Markov Chain Monte Carlo Posterior Sampling with the Hamiltonian Method

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ISBN 13 :
Total Pages : 5 pages
Book Rating : 4.:/5 (893 download)

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Book Synopsis Markov Chain Monte Carlo Posterior Sampling with the Hamiltonian Method by :

Download or read book Markov Chain Monte Carlo Posterior Sampling with the Hamiltonian Method written by and published by . This book was released on 2001 with total page 5 pages. Available in PDF, EPUB and Kindle. Book excerpt: A major advantage of Bayesian data analysis is that provides a characterization of the uncertainty in the model parameters estimated from a given set of measurements in the form of a posterior probability distribution. When the analysis involves a complicated physical phenomenon, the posterior may not be available in analytic form, but only calculable by means of a simulation code. In such cases, the uncertainty in inferred model parameters requires characterization of a calculated functional. An appealing way to explore the posterior, and hence characterize the uncertainty, is to employ the Markov Chain Monte Carlo technique. The goal of MCMC is to generate a sequence random of parameter x samples from a target pdf (probability density function), [pi](x). In Bayesian analysis, this sequence corresponds to a set of model realizations that follow the posterior distribution. There are two basic MCMC techniques. In Gibbs sampling, typically one parameter is drawn from the conditional pdf at a time, holding all others fixed. In the Metropolis algorithm, all the parameters can be varied at once. The parameter vector is perturbed from the current sequence point by adding a trial step drawn randomly from a symmetric pdf. The trial position is either accepted or rejected on the basis of the probability at the trial position relative to the current one. The Metropolis algorithm is often employed because of its simplicity. The aim of this work is to develop MCMC methods that are useful for large numbers of parameters, n, say hundreds or more. In this regime the Metropolis algorithm can be unsuitable, because its efficiency drops as 0.3/n. The efficiency is defined as the reciprocal of the number of steps in the sequence needed to effectively provide a statistically independent sample from [pi].

Handbook of Markov Chain Monte Carlo

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Publisher : CRC Press
ISBN 13 : 1420079425
Total Pages : 620 pages
Book Rating : 4.4/5 (2 download)

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Book Synopsis Handbook of Markov Chain Monte Carlo by : Steve Brooks

Download or read book Handbook of Markov Chain Monte Carlo written by Steve Brooks and published by CRC Press. This book was released on 2011-05-10 with total page 620 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since their popularization in the 1990s, Markov chain Monte Carlo (MCMC) methods have revolutionized statistical computing and have had an especially profound impact on the practice of Bayesian statistics. Furthermore, MCMC methods have enabled the development and use of intricate models in an astonishing array of disciplines as diverse as fisherie

Monte Carlo Methods

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Publisher : Springer Nature
ISBN 13 : 9811329710
Total Pages : 433 pages
Book Rating : 4.8/5 (113 download)

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Book Synopsis Monte Carlo Methods by : Adrian Barbu

Download or read book Monte Carlo Methods written by Adrian Barbu and published by Springer Nature. This book was released on 2020-02-24 with total page 433 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book seeks to bridge the gap between statistics and computer science. It provides an overview of Monte Carlo methods, including Sequential Monte Carlo, Markov Chain Monte Carlo, Metropolis-Hastings, Gibbs Sampler, Cluster Sampling, Data Driven MCMC, Stochastic Gradient descent, Langevin Monte Carlo, Hamiltonian Monte Carlo, and energy landscape mapping. Due to its comprehensive nature, the book is suitable for developing and teaching graduate courses on Monte Carlo methods. To facilitate learning, each chapter includes several representative application examples from various fields. The book pursues two main goals: (1) It introduces researchers to applying Monte Carlo methods to broader problems in areas such as Computer Vision, Computer Graphics, Machine Learning, Robotics, Artificial Intelligence, etc.; and (2) it makes it easier for scientists and engineers working in these areas to employ Monte Carlo methods to enhance their research.

