Archive for Bayesian Analysis

Bayes’ Rule [book review]

Posted in Books, Statistics, University life with tags , , , , , , , , , , on July 10, 2014 by xi'an

This introduction to Bayesian Analysis, Bayes’ Rule, was written by James Stone from the University of Sheffield, who contacted CHANCE suggesting a review of his book. I thus bought it from amazon to check the contents. And write a review.

First, the format of the book. It is a short paper of 127 pages, plus 40 pages of glossary, appendices, references and index. I eventually found the name of the publisher, Sebtel Press, but for a while thought the book was self-produced. While the LaTeX output is fine and the (Matlab) graphs readable, pictures are not of the best quality and the display editing is minimal in that there are several huge white spaces between pages. Nothing major there, obviously, it simply makes the book look like course notes, but this is in no way detrimental to its potential appeal. (I will not comment on the numerous appearances of Bayes’ alleged portrait in the book.)

“… (on average) the adjusted value θMAP is more accurate than θMLE.” (p.82)

Bayes’ Rule has the interesting feature that, in the very first chapter, after spending a rather long time on Bayes’ formula, it introduces Bayes factors (p.15).  With the somewhat confusing choice of calling the prior probabilities of hypotheses marginal probabilities. Even though they are indeed marginal given the joint, marginal is usually reserved for the sample, as in marginal likelihood. Before returning to more (binary) applications of Bayes’ formula for the rest of the chapter. The second chapter is about probability theory, which means here introducing the three axioms of probability and discussing geometric interpretations of those axioms and Bayes’ rule. Chapter 3 moves to the case of discrete random variables with more than two values, i.e. contingency tables, on which the range of probability distributions is (re-)defined and produces a new entry to Bayes’ rule. And to the MAP. Given this pattern, it is not surprising that Chapter 4 does the same for continuous parameters. The parameter of a coin flip.  This allows for discussion of uniform and reference priors. Including maximum entropy priors à la Jaynes. And bootstrap samples presented as approximating the posterior distribution under the “fairest prior”. And even two pages on standard loss functions. This chapter is followed by a short chapter dedicated to estimating a normal mean, then another short one on exploring the notion of a continuous joint (Gaussian) density.

“To some people the word Bayesian is like a red rag to a bull.” (p.119)

Bayes’ Rule concludes with a chapter entitled Bayesian wars. A rather surprising choice, given the intended audience. Which is rather bound to confuse this audience… The first part is about probabilistic ways of representing information, leading to subjective probability. The discussion goes on for a few pages to justify the use of priors but I find completely unfair the argument that because Bayes’ rule is a mathematical theorem, it “has been proven to be true”. It is indeed a maths theorem, however that does not imply that any inference based on this theorem is correct!  (A surprising parallel is Kadane’s Principles of Uncertainty with its anti-objective final chapter.)

All in all, I remain puzzled after reading Bayes’ Rule. Puzzled by the intended audience, as contrary to other books I recently reviewed, the author does not shy away from mathematical notations and concepts, even though he proceeds quite gently through the basics of probability. Therefore, potential readers need some modicum of mathematical background that some students may miss (although it actually corresponds to what my kids would have learned in high school). It could thus constitute a soft entry to Bayesian concepts, before taking a formal course on Bayesian analysis. Hence doing no harm to the perception of the field.

did I mean endemic? [pardon my French!]

Posted in Books, Statistics, University life with tags , , , , , , , , , , , on June 26, 2014 by xi'an

clouds, Nov. 02, 2011Deborah Mayo wrote a Saturday night special column on our Big Bayes stories issue in Statistical Science. She (predictably?) focussed on the critical discussions, esp. David Hand’s most forceful arguments where he essentially considers that, due to our (special issue editors’) selection of successful stories, we biased the debate by providing a “one-sided” story. And that we or the editor of Statistical Science should also have included frequentist stories. To which Deborah points out that demonstrating that “only” a frequentist solution is available may be beyond the possible. And still, I could think of partial information and partial inference problems like the “paradox” raised by Jamie Robbins and Larry Wasserman in the past years. (Not the normalising constant paradox but the one about censoring.) Anyway, the goal of this special issue was to provide a range of realistic illustrations where Bayesian analysis was a most reasonable approach, not to raise the Bayesian flag against other perspectives: in an ideal world it would have been more interesting to get discussants produce alternative analyses bypassing the Bayesian modelling but obviously discussants only have a limited amount of time to dedicate to their discussion(s) and the problems were complex enough to deter any attempt in this direction.

