Showing posts with label mcmc. Show all posts
Showing posts with label mcmc. Show all posts

Bayesian Data Analysis, Second Edition (Chapman & Hall/CRC Texts in Statistical Science) Review

Bayesian Data Analysis, Second Edition (Chapman and Hall/CRC Texts in Statistical Science)
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Note, this is a review of the first edition.
Overview
This book was the textbook used at the University of Wisconsin-Madison for the graduate course in Bayesian Decision and Control I during the fall of 2001 and 2002. It strikes a good balance between theory and practical example, making it ideal for a first course in Bayesian theory at an intermediate-advanced graduate level. Its emphasis is on Bayesian modeling and to some degree computation.
Prerequisites
While no Bayesian theory is assumed, it is assumed that the reader has a background in mathematical statistics, probability and continuous multi-variate distributions at a beginning or intermediate graduate level. The mathematics used in the book is basic probability and statistics, elementary calculus and linear algebra.
Intended audience
This book is primarily for graduate students, statisticians and applied researchers who wish to learn Bayesian methods as opposed to the more classical frequentist methods.
Material covered
It covers the fundamentals starting from first principles, single-parameter models, multi-parameter models, large sample inference, hierarchical models, model checking and sensitivity analysis (model checking and sensitivity analysis are especially well covered), study design, regression models, generalized linear models, mixture models and models for missing data. In addition it covers posterior simulation and integration using rejection sampling and importance sampling. There is one chapter on Markov chain Monte Carlo simulation (MCMC) covering the generalized Metropolis algorithm and the Gibbs sampler.
Over 38 models are covered, 33 detailed examples from a wide range of fields (especially biostatistics). Each of the 18 chapter has a bibliographic note at the end. There are two appendixes: A) a very helpful list of standard probability distributions and B) outline of proofs of asymptotic theorems.
Sixteen of the 18 chapters end with a set of exercises that range from easy to quite difficult. Most of the students in my fall 2001 class used the statistical language R to do the exercises.
The book's emphasis is on applied Bayesian analysis. There are no heavy advanced proofs in the book. While the proofs of the basic algorithms are covered there are no algorithms written in pseudo code...Additional books of related interest
1) Statistical Decision Theory and Bayesian Analysis, James Berger, second edition. Emphasis on decision theory and more difficult to follow than Gelman's book. Covers empirical and hierarchical Bayes analysis. More philosophical challenging than Gelman's book.
2) Monte Carlo Statistical Methods, Robert and Casella. Very mathematically oriented book. Does a good job of covering MCMC.
3) Monte Carlo Methods in Bayesian Computation, Ming-Hui Chen, Qi-Man Shao, Joseph George Ibrahim. An enormous number of algorithms related to MCMC not covered elsewhere. If you need MCMC and need an algorithm to implement MCMC this is the book to read.
4) Monte Carlo Strategies in Scientific Computing, Jun S. Liu. Covers a wide range of scientific disciplines and how Monte Carlo methods can be used to solve real world problems. Includes hot topics such as bioinformatics. Very concise. Well written, but requires effort to understand as so many different topics are covered. This book is my most often borrowed book on Monte Carlo methods. Jun S. Liu is a big gun at Harvard.
5) Probabilistic Networks and Expert Systems. Cowell, Dawid, Lauritzen, Spiegelhalter. Covers the theory and methodology of building Bayesian networks (probabilistic networks).

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Incorporating new and updated information, this second edition of THE bestselling text in Bayesian data analysis continues to emphasize practice over theory, describing how to conceptualize, perform, and critique statistical analyses from a Bayesian perspective. Its world-class authors provide guidance on all aspects of Bayesian data analysis and include examples of real statistical analyses, based on their own research, that demonstrate how to solve complicated problems. Changes in the new edition include:
Stronger focus on MCMC
Revision of the computational advice in Part III
New chapters on nonlinear models and decision analysis
Several additional applied examples from the authors' recent research
Additional chapters on current models for Bayesian data analysis such as nonlinear models, generalized linear mixed models, and more
Reorganization of chapters 6 and 7 on model checking and data collectionBayesian computation is currently at a stage where there are many reasonable ways to compute any given posterior distribution. However, the best approach is not always clear ahead of time. Reflecting this, the new edition offers a more pluralistic presentation, giving advice on performing computations from many perspectives while making clear the importance of being aware that there are different ways to implement any given iterative simulation computation. The new approach, additional examples, and updated information make Bayesian Data Analysis an excellent introductory text and a reference that working scientists will use throughout their professional life.