MCMC from Scratch

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Publisher : Springer Nature
ISBN 13 : 9811927154
Total Pages : 198 pages
Book Rating : 4.8/5 (119 download)

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Book Synopsis MCMC from Scratch by : Masanori Hanada

Download or read book MCMC from Scratch written by Masanori Hanada and published by Springer Nature. This book was released on 2022-10-20 with total page 198 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook explains the fundamentals of Markov Chain Monte Carlo (MCMC) without assuming advanced knowledge of mathematics and programming. MCMC is a powerful technique that can be used to integrate complicated functions or to handle complicated probability distributions. MCMC is frequently used in diverse fields where statistical methods are important – e.g. Bayesian statistics, quantum physics, machine learning, computer science, computational biology, and mathematical economics. This book aims to equip readers with a sound understanding of MCMC and enable them to write simulation codes by themselves. The content consists of six chapters. Following Chap. 2, which introduces readers to the Monte Carlo algorithm and highlights the advantages of MCMC, Chap. 3 presents the general aspects of MCMC. Chap. 4 illustrates the essence of MCMC through the simple example of the Metropolis algorithm. In turn, Chap. 5 explains the HMC algorithm, Gibbs sampling algorithm and Metropolis-Hastings algorithm, discussing their pros, cons and pitfalls. Lastly, Chap. 6 presents several applications of MCMC. Including a wealth of examples and exercises with solutions, as well as sample codes and further math topics in the Appendix, this book offers a valuable asset for students and beginners in various fields.

Advanced Markov Chain Monte Carlo Methods

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Publisher : John Wiley & Sons
ISBN 13 : 1119956803
Total Pages : 308 pages
Book Rating : 4.1/5 (199 download)

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Book Synopsis Advanced Markov Chain Monte Carlo Methods by : Faming Liang

Download or read book Advanced Markov Chain Monte Carlo Methods written by Faming Liang and published by John Wiley & Sons. This book was released on 2011-07-05 with total page 308 pages. Available in PDF, EPUB and Kindle. Book excerpt: Markov Chain Monte Carlo (MCMC) methods are now an indispensable tool in scientific computing. This book discusses recent developments of MCMC methods with an emphasis on those making use of past sample information during simulations. The application examples are drawn from diverse fields such as bioinformatics, machine learning, social science, combinatorial optimization, and computational physics. Key Features: Expanded coverage of the stochastic approximation Monte Carlo and dynamic weighting algorithms that are essentially immune to local trap problems. A detailed discussion of the Monte Carlo Metropolis-Hastings algorithm that can be used for sampling from distributions with intractable normalizing constants. Up-to-date accounts of recent developments of the Gibbs sampler. Comprehensive overviews of the population-based MCMC algorithms and the MCMC algorithms with adaptive proposals. This book can be used as a textbook or a reference book for a one-semester graduate course in statistics, computational biology, engineering, and computer sciences. Applied or theoretical researchers will also find this book beneficial.

Bayesian Data Analysis, Third Edition

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Publisher : CRC Press
ISBN 13 : 1439840954
Total Pages : 677 pages
Book Rating : 4.4/5 (398 download)

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Book Synopsis Bayesian Data Analysis, Third Edition by : Andrew Gelman

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.

Pseudo-Marginal Hamiltonian Monte Carlo with Efficient Importance Sampling

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Publisher :
ISBN 13 :
Total Pages : 29 pages
Book Rating : 4.:/5 (13 download)

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Book Synopsis Pseudo-Marginal Hamiltonian Monte Carlo with Efficient Importance Sampling by : Kjartan Kloster Osmundsen

Download or read book Pseudo-Marginal Hamiltonian Monte Carlo with Efficient Importance Sampling written by Kjartan Kloster Osmundsen and published by . This book was released on 2019 with total page 29 pages. Available in PDF, EPUB and Kindle. Book excerpt: The joint posterior of latent variables and parameters in Bayesian hierarchical models often has a strong nonlinear dependence structure, thus making it a challenging target for standard Markov-chain Monte-Carlo methods. Pseudo-marginal methods aim at effectively exploring such target distributions, by marginalizing the latent variables using Monte-Carlo integration and directly targeting the marginal posterior of the parameters. We follow this approach and propose a generic pseudo-marginal algorithm for efficiently simulating from the posterior of the parameters. It combines efficient importance sampling, for accurately marginalizing the latent variables, with the recently developed pseudo-marginal Hamiltonian Monte Carlo approach. We illustrate our algorithm in applications to dynamic state space models, where it shows a very high simulation efficiency even in challenging scenarios with complex dependence structures.

Bayes Rules!

