**I**n conjunction with the recent PNAS paper on massive model choice, Rob Johnson†, Paul Kirk and Michael Stumpf published in Bioinformatics an implementation of nested sampling that is designed for biological applications, called SYSBIONS. Hence the NS for nested sampling! The C software is available on-line. (I had planned to post this news next to my earlier comments but it went under the radar…)

## Archive for Bayesian model choice

## nested sampling for systems biology

Posted in Books, Statistics, University life with tags Bayesian model choice, bioinformatics, nested sampling, PNAS, SYSBIONS on January 14, 2015 by xi'an## full Bayesian significance test

Posted in Books, Statistics with tags Bayes factor, Bayesian Analysis, Bayesian model choice, e-values, full Bayesian significance test, logic journal of the IGPL, measure theory, Murray Aitkin, p-values, São Paulo, statistical inference on December 18, 2014 by xi'an**A**mong the many comments (thanks!) I received when posting our Testing via mixture estimation paper came the suggestion to relate this approach to the notion of full Bayesian significance test (FBST) developed by (Julio, not Hal) Stern and Pereira, from São Paulo, Brazil. I thus had a look at this alternative and read the Bayesian Analysis paper they published in 2008, as well as a paper recently published in Logic Journal of IGPL. (I could not find what the IGPL stands for.) The central notion in these papers is the *e-value*, which provides the *posterior probability that the posterior density is larger than the largest posterior density over the null set*. This definition bothers me, first because the *null* set has a measure equal to zero under an absolutely continuous prior (BA, p.82). Hence the posterior density is defined in an arbitrary manner over the *null* set and the maximum is itself arbitrary. (An issue that invalidates my 1993 version of the Lindley-Jeffreys paradox!) And second because it considers the posterior probability of an event that does not exist a priori, being conditional on the data. This sounds in fact quite similar to *Statistical Inference*, Murray Aitkin’s (2009) book using a posterior distribution of the likelihood function. With the same drawback of using the data twice. And the other issues discussed in our commentary of the book. (As a side-much-on-the-side remark, the authors incidentally forgot me when citing our 1992 Annals of Statistics paper about decision theory on accuracy estimators..!)

## postdoc in Paris?

Posted in Kids, Statistics, Travel, University life with tags ABC, Bayesian model choice, Fondation Sciences Mathématiques de Paris, MCMC, Monte Carlo Statistical Methods, Paris, postdoctoral position, Université Paris Dauphine on November 4, 2014 by xi'an**T**here is an open call of the Fondation Sciences Mathématiques de Paris (FSMP) about a postdoctoral funding program with 18 position-years available for staying in Université Paris-Dauphine (and other participating universities). The net support is quite decent (wrt French terms and academic salaries) and the application form easy to fill. So, if you are interested in coming to Paris to work on ABC, MCMC, Bayesian model choice, &tc., feel free to contact me (or another Parisian statistician) and to apply! The deadline is December 01, 2014. And the decision will be made by January 15, 2015. The starting date for the postdoc is October 01, 2015.

## all models are wrong

Posted in Statistics, University life with tags ABC, Bayes factor, Bayesian model choice, George Box, model posterior probabilities, Molecular Ecology, phylogenetic model, phylogeography on September 27, 2014 by xi'an

“Using ABC to evaluate competing models has various hazards and comes with recommended precautions (Robert et al. 2011), and unsurprisingly, many if not most researchers have a healthy scepticism as these tools continue to mature.”

**M**ichael Hickerson just published an open-access letter with the above title in Molecular Ecology. (As in several earlier papers, incl. the (in)famous ones by Templeton, Hickerson confuses running an ABC algorithm with conducting Bayesian model comparison, but this is not the main point of this post.)

“Rather than using ABC with weighted model averaging to obtain the three corresponding posterior model probabilities while allowing for the handful of model parameters (θ, τ, γ, Μ) to be estimated under each model conditioned on each model’s posterior probability, these three models are sliced up into 143 ‘submodels’ according to various parameter ranges.”