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Bayesian Core: A Practical Approach to Computational Bayesian Statistics (Springer Texts in Statistics) Review

Bayesian Core: A Practical Approach to Computational Bayesian Statistics (Springer Texts in Statistics)
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I have used 'Bayesian Core' to teach Bayesian statistics to a class of Masters students majoring in finance, statistics or business with an undergraduate mathematics/statistics background and found it to be quite a good book for this purpose. I would have to disagree though with the previous reviewer (A.L.H Mayne) and suggest that this book could also be good for a practitioner, provided they have some prior statistical and mathematical understanding. A limitation for self guided study is the absence of solutions to exercises or hints necessary to ensure understanding for some of the exercises. I would also have to disagree with the previous reviewer over what is or what is not discussed in the book! The statement "conjugacy is mentioned in exercise 2.10 on page 22 with no discussion" is simply not true, the entire page preceding this exercise discusses conjugate priors in particular and they are subsequently used and outlined in the following chapters. There is also considerable attention paid in the book to the use of improper priors, in particular with respect to the implications of using improper priors for the estimation of Bayes factors (Chapter 3). A more thorough description of Jeffrey's Lindley paradox could be provided but a more complete discussion of this seems outside the scope of the book. Similarly, outlining the "historical antecedents ..." and more "...theory" about Jeffrey's prior than what is already provided, while interesting and important in its own right, is not necessarily mandatory reading for the student or practitioner who seeks a practical introduction to the Bayesian approach. To highlight "The implementation of the Monte Carlo method is straightforward" without adding the next few words used in the book "at least on a formal basis" seems terribly insincere and pedantic.
What the book is? The book presents a Bayesian approach to the analysis of topics commonly analysed in statistics designed to allow the reader to quickly grasp the essential elements of Bayesian principles and to put this into practice with examples using R code (simple computing syntax) provided on the website. There are surely limitations of this approach (albeit also acknowledged by the authors!) namely a less than full treatment of topics and of theoretical derivations for approaches. Some of the exercises are also difficult and these exercises could well do with hints being provided or a short statistical annotation.



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This Bayesian modeling book is intended for practitioners and applied statisticians looking for a self-contained entry to computational Bayesian statistics. Focusing on standard statistical models and backed up by discussed real datasets available from the book website, it provides an operational methodology for conducting Bayesian inference, rather than focusing on its theoretical justifications. Special attention is paid to the derivation of prior distributions in each case and specific reference solutions are given for each of the models. Similarly, computational details are worked out to lead the reader towards an effective programming of the methods given in the book.

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Handbook of Parallel Computing and Statistics (Statistics: A Series of Textbooks and Monographs) Review

Handbook of Parallel Computing and Statistics (Statistics:  A Series of Textbooks and Monographs)
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It came as somewhat of a surprise to the industry that coupling together several PC's enabled the construction of what was in effect a supercomputer at a small fraction of the cost.
What began twenty or so years ago has now influenced the design of CPU's and the intereconnection 'LANs' that facilitate the transfer of data between the processors. And this clearly hasn't stopped. The AMD Opteron CPU's and Intel's PCI-Express are simply the latest innovations in silicon, and more is coming.
From a system architecture standpoint, we have (and the book discusses) clusters, Grids, and distributed processor systems -- all of which are fairly loosely defined with plenty of room for very good discussions over several beer.
What this book brings is an excellent introduction into the state of the art in parallel computers as it exists today. As is often the case with books that are pushing the state of the art, it is written by a large numnber of experts and edited together. Each chapter covers a particular area in depth from the design of the hardware to the languages (primarily Fortran and Java), to the solution of a series of common problems that are frequent in several different application areas.
This book is an excellent summary of parallel computing as it exists today. It would be of particular help to the person responsible for writing the proposal for an organization to buy/build one. The book is probably a bit too advanced for a course at an undergraduate level, but would be excellent for first year graduate students in a wide variety of fields from computer science to bio-informatics, data mining, cryptography or any number of other fields requiring heavy duty computation.

