Archive for Bayesian testing

on stopping rules

Posted in Books, Statistics with tags , , , , , , , , , , , , , , , , , on August 3, 2025 by xi'an

The workshop in Chennai and its focus on sequential procedures made me realise (among other things) I had never read Cornfield’s 1966 TAS paper on sequential testing and the likelihood principle:

“By sequential analysis I mean any form of analysis in which the conclusion depends not only on the data, but also on the stopping rule.”

Written with little maths and formalism, this paper argues that keeping a fixed critical level amounts to keeping a fixed amount of evidence. Hence constituting an early critique of p-values even though not expressed in such terms. The part of the paper related with the likelihood principle does not address testing or evidence in a Bayesian way. As a side (late awakening) remark, iid observations in sequential settings are not longer independent, conditional on the stopping rule realisation N=n, since they are constrained by the fact that the stopping rule realisation is n and not n-1, n-2, …  For a short while, I thought it was in turn impacting the distribution of any “sufficient” statistic one may propose, with a normalising constant that depends on the unknown parameter and hence cannot be neglected. Over all those years, I had never though of the modification of sufficiency characteristics in such contexts. But in fine the pair made of the value of the stopping rule and of the unsequential sufficient statistics proves enough. And the normalisation constant is the probability that the stopping rule.. stops!, which is equal to one! For the same short while, I was then wondering that the stopping rule principle!

“my second line of argument that there is a reasonable alternative explication of the idea of inference and one which leads to the rejection of sequential analysis. This explication is provided by the likelihood principle—which states that all observations leading to the same likelihood function should lead to the same conclusion.”

I thus went back to the fundamentals (!), namely [freely available] Bernardo’s and Smith’s Section 5.1.4 (reproduced in EJ’s Stopping rule appendix, also citing Cornfield at length), where the likelihood is properly defined by the joint density of the stopping rule τ and the attached sample at their realised values. And failing in the end (and a discussion with Judith)nto spot a missing normalisation constant.

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.]

a lesser-known correlate of the Jeffreys-Lindley paradox (with discussion)

Posted in Books, pictures, Statistics, University life with tags , , , , , , , , , , , , , , , on October 19, 2024 by xi'an

Two UBC faculty, Harlan Campbell and Paul Gustafson, wrote a paper entitled “Defining a Credible Interval Is Not Always Possible with “Point-Null” Priors: A Lesser-Known Correlate of the Jeffreys-Lindley Paradox” in Bayesian Analysis (2024, 19, Number 3, pp. 925–984), which got discussed and presented on the BA webinar yesterday. I missed the call for discussion, on a topic I would have liked very much to discuss and an analysis I strongly disagree with. Fortunately, several of the discussants in the webinar and in the printed version advanced some of my points (as. e.g., Bertrand Clarke in the above slide screen-shot from the on-line video).

I find the paper somewhat missing in linking with the history of the topic, with no mention of Berger & Sellke (1987) that comes as a counterpoint to Casella &—the other—Berger (1987), opposing one sided to two sided tests. Or of matching priors, which connect credible and confidence intervals to higher orders. But the central issue with the apparent contradiction between rejecting the point null hypothesis and returning a credible interval that contains the null is that the construction proceeds from a model averaged posterior. Which fundamentally contradicts the construct of a pair of priors attached with each model towards selecting the fittest one. And requires a far-from-innocent choice of respective prior weights for both models, an ill-defined notion I have repeatedly criticised here and elsewhere. Model averaging clashes with model selection in both decision-theoretic and modelling terms. In model averaging terms, the disappearance of the opposition exhibited by the authors in the predictive distribution, as shown by discussants Held and Pawel, is unsurprising. And makes the spike-and-slab prior far of a necessity. Contrariwise to the model selection case where it proves unavoidable. And for which a merged credible interval does not make sense (to me at least) since it should be constructed once one (and only one) of the two models is chosen. At this point, that the other model ever was considered should not impact subsequent inference. And within that perspective I do not see the relevance of agnostic (ignoring the model choice ation) 5% confidence or credible regions.

“…considers the regime of a fixed true parameter value as n increases [and] of a fixed p-value…” (p928)

With regards with the connection with the Jeffreys-Lindley (or Lindley-Jeffreys) so-called paradox, on which I have already written a lot (or even too much!), many of the earlier objections resurface. Like the measure-theoretic difficulty in including within a continuous interval an atom, i.e., a value with a point mass. Which isolates this atom away from any other value in the interval (and of course creates discontinuities). Or fixing the p-value forever after (when n goes to infinity), as in the graph below (p929). Or treating an improper prior without further caution than with a proper prior. Especially when these are “created” by the decision problem itself.

 

advancements in Bayesian methods and implementations

Posted in Books, Statistics, University life with tags , , , , , , , , on November 10, 2022 by xi'an

The handbook of (recent) advances in Bayesian methods is now out (at the Elsevierian price of $250!) with chapters on Gibbs posteriors [Ryan Martin & Nicolas Syring], martingale distributions [Walker], selective inference [Daniel García Racines & Alastair Young], manifold simulations [Sumio Watanabe], MCMC for GLMMs [Vivek Roy] and multiple testing [Noirrit Chandra and Sourabh Bhattacharya]. (Along with my chapter on 50 shades of Bayesian testing.) Celebrating 102 years for C.R. Rao, one of the three editors of this volume (as well as the series) along with Arni Srivastava Rao and Alastair Young.

Advancements in Bayesian Methods and Implementations [to appear]

Posted in Books, Statistics with tags , , , , , on July 17, 2022 by xi'an

As noted in another post, I wrote a chapter on Bayesian testing for an incoming handbook, Advancements in Bayesian methods and implementations which is published by Elsevier at an atrocious price (as usual). Here is the table of contents:

1. Fisher Information, Cramèr-Rao and Bayesian Paradigm by Roy Frieden
2. Compound beta binomial distribution functions by Angelo Plastino
3. MCMC for GLMMS by Vivekananda Roy
4. Signal Processing and Bayesian by Chandra Murthy
5. Mathematical theory of Bayesian statistics where all models are wrong by Sumio Watanabe
6. Machine Learning and Bayesian by Jun Zhu
7. Non-parametric Bayes by Stephen Walker
8. [50 shades of] Bayesian testing [of hypotheses] by Christian P. Robert
9. Data Analysis with humans by Sumio Kaski
10. Bayesian Inference under selection by G. Alastair Young
10. Variational inference or Functional horseshoe by Anirban Bhattacharya
11. Generalized Bayes by Ryan Martin

and my chapter is also available on arXiv, quickly gathered from earlier short courses at O’Bayes meetings and some xianblog entries on the topic, hence not containing much novelty!