Archive for Jeffreys priors

model uncertainty and missing data: an objective BAyesian perspective

Posted in Books, Statistics, Travel, University life with tags , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , on September 16, 2025 by xi'an

My Spanish and objective Bayesian friends Gonzalo García-Donato, María Eugenia Castellanos, Stefano Cabras, Alicia Quirós, and Anabel Forte wrote an fairly exciting paper in BA that is open to discussion (for a few more days), to be discussed on 05 November (4:00 PM UTC | 11:00 AM EST | 5:00 PM CET).

The interplay between missing data and model uncertainty—two classic statistical problems—leads to primary questions that we formally address from an objective Bayesian perspective. For the general regression problem, we discuss the probabilistic justification of Rubin’s rules applied to the usual components of Bayesian variable selection, arguing that prior predictive marginals should be central to the pursued methodology. In the regression settings, we explore the conditions of prior distributions that make the missing data mechanism ignorable, provided that it is missing at random or completely at random. Moreover, when comparing multiple linear models, we provide a complete methodology for dealing with special cases, such as variable selection or uncertainty regarding model errors. In numerous simulation experiments, we demonstrate that our method outperforms or equals others, in consistently producing results close to those obtained using the full dataset. In general, the difference increases with the percentage of missing data and the correlation between the variables used for imputation.

The so-called Rubin’s identity is simply the representation of the posterior probability of a model γ given the observed data x⁰, p(γ|x⁰), as the integrated posterior probability of a model given both observed and latent data,  p(γ|x⁰, x¹), against the marginal of latent x¹ given observed x⁰. Since this marginal involves the probabilities p(γ|x⁰), this representation is not directly useful for a numerical implementation.

In this paper, missingness relates to some entries of either the covariates or the response variate. Which is less common but more realistic, especially if some covariates do not contribute to the response. (The missingness mechanism does not matter if the data is missing at random (à la Rubin). The computational solution (p9) is rather standard, simulating the missing variables given the observed variables. In my opinion, the elephant in the room is the super-delicate selection of a prior distribution on the missing covariates, as methinks this impacts in a considerable manner the actual value of the Bayes factor, hence the selection of the surviving model. (As a side remark, we are credited in Celeux et al. (2006) to have “extended DIC for missing data models or when missing data were present”, but our point was instead to point out the arbitrariness of the very definition of DIC in such contexts.)

“The standard Bayesian method for addressing the absence of prior information uses improper distributions. In estimation problems (the model is fixed), the impropriety of priors does not imply any additional difficulty as long as the posterior is proper” (p9)

The authors point out the well-known difficulty with improper priors but still resort to improper priors on the parameters shared by all models—which I dispute as being adequate, despite the arguments put forward on p15, right Haar measure or not—, while sticking to proper priors on the model-dependent parameters. Which unsurprisingly become Zellner’s g-priors. Or rather g’-priors, although the discussion seems to resolve into the (model-free) factor g’ being equal to 1 as for the g-priors. Again a strong term in the derivation of the Bayes factor.

Bayesian Inference: Theory, Methods, Computations [book review]

Posted in Statistics with tags , , , , , , , , , , , , , , , , , , , , , on November 12, 2024 by xi'an

Bayesian Inference: Theory, Methods, Computations by Silvelyn Zwanzig and Rauf Ahmad, both from Uppsala University, is a recent book published by Chapman & Hall / CRC Press. About 300p long (plus appendices), it covers the core aspects of Bayesian inference, namely the decision theoretic motivations, its asymptotic validation, the specifics of estimation and testing, and the computational approximations (MC, MCMC, ABC, VB), with entries on prior specification and Normal linear models. And some R codes. It is (and feels like) constructed from Master and PhD courses (at Uppsala University), with a rigorous mathematical presentation and many examples, some related to biostatistics. Drawings from the first author’s daughter are included in most chapters, to this reviewer’s bemusement. From a further personal viewpoint, the book also reads rather close to my (Bayesian) choice of a Bayesian textbook, which proves rather accurate since several chapters are inspired by my own Bayesian Choice. as acknowledged therein. As well as by the more recent Statistical Decision Theory: Estimation, Testing, and Selection by Liese & Miescke (2008) and Introduction to the Theory of Statistical Inference by Liero & Zwanzig (2011). Witness, for instance, an example of prior construction for capture-recapture experiments on lizards as analysed by my PhD student Dupuis (1995) [with a curious switch to the authors on p.263] and  also included in The Bayesian Choice (with drawing 2.9 incorrect in that the lizards there have marks on their backs, instead of the code adopted by the ecologists, namely cutting one specific phalange for each capture).

