, M; Ligęza, A; López-González, A A; Aguiló, A

    2016-04-01

    An extensive, in-depth study of cardiovascular risk factors (CVRF) seems to be of crucial importance in the research of cardiovascular disease (CVD) in order to prevent (or reduce) the chance of developing or dying from CVD. The main focus of data analysis is on the use of models able to discover and understand the relationships between different CVRF. In this paper a report on applying Bayesian network (BN) modeling to discover the relationships among thirteen relevant epidemiological features of heart age domain in order to analyze cardiovascular lost years (CVLY), cardiovascular risk score (CVRS), and metabolic syndrome (MetS) is presented. Furthermore, the induced BN was used to make inference taking into account three reasoning patterns: causal reasoning, evidential reasoning, and intercausal reasoning. Application of BN tools has led to discovery of several direct and indirect relationships between different CVRF. The BN analysis showed several interesting results, among them: CVLY was highly influenced by smoking being the group of men the one with highest risk in CVLY; MetS was highly influence by physical activity (PA) being again the group of men the one with highest risk in MetS, and smoking did not show any influence. BNs produce an intuitive, transparent, graphical representation of the relationships between different CVRF. The ability of BNs to predict new scenarios when hypothetical information is introduced makes BN modeling an Artificial Intelligence (AI) tool of special interest in epidemiological studies. As CVD is multifactorial the use of BNs seems to be an adequate modeling tool. PMID:26777431

  13. Prediction of near-term breast cancer risk using a Bayesian belief network

    NASA Astrophysics Data System (ADS)

    Zheng, Bin; Ramalingam, Pandiyarajan; Hariharan, Harishwaran; Leader, Joseph K.; Gur, David

    2013-03-01

    Accurately predicting near-term breast cancer risk is an important prerequisite for establishing an optimal personalized breast cancer screening paradigm. In previous studies, we investigated and tested the feasibility of developing a unique near-term breast cancer risk prediction model based on a new risk factor associated with bilateral mammographic density asymmetry between the left and right breasts of a woman using a single feature. In this study we developed a multi-feature based Bayesian belief network (BBN) that combines bilateral mammographic density asymmetry with three other popular risk factors, namely (1) age, (2) family history, and (3) average breast density, to further increase the discriminatory power of our cancer risk model. A dataset involving "prior" negative mammography examinations of 348 women was used in the study. Among these women, 174 had breast cancer detected and verified in the next sequential screening examinations, and 174 remained negative (cancer-free). A BBN was applied to predict the risk of each woman having cancer detected six to 18 months later following the negative screening mammography. The prediction results were compared with those using single features. The prediction accuracy was significantly increased when using the BBN. The area under the ROC curve increased from an AUC=0.70 to 0.84 (p<0.01), while the positive predictive value (PPV) and negative predictive value (NPV) also increased from a PPV=0.61 to 0.78 and an NPV=0.65 to 0.75, respectively. This study demonstrates that a multi-feature based BBN can more accurately predict the near-term breast cancer risk than with a single feature.

  14. A Bayesian belief network approach for assessing uncertainty in conceptual site models at contaminated sites

    NASA Astrophysics Data System (ADS)

    Thomsen, Nanna I.; Binning, Philip J.; McKnight, Ursula S.; Tuxen, Nina; Bjerg, Poul L.; Troldborg, Mads

    2016-05-01

    A key component in risk assessment of contaminated sites is in the formulation of a conceptual site model (CSM). A CSM is a simplified representation of reality and forms the basis for the mathematical modeling of contaminant fate and transport at the site. The CSM should therefore identify the most important site-specific features and processes that may affect the contaminant transport behavior at the site. However, the development of a CSM will always be associated with uncertainties due to limited data and lack of understanding of the site conditions. CSM uncertainty is often found to be a major source of model error and it should therefore be accounted for when evaluating uncertainties in risk assessments. We present a Bayesian belief network (BBN) approach for constructing CSMs and assessing their uncertainty at contaminated sites. BBNs are graphical probabilistic models that are effective for integrating quantitative and qualitative information, and thus can strengthen decisions when empirical data are lacking. The proposed BBN approach facilitates a systematic construction of multiple CSMs, and then determines the belief in each CSM using a variety of data types and/or expert opinion at different knowledge levels. The developed BBNs combine data from desktop studies and initial site investigations with expert opinion to assess which of the CSMs are more likely to reflect the actual site conditions. The method is demonstrated on a Danish field site, contaminated with chlorinated ethenes. Four different CSMs are developed by combining two contaminant source zone interpretations (presence or absence of a separate phase contamination) and two geological interpretations (fractured or unfractured clay till). The beliefs in each of the CSMs are assessed sequentially based on data from three investigation stages (a screening investigation, a more detailed investigation, and an expert consultation) to demonstrate that the belief can be updated as more information

  15. Using Bayesian Belief Networks To Assess Volcano State from Multiple Monitoring Timeseries And Other Evidence

    NASA Astrophysics Data System (ADS)

    Odbert, Henry; Aspinall, Willy

    2013-04-01

    When volcanoes exhibit unrest or become eruptively active, science-based decision support invariably is sought by civil authorities. Evidence available to scientists about a volcano's internal state is usually indirect, secondary or very nebulous.Advancement of volcano monitoring technology in recent decades has increased the variety and resolution of multi-parameter timeseries data recorded at volcanoes. Monitoring timeseries may be interpreted in real time by observatory staff and are often later subjected to further analytic scrutiny by the research community at large. With increasing variety and resolution of data, interpreting these multiple strands of parallel, partial evidence has become increasingly complex. In practice, interpretation of many timeseries involves familiarity with the idiosyncracies of the volcano, the monitoring techniques, the configuration of the recording instrumentation, observations from other datasets, and so on. Assimilation of this knowledge is necessary in order to select and apply the appropriate statistical techniques required to extract the required information. Bayesian Belief Networks (BBNs) use probability theory to treat and evaluate uncertainties in a rational and auditable scientific manner, but only to the extent warranted by the strength of the available evidence. The concept is a suitable framework for marshalling multiple observations, model results and interpretations - and associated uncertainties - in a methodical manner. The formulation is usually implemented in graphical form and could be developed as a tool for near real-time, ongoing use in a volcano observatory, for example. We explore the application of BBNs in analysing volcanic timeseries, the certainty with which inferences may be drawn, and how they can be updated dynamically. Such approaches provide a route to developing analytical interface(s) between volcano monitoring analyses and probabilistic hazard analysis. We discuss the use of BBNs in hazard

  16. A Bayesian belief network approach for assessing uncertainty in conceptual site models at contaminated sites.

    PubMed

    Thomsen, Nanna I; Binning, Philip J; McKnight, Ursula S; Tuxen, Nina; Bjerg, Poul L; Troldborg, Mads

    2016-05-01

    A key component in risk assessment of contaminated sites is in the formulation of a conceptual site model (CSM). A CSM is a simplified representation of reality and forms the basis for the mathematical modeling of contaminant fate and transport at the site. The CSM should therefore identify the most important site-specific features and processes that may affect the contaminant transport behavior at the site. However, the development of a CSM will always be associated with uncertainties due to limited data and lack of understanding of the site conditions. CSM uncertainty is often found to be a major source of model error and it should therefore be accounted for when evaluating uncertainties in risk assessments. We present a Bayesian belief network (BBN) approach for constructing CSMs and assessing their uncertainty at contaminated sites. BBNs are graphical probabilistic models that are effective for integrating quantitative and qualitative information, and thus can strengthen decisions when empirical data are lacking. The proposed BBN approach facilitates a systematic construction of multiple CSMs, and then determines the belief in each CSM using a variety of data types and/or expert opinion at different knowledge levels. The developed BBNs combine data from desktop studies and initial site investigations with expert opinion to assess which of the CSMs are more likely to reflect the actual site conditions. The method is demonstrated on a Danish field site, contaminated with chlorinated ethenes. Four different CSMs are developed by combining two contaminant source zone interpretations (presence or absence of a separate phase contamination) and two geological interpretations (fractured or unfractured clay till). The beliefs in each of the CSMs are assessed sequentially based on data from three investigation stages (a screening investigation, a more detailed investigation, and an expert consultation) to demonstrate that the belief can be updated as more information

  17. Overextension in Verb Conjunctions

    ERIC Educational Resources Information Center

    Jönsson, Martin L.

    2015-01-01

    Hampton (1988) discovered that people are subject to "overextension"--they categorize some things as falling under a conjunction (e.g., they categorize chess as a "sport which is also a game") but not as falling under both of the corresponding conjuncts (e.g., they do not categorize chess as a "sport"). Although…

  18. Monitoring Network Design for Discriminating and Reducing Models in Bayesian Model Averaging Paradigm

    NASA Astrophysics Data System (ADS)

    Tsai, F. T.; Pham, H. V.

    2013-12-01

    Bayesian model averaging (BMA) is often adopted to quantify model prediction and uncertainty using multiple models generated from various sources of uncertainty. Due to the lack of data and knowledge, the number of models with non-dominant posterior model probabilities can be overwhelming. Conducting prediction and uncertainty analysis using a great deal of computationally intensive simulation models (e.g., groundwater models) can become intractable under the BMA framework. Moreover, prediction results using the BMA can be useless when prediction uncertainty is very high. This study implements a monitoring network design under the BMA framework to discriminate groundwater models and in turn reduce the number of models. The posterior model probabilities are re-evaluated by using BMA prediction as 'future observation data' and historical data. Given a design criterion of posterior model probability (e.g. 85%), the monitoring network design aims to find the optimal number and location of monitoring wells at existing wells for continuous observation. If using existing wells cannot achieve the design criterion, then exploration of new monitoring well location is necessary. Once the design criterion is met, other models will be discriminated from the best model. Between-model variance will be significantly reduced. We use the monitoring network design to discriminate 18 complex groundwater models that include the '1,200-foot', '1,500-foot', and '1,700-foot' sands in the Baton Rouge area, southeastern Louisiana. The sources of uncertainty that creates the groundwater models are from hydrostratigraphic architecture, fault permeability architecture, and boundary conditions. To speed up model calibration, we develop a parallel version of CMA-ES and implement it to SuperMike II cluster at Louisiana State University. Results show that in the model calibration period from 1975 to 2010, eleven models have posterior model probabilities ranging from 3.5% to 17.4%. The purpose of

  19. Bayesian inference of Earth's radial seismic structure from body-wave traveltimes using neural networks

    NASA Astrophysics Data System (ADS)

    de Wit, Ralph W. L.; Valentine, Andrew P.; Trampert, Jeannot

    2013-10-01

    How do body-wave traveltimes constrain the Earth's radial (1-D) seismic structure? Existing 1-D seismological models underpin 3-D seismic tomography and earthquake location algorithms. It is therefore crucial to assess the quality of such 1-D models, yet quantifying uncertainties in seismological models is challenging and thus often ignored. Ideally, quality assessment should be an integral part of the inverse method. Our aim in this study is twofold: (i) we show how to solve a general Bayesian non-linear inverse problem and quantify model uncertainties, and (ii) we investigate the constraint on spherically symmetric P-wave velocity (VP) structure provided by body-wave traveltimes from the EHB bulletin (phases Pn, P, PP and PKP). Our approach is based on artificial neural networks, which are very common in pattern recognition problems and can be used to approximate an arbitrary function. We use a Mixture Density Network to obtain 1-D marginal posterior probability density functions (pdfs), which provide a quantitative description of our knowledge on the individual Earth parameters. No linearization or model damping is required, which allows us to infer a model which is constrained purely by the data. We present 1-D marginal posterior pdfs for the 22 VP parameters and seven discontinuity depths in our model. P-wave velocities in the inner core, outer core and lower mantle are resolved well, with standard deviations of ˜0.2 to 1 per cent with respect to the mean of the posterior pdfs. The maximum likelihoods of VP are in general similar to the corresponding ak135 values, which lie within one or two standard deviations from the posterior means, thus providing an independent validation of ak135 in this part of the radial model. Conversely, the data contain little or no information on P-wave velocity in the D'' layer, the upper mantle and the homogeneous crustal layers. Further, the data do not constrain the depth of the discontinuities in our model. Using additional

  20. Expert system support using a Bayesian belief network for the classification of endometrial hyperplasia.

    PubMed

    Morrison, M L; McCluggage, W G; Price, G J; Diamond, J; Sheeran, M R M; Mulholland, K M; Walsh, M Y; Montironi, R; Bartels, P H; Thompson, D; Hamilton, P W

    2002-07-01

    Accurate morphological classification of endometrial hyperplasia is crucial as treatments vary widely between the different categories of hyperplasia and are dependent, in part, on the histological diagnosis. However, previous studies have shown considerable inter-observer variation in the classification of endometrial hyperplasias. The aim of this study was to develop a decision support system (DSS) for the classification of endometrial hyperplasias. The system used a Bayesian belief network to distinguish proliferative endometrium, simple hyperplasia, complex hyperplasia, atypical hyperplasia and grade 1 endometrioid adenocarcinoma. These diagnostic outcomes were held in the decision node. Four morphological features were selected as diagnostic clues used routinely in the discrimination of endometrial hyperplasias. These represented the evidence nodes and were linked to the decision node by conditional probability matrices. The system was designed with a computer user interface (CytoInform) where reference images for a given clue were displayed to assist the pathologist in entering evidence into the network. Reproducibility of diagnostic classification was tested on 50 cases chosen by a gynaecological pathologist. These comprised ten cases each of proliferative endometrium, simple hyperplasia, complex hyperplasia, atypical hyperplasia and grade 1 endometrioid adenocarcinoma. The DSS was tested by two consultant pathologists, two junior pathologists and two medical students. Intra- and inter-observer agreement was calculated following conventional histological examination of the slides on two occasions by the consultants and junior pathologists without the use of the DSS. All six participants then assessed the slides using the expert system on two occasions, enabling inter- and intra-observer agreement to be calculated. Using unaided conventional diagnosis, weighted kappa values for intra-observer agreement ranged from 0.645 to 0.901. Using the DSS, the results

  1. Measuring the consequences of wildfires in a Bayesian network with vulnerability and exposure indicators

    NASA Astrophysics Data System (ADS)

    Papakosta, Panagiota; Botzler, Sebastian; Krug, Kai; Straub, Daniel

    2013-04-01

    areas and rare species is also included. Presence of cultural heritage sites, power stations and power line network influence social exposure. The conceptual framework is demonstrated with a Bayesian Network (BN). The BN model incorporates empirical observation, physical models and expert knowledge; it can also explicitly account for uncertainty in the indicators. The proposed model is applied to the island of Cyprus. Maps support the demonstration of results. [1] Keeley, J.E.; Bond, W.J.; Bradstock, R.A.; Pausas, J.G.; Rundel, P.W. (2012): Fire in Mediterranean ecosystems: ecology, evolution and management. Cambridge University Press, New York, USA. [2] UN/ISDR (International Strategy for Disaster Reduction (2004): Living with Risk: A Global Review of Disaster Reduction Initiatives, Geneva, UN Publications. [3] Birkmann, J. (2006): Measuring vulnerability to natural hazards: towards disaster resilient societies. United Nations University Press, Tokyo, Japan.

  2. A Bayesian Approach for Modeling Cattle Movements in the United States: Scaling up a Partially Observed Network

    PubMed Central

    Lindström, Tom; Grear, Daniel A.; Buhnerkempe, Michael; Webb, Colleen T.; Miller, Ryan S.; Portacci, Katie; Wennergren, Uno

    2013-01-01

    Networks are rarely completely observed and prediction of unobserved edges is an important problem, especially in disease spread modeling where networks are used to represent the pattern of contacts. We focus on a partially observed cattle movement network in the U.S. and present a method for scaling up to a full network based on Bayesian inference, with the aim of informing epidemic disease spread models in the United States. The observed network is a 10% state stratified sample of Interstate Certificates of Veterinary Inspection that are required for interstate movement; describing approximately 20,000 movements from 47 of the contiguous states, with origins and destinations aggregated at the county level. We address how to scale up the 10% sample and predict unobserved intrastate movements based on observed movement distances. Edge prediction based on a distance kernel is not straightforward because the probability of movement does not always decline monotonically with distance due to underlying industry infrastructure. Hence, we propose a spatially explicit model where the probability of movement depends on distance, number of premises per county and historical imports of animals. Our model performs well in recapturing overall metrics of the observed network at the node level (U.S. counties), including degree centrality and betweenness; and performs better compared to randomized networks. Kernel generated movement networks also recapture observed global network metrics, including network size, transitivity, reciprocity, and assortativity better than randomized networks. In addition, predicted movements are similar to observed when aggregated at the state level (a broader geographic level relevant for policy) and are concentrated around states where key infrastructures, such as feedlots, are common. We conclude that the method generally performs well in predicting both coarse geographical patterns and network structure and is a promising method to generate full

  3. A Bayesian network model for the diagnosis of the caring procedure for wheelchair users with spinal injury.

    PubMed

    Athanasiou, Maria; Clark, Jonathan Y

    2009-08-01

    This paper describes a probabilistic causal model for the caring procedure to be followed on wheelchair users with spinal injury. Due to loss of sensation and movement caused by spinal cord injuries, the information extracted about patient findings (i.e. the signs and symptoms) can often be incomplete. This, in turn, introduces uncertainty in assessing the existence and severity of a given condition-and thus, employment of the appropriate caring procedure. Bayesian networks are a framework that enables probabilistic inference; therefore, they are useful for diagnostic reasoning and selection of the appropriate caring procedure in the face of uncertainty. The network structure and numerical parameters are based on data elicited from the qualified staff nurses and available literature of the National Spinal Injury Centre, Stoke Mandeville Hospital, Aylesbury, UK, as well as the compiled knowledge base within the DIMITRA rule-based expert system [M. Athanasiou, J.Y. Clark, DIMITRA: an online expert system for carers of paraplegics and quadriplegics, International Journal of Healthcare Technology and Management 7(5) (2006) 44-451]. We also present the model and report the results of the diagnostic performance tests using the AgenaRiskn [Agena Limited, AgenaRisk Software Package, http://www.agena.co.uk] Bayesian network package. PMID:19409641

  4. Application of Bayesian neural networks to energy reconstruction in EAS experiments for ground-based TeV astrophysics

    NASA Astrophysics Data System (ADS)

    Bai, Y.; Xu, Y.; Pan, J.; Lan, J. Q.; Gao, W. W.

    2016-07-01

    A toy detector array is designed to detect a shower generated by the interaction between a TeV cosmic ray and the atmosphere. In the present paper, the primary energies of showers detected by the detector array are reconstructed with the algorithm of Bayesian neural networks (BNNs) and a standard method like the LHAASO experiment [1], respectively. Compared to the standard method, the energy resolutions are significantly improved using the BNNs. And the improvement is more obvious for the high energy showers than the low energy ones.

  5. Overextension in verb conjunctions.

    PubMed

    Jönsson, Martin L

    2015-11-01

    Hampton (1988) discovered that people are subject to overextension-they categorize some things as falling under a conjunction (e.g., they categorize chess as a sport which is also a game) but not as falling under both of the corresponding conjuncts (e.g., they do not categorize chess as a sport). Although subsequent literature has replicated this effect with a wider range of constructions than those originally used by Hampton, the research so far has been exclusively concerned with various forms of noun compounds. This article generalizes the previous findings to the domain of verb conjunctions. By using a novel paradigm for studying overextension effects, this study demonstrates a very strong overextension effect for conjunctions of gerunds (e.g., walking and smoking). The author discusses the implications of the new findings for available explanations of overextension. PMID:26052787

  6. Rainfall-Runoff Forecast and Model Parameter Estimation: a Dynamic Bayesian Networks Approach

    NASA Astrophysics Data System (ADS)

    Canon Barriga, J. E.; Morillo Leon, F. C.

    2013-12-01

    The suggested climate-driven non-stationarities and intrinsic uncertainties of hydrological processes such as precipitation (P) and runoff (R), represent a fruitful context to develop new methods that may be able to detect parametric variations in time series and incorporate them into forecasts. In this research, we developed a method to forecast runoff from precipitation time series based on Dynamic Bayesian Networks (DBN). The purpose of the research was to determine an appropriate structure of the DBN and the optimal lengths of hydrological time series required to establish statistical parameters (i.e., first two moments) of P and optimal fits of forecasted R at daily and weekly intervals. A DBN can be briefly interpreted as a set of nodes (representing conditional probabilistic variables) connected by arrows that establish a causal, time-oriented, relationship among them. A DBN is defined by two components: a static network (structure) and a transition probability matrix between consecutive stages. Similarly to neural networks, DBN must be trained in order to learn about the subjacent process and make useful predictions. To determine the ability of the DBN to forecast R from P we initially generated long synthetic P series and run a deterministic model (HEC-HMS) to generate R. The DBN were then trained with different lengths of these synthetic series to forecast R (using smoothing and filtering methods). Two structures were considered: 1) DBN with P(t), P(t-1) and R(t-1) and 2) DBN with P(t), P(t-1), R(t-1) and ΔR=[R(t-1)-R(t-2)]. Both smoothing and filtering methods were appropriate to make predictions on a daily and weekly basis (filtration performing better). Setting the complexity (number of states of the random variables) in a DBN proves to be a critical issue, since an increase in the number of states, which implies larger training sets, does not always mean an improvement in the prediction. We found that acceptable results could be obtained from DBN

  7. Development and Execution of the RUNSAFE Runway Safety Bayesian Belief Network Model

    NASA Technical Reports Server (NTRS)

    Green, Lawrence L.

    2015-01-01

    One focus area of the National Aeronautics and Space Administration (NASA) is to improve aviation safety. Runway safety is one such thrust of investigation and research. The two primary components of this runway safety research are in runway incursion (RI) and runway excursion (RE) events. These are adverse ground-based aviation incidents that endanger crew, passengers, aircraft and perhaps other nearby people or property. A runway incursion is the incorrect presence of an aircraft, vehicle or person on the protected area of a surface designated for the landing and take-off of aircraft; one class of RI events simultaneously involves two aircraft, such as one aircraft incorrectly landing on a runway while another aircraft is taking off from the same runway. A runway excursion is an incident involving only a single aircraft defined as a veer-off or overrun off the runway surface. Within the scope of this effort at NASA Langley Research Center (LaRC), generic RI, RE and combined (RI plus RE, or RUNSAFE) event models have each been developed and implemented as a Bayesian Belief Network (BBN). Descriptions of runway safety issues from the literature searches have been used to develop the BBN models. Numerous considerations surrounding the process of developing the event models have been documented in this report. The event models were then thoroughly reviewed by a Subject Matter Expert (SME) panel through multiple knowledge elicitation sessions. Numerous improvements to the model structure (definitions, node names, node states and the connecting link topology) were made by the SME panel. Sample executions of the final RUNSAFE model have been presented herein for baseline and worst-case scenarios. Finally, a parameter sensitivity analysis for a given scenario was performed to show the risk drivers. The NASA and LaRC research in runway safety event modeling through the use of BBN technology is important for several reasons. These include: 1) providing a means to clearly

  8. Bayesian network ensemble as a multivariate strategy to predict radiation pneumonitis risk

    SciTech Connect

    Lee, Sangkyu Ybarra, Norma; Jeyaseelan, Krishinima; Seuntjens, Jan; El Naqa, Issam; Faria, Sergio; Kopek, Neil; Brisebois, Pascale; Bradley, Jeffrey D.; Robinson, Clifford

    2015-05-15

    Purpose: Prediction of radiation pneumonitis (RP) has been shown to be challenging due to the involvement of a variety of factors including dose–volume metrics and radiosensitivity biomarkers. Some of these factors are highly correlated and might affect prediction results when combined. Bayesian network (BN) provides a probabilistic framework to represent variable dependencies in a directed acyclic graph. The aim of this study is to integrate the BN framework and a systems’ biology approach to detect possible interactions among RP risk factors and exploit these relationships to enhance both the understanding and prediction of RP. Methods: The authors studied 54 nonsmall-cell lung cancer patients who received curative 3D-conformal radiotherapy. Nineteen RP events were observed (common toxicity criteria for adverse events grade 2 or higher). Serum concentration of the following four candidate biomarkers were measured at baseline and midtreatment: alpha-2-macroglobulin, angiotensin converting enzyme (ACE), transforming growth factor, interleukin-6. Dose-volumetric and clinical parameters were also included as covariates. Feature selection was performed using a Markov blanket approach based on the Koller–Sahami filter. The Markov chain Monte Carlo technique estimated the posterior distribution of BN graphs built from the observed data of the selected variables and causality constraints. RP probability was estimated using a limited number of high posterior graphs (ensemble) and was averaged for the final RP estimate using Bayes’ rule. A resampling method based on bootstrapping was applied to model training and validation in order to control under- and overfit pitfalls. Results: RP prediction power of the BN ensemble approach reached its optimum at a size of 200. The optimized performance of the BN model recorded an area under the receiver operating characteristic curve (AUC) of 0.83, which was significantly higher than multivariate logistic regression (0

  9. A Sequential Dynamic Bayesian Network for Pore Pressure Prediction and Quantification of Uncertainty.

    NASA Astrophysics Data System (ADS)

    Oughton, R. H.; Wooff, D. A.; Hobbs, R. W.; Swarbrick, R. E.