**T**he letter is in fact a supporting argument for the earlier paper of Pelletier and Carstens (2014, Molecular Ecology) which conducted the above splitting experiment. I could not read this paper so cannot judge of the relevance of splitting this way the parameter range. From what I understand it amounts to using mutually exclusive priors by using different supports.

“Specifically, they demonstrate that as greater numbers of the 143 sub-models areevaluated, the inference from their ABC model choice procedure becomes increasingly.”

**A**n interestingly cut sentence. Increasingly unreliable? mediocre? weak?

“…with greater numbers of models being compared, the most probable models are assigned diminishing levels of posterior probability. This is an expected result…”

**T**rue, if the number of models under consideration increases, under a uniform prior over model indices, the posterior probability of a given model mechanically decreases. But the pairwise Bayes factors should not be impacted by the number of models under comparison and the letter by Hickerson states that Pelletier and Carstens found the opposite:

“…pairwise Bayes factor[s] will always be more conservative except in cases when the posterior probabilities are equal for all models that are less probable than the most probable model.”

**W**hich means that the “Bayes factor” in this study is computed as the ratio of a marginal likelihood and of a compound (or super-marginal) likelihood, averaged over all models and hence incorporating the prior probabilities of the model indices as well. I had never encountered such a proposal before. Contrary to the letter’s claim:

“…using the Bayes factor, incorporating all models is perhaps more consistent with the Bayesian approach of incorporating all uncertainty associated with the ABC model choice procedure.”

**B**esides the needless inclusion of ABC in this sentence, a somewhat confusing sentence, as Bayes factors are not, *stricto sensu*, Bayesian procedures since they remove the prior probabilities from the picture.

“Although the outcome of model comparison with ABC or other similar likelihood-based methods will always be dependent on the composition of the model set, and parameter estimates will only be as good as the models that are used, model-based inference provides a number of benefits.”

**A**ll models are wrong but the very fact that they are models allows for producing pseudo-data from those models and for checking if the pseudo-data is similar enough to the observed data. In components that matters the most for the experimenter. Hence a loss function of sorts…

## R/Rmetrics in Paris [alas!]

Posted in Mountains, pictures, R, Statistics, Travel, University life with tags ABC, andouille de Vire, Bayesian econometrics, Bayesian model choice, Bernese Alps, cmpfun(), Collège des Bernardins, compiler, Eiger, importance sampling, Interlaken, Meielisalp, Mittelegi ridge, Paris, R, Rmetrics, San Antonio, Switzerland, system.time, Thun Lake on June 30, 2014 by xi'an**T**oday I gave a talk on Bayesian model choice in a fabulous 13th Century former monastery in the Latin Quarter of Paris… It is the Collège des Bernardins, close to Jussieu and Collège de France, unbelievably hidden to the point I was not aware of its existence despite having studied and worked in Jussieu since 1982… I mixed my earlier San Antonio survey on importance sampling approximations to Bayes factors with an entry to our most recent work on ABC with random forests. This was the first talk of the 8th R/Rmetrics workshop taking place in Paris this year. (Rmetrics is aiming at aggregating R packages with econometrics and finance applications.) And I had a full hour and a half to deliver my lecture to the workshop audience. Nice place, nice people, new faces and topics (and even andouille de Vire for lunch!): why should I complain with an alas in the title?!**W**hat happened is that the R/Rmetrics meetings have been till this year organised in Meielisalp, Switzerland. Which stands on top of Thuner See and… just next to the most famous peaks of the Bernese Alps! And that I had been invited last year but could not make it… Meaning I lost a genuine opportunity to climb one of my five dream routes, the Mittelegi ridge of the Eiger. As the future R/Rmetrics meetings will not take place there.

**A** lunch discussion at the workshop led me to experiment the compiler library in R, library that I was unaware of. The impact on the running time is obvious: recycling the fowler function from the last Le Monde puzzle,

> bowler=cmpfun(fowler) > N=20;n=10;system.time(fowler(pred=N)) user system elapsed 52.647 0.076 56.332 > N=20;n=10;system.time(bowler(pred=N)) user system elapsed 51.631 0.004 51.768 > N=20;n=15;system.time(bowler(pred=N)) user system elapsed 51.924 0.024 52.429 > N=20;n=15;system.time(fowler(pred=N)) user system elapsed 52.919 0.200 61.960

shows a ten- to twenty-fold gain in system time, if not in elapsed time (re-alas!).

