Sparse Model Building From Genome Wide Variation With Graphical Models
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Sparse Model Building From Genome Wide Variation With Graphical Models
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Author : Benjamin Alexander Logsdon
language : en
Publisher:
Release Date : 2011
Sparse Model Building From Genome Wide Variation With Graphical Models written by Benjamin Alexander Logsdon and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011 with categories.
High throughput sequencing and expression characterization have lead to an explosion of phenotypic and genotypic molecular data underlying both experimental studies and outbred populations. We develop a novel class of algorithms to reconstruct sparse models among these molecular phenotypes (e.g. expression products) and genotypes (e.g. single nucleotide polymorphisms), via both a Bayesian hierarchical model, when the sample size is much smaller than the model dimension (i.e. p n) and the well characterized adaptive lasso algo- rithm. Specifically, we propose novel approaches to the problems of increasing power to detect additional loci in genome-wide association studies using our variational algorithm, efficiently learning directed cyclic graphs from expression and genotype data using the adaptive lasso, and constructing genomewide undirected graphs among genotype, expression and downstream phenotype data using an extension of the variational feature selection algorithm. The Bayesian hierarchical model is derived for a parametric multiple regression model with a mixture prior of a point mass and normal distribution for each regression coefficient, and appropriate priors for the set of hyperparameters. When combined with a probabilistic consistency bound on the model dimension, this approach leads to very sparse solutions without the need for cross validation. We use a variational Bayes approximate inference approach in our algorithm, where we impose a complete factorization across all parameters for the approximate posterior distribution, and then minimize the KullbackLeibler divergence between the approximate and true posterior distributions. Since the prior distribution is non-convex, we restart the algorithm many times to find multiple posterior modes, and combine information across all discovered modes in an approximate Bayesian model averaging framework, to reduce the variance of the posterior probability estimates. We perform analysis of three major publicly available data-sets: the HapMap 2 genotype and expression data collected on immortalized lymphoblastoid cell lines, the genome-wide gene expression and genetic marker data collected for a yeast intercross, and genomewide gene expression, genetic marker, and downstream phenotypes related to weight in a mouse F2 intercross. Based on both simulations and data analysis we show that our algorithms can outperform other state of the art model selection procedures when including thousands to hundreds of thousands of genotypes and expression traits, in terms of aggressively controlling false discovery rate, and generating rich simultaneous statistical models.
Probabilistic Graphical Models For Genetics Genomics And Postgenomics
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Author : Christine Sinoquet
language : en
Publisher: OUP Oxford
Release Date : 2014-09-18
Probabilistic Graphical Models For Genetics Genomics And Postgenomics written by Christine Sinoquet and has been published by OUP Oxford this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-09-18 with Science categories.
Nowadays bioinformaticians and geneticists are faced with myriad high-throughput data usually presenting the characteristics of uncertainty, high dimensionality and large complexity. These data will only allow insights into this wealth of so-called 'omics' data if represented by flexible and scalable models, prior to any further analysis. At the interface between statistics and machine learning, probabilistic graphical models (PGMs) represent a powerful formalism to discover complex networks of relations. These models are also amenable to incorporating a priori biological information. Network reconstruction from gene expression data represents perhaps the most emblematic area of research where PGMs have been successfully applied. However these models have also created renewed interest in genetics in the broad sense, in particular regarding association genetics, causality discovery, prediction of outcomes, detection of copy number variations, and epigenetics. This book provides an overview of the applications of PGMs to genetics, genomics and postgenomics to meet this increased interest. A salient feature of bioinformatics, interdisciplinarity, reaches its limit when an intricate cooperation between domain specialists is requested. Currently, few people are specialists in the design of advanced methods using probabilistic graphical models for postgenomics or genetics. This book deciphers such models so that their perceived difficulty no longer hinders their use and focuses on fifteen illustrations showing the mechanisms behind the models. Probabilistic Graphical Models for Genetics, Genomics and Postgenomics covers six main themes: (1) Gene network inference (2) Causality discovery (3) Association genetics (4) Epigenetics (5) Detection of copy number variations (6) Prediction of outcomes from high-dimensional genomic data. Written by leading international experts, this is a collection of the most advanced work at the crossroads of probabilistic graphical models and genetics, genomics, and postgenomics. The self-contained chapters provide an enlightened account of the pros and cons of applying these powerful techniques.
Statistical Analysis For High Dimensional Data
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Author : Arnoldo Frigessi
language : en
Publisher: Springer
Release Date : 2016-02-16
Statistical Analysis For High Dimensional Data written by Arnoldo Frigessi and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-02-16 with Mathematics categories.
This book features research contributions from The Abel Symposium on Statistical Analysis for High Dimensional Data, held in Nyvågar, Lofoten, Norway, in May 2014. The focus of the symposium was on statistical and machine learning methodologies specifically developed for inference in “big data” situations, with particular reference to genomic applications. The contributors, who are among the most prominent researchers on the theory of statistics for high dimensional inference, present new theories and methods, as well as challenging applications and computational solutions. Specific themes include, among others, variable selection and screening, penalised regression, sparsity, thresholding, low dimensional structures, computational challenges, non-convex situations, learning graphical models, sparse covariance and precision matrices, semi- and non-parametric formulations, multiple testing, classification, factor models, clustering, and preselection. Highlighting cutting-edge research and casting light on future research directions, the contributions will benefit graduate students and researchers in computational biology, statistics and the machine learning community.
