Archive for subjective versus objective Bayes

O’Bayes 2019 has now started!

Posted in pictures, Running, Statistics, Travel, University life with tags , , , , , , , , , on June 28, 2019 by xi'an

The O’Bayes 2019 conference in Warwick University has now started, with about 100 participants meeting over four days (plus one of tutorials) in the Zeeman maths building of the University. Quite a change of location and weather when compared with the previous one in Austin. As an organiser I hope all goes well at the practical level and want to thank the other persons who helped me towards this goal, first and foremost Paula Matthews who solved web and lodging and planning issues all over these past months, as well as Mark Steel and Cristiano Villa. As a member of the scientific committee, I am looking forward the talks and discussants along the coming four days, again hoping all speakers and discussants show up and are not hindered by travel or visa issues…

Computational Bayesian Statistics [book review]

Posted in Books, Statistics with tags , , , , , , , , , , , , , , , , , , , , , , , , , , , , on February 1, 2019 by xi'an

This Cambridge University Press book by M. Antónia Amaral Turkman, Carlos Daniel Paulino, and Peter Müller is an enlarged translation of a set of lecture notes in Portuguese. (Warning: I have known Peter Müller from his PhD years in Purdue University and cannot pretend to perfect objectivity. For one thing, Peter once brought me frozen-solid beer: revenge can also be served cold!) Which reminds me of my 1994 French edition of Méthodes de Monte Carlo par chaînes de Markov, considerably upgraded into Monte Carlo Statistical Methods (1998) thanks to the input of George Casella. (Re-warning: As an author of books on the same topic(s), I can even less pretend to objectivity.)

“The “great idea” behind the development of computational Bayesian statistics is the recognition that Bayesian inference can be implemented by way of simulation from the posterior distribution.”

The book is written from a strong, almost militant, subjective Bayesian perspective (as, e.g., when half-Bayesians are mentioned!). Subjective (and militant) as in Dennis Lindley‘s writings, eminently quoted therein. As well as in Tony O’Hagan‘s. Arguing that the sole notion of a Bayesian estimator is the entire posterior distribution. Unless one brings in a loss function. The book also discusses the Bayes factor in a critical manner, which is fine from my perspective.  (Although the ban on improper priors makes its appearance in a very indirect way at the end of the last exercise of the first chapter.)

Somewhat at odds with the subjectivist stance of the previous chapter, the chapter on prior construction only considers non-informative and conjugate priors. Which, while understandable in an introductory book, is a wee bit disappointing. (When mentioning Jeffreys’ prior in multidimensional settings, the authors allude to using univariate Jeffreys’ rules for the marginal prior distributions, which is not a well-defined concept or else Bernardo’s and Berger’s reference priors would not have been considered.) The chapter also mentions the likelihood principle at the end of the last exercise, without a mention of the debate about its derivation by Birnbaum. Or Deborah Mayo’s recent reassessment of the strong likelihood principle. The following chapter is a sequence of illustrations in classical exponential family models, classical in that it is found in many Bayesian textbooks. (Except for the Poison model found in Exercise 3.3!)

Nothing to complain (!) about the introduction of Monte Carlo methods in the next chapter, especially about the notion of inference by Monte Carlo methods. And the illustration by Bayesian design. The chapter also introduces Rao-Blackwellisation [prior to introducing Gibbs sampling!]. And the simplest form of bridge sampling. (Resuscitating the weighted bootstrap of Gelfand and Smith (1990) may not be particularly urgent for an introduction to the topic.) There is furthermore a section on sequential Monte Carlo, including the Kalman filter and particle filters, in the spirit of Pitt and Shephard (1999). This chapter is thus rather ambitious in the amount of material covered with a mere 25 pages. Consensus Monte Carlo is even mentioned in the exercise section.

“This and other aspects that could be criticized should not prevent one from using this [Bayes factor] method in some contexts, with due caution.”