As an aside and in explanation of the cryptic title of this post, Deborah wonders at my use of endemic in the preface and at the possible mis-translation from the French. I did mean endemic (and endémique) in a half-joking reference to a disease one cannot completely get rid of. At least in French, the term extends beyond diseases, but presumably pervasive would have been less confusing… Or ubiquitous (as in Ubiquitous Chip for those with Glaswegian ties!). She also expresses “surprise at the choice of name for the special issue. Incidentally, the “big” refers to the bigness of the problem, not big data. Not sure about “stories”.” Maybe another occurrence of lost in translation… I had indeed no intent of connection with the “big” of “Big Data”, but wanted to convey the notion of a big as in major problem. And of a story explaining why the problem was considered and how the authors reached a satisfactory analysis. The story of the Air France Rio-Paris crash resolution is representative of that intent. (Hence the explanation for the above picture.)

early rejection MCMC

Posted in Books, Statistics, University life with tags , , , , , , , , on June 16, 2014 by xi'an

In a (relatively) recent Bayesian Analysis paper on efficient MCMC algorithms for climate models, Antti Solonen, Pirkka Ollinaho, Marko Laine, Heikki Haario, Johanna Tamminen and Heikki Järvinen propose an early rejection scheme to speed up Metropolis-Hastings algorithms. The idea is to consider a posterior distribution (proportional to)

\pi(\theta|y)= \prod_{k=1}^nL_i(\theta|y)

such that all terms in the product are less than one and to compare the uniform u in the acceptance step of the Metropolis-Hastings algorithm to

L_1(\theta'|y)/\pi(\theta|y),

then, if u is smaller than the ratio, to

L_1(\theta'|y)L_2(\theta'|y)/\pi(\theta|y),

and so on, until the new value has been rejected or all terms have been evaluated. The scheme obviously stops earlier than the regular Metropolis-Hastings algorithm, at no significant extra cost when the product above does not factor through a sufficient statistic. Solonen et al.  suggest ordering the terms so that the computationally simpler ones are computed first. The upper bound assumption requires and is equivalent to finding the maximum on each term of the product, though, which may be costly in its own for non-standard distributions. With my students Marco Banterle and Clara Grazian, we actually came upon this paper when preparing our delayed acceptance paper as (a) it belongs to the same category of accelerated MCMC methods (delayed acceptance and early rejection are somehow synonymous!) and (b) it mentions the early prefetching papers of Brockwell (2005) and Strid (2009).

“The acceptance probability in ABC is commonly very low, and many proposals are rejected, and ER can potentially help to detect the rejections sooner.”

In the conclusion, Solonen et al. point out a possible link with ABC but, apart from the general idea of rejecting earlier by looking at a subsample or at a proxy simulation of a summary statistics, which is also the idea at the core of Dennis Prangle’s lazy ABC, there is no obvious impact on a likelihood-free method like ABC.

David Blei smile in Paris (seminar)

Posted in Statistics, Travel, University life with tags , , , , , , , , on October 30, 2013 by xi'an

Nicolas Chopin just reminded me of a seminar given by David Blei in Paris tomorrow (at 4pm, SMILE seminarINRIA 23 avenue d’Italie, 5th floor, orange room) on Stochastic Variational Inference and Scalable Topic Models, machine learning seminar that I will alas miss, being busy on giving mine at CMU. Here is the abstract:

Probabilistic topic modeling provides a suite of tools for analyzing
large collections of electronic documents.  With a collection as
input, topic modeling algorithms uncover its underlying themes and
decompose its documents according to those themes.  We can use topic
models to explore the thematic structure of a large collection of
documents or to solve a variety of prediction problems about text.

