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Bayesian Modeling in Bioinformatics

Bayesian Modeling in Bioinformatics
Author: Dipak K. Dey
Publisher: CRC Press
Total Pages: 466
Release: 2010-09-03
Genre: Mathematics
ISBN: 1420070185

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Bayesian Modeling in Bioinformatics discusses the development and application of Bayesian statistical methods for the analysis of high-throughput bioinformatics data arising from problems in molecular and structural biology and disease-related medical research, such as cancer. It presents a broad overview of statistical inference, clustering, and c


Bayesian Methods in Structural Bioinformatics

Bayesian Methods in Structural Bioinformatics
Author: Thomas Hamelryck
Publisher: Springer
Total Pages: 399
Release: 2012-03-23
Genre: Medical
ISBN: 3642272258

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This book is an edited volume, the goal of which is to provide an overview of the current state-of-the-art in statistical methods applied to problems in structural bioinformatics (and in particular protein structure prediction, simulation, experimental structure determination and analysis). It focuses on statistical methods that have a clear interpretation in the framework of statistical physics, rather than ad hoc, black box methods based on neural networks or support vector machines. In addition, the emphasis is on methods that deal with biomolecular structure in atomic detail. The book is highly accessible, and only assumes background knowledge on protein structure, with a minimum of mathematical knowledge. Therefore, the book includes introductory chapters that contain a solid introduction to key topics such as Bayesian statistics and concepts in machine learning and statistical physics.


Probabilistic Modeling in Bioinformatics and Medical Informatics

Probabilistic Modeling in Bioinformatics and Medical Informatics
Author: Dirk Husmeier
Publisher: Springer Science & Business Media
Total Pages: 511
Release: 2006-05-06
Genre: Computers
ISBN: 1846281199

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Probabilistic Modelling in Bioinformatics and Medical Informatics has been written for researchers and students in statistics, machine learning, and the biological sciences. The first part of this book provides a self-contained introduction to the methodology of Bayesian networks. The following parts demonstrate how these methods are applied in bioinformatics and medical informatics. All three fields - the methodology of probabilistic modeling, bioinformatics, and medical informatics - are evolving very quickly. The text should therefore be seen as an introduction, offering both elementary tutorials as well as more advanced applications and case studies.


Bayesian Inference for Gene Expression and Proteomics

Bayesian Inference for Gene Expression and Proteomics
Author: Kim-Anh Do
Publisher: Cambridge University Press
Total Pages: 437
Release: 2006-07-24
Genre: Mathematics
ISBN: 052186092X

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Expert overviews of Bayesian methodology, tools and software for multi-platform high-throughput experimentation.


Probabilistic Methods for Bioinformatics

Probabilistic Methods for Bioinformatics
Author: Richard E. Neapolitan
Publisher: Morgan Kaufmann
Total Pages: 421
Release: 2009-06-12
Genre: Computers
ISBN: 0080919367

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The Bayesian network is one of the most important architectures for representing and reasoning with multivariate probability distributions. When used in conjunction with specialized informatics, possibilities of real-world applications are achieved. Probabilistic Methods for BioInformatics explains the application of probability and statistics, in particular Bayesian networks, to genetics. This book provides background material on probability, statistics, and genetics, and then moves on to discuss Bayesian networks and applications to bioinformatics. Rather than getting bogged down in proofs and algorithms, probabilistic methods used for biological information and Bayesian networks are explained in an accessible way using applications and case studies. The many useful applications of Bayesian networks that have been developed in the past 10 years are discussed. Forming a review of all the significant work in the field that will arguably become the most prevalent method in biological data analysis. Unique coverage of probabilistic reasoning methods applied to bioinformatics data--those methods that are likely to become the standard analysis tools for bioinformatics. Shares insights about when and why probabilistic methods can and cannot be used effectively; Complete review of Bayesian networks and probabilistic methods with a practical approach.


Bayesian Analysis of Gene Expression Data

Bayesian Analysis of Gene Expression Data
Author: Bani K. Mallick
Publisher: John Wiley & Sons
Total Pages: 252
Release: 2009-07-20
Genre: Mathematics
ISBN: 9780470742815

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The field of high-throughput genetic experimentation is evolving rapidly, with the advent of new technologies and new venues for data mining. Bayesian methods play a role central to the future of data and knowledge integration in the field of Bioinformatics. This book is devoted exclusively to Bayesian methods of analysis for applications to high-throughput gene expression data, exploring the relevant methods that are changing Bioinformatics. Case studies, illustrating Bayesian analyses of public gene expression data, provide the backdrop for students to develop analytical skills, while the more experienced readers will find the review of advanced methods challenging and attainable. This book: Introduces the fundamentals in Bayesian methods of analysis for applications to high-throughput gene expression data. Provides an extensive review of Bayesian analysis and advanced topics for Bioinformatics, including examples that extensively detail the necessary applications. Accompanied by website featuring datasets, exercises and solutions. Bayesian Analysis of Gene Expression Data offers a unique introduction to both Bayesian analysis and gene expression, aimed at graduate students in Statistics, Biomedical Engineers, Computer Scientists, Biostatisticians, Statistical Geneticists, Computational Biologists, applied Mathematicians and Medical consultants working in genomics. Bioinformatics researchers from many fields will find much value in this book.


