Archive for model misspecification

safe Bayes & e-values & least favourable priors

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

The paper by Peter Grünwald, Rianne de Heide and Wouter Koolen on safe testing was read before The Royal Statistical Society at a meeting organized by the Research Section on Wednesday, 24th January, 2024, after many years in the making, to the point that several papers based on this initial one have appeared in the meanwhile, incl. some submissions to Biometrika. Like this one in the current issue of Statistical Science dedicated to reproducibility and replicability. Joshua Bon and I wrote a discussion that synthesised the following and sometimes rambling remarks.

Overall, this is a mind-challenging paper with definitely original style and contents for which the authors are to be congratulated!

“…p-values are interpreted as indicating amounts of evidence against the null, and their definition does not need to refer to any specific alternative H¹. Exactly the same holds for e-values: the basic interpretation ‘a large e-value provides evidence against H⁰’ holds no matter how the e-variable is defined, as long as it satisfies (1). If they are defined relative to H¹ that is close to the actual process generating the data they will grow fast and provide a lot of evidence, but the basic interpretation holds regardless.”

About the entry section, one may ask why would a Bayesian want to test the veracity of a null hypothesis. The debate has been raging since the early days, although Jeffreys spent two chapters of his book on the topic of testing. (While appearing in Example 5 p.14 for his point estimation prior.) From an opposite viewpoint, the construction of e-values and such in the paper is highly model dependent, but all models are wrong! and more to the point both hypotheses may turn out to be wrong for misspecified cases. The notion thus seems on the opposite to be very M-close, with no idea of what is happening under misspecified models or why is rejecting H⁰ the ultimate argument.

When introducing e-values, (1) is not a definition per se, since otherwise E≡1 would be an e-value. This is unfortunate as the topic is already confusing enough. E[E] must be larger than 1 under H¹, otherwise product of e-values would always degenerate to zero (?)

The points

  1. behaviour under optional continuation [by a martingale reasoning]
  2. interpretation as ‘evidence against the null’ as gambling [unethical!]
  3. in all cases preserving frequentist Type I error guarantees
  4. e-variables turn out to be Bayes factors based on the right Haar prior [rather than sometimes with highly unusual (e.g. degenerate) priors? p.4]
  5. e-variables need more extreme data than p-values in order to reject the null

are rather worthwhile, even though 2. is vague and 3. is firmly frequentist. Any theory involving Haar priors (and even better amenability) cannot be all wrong, though, even considering that Haar priors are improper. The optional continuation in 1. is a nice argument from a Bayesian viewpoint since it has also been used to defend the Bayesian approach. Point 4. brings a formal way to define least favourable priors in the testing sense. One may then wonder at the connection with the solution of Bayarri and Garcia-Donato (Biometrika, 2007). The perspective adopted therein is somehow an inverse of the more common stance when the prior on H⁰ is the starting point [and obviously known]. So, is there any dual version of e-values where this would happen, i.e. leading to deriving the optimal prior on H¹ for a given prior on H⁰? (Which would further offer a maximin interpretation.) Theorem 1 indeed sounds like the minimax=maximin result for test settings. (In Corollary 2, why is (10) necessarily a Bayes factor, given the two models?)

While I first thought that the approach leads to finding a proper prior, the “Almost Bayesian Case” [p.17] (ABC!!) comes to justify the use of a “common” improper prior over nuisance parameters under both hypotheses, which while more justifiable than in the original objective Bayes literature, remains unsatisfactory to me. But I like the notion in 2.2 [p.10] that a prior chosen on H¹ forces one to adopt a particular corresponding prior on H⁰, as it defines a form of automated projection that we also considered in Goutis [RIP] and Robert (Biometrika, 1998). Corollary 2 is most interesting as well. However, taking the toy example of H⁰ being a normal mean standing in (-a,a) seems to lead to the optimal prior on H⁰ being a point mass at +/- a for any marginal m(y) centred at zero. Which is a disappointing outcome when compared with the point mass situation. It is another disappointment that the Bayes Factor cannot be an e-value since (6) fails to hold, but (1) is not (6) and one could argue that the BF is an e-value when integrating under the marginals!

As a marginalia, the paper made me learn about the term (and theme) tragedy of the commons, a concept developed by [the neomalthusian and eugenist] Garett Hardin.

In conclusion, we congratulate the authors on this endeavour but it remains unclear to us (as Bayesians) (i) how to construct the least favourable prior on H0 on a general basis, especially from a computational viewpoint, and, more importantly, (ii) whether it is at all of inferential interest [i.e., whether it degenerates into a point mass]. With respect to the sequential directions of the paper, we also wonder at the potential connections with sequential Monte Carlo, for instance, towards conducting sequential model choice by constructing efficiently an amalgamated evidence value when the product of Bayes factors is not a Bayes factor (see Buchholz et al., 2023).

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.