*[Heading off to mountainous areas with no Internet or phone connection, I posted a series of entries for the following week, starting with this brilliant trailer of Michael:]*

## Archive for Andrew Gelman

## STAN trailer [PG+53]

Posted in Kids, R, Statistics, University life with tags Andrew Gelman, Hamiltonian Monte Carlo, STAN, statistical software, trailer on August 14, 2015 by xi'an## also sprach Nietzsche

Posted in Books, Kids, pictures with tags Andrew Gelman, atheism, Friedrich Nietzsche, graphical novel, Maximilien Le Roy, Michel Onfray, Philosophenweg on March 30, 2015 by xi'an## Statistics done wrong [book review]

Posted in Books, Kids, pictures, Statistics, University life with tags Andrew Gelman, book reviews, Carnegie Mellon University, CHANCE, consulting, no starch press, p-values, physics, Statistics done wrong, textbook on March 16, 2015 by xi'anno starch press (!) sent me the pdf version of this incoming book, *Statistics done wrong*, by Alex Reinhart, towards writing a book review for CHANCE, and I read it over two flights, one from Montpellier to Paris last week, and from Paris to B’ham this morning. The book is due to appear on March 16. It expands on a still existing website developed by Reinhart. (Discussed a year or so away on Andrew’s blog, most in comments, witness Andrew’s comment below.) Reinhart who is, incidentally or not, is a PhD candidate in statistics at Carnegie Mellon University. After apparently a rather consequent undergraduate foray into physics. Quite an unusual level of maturity and perspective for a PhD student..!

“It’s hard for me to evaluate because I am so close to the material. But on first glance it looks pretty reasonable to me.” A. Gelman

Overall, I found myself enjoying reading the book, even though I found the overall picture of the infinitely many mis-uses of statistics rather grim and a recipe for despairing of ever setting things straight..! Somehow, this is an anti-textbook, in that it warns about many ways of applying the right statistical technique in the wrong setting, without ever describing those statistical techniques. Actually without using a single maths equation. Which should be a reason good enough for me to let all hell break loose on that book! But, no, not really, I felt no compunction about agreeing with Reinhart’s warning and if you have reading Andrew’s blog for a while you should feel the same…

“Then again for a symptom like spontaneous human combustion you might get excited about any improvement.” A. Reinhart (p.13)

Maybe the limitation in the exercise is that statistics appears so much fraught with dangers of over-interpretation and false positive and that everyone (except physicists!) is bound to make such invalidated leaps in conclusion, willingly or not, that it sounds like the statistical side of Gödel’s impossibility theorem! Further, the book moves from recommendation at the individual level, i.e., on how one should conduct an experiment and separate data for hypothesis building from data for hypothesis testing, to a universal criticism of the poor standards of scientific publishing and the unavailability of most datasets and codes. Hence calling for universal reproducibility protocols that reminded of the directions explored in this recent book I reviewed on that topic. (The one the rogue bird did not like.) It may be missing on the bright side of things, for instance the wonderful possibility to use statistical models to produce simulated datasets that allow for an evaluation of the performances of a given procedure in the ideal setting. Which would have helped the increasingly depressed reader in finding ways of checking how wrongs things could get..! But also on the dark side, as it does not say much about the fact that a statistical model is most presumably wrong. (Maybe a physicist’s idiosyncrasy!) There is a chapter entitled Model Abuse, but all it does is criticise stepwise regression and somehow botches the description of Simpson’s paradox.

“You can likely get good advice in exchange for some chocolates or a beer or perhaps coauthorship on your next paper.” A. Reinhart (p.127)

The final pages are however quite redeeming in that they acknowledge that scientists from other fields cannot afford a solid enough training in statistics and hence should hire statisticians as consultants for the data collection, analysis and interpretation of their experiments. A most reasonable recommendation!