Advances In Systems Immunology And Cancer
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Author : Masaru Tomita
language : en
Publisher: Frontiers E-books
Release Date : 2014-12-17
Advances In Systems Immunology And Cancer written by Masaru Tomita and has been published by Frontiers E-books this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-12-17 with Biology (General) categories.
Cladag 2017 Book Of Short Papers
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Author : Francesca Greselin
language : en
Publisher: Universitas Studiorum
Release Date : 2017-09-29
Cladag 2017 Book Of Short Papers written by Francesca Greselin and has been published by Universitas Studiorum this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-09-29 with Mathematics categories.
This book is the collection of the Abstract / Short Papers submitted by the authors of the International Conference of The CLAssification and Data Analysis Group (CLADAG) of the Italian Statistical Society (SIS), held in Milan (Italy) on September 13-15, 2017.
Comprehensive Chemometrics
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Author : Steven Brown
language : en
Publisher: Elsevier
Release Date : 2020-05-26
Comprehensive Chemometrics written by Steven Brown and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-05-26 with Science categories.
Comprehensive Chemometrics, Second Edition, Four Volume Set features expanded and updated coverage, along with new content that covers advances in the field since the previous edition published in 2009. Subject of note include updates in the fields of multidimensional and megavariate data analysis, omics data analysis, big chemical and biochemical data analysis, data fusion and sparse methods. The book follows a similar structure to the previous edition, using the same section titles to frame articles. Many chapters from the previous edition are updated, but there are also many new chapters on the latest developments. Presents integrated reviews of each chemical and biological method, examining their merits and limitations through practical examples and extensive visuals Bridges a gap in knowledge, covering developments in the field since the first edition published in 2009 Meticulously organized, with articles split into 4 sections and 12 sub-sections on key topics to allow students, researchers and professionals to find relevant information quickly and easily Written by academics and practitioners from various fields and regions to ensure that the knowledge within is easily understood and applicable to a large audience Presents integrated reviews of each chemical and biological method, examining their merits and limitations through practical examples and extensive visuals Bridges a gap in knowledge, covering developments in the field since the first edition published in 2009 Meticulously organized, with articles split into 4 sections and 12 sub-sections on key topics to allow students, researchers and professionals to find relevant information quickly and easily Written by academics and practitioners from various fields and regions to ensure that the knowledge within is easily understood and applicable to a large audience
Computational Evolution Of Neural And Morphological Development
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Author : Yaochu Jin
language : en
Publisher: Springer Nature
Release Date : 2023-07-14
Computational Evolution Of Neural And Morphological Development written by Yaochu Jin and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-07-14 with Computers categories.
This book provides a basic yet unified overview of theory and methodologies for evolutionary developmental systems. Based on the author’s extensive research into the synergies between various approaches to artificial intelligence including evolutionary computation, artificial neural networks, and systems biology, it also examines the inherent links between biological intelligence and artificial intelligence. The book begins with an introduction to computational algorithms used to understand and simulate biological evolution and development, including evolutionary algorithms, gene regulatory network models, multi-cellular models for neural and morphological development, and computational models of neural plasticity. Chap. 2 discusses important properties of biological gene regulatory systems, including network motifs, network connectivity, robustness and evolvability. Going a step further, Chap. 3 presents methods for synthesizing regulatory motifs from scratch and creating more complex regulatory dynamics by combining basic regulatory motifs using evolutionary algorithms. Multi-cellular growth models, which can be used to simulate either neural or morphological development, are presented in Chapters 4 and 5. Chap. 6 examines the synergies and coupling between neural and morphological evolution and development. In turn, Chap. 7 provides preliminary yet promising examples of how evolutionary developmental systems can help in self-organized pattern generation, referred to as morphogenetic self-organization, highlighting the great potentials of evolutionary developmental systems. Finally, Chap. 8 rounds out the book, stressing the importance and promise of the evolutionary developmental approach to artificial intelligence. Featuring a wealth of diagrams, graphs and charts to aid in comprehension, this book offers a valuable asset for graduate students, researchers and practitioners who are interested in pursuing a different approach to artificial intelligence.
Genome Scale Algorithm Design
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Author : Veli Mäkinen
language : en
Publisher: Cambridge University Press
Release Date : 2023-10-12
Genome Scale Algorithm Design written by Veli Mäkinen and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-10-12 with Computers categories.
The fundamental algorithms and data structures that power standard bioscience workflows, with rigorous computer science formulations.
Biocomputing 2019 Proceedings Of The Pacific Symposium
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Author : Russ B Altman
language : en
Publisher: World Scientific
Release Date : 2018-11-28
Biocomputing 2019 Proceedings Of The Pacific Symposium written by Russ B Altman and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-11-28 with Computers categories.
The Pacific Symposium on Biocomputing (PSB) 2019 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2019 will be held on January 3 - 7, 2019 in Kohala Coast, Hawaii. Tutorials and workshops will be offered prior to the start of the conference.PSB 2019 will bring together top researchers from the US, the Asian Pacific nations, and around the world to exchange research results and address open issues in all aspects of computational biology. It is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling, and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology.The PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing. For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals. PSB sessions are organized by leaders of research in biocomputing's 'hot topics.' In this way, the meeting provides an early forum for serious examination of emerging methods and approaches in this rapidly changing field.
Neuroimaging Approaches To The Study Of Cognitive Aging
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Author : Ronald Cohen
language : en
Publisher: Frontiers Media SA
Release Date : 2020-07-29
Neuroimaging Approaches To The Study Of Cognitive Aging written by Ronald Cohen and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-07-29 with categories.