Download or read book Large scale Variational Inference for Bayesian Joint Regression Modelling of High dimensional Genetic Data written by Hélène Ruffieux and published by . This book was released on 2019 with total page 192 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mots-clés de l'auteur: Bayesian sparse regression ; Hierarchical model ; High-dimensional data ; Molecular quantitative trait locus analysis ; Pleiotropy ; Statistical genetics ; Variable selection ; Variational inference.
Download or read book Statistical Analysis for High Dimensional Data written by Arnoldo Frigessi and published by Springer. This book was released on 2016-02-16 with total page 313 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Frontiers in Massive Data Analysis written by National Research Council and published by National Academies Press. This book was released on 2013-09-03 with total page 191 pages. Available in PDF, EPUB and Kindle. Book excerpt: Data mining of massive data sets is transforming the way we think about crisis response, marketing, entertainment, cybersecurity and national intelligence. Collections of documents, images, videos, and networks are being thought of not merely as bit strings to be stored, indexed, and retrieved, but as potential sources of discovery and knowledge, requiring sophisticated analysis techniques that go far beyond classical indexing and keyword counting, aiming to find relational and semantic interpretations of the phenomena underlying the data. Frontiers in Massive Data Analysis examines the frontier of analyzing massive amounts of data, whether in a static database or streaming through a system. Data at that scale-terabytes and petabytes-is increasingly common in science (e.g., particle physics, remote sensing, genomics), Internet commerce, business analytics, national security, communications, and elsewhere. The tools that work to infer knowledge from data at smaller scales do not necessarily work, or work well, at such massive scale. New tools, skills, and approaches are necessary, and this report identifies many of them, plus promising research directions to explore. Frontiers in Massive Data Analysis discusses pitfalls in trying to infer knowledge from massive data, and it characterizes seven major classes of computation that are common in the analysis of massive data. Overall, this report illustrates the cross-disciplinary knowledge-from computer science, statistics, machine learning, and application disciplines-that must be brought to bear to make useful inferences from massive data.
Download or read book Probabilistic Graphical Models for Genetics Genomics and Postgenomics written by Christine Sinoquet and published by OUP Oxford. This book was released on 2014-09-18 with total page 415 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Models of Neural Networks III written by Eytan Domany and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: One of the most challenging and fascinating problems of the theory of neural nets is that of asymptotic behavior, of how a system behaves as time proceeds. This is of particular relevance to many practical applications. Here we focus on association, generalization, and representation. We turn to the last topic first. The introductory chapter, "Global Analysis of Recurrent Neural Net works," by Andreas Herz presents an in-depth analysis of how to construct a Lyapunov function for various types of dynamics and neural coding. It includes a review of the recent work with John Hopfield on integrate-and fire neurons with local interactions. The chapter, "Receptive Fields and Maps in the Visual Cortex: Models of Ocular Dominance and Orientation Columns" by Ken Miller, explains how the primary visual cortex may asymptotically gain its specific structure through a self-organization process based on Hebbian learning. His argu ment since has been shown to be rather susceptible to generalization.
Download or read book A Bayesian Large Scale Multiple Regression Model for Genome Wide Association Summary Statistics written by Xiang Zhu and published by . This book was released on 2017 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt: We apply RSS methods to analyze published GWAS summary statistics of 1.1 millions common variants from 31 human phenotypes, 3,913 biological pathways retrieved from nine public databases, and 113 tissue-associated gene sets derived from gene expression profiles of 53 human tissues. We identify many previously-unreported genes, pathways and tissues that show strong evidence for association with complex traits in our large-scale integrated analyses. Software is available at https://github.com/stephenslab/rss.
Download or read book Modeling and Analysis of Bio molecular Networks written by Jinhu Lü and published by Springer Nature. This book was released on 2020-12-06 with total page 464 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book addresses a number of questions from the perspective of complex systems: How can we quantitatively understand the life phenomena? How can we model life systems as complex bio-molecular networks? Are there any methods to clarify the relationships among the structures, dynamics and functions of bio-molecular networks? How can we statistically analyse large-scale bio-molecular networks? Focusing on the modeling and analysis of bio-molecular networks, the book presents various sophisticated mathematical and statistical approaches. The life system can be described using various levels of bio-molecular networks, including gene regulatory networks, and protein-protein interaction networks. It first provides an overview of approaches to reconstruct various bio-molecular networks, and then discusses the modeling and dynamical analysis of simple genetic circuits, coupled genetic circuits, middle-sized and large-scale biological networks, clarifying the relationships between the structures, dynamics and functions of the networks covered. In the context of large-scale bio-molecular networks, it introduces a number of statistical methods for exploring important bioinformatics applications, including the identification of significant bio-molecules for network medicine and genetic engineering. Lastly, the book describes various state-of-art statistical methods for analysing omics data generated by high-throughput sequencing. This book is a valuable resource for readers interested in applying systems biology, dynamical systems or complex networks to explore the truth of nature.