Bayesian Statistical Methods

Bayesian Statistical Methods
Author: Brian J. Reich
Publisher: CRC Press
Total Pages: 288
Release: 2019-04-12
Genre: Mathematics
ISBN: 0429510918

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Bayesian Statistical Methods provides data scientists with the foundational and computational tools needed to carry out a Bayesian analysis. This book focuses on Bayesian methods applied routinely in practice including multiple linear regression, mixed effects models and generalized linear models (GLM). The authors include many examples with complete R code and comparisons with analogous frequentist procedures. In addition to the basic concepts of Bayesian inferential methods, the book covers many general topics: Advice on selecting prior distributions Computational methods including Markov chain Monte Carlo (MCMC) Model-comparison and goodness-of-fit measures, including sensitivity to priors Frequentist properties of Bayesian methods Case studies covering advanced topics illustrate the flexibility of the Bayesian approach: Semiparametric regression Handling of missing data using predictive distributions Priors for high-dimensional regression models Computational techniques for large datasets Spatial data analysis The advanced topics are presented with sufficient conceptual depth that the reader will be able to carry out such analysis and argue the relative merits of Bayesian and classical methods. A repository of R code, motivating data sets, and complete data analyses are available on the book’s website. Brian J. Reich, Associate Professor of Statistics at North Carolina State University, is currently the editor-in-chief of the Journal of Agricultural, Biological, and Environmental Statistics and was awarded the LeRoy & Elva Martin Teaching Award. Sujit K. Ghosh, Professor of Statistics at North Carolina State University, has over 22 years of research and teaching experience in conducting Bayesian analyses, received the Cavell Brownie mentoring award, and served as the Deputy Director at the Statistical and Applied Mathematical Sciences Institute.


Bayesian Modeling and Computation in Python

Bayesian Modeling and Computation in Python
Author: Osvaldo A. Martin
Publisher: CRC Press
Total Pages: 420
Release: 2021-12-28
Genre: Computers
ISBN: 1000520048

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Bayesian Modeling and Computation in Python aims to help beginner Bayesian practitioners to become intermediate modelers. It uses a hands on approach with PyMC3, Tensorflow Probability, ArviZ and other libraries focusing on the practice of applied statistics with references to the underlying mathematical theory. The book starts with a refresher of the Bayesian Inference concepts. The second chapter introduces modern methods for Exploratory Analysis of Bayesian Models. With an understanding of these two fundamentals the subsequent chapters talk through various models including linear regressions, splines, time series, Bayesian additive regression trees. The final chapters include Approximate Bayesian Computation, end to end case studies showing how to apply Bayesian modelling in different settings, and a chapter about the internals of probabilistic programming languages. Finally the last chapter serves as a reference for the rest of the book by getting closer into mathematical aspects or by extending the discussion of certain topics. This book is written by contributors of PyMC3, ArviZ, Bambi, and Tensorflow Probability among other libraries.


Bayesian Phylogenetics

Bayesian Phylogenetics
Author: Ming-Hui Chen
Publisher: CRC Press
Total Pages: 398
Release: 2014-05-27
Genre: Mathematics
ISBN: 1466500794

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Offering a rich diversity of models, Bayesian phylogenetics allows evolutionary biologists, systematists, ecologists, and epidemiologists to obtain answers to very detailed phylogenetic questions. Suitable for graduate-level researchers in statistics and biology, Bayesian Phylogenetics: Methods, Algorithms, and Applications presents a snapshot of current trends in Bayesian phylogenetic research. Encouraging interdisciplinary research, this book introduces state-of-the-art phylogenetics to the Bayesian statistical community and, likewise, presents state-of-the-art Bayesian statistics to the phylogenetics community. The book emphasizes model selection, reflecting recent interest in accurately estimating marginal likelihoods. It also discusses new approaches to improve mixing in Bayesian phylogenetic analyses in which the tree topology varies. In addition, the book covers divergence time estimation, biologically realistic models, and the burgeoning interface between phylogenetics and population genetics.


Bayesian Time Series Models

Bayesian Time Series Models
Author: David Barber
Publisher: Cambridge University Press
Total Pages: 432
Release: 2011-08-11
Genre: Computers
ISBN: 0521196760

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The first unified treatment of time series modelling techniques spanning machine learning, statistics, engineering and computer science.