Topic models are based on hierarchical mixed-membership models,
statistical models where each document expresses a set of components
(called topics) with individual per-document proportions. The
computational problem is to condition on a collection of observed
documents and estimate the posterior distribution of the topics and
per-document proportions. In modern data sets, this amounts to
posterior inference with billions of latent variables.

How can we cope with such data?  In this talk I will describe
stochastic variational inference, a general algorithm for
approximating posterior distributions that are conditioned on massive
data sets.  Stochastic inference is easily applied to a large class of
hierarchical models, including time-series models, factor models, and
Bayesian nonparametric models.  I will demonstrate its application to
topic models fit with millions of articles.  Stochastic inference
opens the door to scalable Bayesian computation for modern data

Statistics for spatio-temporal data [book review]

Posted in Books, Statistics, University life with tags , , , , , , on October 14, 2013 by xi'an

Here is the new reference book about spatial and spatio-temporal statistical modelling!  Noel Cressie wrote the earlier classic Statistics for Spatial Data in 1993 and he has now co-authored with Christopher Wikle (a plenary speaker at ISBA 2014 in Cancún) the new bible on the topic. And with a very nice cover of a Guatemaltec lienzo about the Spanish conquest. (Disclaimer: as I am a good friend of Noel, do not expect this review to remain unbiased!)

“…we state the obvious, that political boundaries cannot hold back a one-meter rise in sea level; our environment is ultimately a global resource and its stewardship is an international responsibility.” (p.11)

The book is a sum (in the French/Latin meaning of somme/summa when applied to books—I am not sure this explanation makes any sense!) and, as its predecessor, it covers an enormous range of topics and methods. So do not expect a textbook coverage of most notions and prepare to read further articles referenced in the text. One of the many differences with the earlier book is that MCMC appears from the start as a stepping stone that is necessary to handle

“…there are model-selection criteria that could be invoked (e.g., AIC, BIC, DIC, etc.), which concentrate on the twin pillars of predictability and parsimony. But they do not address the third pillar, namely scientific interpretability (i.e., knowledge).” (p.33)

The first chapter of the book is actually a preface motivating the topics covered by the book, which may be confusing on a first read, esp. for a graduate student, as there is no math formula and no model introduced at this stage. Anyway, this is not really a book made for a linear read. It is quite  witty (with too many quotes to report here!) and often funny (I learned for instance that Einstein’s quote “Everything should be made as simple as possible, but not simpler” was a paraphrase of an earlier lecture, invented by the Reader’s Digest!).

“Thus, we believe that it is not helpful to try to classify probability distributions that determine the statistical models, as subjective or objective. Better questions to ask are about the sensitivity of inferences to model choices and whether such choices make sense scientifically.” (p.32)

The overall tone of the book is mostly Bayesian, in a non-conflictual conditional probability way, insisting on hierarchical (Bayesian) model building. Incidentally, it uses the same bracket notation for generic distributions (densities) as in Gelfand and Smith (JASA, 1990), i.e. [X|Y] and [X|Z,y][Z|y,θ], notation that did not get much of a fan club. (I actually do not know where it stemmed from.) The second chapter contains an illustration of the search for the USS Scorpion using a Bayesian model (including priors built from experts’ opinions), example which is also covered [without the maths!] in Sharon McGrayne’s Theory that would not die.

The book is too rich and my time is too tight (!) to cover each chapter in details.  (For instance, I am not so happy with the temporal chapter in that it moves away from the Bayesian perspective without much of a justification.) Suffice to say then that it appears like an updated and improved version of its predecessor, with 45 pages of references, some of them quite recent. If I was to teach from this book at a Master level, it would take the whole academic year and then some, assuming enough mathematical culture from the student audience.

As an addendum, I noticed several negative reviews on amazon due to the poor quality of the printing, but the copy I received from John Wiley was quite fine, with the many colour graphs well-rendered. Maybe an earlier printing or a different printing agreement?

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