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Technological improvements continue to push back the frontier of processor speed in modern computers. Unfortunately, the computational intensity demanded by modern research problems grows even faster. Parallel computing has emerged as the most successful bridge to this computational gap, and many popular solutions have emerged based on its concepts, such as grid computing and massively parallel supercomputers. The Handbook of Parallel Computing and Statistics systematically applies the principles of parallel computing for solving increasingly complex problems in statistics research.
This unique reference weaves together the principles and theoretical models of parallel computing with the design, analysis, and application of algorithms for solving statistical problems. After a brief introduction to parallel computing, the book explores the architecture, programming, and computational aspects of parallel processing. Focus then turns to optimization methods followed by statistical applications. These applications include algorithms for predictive modeling, adaptive design, real-time estimation of higher-order moments and cumulants, data mining, econometrics, and Bayesian computation. Expert contributors summarize recent results and explore new directions in these areas.
Its intricate combination of theory and practical applications makes the Handbook of Parallel Computing and Statistics an ideal companion for helping solve the abundance of computation-intensive statistical problems arising in a variety of fields.

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Bayesian Statistical Modelling (Wiley Series in Probability and Statistics) Review

Bayesian Statistical Modelling (Wiley Series in Probability and Statistics)
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Congdon presents a very nice and modern treatment of Bayesian methods and models emphasizing implementation using BUGS or WINBUGS. The book covers Bayesian models for regression including linear, log-linear, robust and nonparametric regression. Covers association and classification, mixture models, latent variables, problems of missing data, survival analysis, hierarchical models for pooling information, time series and other correlated data methods (e.g. spatial processes), multivariate analysis, growth curves and model assessment criteria.
The book is loaded with techniques and applications covering a wide variety of topics with reasonable depth.
It also has a very large bibliography with many very relevant and useful references. But there is also a negative side to the bibliography. It was not carefully proofread and there are some annoyances as you will see the same reference listed two, three or more times in the bibliography. Also for such a nice reference text it should have included an author index as well as an ordinary index.
Gibbs sampling is one of the primary estimation techniques in the book but the details are put off until section 10.1 where we get a nice introduction to Gibbs sampling and also the Metropolis algorithm with several excellent references.
This is a good book to start implementing Bayesian methods through the MCMC technique. It contains mostly medical applications which is a nice feature for biostatisticians.


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Bayesian methods combine the evidence from the data at hand with previous quantitative knowledge to analyse practical problems in a wide range of areas. The calculations were previously complex, but it is now possible to routinely apply Bayesian methods due to advances in computing technology and the use of new sampling methods for estimating parameters. Such developments together with the availability of freeware such as WINBUGS and R have facilitated a rapid growth in the use of Bayesian methods, allowing their application in many scientific disciplines, including applied statistics, public health research, medical science, the social sciences and economics.
Following the success of the first edition, this reworked and updated book provides an accessible approach to Bayesian computing and analysis, with an emphasis on the principles of prior selection, identification and the interpretation of real data sets.
The second edition:
Provides an integrated presentation of theory, examples, applications and computer algorithms.
Discusses the role of Markov Chain Monte Carlo methods in computing and estimation.
Includes a wide range of interdisciplinary applications, and a large selection of worked examples from the health and social sciences.
Features a comprehensive range of methodologies and modelling techniques, and examines model fitting in practice using Bayesian principles.
Provides exercises designed to help reinforce the reader's knowledge and a supplementary website containing data sets and relevant programs.

Bayesian Statistical Modelling is ideal for researchers in applied statistics, medical science, public health and the social sciences, who will benefit greatly from the examples and applications featured. The book will also appeal to graduate students of applied statistics, data analysis and Bayesian methods, and will provide a great source of reference for both researchers and students.
Praise for the First Edition:
"It is a remarkable achievement to have carried out such a range of analysis on such a range of data sets. I found this book comprehensive and stimulating, and was thoroughly impressed with both the depth and the range of the discussions it contains." – ISI - Short Book Reviews
"This is an excellent introductory book on Bayesian modelling techniques and data analysis" – Biometrics
"The book fills an important niche in the statistical literature and should be a very valuable resource for students and professionals who are utilizing Bayesian methods." – Journal of Mathematical Psychology

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Bayesian Adaptive Methods for Clinical Trials (Chapman & Hall/CRC Biostatistics Series) Review

