Archive for Bayes(Pharma)

Insufficient Gibbs sampling [at COMPSTAT 2024]

Posted in pictures, Statistics, Travel, University life with tags , , , , , , , , , , , , , on August 29, 2024 by xi'an


The COMPSTAT 2024 programme proved somewhat remote from my interests, far from the 1998 version I attended that was buzzing and brimming with MCMC sessions! (Correlatively, apart from the speakers in my own session, I hardly knew anyone there.) I however [missed a Bayesian session as I] attended a session on change-point detection, with a talk by Ziyang Yang (Lancaster University) on an acceleration proposal when the data size is too much, by aggregating similar datapoints, for which I would like to see a theoretical analysis of the impact of this aggregation on the quality (and consistency) of the attached Bayes factor. In my own session, I did not feel overly comfortable with the presentation of a commercial [i.e., for sale] software for pharmacokinetics.

I also enjoyed spending the day in Gießen, from running to the top of nearby Burg Glieberg at sunrise to swimming outdoor in the local 50m Freibad.

Bayesian biostatistics in Lyon 2019

Posted in pictures, Statistics, Travel, University life with tags , , , , , on November 8, 2018 by xi'an

Bayes, reproducibility, and the quest for truth

Posted in Books, Kids, Statistics, University life with tags , , , , , , , , , on September 2, 2016 by xi'an

“Avoid opinion priors, you could be held legally or otherwise responsible.”

Don Fraser, Mylène Bedard, Augustine Wong, Wei Lin, and Ailana Fraser wrote a paper to appear in Statistical Science, with the above title. This paper is a continuation of Don’s assessment of Bayes procedures in earlier Statistical Science [which I discussed] and Science 2013 papers, which I would qualify with all due respect of a demolition enterprise [of the Bayesian approach to statistics]…  The argument therein is similar in that “reproducibility” is to be understood therein as providing frequentist confidence assessment. The authors also use “accuracy” in this sense. (As far as I know, there is no definition of reproducibility to be found in the paper.) Some priors are matching priors, in the (restricted) sense that they give second-order accurate frequentist coverage. Most are not matching and none is third-order accurate, a level that may be attained by alternative approaches. As far as the abstract goes, this seems to be the crux of the paper. Which is fine, but does not qualify in my opinion as a criticism of the Bayesian paradigm, given that (a) it makes no claim at frequentist coverage and (b) I see no reason in proper coverage being connected with “truth” or “accuracy”. It truly makes no sense to me to attempt either to put a frequentist hat on posterior distributions or to check whether or not the posterior is “valid”, “true” or “actual”. I similarly consider that Efron‘s “genuine priors” do not belong to the Bayesian paradigm but are on the opposite anti-Bayesian in that they suggest all priors should stem from frequency modelling, to borrow the terms from the current paper. (This is also the position of the authors, who consider they have “no Bayes content”.)

Among their arguments, the authors refer to two tragic real cases: the earthquake at L’Aquila, where seismologists were charged (and then discharged) with manslaughter for asserting there was little risk of a major earthquake, and the indictment of the pharmaceutical company Merck for the deadly side-effects of their drug Vioxx. The paper however never return to those cases and fails to explain in which sense this is connected with the lack of reproducibility or of truth(fullness) of Bayesian procedures. If anything, the morale of the Aquila story is that statisticians should not draw definitive conclusions like there is no risk of a major earthquake or that it was improbable. There is a strange if human tendency for experts to reach definitive conclusions and to omit the many layers of uncertainty in their models and analyses. In the earthquake case, seismologists do not know how to predict major quakes from the previous activity and that should have been the [non-]conclusion of the experts. Which could possibly have been reached by a Bayesian modelling that always includes uncertainty. But the current paper is not at all operating at this (epistemic?) level, as it never ever questions the impact of the choice of a likelihood function or of a statistical model in the reproducibility framework. First, third or 47th order accuracy nonetheless operates strictly within the referential of the chosen model and providing the data to another group of scientists, experts or statisticians will invariably produce a different statistical modelling. So much for reproducibility or truth.

ISBA [officially] on drugs

Posted in pictures, Statistics, University life with tags , , , , on September 11, 2012 by xi'an

Following a call in June for sponsoring a new ISBA section on biostatistics and pharmaceutical statistics, relayed by this blog, the process has now reached its natural conclusion and ISBA/BioPharm is now an official session of ISBA! It is quite straightforward to become a (founding) member, just one click away… Just to borrow from the initial call:

An important aspect of biostat and pharmaceutical statistics is the presence of strong communities in academics, industry and government agencies. We hope that the new section will play an important role in connecting folks across these different communities and giving a platform to related intiatives. The initial officers of the section are

*  Section chair: Donald A. Berry (Term: August 2012-December 2014)
*  Program chair: Telba Z. Irony (Term: July 2012-December 2013)
*  Secretary: Peter Mueller (Term: July 2012-December 2014)
*  Treasurer: Kathryn Chaloner (Term: July 2012-December 2013)

Please join now to participate in the first election this October of the new chair elect!  Lifetime memberships are $200 while annual memberships are $10. All new memberships after September 1 will be extended until Dec 31, 2013!

Note that we should pretty soon be allowed to announce a similar creation for BayesComp, the computational Bayes section of ISBA!

Biostat/Pharma is coming to ISBA [guest post]

Posted in Statistics, Travel, University life with tags , , , , on June 19, 2012 by xi'an

This post is written by Julien Cornebise :

Along with Telba Irony, Peter Mueller, and Gary Rosner, I have the pleasure to be co-founding a dedicated Biostat/Pharma section of ISBA.

Its aim is to help network and federate under a common well-known “brand” the many initiatives to spread Bayesian methods and ideas in Biostats and Pharmacological stats: for example workshops, short courses, continuing education, sessions within larger conferences, etc.

We also want to help bridge academic and industry in this regard: there are plenty of people on both sides with excellent ideas and stimulating problems, and we think that such an ISBA’s section could help connecting them.

You can already sign the opening petition: we aim to have this section open by the end of the summer. Besides, I will be in ISBA 2012 in Kyoto next week: if you have questions, suggestions, or existing initiatives that could benefit from this branding, I will be glad to meet with yoi!

Post-scriptum: to sign the opening petition, you need to already be or become an ISBA member (50 USD, much worth it!)