This book is a thorough introduction to the formal foundations and practical applications of Bayesian networks. It provides an extensive discussion of techniques for building Bayesian networks that ...model real-world situations, including techniques for synthesizing models from design, learning models from data, and debugging models using sensitivity analysis. It also treats exact and approximate inference algorithms at both theoretical and practical levels. The treatment of exact algorithms covers the main inference paradigms based on elimination and conditioning and includes advanced methods for compiling Bayesian networks, time-space tradeoffs, and exploiting local structure of massively connected networks. The treatment of approximate algorithms covers the main inference paradigms based on sampling and optimization and includes influential algorithms such as importance sampling, MCMC, and belief propagation. The author assumes very little background on the covered subjects, supplying in-depth discussions for theoretically inclined readers and enough practical details to provide an algorithmic cookbook for the system developer.
Bayes' rule appears to be a straightforward, one-line theorem: by updating our initial beliefs with objective new information, we get a new and improved belief. To its adherents, it is an elegant ...statement about learning from experience. To its opponents, it is subjectivity run amok.
In the first-ever account of Bayes' rule for general readers, Sharon Bertsch McGrayne explores this controversial theorem and the human obsessions surrounding it. She traces its discovery by an amateur mathematician in the 1740s through its development into roughly its modern form by French scientist Pierre Simon Laplace. She reveals why respected statisticians rendered it professionally taboo for 150 years-at the same time that practitioners relied on it to solve crises involving great uncertainty and scanty information (Alan Turing's role in breaking Germany's Enigma code during World War II), and explains how the advent of off-the-shelf computer technology in the 1980s proved to be a game-changer. Today, Bayes' rule is used everywhere from DNA de-coding to Homeland Security.
Drawing on primary source material and interviews with statisticians and other scientists,The Theory That Would Not Dieis the riveting account of how a seemingly simple theorem ignited one of the greatest controversies of all time.
Datasets collected by high-throughput sequencing (HTS) of 16S rRNA gene amplimers, metagenomes or metatranscriptomes are commonplace and being used to study human disease states, ecological ...differences between sites, and the built environment. There is increasing awareness that microbiome datasets generated by HTS are compositional because they have an arbitrary total imposed by the instrument. However, many investigators are either unaware of this or assume specific properties of the compositional data. The purpose of this review is to alert investigators to the dangers inherent in ignoring the compositional nature of the data, and point out that HTS datasets derived from microbiome studies can and should be treated as compositions at all stages of analysis. We briefly introduce compositional data, illustrate the pathologies that occur when compositional data are analyzed inappropriately, and finally give guidance and point to resources and examples for the analysis of microbiome datasets using compositional data analysis.
Pretimed signalized intersection is known as a common source of congestion, especially in urban heterogeneous traffic. Furthermore, the accuracy of saturation flow rate is found to cause efficient ...and vital capacity estimation, in order to ensure optimal design and operation of the signal timings. Presently, the traffic also consists of diverse vehicle presence, each with its own static and dynamic characteristics. The passenger car equivalent (PCE) in an essential unit is also used to measure heterogenous traffic into the PCU (Passenger Car Unit). Based on the collection of observed data at three targets in Banda Aceh City, this study aims to redetermine the PCEs by using Bayesian linear regression, through the Random-walk Metropolis-Hastings and Gibbs sampling. The result showed that the obtained PCE values were 0.24, 1.0, and 0.80 for motorcycle (MC), passenger car (PC), and motorized rickshaw (MR), respectively. It also showed that a significant deviation was found between new and IHCM PCEs, as the source of error was partially due to the vehicle compositions. The present traffic characteristics were also substantially different from the prevailing conditions of IHCM 1997. Therefore, the proposed PCEs enhanced the accuracy of base saturation flow prediction, provided support for traffic operation design, alleviated congestion, and reduced delay within the city, which in turn improved the estimation of signalized intersection capacity.
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This work aimed to use the Bayesian approach to discriminate 43 genotypes of Coffea canephora cv. Conilon, which were cultivated in two producing regions to identify the most stable and productive ...genotypes. The experiment was a randomized block design with three replications and seven plants per plot, carried out in the south of Bahia and the north of Espírito Santo, environments with different climatic conditions, and evaluated during four harvests. The proposed Bayesian methodology was implemented in R language, using the MCMCglmm package. This approach made it possible to find great genetic divergence between the materials, and detect significant effects for both genotype, environment, and year, but the hyper-parametrized models (block effect) presented problems of singularity and convergence. It was also possible to detect a few differences between crops within the same environment. With a model with lower residual, it was possible to recommend the most productive genotypes for both environments: LB1, AD1, Peneirão, Z21, and P2.
We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. This software platform is a re-design of the popular BEAST 1 platform to ...correct structural deficiencies that became evident as the BEAST 1 software evolved. Key among those deficiencies was the lack of post-deployment extensibility. BEAST 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform. This package architecture is showcased with a number of recently published new models encompassing birth-death-sampling tree priors, phylodynamics and model averaging for substitution models and site partitioning. A second major improvement is the ability to read/write the entire state of the MCMC chain to/from disk allowing it to be easily shared between multiple instances of the BEAST software. This facilitates checkpointing and better support for multi-processor and high-end computing extensions. Finally, the functionality in new packages can be easily added to the user interface (BEAUti 2) by a simple XML template-based mechanism because BEAST 2 has been re-designed to provide greater integration between the analysis engine and the user interface so that, for example BEAST and BEAUti use exactly the same XML file format.
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Genetic association studies, in particular the genome-wide association study (GWAS) design, have provided a wealth of novel insights into the aetiology of a wide range of human diseases and traits, ...in particular cardiovascular diseases and lipid biomarkers. The next challenge consists of understanding the molecular basis of these associations. The integration of multiple association datasets, including gene expression datasets, can contribute to this goal. We have developed a novel statistical methodology to assess whether two association signals are consistent with a shared causal variant. An application is the integration of disease scans with expression quantitative trait locus (eQTL) studies, but any pair of GWAS datasets can be integrated in this framework. We demonstrate the value of the approach by re-analysing a gene expression dataset in 966 liver samples with a published meta-analysis of lipid traits including >100,000 individuals of European ancestry. Combining all lipid biomarkers, our re-analysis supported 26 out of 38 reported colocalisation results with eQTLs and identified 14 new colocalisation results, hence highlighting the value of a formal statistical test. In three cases of reported eQTL-lipid pairs (SYPL2, IFT172, TBKBP1) for which our analysis suggests that the eQTL pattern is not consistent with the lipid association, we identify alternative colocalisation results with SORT1, GCKR, and KPNB1, indicating that these genes are more likely to be causal in these genomic intervals. A key feature of the method is the ability to derive the output statistics from single SNP summary statistics, hence making it possible to perform systematic meta-analysis type comparisons across multiple GWAS datasets (implemented online at http://coloc.cs.ucl.ac.uk/coloc/). Our methodology provides information about candidate causal genes in associated intervals and has direct implications for the understanding of complex diseases as well as the design of drugs to target disease pathways.
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