Bayesian Adaptive Methods for Clinical Trials (Chapman and Hall/CRC Biostatistics Series)
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In the pharmaceutical industry adaptive designs are currently the rage because of their many potential advantages due to their flexibility. It allows you to stop early for efficacy or futility. It can do drug dose selection more easily and may have patients on inferior treatment for smaller amounts of time. There have already been four or five books published from the frequentist point of view. This is the first serious text on adaptive designs using the Bayesian approach. Pharmaceutical companies including Johnson and Johnson, Eli Lilly, Pfizer, Merck, Novartis, Novo Nordisk, Millennium, AMAG and GlaxoSmithKline have all been successful at running adaptive trials. Merck for example has already completed more than 40 adaptive design trials. Such trials can be done in phase II, phase III or a combining of phases II and III in a single adaptive trial. Merck claims to have completed over 40 adaptive trials. The M D Anderson Medical Center at UT Houston runs hundreds of adaptive trials (all as far as I know using the Bayesian methodology). Don Berry runs the biostatistics group at M D Anderson and he and his son scott own a consulting group that helps companies run Bayesian adaptive designs. Eli Lilly has been one of their clients on a drug trial and Biosense Webster, a J& J company, used them for a Bayesian trial on one of their ablation catheters. Scott Berry isone of the authors of this book and a lot of the book is devoted to work of Berry first at Duke and then later at M D Anderson and Berry Consultants.
Adaptive designs have logistic problems but companies have been able to overcome the problems motivated by the overall time and money saving benefits. All types of studies are illustrated from phase I through phase III and the examples are real and practical. Even when taking the Bayesian approach issues of frequentist properties for the designs comes up. Missing data, multiple testing, type I error and power of the test conditional and unconidtional are important when the frequentist approach is applied. The authors admit that both frequentist and Bayesian properties for a design are important and can be evaluated through simulation.
Although adaptive designs can be implemented effectively using either the Bayesian or the frequentist approaches. But Bayesian trials are a little more natural and simpler. This is the right book to get if you are interested in Bayesian methods.

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Monte Carlo Simulation in Statistical Physics: An Introduction (Graduate Texts in Physics) Review

Monte Carlo Simulation in Statistical Physics: An Introduction (Graduate Texts in Physics)
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This is a nice little book written by two experts of the field. This edition is only an expanded version of earlier editions (by addition of two new chapters, the core of the book chapter 1 to 3 hasn't change at all). The book covers monte carlo techniques through various well-known examples (Ising model, random walk, percolation, self-avoiding random walk). I enjoyed reading the first 3 chapters of the book. In particular, chapter 3 guides the readers and gives them the chance to practice what they should have learned in previous chapter (through 53 exercises). The following 2 chapters (chapter 4 and 5) are not as nicely written. Moreover, there are some serious shortcoming in the book. (1) All codes are written in Fortran. While everyone who can program can easily understand the codes, Fortran belongs to the past and could have been ok for physics students during late 80's (first edition) but not for those at 2006. (2) The guide (chapter 3) should have been the last chapter and have covered subjects in chapters 4 and 5 (3) As I mentioned before, chapter 4 and 5 are not well-organized. (4) The book in general stresses too much on finite-size effects. However, it is an important subject and it tells us how we can scale our simulation result to more realistic cases. By my judgement, the book gives wrong impression about the degree of its importance.
I recommend graduate students who are serious about learning monte carlo methods to read Newman and Barkema book (Monte Carlo Methods in Statistical Physics) instead since it provides a broader view about the subject. Although I highly recommend those who are interested in the subject to go through chapter 3. It is fun and very instructive.


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Probability, Markov Chains, Queues, and Simulation: The Mathematical Basis of Performance Modeling Review

Probability, Markov Chains, Queues, and Simulation: The Mathematical Basis of Performance Modeling
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This is the most succinct, clear mathematics book I have ever own. Unlike many mathematics books whose mathematical derivations usually have several missing yet important steps make people scratching their heads, this books is not one of them. All the derivations are very detailed along with great explanations and numerical examples. It is a rare gem in mathematical literature and I salute Prof. Stewart for his great achievement.

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Probability, Markov Chains, Queues, and Simulation provides a modern and authoritative treatment of the mathematical processes that underlie performance modeling. The detailed explanations of mathematical derivations and numerous illustrative examples make this textbook readily accessible to graduate and advanced undergraduate students taking courses in which stochastic processes play a fundamental role. The textbook is relevant to a wide variety of fields, including computer science, engineering, operations research, statistics, and mathematics.

The textbook looks at the fundamentals of probability theory, from the basic concepts of set-based probability, through probability distributions, to bounds, limit theorems, and the laws of large numbers. Discrete and continuous-time Markov chains are analyzed from a theoretical and computational point of view. Topics include the Chapman-Kolmogorov equations; irreducibility; the potential, fundamental, and reachability matrices; random walk problems; reversibility; renewal processes; and the numerical computation of stationary and transient distributions. The M/M/1 queue and its extensions to more general birth-death processes are analyzed in detail, as are queues with phase-type arrival and service processes. The M/G/1 and G/M/1 queues are solved using embedded Markov chains; the busy period, residual service time, and priority scheduling are treated. Open and closed queueing networks are analyzed. The final part of the book addresses the mathematical basis of simulation.