    2014-12-01

    Pore pressure prediction is vital when drilling a well, as unexpected overpressure can cause drilling challenges and uncontrolled hydrocarbon leakage. One cause of overpressure is when pore fluid is trapped during burial and takes on part of the lithostatic load. Predictions often use porosity-based techniques, such as the Eaton Ratio method and equivalent depth method. These rely on an idealised compaction trend and use a single wireline log as a proxy for porosity. Such methods do not account for the many sources of uncertainty, or for the multivariate nature of the system. We propose a sequential dynamic Bayesian network (SDBN) as a solution to these issues. The SDBN models the quantities in the system (such as pressures, porosity, lithology, wireline logs, fluid properties and so on) using conditional probability distributions to capture their joint behaviour. A compaction model is central to the SDBN, relating porosity to vertical effective stress, with uncertainty in the relationship, so that the logic is similar to that of the equivalent depth method. The probability distribution for porosity depends on VES and lithology, with much more uncertainty in sandstone-like rocks than in shales to reflect a general lack of understanding of sandstone compaction. The distributions of the wireline logs depend on porosity and lithology, along with other quantities, and so when they are observed the SDBN learns about porosity and lithology and in turn VES and pore pressure, using Bayes theorem. The probability distribution for each quantity in the SDBN is updated in light of any data, so that rather than giving a single-valued prediction for pore pressure, the SDBN gives a prediction with uncertainty that takes into account the whole system, knowledge and data. The dynamic nature of the SDBN enables it to use the bulk density to calculate total vertical stress, and to account for the dissipation of pore pressure. The vertical correlation in the SDBN means it is suited to

  10. Integration of Geophysical Data into Structural Geological Modelling through Bayesian Networks

    NASA Astrophysics Data System (ADS)

    de la Varga, Miguel; Wellmann, Florian; Murdie, Ruth

    2016-04-01

    Structural geological models are widely used to represent the spatial distribution of relevant geological features. Several techniques exist to construct these models on the basis of different assumptions and different types of geological observations (e.g. Jessell et al., 2014). However, two problems are prevalent when constructing models: (i) observations and assumptions, and therefore also the constructed model, are subject to uncertainties, and (ii) additional information, such as geophysical data, is often available, but cannot be considered directly in the geological modelling step. In our work, we propose the integration of all available data into a Bayesian network including the generation of the implicit geological method by means of interpolation functions (Mallet, 1992; Lajaunie et al., 1997; Mallet, 2004; Carr et al., 2001; Hillier et al., 2014). As a result, we are able to increase the certainty of the resultant models as well as potentially learn features of our regional geology through data mining and information theory techniques. MCMC methods are used in order to optimize computational time and assure the validity of the results. Here, we apply the aforementioned concepts in a 3-D model of the Sandstone Greenstone Belt in the Archean Yilgarn Craton in Western Australia. The example given, defines the uncertainty in the thickness of greenstone as limited by Bouguer anomaly and the internal structure of the greenstone as limited by the magnetic signature of a banded iron formation. The incorporation of the additional data and specially the gravity provides an important reduction of the possible outcomes and therefore the overall uncertainty. References Carr, C. J., K. R. Beatson, B. J. Cherrie, J. T. Mitchell, R. W. Fright, C. B. McCallum, and R. T. Evans, 2001, Reconstruction and representation of 3D objects with radial basis functions: Proceedings of the 28th annual conference on Computer graphics and interactive techniques, 67-76. Jessell, M

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  12. Linking hydrology, ecosystem function, and livelihood sustainability in African papyrus wetlands using a Bayesian Network Model

    NASA Astrophysics Data System (ADS)

    van Dam, A.; Gettel, G. M.; Kipkemboi, J.; Rahman, M. M.

    2011-12-01

    Papyrus wetlands in East Africa provide ecosystem services supporting the livelihoods of millions but are rapidly degrading due to economic development. For ecosystem conservation, an integrated understanding of the natural and social processes driving ecosystem change is needed. This research focuses on integrating the causal relationships between hydrology, ecosystem function, and livelihood sustainability in Nyando wetland, western Kenya. Livelihood sustainability is based on ecosystem services that include plant and animal harvest for building material and food, conversion of wetlands to crop and grazing land, water supply, and water quality regulation. Specific objectives were: to integrate studies of hydrology, ecology, and livelihood activities using a Bayesian Network (BN) model and include stakeholder involvement in model development. The BN model (Netica 4.16) had 35 nodes with seven decision nodes describing demography, economy, papyrus market, and rainfall, and two target nodes describing ecosystem function (defined by groundwater recharge, nutrient and sediment retention, and biodiversity) and livelihood sustainability (drinking water supply, crop production, livestock production, and papyrus yield). The conditional probability tables were populated using results of ecohydrological and socio-economic field work and consultations with stakeholders. The model was evaluated for an average year with decision node probabilities set according to data from research, expert opinion, and stakeholders' views. Then, scenarios for dry and wet seasons and for economic development (low population growth and unemployment) and policy development (more awareness of wetland value) were evaluated. In an average year, the probability for maintaining a "good" level of sediment and nutrient retention functions, groundwater recharge, and biodiversity was about 60%. ("Good" is defined by expert opinion based on ongoing field research.) In the dry season, the probability was

  13. A Bayesian Belief Network approach to assess the potential of non wood forest products for small scale forest owners

    NASA Astrophysics Data System (ADS)

    Vacik, Harald; Huber, Patrick; Hujala, Teppo; Kurtilla, Mikko; Wolfslehner, Bernhard

    2015-04-01

    It is an integral element of the European understanding of sustainable forest management to foster the design and marketing of forest products, non-wood forest products (NWFPs) and services that go beyond the production of timber. Despite the relevance of NWFPs in Europe, forest management and planning methods have been traditionally tailored towards wood and wood products, because most forest management models and silviculture techniques were developed to ensure a sustained production of timber. Although several approaches exist which explicitly consider NWFPs as management objectives in forest planning, specific models are needed for the assessment of their production potential in different environmental contexts and for different management regimes. Empirical data supporting a comprehensive assessment of the potential of NWFPs are rare, thus making development of statistical models particularly problematic. However, the complex causal relationships between the sustained production of NWFPs, the available ecological resources, as well as the organizational and the market potential of forest management regimes are well suited for knowledge-based expert models. Bayesian belief networks (BBNs) are a kind of probabilistic graphical model that have become very popular to practitioners and scientists mainly due to the powerful probability theory involved, which makes BBNs suitable to deal with a wide range of environmental problems. In this contribution we present the development of a Bayesian belief network to assess the potential of NWFPs for small scale forest owners. A three stage iterative process with stakeholder and expert participation was used to develop the Bayesian Network within the frame of the StarTree Project. The group of participants varied in the stages of the modelling process. A core team, consisting of one technical expert and two domain experts was responsible for the entire modelling process as well as for the first prototype of the network

  14. Bias in identification of the best treatment in a Bayesian network meta-analysis for binary outcome: a simulation study.

    PubMed

    Kibret, Taddele; Richer, Danielle; Beyene, Joseph

    2014-01-01

    Network meta-analysis (NMA) has emerged as a useful analytical tool allowing comparison of multiple treatments based on direct and indirect evidence. Commonly, a hierarchical Bayesian NMA model is used, which allows rank probabilities (the probability that each treatment is best, second best, and so on) to be calculated for decision making. However, the statistical properties of rank probabilities are not well understood. This study investigates how rank probabilities are affected by various factors such as unequal number of studies per comparison in the network, the sample size of individual studies, the network configuration, and effect sizes between treatments. In order to explore these factors, a simulation study of four treatments (three equally effective treatments and one less effective reference) was conducted. The simulation illustrated that estimates of rank probabilities are highly sensitive to both the number of studies per comparison and the overall network configuration. An unequal number of studies per comparison resulted in biased estimates of treatment rank probabilities for every network considered. The rank probability for the treatment that was included in the fewest number of studies was biased upward. Conversely, the rank of the treatment included in the most number of studies was consistently underestimated. When the simulation was altered to include three equally effective treatments and one superior treatment, the hierarchical Bayesian NMA model correctly identified the most effective treatment, regardless of all factors varied. The results of this study offer important insight into the ability of NMA models to rank treatments accurately under several scenarios. The authors recommend that health researchers use rank probabilities cautiously in making important decisions. PMID:25506247

  15. miRNA-target gene regulatory networks: A Bayesian integrative approach to biomarker selection with application to kidney cancer.

    PubMed

    Chekouo, Thierry; Stingo, Francesco C; Doecke, James D; Do, Kim-Anh

    2015-06-01

    The availability of cross-platform, large-scale genomic data has enabled the investigation of complex biological relationships for many cancers. Identification of reliable cancer-related biomarkers requires the characterization of multiple interactions across complex genetic networks. MicroRNAs are small non-coding RNAs that regulate gene expression; however, the direct relationship between a microRNA and its target gene is difficult to measure. We propose a novel Bayesian model to identify microRNAs and their target genes that are associated with survival time by incorporating the microRNA regulatory network through prior distributions. We assume that biomarkers involved in regulatory networks are likely associated with survival time. We employ non-local prior distributions and a stochastic search method for the selection of biomarkers associated with the survival outcome. We use KEGG pathway information to incorporate correlated gene effects within regulatory networks. Using simulation studies, we assess the performance of our method, and apply it to experimental data of kidney renal cell carcinoma (KIRC) obtained from The Cancer Genome Atlas. Our novel method validates previously identified cancer biomarkers and identifies biomarkers specific to KIRC progression that were not previously discovered. Using the KIRC data, we confirm that biomarkers involved in regulatory networks are more likely to be associated with survival time, showing connections in one regulatory network for five out of six such genes we identified. PMID:25639276

  16. miRNA-Target Gene Regulatory Networks: A Bayesian Integrative Approach to Biomarker Selection with Application to Kidney Cancer

    PubMed Central

    Chekouo, Thierry; Stingo, Francesco C.; Doecke, James D.; Do, Kim-Anh

    2015-01-01

    Summary The availability of cross-platform, large-scale genomic data has enabled the investigation of complex biological relationships for many cancers. Identification of reliable cancer-related biomarkers requires the characterization of multiple interactions across complex genetic networks. MicroRNAs are small non-coding RNAs that regulate gene expression; however, the direct relationship between a microRNA and its target gene is difficult to measure. We propose a novel Bayesian model to identify microRNAs and their target genes that are associated with survival time by incorporating the microRNA regulatory network through prior distributions. We assume that biomarkers involved in regulatory networks are likely associated with survival time. We employ non-local prior distributions and a stochastic search method for the selection of biomarkers associated with the survival outcome. We use KEGG pathway information to incorporate correlated gene effects within regulatory networks. Using simulation studies, we assess the performance of our method, and apply it to experimental data of kidney renal cell carcinoma (KIRC) obtained from The Cancer Genome Atlas. Our novel method validates previously identified cancer biomarkers and identifies biomarkers specific to KIRC progression that were not previously discovered. Using the KIRC data, we confirm that biomarkers involved in regulatory networks are more likely to be associated with survival time, showing connections in one regulatory network for five out of six such genes we identified. PMID:25639276

  17. Bayesian networks and agent-based modeling approach for urban land-use and population density change: a BNAS model

    NASA Astrophysics Data System (ADS)

    Kocabas, Verda; Dragicevic, Suzana

    2013-10-01

    Land-use change models grounded in complexity theory such as agent-based models (ABMs) are increasingly being used to examine evolving urban systems. The objective of this study is to develop a spatial model that simulates land-use change under the influence of human land-use choice behavior. This is achieved by integrating the key physical and social drivers of land-use change using Bayesian networks (BNs) coupled with agent-based modeling. The BNAS model, integrated Bayesian network-based agent system, presented in this study uses geographic information systems, ABMs, BNs, and influence diagram principles to model population change on an irregular spatial structure. The model is parameterized with historical data and then used to simulate 20 years of future population and land-use change for the City of Surrey, British Columbia, Canada. The simulation results identify feasible new urban areas for development around the main transportation corridors. The obtained new development areas and the projected population trajectories with the“what-if” scenario capabilities can provide insights into urban planners for better and more informed land-use policy or decision-making processes.

  18. Capturing ecosystem services, stakeholders' preferences and trade-offs in coastal aquaculture decisions: a Bayesian belief network application.

    PubMed

    Schmitt, Laetitia Helene Marie; Brugere, Cecile

    2013-01-01

    Aquaculture activities are embedded in complex social-ecological systems. However, aquaculture development decisions have tended to be driven by revenue generation, failing to account for interactions with the environment and the full value of the benefits derived from services provided by local ecosystems. Trade-offs resulting from changes in ecosystem services provision and associated impacts on livelihoods are also often overlooked. This paper proposes an innovative application of Bayesian belief networks - influence diagrams - as a decision support system for mediating trade-offs arising from the development of shrimp aquaculture in Thailand. Senior experts were consulted (n = 12) and primary farm data on the economics of shrimp farming (n = 20) were collected alongside secondary information on ecosystem services, in order to construct and populate the network. Trade-offs were quantitatively assessed through the generation of a probabilistic impact matrix. This matrix captures nonlinearity and uncertainty and describes the relative performance and impacts of shrimp farming management scenarios on local livelihoods. It also incorporates export revenues and provision and value of ecosystem services such as coastal protection and biodiversity. This research shows that Bayesian belief modeling can support complex decision-making on pathways for sustainable coastal aquaculture development and thus contributes to the debate on the role of aquaculture in social-ecological resilience and economic development. PMID:24155876

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

    PubMed

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

    2016-01-01

    An integrated methodology, based on linking Bayesian belief networks (BBN) with GIS, is proposed for combining available evidence to help forest managers evaluate implications and trade-offs between forest production and conservation measures to preserve biodiversity in forested habitats. A Bayesian belief network is a probabilistic graphical model that represents variables and their dependencies through specifying probabilistic relationships. In spatially explicit decision problems where it is difficult to choose appropriate combinations of interventions, the proposed integration of a BBN with GIS helped to facilitate shared understanding of the human-landscape relationships, while fostering collective management that can be incorporated into landscape planning processes. Trades-offs become more and more relevant in these landscape contexts where the participation of many and varied stakeholder groups is indispensable. With these challenges in mind, our integrated approach incorporates GIS-based data with expert knowledge to consider two different land use interests - biodiversity value for conservation and timber production potential - with the focus on a complex mountain landscape in the French Alps. The spatial models produced provided different alternatives of suitable sites that can be used by policy makers in order to support conservation priorities while addressing management options. The approach provided provide a common reasoning language among different experts from different backgrounds while helped to identify spatially explicit conflictive areas. PMID:26597639

  20. Capturing Ecosystem Services, Stakeholders' Preferences and Trade-Offs in Coastal Aquaculture Decisions: A Bayesian Belief Network Application

    PubMed Central

    Schmitt, Laetitia Helene Marie; Brugere, Cecile

    2013-01-01

    Aquaculture activities are embedded in complex social-ecological systems. However, aquaculture development decisions have tended to be driven by revenue generation, failing to account for interactions with the environment and the full value of the benefits derived from services provided by local ecosystems. Trade-offs resulting from changes in ecosystem services provision and associated impacts on livelihoods are also often overlooked. This paper proposes an innovative application of Bayesian belief networks - influence diagrams - as a decision support system for mediating trade-offs arising from the development of shrimp aquaculture in Thailand. Senior experts were consulted (n = 12) and primary farm data on the economics of shrimp farming (n = 20) were collected alongside secondary information on ecosystem services, in order to construct and populate the network. Trade-offs were quantitatively assessed through the generation of a probabilistic impact matrix. This matrix captures nonlinearity and uncertainty and describes the relative performance and impacts of shrimp farming management scenarios on local livelihoods. It also incorporates export revenues and provision and value of ecosystem services such as coastal protection and biodiversity. This research shows that Bayesian belief modeling can support complex decision-making on pathways for sustainable coastal aquaculture development and thus contributes to the debate on the role of aquaculture in social-ecological resilience and economic development. PMID:24155876

  1. Using of bayesian networks to estimate the probability of "NATECH" scenario occurrence

    NASA Astrophysics Data System (ADS)

    Dobes, Pavel; Dlabka, Jakub; Jelšovská, Katarína; Polorecká, Mária; Baudišová, Barbora; Danihelka, Pavel

    2015-04-01

    In the twentieth century, implementation of Bayesian statistics and probability was not much used (may be it wasn't a preferred approach) in the area of natural and industrial risk analysis and management. Neither it was used within analysis of so called NATECH accidents (chemical accidents triggered by natural events, such as e.g. earthquakes, floods, lightning etc.; ref. E. Krausmann, 2011, doi:10.5194/nhess-11-921-2011). Main role, from the beginning, played here so called "classical" frequentist probability (ref. Neyman, 1937), which rely up to now especially on the right/false results of experiments and monitoring and didn't enable to count on expert's beliefs, expectations and judgements (which is, on the other hand, one of the once again well known pillars of Bayessian approach to probability). In the last 20 or 30 years, there is possible to observe, through publications and conferences, the Renaissance of Baysssian statistics into many scientific disciplines (also into various branches of geosciences). The necessity of a certain level of trust in expert judgment within risk analysis is back? After several decades of development on this field, it could be proposed following hypothesis (to be checked): "We couldn't estimate probabilities of complex crisis situations and their TOP events (many NATECH events could be classified as crisis situations or emergencies), only by classical frequentist approach, but also by using of Bayessian approach (i.e. with help of prestaged Bayessian Network including expert belief and expectation as well as classical frequentist inputs). Because - there is not always enough quantitative information from monitoring of historical emergencies, there could be several dependant or independant variables necessary to consider and in generally - every emergency situation always have a little different run." In this topic, team of authors presents its proposal of prestaged typized Bayessian network model for specified NATECH scenario

  2. Potential Use of a Bayesian Network for Discriminating Flash Type from Future GOES-R Geostationary Lightning Mapper (GLM) data

    NASA Technical Reports Server (NTRS)

    Solakiewiz, Richard; Koshak, William

    2008-01-01

    Continuous monitoring of the ratio of cloud flashes to ground flashes may provide a better understanding of thunderstorm dynamics, intensification, and evolution, and it may be useful in severe weather warning. The National Lighting Detection Network TM (NLDN) senses ground flashes with exceptional detection efficiency and accuracy over most of the continental United States. A proposed Geostationary Lightning Mapper (GLM) aboard the Geostationary Operational Environmental Satellite (GOES-R) will look at the western hemisphere, and among the lightning data products to be made available will be the fundamental optical flash parameters for both cloud and ground flashes: radiance, area, duration, number of optical groups, and number of optical events. Previous studies have demonstrated that the optical flash parameter statistics of ground and cloud lightning, which are observable from space, are significantly different. This study investigates a Bayesian network methodology for discriminating lightning flash type (ground or cloud) using the lightning optical data and ancillary GOES-R data. A Directed Acyclic Graph (DAG) is set up with lightning as a "root" and data observed by GLM as the "leaves." This allows for a direct calculation of the joint probability distribution function for the lighting type and radiance, area, etc. Initially, the conditional probabilities that will be required can be estimated from the Lightning Imaging Sensor (LIS) and the Optical Transient Detector (OTD) together with NLDN data. Directly manipulating the joint distribution will yield the conditional probability that a lightning flash is a ground flash given the evidence, which consists of the observed lightning optical data [and possibly cloud data retrieved from the GOES-R Advanced Baseline Imager (ABI) in a more mature Bayesian network configuration]. Later, actual GLM and NLDN data can be used to refine the estimates of the conditional probabilities used in the model; i.e., the Bayesian

  3. A study of anthropogenic and climatic disturbance of the New River Estuary using a Bayesian belief network.

    PubMed

    Nojavan A, Farnaz; Qian, Song S; Paerl, Hans W; Reckhow, Kenneth H; Albright, Elizabeth A

    2014-06-15

    The present paper utilizes a Bayesian Belief Network (BBN) approach to intuitively present and quantify our current understanding of the complex physical, chemical, and biological processes that lead to eutrophication in an estuarine ecosystem (New River Estuary, North Carolina, USA). The model is further used to explore the effects of plausible future climatic and nutrient pollution management scenarios on water quality indicators. The BBN, through visualizing the structure of the network, facilitates knowledge communication with managers/stakeholders who might not be experts in the underlying scientific disciplines. Moreover, the developed structure of the BBN is transferable to other comparable estuaries. The BBN nodes are discretized exploring a new approach called moment matching method. The conditional probability tables of the variables are driven by a large dataset (four years). Our results show interaction among various predictors and their impact on water quality indicators. The synergistic effects caution future management actions. PMID:24814252

  4. A Bayesian network approach to linear and nonlinear acoustic echo cancellation

    NASA Astrophysics Data System (ADS)

    Huemmer, Christian; Maas, Roland; Hofmann, Christian; Kellermann, Walter

    2015-12-01

    This article provides a general Bayesian approach to the tasks of linear and nonlinear acoustic echo cancellation (AEC). We introduce a state-space model with latent state vector modeling all relevant information of the unknown system. Based on three cases for defining the state vector (to model a linear or nonlinear echo path) and its mathematical relation to the observation, it is shown that the normalized least mean square algorithm (with fixed and adaptive stepsize), the Hammerstein group model, and a numerical sampling scheme for nonlinear AEC can be derived by applying fundamental techniques for probabilistic graphical models. As a consequence, the major contribution of this Bayesian approach is a unifying graphical-model perspective which may serve as a powerful framework for future work in linear and nonlinear AEC.

  5. Conjunctivitis (Pink Eye)

    MedlinePlus

    ... message, please visit this page: About CDC.gov . Language: English Español (Spanish) Recommend on Facebook Tweet Share Compartir ... Treatment For Clinicians Conjunctivitis in Newborns Multimedia References Language: English Español (Spanish) File Formats Help: How do I ...

  6. The Inverse Conjunction Fallacy

    ERIC Educational Resources Information Center

    Jonsson, Martin L.; Hampton, James A.

    2006-01-01

    If people believe that some property is true of all members of a class such as sofas, then they should also believe that the same property is true of all members of a conjunctively defined subset of that class such as uncomfortable handmade sofas. A series of experiments demonstrated a failure to observe this constraint, leading to what is termed…

  7. 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

  8. Dynamic Bayesian Networks as a Decision Support tool for assessing Climate Change impacts on highly stressed groundwater systems

    NASA Astrophysics Data System (ADS)

    Molina, José-Luis; Pulido-Velázquez, David; García-Aróstegui, José Luis; Pulido-Velázquez, Manuel

    2013-02-01

    SummaryBayesian Networks (BNs) are powerful tools for assessing and predicting consequences of water management scenarios and uncertain drivers like climate change, integrating available scientific knowledge with the interests of the multiple stakeholders. However, among their major limitations, the non-transient treatment of the cause-effect relationship stands out. A Decision Support System (DSS) based on Dynamic Bayesian Networks (DBNs) is proposed here aimed to palliate that limitation through time slicing technique. The DSS comprises several classes (Object-Oriented BN networks), especially designed for future 5 years length time steps (time slices), covering a total control period of 30 years (2070-2100). The DSS has been developed for assessing impacts generated by different Climate Change (CC) scenarios (generated from several Regional Climatic Models (RCMs) under two emission scenarios, A1B and A2) in an aquifer system (Serral-Salinas) affected by intensive groundwater use over the last 30 years. A calibrated continuous water balance model was used to generate hydrological CC scenarios, and then a groundwater flow model (MODFLOW) was employed in order to analyze the aquifer behavior under CC conditions. Results obtained from both models were used as input for the DSS, considering rainfall, aquifer recharge, variation of piezometric levels and temporal evolution of aquifer storage as the main hydrological components of the aquifer system. Results show the evolution of the aquifer storage for each future time step under different climate change conditions and under controlled water management interventions. This type of applications would allow establishing potential adaptation strategies for aquifer systems as the CC comes into effect.

  9. Conjunctivitis (Pink Eye) in Newborns

    MedlinePlus

    ... Antibiotics Work Adenovirus Non-Polio Enterovirus Parent Portal Conjunctivitis (Pink Eye) in Newborns Language: English Español (Spanish) ... can be very serious. Symptoms and Causes of Conjunctivitis in Newborns Newborns with conjunctivitis develop drainage from ...

  10. Are Student Evaluations of Teaching Effectiveness Valid for Measuring Student Learning Outcomes in Business Related Classes? A Neural Network and Bayesian Analyses

    ERIC Educational Resources Information Center

    Galbraith, Craig S.; Merrill, Gregory B.; Kline, Doug M.

    2012-01-01

    In this study we investigate the underlying relational structure between student evaluations of teaching effectiveness (SETEs) and achievement of student learning outcomes in 116 business related courses. Utilizing traditional statistical techniques, a neural network analysis and a Bayesian data reduction and classification algorithm, we find…

  11. A Bayesian Belief Network Approach to Explore Alternative Decisions for Sediment Control and water Storage Capacity at Lago Lucchetti, Puerto Rico

    EPA Science Inventory

    A Bayesian belief network (BBN) was developed to characterize the effects of sediment accumulation on the water storage capacity of Lago Lucchetti (located in southwest Puerto Rico) and to forecast the life expectancy (usefulness) of the reservoir under different management scena...

  12. Velocity estimation using a Bayesian network in a critical-habitat reach of the Kootenai River, Idaho

    NASA Astrophysics Data System (ADS)

    Palmsten, Margaret L.; Todd Holland, K.; Plant, Nathaniel G.

    2013-09-01

    Numerous numerical modeling studies have been completed in support of an extensive recovery program for the endangered white sturgeon (Acipenser transmontanus) on the Kootenai River near Bonner's Ferry, ID. A technical hurdle in the interpretation of these model results is the transfer of information from the specialist to nonspecialist such that practical decisions utilizing the numerical simulations can be made. To address this, we designed and trained a Bayesian network to provide probabilistic prediction of depth-averaged velocity. Prediction of this critical parameter governing suitable spawning habitat was obtained by exploiting the dynamic relationships between variables derived from model simulations with associated parameter uncertainties. Postdesign assessment indicates that the most influential environmental variables in order of importance are river discharge, depth, and width, and water surface slope. We demonstrate that the probabilistic network not only reproduces the training data with accuracy similar to the accuracy of a numerical model (root-mean-squared error of 0.10 m/s), but that it makes reliable predictions on the same river at times and locations other than where the network was trained (root mean squared error of 0.09 m/s). Additionally, the network showed similar skill (root mean square error of 0.04 m/s) when predicting velocity on the Apalachicola River, FL, a river of similar shape and size to the Kootenai River where a related sturgeon population is also threatened.

  13. Immigrant maternal depression and social networks. A multilevel Bayesian spatial logistic regression in South Western Sydney, Australia.

    PubMed

    Eastwood, John G; Jalaludin, Bin B; Kemp, Lynn A; Phung, Hai N; Barnett, Bryanne E W

    2013-09-01

    The purpose is to explore the multilevel spatial distribution of depressive symptoms among migrant mothers in South Western Sydney and to identify any group level associations that could inform subsequent theory building and local public health interventions. Migrant mothers (n=7256) delivering in 2002 and 2003 were assessed at 2-3 weeks after delivery for risk factors for depressive symptoms. The binary outcome variables were Edinburgh Postnatal Depression Scale scores (EPDS) of >9 and >12. Individual level variables included were: financial income, self-reported maternal health, social support network, emotional support, practical support, baby trouble sleeping, baby demanding and baby not content. The group level variable reported here is aggregated social support networks. We used Bayesian hierarchical multilevel spatial modelling with conditional autoregression. Migrant mothers were at higher risk of having depressive symptoms if they lived in a community with predominantly Australian-born mothers and strong social capital as measured by aggregated social networks. These findings suggest that migrant mothers are socially isolated and current home visiting services should be strengthened for migrant mothers living in communities where they may have poor social networks. PMID:23973180

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

    PubMed Central

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

    2016-01-01

    Background Traumatic brain injury remains a global health problem. Understanding the relative importance of outcome predictors helps optimize our treatment strategies by informing assessment protocols, clinical decisions and trial designs. In this study we establish importance ranking for outcome predictors based on receiver operating indices to identify key predictors of outcome and create simple predictive models. We then explore the associations between key outcome predictors using Bayesian networks to gain further insight into predictor importance. Methods We analyzed the corticosteroid randomization after significant head injury (CRASH) trial database of 10008 patients and included patients for whom demographics, injury characteristics, computer tomography (CT) findings and Glasgow Outcome Scale (GCS) were recorded (total of 13 predictors, which would be available to clinicians within a few hours following the injury in 6945 patients). Predictions of clinical outcome (death or severe disability at 6 months) were performed using logistic regression models with 5-fold cross validation. Predictive performance was measured using standardized partial area (pAUC) under the receiver operating curve (ROC) and we used Delong test for comparisons. Variable importance ranking was based on pAUC targeted at specificity (pAUCSP) and sensitivity (pAUCSE) intervals of 90–100%. Probabilistic associations were depicted using Bayesian networks. Results Complete AUC analysis showed very good predictive power (AUC = 0.8237, 95% CI: 0.8138–0.8336) for the complete model. Specificity focused importance ranking highlighted age, pupillary, motor responses, obliteration of basal cisterns/3rd ventricle and midline shift. Interestingly when targeting model sensitivity, the highest-ranking variables were age, severe extracranial injury, verbal response, hematoma on CT and motor response. Simplified models, which included only these key predictors, had similar performance (pAUCSP = 0

  15. Web-tool to Support Medical Experts in Probabilistic Modelling Using Large Bayesian Networks With an Example of Hinosinusitis.