Chapter 5 turns back to inference with model assessment. Using Bayesian p-values for model assessment. (With an harmonic mean spotted in Example 5.1!, with no warning about the risks, except later in 5.3.2.) And model comparison. Presenting the whole collection of xIC information criteria. from AIC to WAIC, including a criticism of DIC. The chapter feels somewhat inconclusive but methinks this is the right feeling on the current state of the methodology for running inference about the model itself.

“Hint: There is a very easy answer.”

Chapter 6 is also a mostly standard introduction to Metropolis-Hastings algorithms and the Gibbs sampler. (The argument given later of a Metropolis-Hastings algorithm with acceptance probability one does not work.) The Gibbs section also mentions demarginalization as a [latent or auxiliary variable] way to simulate from complex distributions [as we do], but without defining the notion. It also references the precursor paper of Tanner and Wong (1987). The chapter further covers slice sampling and Hamiltonian Monte Carlo, the later with sufficient details to lead to reproducible implementations. Followed by another standard section on convergence assessment, returning to the 1990’s feud of single versus multiple chain(s). The exercise section gets much larger than in earlier chapters with several pages dedicated to most problems. Including one on ABC, maybe not very helpful in this context!

“…dimension padding (…) is essentially all that is to be said about the reversible jump. The rest are details.”

The next chapter is (somewhat logically) the follow-up for trans-dimensional problems and marginal likelihood approximations. Including Chib’s (1995) method [with no warning about potential biases], the spike & slab approach of George and McCulloch (1993) that I remember reading in a café at the University of Wyoming!, the somewhat antiquated MC³ of Madigan and York (1995). And then the much more recent array of Bayesian lasso techniques. The trans-dimensional issues are covered by the pseudo-priors of Carlin and Chib (1995) and the reversible jump MCMC approach of Green (1995), the later being much more widely employed in the literature, albeit difficult to tune [and even to comprehensively describe, as shown by the algorithmic representation in the book] and only recommended for a large number of models under comparison. Once again the exercise section is most detailed, with recent entries like the EM-like variable selection algorithm of Ročková and George (2014).

The book also includes a chapter on analytical approximations, which is also the case in ours [with George Casella] despite my reluctance to bring them next to exact (simulation) methods. The central object is the INLA methodology of Rue et al. (2009) [absent from our book for obvious calendar reasons, although Laplace and saddlepoint approximations are found there as well]. With a reasonable amount of details, although stopping short of implementable reproducibility. Variational Bayes also makes an appearance, mostly following the very recent Blei et al. (2017).

The gem and originality of the book are primarily to be found in the final and ninth chapter where four software are described, all with interfaces to R: OpenBUGS, JAGS, BayesX, and Stan, plus R-INLA which is processed in the second half of the chapter (because this is not a simulation method). As in the remainder of the book, the illustrations are related to medical applications. Worth mentioning is the reminder that BUGS came in parallel with Gelfand and Smith (1990) Gibbs sampler rather than as a consequence. Even though the formalisation of the Markov chain Monte Carlo principle by the later helped in boosting the power of this software. (I also appreciated the mention made of Sylvia Richardson’s role in this story.) Since every software is illustrated in depth with relevant code and output, and even with the shortest possible description of its principle and modus vivendi, the chapter is 60 pages long [and missing a comparative conclusion]. Given my total ignorance of the very existence of the BayesX software, I am wondering at the relevance of its inclusion in this description rather than, say, other general R packages developed by authors of books such as Peter Rossi. The chapter also includes a description of CODA, with an R version developed by Martin Plummer [now a Warwick colleague].

In conclusion, this is a high-quality and all-inclusive introduction to Bayesian statistics and its computational aspects. By comparison, I find it much more ambitious and informative than Albert’s. If somehow less pedagogical than the thicker book of Richard McElreath. (The repeated references to Paulino et al.  (2018) in the text do not strike me as particularly useful given that this other book is written in Portuguese. Unless an English translation is in preparation.)