## Bayesian Data Analysis [BDA3 – part #2]

Posted in Books, Kids, R, Statistics, University life with tags Andrew Gelman, Bayesian data analysis, Bayesian model choice, Bayesian predictive, finite mixtures, graduate course, hierarchical Bayesian modelling, rats, STAN on March 31, 2014 by xi'an**H**ere is the second part of my review of Gelman et al.’ *Bayesian Data Analysis* (third edition):

“When an iterative simulation algorithm is “tuned” (…) the iterations will not in general converge to the target distribution.” (p.297)

**P**art III covers advanced computation, obviously including MCMC but also model approximations like variational Bayes and expectation propagation (EP), with even a few words on ABC. The novelties in this part are centred at Stan, the language Andrew is developing around Hamiltonian Monte Carlo techniques, a sort of BUGS of the 10’s! (And of course Hamiltonian Monte Carlo techniques themselves. A few (nit)pickings: the book advises important resampling without replacement (p.266) which makes some sense when using a poor importance function but ruins the fundamentals of importance sampling. Plus, no trace of infinite variance importance sampling? of harmonic means and their dangers? In the Metropolis-Hastings algorithm, the proposal is called the jumping rule and denoted by J_{t}, which, besides giving the impression of a Jacobian, seems to allow for time-varying proposals and hence time-inhomogeneous Markov chains, which convergence properties are much hairier. (The warning comes much later, as exemplified in the above quote.) Moving from “burn-in” to “warm-up” to describe the beginning of an MCMC simulation. Being somewhat 90’s about convergence diagnoses (as shown by the references in Section 11.7), although the book also proposes new diagnoses and relies much more on effective sample sizes. Particle filters are evacuated in hardly half-a-page. Maybe because Stan does not handle particle filters. A lack of intuition about the Hamiltonian Monte Carlo algorithms, as the book plunges immediately into a two-page pseudo-code description. Still using physics vocabulary that put *me* (and maybe only *me*) off. Although I appreciated the advice to check analytical gradients against their numerical counterpart.

“In principle there is no limit to the number of levels of variation that can be handled in this way. Bayesian methods provide ready guidance in handling the estimation of the unknown parameters.” (p.381)

**I** also enjoyed reading the part about modes that stand at the boundary of the parameter space (Section 13.2), even though I do not think modes are great summaries in Bayesian frameworks and while I do not see how picking the prior to avoid modes at the boundary avoids the data impacting the prior, *in fine*. The variational Bayes section (13.7) is equally enjoyable, with a proper spelled-out illustration, introducing an unusual feature for Bayesian textbooks. (Except that sampling without replacement is back!) Same comments for the Expectation Propagation (EP) section (13.8) that covers brand new notions. (Will they stand the test of time?!)

“Geometrically, if β-space is thought of as a room, the model implied by classical model selection claims that the true β has certain prior probabilities of being in the room, on the floor, on the walls, in the edge of the room, or in a corner.” (p.368)