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Publisher : CRC Press
ISBN 13 : 1000529568
Total Pages : 606 pages
Book Rating : 4.0/5 (5 download)

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Book Synopsis Bayes Rules! by : Alicia A. Johnson

Download or read book Bayes Rules! written by Alicia A. Johnson and published by CRC Press. This book was released on 2022-03-03 with total page 606 pages. Available in PDF, EPUB and Kindle. Book excerpt: Praise for Bayes Rules!: An Introduction to Applied Bayesian Modeling “A thoughtful and entertaining book, and a great way to get started with Bayesian analysis.” Andrew Gelman, Columbia University “The examples are modern, and even many frequentist intro books ignore important topics (like the great p-value debate) that the authors address. The focus on simulation for understanding is excellent.” Amy Herring, Duke University “I sincerely believe that a generation of students will cite this book as inspiration for their use of – and love for – Bayesian statistics. The narrative holds the reader’s attention and flows naturally – almost conversationally. Put simply, this is perhaps the most engaging introductory statistics textbook I have ever read. [It] is a natural choice for an introductory undergraduate course in applied Bayesian statistics." Yue Jiang, Duke University “This is by far the best book I’ve seen on how to (and how to teach students to) do Bayesian modeling and understand the underlying mathematics and computation. The authors build intuition and scaffold ideas expertly, using interesting real case studies, insightful graphics, and clear explanations. The scope of this book is vast – from basic building blocks to hierarchical modeling, but the authors’ thoughtful organization allows the reader to navigate this journey smoothly. And impressively, by the end of the book, one can run sophisticated Bayesian models and actually understand the whys, whats, and hows.” Paul Roback, St. Olaf College “The authors provide a compelling, integrated, accessible, and non-religious introduction to statistical modeling using a Bayesian approach. They outline a principled approach that features computational implementations and model assessment with ethical implications interwoven throughout. Students and instructors will find the conceptual and computational exercises to be fresh and engaging.” Nicholas Horton, Amherst College An engaging, sophisticated, and fun introduction to the field of Bayesian statistics, Bayes Rules!: An Introduction to Applied Bayesian Modeling brings the power of modern Bayesian thinking, modeling, and computing to a broad audience. In particular, the book is an ideal resource for advanced undergraduate statistics students and practitioners with comparable experience. Bayes Rules! empowers readers to weave Bayesian approaches into their everyday practice. Discussions and applications are data driven. A natural progression from fundamental to multivariable, hierarchical models emphasizes a practical and generalizable model building process. The evaluation of these Bayesian models reflects the fact that a data analysis does not exist in a vacuum. Features • Utilizes data-driven examples and exercises. • Emphasizes the iterative model building and evaluation process. • Surveys an interconnected range of multivariable regression and classification models. • Presents fundamental Markov chain Monte Carlo simulation. • Integrates R code, including RStan modeling tools and the bayesrules package. • Encourages readers to tap into their intuition and learn by doing. • Provides a friendly and inclusive introduction to technical Bayesian concepts. • Supports Bayesian applications with foundational Bayesian theory.

Markov Chain Monte Carlo

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Publisher : CRC Press
ISBN 13 : 148229642X
Total Pages : 342 pages
Book Rating : 4.4/5 (822 download)

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Book Synopsis Markov Chain Monte Carlo by : Dani Gamerman

Download or read book Markov Chain Monte Carlo written by Dani Gamerman and published by CRC Press. This book was released on 2006-05-10 with total page 342 pages. Available in PDF, EPUB and Kindle. Book excerpt: While there have been few theoretical contributions on the Markov Chain Monte Carlo (MCMC) methods in the past decade, current understanding and application of MCMC to the solution of inference problems has increased by leaps and bounds. Incorporating changes in theory and highlighting new applications, Markov Chain Monte Carlo: Stochastic Simul

Statistical Rethinking

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Publisher : CRC Press
ISBN 13 : 1315362619
Total Pages : 488 pages
Book Rating : 4.3/5 (153 download)

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Book Synopsis Statistical Rethinking by : Richard McElreath

Download or read book Statistical Rethinking written by Richard McElreath and published by CRC Press. This book was released on 2018-01-03 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: Statistical Rethinking: A Bayesian Course with Examples in R and Stan builds readers’ knowledge of and confidence in statistical modeling. Reflecting the need for even minor programming in today’s model-based statistics, the book pushes readers to perform step-by-step calculations that are usually automated. This unique computational approach ensures that readers understand enough of the details to make reasonable choices and interpretations in their own modeling work. The text presents generalized linear multilevel models from a Bayesian perspective, relying on a simple logical interpretation of Bayesian probability and maximum entropy. It covers from the basics of regression to multilevel models. The author also discusses measurement error, missing data, and Gaussian process models for spatial and network autocorrelation. By using complete R code examples throughout, this book provides a practical foundation for performing statistical inference. Designed for both PhD students and seasoned professionals in the natural and social sciences, it prepares them for more advanced or specialized statistical modeling. Web Resource The book is accompanied by an R package (rethinking) that is available on the author’s website and GitHub. The two core functions (map and map2stan) of this package allow a variety of statistical models to be constructed from standard model formulas.

