Bayes on drugs (guest post)

This post is written by Julien Cornebise.

Last week in Aachen was the 3rd Edition of the Bayes(Pharma) workshop. Its specificity: half-and-half industry/academic participants and speakers, all in Pharmaceutical statistics, with a great care to welcome newcomers to Bayes, so as to spread as much as possible the love where it will actually be used. First things first: all the slides are available online, thanks to the speakers for sharing those. Full disclaimer: being part of the scientific committee of the workshop, I had a strong subjective prior.

3 days, 70 participants, we were fully booked, and even regretfully had to refuse inscriptions due to lack of room-space (!! German regulations are quite… enforced). Time to size it up for next year, maybe?

My most vivid impression overall: I was struck by the interactivity of the questions/answers after each talk. Rarely fewer than 5 questions per talk (come on, we’ve all attended sessions where the chairman is forced to ask the lone question — no such thing here!), on all points of each talk, with cross-references from one question to the other, even from one *talk* to the other! Seeing so much interaction and discussion in spite of (or, probably, thanks to ?) the diversity of the audience was a real treat: not only did the questions bring up additional details about the talk, they were, more importantly, bringing very precious highlight on the questioners’ mindsets, their practical concerns and needs. Both academics and industrials were learning on all counts — and, for having sometimes seen failed marriages of the kind in the past (either a French round-table degenerating in nasty polemic on “research-induced tax credit”, or just plain mismatch of interests), I was quite impressed that we were purely and simply all interested in multiple facets of the very same thing: the interface between pharma and stats.

As is now a tradition, the first day was a short course, this time by Pr. Emmanuel Lessaffre: based on his upcoming book on Bayesian Biostatistics (Xian, maybe a review someday?), it was meant to be introductory for newcomers to Bayes, but was still packed with enough “tricks of the trades” that even seasoned Bayesians could get something out of it. I very much appreciated the pedagogy in the “live” examples, with clear convergence caveats based on traceplots of common software (WinBUGS). The most vivid memory: his strong spotlight on INLA as “the future of Bayesian computation”. Although my research is mostly on MCMC/SMC, I’m now damn curious to give it a serious try — this was further reinforced by late evening discussions with Gianluca BaioM, who revealed that all his results that were all obtained in seconds of INLA computing.

Day 2 and half-day 3 were invited and contributed talks, all motivated by top-level applications. No convergence theorems here, but practical issues, with constraints that theoreticians (including myself!) would hardly guess exist: very small sample sizes, regulatory issues, concurrence with legacy methodology with only seconds-long runtime (impossible to run 1 million MCMC steps!), and sometimes even imposed software due to validation processes! Again, as stated above, the number and quality of questions is really what I will keep from those 2 days.

If I had to state one regret, maybe, it would be this unsatisfactory feeling that, for many newcomers, MCMC = WinBUGS — with its obvious restrictions. The lesson I learned: all the great methodological advances of the last 10 years, especially in Adaptive MCMC, have not yet reached most practitioners yet, since they need *tools* they can use. It may be a sign that, as methodological researchers, we should maybe put a stronger emphasis on bringing software packages forward (for R, of course, but also for JAGS or OpenBUGS!); not only a zip-file with our article’s codes, but a full-fledged package, with ongoing support, maintenance, and forum. That’s a tough balance to find, since the time maintaining a package does not count in the holy-bibliometry… but doesn’t it have more actual impact? Besides, more packages = less papers but also = more citations of the corresponding paper. Some do take this road (Robert Gramacy’s packages were cited last week as examples of great support, and Andy Gelman and Matt Hoffman are working on the much-expected STAN, and I mentioned above Havard Rue’s R-INLA), but I don’t think it is yet considered “best practices”.

As a conclusion, this Bayes-Pharma 2012 workshop reminded me a lot of the SAMSI 2010 Summer Program: while Bayes-Pharma aims to be much more introductory, they had in common this same success in blending pharma-industry and academy. Could it be a specificity of pharma? In which case, I’m looking very much forward opening ISBA’s Specialized Section on Biostat/Pharmastat that a few colleagues and I are currently working on (more on this here soon). With such a crowd on both sides of the Atlantic, and a looming Bayes 2013 in the Netherlands, that will be exciting.

4 Responses to “Bayes on drugs (guest post)”

  1. Julien, you should check out Pierre and my recent R package, “PAWL”. It does parallel adaptive Wang-Landau as well as adaptive MH.

    http://cran.r-project.org/web/packages/PAWL/index.html

  2. I’m happy to receive suggestions for future JAGS development. JAGS was always intended to be an extensible platform, not just end-user software. Unfortunately, the demands of maintaining it are substantial and I have not made as much progress in that direction as I wanted.

    As an example, two weeks ago I was in Vienna, where Sylvia Fruehwirth-Schnatter brought me up to date with the latest developments in auxiliary variable mixture sampling. These will be incorporated into the next major release.

    • Hi Martyn, thanks for answering.
      Actually, the job you’ve done with JAGS is impressive. I have posted on your forum a question about contributing to the code, but have since then realized that indeed, you’re the one and only main coder, which is a remarkable feat!
      I think the great strength of JAGS is that it indeed has the potential to gather much more contributors/extenders than OpenBUGS, thanks to its use of the widespread C++ rather than Component Pascal. Have you had people asking to contribute modules, in the past?

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