Archive for survey

Computing Bayes: Bayesian Computation from 1763 to the 21st Century

Posted in Books, pictures, Statistics, Travel, University life with tags , , , , , , on April 16, 2020 by xi'an

Last night, Gael Martin, David Frazier (from Monash U) and myself arXived a survey on the history of Bayesian computations. This project started when Gael presented a historical overview of Bayesian computation, then entitled ‘Computing Bayes: Bayesian Computation from 1763 to 2017!’, at ‘Bayes on the Beach’ (Queensland, November, 2017). She then decided to build a survey from the material she had gathered, with her usual dedication and stamina. Asking David and I to join forces and bring additional perspectives on this history. While this is a short and hence necessary incomplete history (of not everything!), it hopefully brings some different threads together in an original enough fashion (as I think there is little overlap with recent surveys I wrote). We welcome comments about aspects we missed, skipped or misrepresented, most obviously!

Rao-Blackwellisation, a review in the making

Posted in Statistics with tags , , , , , , , , , , on March 17, 2020 by xi'an

Recently, I have been contacted by a mainstream statistics journal to write a review of Rao-Blackwellisation techniques in computational statistics, in connection with an issue celebrating C.R. Rao’s 100th birthday. As many many techniques can be interpreted as weak forms of Rao-Blackwellisation, as e.g. all auxiliary variable approaches, I am clearly facing an abundance of riches and would thus welcome suggestions from Og’s readers on the major advances in Monte Carlo methods that can be connected with the Rao-Blackwell-Kolmogorov theorem. (On the personal and anecdotal side, I only met C.R. Rao once, in 1988, when he came for a seminar at Purdue University where I was spending the year.)

MCMC, with common misunderstandings

Posted in Books, pictures, R, Statistics, University life with tags , , , , , , , , , , , , on January 27, 2020 by xi'an

As I was asked to write a chapter on MCMC methods for an incoming Handbook of Computational Statistics and Data Science, published by Wiley, rather than cautiously declining!, I decided to recycle the answers I wrote on X validated to what I considered to be the most characteristic misunderstandings about MCMC and other computing methods, using as background the introduction produced by Wu Changye in his PhD thesis. Waiting for the opinion of the editors of the Handbook on this Q&A style. The outcome is certainly lighter than other recent surveys like the one we wrote with Peter Green, Krys Latuszinski, and Marcelo Pereyra, for Statistics and Computing, or the one with Victor Elvira, Nick Tawn, and Changye Wu.

approximate likelihood perspective on ABC

Posted in Books, Statistics, University life with tags , , , , , , , , , , , , , , on December 20, 2018 by xi'an

George Karabatsos and Fabrizio Leisen have recently published in Statistics Surveys a fairly complete survey on ABC methods [which earlier arXival I had missed]. Listing within an extensive bibliography of 20 pages some twenty-plus earlier reviews on ABC (with further ones in applied domains)!

“(…) any ABC method (algorithm) can be categorized as either (1) rejection-, (2) kernel-, and (3) coupled ABC; and (4) synthetic-, (5) empirical- and (6) bootstrap-likelihood methods; and can be combined with classical MC or VI algorithms [and] all 22 reviews of ABC methods have covered rejection and kernel ABC methods, but only three covered synthetic likelihood, one reviewed the empirical likelihood, and none have reviewed coupled ABC and bootstrap likelihood methods.”

The motivation for using approximate likelihood methods is provided by the examples of g-and-k distributions, although the likelihood can be efficiently derived by numerical means, as shown by Pierre Jacob‘s winference package, of mixed effect linear models, although a completion by the mixed effects themselves is available for Gibbs sampling as in Zeger and Karim (1991), and of the hidden Potts model, which we covered by pre-processing in our 2015 paper with Matt Moores, Chris Drovandi, Kerrie Mengersen. The paper produces a general representation of the approximate likelihood that covers the algorithms listed above as through the table below (where t(.) denotes the summary statistic):

The table looks a wee bit challenging simply because the review includes the synthetic likelihood approach of Wood (2010), which figured preeminently in the 2012 Read Paper discussion but opens the door to all kinds of approximations of the likelihood function, including variational Bayes and non-parametric versions. After a description of the above versions (including a rather ignored coupled version) and the special issue of ABC model choice,  the authors expand on the difficulties with running ABC, from multiple tuning issues, to the genuine curse of dimensionality in the parameter (with unnecessary remarks on low-dimension sufficient statistics since they are almost surely inexistent in most realistic settings), to the mis-specified case (on which we are currently working with David Frazier and Judith Rousseau). To conclude, an worthwhile update on ABC and on the side a funny typo from the reference list!