Download or read book Bayesian Data Analysis Third Edition written by Andrew Gelman and published by CRC Press. This book was released on 2013-11-01 with total page 677 pages. Available in PDF, EPUB and Kindle. Book excerpt: Now in its third edition, this classic book is widely considered the leading text on Bayesian methods, lauded for its accessible, practical approach to analyzing data and solving research problems. Bayesian Data Analysis, Third Edition continues to take an applied approach to analysis using up-to-date Bayesian methods. The authors—all leaders in the statistics community—introduce basic concepts from a data-analytic perspective before presenting advanced methods. Throughout the text, numerous worked examples drawn from real applications and research emphasize the use of Bayesian inference in practice. New to the Third Edition Four new chapters on nonparametric modeling Coverage of weakly informative priors and boundary-avoiding priors Updated discussion of cross-validation and predictive information criteria Improved convergence monitoring and effective sample size calculations for iterative simulation Presentations of Hamiltonian Monte Carlo, variational Bayes, and expectation propagation New and revised software code The book can be used in three different ways. For undergraduate students, it introduces Bayesian inference starting from first principles. For graduate students, the text presents effective current approaches to Bayesian modeling and computation in statistics and related fields. For researchers, it provides an assortment of Bayesian methods in applied statistics. Additional materials, including data sets used in the examples, solutions to selected exercises, and software instructions, are available on the book’s web page.
Download or read book Bayesian Inference for Gene Expression and Proteomics written by Kim-Anh Do and published by Cambridge University Press. This book was released on 2006-07-24 with total page 437 pages. Available in PDF, EPUB and Kindle. Book excerpt: Expert overviews of Bayesian methodology, tools and software for multi-platform high-throughput experimentation.
Download or read book Analysis of Large Scale Genetic Perturbation with Linear Regression of Microarray and Bayesian Networks written by Ruifu Jiang and published by . This book was released on 2018 with total page 33 pages. Available in PDF, EPUB and Kindle. Book excerpt: This paper aims to examine how large-scale genetic perturbations reveal regulatory network and an abundance of gene-specific repressors by analyzing data from a published paper (Kemmeren et al., 2014) . The main goal is to uniformly determine the effect of different components on the expression of all other genes. The idea of their experiment is doing gene deletion of one-quarter of yeast genes individually and then observing the mRNA expression genomewide. Then genetic perturbation would be resulted, which also shows some properties including the architecture of protein complexes and pathways, identification of expression changes compatible with viability, and the varying responsiveness to genetic perturbation. And all data collected from this experiment is constructed as a genetic perturbation network which present a varying connectivities among regulators. Finally it provides a regulation network with analysis result from R package limma and sparsebn.
Download or read book Large scale Inference of Correlation Between Complex Biological Traits written by Zhenyu Zhang and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Inferring dependencies between complex biological traits while accounting for evolutionary relationships among specimens is of great scientific interest, yet remains infeasible when trait and specimen counts grow large. I aim to develop a scalable Bayesian inference framework to assess correlation between complex traits along the evolutionary tree relating the specimens and informed by molecular sequences. To accommodate discrete and continuous traits, I posit a phylogenetic multivariate probit model that uses a latent variable framework. Posterior computation under this model requires integrating many latent variables, or equivalently making many computationally expensive draws from a high-dimensional multivariate truncated normal distribution (MTN). To tackle this challenge, I propose an inference scheme that exploits 1) representative cutting-edge Markov chain Monte Carlo (MCMC) methods including the bouncy particle sampler (BPS), the Markovian Zigzag sampler (ZZ), and the Zigzag Hamiltonian Monte Carlo (Zigzag-HMC) that can simultaneously sample all truncated normal dimensions, and 2) novel dynamic programming strategies that reduce the cost of likelihood and gradient evaluations for all three samplers to linear in sample size. Compared to the previous best practices that employ multiple-try rejection sampling, my approach achieves an order-of-magnitude speedup, allowing us to tackle previously unworkable large-scale problems. In an application with 535 HIV-1 viruses and 24 traits that necessitates sampling from a 11,235-dimensional MTN, my method makes it possible to examine the conditional dependencies between 21 immune escape mutations and 3 virulence measurements. In a second application I study the evolution of influenza H1N1 glycosylations using around 900 viruses. Lastly, I extend the phylogenetic probit model to incorporate categorical traits and demonstrate its use to investigate Aquilegia flower and pollinator coevolution. In summary, the contribution of this dissertation is two-fold. First, I develop a state-of-the-art solution for the long-standing problem in Bayesian phylogenetics | learning correlation among complex biological traits with joint tree modeling. Second, further empirical and theoretical investigation of BPS, ZZ, and Zigzag-HMC yield insight into the differences and similarities between these recently developed MCMC samplers. As Zigzag-HMC outperforms the other two on MTNs, I also implement this approach in a standalone R package, aiming to provide a general efficient tool for high-dimensional MTN simulation.