Disclaimer: this book was sent to me by CUP for endorsement and here is what I wrote in reply for a back-cover entry:

An introduction to computational Bayesian statistics cooked to perfection, with the right mix of ingredients, from the spirited defense of the Bayesian approach, to the description of the tools of the Bayesian trade, to a definitely broad and very much up-to-date presentation of Monte Carlo and Laplace approximation methods, to an helpful description of the most common software. And spiced up with critical perspectives on some common practices and an healthy focus on model assessment and model selection. Highly recommended on the menu of Bayesian textbooks!

And this review is likely to appear in CHANCE, in my book reviews column.

Practicals of Uncertainty [book review]

Posted in Books, Statistics, University life with tags , , , , , , , on December 22, 2017 by xi'an

On my way to the O’Bayes 2017 conference in Austin, I [paradoxically!] went through Jay Kadane’s Pragmatics of Uncertainty, which had been published earlier this year by CRC Press. The book is to be seen as a practical illustration of the Principles of Uncertainty Jay wrote in 2011 (and I reviewed for CHANCE). The avowed purpose is to allow the reader to check through Jay’s applied work whether or not he had “made good” on setting out clearly the motivations for his subjective Bayesian modelling. (While I presume the use of the same P of U in both books is mostly a coincidence, I started wondering how a third P of U volume could be called. Perils of Uncertainty? Peddlers of Uncertainty? The game is afoot!)

The structure of the book is a collection of fifteen case studies undertaken by Jay over the past 30 years, covering paleontology, survey sampling, legal expertises, physics, climate, and even medieval Norwegian history. Each chapter starts with a short introduction that often explains how he came by the problem (most often as an interesting PhD student consulting project at CMU), what were the difficulties in the analysis, and what became of his co-authors. As noted by the author, the main bulk of each chapter is the reprint (in a unified style) of the paper and most of these papers are actually and freely available on-line. The chapter always concludes with an epilogue (or post-mortem) that re-considers (very briefly) what had been done and what could have been done and whether or not the Bayesian perspective was useful for the problem (unsurprisingly so for the majority of the chapters!). There are also reading suggestions in the other P of U and a few exercises.

“The purpose of the book is philosophical, to address, with specific examples, the question of whether Bayesian statistics is ready for prime time. Can it be used in a variety of applied settings to address real applied problems?”

The book thus comes as a logical complement of the Principles, to demonstrate how Jay himself did apply his Bayesian principles to specific cases and how one can set the construction of a prior, of a loss function or of a statistical model in identifiable parts that can then be criticised or reanalysed. I find browsing through this series of fourteen different problems fascinating and exhilarating, while I admire the dedication of Jay to every case he presents in the book. I also feel that this comes as a perfect complement to the earlier P of U, in that it makes refering to a complete application of a given principle most straightforward, the problem being entirely described, analysed, and in most cases solved within a given chapter. A few chapters have discussions, being published in the Valencia meeting proceedings or another journal with discussions.

While all papers have been reset in the book style, I wish the graphs had been edited as well as they do not always look pretty. Although this would have implied a massive effort, it would have also been great had each chapter and problem been re-analysed or at least discussed by another fellow (?!) Bayesian in order to illustrate the impact of individual modelling sensibilities. This may however be a future project for a graduate class. Assuming all datasets are available, which is unclear from the text.

“We think however that Bayes factors are overemphasized. In the very special case in which there are only two possible “states of the world”, Bayes factors are sufficient. However in the typical case in which there are many possible states of the world, Bayes factors are sufficient only when the decision-maker’s loss has only two values.” (p. 278)

The above is in Jay’s reply to a comment from John Skilling regretting the absence of marginal likelihoods in the chapter. Reply to which I completely subscribe.