    PubMed

    Cypko, Mario A; Hirsch, David; Koch, Lucas; Stoehr, Matthaeus; Strauss, Gero; Denecke, Kerstin

    2015-01-01

    For many complex diseases, finding the best patient-specific treatment decision is difficult for physicians due to limited mental capacity. Clinical decision support systems based on Bayesian networks (BN) can provide a probabilistic graphical model integrating all necessary aspects relevant for decision making. Such models are often manually created by clinical experts. The modeling process consists of graphical modeling conducted by collecting of information entities, and probabilistic modeling achieved through defining the relations of information entities to their direct causes. Such expert-based probabilistic modelling with BNs is very time intensive and requires knowledge about the underlying modeling method. We introduce in this paper an intuitive web-based system for helping medical experts generate decision models based on BNs. Using the tool, no special knowledge about the underlying model or BN is necessary. We tested the tool with an example of modeling treatment decisions of Rhinosinusitis and studied its usability. PMID:26262051

  16. Design and Evaluation of the User-Adapted Program Scheduling system based on Bayesian Network and Constraint Satisfaction

    NASA Astrophysics Data System (ADS)

    Iwasaki, Hirotoshi; Sega, Shinichiro; Hiraishi, Hironori; Mizoguchi, Fumio

    In recent years, lots of music content can be stored in mobile computing devices, such as a portable digital music player and a car navigation system. Moreover, various information content like news or traffic information can be acquired always anywhere by a cellular communication and a wireless LAN. However, usability issues arise from the simple interfaces of mobile computing devices. Moreover, retrieving and selecting such content poses safety issues, especially while driving. Thus, it is important for the mobile system to recommend content automatically adapted to user's preference and situation. In this paper, we present the user-adapted program scheduling that generates sequences of content (Program) suiting user's preference and situation based on the Bayesian network and the Constraint Satisfaction Problem (CSP) technique. We also describe the design and evaluation of its realization system, the Personal Program Producer (P3). First, preference such as a genre ratio of content in a program is learned as a Bayesian network model using simple operations such as a skip behavior. A model including each content tends to become large-scale. In order to make it small, we present the model separation method that carries out losslessly compression of the model. Using the model, probabilistic distributions of preference to generate constraints are inferred. Finally satisfying the constraints, a program is produced. This kind of CSP has an issue of which the number of variables is not fixedness. In order to make it variable, we propose a method using metavariables. To evaluate the above methods, we applied them to P3 on a car navigation system. User evaluations helped us clarify that the P3 can produce the program that a user prefers and adapt it to the user.

  17. Use of Bayesian Networks to Combine USGS Surface Water Observations with Hydraulic Geometry Models towards Riverine Discharge Estimation

    NASA Astrophysics Data System (ADS)

    Holland, K. T.; Palmsten, M. L.

    2014-12-01

    We have developed a probabilistic framework for riverine discharge estimation that describes more than 725,000 average daily streamflow observations from the U.S. Geological Survey's Surface Water Field Measurement Program at 1999 sites located throughout the continental United States and collected since 2000. These data, combined with geomorphic parameter information obtained from the National Hydrography Dataset and the National Elevation Dataset, were used to train Bayesian Networks consisting of 9-15 parameters. Hydraulic geometry relationships were used to constrain power law coefficients such that observed time series representing the measured daily discharge could be correlated with synthetic time series governing hydraulic width, depth and velocity at each site. This approach allows the training set to represent natural flow conditions and not the somewhat irregular timing of the field surveys. Sensitivity analysis of network is presented, along with over 500 worldwide validation cases to demonstrate network accuracy when confidently constrained. Making discharge predictions that combine field data with empirical relations though the use of a probabilistic framework is advantageous in that it explicitly accounts for uncertainty in the interpretation of results. This allows objective assessment of the predictive performance when applied to qualitative decisions relevant to environmental managers.

  18. Expert system support using Bayesian belief networks in the diagnosis of fine needle aspiration biopsy specimens of the breast.

    PubMed Central

    Hamilton, P W; Anderson, N; Bartels, P H; Thompson, D

    1994-01-01

    AIM--To develop an expert system model for the diagnosis of fine needle aspiration cytology (FNAC) of the breast. METHODS--Knowledge and uncertainty were represented in the form of a Bayesian belief network which permitted the combination of diagnostic evidence in a cumulative manner and provided a final probability for the possible diagnostic outcomes. The network comprised 10 cytological features (evidence nodes), each independently linked to the diagnosis (decision node) by a conditional probability matrix. The system was designed to be interactive in that the cytopathologist entered evidence into the network in the form of likelihood ratios for the outcomes at each evidence node. RESULTS--The efficiency of the network was tested on a series of 40 breast FNAC specimens. The highest diagnostic probability provided by the network agreed with the cytopathologists' diagnosis in 100% of cases for the assessment of discrete, benign, and malignant aspirates. Atypical probably benign cases were given probabilities in favour of a benign diagnosis. Suspicious cases tended to have similar probabilities for both diagnostic outcomes and so, correctly, could not be assigned as benign or malignant. A closer examination of cumulative belief graphs for the diagnostic sequence of each case provided insight into the diagnostic process, and quantitative data which improved the identification of suspicious cases. CONCLUSION--The further development of such a system will have three important roles in breast cytodiagnosis: (1) to aid the cytologist in making a more consistent and objective diagnosis; (2) to provide a teaching tool on breast cytological diagnosis for the non-expert; and (3) it is the first stage in the development of a system capable of automated diagnosis through the use of expert system machine vision. PMID:8027370

  19. Giant papillary conjunctivitis.

    PubMed Central

    Donshik, P C

    1994-01-01

    Giant papillary conjunctivitis is a syndrome found frequently as a complication of contact lenses. Many variables can affect the onset and severity of the presenting signs and symptoms. Rigid gas permeable contact lenses appear to result in less severe signs and symptoms, with a longer time before the development of giant papillary conjunctivitis. Nonionic, low-water-content soft contact lenses tend to produce less severe signs and symptoms than ionic, low-water-content soft contact lenses. Enzymatic treatment appears to lessen the severity of signs and symptoms. The association of an allergy appears to play a role in the onset of the severity of the signs and symptoms but does not appear to affect the final ability of the individual to wear contact lenses. Using multiple treatment options, such as changing the polymer to a glyceryl methyl methacrylate or a rigid lens, or utilizing a soft lens on a frequent-replacement basis, can result in a success rate of over 90%. In individuals who still have a return of symptoms, the use of topical mast cell stabilizers or a nonsteroidal anti-inflammatory drug as an adjunctive therapy offers the added possibility of keeping these patients in contact lenses. Images FIGURE 1 FIGURE 2 FIGURE 3 FIGURE 4 FIGURE 5 FIGURE 6 FIGURE 7 FIGURE 11 A FIGURE 11 B FIGURE 11 C FIGURE 11 D PMID:7886881

  20. Conjunctive management of surface and groundwater resources under projected future climate change scenarios

    DOE PAGESBeta

    Mani, Amir; Tsai, Frank T. -C.; Kao, Shih-Chieh; Naz, Bibi S.; Ashfaq, Moetasim; Rastogi, Deeksha

    2016-06-16

    Our study introduces a mixed integer linear fractional programming (MILFP) method to optimize conjunctive use of future surface water and groundwater resources under projected climate change scenarios. The conjunctive management model maximizes the ratio of groundwater usage to reservoir water usage. Future inflows to the reservoirs were estimated from the future runoffs projected through hydroclimate modeling considering the Variable Infiltration Capacity model, and 11 sets of downscaled Coupled Model Intercomparison Project phase 5 global climate model projections. Bayesian model averaging was adopted to quantify uncertainty in future runoff projections and reservoir inflow projections due to uncertain future climate projections. Optimizedmore » conjunctive management solutions were investigated for a water supply network in northern Louisiana which includes the Sparta aquifer. Runoff projections under climate change scenarios indicate that runoff will likely decrease in winter and increase in other seasons. Ultimately, results from the developed conjunctive management model with MILFP indicate that the future reservoir water, even at 2.5% low inflow cumulative probability level, could counterbalance groundwater pumping reduction to satisfy demands while improving the Sparta aquifer through conditional groundwater head constraint.« less

  1. Conjunctive management of surface and groundwater resources under projected future climate change scenarios

    SciTech Connect

    Mani, Amir; Tsai, Frank T.-C.; Kao, Shih-Chieh; Ashfaq, Moetasim; Rastogi, Deeksha

    2016-01-01

    This study introduces a mixed integer linear fractional programming (MILFP) method to optimize conjunctive use of future surface water and groundwater resources under projected climate change scenarios. The conjunctive management model maximizes the ratio of groundwater usage to reservoir water usage. Future inflows to the reservoirs were estimated from the future runoffs projected through hydroclimate modeling considering the Variable Infiltration Capacity model, and 11 sets of downscaled Coupled Model Intercomparison Project phase 5 global climate model projections. Bayesian model averaging was adopted to quantify uncertainty in future runoff projections and reservoir inflow projections due to uncertain future climate projections. Optimized conjunctive management solutions were investigated for a water supply network in northern Louisiana which includes the Sparta aquifer. Runoff projections under climate change scenarios indicate that runoff will likely decrease in winter and increase in other seasons. Results from the developed conjunctive management model with MILFP indicate that the future reservoir water, even at 2.5% low inflow cumulative probability level, could counterbalance groundwater pumping reduction to satisfy demands while improving the Sparta aquifer through conditional groundwater head constraint.

  2. Conjunctive management of surface and groundwater resources under projected future climate change scenarios

    NASA Astrophysics Data System (ADS)

    Mani, Amir; Tsai, Frank T.-C.; Kao, Shih-Chieh; Naz, Bibi S.; Ashfaq, Moetasim; Rastogi, Deeksha

    2016-09-01

    This study introduces a mixed integer linear fractional programming (MILFP) method to optimize conjunctive use of future surface water and groundwater resources under projected climate change scenarios. The conjunctive management model maximizes the ratio of groundwater usage to reservoir water usage. Future inflows to the reservoirs were estimated from the future runoffs projected through hydroclimate modeling considering the Variable Infiltration Capacity model, and 11 sets of downscaled Coupled Model Intercomparison Project phase 5 global climate model projections. Bayesian model averaging was adopted to quantify uncertainty in future runoff projections and reservoir inflow projections due to uncertain future climate projections. Optimized conjunctive management solutions were investigated for a water supply network in northern Louisiana which includes the Sparta aquifer. Runoff projections under climate change scenarios indicate that runoff will likely decrease in winter and increase in other seasons. Results from the developed conjunctive management model with MILFP indicate that the future reservoir water, even at 2.5% low inflow cumulative probability level, could counterbalance groundwater pumping reduction to satisfy demands while improving the Sparta aquifer through conditional groundwater head constraints.

  3. How Good Is Crude MDL for Solving the Bias-Variance Dilemma? An Empirical Investigation Based on Bayesian Networks

    PubMed Central

    Cruz-Ramírez, Nicandro; Acosta-Mesa, Héctor Gabriel; Mezura-Montes, Efrén; Guerra-Hernández, Alejandro; Hoyos-Rivera, Guillermo de Jesús; Barrientos-Martínez, Rocío Erandi; Gutiérrez-Fragoso, Karina; Nava-Fernández, Luis Alonso; González-Gaspar, Patricia; Novoa-del-Toro, Elva María; Aguilera-Rueda, Vicente Josué; Ameca-Alducin, María Yaneli

    2014-01-01

    The bias-variance dilemma is a well-known and important problem in Machine Learning. It basically relates the generalization capability (goodness of fit) of a learning method to its corresponding complexity. When we have enough data at hand, it is possible to use these data in such a way so as to minimize overfitting (the risk of selecting a complex model that generalizes poorly). Unfortunately, there are many situations where we simply do not have this required amount of data. Thus, we need to find methods capable of efficiently exploiting the available data while avoiding overfitting. Different metrics have been proposed to achieve this goal: the Minimum Description Length principle (MDL), Akaike’s Information Criterion (AIC) and Bayesian Information Criterion (BIC), among others. In this paper, we focus on crude MDL and empirically evaluate its performance in selecting models with a good balance between goodness of fit and complexity: the so-called bias-variance dilemma, decomposition or tradeoff. Although the graphical interaction between these dimensions (bias and variance) is ubiquitous in the Machine Learning literature, few works present experimental evidence to recover such interaction. In our experiments, we argue that the resulting graphs allow us to gain insights that are difficult to unveil otherwise: that crude MDL naturally selects balanced models in terms of bias-variance, which not necessarily need be the gold-standard ones. We carry out these experiments using a specific model: a Bayesian network. In spite of these motivating results, we also should not overlook three other components that may significantly affect the final model selection: the search procedure, the noise rate and the sample size. PMID:24671204

  4. How good is crude MDL for solving the bias-variance dilemma? An empirical investigation based on Bayesian networks.

    PubMed

    Cruz-Ramírez, Nicandro; Acosta-Mesa, Héctor Gabriel; Mezura-Montes, Efrén; Guerra-Hernández, Alejandro; Hoyos-Rivera, Guillermo de Jesús; Barrientos-Martínez, Rocío Erandi; Gutiérrez-Fragoso, Karina; Nava-Fernández, Luis Alonso; González-Gaspar, Patricia; Novoa-del-Toro, Elva María; Aguilera-Rueda, Vicente Josué; Ameca-Alducin, María Yaneli

    2014-01-01

    The bias-variance dilemma is a well-known and important problem in Machine Learning. It basically relates the generalization capability (goodness of fit) of a learning method to its corresponding complexity. When we have enough data at hand, it is possible to use these data in such a way so as to minimize overfitting (the risk of selecting a complex model that generalizes poorly). Unfortunately, there are many situations where we simply do not have this required amount of data. Thus, we need to find methods capable of efficiently exploiting the available data while avoiding overfitting. Different metrics have been proposed to achieve this goal: the Minimum Description Length principle (MDL), Akaike's Information Criterion (AIC) and Bayesian Information Criterion (BIC), among others. In this paper, we focus on crude MDL and empirically evaluate its performance in selecting models with a good balance between goodness of fit and complexity: the so-called bias-variance dilemma, decomposition or tradeoff. Although the graphical interaction between these dimensions (bias and variance) is ubiquitous in the Machine Learning literature, few works present experimental evidence to recover such interaction. In our experiments, we argue that the resulting graphs allow us to gain insights that are difficult to unveil otherwise: that crude MDL naturally selects balanced models in terms of bias-variance, which not necessarily need be the gold-standard ones. We carry out these experiments using a specific model: a Bayesian network. In spite of these motivating results, we also should not overlook three other components that may significantly affect the final model selection: the search procedure, the noise rate and the sample size. PMID:24671204

  5. A hybrid approach to monthly streamflow forecasting: Integrating hydrological model outputs into a Bayesian artificial neural network

    NASA Astrophysics Data System (ADS)

    Humphrey, Greer B.; Gibbs, Matthew S.; Dandy, Graeme C.; Maier, Holger R.

    2016-09-01

    Monthly streamflow forecasts are needed to support water resources decision making in the South East of South Australia, where baseflow represents a significant proportion of the total streamflow and soil moisture and groundwater are important predictors of runoff. To address this requirement, the utility of a hybrid monthly streamflow forecasting approach is explored, whereby simulated soil moisture from the GR4J conceptual rainfall-runoff model is used to represent initial catchment conditions in a Bayesian artificial neural network (ANN) statistical forecasting model. To assess the performance of this hybrid forecasting method, a comparison is undertaken of the relative performances of the Bayesian ANN, the GR4J conceptual model and the hybrid streamflow forecasting approach for producing 1-month ahead streamflow forecasts at three key locations in the South East of South Australia. Particular attention is paid to the quantification of uncertainty in each of the forecast models and the potential for reducing forecast uncertainty by using the hybrid approach is considered. Case study results suggest that the hybrid models developed in this study are able to take advantage of the complementary strengths of both the ANN models and the GR4J conceptual models. This was particularly the case when forecasting high flows, where the hybrid models were shown to outperform the two individual modelling approaches in terms of the accuracy of the median forecasts, as well as reliability and resolution of the forecast distributions. In addition, the forecast distributions generated by the hybrid models were up to 8 times more precise than those based on climatology; thus, providing a significant improvement on the information currently available to decision makers.

  6. Towards a Fuzzy Bayesian Network Based Approach for Safety Risk Analysis of Tunnel-Induced Pipeline Damage.

    PubMed

    Zhang, Limao; Wu, Xianguo; Qin, Yawei; Skibniewski, Miroslaw J; Liu, Wenli

    2016-02-01

    Tunneling excavation is bound to produce significant disturbances to surrounding environments, and the tunnel-induced damage to adjacent underground buried pipelines is of considerable importance for geotechnical practice. A fuzzy Bayesian networks (FBNs) based approach for safety risk analysis is developed in this article with detailed step-by-step procedures, consisting of risk mechanism analysis, the FBN model establishment, fuzzification, FBN-based inference, defuzzification, and decision making. In accordance with the failure mechanism analysis, a tunnel-induced pipeline damage model is proposed to reveal the cause-effect relationships between the pipeline damage and its influential variables. In terms of the fuzzification process, an expert confidence indicator is proposed to reveal the reliability of the data when determining the fuzzy probability of occurrence of basic events, with both the judgment ability level and the subjectivity reliability level taken into account. By means of the fuzzy Bayesian inference, the approach proposed in this article is capable of calculating the probability distribution of potential safety risks and identifying the most likely potential causes of accidents under both prior knowledge and given evidence circumstances. A case concerning the safety analysis of underground buried pipelines adjacent to the construction of the Wuhan Yangtze River Tunnel is presented. The results demonstrate the feasibility of the proposed FBN approach and its application potential. The proposed approach can be used as a decision tool to provide support for safety assurance and management in tunnel construction, and thus increase the likelihood of a successful project in a complex project environment. PMID:26224125

  7. NASA Human Spaceflight Conjunction Assessment: Recent Conjunctions of Interest

    NASA Technical Reports Server (NTRS)

    Browns, Ansley C.

    2010-01-01

    This viewgraph presentation discusses a brief history of NASA Human Spaceflight Conjunction Assessment (CA) activities, an overview of NASA CA process for ISS and Shuttle, and recent examples from Human Spaceflight conjunctions.

  8. A Bayesian Approach to the Evolution of Metabolic Networks on a Phylogeny

    PubMed Central

    Mithani, Aziz; Preston, Gail M.; Hein, Jotun

    2010-01-01

    The availability of genomes of many closely related bacteria with diverse metabolic capabilities offers the possibility of tracing metabolic evolution on a phylogeny relating the genomes to understand the evolutionary processes and constraints that affect the evolution of metabolic networks. Using simple (independent loss/gain of reactions) or complex (incorporating dependencies among reactions) stochastic models of metabolic evolution, it is possible to study how metabolic networks evolve over time. Here, we describe a model that takes the reaction neighborhood into account when modeling metabolic evolution. The model also allows estimation of the strength of the neighborhood effect during the course of evolution. We present Gibbs samplers for sampling networks at the internal node of a phylogeny and for estimating the parameters of evolution over a phylogeny without exploring the whole search space by iteratively sampling from the conditional distributions of the internal networks and parameters. The samplers are used to estimate the parameters of evolution of metabolic networks of bacteria in the genus Pseudomonas and to infer the metabolic networks of the ancestral pseudomonads. The results suggest that pathway maps that are conserved across the Pseudomonas phylogeny have a stronger neighborhood structure than those which have a variable distribution of reactions across the phylogeny, and that some Pseudomonas lineages are going through genome reduction resulting in the loss of a number of reactions from their metabolic networks. PMID:20700467

  9. Characterization of aluminum hydroxide particles from the Bayer process using neural network and Bayesian classifiers.

    PubMed

    Zaknich, A

    1997-01-01

    An automatic process of isolating and characterizing individual aluminum hydroxide particles from the Bayer process in scanning electron microscope gray-scale images of samples is described. It uses image processing algorithms, neural nets and Bayesian classifiers. As the particles are amorphous and different greatly, there were complex nonlinear decisions and anomalies. The process is in two stages; isolation of particles, and classification of each particle. The isolation process correctly identifies 96.9% of the objects as complete and single particles after a 15.5% rejection of questionable objects. The sample set had a possible 2455 particles taken from 384 256x256-pixel images. Of the 15.5%, 14.2% were correctly rejected. With no rejection the accuracy drops to 91.8% which represents the accuracy of the isolation process alone. The isolated particles are classified by shape, single crystal protrusions, texture, crystal size, and agglomeration. The particle samples were preclassified by a human expert and the data were used to train the five classifiers to embody the expert knowledge. The system was designed to be used as a research tool to determine and study relationships between particle properties and plant parameters in the production of smelting grade alumina by the Bayer process. PMID:18255695

  10. Developing a Methodology for Eliciting Subjective Probability Estimates During Expert Evaluations of Safety Interventions: Application for Bayesian Belief Networks

    NASA Technical Reports Server (NTRS)

    Wiegmann, Douglas A.a

    2005-01-01

    The NASA Aviation Safety Program (AvSP) has defined several products that will potentially modify airline and/or ATC operations, enhance aircraft systems, and improve the identification of potential hazardous situations within the National Airspace System (NAS). Consequently, there is a need to develop methods for evaluating the potential safety benefit of each of these intervention products so that resources can be effectively invested to produce the judgments to develop Bayesian Belief Networks (BBN's) that model the potential impact that specific interventions may have. Specifically, the present report summarizes methodologies for improving the elicitation of probability estimates during expert evaluations of AvSP products for use in BBN's. The work involved joint efforts between Professor James Luxhoj from Rutgers University and researchers at the University of Illinois. The Rutgers' project to develop BBN's received funding by NASA entitled "Probabilistic Decision Support for Evaluating Technology Insertion and Assessing Aviation Safety System Risk." The proposed project was funded separately but supported the existing Rutgers' program.

  11. Modeling and predicting the occurrence of brain metastasis from lung cancer by Bayesian network: a case study of Taiwan.

    PubMed

    Wang, Kung-Jeng; Makond, Bunjira; Wang, Kung-Min

    2014-04-01

    The Bayesian network (BN) is a promising method for modeling cancer metastasis under uncertainty. BN is graphically represented using bioinformatics variables and can be used to support an informative medical decision/observation by using probabilistic reasoning. In this study, we propose such a BN to describe and predict the occurrence of brain metastasis from lung cancer. A nationwide database containing more than 50,000 cases of cancer patients from 1996 to 2010 in Taiwan was used in this study. The BN topology for studying brain metastasis from lung cancer was rigorously examined by domain experts/doctors. We used three statistical measures, namely, the accuracy, sensitivity, and specificity, to evaluate the performances of the proposed BN model and to compare it with three competitive approaches, namely, naive Bayes (NB), logistic regression (LR) and support vector machine (SVM). Experimental results show that no significant differences are observed in accuracy or specificity among the four models, while the proposed BN outperforms the others in terms of sampled average sensitivity. Moreover the proposed BN has advantages compared with the other approaches in interpreting how brain metastasis develops from lung cancer. It is shown to be easily understood by physicians, to be efficient in modeling non-linear situations, capable of solving stochastic medical problems, and handling situations wherein information are missing in the context of the occurrence of brain metastasis from lung cancer. PMID:24607682

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

    PubMed

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

    2016-09-01

    Identifying areas that have a high risk of burning is a main component of fire management planning. Although the available tools can predict the fire risks, these are poor in accommodating uncertainties in their predictions. In this study, we accommodated uncertainty in wildfire prediction using Bayesian belief networks (BBNs). An influence diagram was developed to identify the factors influencing wildfire in arid and semi-arid areas of Iran, and it was populated with probabilities to produce a BBNs model. The behavior of the model was tested using scenario and sensitivity analysis. Land cover/use, mean annual rainfall, mean annual temperature, elevation, and livestock density were recognized as the main variables determining wildfire occurrence. The produced model had good accuracy as its ROC area under the curve was 0.986. The model could be applied in both predictive and diagnostic analysis for answering "what if" and "how" questions. The probabilistic relationships within the model can be updated over time using observation and monitoring data. The wildfire BBN model may be updated as new knowledge emerges; hence, it can be used to support the process of adaptive management. PMID:27553945

  13. Bayesian network meta-analysis suggests a similar effectiveness between a monovalent and a pentavalent rotavirus vaccine

    PubMed Central

    Takeuchi, Masato

    2014-01-01

    To assess the comparative effectiveness of a monovalent and a pentavalent rotavirus vaccine (RV1 and RV5), a Bayesian network meta-analysis was conducted. Data of randomized trials from the Cochrane Review in 2012 were extracted and synthesized. For the prevention of severe rotavirus disease up to 2 years, no statistical difference was found in the effectiveness between the 2 types of vaccine (odds ratio: 2.23, 95% credible interval: 0.71–5.20). Similarly, the comparative effectiveness of RV1 and RV5 appeared equivalent for other rotavirus-associated outcome measures, such as prevention of severe disease up to 1 year and all severity of rotavirus infections for up to both 1- and 2-year follow-ups. These results indicates that, overall, RV1 and RV5 offer similar benefits to prevent rotavirus diseases; nonetheless, credible intervals are generally wide, highlighting the necessity of further meta-analyses including updated information or, ideally, controlled trials comparing both vaccines directly. PMID:24608099

  14. Integrating Expert Knowledge with Data in Bayesian Networks: Preserving Data-Driven Expectations when the Expert Variables Remain Unobserved

    PubMed Central

    Constantinou, Anthony Costa; Fenton, Norman; Neil, Martin

    2016-01-01

    When developing a causal probabilistic model, i.e. a Bayesian network (BN), it is common to incorporate expert knowledge of factors that are important for decision analysis but where historical data are unavailable or difficult to obtain. This paper focuses on the problem whereby the distribution of some continuous variable in a BN is known from data, but where we wish to explicitly model the impact of some additional expert variable (for which there is expert judgment but no data). Because the statistical outcomes are already influenced by the causes an expert might identify as variables missing from the dataset, the incentive here is to add the expert factor to the model in such a way that the distribution of the data variable is preserved when the expert factor remains unobserved. We provide a method for eliciting expert judgment that ensures the expected values of a data variable are preserved under all the known conditions. We show that it is generally neither possible, nor realistic, to preserve the variance of the data variable, but we provide a method towards determining the accuracy of expertise in terms of the extent to which the variability of the revised empirical distribution is minimised. We also describe how to incorporate the assessment of extremely rare or previously unobserved events. PMID:27378822

  15. A General Bayesian Network Approach to Analyzing Online Game Item Values and Its Influence on Consumer Satisfaction and Purchase Intention

    NASA Astrophysics Data System (ADS)

    Lee, Kun Chang; Park, Bong-Won

    Many online game users purchase game items with which to play free-to-play games. Because of a lack of research into which there is no specified framework for categorizing the values of game items, this study proposes four types of online game item values based on an analysis of literature regarding online game characteristics. It then proposes to investigate how online game users perceive satisfaction and purchase intention from the proposed four types of online game item values. Though regression analysis has been used frequently to answer this kind of research question, we propose a new approach, a General Bayesian Network (GBN), which can be performed in an understandable way without sacrificing predictive accuracy. Conventional techniques, such as regression analysis, do not provide significant explanation for this kind of problem because they are fixed to a linear structure and are limited in explaining why customers are likely to purchase game items and if they are satisfied with their purchases. In contrast, the proposed GBN provides a flexible underlying structure based on questionnaire survey data and offers robust decision support on this kind of research question by identifying its causal relationships. To illustrate the validity of GBN in solving the research question in this study, 327 valid questionnaires were analyzed using GBN with what-if and goal-seeking approaches. The experimental results were promising and meaningful in comparison with regression analysis results.