Other minor quandaries: The usual issue of quoting the wrong edition for creating a method, as when citing Jeffreys (1946) for inventing non-informative priors [p.53], failing to point out the parameterisation invariance of intrinsic losses [p.95]considering that Bayes factors are only relevant for obtaining evidence against the null hypothesis [p.216], recommending BIC and DIC (!) [pp.232-6], advocating sampling importance resampling (SIR) for approximate sampling from the target (omitting infinite variance issues) [p.253], defining annealing as using “several trial distributions” [p.261], a mistake in ABC-MCMC [p.274] since the case when the simulated data is too far from the actual data should lead to a repetition rather than a pure rejection.

All in all, a reasonable textbook with some recent input, but still lacking in originality, if I may subjectively say so.

[Disclaimer about potential self-plagiarism: this post or an edited version of it could possibly appear in my Books Review section in CHANCE.]

Objective Bayesian Inference [book review]

Posted in Books, Statistics, University life with tags , , , , , , , , , , , , , , , , , , , , , on July 2, 2024 by xi'an

As advertised earlier on the ‘Og, the reference book on reference priors and relatives by my long-time friends Jim Berger, José Bernardo, and Dongchu Sun is at last out! I received a copy from the editor, World Scientific, and read through it, mostly in train rides to Normandy and Brittany. The construction of this book took decades and I remember many O’Bayes meetings when we were discussing of the progress made that far. As I knew from a few months back that the book was at last completed, I was quite eager to dig into it. And get this review ready for ISBA 2024. Given this prior knowledge, completed with sequential observations, I thus fear my review will be far from objective! And most likely more critical than it should be as fantasying how I would have written a book on that topic…

“Some of the best statisticians (not named Fisher or Neyman)…” (p1)

The book covers traditional approaches to principled ways of selecting prior distributions, culminating with the reference prior introduced by José Bernardo in his PhD thesis in the late 1970’s and expanded by all three authors over their academic careers. (Why is the acute accent missing from José on the front pages?!) The cover connects to the three founding fathers of objective Bayesian inference, Bayes, Laplace, and Jeffreys. The contents are not overly surprising from a personal viewpoint, i.e. as a card-carrying O’Bayes member. Namely that the chapters set the scene of parametric models and Bayesian inference (“a data driven probability transformation machine”), mostly supported by decision theory (including intrinsic losses!) but skipping testing and (mostly) model choice. This is unsurprisingly in the same spirit as Berger (1985) and Bernardo & Smith (1992). Not covering advanced Bayesian asymptotics, any flavour of Bayesian nonparametrics, the more recent generalized Bayesian inference, and the impact of misspecified models. The likelihood section does not mention Deborah Mayo’s criticism of the Likelihood Principle, or the Pitman Koopman lemma (although the examples are predominantly connected with exponential families).  The section (1.8) on MCMC implies that the Metropolis algorithm is less accurate that the Gibbs sampler, which is an exaggerated generalisation from a simple example, accrued by a comparison that does not seem to account for mixing behaviours.

“Our own belief is that the effort [seeking objective prior distributions] is a misguided search for the holy grail” (p.68)

The basics of objective priors repeats the useful warning that a truncation of parameter space is far from advised, as is the call for vague proper priors à la BUGS (a “nonsense”). A remark on the alternative weakly informative priors à la BDA require subjective input, a whole section on the legitimacy of improper priors as KL limits of sequences of proper priors. Plus a nice recall of the data dependent prior of Wasserman (2000) forcing mixtures to avoid empty clusters. This was the prior Jean Diebolt and I implemented in our 1990 Gibbs sampling paper. (I do not really see it as data dependent to impose that no component comes empty in the sample, but rather as a different model removing some terms from the likelihood.) There is even a chapter dedicated to constant priors—the historical meaning of inverse probability—, with a section on the modern advocates of this constant prior, that mostly focus on Binomial model. The book goes on justifying this prior by an invariance under reparameterisation argument (p108), but the discussion may seem stretched for some newcomers. This is followed by a nice chapter on frequentist matching, covering the bivariate Normal case and some asymptotics, followed by confidence distributions, quite topical and then fiducial inference, that imagines a posterior without a prior, one short too short chapter on invariance priors arguing for the right-Haar vs the left-Haar prior measure in invariance settings as exact matching, completed by a useful if short chapter—I would not have thought of including—on the performances of objective priors, like over-dispersion or under-dispersion. A mention is made there of the (now well-known) danger of using MCMC with improper posteriors as the issue potentially goes undetected, as it did in the early 1990s. Within its coherence section, the authors recall the fundamentals of the lovely marginalisation paradoxes. While addressing some computational issues, the book does not mention the derivation of the Jeffreys prior for mixtures Clara Grazian and I examined. The chapter ends by a rather expedited dismissal of maximum entropy. Which many still regard as the default approach to (partly informed) objective prior modelling. (They’ll be back in Chapter 13.)