Li, W. and Fearnhead, P. (2018, in press). On the asymptotic efficiency
of approximate Bayesian computation estimators. Biometrika na na-na.

support for Remain comes first in latest YouGov survey

Posted in pictures, Travel with tags , , , , , , , on December 6, 2018 by xi'an

ABC intro for Astrophysics

Posted in Books, Kids, Mountains, R, Running, Statistics, University life with tags , , , , , , , , , , , on October 15, 2018 by xi'an

Today I received in the mail a copy of the short book published by edp sciences after the courses we gave last year at the astrophysics summer school, in Autrans. Which contains a quick introduction to ABC extracted from my notes (which I still hope to turn into a book!). As well as a longer coverage of Bayesian foundations and computations by David Stenning and David van Dyk.

look, look, confidence! [book review]

Posted in Books, Statistics, University life with tags , , , , , , , , , , , , , , , , on April 23, 2018 by xi'an

As it happens, I recently bought [with Amazon Associate earnings] a (used) copy of Confidence, Likelihood, Probability (Statistical Inference with Confidence Distributions), by Tore Schweder and Nils Hjort, to try to understand this confusing notion of confidence distributions. (And hence did not get the book from CUP or anyone else towards purposely writing a review. Or a ½-review like the one below.)

“Fisher squared the circle and obtained a posterior without a prior.” (p.419)

Now that I have gone through a few chapters, I am no less confused about the point of this notion. Which seems to rely on the availability of confidence intervals. Exact or asymptotic ones. The authors plainly recognise (p.61) that a confidence distribution is neither a posterior distribution nor a fiducial distribution, hence cutting off any possible Bayesian usage of the approach. Which seems right in that there is no coherence behind the construct, meaning for instance there is no joint distribution corresponding to the resulting marginals. Or even a specific dominating measure in the parameter space. (Always go looking for the dominating measure!) As usual with frequentist procedures, there is always a feeling of arbitrariness in the resolution, as for instance in the Neyman-Scott problem (p.112) where the profile likelihood and the deviance do not work, but considering directly the distribution of the (inconsistent) MLE of the variance “saves the day”, which sounds a bit like starting from the solution. Another statistical freak, the Fieller-Creasy problem (p.116) remains a freak in this context as it does not seem to allow for a confidence distribution. I also notice an ambivalence in the discourse of the authors of this book, namely that while they claim confidence distributions are both outside a probabilisation of the parameter and inside, “producing distributions for parameters of interest given the data (…) with fewer philosophical and interpretational obstacles” (p.428).

“Bias is particularly difficult to discuss for Bayesian methods, and seems not to be a worry for most Bayesian statisticians.” (p.10)

The discussions as to whether or not confidence distributions form a synthesis of Bayesianism and frequentism always fall short from being convincing, the choice of (or the dependence on) a prior distribution appearing to the authors as a failure of the former approach. Or unnecessarily complicated when there are nuisance parameters. Apparently missing on the (high) degree of subjectivity involved in creating the confidence procedures. Chapter 1 contains a section on “Why not go Bayesian?” that starts from Chris Sims‘ Nobel Lecture on the appeal of Bayesian methods and goes [softly] rampaging through each item. One point (3) is recurrent in many criticisms of B and I always wonder whether or not it is tongue-in-cheek-y… Namely the fact that parameters of a model are rarely if ever stochastic. This is a misrepresentation of the use of prior and posterior distributions [which are in fact] as summaries of information cum uncertainty. About a true fixed parameter. Refusing as does the book to endow posteriors with an epistemic meaning (except for “Bayesian of the Lindley breed” (p.419) is thus most curious. (The debate is repeating in the final(e) chapter as “why the world need not be Bayesian after all”.)

“To obtain frequentist unbiasedness, the Bayesian will have to choose her prior with unbiasedness in mind. Is she then a Bayesian?” (p.430)

A general puzzling feature of the book is that notions are not always immediately defined, but rather discussed and illustrated first. As for instance for the central notion of fiducial probability (Section 1.7, then Chapter 6), maybe because Fisher himself did not have a general principle to advance. The construction of a confidence distribution most often keeps a measure of mystery (and arbitrariness), outside the rather stylised setting of exponential families and sufficient (conditionally so) statistics. (Incidentally, our 2012 ABC survey is [kindly] quoted in relation with approximate sufficiency (p.180), while it does not sound particularly related to this part of the book. Now, is there an ABC version of confidence distributions? Or an ABC derivation?) This is not to imply that the book is uninteresting!, as I found reading it quite entertaining, with many humorous and tongue-in-cheek remarks, like “From Fraser (1961a) and until Fraser (2011), and hopefully even further” (p.92), and great datasets. (Including one entitled Pornoscope, which is about drosophilia mating.) And also datasets with lesser greatness, like the 3000 mink whales that were killed for Example 8.5, where the authors if not the whales “are saved by a large and informative dataset”… (Whaling is a recurrent [national?] theme throughout the book, along with sport statistics usually involving Norway!)

Miscellanea: The interest of the authors in the topic is credited to bowhead whales, more precisely to Adrian Raftery’s geometric merging (or melding) of two priors and to the resulting Borel paradox (xiii). Proposal that I remember Adrian presenting in Luminy, presumably in 1994. Or maybe in Aussois the year after. The book also repeats Don Fraser’s notion that the likelihood is a sufficient statistic, a point that still bothers me. (On the side, I realised while reading Confidence, &tc., that ABC cannot comply with the likelihood principle.) To end up on a French nitpicking note (!), Quenouille is typ(o)ed Quenoille in the main text, the references and the index. (Blame the .bib file!)