  16. Integrating indigenous ecological and scientific hydro-geological knowledge using a Bayesian Network in the context of water resource development

    NASA Astrophysics Data System (ADS)

    Liedloff, A. C.; Woodward, E. L.; Harrington, G. A.; Jackson, S.

    2013-08-01

    The contributions indigenous ecological knowledge can make to better inform water management decisions are currently undervalued leading to an underrepresentation of indigenous values in water planning and policy. This paper outlines a novel approach in which indigenous ecological knowledge informs cause and effect relationships between species and aquatic habitats to promote broader ecosystem understanding. A Bayesian Network was developed to synthesise the seasonal aquatic knowledge of a group of Gooniyandi Aboriginal language speakers, including fish species’ availability, condition and required habitat, and integrate it with hydrogeological understanding obtained from research undertaken in a stretch of the Fitzroy River, Western Australia. This river system, like most in northern Australia, is highly seasonal and entirely dependent upon groundwater for maintaining flow during prolonged dry seasons. We found that potential changes in river flow rates caused by future water resource development, such as groundwater extraction and surface water diversion, may have detrimental effects on the ability to catch the high value aquatic food species such as Barramundi and Sawfish, but also that species such as Black Bream may benefit. These findings result from changes in availability of habitats at times when Gooniyandi understanding shows they are important for providing aquatic resources in good condition. This study raises awareness of the potential outcomes of future water management and stimulates communication between indigenous people, the scientific community and water managers by developing a model of indigenous understanding from which to predict eco-hydrological change.

  17. A spatial Bayesian network model to assess the benefits of early warning for urban flood risk to people

    NASA Astrophysics Data System (ADS)

    Balbi, Stefano; Villa, Ferdinando; Mojtahed, Vahid; Hegetschweiler, Karin Tessa; Giupponi, Carlo

    2016-06-01

    This article presents a novel methodology to assess flood risk to people by integrating people's vulnerability and ability to cushion hazards through coping and adapting. The proposed approach extends traditional risk assessments beyond material damages; complements quantitative and semi-quantitative data with subjective and local knowledge, improving the use of commonly available information; and produces estimates of model uncertainty by providing probability distributions for all of its outputs. Flood risk to people is modeled using a spatially explicit Bayesian network model calibrated on expert opinion. Risk is assessed in terms of (1) likelihood of non-fatal physical injury, (2) likelihood of post-traumatic stress disorder and (3) likelihood of death. The study area covers the lower part of the Sihl valley (Switzerland) including the city of Zurich. The model is used to estimate the effect of improving an existing early warning system, taking into account the reliability, lead time and scope (i.e., coverage of people reached by the warning). Model results indicate that the potential benefits of an improved early warning in terms of avoided human impacts are particularly relevant in case of a major flood event.

  18. A spatial Bayesian network model to assess the benefits of early warning for urban flood risk to people

    NASA Astrophysics Data System (ADS)

    Balbi, S.; Villa, F.; Mojtahed, V.; Hegetschweiler, K. T.; Giupponi, C.

    2015-10-01

    This article presents a novel methodology to assess flood risk to people by integrating people's vulnerability and ability to cushion hazards through coping and adapting. The proposed approach extends traditional risk assessments beyond material damages; complements quantitative and semi-quantitative data with subjective and local knowledge, improving the use of commonly available information; produces estimates of model uncertainty by providing probability distributions for all of its outputs. Flood risk to people is modeled using a spatially explicit Bayesian network model calibrated on expert opinion. Risk is assessed in terms of: (1) likelihood of non-fatal physical injury; (2) likelihood of post-traumatic stress disorder; (3) likelihood of death. The study area covers the lower part of the Sihl valley (Switzerland) including the city of Zurich. The model is used to estimate the benefits of improving an existing Early Warning System, taking into account the reliability, lead-time and scope (i.e. coverage of people reached by the warning). Model results indicate that the potential benefits of an improved early warning in terms of avoided human impacts are particularly relevant in case of a major flood event: about 75 % of fatalities, 25 % of injuries and 18 % of post-traumatic stress disorders could be avoided.

  19. Developing best-practice Bayesian Belief Networks in ecological risk assessments for freshwater and estuarine ecosystems: a quantitative review.

    PubMed

    McDonald, K S; Ryder, D S; Tighe, M

    2015-05-01

    Bayesian Belief Networks (BBNs) are being increasingly used to develop a range of predictive models and risk assessments for ecological systems. Ecological BBNs can be applied to complex catchment and water quality issues, integrating multiple spatial and temporal variables within social, economic and environmental decision making processes. This paper reviews the essential components required for ecologists to design a best-practice predictive BBN in an ecological risk assessment (ERA) framework for aquatic ecosystems, outlining: (1) how to create a BBN for an aquatic ERA?; (2) what are the challenges for aquatic ecologists in adopting the best-practice applications of BBNs to ERAs?; and (3) how can BBNs in ERAs influence the science/management interface into the future? The aims of this paper are achieved using three approaches. The first is to demonstrate the best-practice development of BBNs in aquatic sciences using a simple nutrient model. The second is to discuss the limitations and challenges aquatic ecologists encounter when applying BBNs to ERAs. The third is to provide a framework for integrating best-practice BBNs into ERAs and the management of aquatic ecosystems. A quantitative review of the application and development of BBNs in aquatic science from 2002 to 2014 was conducted to identify areas where continued best-practice development is required. We outline a best-practice framework for the integration of BBNs into ERAs and study of complex aquatic systems. PMID:25733196

  20. Impact assessment of emission management strategies of the pharmaceuticals Metformin and Metoprolol to the aquatic environment using Bayesian networks.

    PubMed

    Brandmayr, Caterina; Kerber, Heide; Winker, Martina; Schramm, Engelbert

    2015-11-01

    The issue of pharmaceuticals in the environment has caused increasing concern in the recent years and various strategies have been proposed to tackle this problem. This work describes a Bayesian network (BN)-based socio-ecological impact assessment of a set of measures aimed at reducing the entry of pharmaceuticals in the aquatic environment. The measures investigated were selected across three sectors: public health market, environmental politics and drug design innovation. The BN model was developed for two drugs, Metformin and Metoprolol, and it models the distribution of the Predicted Environmental Concentration (PEC) values as a function of different measures. Results show that the sensitivity of the PEC for the two drugs to the measures investigated reflects the distinct drug characteristics, suggesting that in order to ensure the successful reduction of a broad range of substances, a spectrum of measures targeting the entire lifecycle of a pharmaceutical should be implemented. Furthermore, evaluation of two scenarios reflecting different emission management strategies highlights that the integrated implementation of a comprehensive set of measures across the three sectors results in a more extensive reduction of the contamination. Finally, the BN provides an initial forecasting tool to model the PEC of a drug as a function of a combination of measures in a context-specific manner and possible adaptations of the model are proposed. PMID:26115339

  1. Landslide susceptibility assessment in the Hoa Binh province of Vietnam: A comparison of the Levenberg-Marquardt and Bayesian regularized neural networks

    NASA Astrophysics Data System (ADS)

    Tien Bui, Dieu; Pradhan, Biswajeet; Lofman, Owe; Revhaug, Inge; Dick, Oystein B.

    2012-10-01

    This study investigates the potential application of artificial neural networks in landslide susceptibility mapping in the Hoa Binh province of Vietnam. A landslide inventory map of the study area was prepared by combining landslide locations investigated through three projects during the last 10 years. Some recent landslide locations were identified based on SPOT satellite images, field surveys, and existing literature. The images have a spatial resolution of 2.5 m. Ten landslide conditioning factors were utilized in the multilayer feed-forward neural network analysis: slope, aspect, relief amplitude, lithology, land use, soil type, rainfall, distance to roads, distance to rivers and distance to faults. Two back-propagation training algorithms, Levenberg-Marquardt and Bayesian regularization, were utilized to determine synoptic weights using a training dataset. Relative importance of each landslide conditioning factor was assessed using the above mentioned synoptic weights. The final connection weights obtained in the training phase were applied to the entire study area to produce landslide susceptibility indexes. The results were then imported to a GIS and landslide susceptibility maps were constructed. Landslide locations not used in the training phase were used to verify and compare the results of the landslide susceptibility maps. Finally, the two landslide susceptibility maps were validated using the prediction-rate method. Subsequently, areas under the prediction curves were assessed. The prediction accuracy of landslide susceptibility maps produced by the Bayesian regularization neural network and the Levenberg-Marquardt neural network were 90.3% and 86.1% respectively. These results indicate that the two models seem to have good predictive capability. The Bayesian regularization network model appears more robust and efficient than the Levenberg-Marquardt network model for landslide susceptibility mapping.

  2. Updating Parameters for Volcanic Hazard Assessment Using Multi-parameter Monitoring Data Streams And Bayesian Belief Networks

    NASA Astrophysics Data System (ADS)

    Odbert, Henry; Aspinall, Willy

    2014-05-01

    Evidence-based hazard assessment at volcanoes assimilates knowledge about the physical processes of hazardous phenomena and observations that indicate the current state of a volcano. Incorporating both these lines of evidence can inform our belief about the likelihood (probability) and consequences (impact) of possible hazardous scenarios, forming a basis for formal quantitative hazard assessment. However, such evidence is often uncertain, indirect or incomplete. Approaches to volcano monitoring have advanced substantially in recent decades, increasing the variety and resolution of multi-parameter timeseries data recorded at volcanoes. Interpreting these multiple strands of parallel, partial evidence thus becomes increasingly complex. In practice, interpreting many timeseries requires an individual to be familiar with the idiosyncrasies of the volcano, monitoring techniques, configuration of recording instruments, observations from other datasets, and so on. In making such interpretations, an individual must consider how different volcanic processes may manifest as measureable observations, and then infer from the available data what can or cannot be deduced about those processes. We examine how parts of this process may be synthesised algorithmically using Bayesian inference. Bayesian Belief Networks (BBNs) use probability theory to treat and evaluate uncertainties in a rational and auditable scientific manner, but only to the extent warranted by the strength of the available evidence. The concept is a suitable framework for marshalling multiple strands of evidence (e.g. observations, model results and interpretations) and their associated uncertainties in a methodical manner. BBNs are usually implemented in graphical form and could be developed as a tool for near real-time, ongoing use in a volcano observatory, for example. We explore the application of BBNs in analysing volcanic data from the long-lived eruption at Soufriere Hills Volcano, Montserrat. We discuss

  3. Study of Single Top Quark Production Using Bayesian Neural Networks With D0 Detector at the Tevatron

    SciTech Connect

    Joshi, Jyoti

    2012-01-01

    Top quark, the heaviest and most intriguing among the six known quarks, can be created via two independent production mechanisms in {\\pp} collisions. The primary mode, strong {\\ttbar} pair production from a $gtt$ vertex, was used by the {\\d0} and CDF collaborations to establish the existence of the top quark in March 1995. The second mode is the electroweak production of a single top quark or antiquark, which has been observed recently in March 2009. Since single top quarks are produced at hadron colliders through a $Wtb$ vertex, thereby provide a direct probe of the nature of $Wtb$ coupling and of the Cabibbo-Kobayashi-Maskawa matrix element, $V_{tb}$. So this mechanism provides a sensitive probe for several, standard model and beyond standard model, parameters such as anomalous $Wtb$ couplings. In this thesis, we measure the cross section of the electroweak produced top quark in three different production modes, $s+t$, $s$ and $t$-channels using a technique based on the Bayesian neural networks. This technique is applied for analysis of the 5.4 $fb^{-1}$ of data collected by the {\\d0} detector. From a comparison of the Bayesian neural networks discriminants between data and the signal-background model using Bayesian statistics, the cross sections of the top quark produced through the electroweak mechanism have been measured as: \\[\\sigma(p\\bar{p}→tb+X,tqb+X) = 3.11^{+0.77}_{-0.71}\\;\\rm pb\\] \\[\\sigma(p\\bar{p}→tb+X) = 0.72^{+0.44}_{-0.43}\\;\\rm pb\\] \\[\\sigma(p\\bar{p}→tqb+X) = 2.92^{+0.87}_{-0.73}\\;\\rm pb\\] % The $s+t$-channel has a gaussian significance of $4.7\\sigma$, the $s$-channel $0.9\\sigma$ and the $t$-channel~$4.7\\sigma$. The results are consistent with the standard model predictions within one standard deviation. By combining these results with the results for two other analyses (using different MVA techniques) improved results \\[\\sigma(p\\bar{p}→tb+X,tqb+X) = 3.43^{+0.73}_{-0.74}\\;\\rm pb\\] \\[\\sigma

  4. Conjunction Illusions and Conjunction Fallacies in Episodic Memory

    ERIC Educational Resources Information Center

    Brainerd, C. J.; Holliday, Robyn E.; Nakamura, Koyuki; Reyna, Valerie F.

    2014-01-01

    Recent research on the overdistribution principle implies that episodic memory is infected by conjunction illusions. These are instances in which an item that was presented in a single context (e.g., List 1) is falsely remembered as having been presented in multiple contexts (e.g., List 1 and List 2). Robust conjunction illusions were detected in…

  5. Reverse Engineering of Modified Genes by Bayesian Network Analysis Defines Molecular Determinants Critical to the Development of Glioblastoma

    PubMed Central

    Kunkle, Brian W.; Yoo, Changwon; Roy, Deodutta

    2013-01-01

    In this study we have identified key genes that are critical in development of astrocytic tumors. Meta-analysis of microarray studies which compared normal tissue to astrocytoma revealed a set of 646 differentially expressed genes in the majority of astrocytoma. Reverse engineering of these 646 genes using Bayesian network analysis produced a gene network for each grade of astrocytoma (Grade I–IV), and ‘key genes’ within each grade were identified. Genes found to be most influential to development of the highest grade of astrocytoma, Glioblastoma multiforme were: COL4A1, EGFR, BTF3, MPP2, RAB31, CDK4, CD99, ANXA2, TOP2A, and SERBP1. All of these genes were up-regulated, except MPP2 (down regulated). These 10 genes were able to predict tumor status with 96–100% confidence when using logistic regression, cross validation, and the support vector machine analysis. Markov genes interact with NFkβ, ERK, MAPK, VEGF, growth hormone and collagen to produce a network whose top biological functions are cancer, neurological disease, and cellular movement. Three of the 10 genes - EGFR, COL4A1, and CDK4, in particular, seemed to be potential ‘hubs of activity’. Modified expression of these 10 Markov Blanket genes increases lifetime risk of developing glioblastoma compared to the normal population. The glioblastoma risk estimates were dramatically increased with joint effects of 4 or more than 4 Markov Blanket genes. Joint interaction effects of 4, 5, 6, 7, 8, 9 or 10 Markov Blanket genes produced 9, 13, 20.9, 26.7, 52.8, 53.2, 78.1 or 85.9%, respectively, increase in lifetime risk of developing glioblastoma compared to normal population. In summary, it appears that modified expression of several ‘key genes’ may be required for the development of glioblastoma. Further studies are needed to validate these ‘key genes’ as useful tools for early detection and novel therapeutic options for these tumors. PMID:23737970

  6. Brain Decoding-Classification of Hand Written Digits from fMRI Data Employing Bayesian Networks.

    PubMed

    Yargholi, Elahe'; Hossein-Zadeh, Gholam-Ali

    2016-01-01

    We are frequently exposed to hand written digits 0-9 in today's modern life. Success in decoding-classification of hand written digits helps us understand the corresponding brain mechanisms and processes and assists seriously in designing more efficient brain-computer interfaces. However, all digits belong to the same semantic category and similarity in appearance of hand written digits makes this decoding-classification a challenging problem. In present study, for the first time, augmented naïve Bayes classifier is used for classification of functional Magnetic Resonance Imaging (fMRI) measurements to decode the hand written digits which took advantage of brain connectivity information in decoding-classification. fMRI was recorded from three healthy participants, with an age range of 25-30. Results in different brain lobes (frontal, occipital, parietal, and temporal) show that utilizing connectivity information significantly improves decoding-classification and capability of different brain lobes in decoding-classification of hand written digits were compared to each other. In addition, in each lobe the most contributing areas and brain connectivities were determined and connectivities with short distances between their endpoints were recognized to be more efficient. Moreover, data driven method was applied to investigate the similarity of brain areas in responding to stimuli and this revealed both similarly active areas and active mechanisms during this experiment. Interesting finding was that during the experiment of watching hand written digits, there were some active networks (visual, working memory, motor, and language processing), but the most relevant one to the task was language processing network according to the voxel selection. PMID:27468261

  7. Brain Decoding-Classification of Hand Written Digits from fMRI Data Employing Bayesian Networks

    PubMed Central

    Yargholi, Elahe'; Hossein-Zadeh, Gholam-Ali

    2016-01-01

    We are frequently exposed to hand written digits 0–9 in today's modern life. Success in decoding-classification of hand written digits helps us understand the corresponding brain mechanisms and processes and assists seriously in designing more efficient brain–computer interfaces. However, all digits belong to the same semantic category and similarity in appearance of hand written digits makes this decoding-classification a challenging problem. In present study, for the first time, augmented naïve Bayes classifier is used for classification of functional Magnetic Resonance Imaging (fMRI) measurements to decode the hand written digits which took advantage of brain connectivity information in decoding-classification. fMRI was recorded from three healthy participants, with an age range of 25–30. Results in different brain lobes (frontal, occipital, parietal, and temporal) show that utilizing connectivity information significantly improves decoding-classification and capability of different brain lobes in decoding-classification of hand written digits were compared to each other. In addition, in each lobe the most contributing areas and brain connectivities were determined and connectivities with short distances between their endpoints were recognized to be more efficient. Moreover, data driven method was applied to investigate the similarity of brain areas in responding to stimuli and this revealed both similarly active areas and active mechanisms during this experiment. Interesting finding was that during the experiment of watching hand written digits, there were some active networks (visual, working memory, motor, and language processing), but the most relevant one to the task was language processing network according to the voxel selection. PMID:27468261

  8. Comparative effectiveness of inhaled corticosteroids for paediatric asthma: protocol for a systematic review and Bayesian network meta-analysis

    PubMed Central

    Takeuchi, Masato; Kano, Hirotsugu; Takahashi, Kenzo; Iwata, Tsutomu

    2015-01-01

    Introduction Use of inhaled corticosteroid (ICS) is the mainstream maintenance therapy for paediatric asthma. Several forms of ICS are available, but the relative effectiveness among ICS has not been well investigated in published, randomised, controlled trials. The paucity of direct comparisons between ICS may have resulted in insufficient estimation in former systematic reviews/meta-analyses. To supplement the information on the comparative effectiveness of ICS for paediatric asthma, we plan to conduct a network meta-analysis that will enable summary of direct and indirect evidence. Methods and analysis We will retrieve randomised, controlled trials that examined the effectiveness of ICS for paediatric asthma from the PubMed and Cochrane Central Register of Controlled Trials. After one author scans the title and abstract for eligible studies, two authors will independently review study data and assess the quality of the study. Studies of children (≤18 years old) with chronic asthma or recurrent wheezing episodes will be included if they used ICS for ≥4 weeks. We will define a priori core outcomes and supplemental outcomes of paediatric asthma, including exacerbation, healthcare use and pulmonary function. Studies reporting a minimum of one core outcome will be entered into the systematic review. After the systematic review is performed, extracted data of relevant studies will be synthesised in the Bayesian framework using a random-effects model. Ethics and dissemination The results will be disseminated through peer-reviewed publications and conference presentations. Protocol registration number UMIN (000016724) and PROSPERO (CRD42015025889). PMID:26493456

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

    NASA Astrophysics Data System (ADS)

    Scherb, Anke; Papakosta, Panagiota; Straub, Daniel

    2014-05-01

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

  10. Bayesian network for point and diffuse source phosphorus transfer from dairy pastures in South otago, new zealand.

    PubMed

    Lucci, Gina M; Nash, David; McDowell, Richard W; Condron, Leo M

    2014-07-01

    Many factors affect the magnitude of nutrient losses from dairy farm systems. Bayesian Networks (BNs) are an alternative to conventional modeling that can evaluate complex multifactor problems using forward and backward reasoning. A BN of annual total phosphorus (TP) exports was developed for a hypothetical dairy farm in the south Otago region of New Zealand and was used to investigate and integrate the effects of different management options under contrasting rainfall and drainage regimes. Published literature was consulted to quantify the relationships that underpin the BN, with preference given to data and relationships derived from the Otago region. In its default state, the BN estimated loads of 0.34 ± 0.42 kg TP ha for overland flow and 0.30 ± 0.19 kg TP ha for subsurface flow, which are in line with reported TP losses in overland flow (0-1.1 kg TP ha) and in drainage (0.15-2.2 kg TP ha). Site attributes that cannot be managed, like annual rainfall and the average slope of the farm, were found to affect the loads of TP lost from dairy farms. The greatest loads (13.4 kg TP ha) were predicted to occur with above-average annual rainfall (970 mm), where irrigation of farm dairy effluent was managed poorly, and where Olsen P concentrations were above pasture requirements (60 mg kg). Most of this loading was attributed to contributions from overland flow. This study demonstrates the value of using a BN to understand the complex interactions between site variables affecting P loss and their relative importance. PMID:25603084

  11. Using Bayesian networks to explore the role of weather as a potential determinant of disease in pigs

    PubMed Central

    McCormick, B.J.J.; Sanchez-Vazquez, M.J.; Lewis, F.I.

    2013-01-01

    Many pathogens are sensitive to climatic variables and this is reflected in their seasonality of occurrence and transmission. The identification of environmental conditions that influence disease occurrence can be subtle, particularly considering their complex interdependencies in addition to those relationships between climate and disease. Statistical treatment of environmental variables is often dependent on their correlations and thus descriptions of climate are often restricted to means rather than accounting for the more precise aspects (including mean, maximum, minimum, variability). Here we utilize a novel multivariate statistical modelling approach, additive Bayesian network (ABN) analyses, to identify the inter-linkages of different weather variables to better capture short-term environmental conditions that are important drivers of disease. We present a case study that explores weather as a driver of disease in livestock systems. We utilize quality assurance health scheme data on ten major diseases of pigs from 875 finishing pig herds distributed across the United Kingdom over 7 years (2005–2011). We examine the relationship between the occurrence of these pathologies and contemporary weather conditions measured by local meteorological stations. All ten pathologies were associated with at least 2 other pathologies (maximum 6). Three pathologies were associated directly with temperature variables: papular dermatitis, enzootic pneumonia and milk spots. Latitude was strongly associated with multiple pathologies, though associations with longitude were eliminated when clustering for repeated observations of farms was assessed. The identification of relationships between climatic factors and different (potentially related) diseases offers a more comprehensive insight into the complex role of seasonal drivers and herd health status than traditional analytical methods. PMID:23465608

  12. Predicting severity of pathological scarring due to burn injuries: a clinical decision making tool using Bayesian networks.

    PubMed

    Berchialla, Paola; Gangemi, Ezio Nicola; Foltran, Francesca; Haxhiaj, Arber; Buja, Alessandra; Lazzarato, Fulvio; Stella, Maurizio; Gregori, Dario

    2014-06-01

    It is important for clinicians to understand which are the clinical signs, the patient characteristics and the procedures that are related with the occurrence of hypertrophic burn scars in order to carry out a possible prognostic assessment. Providing clinicians with an easy-to- use tool for predicting the risk of pathological scars. A total of 703 patients with 2440 anatomical burn sites who were admitted to the Department of Plastic and Reconstructive Surgery, Burn Center of the Traumatological Hospital in Torino between January 1994 and May 2006 were included in the analysis. A Bayesian network (BN) model was implemented. The probability of developing a hypertrophic scar was evaluated on a number of scenarios. The error rate of the BN model was assessed internally and it was equal to 24·83%. While classical statistical method as logistic models can infer only which variables are related to the final outcome, the BN approach displays a set of relationships between the final outcome (scar type) and the explanatory covariates (patient's age and gender, burn surface area, full-thickness burn surface area, burn anatomical area and wound-healing time; burn treatment options such as advanced dressings, type of surgical approach, number of surgical procedures, type of skin graft, excision and coverage timing). A web-based interface to handle the BN model was developed on the website www.pubchild.org (burns header). Clinicians who registered at the website could submit their data in order to get from the BN model the predicted probability of observing a pathological scar type. PMID:22958613

  13. Evaluating nonindigenous species management in a Bayesian networks derived relative risk framework for Padilla Bay, WA, USA.