The last hundred pages (Chap. 9-14) of the book are focussing on reference priors, as should be given the priorities of the authors. Starting with the rather convincing concept of maximising missing information, getting asymptotic to remove the impact of the data, and turning recursive in case of multidimensional parameters, while resorting to compact parameter spaces to avoid improprieties (the Achille’s heel of reference priors!). Reaching a definition (p176) in the univariate case that coherently does not depend on the sample size but on an arbitrary dominating measure (p179), interestingly sharing this feature with the definition of conjugate priors. In multivariate settings, things get… more complicated! And force a separation between nuisance and interesting parameters lest the resulting priors prove underperforming. Asymptotic normality again helps, but the derivation remains involved witness a one page (p201) theorem (Proposition 10.2).  My favourite example of selecting the prior for a Normal mean squared norm is there, with the original Jeffreys prior based on the Normal vector failing badly while the reference prior based on the norm of the observation does much better! (An open problem is the construction of the Jeffreys prior in that example.) A large table (p210) illustrates the plethora of reference priors depending on the parameter ordering. A short chapter (11) specialises on discrete parameters as in population sizes. And in model choice, a resolution I had not seen previously, with prior weights depending on the number of parameters in the respective models. But not accounting for embedded models. Chapter 12 addresses the “overall objective” prior construction when all parameters are equal (and none more equal than others). Supporting in the end the best overall prior defined in terms of distance to a family of reference priors. With a special treatment of the hierarchical Normal model following Berger & al. (2020). Chapter 13 is a short incursion into partial information reference priors, incl. maxent priors. Chapter 14 is about special reference priors exploiting special structures. And, at last, Chapter 15 a non-chapter pointing out to a catalogue of objective priors, following Yang & Berger (1997) as well as an initiative set during one of the O’Bayes meetings.

On the minor (nitpicking) side, I found a few “the the” (the typo no one can escape!) throughout the book, informality in some statements like Proposition 1.6, whose limit (in n) depends on n (a shortcut from which we try to wean our students). Also a somewhat anecdotal appearance of the ratio of uniforms algorithm with a mistaken statement that the method doesn’t depend on a proposal (p61), the references to Jeffreys’ main book clashing between the 1930s  and 1961 (final edition). The “random posterior” section 1.8 6 seems unfinished.

In conclusion, this much awaited reference book does deliver! It brings a perspective on reference priors that no other book does and reflects (well) on the authors’ careful completion of a coherent theory, hence should appeal to anyone working on the foundations and principles of Bayesian inference. Obviously, it will not change the position of strict subjectivists, nor convince non-Bayesians, but it should inspire current and future researchers, as well as complement graduate courses on Bayesian inference. In addition, the huge bibliography retraces the work in the area till today (if less intensely in the most recent years). Kudos to the authors, then!

[Disclaimer about potential self-plagiarism: this post or an edited version will eventually appear in my Books Review section in CHANCE!]

it’s objectively out!

Posted in Books, Statistics, University life with tags , , , , , , , , , , , , , , on June 13, 2024 by xi'an

statistical modeling with R [book review]

Posted in Books, Statistics with tags , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , on June 10, 2023 by xi'an

Statistical Modeling with R (A dual frequentist and Bayesian approach for life scientists) is a recent book written by Pablo Inchausti, from Uruguay. In a highly personal and congenial style (witness the preface), with references to (fiction) books that enticed me to buy them. The book was sent to me by the JASA book editor for review and I went through the whole of it during my flight back from Jeddah. [Disclaimer about potential self-plagiarism: this post or a likely edited version of it will eventually appear in JASA. If not CHANCE, for once.]