Download or read book Probabilistic Graphical Models written by Daphne Koller and published by MIT Press. This book was released on 2009-07-31 with total page 1270 pages. Available in PDF, EPUB and Kindle. Book excerpt: A general framework for constructing and using probabilistic models of complex systems that would enable a computer to use available information for making decisions. Most tasks require a person or an automated system to reason—to reach conclusions based on available information. The framework of probabilistic graphical models, presented in this book, provides a general approach for this task. The approach is model-based, allowing interpretable models to be constructed and then manipulated by reasoning algorithms. These models can also be learned automatically from data, allowing the approach to be used in cases where manually constructing a model is difficult or even impossible. Because uncertainty is an inescapable aspect of most real-world applications, the book focuses on probabilistic models, which make the uncertainty explicit and provide models that are more faithful to reality. Probabilistic Graphical Models discusses a variety of models, spanning Bayesian networks, undirected Markov networks, discrete and continuous models, and extensions to deal with dynamical systems and relational data. For each class of models, the text describes the three fundamental cornerstones: representation, inference, and learning, presenting both basic concepts and advanced techniques. Finally, the book considers the use of the proposed framework for causal reasoning and decision making under uncertainty. The main text in each chapter provides the detailed technical development of the key ideas. Most chapters also include boxes with additional material: skill boxes, which describe techniques; case study boxes, which discuss empirical cases related to the approach described in the text, including applications in computer vision, robotics, natural language understanding, and computational biology; and concept boxes, which present significant concepts drawn from the material in the chapter. Instructors (and readers) can group chapters in various combinations, from core topics to more technically advanced material, to suit their particular needs.
Download or read book New Statistical Perspectives on Efficient Big Data Algorithms for High dimensional Bayesian Regression and Model Selection written by Daniel Christian Ahfock and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Understanding and Interpreting Machine Learning in Medical Image Computing Applications written by Danail Stoyanov and published by Springer. This book was released on 2018-10-23 with total page 158 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed joint proceedings of the First International Workshop on Machine Learning in Clinical Neuroimaging, MLCN 2018, the First International Workshop on Deep Learning Fails, DLF 2018, and the First International Workshop on Interpretability of Machine Intelligence in Medical Image Computing, iMIMIC 2018, held in conjunction with the 21st International Conference on Medical Imaging and Computer-Assisted Intervention, MICCAI 2018, in Granada, Spain, in September 2018. The 4 full MLCN papers, the 6 full DLF papers, and the 6 full iMIMIC papers included in this volume were carefully reviewed and selected. The MLCN contributions develop state-of-the-art machine learning methods such as spatio-temporal Gaussian process analysis, stochastic variational inference, and deep learning for applications in Alzheimer's disease diagnosis and multi-site neuroimaging data analysis; the DLF papers evaluate the strengths and weaknesses of DL and identify the main challenges in the current state of the art and future directions; the iMIMIC papers cover a large range of topics in the field of interpretability of machine learning in the context of medical image analysis.
Download or read book Multidimensional Item Response Theory written by M.D. Reckase and published by Springer Science & Business Media. This book was released on 2009-07-07 with total page 355 pages. Available in PDF, EPUB and Kindle. Book excerpt: First thorough treatment of multidimensional item response theory Description of methods is supported by numerous practical examples Describes procedures for multidimensional computerized adaptive testing
Download or read book Large Scale Variational Bayesian Inference with Applications to Image Deblurring written by Brian Jonathan Verbaken and published by . This book was released on 2011 with total page 78 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Advances in Neural Information Processing Systems 19 written by Bernhard Schölkopf and published by MIT Press. This book was released on 2007 with total page 1668 pages. Available in PDF, EPUB and Kindle. Book excerpt: The annual Neural Information Processing Systems (NIPS) conference is the flagship meeting on neural computation and machine learning. This volume contains the papers presented at the December 2006 meeting, held in Vancouver.