    PubMed

    Herring, Carlie E; Stinson, Jonah; Landis, Wayne G

    2015-10-01

    Many coastal regions are encountering issues with the spread of nonindigenous species (NIS). In this study, we conducted a regional risk assessment using a Bayesian network relative risk model (BN-RRM) to analyze multiple vectors of NIS introductions to Padilla Bay, Washington, a National Estuarine Research Reserve. We had 3 objectives in this study. The 1st objective was to determine whether the BN-RRM could be used to calculate risk from NIS introductions for Padilla Bay. Our 2nd objective was to determine which regions and endpoints were at greatest risk from NIS introductions. Our 3rd objective was to incorporate a management option into the model and predict endpoint risk if it were to be implemented. Eradication can occur at different stages of NIS invasions, such as the elimination of these species before being introduced to the habitat or removal of the species after settlement. We incorporated the ballast water treatment management scenario into the model, observed the risk to the endpoints, and compared this risk with the initial risk estimates. The model results indicated that the southern portion of the bay was at greatest risk because of NIS. Changes in community composition, Dungeness crab, and eelgrass were the endpoints most at risk from NIS introductions. The currents node, which controls the exposure of NIS to the bay from the surrounding marine environment, was the parameter that had the greatest influence on risk. The ballast water management scenario displayed an approximate 1% reduction in risk in this Padilla Bay case study. The models we developed provide an adaptable template for decision makers interested in managing NIS in other coastal regions and large bodies of water. PMID:25845995

  14. Non-Invasive Clinical Parameters for the Prediction of Urodynamic Bladder Outlet Obstruction: Analysis Using Causal Bayesian Networks

    PubMed Central

    Kim, Myong; Cheeti, Abhilash; Yoo, Changwon; Choo, Minsoo; Paick, Jae-Seung; Oh, Seung-June

    2014-01-01

    Purpose To identify non-invasive clinical parameters to predict urodynamic bladder outlet obstruction (BOO) in patients with benign prostatic hyperplasia (BPH) using causal Bayesian networks (CBN). Subjects and Methods From October 2004 to August 2013, 1,381 eligible BPH patients with complete data were selected for analysis. The following clinical variables were considered: age, total prostate volume (TPV), transition zone volume (TZV), prostate specific antigen (PSA), maximum flow rate (Qmax), and post-void residual volume (PVR) on uroflowmetry, and International Prostate Symptom Score (IPSS). Among these variables, the independent predictors of BOO were selected using the CBN model. The predictive performance of the CBN model using the selected variables was verified through a logistic regression (LR) model with the same dataset. Results Mean age, TPV, and IPSS were 6.2 (±7.3, SD) years, 48.5 (±25.9) ml, and 17.9 (±7.9), respectively. The mean BOO index was 35.1 (±25.2) and 477 patients (34.5%) had urodynamic BOO (BOO index ≥40). By using the CBN model, we identified TPV, Qmax, and PVR as independent predictors of BOO. With these three variables, the BOO prediction accuracy was 73.5%. The LR model showed a similar accuracy (77.0%). However, the area under the receiver operating characteristic curve of the CBN model was statistically smaller than that of the LR model (0.772 vs. 0.798, p = 0.020). Conclusions Our study demonstrated that TPV, Qmax, and PVR are independent predictors of urodynamic BOO. PMID:25397903

  15. Evaluation of the imminence of a tsunami based on real-time seismic source parameter estimates - a Bayesian network approach

    NASA Astrophysics Data System (ADS)

    Blaser, Lilian; Ohrnberger, Matthias; Scherbaum, Frank

    2010-05-01

    Tsunami early warnings are based on co-seismic evidences being the earliest available information from a hazardous earthquake with the potential of causing a tsunami. Evaluations are generally done by applying rules derived from historic observation and making use of seismological expertise regarding regional tectonic contexts, faulting styles, occurrence frequency of large earthquakes and more. However, the co-seismic generation of a tsunami as well as the estimation of a potentially tsunamigenic event is prone to various uncertainties. As Bayesian networks (BNs) allow for integration and quantification of the uncertainties within the framework of probabilistic graphical models, we propose the usage of BNs for evaluating the imminence of a tsunami based on real-time seismic source parameter estimates. Earthquake parameter estimates (including uncertainties) are evaluated in real-time and the probabilities of tsunami threat levels are calculated and updated whenever new co-seismic evidence is available. The fast and efficient method gives an important additional information for the staff members at tsunami warning centers as it provides a probabilistic overview on the imminence of a tsunami for some particular costal region. In our work, we have developed a preliminary BN tsunami warning system for the region of Sumatra by extracting knowledge from a set of formulas describing the physical process from earthquake rupture to sea-floor deformation to tsunami wave propagation and finally shoaling at the coast. The physical knowledge was transformed by ancestral sampling to a synthetic database and thereof BNs were learned for several sites of interest along the Sumatran coast and the fore-arc islands. To determine the conditional probability of the tsunami amplitude a set of seven co-seismic variables was defined: epicenter, centroid, magnitude, hypocentral depth, rupture direction, rupture length and width. We illustrate the advantages of this approach by case

  16. 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

  17. Inferring functional connectivity in MRI using Bayesian network structure learning with a modified PC algorithm.

    PubMed

    Iyer, Swathi P; Shafran, Izhak; Grayson, David; Gates, Kathleen; Nigg, Joel T; Fair, Damien A

    2013-07-15

    Resting state functional connectivity MRI (rs-fcMRI) is a popular technique used to gauge the functional relatedness between regions in the brain for typical and special populations. Most of the work to date determines this relationship by using Pearson's correlation on BOLD fMRI timeseries. However, it has been recognized that there are at least two key limitations to this method. First, it is not possible to resolve the direct and indirect connections/influences. Second, the direction of information flow between the regions cannot be differentiated. In the current paper, we follow-up on recent work by Smith et al. (2011), and apply PC algorithm to both simulated data and empirical data to determine whether these two factors can be discerned with group average, as opposed to single subject, functional connectivity data. When applied on simulated individual subjects, the algorithm performs well determining indirect and direct connection but fails in determining directionality. However, when applied at group level, PC algorithm gives strong results for both indirect and direct connections and the direction of information flow. Applying the algorithm on empirical data, using a diffusion-weighted imaging (DWI) structural connectivity matrix as the baseline, the PC algorithm outperformed the direct correlations. We conclude that, under certain conditions, the PC algorithm leads to an improved estimate of brain network structure compared to the traditional connectivity analysis based on correlations. PMID:23501054

  18. Bayesian Statistics.

    ERIC Educational Resources Information Center

    Meyer, Donald L.

    Bayesian statistical methodology and its possible uses in the behavioral sciences are discussed in relation to the solution of problems in both the use and teaching of fundamental statistical methods, including confidence intervals, significance tests, and sampling. The Bayesian model explains these statistical methods and offers a consistent…

  19. Conjunctions of Jupiter and Saturn

    NASA Astrophysics Data System (ADS)

    Etz, Donald V.

    2000-08-01

    This year's Jupiter-Saturn conjunction is an astronomical event that has been noted in yearbooks, even though it occurred too close to the Sun to be readily visible. Astronomical conjunctions are often loosely defined. Four questions need to be answered: Which two astronomical bodies are involved? What co-ordinate system is used to define the conjunction? From what astronomical body is the event observed? Is the event described apparent or real? Jupiter-Saturn conjunctions are among the most impressive such events, occurring about every 20 years and involving the two outermost visible planets. The timing of apparent retrograde motion of the two planets can also produce an apparent triple conjunction, as happened in 1980-81. Triple conjunctions occur at irregular multiples of the conjunction interval. Occasionally a close grouping of Jupiter, Saturn, and Mars is also referred to as a triple conjunction. Successive Jupiter-Saturn conjunctions, slightly more than 240 deg apart, develop an interesting pattern as they step around the ecliptic, a rotating triangle with legs about 120 deg apart. In relation to the fixed stars, it takes about 854 or 913 years for the event to return to a point near the start of the sequence. Some scholars have given it as 960 years. Relative to a precessing co-ordinate system, it takes about 800 (794) years. Medieval scholars in Europe and the Near East were impressed by the above conjunction sequence, and tried to relate it to major events in world history. The earliest known attempts come from 8th century Baghdad, but their explanation may have originated in Iran (3rd to 7th centuries). It persisted in Europe into the 17th century.

  20. Conjunction Illusions and Conjunction Fallacies in Episodic Memory

    PubMed Central

    Brainerd, C. J.; Holliday, R. E.; Nakamura, K.; Reyna, V. F.

    2014-01-01

    Recent research on the overdistribution principle implies that episodic memory is infected by conjunction illusions. These are instances in which an item that was presented in a single context (e.g., List 1) is falsely remembered as having been presented in multiple contexts (e.g., List 1 and List 2). Robust conjunction illusions were detected in source-monitoring designs in which conjunctive probes (Was bagpipe presented on List 1 and List 2?) were added to the traditional nonconjunctive probes (Was bagpipe presented on List 1?). In Experiment 1, the levels of those illusions were comparable to what would be expected on the basis of results from prior overdistribution experiments. In Experiments 2 and 3, conjunction illusions were neither eliminated nor reduced by a manipulation that should have had such effects if the illusions are by-products of subjective differences in retrieved memory support. Also, conjunction illusions sometimes rose to the level of conjunction fallacies: In certain conditions, subjects thought that items were more likely to have occurred in all the presentation contexts than in any single context, which is impossible. Two general approaches to explaining overdistribution, representational accounts and retrieval accounts, are considered. PMID:24911136

  1. Mars solar conjunction prediction modeling

    NASA Astrophysics Data System (ADS)

    Srivastava, Vineet K.; Kumar, Jai; Kulshrestha, Shivali; Kushvah, Badam Singh

    2016-01-01

    During the Mars solar conjunction, telecommunication and tracking between the spacecraft and the Earth degrades significantly. The radio signal degradation depends on the angular separation between the Sun, Earth and probe (SEP), the signal frequency band and the solar activity. All radiometric tracking data types display increased noise and signatures for smaller SEP angles. Due to scintillation, telemetry frame errors increase significantly when solar elongation becomes small enough. This degradation in telemetry data return starts at solar elongation angles of around 5° at S-band, around 2° at X-band and about 1° at Ka-band. This paper presents a mathematical model for predicting Mars superior solar conjunction for any Mars orbiting spacecraft. The described model is simulated for the Mars Orbiter Mission which experienced Mars solar conjunction during May-July 2015. Such a model may be useful to flight projects and design engineers in the planning of Mars solar conjunction operational scenarios.

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

    PubMed

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

    2014-12-01

    Freshwater ponds deliver a broad range of ecosystem services (ESS). Taking into account this broad range of services to attain cost-effective ESS delivery is an important challenge facing integrated pond management. To assess the strengths and weaknesses of an ESS approach to support decisions in integrated pond management, we applied it on a small case study in Flanders, Belgium. A Bayesian belief network model was developed to assess ESS delivery under three alternative pond management scenarios: intensive fish farming (IFF), extensive fish farming (EFF) and nature conservation management (NCM). A probabilistic cost-benefit analysis was performed that includes both costs associated with pond management practices and benefits associated with ESS delivery. Whether or not a particular ESS is included in the analysis affects the identification of the most preferable management scenario by the model. Assessing the delivery of a more complete set of ecosystem services tends to shift the results away from intensive management to more biodiversity-oriented management scenarios. The proposed methodology illustrates the potential of Bayesian belief networks. BBNs facilitate knowledge integration and their modular nature encourages future model expansion to more encompassing sets of services. Yet, we also illustrate the key weaknesses of such exercises, being that the choice whether or not to include a particular ecosystem service may determine the suggested optimal management practice. PMID:25005053

  3. Bayesian networks modelling in support to cross cutting analysis of water supply and sanitation in developing countries

    NASA Astrophysics Data System (ADS)

    Dondeynaz, C.; López Puga, J.; Carmona Moreno, C.

    2013-02-01

    Despite the efforts made towards the millennium goals targets during the last decade, access to improved water supply or basic sanitation remains still not accessible for millions of people across the world. This paper proposes a set of models that use 25 key variables from the WatSan4Dev dataset and country profiles involving Water Supply and Sanitation (Dondeynaz et al., 2012). This paper proposes the use of Bayesian Network modelling methods because adapted to the management of non-normal distribution, and integrate a qualitative approach for data analysis. They also offer the advantage to integrate preliminary knowledge into the probabilistic models. The statistical performance of the proposed models ranges between 80 and 95% which is very satisfactory taking into account the strong heterogeneity of variables. Probabilistic scenarios run from the models allow a quantification of the relationships between human development, external support, governance aspects, economic activities and Water Supply and Sanitation (WSS) access. According to models proposed in this paper, a strong poverty reduction will induce an increment of the WSS access equal to 75-76% through: (1) the organisation of on-going urbanisation process to avoid slums development; and, (2) the improvement of health care for instance for children. On one side, improving governance, such as institutional efficiency, capacities to make and apply rules or control of corruption will also have a positive impact on WSS sustainable development. The first condition for an increment of the WSS access remains of course an improvement of the economic development with an increment of household income. Moreover, a significant country environmental commitment associated with civil society freedom of expression constitutes a favourable environment for sustainable WSS services delivery. Intensive agriculture through irrigation practises also appears as a mean for sustainable WSS thanks to multi-uses and

  4. Bayesian networks modelling in support to cross-cutting analysis of water supply and sanitation in developing countries

    NASA Astrophysics Data System (ADS)

    Dondeynaz, C.; López Puga, J.; Carmona Moreno, C.

    2013-09-01

    Despite the efforts made towards the Millennium Development Goals targets during the last decade, improved access to water supply or basic sanitation still remains unavailable for millions of people across the world. This paper proposes a set of models that use 25 key variables and country profiles from the WatSan4Dev data set involving water supply and sanitation (Dondeynaz et al., 2012). This paper suggests the use of Bayesian network modelling methods because they are more easily adapted to deal with non-normal distributions, and integrate a qualitative approach for data analysis. They also offer the advantage of integrating preliminary knowledge into the probabilistic models. The statistical performance of the proposed models ranges between 20 and 5% error rates, which are very satisfactory taking into account the strong heterogeneity of variables. Probabilistic scenarios run from the models allow an assessment of the relationships between human development, external support, governance aspects, economic activities and water supply and sanitation (WSS) access. According to models proposed in this paper, gaining a strong poverty reduction will require the WSS access to reach 75-76% through: (1) the management of ongoing urbanisation processes to avoid slums development; and (2) the improvement of health care, for instance for children. Improving governance, such as institutional efficiency, capacities to make and apply rules, or control of corruption is positively associated with WSS sustainable development. The first condition for an increment of the HDP (human development and poverty) remains of course an improvement of the economic conditions with higher household incomes. Moreover, a significant country commitment to the environment, associated with civil society freedom of expression constitutes a favourable setting for sustainable WSS services delivery. Intensive agriculture using irrigation practises also appears as a mean for sustainable WSS thanks to

  5. Language Teaching: Prepositions and Conjunctives.

    ERIC Educational Resources Information Center

    Hobson, Arline B.

    This bulletin is the first of three designed to give detailed help on fostering language competence in 4- to 6-year-old school children. The bulletin introduces the teacher to a group of prepositions and conjunctions (chosen from the Dolch Basic Sight Vocabulary List of 220 Words) which are important to the meaning of sentences. The list was…

  6. Quantum Phenomenology of Conjunction Fallacy

    NASA Astrophysics Data System (ADS)

    Cheon, Taksu; Takahashi, Taiki

    2012-10-01

    A quantum-like description of human decision process is developed, and a heuristic argument supporting the theory as sound phenomenology is given. It is shown to be capable of quantitatively explaining the conjunction fallacy in the same footing as the violation of sure-thing principle.

  7. Analysis of regional scale risk of whirling disease in populations of Colorado and Rio Grande cutthroat trout using a Bayesian belief network model.

    PubMed

    Ayre, Kimberley Kolb; Caldwell, Colleen A; Stinson, Jonah; Landis, Wayne G

    2014-09-01

    Introduction and spread of the parasite Myxobolus cerebralis, the causative agent of whirling disease, has contributed to the collapse of wild trout populations throughout the intermountain west. Of concern is the risk the disease may have on conservation and recovery of native cutthroat trout. We employed a Bayesian belief network to assess probability of whirling disease in Colorado River and Rio Grande cutthroat trout (Oncorhynchus clarkii pleuriticus and Oncorhynchus clarkii virginalis, respectively) within their current ranges in the southwest United States. Available habitat (as defined by gradient and elevation) for intermediate oligochaete worm host, Tubifex tubifex, exerted the greatest influence on the likelihood of infection, yet prevalence of stream barriers also affected the risk outcome. Management areas that had the highest likelihood of infected Colorado River cutthroat trout were in the eastern portion of their range, although the probability of infection was highest for populations in the southern, San Juan subbasin. Rio Grande cutthroat trout had a relatively low likelihood of infection, with populations in the southernmost Pecos management area predicted to be at greatest risk. The Bayesian risk assessment model predicted the likelihood of whirling disease infection from its principal transmission vector, fish movement, and suggested that barriers may be effective in reducing risk of exposure to native trout populations. Data gaps, especially with regard to location of spawning, highlighted the importance in developing monitoring plans that support future risk assessments and adaptive management for subspecies of cutthroat trout. PMID:24660663

  8. Analysis of regional scale risk to whirling disease in populations of Colorado and Rio Grande cutthroat trout using Bayesian belief network model

    USGS Publications Warehouse

    Kolb Ayre, Kimberley; Caldwell, Colleen A.; Stinson, Jonah; Landis, Wayne G.

    2014-01-01

    Introduction and spread of the parasite Myxobolus cerebralis, the causative agent of whirling disease, has contributed to the collapse of wild trout populations throughout the intermountain west. Of concern is the risk the disease may have on conservation and recovery of native cutthroat trout. We employed a Bayesian belief network to assess probability of whirling disease in Colorado River and Rio Grande cutthroat trout (Oncorhynchus clarkii pleuriticus and Oncorhynchus clarkii virginalis, respectively) within their current ranges in the southwest United States. Available habitat (as defined by gradient and elevation) for intermediate oligochaete worm host, Tubifex tubifex, exerted the greatest influence on the likelihood of infection, yet prevalence of stream barriers also affected the risk outcome. Management areas that had the highest likelihood of infected Colorado River cutthroat trout were in the eastern portion of their range, although the probability of infection was highest for populations in the southern, San Juan subbasin. Rio Grande cutthroat trout had a relatively low likelihood of infection, with populations in the southernmost Pecos management area predicted to be at greatest risk. The Bayesian risk assessment model predicted the likelihood of whirling disease infection from its principal transmission vector, fish movement, and suggested that barriers may be effective in reducing risk of exposure to native trout populations. Data gaps, especially with regard to location of spawning, highlighted the importance in developing monitoring plans that support future risk assessments and adaptive management for subspecies of cutthroat trout.

  9. Distinguishing Parkinson's disease from atypical parkinsonian syndromes using PET data and a computer system based on support vector machines and Bayesian networks

    PubMed Central

    Segovia, Fermín; Illán, Ignacio A.; Górriz, Juan M.; Ramírez, Javier; Rominger, Axel; Levin, Johannes

    2015-01-01

    Differentiating between Parkinson's disease (PD) and atypical parkinsonian syndromes (APS) is still a challenge, specially at early stages when the patients show similar symptoms. During last years, several computer systems have been proposed in order to improve the diagnosis of PD, but their accuracy is still limited. In this work we demonstrate a full automatic computer system to assist the diagnosis of PD using 18F-DMFP PET data. First, a few regions of interest are selected by means of a two-sample t-test. The accuracy of the selected regions to separate PD from APS patients is then computed using a support vector machine classifier. The accuracy values are finally used to train a Bayesian network that can be used to predict the class of new unseen data. This methodology was evaluated using a database with 87 neuroimages, achieving accuracy rates over 78%. A fair comparison with other similar approaches is also provided. PMID:26594165

  10. Distinguishing Parkinson's disease from atypical parkinsonian syndromes using PET data and a computer system based on support vector machines and Bayesian networks.

    PubMed

    Segovia, Fermín; Illán, Ignacio A; Górriz, Juan M; Ramírez, Javier; Rominger, Axel; Levin, Johannes

    2015-01-01

    Differentiating between Parkinson's disease (PD) and atypical parkinsonian syndromes (APS) is still a challenge, specially at early stages when the patients show similar symptoms. During last years, several computer systems have been proposed in order to improve the diagnosis of PD, but their accuracy is still limited. In this work we demonstrate a full automatic computer system to assist the diagnosis of PD using (18)F-DMFP PET data. First, a few regions of interest are selected by means of a two-sample t-test. The accuracy of the selected regions to separate PD from APS patients is then computed using a support vector machine classifier. The accuracy values are finally used to train a Bayesian network that can be used to predict the class of new unseen data. This methodology was evaluated using a database with 87 neuroimages, achieving accuracy rates over 78%. A fair comparison with other similar approaches is also provided. PMID:26594165

  11. Using Current and Historic Climate Data and Bayesian Belief Networks to Predict Optimum Satellite Image Acquisition Periods for Detecting Cheatgrass on the Snake River Plain, Idaho

    NASA Astrophysics Data System (ADS)

    Rope, R. C.; Ames, D. P.; Jerry, T. D.; Cherry, S. J.

    2005-12-01

    Invasive plant species, such as Bromus tectorum (cheatgrass), cost the United States over $36 billion per year and have encroached upon over 100 million acres while impacting range site productivity, disturbing wildlife habitat, altering the wildland fire regime and frequencies, and reducing biodiversity. Because of these adverse impacts, federal, tribal, state, and county land managers are faced with the challenge of prevention, early detection, management, and monitoring of invasive plants. Often these managers rely on the analysis of remotely sensed imagery as part of their management plan. However, it's difficult to predict specific phenological events that allow for the spectral discrimination of invasive species using only remotely sensed imagery. To address this issue tools are being developed to model and view optimal periods to collect high spatial and/or spectral resolution remotely sensed data for refined detection and mapping of invasive species and for use as a decision support tool for land managers. These tools involve the integration of historic and current climate data (cumulative growing days and precipitation) satellite imagery (MODIS) and Bayesian Belief Networks, and a web ArcIMS application to distribute the information. The general approach is to issue an initial forecast early in the year based on the previous years' data. As the year progresses, air temperature, precipitation and newly acquired low resolution MODIS satellite imagery will be used to update the prediction. Updating will be accomplished using a Bayesian Belief Network model that indicates the probabilistic relationships between prior years' conditions and those of the current year. These tools have specific application in providing a means for which land managers can efficiently and effectively detect, map, and monitor invasive plant species, specifically cheatgrass, in western rangelands. This information can then be integrated into management studies and plans to help land

  12. Bayesian learning

    NASA Technical Reports Server (NTRS)

    Denning, Peter J.

    1989-01-01

    In 1983 and 1984, the Infrared Astronomical Satellite (IRAS) detected 5,425 stellar objects and measured their infrared spectra. In 1987 a program called AUTOCLASS used Bayesian inference methods to discover the classes present in these data and determine the most probable class of each object, revealing unknown phenomena in astronomy. AUTOCLASS has rekindled the old debate on the suitability of Bayesian methods, which are computationally intensive, interpret probabilities as plausibility measures rather than frequencies, and appear to depend on a subjective assessment of the probability of a hypothesis before the data were collected. Modern statistical methods have, however, recently been shown to also depend on subjective elements. These debates bring into question the whole tradition of scientific objectivity and offer scientists a new way to take responsibility for their findings and conclusions.

  13. Efficacy of the Additional Neoadjuvant Chemotherapy to Concurrent Chemoradiotherapy for Patients with Locoregionally Advanced Nasopharyngeal Carcinoma: a Bayesian Network Meta-analysis of Randomized Controlled Trials

    PubMed Central

    Chen, Yu-Pei; Guo, Rui; Liu, Na; Liu, Xu; Mao, Yan-Ping; Tang, Ling-Long; Zhou, Guan-Qun; Lin, Ai-Hua; Sun, Ying; Ma, Jun

    2015-01-01

    Background: Due to the lack of studies, it remains unclear whether the additional neoadjuvant chemotherapy (NACT) to concurrent chemoradiotherapy (CCRT) is superior to CCRT alone for locoregionally advanced nasopharyngeal carcinoma (NPC). The main objective of this Bayesian network meta-analysis was to determine the efficacy of NACT+CCRT as compared with CCRT alone. Methods: We comprehensively searched databases and extracted data from randomized controlled trials involving NPC patients who received NACT+CCRT, CCRT, NACT+radiotherapy (RT), or RT. Overall survival (OS) with hazard ratio (HR), and locoregional recurrence rate (LRR) and distant metastasis rate (DMR) with relative risks (RRs), were concerned. Results: Nine trials involving 1988 patients were analyzed. In the network meta-analysis, there was significant benefit of NACT+CCRT over CCRT for DMR (RR=0.54, 95% credible interval [CrI]=0.27-0.94). However, NACT+CCRT had a tendency to worsen locoregional control significantly as compared with CCRT (RR =1.71, 95%CrI =0.94-2.84), and no significant improvement in OS was found (HR =0.73, 95%CrI=0.40-1.23). Conclusions: NACT+CCRT is associated with reduced distant failure as compared with CCRT alone, and whether the additional NACT can improve survival for locoregionally advanced NPC should be further explored. Optimizing regimens and identifying patients at high risk of metastasis may enhance the efficacy of NACT+CCRT. PMID:26284140

  14. Projection of future climate change conditions using IPCC simulations, neural networks and Bayesian statistics. Part 2: Precipitation mean state and seasonal cycle in South America

    NASA Astrophysics Data System (ADS)

    Boulanger, Jean-Philippe; Martinez, Fernando; Segura, Enrique C.

    2007-02-01

    Evaluating the response of climate to greenhouse gas forcing is a major objective of the climate community, and the use of large ensemble of simulations is considered as a significant step toward that goal. The present paper thus discusses a new methodology based on neural network to mix ensemble of climate model simulations. Our analysis consists of one simulation of seven Atmosphere Ocean Global Climate Models, which participated in the IPCC Project and provided at least one simulation for the twentieth century (20c3m) and one simulation for each of three SRES scenarios: A2, A1B and B1. Our statistical method based on neural networks and Bayesian statistics computes a transfer function between models and observations. Such a transfer function was then used to project future conditions and to derive what we would call the optimal ensemble combination for twenty-first century climate change projections. Our approach is therefore based on one statement and one hypothesis. The statement is that an optimal ensemble projection should be built by giving larger weights to models, which have more skill in representing present climate conditions. The hypothesis is that our method based on neural network is actually weighting the models that way. While the statement is actually an open question, which answer may vary according to the region or climate signal under study, our results demonstrate that the neural network approach indeed allows to weighting models according to their skills. As such, our method is an improvement of existing Bayesian methods developed to mix ensembles of simulations. However, the general low skill of climate models in simulating precipitation mean climatology implies that the final projection maps (whatever the method used to compute them) may significantly change in the future as models improve. Therefore, the projection results for late twenty-first century conditions are presented as possible projections based on the “state-of-the-art” of

  15. A Bayesian network based framework for real-time crash prediction on the basic freeway segments of urban expressways.