The very first sentence (after the preface) quotes my late friend Steve Fienberg, which is definitely starting on the right foot. The exposition of the motivations for writing the book is quite convincing, with more emphasis than usual put on the notion and limitations of modeling. The discourse is overall inspirational and contains many relevant remarks and links that make it worth reading it as a whole. While heavily connected with a few R packages like fitdist, fitistrplus, brms (a  front for Stan), glm, glmer, the book is wisely bypassing the perilous reef of recalling R bases. Similarly for the foundations of probability and statistics. While lacking in formal definitions, in my opinion, it reads well enough to somehow compensate for this very lack. I also appreciate the coherent and throughout continuation of the parallel description of Bayesian and non-Bayesian analyses, an attempt that often too often quickly disappear in other books. (As an aside, note that hardly anyone claims to be a frequentist, except maybe Deborah Mayo.) A new model is almost invariably backed by a new dataset, if a few being somewhat inappropriate as in the mammal sleep patterns of Chapter 5. Or in Fig. 6.1.

Given that the main motivation for the book (when compared with references like BDA) is heavily towards the practical implementation of statistical modelling via R packages, it is inevitable that a large fraction of Statistical Modeling with R is spent on the analysis of R outputs, even though it sometimes feels a wee bit too heavy for yours truly.  The R screen-copies are however produced in moderate quantity and size, even though the variations in typography/fonts (at least on my copy?!) may prove confusing. Obviously the high (explosive?) distinction between regression models may eventually prove challenging for the novice reader. The specific issue of prior input (or “defining priors”) is briefly addressed in a non-chapter (p.323), although mentions are made throughout preceding chapters. I note the nice appearance of hierarchical models and experimental designs towards the end, but would have appreciated some discussions on missing topics such as time series, causality, connections with machine learning, non-parametrics, model misspecification. As an aside, I appreciated being reminded about the apocryphal nature of Ockham’s much cited quote “Pluralitas non est ponenda sine necessitate“.

Typo Jeffries found in Fig. 2.1, along with a rather sketchy representation of the history of both frequentist and Bayesian statistics. And Jon Wakefield’s book (with related purpose of presenting both versions of parametric inference) was mistakenly entered as Wakenfield’s in the bibliography file. Some repetitions occur. I do not like the use of the equivalence symbol ≈ for proportionality. And I found two occurrences of the unavoidable “the the” typo (p.174 and p.422). I also had trouble with some sentences like “long-run, hypothetical distribution of parameter estimates known as the sampling distribution” (p.27), “maximum likelihood estimates [being] sufficient” (p.28), “Jeffreys’ (1939) conjugate priors” [which were introduced by Raiffa and Schlaifer] (p.35), “A posteriori tests in frequentist models” (p.130), “exponential families [having] limited practical implications for non-statisticians” (p.190), “choice of priors being correct” (p.339), or calling MCMC sample terms “estimates” (p.42), and issues with some repetitions, missing indices for acronyms, packages, datasets, but did not bemoan the lack homework sections (beyond suggesting new datasets for analysis).

A problematic MCMC entry is found when calibrating the choice of the Metropolis-Hastings proposal towards avoiding negative values “that will generate an error when calculating the log-likelihood” (p.43) since it suggests proposed values should not exceed the support of the posterior (and indicates a poor coding of the log-likelihood!). I also find the motivation for the full conditional decomposition behind the Gibbs sampler (p.47) unnecessarily confusing. (And automatically having a Metropolis-Hastings step within Gibbs as on Fig. 3.9 brings another magnitude of confusion.) The Bayes factor section is very terse. The derivation of the Kullback-Leibler representation (7.3) as an expected log likelihood ratio seems to be missing a reference measure. Of course, seeing a detailed coverage of DIC (Section 7.4) did not suit me either, even though the issue with mixtures was alluded to (with no detail whatsoever). The Nelder presentation of the generalised linear models felt somewhat antiquated, since the addition of the scale factor a(φ) sounds over-parameterized.

But those are minor quibble in relation to a book that should attract curious minds of various background knowledge and expertise in statistics, as well as work nicely to support an enthusiastic teacher of statistical modelling. I thus recommend this book most enthusiastically.