[Usual warning: this review should find its way into CHANCE book reviews at some point, with a fairly similar content.]

beyond objectivity, subjectivity, and other ‘bjectivities

Posted in Statistics with tags , , , , , , , , , , , , , on April 12, 2017 by xi'an

Here is my discussion of Gelman and Hennig at the Royal Statistical Society, which I am about to deliver!

objective and subjective RSS Read Paper next week

Posted in Books, pictures, Statistics, Travel, University life, Wines with tags , , , , , , , , , , , , , , on April 5, 2017 by xi'an

Andrew Gelman and Christian Hennig will give a Read Paper presentation next Wednesday, April 12, 5pm, at the Royal Statistical Society, London, on their paper “Beyond subjective and objective in statistics“. Which I hope to attend and else to write a discussion. Since the discussion (to published in Series A) is open to everyone, I strongly encourage ‘Og’s readers to take a look at the paper and the “radical” views therein to hopefully contribute to this discussion. Either as a written discussion or as comments on this very post.

round-table on Bayes[ian[ism]]

Posted in Books, pictures, Statistics, University life with tags , , , , , , , , , , , , , , on March 7, 2017 by xi'an

In a [sort of] coincidence, shortly after writing my review on Le bayésianisme aujourd’hui, I got invited by the book editor, Isabelle Drouet, to take part in a round-table on Bayesianism in La Sorbonne. Which constituted the first seminar in the monthly series of the séminaire “Probabilités, Décision, Incertitude”. Invitation that I accepted and honoured by taking place in this public debate (if not dispute) on all [or most] things Bayes. Along with Paul Egré (CNRS, Institut Jean Nicod) and Pascal Pernot (CNRS, Laboratoire de chimie physique). And without a neuroscientist, who could not or would not attend.

While nothing earthshaking came out of the seminar, and certainly not from me!, it was interesting to hear of the perspectives of my philosophy+psychology and chemistry colleagues, the former explaining his path from classical to Bayesian testing—while mentioning trying to read the book Statistical rethinking reviewed a few months ago—and the later the difficulty to teach both colleagues and students the need for an assessment of uncertainty in measurements. And alluding to GUM, developed by the Bureau International des Poids et Mesures I visited last year. I tried to present my relativity viewpoints on the [relative] nature of the prior, to avoid the usual morass of debates on the nature and subjectivity of the prior, tried to explain Bayesian posteriors via ABC, mentioned examples from The Theorem that Would not Die, yet untranslated into French, and expressed reserves about the glorious future of Bayesian statistics as we know it. This seminar was fairly enjoyable, with none of the stress induced by the constraints of a radio-show. Just too bad it did not attract a wider audience!

le bayésianisme aujourd’hui [book review]

Posted in Books, pictures, Statistics, University life with tags , , , , , , , , , , , , , , , , , , on March 4, 2017 by xi'an

It is quite rare to see a book published in French about Bayesian statistics and even rarer to find one that connects philosophy of science, foundations of probability, statistics, and applications in neurosciences and artificial intelligence. Le bayésianisme aujourd’hui (Bayesianism today) was edited by Isabelle Drouet, a Reader in Philosophy at La Sorbonne. And includes a chapter of mine on the basics of Bayesian inference (à la Bayesian Choice), written in French like the rest of the book.

The title of the book is rather surprising (to me) as I had never heard the term Bayesianism mentioned before. As shown by this link, the term apparently exists. (Even though I dislike the sound of it!) The notion is one of a probabilistic structure of knowledge and learning, à la Poincaré. As described in the beginning of the book. But I fear the arguments minimising the subjectivity of the Bayesian approach should not be advanced, following my new stance on the relativity of probabilistic statements, if only because they are defensive and open the path all too easily to counterarguments. Similarly, the argument according to which the “Big Data” era makesp the impact of the prior negligible and paradoxically justifies the use of Bayesian methods is limited to the case of little Big Data, i.e., when the observations are more or less iid with a limited number of parameters. Not when the number of parameters explodes. Another set of arguments that I find both more modern and compelling [for being modern is not necessarily a plus!] is the ease with which the Bayesian framework allows for integrative and cooperative learning. Along with its ultimate modularity, since each component of the learning mechanism can be extracted and replaced with an alternative. Continue reading