    PubMed

    Hossain, Moinul; Muromachi, Yasunori

    2012-03-01

    The concept of measuring the crash risk for a very short time window in near future is gaining more practicality due to the recent advancements in the fields of information systems and traffic sensor technology. Although some real-time crash prediction models have already been proposed, they are still primitive in nature and require substantial improvements to be implemented in real-life. This manuscript investigates the major shortcomings of the existing models and offers solutions to overcome them with an improved framework and modeling method. It employs random multinomial logit model to identify the most important predictors as well as the most suitable detector locations to acquire data to build such a model. Afterwards, it applies Bayesian belief net (BBN) to build the real-time crash prediction model. The model has been constructed using high resolution detector data collected from Shibuya 3 and Shinjuku 4 expressways under the jurisdiction of Tokyo Metropolitan Expressway Company Limited, Japan. It has been specifically built for the basic freeway segments and it predicts the chance of formation of a hazardous traffic condition within the next 4-9 min for a particular 250 meter long road section. The performance evaluation results reflect that at an average threshold value the model is able to successful classify 66% of the future crashes with a false alarm rate less than 20%. PMID:22269521

  16. A Bayesian network approach to predicting nest presence of thefederally-threatened piping plover (Charadrius melodus)using barrier island features

    USGS Publications Warehouse

    Gieder, Katherina D.; Karpanty, Sarah M.; Frasera, James D.; Catlin, Daniel H.; Gutierrez, Benjamin T.; Plant, Nathaniel G.; Turecek, Aaron M.; Thieler, E. Robert

    2014-01-01

    Sea-level rise and human development pose significant threats to shorebirds, particularly for species that utilize barrier island habitat. The piping plover (Charadrius melodus) is a federally-listed shorebird that nests on barrier islands and rapidly responds to changes in its physical environment, making it an excellent species with which to model how shorebird species may respond to habitat change related to sea-level rise and human development. The uncertainty and complexity in predicting sea-level rise, the responses of barrier island habitats to sea-level rise, and the responses of species to sea-level rise and human development necessitate a modelling approach that can link species to the physical habitat features that will be altered by changes in sea level and human development. We used a Bayesian network framework to develop a model that links piping plover nest presence to the physical features of their nesting habitat on a barrier island that is impacted by sea-level rise and human development, using three years of data (1999, 2002, and 2008) from Assateague Island National Seashore in Maryland. Our model performance results showed that we were able to successfully predict nest presence given a wide range of physical conditions within the model’s dataset. We found that model predictions were more successful when the range of physical conditions included in model development was varied rather than when those physical conditions were narrow. We also found that all model predictions had fewer false negatives (nests predicted to be absent when they were actually present in the dataset) than false positives (nests predicted to be present when they were actually absent in the dataset), indicating that our model correctly predicted nest presence better than nest absence. These results indicated that our approach of using a Bayesian network to link specific physical features to nest presence will be useful for modelling impacts of sea-level rise- or human

  17. Using a Bayesian Network to predict shore-line change vulnerability to sea-level rise for the coasts of the United States

    USGS Publications Warehouse

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

    2014-01-01

    Sea-level rise is an ongoing phenomenon that is expected to continue and is projected to have a wide range of effects on coastal environments and infrastructure during the 21st century and beyond. Consequently, there is a need to assemble relevant datasets and to develop modeling or other analytical approaches to evaluate the likelihood of particular sea-level rise impacts, such as coastal erosion, and to inform coastal management decisions with this information. This report builds on previous work that compiled oceanographic and geomorphic data as part of the U.S. Geological Survey’s Coastal Vulnerability Index (CVI) for the U.S. Atlantic coast, and developed a Bayesian Network to predict shoreline-change rates based on sea-level rise plus variables that describe the hydrodynamic and geologic setting. This report extends the previous analysis to include the Gulf and Pacific coasts of the continental United States and Alaska and Hawaii, which required using methods applied to the USGS CVI dataset to extract data for these regions. The Bayesian Network converts inputs that include observations of local rates of relative sea-level change, mean wave height, mean tide range, a geomorphic classification, coastal slope, and observed shoreline-change rates to calculate the probability of the shoreline-erosion rate exceeding a threshold level of 1 meter per year for the coasts of the United States. The calculated probabilities were compared to the historical observations of shoreline change to evaluate the hindcast success rate of the most likely probability of shoreline change. Highest accuracy was determined for the coast of Hawaii (98 percent success rate) and lowest accuracy was determined for the Gulf of Mexico (34 percent success rate). The minimum success rate rose to nearly 80 percent (Atlantic and Gulf coasts) when success included shoreline-change outcomes that were adjacent to the most likely outcome. Additionally, the probabilistic approach determines the

  18. Bayesian belief network for CO2 leak detection by near-surface flux rates for CO2 and perfluorocarbon (PFC) tracer

    NASA Astrophysics Data System (ADS)

    Yang, Y.; Small, M. J.; Ogretim, E.; Gray, D. D.; Bromhal, G. S.; Strazisar, B. R.; Wells, A. W.

    2010-12-01

    To incorporate the use of multiple geologic sequestration monitoring techniques, a Bayesian Belief Network (BBN) for leak detection inference is applied to integrate the information provided by different techniques deployed at a site. In this study, two monitoring methods, near-surface soil CO2 flux and perfluorocarbon (PFC) tracer concentration, are included in the BBN. First, possible near-surface flux rates for CO2 and PFC tracer as a function of distance from a leakage point are simulated by TOUGH2, given different leakage rates and permeabilities. Then, the natural near-surface CO2 flux and background PFC tracer concentration measured at the Zero Emission Research and Technology (ZERT) site are used to determine critical values for leak inference and to calculate the probabilities of leak detection given a monitoring network. A BBN of leak detection is established by combing the TOUGH2 simulations and the background characterization of near-surface CO2 flux and PFC tracer at the sequestration site. The results show a positive correlation between the detection abilities of PFC tracer and soil CO2 flux, but the PFC tracer is more sensitive for detecting a leak in most cases. The BBN of leak detection including both soil CO2 flux and PFC tracer concentration gives an integrated probability estimation of leak detection for different permeability and leakage rates for a given monitoring network. A BBN developed using the proposed methodology can be used to help site engineers and decision makers to evaluate leakage signals and the risk of undetected leakage, given a suite of monitoring techniques and site conditions.

  19. Multivariate Analysis of the Determinants of the End-Product Quality of Manure-Based Composts and Vermicomposts Using Bayesian Network Modelling

    PubMed Central

    Faverial, Julie; Cornet, Denis; Paul, Jacky

    2016-01-01

    Previous studies indicated that the quality of tropical composts is poorer than that of composts produced in temperate regions. The aim of this study was to test the type of manure, the use of co-composting with green waste, and the stabilization method for their ability to improve compost quality in the tropics. We produced 68 composts and vermicomposts that were analysed for their C, lignin and NPK contents throughout the composting process. Bayesian networks were used to assess the mechanisms controlling compost quality. The concentration effect, for C and lignin, and the initial blend quality, for NPK content, were the main factors affecting compost quality. Cattle manure composts presented the highest C and lignin contents, and poultry litter composts exhibited the highest NPK content. Co-composting improved quality by enhancing the concentration effect, which reduced the impact of C and nutrient losses. Vermicomposting did not improve compost quality; co-composting without earthworms thus appears to be a suitable stabilization method under the conditions of this study because it produced high quality composts and is easier to implement. PMID:27314950

  20. Multivariate Analysis of the Determinants of the End-Product Quality of Manure-Based Composts and Vermicomposts Using Bayesian Network Modelling.

    PubMed

    Faverial, Julie; Cornet, Denis; Paul, Jacky; Sierra, Jorge

    2016-01-01

    Previous studies indicated that the quality of tropical composts is poorer than that of composts produced in temperate regions. The aim of this study was to test the type of manure, the use of co-composting with green waste, and the stabilization method for their ability to improve compost quality in the tropics. We produced 68 composts and vermicomposts that were analysed for their C, lignin and NPK contents throughout the composting process. Bayesian networks were used to assess the mechanisms controlling compost quality. The concentration effect, for C and lignin, and the initial blend quality, for NPK content, were the main factors affecting compost quality. Cattle manure composts presented the highest C and lignin contents, and poultry litter composts exhibited the highest NPK content. Co-composting improved quality by enhancing the concentration effect, which reduced the impact of C and nutrient losses. Vermicomposting did not improve compost quality; co-composting without earthworms thus appears to be a suitable stabilization method under the conditions of this study because it produced high quality composts and is easier to implement. PMID:27314950

  1. Comprehensive analysis of regional human-driven environmental change with multitemporal remote sensing images using observed object-specified dynamic Bayesian network

    NASA Astrophysics Data System (ADS)

    Chen, Hao; Hua, Yi; Ren, Qinglong; Zhang, Ye

    2016-01-01

    Traditional remote sensing change-detection algorithms only generate change-detection map and few quantitative evaluation indicators as the results, but they are unable to provide comprehensive analysis and further understanding of the detected changes. Aiming to assess regional development, we develop a comprehensive analysis method for human-driven environmental change by multitemporal remote sensing images. In order to adapt to analyze the time-varying multiple changed objects, an observed object-specified dynamic Bayesian network (i.e., OOS-DBN) is first proposed to adjust DBN structure and variables. Using semantic analysis for the relationship between multiple changed objects and regional development, all levels of situations and evidences (i.e., detected attributes of changed objects) are extracted as hidden variables and observed variables and inputted to OOS-DBN. Furthermore, conditional probabilities are computed by levels and time slices in OOS-DBN, resulting in the comprehensive analysis results. The experiments on the coastal region in Huludao, China, from 2003 to 2014 demonstrate that comprehensive analysis of changes reflecting that reclamation, construction of infrastructure, and New Huludao port contributed to the regional development. During four time slices, this region experienced rapid and medium-speed development, whose corresponding probabilities are 0.90, 0.87, 0.41, and 0.54, respectively, which is consistent with our field surveys.

  2. Development of intelligent systems based on Bayesian regularization network and neuro-fuzzy models for mass detection in mammograms: A comparative analysis.

    PubMed

    Mahersia, Hela; Boulehmi, Hela; Hamrouni, Kamel

    2016-04-01

    Female breast cancer is the second most common cancer in the world. Several efforts in artificial intelligence have been made to help improving the diagnostic accuracy at earlier stages. However, the identification of breast abnormalities, like masses, on mammographic images is not a trivial task, especially for dense breasts. In this paper we describe our novel mass detection process that includes three successive steps of enhancement, characterization and classification. The proposed enhancement system is based mainly on the analysis of the breast texture. First of all, a filtering step with morphological operators and soft thresholding is achieved. Then, we remove from the filtered breast region, all the details that may interfere with the eventual masses, including pectoral muscle and galactophorous tree. The pixels belonging to this tree will be interpolated and replaced by the average of the neighborhood. In the characterization process, measurement of the Gaussian density in the wavelet domain allows the segmentation of the masses. Finally, a comparative classification mechanism based on the Bayesian regularization back-propagation networks and ANFIS techniques is proposed. The tests were conducted on the MIAS database. The results showed the robustness of the proposed enhancement method. PMID:26831269

  3. Linking urbanization to the Biological Condition Gradient (BCG) for stream ecosystems in the Northeastern United States using a Bayesian network approach

    USGS Publications Warehouse

    Kashuba, Roxolana; McMahon, Gerard; Cuffney, Thomas F.; Qian, Song; Reckhow, Kenneth; Gerritsen, Jeroen; Davies, Susan

    2012-01-01

    In realization of the aforementioned advantages, a Bayesian network model was constructed to characterize the effect of urban development on aquatic macroinvertebrate stream communities through three simultaneous, interacting ecological pathways affecting stream hydrology, habitat, and water quality across watersheds in the Northeastern United States. This model incorporates both empirical data and expert knowledge to calculate the probabilities of attaining desired aquatic ecosystem conditions under different urban stress levels, environmental conditions, and management options. Ecosystem conditions are characterized in terms of standardized Biological Condition Gradient (BCG) management endpoints. This approach to evaluating urban development-induced perturbations in watersheds integrates statistical and mechanistic perspectives, different information sources, and several ecological processes into a comprehensive description of the system that can be used to support decision making. The completed model can be used to infer which management actions would lead to the highest likelihood of desired BCG tier achievement. For example, if best management practices (BMP) were implemented in a highly urbanized watershed to reduce flashiness to medium levels and specific conductance to low levels, the stream would have a 70-percent chance of achieving BCG Tier 3 or better, relative to a 24-percent achievement likelihood for unmanaged high urban land cover. Results are reported probabilistically to account for modeling uncertainty that is inherent in sources such as natural variability and model simplification error.

  4. A methodology for risk analysis based on hybrid Bayesian networks: application to the regasification system of liquefied natural gas onboard a floating storage and regasification unit.

    PubMed

    Martins, Marcelo Ramos; Schleder, Adriana Miralles; Droguett, Enrique López

    2014-12-01

    This article presents an iterative six-step risk analysis methodology based on hybrid Bayesian networks (BNs). In typical risk analysis, systems are usually modeled as discrete and Boolean variables with constant failure rates via fault trees. Nevertheless, in many cases, it is not possible to perform an efficient analysis using only discrete and Boolean variables. The approach put forward by the proposed methodology makes use of BNs and incorporates recent developments that facilitate the use of continuous variables whose values may have any probability distributions. Thus, this approach makes the methodology particularly useful in cases where the available data for quantification of hazardous events probabilities are scarce or nonexistent, there is dependence among events, or when nonbinary events are involved. The methodology is applied to the risk analysis of a regasification system of liquefied natural gas (LNG) on board an FSRU (floating, storage, and regasification unit). LNG is becoming an important energy source option and the world's capacity to produce LNG is surging. Large reserves of natural gas exist worldwide, particularly in areas where the resources exceed the demand. Thus, this natural gas is liquefied for shipping and the storage and regasification process usually occurs at onshore plants. However, a new option for LNG storage and regasification has been proposed: the FSRU. As very few FSRUs have been put into operation, relevant failure data on FSRU systems are scarce. The results show the usefulness of the proposed methodology for cases where the risk analysis must be performed under considerable uncertainty. PMID:25041168

  5. Advance Liquid Metal Reactor Discrete Dynamic Event Tree/Bayesian Network Analysis and Incident Management Guidelines (Risk Management for Sodium Fast Reactors)

    SciTech Connect

    Denman, Matthew R.; Groth, Katrina M.; Cardoni, Jeffrey N.; Wheeler, Timothy A.

    2015-04-01

    Accident management is an important component to maintaining risk at acceptable levels for all complex systems, such as nuclear power plants. With the introduction of self-correcting, or inherently safe, reactor designs the focus has shifted from management by operators to allowing the system's design to manage the accident. Inherently and passively safe designs are laudable, but nonetheless extreme boundary conditions can interfere with the design attributes which facilitate inherent safety, thus resulting in unanticipated and undesirable end states. This report examines an inherently safe and small sodium fast reactor experiencing a beyond design basis seismic event with the intend of exploring two issues : (1) can human intervention either improve or worsen the potential end states and (2) can a Bayesian Network be constructed to infer the state of the reactor to inform (1). ACKNOWLEDGEMENTS The authors would like to acknowledge the U.S. Department of Energy's Office of Nuclear Energy for funding this research through Work Package SR-14SN100303 under the Advanced Reactor Concepts program. The authors also acknowledge the PRA teams at Argonne National Laboratory, Oak Ridge National Laboratory, and Idaho National Laboratory for their continue d contributions to the advanced reactor PRA mission area.

  6. Probabilistic evidential assessment of gunshot residue particle evidence (Part I): likelihood ratio calculation and case pre-assessment using Bayesian networks.

    PubMed

    Biedermann, A; Bozza, S; Taroni, F

    2009-10-30

    Well developed experimental procedures currently exist for retrieving and analyzing particle evidence from hands of individuals suspected of being associated with the discharge of a firearm. Although analytical approaches (e.g. automated Scanning Electron Microscopy with Energy Dispersive X-ray (SEM-EDS) microanalysis) allow the determination of the presence of elements typically found in gunshot residue (GSR) particles, such analyses provide no information about a given particle's actual source. Possible origins for which scientists may need to account for are a primary exposure to the discharge of a firearm or a secondary transfer due to a contaminated environment. In order to approach such sources of uncertainty in the context of evidential assessment, this paper studies the construction and practical implementation of graphical probability models (i.e. Bayesian networks). These can assist forensic scientists in making the issue tractable within a probabilistic perspective. The proposed models focus on likelihood ratio calculations at various levels of detail as well as case pre-assessment. PMID:19592185

  7. The role of induction and adjuvant chemotherapy in combination with concurrent chemoradiotherapy for nasopharyngeal cancer: a Bayesian network meta-analysis of published randomized controlled trials

    PubMed Central

    Yu, Hongliang; Gu, Dayong; He, Xia; Gao, Xianshu; Bian, Xiuhua

    2016-01-01

    Whether the addition of induction chemotherapy (IC) or adjuvant chemotherapy (AC) to concurrent chemoradiotherapy (CCRT) is superior to CCRT alone for locally advanced nasopharyngeal cancer is unknown. A Bayesian network meta-analysis was performed to investigate the efficacy of CCRT, IC + CCRT, and CCRT + AC on locally advanced nasopharyngeal cancer. The overall survival (OS) with hazard ratios (HRs) and locoregional recurrence rates (LRRs) and distant metastasis rates (DMRs) with risk ratios (RRs) were investigated. After a comprehensive database search, eleven studies involving 2,626 assigned patients were included in this network meta-analysis. Compared with CCRT alone, IC + CCRT resulted in no significant improvement in OS or LRR and a marginal improvement in DMR (OS: HR =0.67, 95% credible interval (CrI) 0.32–1.18; LRR: RR =1.79, 95% CrI 0.80–3.51; DMR: RR =1.79, 95% CrI 0.24–1.04) and CCRT + AC exhibited no beneficial effects on any of the endpoints of OS, LRR, or DMR (OS: HR =0.99, 95% CrI 0.64–1.43; LRR: RR =0.78, 95% CrI 0.43–1.32; DMR: RR =0.85, 95% CrI 0.57–1.24). As a conclusion, for locally advanced nasopharyngeal cancer, no significant differences in the treatment efficacies of CCRT, IC + CCRT, and CCRT + AC were found, with the exception of a marginally significant improvement in distant control observed following IC + CCRT compared with CCRT alone. PMID:26793000

  8. Linear and nonlinear modeling of antifungal activity of some heterocyclic ring derivatives using multiple linear regression and Bayesian-regularized neural networks.

    PubMed

    Caballero, Julio; Fernández, Michael

    2006-01-01

    Antifungal activity was modeled for a set of 96 heterocyclic ring derivatives (2,5,6-trisubstituted benzoxazoles, 2,5-disubstituted benzimidazoles, 2-substituted benzothiazoles and 2-substituted oxazolo(4,5-b)pyridines) using multiple linear regression (MLR) and Bayesian-regularized artificial neural network (BRANN) techniques. Inhibitory activity against Candida albicans (log(1/C)) was correlated with 3D descriptors encoding the chemical structures of the heterocyclic compounds. Training and test sets were chosen by means of k-Means Clustering. The most appropriate variables for linear and nonlinear modeling were selected using a genetic algorithm (GA) approach. In addition to the MLR equation (MLR-GA), two nonlinear models were built, model BRANN employing the linear variable subset and an optimum model BRANN-GA obtained by a hybrid method that combined BRANN and GA approaches (BRANN-GA). The linear model fit the training set (n = 80) with r2 = 0.746, while BRANN and BRANN-GA gave higher values of r2 = 0.889 and r2 = 0.937, respectively. Beyond the improvement of training set fitting, the BRANN-GA model was superior to the others by being able to describe 87% of test set (n = 16) variance in comparison with 78 and 81% the MLR-GA and BRANN models, respectively. Our quantitative structure-activity relationship study suggests that the distributions of atomic mass, volume and polarizability have relevant relationships with the antifungal potency of the compounds studied. Furthermore, the ability of the six variables selected nonlinearly to differentiate the data was demonstrated when the total data set was well distributed in a Kohonen self-organizing neural network (KNN). PMID:16205958

  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. 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.

  11. The impact of incorporating Bayesian network meta-analysis in cost-effectiveness analysis - a case study of pharmacotherapies for moderate to severe COPD

    PubMed Central

    2014-01-01

    Objective To evaluate the impact of using network meta-analysis (NMA) versus pair wise meta-analyses (PMA) for evidence synthesis on key outputs of cost-effectiveness analysis (CEA). Methods We conducted Bayesian NMA of randomized clinical trials providing head-to-head and placebo comparisons of the effect of pharmacotherapies on the exacerbation rate in chronic obstructive pulmonary disease (COPD). Separately, the subset of placebo–comparison trials was used in a Bayesian PMA. The pooled rate ratios (RR) were used to populate a decision-analytic model of COPD treatment to predict 10-year outcomes. Results Efficacy estimates from the NMA and PMA were similar, but the NMA provided estimates with higher precision. This resulted in similar incremental cost-effectiveness ratios (ICER). Probabilities of being cost-effective at willingness-to-pay thresholds (WTPs) between $25,000 and $100,000 per quality adjusted life year (QALY) varied considerably between the PMA- and NMA-based approaches. The largest difference in the probabilities of being cost-effective was observed at a WTP of approximately $40,000/QALY. At this threshold, with the PMA-based analysis, ICS, LAMA and placebo had a 43%, 30, and 18% probability of being the most cost-effective. By contrast, with the NMA based approach, ICS, LAMA, and placebo had a 56%, 19%, and 21% probability of being cost-effective. For larger WTP thresholds the probability of LAMA being the most cost-effective became higher than that of ICS. Under the PMA-based analyses the cross-over occurred at a WTP threshold between $60,000/QALY-$65,000/QALY, whereas under the NMA-based approach, the cross-over occurred between $85,000/QALY-$90,000/QALY. Conclusion Use of NMAs in CEAs is feasible and, as our case study showed, can decrease uncertainty around key cost-effectiveness measures compared with the use of PMAs. The approval process of health technologies in many jurisdictions requires estimates of comparative efficacy and cost

  12. Data in support of a central role of plasminogen activator inhibitor-2 polymorphism in recurrent cardiovascular disease risk in the setting of high HDL cholesterol and C-reactive protein using Bayesian network modeling.

    PubMed

    Corsetti, James P; Salzman, Peter; Ryan, Dan; Moss, Arthur J; Zareba, Wojciech; Sparks, Charles E

    2016-09-01

    Data is presented that was utilized as the basis for Bayesian network modeling of influence pathways focusing on the central role of a polymorphism of plasminogen activator inhibitor-2 (PAI-2) on recurrent cardiovascular disease risk in patients with high levels of HDL cholesterol and C-reactive protein (CRP) as a marker of inflammation, "Influences on Plasminogen Activator Inhibitor-2 Polymorphism-Associated Recurrent Cardiovascular Disease Risk in Patients with High HDL Cholesterol and Inflammation" (Corsetti et al., 2016; [1]). The data consist of occurrence of recurrent coronary events in 166 post myocardial infarction patients along with 1. clinical data on gender, race, age, and body mass index; 2. blood level data on 17 biomarkers; and 3. genotype data on 53 presumptive CVD-related single nucleotide polymorphisms. Additionally, a flow diagram of the Bayesian modeling procedure is presented along with Bayesian network subgraphs (root nodes to outcome events) utilized as the data from which PAI-2 associated influence pathways were derived (Corsetti et al., 2016; [1]). PMID:27284570

  13. Efficient Conjunction Assessment using Modified Chebyshev Picard Iteration

    NASA Astrophysics Data System (ADS)

    Probe, A.; Macomber, B.; Read, J.; Woollands, R.; Masher, A.; Junkins, J.

    Conjunction Assessment is one of the most important and computationally expensive components of modern SSA efforts. Timely warnings of potential conjunctions are critical for the protection of valuable space assets. Upgrades to the US Space Surveillance Network (SSN) such as the Space Surveillance Telescope and the new Space Fence become operational, the influx of newly trackable objects will exacerbate the current issues of computational tractability. Modified Chebyshev Picard Iteration (MCPI) is a numerical method for solving ordinary differential equations that can be utilized to efficiently proximate orbits with high accuracy. Unlike, more traditional stepping based integrators; MCPI uses recursive approximation using Chebyshev polynomials to estimate segments of an orbit. The end result of the propagation is orthogonal Chebyshev polynomial approximation of the orbital trajectory; this approximation is analytically differentiable and potentially accurate to machine precision. Once computed, these approximations provide an efficient method for evaluating and comparing the positions of space objects. The reduced cost of catalog propagation and subsequent conjunction probability analysis when using MCPI, allows for significant reduction in the cost to perform high fidelity conjunction assessment. A method for catalog propagation and conjunction assessment using MCPI is presented, along with results from implementation running in a compute cluster environment are presented.

  14. Bayesian superresolution

    NASA Astrophysics Data System (ADS)

    Isakson, Steve Wesley

    2001-12-01

    Well-known principles of physics explain why resolution restrictions occur in images produced by optical diffraction-limited systems. The limitations involved are present in all diffraction-limited imaging systems, including acoustical and microwave. In most circumstances, however, prior knowledge about the object and the imaging system can lead to resolution improvements. In this dissertation I outline a method to incorporate prior information into the process of reconstructing images to superresolve the object beyond the above limitations. This dissertation research develops the details of this methodology. The approach can provide the most-probable global solution employing a finite number of steps in both far-field and near-field images. In addition, in order to overcome the effects of noise present in any imaging system, this technique provides a weighted image that quantifies the likelihood of various imaging solutions. By utilizing Bayesian probability, the procedure is capable of incorporating prior information about both the object and the noise to overcome the resolution limitation present in many imaging systems. Finally I will present an imaging system capable of detecting the evanescent waves missing from far-field systems, thus improving the resolution further.

  15. Comparison of Bayesian network and support vector machine models for two-year survival prediction in lung cancer patients treated with radiotherapy

    SciTech Connect

    Jayasurya, K.; Fung, G.; Yu, S.; Dehing-Oberije, C.; De Ruysscher, D.; Hope, A.; De Neve, W.; Lievens, Y.; Lambin, P.; Dekker, A. L. A. J.