Doing Bayesian Data Analysis

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Publisher : Academic Press
ISBN 13 : 0123814863
Total Pages : 673 pages
Book Rating : 4.1/5 (238 download)

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Book Synopsis Doing Bayesian Data Analysis by : John Kruschke

Download or read book Doing Bayesian Data Analysis written by John Kruschke and published by Academic Press. This book was released on 2010-11-25 with total page 673 pages. Available in PDF, EPUB and Kindle. Book excerpt: There is an explosion of interest in Bayesian statistics, primarily because recently created computational methods have finally made Bayesian analysis tractable and accessible to a wide audience. Doing Bayesian Data Analysis, A Tutorial Introduction with R and BUGS, is for first year graduate students or advanced undergraduates and provides an accessible approach, as all mathematics is explained intuitively and with concrete examples. It assumes only algebra and ‘rusty’ calculus. Unlike other textbooks, this book begins with the basics, including essential concepts of probability and random sampling. The book gradually climbs all the way to advanced hierarchical modeling methods for realistic data. The text provides complete examples with the R programming language and BUGS software (both freeware), and begins with basic programming examples, working up gradually to complete programs for complex analyses and presentation graphics. These templates can be easily adapted for a large variety of students and their own research needs.The textbook bridges the students from their undergraduate training into modern Bayesian methods. Accessible, including the basics of essential concepts of probability and random sampling Examples with R programming language and BUGS software Comprehensive coverage of all scenarios addressed by non-bayesian textbooks- t-tests, analysis of variance (ANOVA) and comparisons in ANOVA, multiple regression, and chi-square (contingency table analysis). Coverage of experiment planning R and BUGS computer programming code on website Exercises have explicit purposes and guidelines for accomplishment

Medical Imaging

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Publisher :
ISBN 13 :
Total Pages : 880 pages
Book Rating : 4.3/5 (91 download)

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Book Synopsis Medical Imaging by :

Download or read book Medical Imaging written by and published by . This book was released on 1995 with total page 880 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Differential Equations, Dynamical Systems, and Linear Algebra

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Publisher : Academic Press
ISBN 13 : 0080873766
Total Pages : 373 pages
Book Rating : 4.0/5 (88 download)

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Book Synopsis Differential Equations, Dynamical Systems, and Linear Algebra by : Morris W. Hirsch

Download or read book Differential Equations, Dynamical Systems, and Linear Algebra written by Morris W. Hirsch and published by Academic Press. This book was released on 1974-06-28 with total page 373 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is about dynamical aspects of ordinary differential equations and the relations between dynamical systems and certain fields outside pure mathematics. A prominent role is played by the structure theory of linear operators on finite-dimensional vector spaces; the authors have included a self-contained treatment of that subject.

Sequential Monte Carlo Methods in Practice

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Publisher : Springer Science & Business Media
ISBN 13 : 1475734379
Total Pages : 590 pages
Book Rating : 4.4/5 (757 download)

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Book Synopsis Sequential Monte Carlo Methods in Practice by : Arnaud Doucet

Download or read book Sequential Monte Carlo Methods in Practice written by Arnaud Doucet and published by Springer Science & Business Media. This book was released on 2013-03-09 with total page 590 pages. Available in PDF, EPUB and Kindle. Book excerpt: Monte Carlo methods are revolutionizing the on-line analysis of data in many fileds. They have made it possible to solve numerically many complex, non-standard problems that were previously intractable. This book presents the first comprehensive treatment of these techniques.