Each chapter of the textbook concludes with an extensive set of exercises. An instructor's solution manual, in which all exercises are completely worked out, is also available (to professors only).

Numerous examples illuminate the mathematical theories
Carefully detailed explanations of mathematical derivations guarantee a valuable pedagogical approach
Each chapter concludes with an extensive set of exercises

Professors: A supplementary Solutions Manual is available for this book. It is restricted to teachers using the text in courses. For information on how to obtain a copy, refer to: http://press.princeton.edu/class_use/solutions.html


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Applied Bayesian Modeling and Causal Inference from Incomplete-Data Perspectives (Wiley Series in Probability and Statistics) Review

Applied Bayesian Modeling and Causal Inference from Incomplete-Data Perspectives (Wiley Series in Probability and Statistics)
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Professor Gelman has edited a book containing 29 articles dealing primarily with real applications of Bayesian methods for causal inference and the treatment of incomplete data.
It contains a collection of the best work in applied statistics by prominent statisticians. In addition to learning the wide variety of problems that have been solved using the Bayesian approach (particularly in the medical field) the reader can learn and appreciate the power and ease of interpretation of Bayesian results.

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This book brings together a collection of articles on statistical methods relating to missing data analysis, including multiple imputation, propensity scores, instrumental variables, and Bayesian inference. Covering new research topics and real-world examples which do not feature in many standard texts. The book is dedicated to Professor Don Rubin (Harvard). Don Rubin has made fundamental contributions to the study of missing data.
Key features of the book include:
Comprehensive coverage of an imporant area for both research and applications.
Adopts a pragmatic approach to describing a wide range of intermediate and advanced statistical techniques.
Covers key topics such as multiple imputation, propensity scores, instrumental variables and Bayesian inference.
Includes a number of applications from the social and health sciences.
Edited and authored by highly respected researchers in the area.


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Molecular Modeling and Simulation Review

Molecular Modeling and Simulation
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... not only to molecular modeling, but to some of the subtleties of DNA and protein behavior and geometry, too.
This book's focus is generally on interactions with large molecules, DNA and proteins, although it does discuss small molecules (drugs, a few dozen to a few hundred atoms) too. That means that it skips most of the quantum mechanical modeling of more advanced computational chemistry texts.
Nothing is lost, because Schlick covers her chosen topic (molecular modeling and dynamics) in such detail. She starts with a very clear discussion of the structure of large biomolecules, with emphasis on the features that need quantitative description for modeling. That covers protein structure at ever level. It also covers DNA/RNA structure in the best detail I've ever seen. The double-helix is the just the starting point. There are alternative helix forms, non-standard binding between nucleotides, and asymmetries caused by nucleotide composition. The next chapters describe the geometric model and, briefly, the forces acting between atoms.
The second half of the book gets down to the nuts and bolts of modeling. This includes numerical techniques, minimization, sampling and Monte Carlo techniques, and the start of dynamics. Schlick attacks some of the nasty points of the calculations, such as modeling of forces that act on very different time scales. As with the simpler material, the development is clear, descriptive, and free of pointless theorems. The meticulous reader should come away able to implement most or all of the techniques described. The level of presentation is consistent and approachable. I think freshman physics should be enough preparation for most students to get most of the value out of the discussion.
The book is written with clarity as a top priority. The glossary is in the front, making sure that the reader knows it's a first-class part of the text. After that, every chapter starts with a list of the mathematical symbols and variables used and a one-line description of each. These are small things, but they increase the book's readability immensely. The illustrations are generally informative enough. On the whole, though, they don't seem quite up to the level of the textual and mathematical presentations.
I needed a crash course in the mathematical techniques used for describing molecular structure and behavior. I should have read this book first - its clarity and thoroughness would have saved me a lot of time. After this one, I can now go back and reread the more complex texts with more hops of understanding. Do yourself a favor and read this one first.

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Very broad overview of the field intended for an interdisciplinary audience; Lively discussion of current challenges written in a colloquial style; Author is a rising star in this discipline; Suitably accessible for beginners and suitably rigorous for experts; Features extensive four-color illustrations; Appendices featuring homework assignments and reading lists complement the material in the main text

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