    2010-04-15

    Purpose: Classic statistical and machine learning models such as support vector machines (SVMs) can be used to predict cancer outcome, but often only perform well if all the input variables are known, which is unlikely in the medical domain. Bayesian network (BN) models have a natural ability to reason under uncertainty and might handle missing data better. In this study, the authors hypothesize that a BN model can predict two-year survival in non-small cell lung cancer (NSCLC) patients as accurately as SVM, but will predict survival more accurately when data are missing. Methods: A BN and SVM model were trained on 322 inoperable NSCLC patients treated with radiotherapy from Maastricht and validated in three independent data sets of 35, 47, and 33 patients from Ghent, Leuven, and Toronto. Missing variables occurred in the data set with only 37, 28, and 24 patients having a complete data set. Results: The BN model structure and parameter learning identified gross tumor volume size, performance status, and number of positive lymph nodes on a PET as prognostic factors for two-year survival. When validated in the full validation set of Ghent, Leuven, and Toronto, the BN model had an AUC of 0.77, 0.72, and 0.70, respectively. A SVM model based on the same variables had an overall worse performance (AUC 0.71, 0.68, and 0.69) especially in the Ghent set, which had the highest percentage of missing the important GTV size data. When only patients with complete data sets were considered, the BN and SVM model performed more alike. Conclusions: Within the limitations of this study, the hypothesis is supported that BN models are better at handling missing data than SVM models and are therefore more suitable for the medical domain. Future works have to focus on improving the BN performance by including more patients, more variables, and more diversity.

  16. Comparative efficacy and tolerability of duloxetine, pregabalin, and milnacipran for the treatment of fibromyalgia: a Bayesian network meta-analysis of randomized controlled trials.

    PubMed

    Lee, Young Ho; Song, Gwan Gyu

    2016-05-01

    The aim of this study was to assess the relative efficacy and tolerability of duloxetine, pregabalin, and milnacipran at the recommended doses in patients with fibromyalgia. Randomized controlled trials (RCTs) examining the efficacy and safety of duloxetine 60 mg, pregabalin 300 mg, pregabalin 150 mg, milnacipran 200 mg, and milnacipran 100 mg compared to placebo in patients with fibromyalgia were included in this Bayesian network meta-analysis. Nine RCTs including 5140 patients met the inclusion criteria. The proportion of patients with >30 % improvement from baseline in pain was significantly higher in the duloxetine 60 mg, pregabalin 300 mg, milnacipran 100 mg, and milnacipran 200 mg groups than in the placebo group [pairwise odds ratio (OR) 2.33, 95 % credible interval (CrI) 1.50-3.67; OR 1.68, 95 % CrI 1.25-2.28; OR 1.62, 95 % CrI 1.16-2.25; and OR 1.61; 95 % CrI 1.15-2.24, respectively]. Ranking probability based on the surface under the cumulative ranking curve (SUCRA) indicated that duloxetine 60 mg had the highest probability of being the best treatment for achieving the response level (SUCRA = 0.9431), followed by pregabalin 300 mg (SUCRA = 0.6300), milnacipran 100 mg (SUCRA = 0.5680), milnacipran 200 mg (SUCRA = 0.5617), pregabalin 150 mg (SUCRA = 0.2392), and placebo (SUCRA = 0.0580). The risk of withdrawal due to adverse events was lower in the placebo group than in the pregabalin 300 mg, duloxetine 60 mg, milnacipran 100 mg, and milnacipran 200 mg groups. However, there was no significant difference in the efficacy and tolerability between the medications at the recommended doses. Duloxetine 60 mg, pregabalin 300 mg, milnacipran 100 mg, and milnacipran 200 mg were more efficacious than placebo. However, there was no significant difference in the efficacy and tolerability between the medications at the recommended doses. PMID:27000046

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  18. The metabolic network of Clostridium acetobutylicum: Comparison of the approximate Bayesian computation via sequential Monte Carlo (ABC-SMC) and profile likelihood estimation (PLE) methods for determinability analysis.

    PubMed

    Thorn, Graeme J; King, John R

    2016-01-01

    The Gram-positive bacterium Clostridium acetobutylicum is an anaerobic endospore-forming species which produces acetone, butanol and ethanol via the acetone-butanol (AB) fermentation process, leading to biofuels including butanol. In previous work we looked to estimate the parameters in an ordinary differential equation model of the glucose metabolism network using data from pH-controlled continuous culture experiments. Here we combine two approaches, namely the approximate Bayesian computation via an existing sequential Monte Carlo (ABC-SMC) method (to compute credible intervals for the parameters), and the profile likelihood estimation (PLE) (to improve the calculation of confidence intervals for the same parameters), the parameters in both cases being derived from experimental data from forward shift experiments. We also apply the ABC-SMC method to investigate which of the models introduced previously (one non-sporulation and four sporulation models) have the greatest strength of evidence. We find that the joint approximate posterior distribution of the parameters determines the same parameters as previously, including all of the basal and increased enzyme production rates and enzyme reaction activity parameters, as well as the Michaelis-Menten kinetic parameters for glucose ingestion, while other parameters are not as well-determined, particularly those connected with the internal metabolites acetyl-CoA, acetoacetyl-CoA and butyryl-CoA. We also find that the approximate posterior is strongly non-Gaussian, indicating that our previous assumption of elliptical contours of the distribution is not valid, which has the effect of reducing the numbers of pairs of parameters that are (linearly) correlated with each other. Calculations of confidence intervals using the PLE method back this up. Finally, we find that all five of our models are equally likely, given the data available at present. PMID:26561777

  19. Decision generation tools and Bayesian inference

    NASA Astrophysics Data System (ADS)

    Jannson, Tomasz; Wang, Wenjian; Forrester, Thomas; Kostrzewski, Andrew; Veeris, Christian; Nielsen, Thomas

    2014-05-01

    Digital Decision Generation (DDG) tools are important software sub-systems of Command and Control (C2) systems and technologies. In this paper, we present a special type of DDGs based on Bayesian Inference, related to adverse (hostile) networks, including such important applications as terrorism-related networks and organized crime ones.

  20. Exploring the Overestimation of Conjunctive Probabilities

    PubMed Central

    Nilsson, Håkan; Rieskamp, Jörg; Jenny, Mirjam A.

    2013-01-01

    People often overestimate probabilities of conjunctive events. The authors explored whether the accuracy of conjunctive probability estimates can be improved by increased experience with relevant constituent events and by using memory aids. The first experiment showed that increased experience with constituent events increased the correlation between the estimated and the objective conjunctive probabilities, but that it did not reduce overestimation of conjunctive probabilities. The second experiment showed that reducing cognitive load with memory aids for the constituent probabilities led to improved estimates of the conjunctive probabilities and to decreased overestimation of conjunctive probabilities. To explain the cognitive process underlying people’s probability estimates, the configural weighted average model was tested against the normative multiplicative model. The configural weighted average model generates conjunctive probabilities that systematically overestimate objective probabilities although the generated probabilities still correlate strongly with the objective probabilities. For the majority of participants this model was better than the multiplicative model in predicting the probability estimates. However, when memory aids were provided, the predictive accuracy of the multiplicative model increased. In sum, memory tools can improve people’s conjunctive probability estimates. PMID:23460026

  1. From genome-scale data to models of infectious disease: A Bayesian network-based strategy to drive model development.

    PubMed

    Yin, Weiwei; Kissinger, Jessica C; Moreno, Alberto; Galinski, Mary R; Styczynski, Mark P

    2015-12-01

    High-throughput, genome-scale data present a unique opportunity to link host to pathogen on a molecular level. Forging such connections will help drive the development of mathematical models to better understand and predict both pathogen behavior and the epidemiology of infectious diseases, including malaria. However, the datasets that can aid in identifying these links and models are vast and not amenable to simple, reductionist, and univariate analyses. These datasets require data mining in order to identify the truly important measurements that best describe clinical and molecular observations. Moreover, these datasets typically have relatively few samples due to experimental limitations (particularly for human studies or in vivo animal experiments), making data mining extremely difficult. Here, after first providing a brief overview of common strategies for data reduction and identification of relationships between variables for inclusion in mathematical models, we present a new generalized strategy for performing these data reduction and relationship inference tasks. Our approach emphasizes the importance of robustness when using data to drive model development, particularly when using genome-scale, small-sample in vivo data. We identify the use of appropriate feature reduction combined with data permutations and subsampling strategies as being critical to enable increasingly robust results from network inference using high-dimensional, low-observation data. PMID:26093035

  2. Is a Complex Neural Network Based Air Quality Prediction Model Better Than a Simple One? A Bayesian Point of View

    NASA Astrophysics Data System (ADS)

    Hoi, K. I.; Yuen, K. V.; Mok, K. M.

    2010-05-01

    In this study the neural network based air quality prediction model was tested in a typical coastal city, Macau, with Latitude 22° 10'N and Longitude 113° 34'E. By using five years of air quality and meteorological data recorded at an ambient air quality monitoring station between 2001 and 2005, it was found that the performance of the ANN model was generally improved by increasing the number of hidden neurons in the training phase. However, the performance of the ANN model was not sensitive to the change in the number of hidden neurons during the prediction phase. Therefore, the improvement in the error statistics for a complex ANN model in the training phase may be only caused by the overfitting of the data. In addition, the posterior PDF of the parameter vector conditional on the training dataset was investigated for different number of hidden neurons. It was found that the parametric space for a simple ANN model was globally identifiable and the Levenberg-Marquardt backpropagation algorithm was able to locate the optimal parameter vector. However, the parameter vector might contain redundant parameters and the parametric space was not globally identifiable when the model class became complex. In addition, the Levenberg-Marquardt backpropagation algorithm was unable to locate the most optimal parameter vector in this situation. Finally, it was concluded that the a more complex MLP model, that fits the data better, is not necessarily better than a simple one.

  3. Scalable Conjunction Processing using Spatiotemporally Indexed Ephemeris Data

    NASA Astrophysics Data System (ADS)

    Budianto-Ho, I.; Johnson, S.; Sivilli, R.; Alberty, C.; Scarberry, R.

    2014-09-01

    The collision warnings produced by the Joint Space Operations Center (JSpOC) are of critical importance in protecting U.S. and allied spacecraft against destructive collisions and protecting the lives of astronauts during space flight. As the Space Surveillance Network (SSN) improves its sensor capabilities for tracking small and dim space objects, the number of tracked objects increases from thousands to hundreds of thousands of objects, while the number of potential conjunctions increases with the square of the number of tracked objects. Classical filtering techniques such as apogee and perigee filters have proven insufficient. Novel and orders of magnitude faster conjunction analysis algorithms are required to find conjunctions in a timely manner. Stellar Science has developed innovative filtering techniques for satellite conjunction processing using spatiotemporally indexed ephemeris data that efficiently and accurately reduces the number of objects requiring high-fidelity and computationally-intensive conjunction analysis. Two such algorithms, one based on the k-d Tree pioneered in robotics applications and the other based on Spatial Hash Tables used in computer gaming and animation, use, at worst, an initial O(N log N) preprocessing pass (where N is the number of tracked objects) to build large O(N) spatial data structures that substantially reduce the required number of O(N^2) computations, substituting linear memory usage for quadratic processing time. The filters have been implemented as Open Services Gateway initiative (OSGi) plug-ins for the Continuous Anomalous Orbital Situation Discriminator (CAOS-D) conjunction analysis architecture. We have demonstrated the effectiveness, efficiency, and scalability of the techniques using a catalog of 100,000 objects, an analysis window of one day, on a 64-core computer with 1TB shared memory. Each algorithm can process the full catalog in 6 minutes or less, almost a twenty-fold performance improvement over the

  4. Bayesianism Versus Confirmation

    NASA Astrophysics Data System (ADS)

    Strevens, Michael

    2014-03-01

    The usual Bayesian approach to understanding the confirmation of scientific theories is inadequate. The problem lies not with Bayesian epistemology, but with a simplistic equation of the subjective, individualistic evidential relevance relation that Bayesianism attempts to capture and the more objective relevance relation of confirmation.

  5. "Adversative Conjunction": The Poetics of Linguistic Opposition.

    ERIC Educational Resources Information Center

    Wallerstein, Nicholas

    1992-01-01

    The general use of adversative conjunction in (primarily) English and U.S. poetry is outlined. The contention is that the adversative is not merely a grammatical convenience but sometimes a highly functional tool of rhetorical strategy. (36 references) (LB)

  6. Immunonutrition Support for Patients Undergoing Surgery for Gastrointestinal Malignancy: Preoperative, Postoperative, or Perioperative? A Bayesian Network Meta-Analysis of Randomized Controlled Trials.

    PubMed

    Song, Guo-Min; Tian, Xu; Zhang, Lei; Ou, Yang-Xiang; Yi, Li-Juan; Shuai, Ting; Zhou, Jian-Guo; Zeng, Zi; Yang, Hong-Ling

    2015-07-01

    Enteral immunonutrition (EIN) has been established to be as a significantly important modality to prevent the postoperative infectious and noninfectious complications, enhance the immunity of host, and eventually improve the prognosis of gastrointestinal (GI) cancer patients undergoing surgery. However, different support routes, which are the optimum option, remain unclear. To evaluate the effects of different EIN support regimes for patients who underwent selective surgery for resectable GI malignancy, a Bayesian network meta-analysis (NMA) of randomized controlled trials (RCTs) was conducted. A search of PubMed, EMBASE, and the Cochrane Central Register of Controlled Trials (CENTRAL) was electronically searched until the end of December 2014. Moreover, we manually checked reference lists of eligible trials and review and retrieval unpublished literature. RCTs which investigated the comparative effects of EIN versus standard enteral nutrition (EN) or different EIN regimes were included if the clinical outcomes information can be extracted from it. A total of 27 RCTs were incorporated into this study. Pair-wise meta-analyses suggested that preoperative (relative risk [RR], 0.58; 95% confidence interval [CI], 0.43-0.78), postoperative (RR, 0.63; 95% CI, 0.52-0.76), and perioperative EIN methods (RR, 0.46; 95% CI, 0.34-0.62) reduced incidence of postoperative infectious complications compared with standard EN. Moreover, perioperative EIN (RR, 0.65; 95% CI, 0.44-0.95) reduced the incidence of postoperative noninfectious complications, and the postoperative (mean difference [MD], -2.38; 95% CI, -3.4 to -1.31) and perioperative EIN (MD, -2.64; 95% CI, -3.28 to -1.99) also shortened the length of postoperative hospitalization compared with standard EN. NMA found that EIN support effectively improved the clinical outcomes of patients who underwent selective surgery for GI cancer compared with standard EN. Our results suggest EIN support is promising alternative for

  7. Use of Bayesian Belief Network techniques to explore the interaction of biosecurity practices on the probability of porcine disease occurrence in Canada.

    PubMed

    Cox, Ruth; Revie, Crawford W; Hurnik, Daniel; Sanchez, Javier

    2016-09-01

    Identification and quantification of pathogen threats need to be a priority for the Canadian swine industry so that resources can be focused where they will be most effective. Here we create a tool based on a Bayesian Belief Network (BBN) to model the interaction between biosecurity practices and the probability of occurrence of four different diseases on Canadian swine farms. The benefits of using this novel approach, in comparison to other methods, is that it enables us to explore both the complex interaction and the relative importance of biosecurity practices on the probability of disease occurrence. In order to build the BBN we used two datasets. The first dataset detailed biosecurity practices employed on 218 commercial swine farms across Canada in 2010. The second dataset detailed animal health status and disease occurrence on 90 of those farms between 2010 and 2012. We used expert judgement to identify 15 biosecurity practices that were considered the most important in mitigating disease occurrence on farms. These included: proximity to other livestock holdings, the health status of purchased stock, manure disposal methods, as well as the procedures for admitting vehicles and staff. Four diseases were included in the BBN: Porcine reproductive and respiratory syndrome (PRRS), (a prevalent endemic aerosol pathogen), Swine influenza (SI) (a viral respiratory aerosol pathogen), Mycoplasma pneumonia (MP) (an endemic respiratory disease spread by close contact and aerosol) and Swine dysentery (SD) (an enteric disease which is re-emerging in North America). This model indicated that the probability of disease occurrence was influenced by a number of manageable biosecurity practices. Increased probability of PRRS and of MP were associated with spilt feed (feed that did not fall directly in a feeding trough), not being disposed of immediately and with manure being brought onto the farm premises and spread on land adjacent to the pigs. Increased probabilities of SI

  8. Identification of reciprocal causality between non-alcoholic fatty liver disease and metabolic syndrome by a simplified Bayesian network in a Chinese population

    PubMed Central

    Zhang, Yongyuan; Zhang, Tao; Zhang, Chengqi; Tang, Fang; Zhong, Nvjuan; Li, Hongkai; Song, Xinhong; Lin, Haiyan; Liu, Yanxun; Xue, Fuzhong

    2015-01-01

    Objectives It remains unclear whether non-alcoholic fatty liver disease (NAFLD) is a cause or a consequence of metabolic syndrome (MetS). We proposed a simplified Bayesian network (BN) and attempted to confirm their reciprocal causality. Setting Bidirectional longitudinal cohorts (subcohorts A and B) were designed and followed up from 2005 to 2011 based on a large-scale health check-up in a Chinese population. Participants Subcohort A (from NAFLD to MetS, n=8426) included the participants with or without NAFLD at baseline to follow-up the incidence of MetS, while subcohort B (from MetS to NAFLD, n=16 110) included the participants with or without MetS at baseline to follow-up the incidence of NAFLD. Results Incidence densities were 2.47 and 17.39 per 100 person-years in subcohorts A and B, respectively. Generalised estimating equation analyses demonstrated that NAFLD was a potential causal factor for MetS (relative risk, RR, 95% CI 5.23, 3.50 to 7.81), while MetS was also a factor for NAFLD (2.55, 2.23 to 2.92). A BN with 5 simplification strategies was used for the reciprocal causal inference. The BN's causal inference illustrated that the total effect of NAFLD on MetS (attributable risks, AR%) was 2.49%, while it was 19.92% for MetS on NAFLD. The total effect of NAFLD on MetS components was different, with dyslipidemia having the greatest (AR%, 10.15%), followed by obesity (7.63%), diabetes (3.90%) and hypertension (3.51%). Similar patterns were inferred for MetS components on NAFLD, with obesity having the greatest (16.37%) effect, followed by diabetes (10.85%), dyslipidemia (10.74%) and hypertension (7.36%). Furthermore, the most important causal pathway from NAFLD to MetS was that NAFLD led to elevated GGT, then to MetS components, while the dominant causal pathway from MetS to NAFLD began with dyslipidaemia. Conclusions The findings suggest a reciprocal causality between NAFLD and MetS, and the effect of MetS on NAFLD is significantly greater than that of

  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. Markov blanket-based approach for learning multi-dimensional Bayesian network classifiers: an application to predict the European Quality of Life-5 Dimensions (EQ-5D) from the 39-item Parkinson's Disease Questionnaire (PDQ-39).

    PubMed

    Borchani, Hanen; Bielza, Concha; Martı Nez-Martı N, Pablo; Larrañaga, Pedro

    2012-12-01

    Multi-dimensional Bayesian network classifiers (MBCs) are probabilistic graphical models recently proposed to deal with multi-dimensional classification problems, where each instance in the data set has to be assigned to more than one class variable. In this paper, we propose a Markov blanket-based approach for learning MBCs from data. Basically, it consists of determining the Markov blanket around each class variable using the HITON algorithm, then specifying the directionality over the MBC subgraphs. Our approach is applied to the prediction problem of the European Quality of Life-5 Dimensions (EQ-5D) from the 39-item Parkinson's Disease Questionnaire (PDQ-39) in order to estimate the health-related quality of life of Parkinson's patients. Fivefold cross-validation experiments were carried out on randomly generated synthetic data sets, Yeast data set, as well as on a real-world Parkinson's disease data set containing 488 patients. The experimental study, including comparison with additional Bayesian network-based approaches, back propagation for multi-label learning, multi-label k-nearest neighbor, multinomial logistic regression, ordinary least squares, and censored least absolute deviations, shows encouraging results in terms of predictive accuracy as well as the identification of dependence relationships among class and feature variables. PMID:22897950

  11. Bayesian Methods in Cosmology

    NASA Astrophysics Data System (ADS)

    Hobson, Michael P.; Jaffe, Andrew H.; Liddle, Andrew R.; Mukherjee, Pia; Parkinson, David

    2014-02-01

    Preface; Part I. Methods: 1. Foundations and algorithms John Skilling; 2. Simple applications of Bayesian methods D. S. Sivia and Steve Rawlings; 3. Parameter estimation using Monte Carlo sampling Antony Lewis and Sarah Bridle; 4. Model selection and multi-model interference Andrew R. Liddle, Pia Mukherjee and David Parkinson; 5. Bayesian experimental design and model selection forecasting Roberto Trotta, Martin Kunz, Pia Mukherjee and David Parkinson; 6. Signal separation in cosmology M. P. Hobson, M. A. J. Ashdown and V. Stolyarov; Part II. Applications: 7. Bayesian source extraction M. P. Hobson, Graça Rocha and R. Savage; 8. Flux measurement Daniel Mortlock; 9. Gravitational wave astronomy Neil Cornish; 10. Bayesian analysis of cosmic microwave background data Andrew H. Jaffe; 11. Bayesian multilevel modelling of cosmological populations Thomas J. Loredo and Martin A. Hendry; 12. A Bayesian approach to galaxy evolution studies Stefano Andreon; 13. Photometric redshift estimation: methods and applications Ofer Lahav, Filipe B. Abdalla and Manda Banerji; Index.

  12. Bayesian Methods in Cosmology

    NASA Astrophysics Data System (ADS)

    Hobson, Michael P.; Jaffe, Andrew H.; Liddle, Andrew R.; Mukherjee, Pia; Parkinson, David

    2009-12-01

    Preface; Part I. Methods: 1. Foundations and algorithms John Skilling; 2. Simple applications of Bayesian methods D. S. Sivia and Steve Rawlings; 3. Parameter estimation using Monte Carlo sampling Antony Lewis and Sarah Bridle; 4. Model selection and multi-model interference Andrew R. Liddle, Pia Mukherjee and David Parkinson; 5. Bayesian experimental design and model selection forecasting Roberto Trotta, Martin Kunz, Pia Mukherjee and David Parkinson; 6. Signal separation in cosmology M. P. Hobson, M. A. J. Ashdown and V. Stolyarov; Part II. Applications: 7. Bayesian source extraction M. P. Hobson, Graça Rocha and R. Savage; 8. Flux measurement Daniel Mortlock; 9. Gravitational wave astronomy Neil Cornish; 10. Bayesian analysis of cosmic microwave background data Andrew H. Jaffe; 11. Bayesian multilevel modelling of cosmological populations Thomas J. Loredo and Martin A. Hendry; 12. A Bayesian approach to galaxy evolution studies Stefano Andreon; 13. Photometric redshift estimation: methods and applications Ofer Lahav, Filipe B. Abdalla and Manda Banerji; Index.

  13. Gestalt Reasoning with Conjunctions and Disjunctions.

    PubMed

    Dumitru, Magda L; Joergensen, Gitte H

    2016-01-01

    Reasoning, solving mathematical equations, or planning written and spoken sentences all must factor in stimuli perceptual properties. Indeed, thinking processes are inspired by and subsequently fitted to concrete objects and situations. It is therefore reasonable to expect that the mental representations evoked when people solve these seemingly abstract tasks should interact with the properties of the manipulated stimuli. Here, we investigated the mental representations evoked by conjunction and disjunction expressions in language-picture matching tasks. We hypothesised that, if these representations have been derived using key Gestalt principles, reasoners should use perceptual compatibility to gauge the goodness of fit between conjunction/disjunction descriptions (e.g., the purple and/ or the green) and corresponding binary visual displays. Indeed, the results of three experimental studies demonstrate that reasoners associate conjunction descriptions with perceptually-dependent stimuli and disjunction descriptions with perceptually-independent stimuli, where visual dependency status follows the key Gestalt principles of common fate, proximity, and similarity. PMID:26986760

  14. Evolution of ESA's SSA Conjunction Prediction Service

    NASA Astrophysics Data System (ADS)

    Escobar, D.; Sancho, A. Tirado, J.; Agueda, A.; Martin, L.; Luque, F.; Fletcher, E.; Navarro, V.

    2013-08-01

    This paper presents the recent evolution of ESA's SSA Conjunction Prediction Service (CPS) as a result of an on-going activity in the Space Surveillance and Tracking (SST) Segment of ESA's Space Situational Awareness (SSA) Programme. The CPS is one of a number of precursor services being developed as part of the SST segment. It has been implemented as a service to provide external users with web-based access to conjunction information and designed with a service-oriented architecture. The paper encompasses the following topics: service functionality enhancements, integration with a live objects catalogue, all vs. all analyses supporting an operational concept based on low and high fidelity screenings, and finally conjunction detection and probability algorithms.

  15. Four cases of Raoultella planticola conjunctivitis.

    PubMed

    Vassallo, J; Vella, M; Cassar, R; Caruana, P

    2016-04-01

    AimsThis brief report of four cases of conjunctivitis caused by Raoultella planticola provides a description of possibly the first documented cases of this eye infection.MethodsThe laboratory database and medical records were used to trace all the R. planticola-positive conjunctival swabs obtained in our institution. Four cases were identified and available relevant information was obtained.ResultsThis organism causes a non-specific purulent conjunctivitis that seems to have a benign course and tends to be responsive to a topical fluoroquinolone.ConclusionsThe possibility of atypical organisms must be considered when managing infective conjunctivitis. Conjunctival swabs should be obtained and topical treatment switched when initial empirical therapy fails. PMID:26742869

  16. Gestalt Reasoning with Conjunctions and Disjunctions

    PubMed Central

    Dumitru, Magda L.; Joergensen, Gitte H.

    2016-01-01

    Reasoning, solving mathematical equations, or planning written and spoken sentences all must factor in stimuli perceptual properties. Indeed, thinking processes are inspired by and subsequently fitted to concrete objects and situations. It is therefore reasonable to expect that the mental representations evoked when people solve these seemingly abstract tasks should interact with the properties of the manipulated stimuli. Here, we investigated the mental representations evoked by conjunction and disjunction expressions in language-picture matching tasks. We hypothesised that, if these representations have been derived using key Gestalt principles, reasoners should use perceptual compatibility to gauge the goodness of fit between conjunction/disjunction descriptions (e.g., the purple and/ or the green) and corresponding binary visual displays. Indeed, the results of three experimental studies demonstrate that reasoners associate conjunction descriptions with perceptually-dependent stimuli and disjunction descriptions with perceptually-independent stimuli, where visual dependency status follows the key Gestalt principles of common fate, proximity, and similarity. PMID:26986760

  17. Collaborative Work Environment for Operational Conjunction Assessment

    NASA Astrophysics Data System (ADS)

    Laporte, F.; Christy, S.