Stochastic Modelling for Systems Biology

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Publisher : CRC Press
ISBN 13 : 9781584885405
Total Pages : 296 pages
Book Rating : 4.8/5 (854 download)

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Book Synopsis Stochastic Modelling for Systems Biology by : Darren J. Wilkinson

Download or read book Stochastic Modelling for Systems Biology written by Darren J. Wilkinson and published by CRC Press. This book was released on 2006-04-18 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt: Although stochastic kinetic models are increasingly accepted as the best way to represent and simulate genetic and biochemical networks, most researchers in the field have limited knowledge of stochastic process theory. The stochastic processes formalism provides a beautiful, elegant, and coherent foundation for chemical kinetics and there is a wealth of associated theory every bit as powerful and elegant as that for conventional continuous deterministic models. The time is right for an introductory text written from this perspective. Stochastic Modelling for Systems Biology presents an accessible introduction to stochastic modelling using examples that are familiar to systems biology researchers. Focusing on computer simulation, the author examines the use of stochastic processes for modelling biological systems. He provides a comprehensive understanding of stochastic kinetic modelling of biological networks in the systems biology context. The text covers the latest simulation techniques and research material, such as parameter inference, and includes many examples and figures as well as software code in R for various applications. While emphasizing the necessary probabilistic and stochastic methods, the author takes a practical approach, rooting his theoretical development in discussions of the intended application. Written with self-study in mind, the book includes technical chapters that deal with the difficult problems of inference for stochastic kinetic models from experimental data. Providing enough background information to make the subject accessible to the non-specialist, the book integrates a fairly diverse literature into a single convenient and notationally consistent source.

Monte Carlo Methods

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Publisher : American Mathematical Soc.
ISBN 13 : 0821819925
Total Pages : 238 pages
Book Rating : 4.8/5 (218 download)

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Book Synopsis Monte Carlo Methods by : Neal Noah Madras

Download or read book Monte Carlo Methods written by Neal Noah Madras and published by American Mathematical Soc.. This book was released on 2000 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume contains the proceedings of the Workshop on Monte Carlo Methods held at The Fields Institute for Research in Mathematical Sciences (Toronto, 1998). The workshop brought together researchers in physics, statistics, and probability. The papers in this volume - of the invited speakers and contributors to the poster session - represent the interdisciplinary emphasis of the conference. Monte Carlo methods have been used intensively in many branches of scientific inquiry. Markov chain methods have been at the forefront of much of this work, serving as the basis of many numerical studies in statistical physics and related areas since the Metropolis algorithm was introduced in 1953. Statisticians and theoretical computer scientists have used these methods in recent years, working on different fundamental research questions, yet using similar Monte Carlo methodology. This volume focuses on Monte Carlo methods that appear to have wide applicability and emphasizes new methods, practical applications and theoretical analysis. It will be of interest to researchers and graduate students who study and/or use Monte Carlo methods in areas of probability, statistics, theoretical physics, or computer science.

Hamiltonian Monte Carlo Methods in Machine Learning

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Publisher : Elsevier
ISBN 13 : 0443190364
Total Pages : 222 pages
Book Rating : 4.4/5 (431 download)

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Book Synopsis Hamiltonian Monte Carlo Methods in Machine Learning by : Tshilidzi Marwala

Download or read book Hamiltonian Monte Carlo Methods in Machine Learning written by Tshilidzi Marwala and published by Elsevier. This book was released on 2023-02-03 with total page 222 pages. Available in PDF, EPUB and Kindle. Book excerpt: Hamiltonian Monte Carlo Methods in Machine Learning introduces methods for optimal tuning of HMC parameters, along with an introduction of Shadow and Non-canonical HMC methods with improvements and speedup. Lastly, the authors address the critical issues of variance reduction for parameter estimates of numerous HMC based samplers. The book offers a comprehensive introduction to Hamiltonian Monte Carlo methods and provides a cutting-edge exposition of the current pathologies of HMC-based methods in both tuning, scaling and sampling complex real-world posteriors. These are mainly in the scaling of inference (e.g., Deep Neural Networks), tuning of performance-sensitive sampling parameters and high sample autocorrelation. Other sections provide numerous solutions to potential pitfalls, presenting advanced HMC methods with applications in renewable energy, finance and image classification for biomedical applications. Readers will get acquainted with both HMC sampling theory and algorithm implementation. Provides in-depth analysis for conducting optimal tuning of Hamiltonian Monte Carlo (HMC) parameters Presents readers with an introduction and improvements on Shadow HMC methods as well as non-canonical HMC methods Demonstrates how to perform variance reduction for numerous HMC-based samplers Includes source code from applications and algorithms