**P**art IV is a series of five chapters about regression(s). This is somewhat of a classic, nonetheless Chapter 14 surprised me with an elaborate election example that dabbles in advanced topics like causality and counterfactuals. I did not spot any reference to the *g*-prior or to its intuitive justifications and the chapter mentions the lasso as a regularisation technique, but without any proper definition of this “popular non-Bayesian form of regularisation” (p.368). In French: with not a single equation! Additional novelty may lie in the numerical prior information about the correlations. What is rather crucially (cruelly?) missing though is a clearer processing of variable selection in regression models. I know Andrew opposes any notion of a coefficient being exactly equal to zero, as ridiculed through the above quote, but the book does not reject model selection, so why not in this context?! Chapter 15 on hierarchical extensions stresses the link with exchangeability, once again. With another neat election example justifying the progressive complexification of the model and the cranks and toggles of model building. (I am not certain the reparameterisation advice on p.394 is easily ingested by a newcomer.) The chapters on robustness (Chap. 17) and missing data (Chap. 18) sound slightly less convincing to me, esp. the one about robustness as I never got how to make robustness agree with my Bayesian perspective. The book states “we do not have to abandon Bayesian principles to handle outliers” (p.436), but I would object that the Bayesian paradigm compels us to define an alternative model for those outliers and the way they are produced. One can always resort to a drudging exploration of which subsample of the dataset is at odds with the model but this may be unrealistic for large datasets and further tells us nothing about how to handle those datapoints. The missing data chapter is certainly relevant to such a comprehensive textbook and I liked the survey illustration where the missing data was in fact made of missing questions. However, I felt the multiple imputation part was not well-presented, fearing readers would not understand how to handle it…

“You can use MCMC, normal approximation, variational Bayes, expectation propagation, Stan, or any other method. But your fit must be Bayesian.” (p.517)

**P**art V concentrates the most advanced material, with Chapter 19 being mostly an illustration of a few complex models, slightly superfluous in my opinion, Chapter 20 a very short introduction to functional bases, including a basis selection section (20.2) that implements the “zero coefficient” variable selection principle refuted in the regression chapter(s), and does not go beyond splines (what about wavelets?), Chapter 21 a (quick) coverage of Gaussian processes with the motivating birth-date example (and two mixture datasets I used eons ago…), Chapter 22 a more (too much?) detailed study of finite mixture models, with no coverage of reversible-jump MCMC, and Chapter 23 an entry on Bayesian non-parametrics through Dirichlet processes.

“In practice, for well separated components, it is common to remain stuck in one labelling across all the samples that are collected. One could argue that the Gibbs sampler has failed in such a case.” (p.535)

**T**o get back to mixtures, I liked the quote about the label switching issue above, as I was “one” who argued that the Gibbs sampler fails to converge! The corresponding section seems to favour providing a density estimate for mixture models, rather than component-wise evaluations, but it nonetheless mentions the relabelling by permutation approach (if missing our 2000 JASA paper). The section about inferring on the unknown number of components suggests conducting a regular Gibbs sampler on a model with an upper bound on the number of components and then checking for empty components, an idea I (briefly) considered in the mid-1990’s before the occurrence of RJMCMC. Of course, the prior on the components matters and the book suggests using a Dirichlet with fixed sum like 1 on the coefficients for all numbers of components.

“14. Objectivity and subjectivity: discuss the statement `People tend to believe results that support their preconceptions and disbelieve results that surprise them. Bayesian methods tend to encourage this undisciplined mode of thinking.’¨ (p.100)

**O**bviously, this being a third edition begets the question, *what’s up, doc?!,* i.e., what’s new [when compared with the second edition]? Quite a lot, even though I am not enough of a Gelmanian exegist to produce a comparision table. Well, for a starter, David Dunson and Aki Vethtari joined the authorship, mostly contributing to the advanced section on non-parametrics, Gaussian processes, EP algorithms. Then the Hamiltonian Monte Carlo methodology and Stan of course, which is now central to Andrew’s interests. The book does include a short Appendix on running computations in R and in Stan. Further novelties were mentioned above, like the vision of weakly informative priors taking over noninformative priors but I think this edition of *Bayesian Data Analysis* puts more stress on clever and critical model construction and on the fact that it can be done in a Bayesian manner. Hence the insistence on predictive and cross-validation tools. The book may be deemed somewhat short on exercices, providing between 3 and 20 mostly well-developed problems per chapter, often associated with datasets, rather than the less exciting counter-example above. Even though Andrew disagrees and his students at ENSAE this year certainly did not complain, I personally feel a total of 220 exercices is not enough for instructors and self-study readers. (At least, this reduces the number of email requests for solutions! Esp. when 50 of those are solved on the book website.) But this aspect is a minor quip: overall this is truly the reference book for a graduate course on Bayesian statistics and not only Bayesian data analysis.