    Conjunction Messages (CM) provided by JSpOC are complete and valuable data to evaluate the level of risk of conjunctions, decide and choose avoidance actions. Nevertheless, conjunction assessment remains a difficult task which requires Middle Man between the CM provider (JSpOC) and Owner/Operators. Operational collision threat characterization is now an essential component of space mission operations. Most spacecraft operators have some sort of a process to evaluate and mitigate high-risk conjunction events. As the size of the space object catalog increases, satellite operators will be faced with more conjunction events to evaluate. Thus more sophisticated collision threat characterization and collision avoidance strategies must be implemented thought Middle Man entities. CAESAR (Conjunction Analysis and Evaluation Service, Alerts and Recommendations) is the French Middle Man. CAESAR relies on a collaborative work environment between all members of CAESAR team and its subscribers. For CAESAR, the collaborative work environment is based on JAC software and a dedicated secure webserver SpOD Space Operational Data. JAC software is not the Main Flight Dynamics (FD) software used by CAESAR team, but it is a light friendly CM dedicated software to be used on a laptop by on-call teams or support dialogue between Middle Man and FD teams. The dedicated secure webserver is a key element to share data and information between actors. This paper presents the main feedbacks from CAESAR team operational experience with regards to its collaborative work environment components: - JAC software which is not a classical Flight Dynamics software, its MMI is designed to be very quickly taken over (by teams not using it on daily basis) while also offering all the expertise levels required by the Middle Man team. JAC is used by CAESAR on-call team and all FD teams who subscribed to CAESAR. JAC is also distributed by CNES and therefore already used by some operational teams for Conjunction

  18. Temporal Phenomena in the Korean Conjunctive Constructions

    ERIC Educational Resources Information Center

    Kim, Dongmin

    2015-01-01

    The goal of this study is to characterize the temporal phenomena in the Korean conjunctive constructions. These constructions consist of three components: a verbal stem, a clause medial temporal suffix, and a clause terminal suffix. This study focuses on both the temporality of the terminal connective suffixes and the grammatical meanings of the…

  19. A New Bayesian Network-Based Risk Stratification Model for Prediction of Short-term and Long-term LVAD Mortality

    PubMed Central

    Loghmanpour, Natasha A.; Kanwar, Manreet K.; Druzdzel, Marek J.; Benza, Raymond L.; Murali, Srinivas; Antaki, James F.

    2015-01-01

    Existing risk assessment tools for patient selection for left ventricular assist devices (LVADs) such as the Destination Therapy Risk Score (DTRS) and HeartMate II Risk Score (HMRS) have limited predictive ability. This study aims to overcome the limitations of traditional statistical methods by performing the first application of Bayesian analysis to the comprehensive INTERMACS dataset and comparing it to HMRS. We retrospectively analyzed 8,050 continuous flow (CF) LVAD patients and 226 pre-implant variables. We then derived Bayesian models for mortality at each of five time endpoints post-implant (30 day, 90 day, 6 month, 1 year, and 2 year), achieving accuracies of 95, 90, 90, 83, and 78%, Kappa values of 0.43, 0.37, 0.37, 0.45, and 0.43, and area under the ROC of 91, 82, 82, 80 and 81% respectively. This was in comparison to the HMRS with an ROC of 57 and 60% at 90-days and 1-year, respectively. Pre-implant interventions such as dialysis, ECMO, and ventilators were major contributing risk markers. Bayesian models have the ability to reliably represent the complex causal relationships of multiple variables on clinical outcomes. Their potential to develop a reliable risk stratification tool for use in clinical decision making on LVAD patients encourages further investigation. PMID:25710772

  20. Bayesian Mediation Analysis

    ERIC Educational Resources Information Center

    Yuan, Ying; MacKinnon, David P.

    2009-01-01

    In this article, we propose Bayesian analysis of mediation effects. Compared with conventional frequentist mediation analysis, the Bayesian approach has several advantages. First, it allows researchers to incorporate prior information into the mediation analysis, thus potentially improving the efficiency of estimates. Second, under the Bayesian…

  1. A New Bayesian Lasso

    PubMed Central

    Mallick, Himel; Yi, Nengjun

    2016-01-01

    Park and Casella (2008) provided the Bayesian lasso for linear models by assigning scale mixture of normal (SMN) priors on the parameters and independent exponential priors on their variances. In this paper, we propose an alternative Bayesian analysis of the lasso problem. A different hierarchical formulation of Bayesian lasso is introduced by utilizing the scale mixture of uniform (SMU) representation of the Laplace density. We consider a fully Bayesian treatment that leads to a new Gibbs sampler with tractable full conditional posterior distributions. Empirical results and real data analyses show that the new algorithm has good mixing property and performs comparably to the existing Bayesian method in terms of both prediction accuracy and variable selection. An ECM algorithm is provided to compute the MAP estimates of the parameters. Easy extension to general models is also briefly discussed.

  2. JAC Software, Solving Conjunction Assessment Issues

    NASA Astrophysics Data System (ADS)

    Laporte, F.

    2014-09-01

    Conjunction Messages (CM) provided by JSpOC are complete and valuable data to evaluate the level of risk of conjunctions, decide and choose avoidance actions. Nevertheless, conjunction assessment remains a difficult task which requires Middle Man between the CM provider (JSpOC) and Owner/Operators. CAESAR (Conjunction Analysis and Evaluation Service, Alerts and Recommendations) is the French Middle Man. CAESAR relies on a collaborative work environment between CAESAR team and its subscribers. For CAESAR, the collaborative work environment is based on JAC software and a dedicated secure webserver. JAC software is not the Main Flight Dynamics (FD) software used by CAESAR team, but it is a light friendly CM dedicated software to be used on laptops by on-call teams or support dialogue between Middle Man and FD teams. This paper presents the main feedbacks from CAESAR team operational experience and how each new encountered issue has enriched JAC Software functions. JAC has got two levels: - JAC Basic version, to be aware of the situation described with CMs : automatic download of CM from websites with secure password management, capacity to manage CM from different providers, management of the downloaded CM database, visualization of the key data given by the different CM related to each close approach, visualization of the evolution of those key data through tables-graphs-3Danimations, capacity to copy/paste and edit CM data to illustrate sensibility of key parameters, capacity to use several pre-defined dispersions for each primary, printable summary of analysis, statistics on CM in database, - JAC Expert version, to take and validate a decision of avoidance action: sensitivity analysis to errors, thresholds chosen by the user, simulation of maneuvers on the satellite of interest to determine their effect in terms of mitigation of the identified risk. JAC Expert version also includes a monitoring capacity to enable 24/7 analysis. JAC Basic and JAC Expert are

  3. Human Spaceflight Recent Conjunctions of Interest

    NASA Technical Reports Server (NTRS)

    Browns, Ansley C.

    2010-01-01

    I. During each nine-hour shift (or upon request), the Orbital Safety Analyst (OSA) at JSpOC updates the entire tracked catalog with the latest tracking data from the SSN and screens this catalog against NASA s assets. a) For ISS operations, a 72-hour advance screening is performed. b) For Shuttle orbit operations, a 36-hour advance screening is performed. c) If a vehicle is performing a maneuver during the screening period, OSA uses post-reboost-trajectory data supplied by Mission Control Center-Houston (MCC-H) for screening. II. An automated process is used to detect any conjunctions within 10 x 40 x 40 km box (centered on the vehicle) using Special Perturbation (SP) processing: a) Box dimensions are Radial x Downtrack x Crosstrack. b) Any object found within this box has the tracking tasking level increased to improve (hopefully) its uncertainty in its current and predicted orbital trajectory. c) OSA informs NASA if any object is found inside a 2 x 25 x 25 km box then creates and sends an Orbital Conjunction Message (OCM) to NASA which contains detailed information about the conjunction. d) For Shuttle, the box size used for screening and reporting is altered for special operations (day of rendezvous, launch screening, etc.).

  4. A case of recalcitrant bacterial conjunctivitis.

    PubMed

    Aboshiha, Jonathan

    2013-01-01

    It is important to be vigilant for retained foreign bodies as a cause of recalcitrant bacterial conjunctivitis, even in the absence of foreign body sensation. A relapsing-remitting history should prompt referral to an ophthalmology department. All patients presenting with a red eye should be asked specifically about contact lens wear, and causes of conjunctivitis other than those bacterial in nature--such as viral and chlamydial infections or allergy--should be borne in mind. Contact lens wear may cause ocular complications, ranging from mild dry eye symptoms to contact lens-associated microbial keratitis, which is an ophthalmic emergency. Contact lens-associated corneal infections caused by Pseudomonas aeruginosa, which can rapidly penetrate the cornea, or Acanthamoeba can be severe and sight threatening. All patients with a history of contact lens wear and red flag symptoms such as eye pain, redness, reduction or change in vision, corneal epithelial defect, discharge, foreign body sensation or failure to respond to antibiotics should be referred for an urgent ophthalmic review. Retained contact lenses are known to cause several ocular complications, such as giant papillary conjunctivitis and ulcerative keratitis which may threaten corneal penetration. Lid eversion may reveal a hidden sub-tarsal contact lens. Use of fluorescein may also allow visualisation of any corneal epithelial defect. A careful slit lamp examination by an ophthalmologist is required to exclude this critical finding definitively. PMID:24555257

  5. Conjunctions and Collision Avoidance with Electrodynamic Tethers

    NASA Astrophysics Data System (ADS)

    Levin, E.

    2013-09-01

    Electrodynamic propulsion technology is currently in development by NASA, ESA, and JAXA for the purpose of affordable removal of large debris objects from LEO. At the same time, the Naval Research Laboratory is preparing a 3U CubeSat with a 1-km electrodynamic tether for a flight demonstration of electrodynamic propulsion. This type of propulsion does not require fuel. The electrodynamic thrust is the Lorentz force acting on the electric current in a long conductor (tether) in the geomagnetic field. Electrons are collected from the ambient plasma on one end and emitted back into the plasma from the other end. The electric current loop is closed through the ionosphere, as demonstrated in two previous flights. The vehicle is solar powered. To support safe navigation of electrodynamic tethers, proper conjunction analysis and collision avoidance strategies are needed. The typical lengths of electrodynamic tethers for near-term applications are measured in kilometers, and the conjunction geometry is very different from the geometry of conjunctions between compact objects. It is commonly thought that the collision cross-section in a conjunction between a tether and a compact object is represented by the product of the tether length and the size of the object. However, rigorous analysis shows that this is not the case, and that the above assumption leads to grossly overestimated collision probabilities. The paper will present the results of a detailed mathematical analysis of the conjunction geometry and collision probabilities in close approaches between electrodynamic tethers and compact objects, such as satellites, rocket bodies, and debris fragments. Electrodynamic spacecraft will not require fuel, and therefore, can thrust constantly. Their orbit transfers can take many days, but can result in major orbit changes, including large rotations of the orbital plane, both in the inclination and the node. During these orbit transfers, the electrodynamic spacecraft will

  6. Peak Pc Prediction in Conjunction Analysis: Conjunction Assessment Risk Analysis. Pc Behavior Prediction Models

    NASA Technical Reports Server (NTRS)

    Vallejo, J.J.; Hejduk, M.D.; Stamey, J. D.

    2015-01-01

    Satellite conjunction risk typically evaluated through the probability of collision (Pc). Considers both conjunction geometry and uncertainties in both state estimates. Conjunction events initially discovered through Joint Space Operations Center (JSpOC) screenings, usually seven days before Time of Closest Approach (TCA). However, JSpOC continues to track objects and issue conjunction updates. Changes in state estimate and reduced propagation time cause Pc to change as event develops. These changes a combination of potentially predictable development and unpredictable changes in state estimate covariance. Operationally useful datum: the peak Pc. If it can reasonably be inferred that the peak Pc value has passed, then risk assessment can be conducted against this peak value. If this value is below remediation level, then event intensity can be relaxed. Can the peak Pc location be reasonably predicted?

  7. Improved Conjunction Analysis via Collaborative Space Situational Awareness

    NASA Astrophysics Data System (ADS)

    Kelso, T.; Vallado, D.; Chan, J.; Buckwalter, B.

    With recent events such as the Chinese ASAT test in 2007 and the USA 193 intercept in 2008, many satellite operators are becoming increasingly aware of the potential threat to their satellites as the result of orbital debris or even other satellites. However, to be successful at conjunction monitoring and collision avoidance requires accurate orbital information for as many space objects (payloads, dead satellites, rocket bodies, and debris) as possible. Given the current capabilities of the US Space Surveillance Network (SSN), approximately 18,500 objects are now being tracked and orbital data (in the form of two-line element sets) is available to satellite operators for 11,750 of them (as of 2008 September 1). The capability to automatically process this orbital data to look for close conjunctions and provide that information to satellite operators via the Internet has been continuously available on CelesTrak, in the form of Satellite Orbital Conjunction Reports Assessing Threatening Encounters in Space (SOCRATES), since May 2004. Those reports are used by many operators as one way to keep apprised of these potential threats. However, the two-line element sets (TLEs) are generated using non-cooperative tracking via the SSN's network of radar and optical sensors. As a result, the relatively low accuracy of the data results in a large number of false alarms that satellite operators must routinely deal with. Yet, satellite operators typically perform orbit maintenance for their own satellites, using active ranging and GPS systems. These data are often an order of magnitude more accurate than those available using TLEs. When combined (in the form of ephemerides) with maneuver planning information, the ability to maintain predictive awareness increases significantly. And when satellite operators share this data, the improved space situational awareness, particularly in the crowded geosynchronous belt, can be dramatic and the number of false alarms can be reduced

  8. 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

  9. Practical Bayesian tomography

    NASA Astrophysics Data System (ADS)

    Granade, Christopher; Combes, Joshua; Cory, D. G.

    2016-03-01

    In recent years, Bayesian methods have been proposed as a solution to a wide range of issues in quantum state and process tomography. State-of-the-art Bayesian tomography solutions suffer from three problems: numerical intractability, a lack of informative prior distributions, and an inability to track time-dependent processes. Here, we address all three problems. First, we use modern statistical methods, as pioneered by Huszár and Houlsby (2012 Phys. Rev. A 85 052120) and by Ferrie (2014 New J. Phys. 16 093035), to make Bayesian tomography numerically tractable. Our approach allows for practical computation of Bayesian point and region estimators for quantum states and channels. Second, we propose the first priors on quantum states and channels that allow for including useful experimental insight. Finally, we develop a method that allows tracking of time-dependent states and estimates the drift and diffusion processes affecting a state. We provide source code and animated visual examples for our methods.

  10. Bayesian inference in physics

    NASA Astrophysics Data System (ADS)

    von Toussaint, Udo

    2011-07-01

    Bayesian inference provides a consistent method for the extraction of information from physics experiments even in ill-conditioned circumstances. The approach provides a unified rationale for data analysis, which both justifies many of the commonly used analysis procedures and reveals some of the implicit underlying assumptions. This review summarizes the general ideas of the Bayesian probability theory with emphasis on the application to the evaluation of experimental data. As case studies for Bayesian parameter estimation techniques examples ranging from extra-solar planet detection to the deconvolution of the apparatus functions for improving the energy resolution and change point estimation in time series are discussed. Special attention is paid to the numerical techniques suited for Bayesian analysis, with a focus on recent developments of Markov chain Monte Carlo algorithms for high-dimensional integration problems. Bayesian model comparison, the quantitative ranking of models for the explanation of a given data set, is illustrated with examples collected from cosmology, mass spectroscopy, and surface physics, covering problems such as background subtraction and automated outlier detection. Additionally the Bayesian inference techniques for the design and optimization of future experiments are introduced. Experiments, instead of being merely passive recording devices, can now be designed to adapt to measured data and to change the measurement strategy on the fly to maximize the information of an experiment. The applied key concepts and necessary numerical tools which provide the means of designing such inference chains and the crucial aspects of data fusion are summarized and some of the expected implications are highlighted.

  11. Incorporating transient storage in conjunctive stream-aquifer modeling

    NASA Astrophysics Data System (ADS)

    Lin, Yi-Chang; Medina, Miguel A.

    2003-09-01

    There has been growing interest in incorporating the transient storage effect into modeling solute transport in streams. In particular, for a smaller mountain stream where flow is fast and the flow field is irregular (a favorable environment to induce dead zones along the stream), long tails are normally observed in the stream tracer data, and adding transient storage terms in the advection-dispersion transport equation can result in more accurate simulation. While previous studies on transient storage modeling account for temporary, localized exchange between the stream and the shallow groundwater in the hyporheic zone, larger-scale exchange with the groundwater in the underlying aquifer has rarely been included or properly coupled to surface water modeling. In this paper, we complement previous modeling efforts by incorporating the transient storage concept in a conjunctive stream-aquifer model. Three well-documented and widely used USGS models have been coupled to form the core of this conjunctive model: MODFLOW handles the groundwater flow in the aquifer; DAFLOW accurately computes unsteady streamflow by means of the diffusive wave routing technique, as well as stream-aquifer exchange simulated as streambed leakage; and MOC3D computes solute transport in the groundwater zone. In addition, an explicit finite difference package was developed to incorporate the one-dimensional transient storage equations for solute transport in streams. The quadratic upstream interpolation (QUICK) algorithm is employed to improve the accuracy of spatial differencing. An adaptive stepsize control algorithm for the Runge-Kutta method is incorporated to increase overall model efficiency. Results show that the conjunctive stream-aquifer model with transient storage can handle well the bank storage effect under a flooding event. When it is applied over a stream network, the results also show that the stream-aquifer interaction acts as a strong source or sink along the stream and is too

  12. Effects of Increasing Drag on Conjunction Assessment

    NASA Technical Reports Server (NTRS)

    Frigm, Ryan Clayton; McKinley, David P.

    2010-01-01

    Conjunction Assessment Risk Analysis relies heavily on the computation of the Probability of Collision (Pc) and the understanding of the sensitivity of this calculation to the position errors as defined by the covariance. In Low Earth Orbit (LEO), covariance is predominantly driven by perturbations due to atmospheric drag. This paper describes the effects of increasing atmospheric drag through Solar Cycle 24 on Pc calculations. The process of determining these effects is found through analyzing solar flux predictions on Energy Dissipation Rate (EDR), historical relationship between EDR and covariance, and the sensitivity of Pc to covariance. It is discovered that while all LEO satellites will be affected by the increase in solar activity, the relative effect is more significant in the LEO regime around 700 kilometers in altitude compared to 400 kilometers. Furthermore, it is shown that higher Pc values can be expected at larger close approach miss distances. Understanding these counter-intuitive results is important to setting Owner/Operator expectations concerning conjunctions as solar maximum approaches.

  13. Immune Regulatory Mechanisms in Allergic Conjunctivitis

    PubMed Central

    Niederkorn, Jerry Y.

    2008-01-01

    Purpose of review This review highlights recent findings regarding the immune regulation of allergic conjunctivitis (AC). Mouse models have facilitated prospective studies that have not been possible in patients. The availability of gene knockout mice and the wealth of monoclonal antibodies have permitted exquisite dissection of the pathophysiology and immune regulation of AC. Recent findings New insights have emerged in three areas: a) role of costimulatory molecules in the induction of Th2 immune responses; b) crucial role of interferon-γ (IFN-γ) in the expression of AC; and c) the function of T regulatory cells in shaping conjunctival inflammation once the immune response has been initiated. Summary Allergic conjunctivitis involves early phase and late phase reactions. The early phase reaction (EPR) is IgE antibody-dependent, while the late phase reaction (LPR) is IgE-independent and is mediated by inflammatory cells, especially eosinophils. Recent studies in mouse models of AC have provided important insights into the immune regulation of both the EPR and LPR of AC. Mounting evidence suggests that IFN-γ is crucial for optimum expression of AC. Costimulatory molecules influence the induction of Th2 immune responses and the EPR while regulatory T cells shape the expression of the LPR of AC. PMID:18769204

  14. Semantic transparency affects memory conjunction errors

    PubMed Central

    Wong, Mungchen; Rotello, Caren M.

    2009-01-01

    Memory conjunction errors occur when aspects of two different events are falsely recognized or recalled as having occurred as parts of the same event. One theoretical account of conjunction errors is rooted in traditional dual-process models of recognition judgments, in which responses are based on an item’s familiarity or the retrieval of recollected details associated with the encoding of that item. We manipulated the familiarity of test probes by varying their semantic overlap with studied items, taking advantage of the inherent semantic transparency of compound words. Transparent compounds are those whose component parts (lexemes) are semantically related to the meaning of the entire word. In contrast, opaque compounds’ lexemes do not contribute directly to the meaning of the compound. We showed that the familiarity of semantically transparent assembly lures created from their lexemes (study dog and house, test on doghouse) is greater than the familiarity of opaque assembly lures (study back and draw, test on drawback). A response-signal experiment revealed no evidence for the use of a recall-to-reject process for either semantically transparent or opaque lures. PMID:19966238

  15. Tuberculous Conjunctivitis in an Anophthalmic Socket.

    PubMed

    Al Habash, Ahmed; Malik, Faisal; Al Abdulsalam, Omar; Al Abdulsalam, Abdulrahim

    2015-01-01

    Tuberculous (TB) conjunctivitis was not an uncommon condition before the early 20(th) century but is currently a rare occurrence, especially in the developed countries. We report a 27-year-old Saudi female who underwent enucleation of the right eye at the age of 20 following a penetrating eye injury. She had a history of miliary TB that was treated at the age of 22. She was presented with chronic purulent discharge from her right an anophthalmic socket for 2 months. Cultures for bacteria and fungi were sterile. There was no response to empirical topical antibiotics and steroids. Direct microscopic examination of conjunctival scrapings with the Ziehl-Neelsen staining revealed no microorganisms. Histopathological examination revealed epithelioid granulomas. Polymerase chain reaction was negative for Mycobacterium tuberculosis DNA. TB conjunctivitis was suspected from the history of miliary TB and presence of epithelioid granulomas. The definitive diagnosis was made after prompt resolution of the ocular signs with no recurrence only after systemic anti-TB therapy. PMID:26692731

  16. [Enteroviruses responsible for acute hemorrhagic conjunctivitis].

    PubMed

    Lévêque, N; Huguet, P; Norder, H; Chomel, J-J

    2010-04-01

    Acute hemorrhagic conjunctivitis (AHC) is an epidemic form of highly contagious conjunctivitis, characterized by conjunctival hemorrhages. The first AHC outbreak was described in 1969 in Ghana, West Africa, and was called Apollo disease, from the Apollo landing on the moon. This outbreak was caused by Enterovirus 70 (EV70) together with a Coxsackievirus A24 (CVA24v) variant, which are the major etiological agents involved in AHC outbreaks worldwide. AHC is known to be directly transmitted by close person-to-person contact or indirectly through soiled ophthalmological materials or unsafe recreational water. Recently, a possible airborne virus spread was suggested which could explain the high transmission rate of the disease. In the absence of a specific antiviral therapy, a rapid diagnosis of the causative agent is required to distinguish AHC due to enteroviruses from other ocular infectious diseases, for there are active drugs, or to quickly implement proper public health measures to limit the extension of the outbreak. However, virus identification remains difficult and time-consuming. Moreover, virological diagnosis is difficult to implement in developing countries where AHC has recently become a major problem for public health. PMID:19836177

  17. Bayesian Test of Significance for Conditional Independence: The Multinomial Model

    NASA Astrophysics Data System (ADS)

    de Morais Andrade, Pablo; Stern, Julio; de Bragança Pereira, Carlos

    2014-03-01

    Conditional independence tests (CI tests) have received special attention lately in Machine Learning and Computational Intelligence related literature as an important indicator of the relationship among the variables used by their models. In the field of Probabilistic Graphical Models (PGM)--which includes Bayesian Networks (BN) models--CI tests are especially important for the task of learning the PGM structure from data. In this paper, we propose the Full Bayesian Significance Test (FBST) for tests of conditional independence for discrete datasets. FBST is a powerful Bayesian test for precise hypothesis, as an alternative to frequentist's significance tests (characterized by the calculation of the \\emph{p-value}).

  18. Graves’ Ophthalmopathy Misdiagnosed as Relapsing Conjunctivitis

    PubMed Central

    Chatziralli, Irini P.; Kanonidou, Evgenia; Keryttopoulos, Petros; Papadopoulou, Dionyssia; Papazisis, Leonidas

    2010-01-01

    A 59-year-old female patient presented at the outpatients’ Department of Ophthalmology with epiphora, eyelid swelling, and a foreign body feeling in the right eye. The symptoms were present for 4 months, and the patient was treated as suffering from relapsing conjunctivitis. The slit lamp examination revealed keratitis due to exposure, related with the deficient closure of the eyelids. There was a 2 mm difference in the readings with the Hertel exophthalmometry examination between the eyes. Her medical history was clear, and she was referred for computed tomography of the orbits and brain and biochemical examinations (FT3, FT4, and TSH) to investigate the presence of an intraorbital mass. FT3 was significantly increased and TSH was accordingly low, indicating the diagnosis of Graves’ disease, which presented without other signs and symptoms apart from ophthalmopathy. Computed tomography scan excluded the diagnosis of an intraorbital mass. Therefore, it is important not to underestimate the ocular manifestations of systemic diseases. PMID:21060773

  19. A New Caching Technique to Support Conjunctive Queries in P2P DHT

    NASA Astrophysics Data System (ADS)

    Kobatake, Koji; Tagashira, Shigeaki; Fujita, Satoshi

    P2P DHT (Peer-to-Peer Distributed Hash Table) is one of typical techniques for realizing an efficient management of shared resources distributed over a network and a keyword search over such networks in a fully distributed manner. In this paper, we propose a new method for supporting conjunctive queries in P2P DHT. The basic idea of the proposed technique is to share a global information on past trials by conducting a local caching of search results for conjunctive queries and by registering the fact to the global DHT. Such a result caching is expected to significantly reduce the amount of transmitted data compared with conventional schemes. The effect of the proposed method is experimentally evaluated by simulation. The result of experiments indicates that by using the proposed method, the amount of returned data is reduced by 60% compared with conventional P2P DHT which does not support conjunctive queries.

  20. BIE: Bayesian Inference Engine

    NASA Astrophysics Data System (ADS)

    Weinberg, Martin D.

    2013-12-01

    The Bayesian Inference Engine (BIE) is an object-oriented library of tools written in C++ designed explicitly to enable Bayesian update and model comparison for astronomical problems. To facilitate "what if" exploration, BIE provides a command line interface (written with Bison and Flex) to run input scripts. The output of the code is a simulation of the Bayesian posterior distribution from which summary statistics e.g. by taking moments, or determine confidence intervals and so forth, can be determined. All of these quantities are fundamentally integrals and the Markov Chain approach produces variates heta distributed according to P( heta|D) so moments are trivially obtained by s