## accelerating Metropolis-Hastings algorithms by delayed acceptance

Posted in Books, Statistics, University life with tags Andrew Gelman, Hamiltonian Monte Carlo, MALA, Metropolis-Hastings algorithm, Montréal, NIPS, Peskun ordering, prefetching, University of Warwick on March 5, 2015 by xi'an**M**arco Banterle, Clara Grazian, Anthony Lee, and myself just arXived our paper “Accelerating Metropolis-Hastings algorithms by delayed acceptance“, which is an major revision and upgrade of our “Delayed acceptance with prefetching” paper of last June. Paper that we submitted at the last minute to NIPS, but which did not get accepted. The difference with this earlier version is the inclusion of convergence results, in particular that, while the original Metropolis-Hastings algorithm dominates the delayed version in Peskun ordering, the later can improve upon the original for an appropriate choice of the early stage acceptance step. We thus included a new section on optimising the design of the delayed step, by picking the optimal scaling à la Roberts, Gelman and Gilks (1997) in the first step and by proposing a ranking of the factors in the Metropolis-Hastings acceptance ratio that speeds up the algorithm. The algorithm thus got adaptive. Compared with the earlier version, we have not pursued the second thread of prefetching as much, simply mentioning that prefetching and delayed acceptance could be merged. We have also included a section on the alternative suggested by Philip Nutzman on the ‘Og of using a growing ratio rather than individual terms, the advantage being the probability of acceptance stabilising when the number of terms grows, with the drawback being that expensive terms are not always computed last. In addition to our logistic and mixture examples, we also study in this version the MALA algorithm, since we can postpone computing the ratio of the proposals till the second step. The gain observed in one experiment is of the order of a ten-fold higher efficiency. By comparison, and in answer to one comment on Andrew’s blog, we did not cover the HMC algorithm, since the preliminary acceptance step would require the construction of a proxy to the acceptance ratio, in order to avoid computing a costly number of derivatives in the discretised Hamiltonian integration.

## Posterior predictive p-values and the convex order

Posted in Books, Statistics, University life with tags Andrew Gelman, arXiv, Bayesian p-values, DIC, posterior predictive, uniformity, University of Bristol, using the data twice, warhammer, Xiao-Li Meng on December 22, 2014 by xi'an**P**atrick Rubin-Delanchy and Daniel Lawson [of Warhammer fame!] recently arXived a paper we had discussed with Patrick when he visited Andrew and I last summer in Paris. The topic is the evaluation of the posterior predictive probability of a larger discrepancy between data and model

which acts like a Bayesian p-value of sorts. I discussed several times the reservations I have about this notion on this blog… Including running one experiment on the uniformity of the ppp while in Duke last year. One item of those reservations being that it evaluates the posterior probability of an event that does not exist a priori. Which is somewhat connected to the issue of using the data “twice”.

“A posterior predictive p-value has a transparent Bayesian interpretation.”

Another item that was suggested [to me] in the current paper is the difficulty in defining the posterior predictive (pp), for instance by including latent variables

which reminds me of the multiple possible avatars of the BIC criterion. The question addressed by Rubin-Delanchy and Lawson is how far from the uniform distribution stands this pp when the model is correct. The main result of their paper is that any sub-uniform distribution can be expressed as a particular posterior predictive. The authors also exhibit the distribution that achieves the bound produced by Xiao-Li Meng, Namely that

where *P* is the above (top) probability. (Hence it is uniform up to a factor 2!) Obviously, the proximity with the upper bound only occurs in a limited number of cases that do not validate the overall use of the ppp. But this is certainly a nice piece of theoretical work.

## importance sampling schemes for evidence approximation [revised]

Posted in Statistics, University life with tags Andrew Gelman, candidate approximation, Chib's approximation, evidence, finite mixtures, label switching, permutations, Rao-Blackwellisation on November 18, 2014 by xi'an**A**fter a rather intense period of new simulations and versions, Juong Een (Kate) Lee and I have now resubmitted our paper on (some) importance sampling schemes for evidence approximation in mixture models to Bayesian Analysis. There is no fundamental change in the new version but rather a more detailed description of what those importance schemes mean in practice. The original idea in the paper is to improve upon the Rao-Blackwellisation solution proposed by Berkoff et al. (2002) and later by Marin et al. (2005) to avoid the impact of label switching on Chib’s formula. The Rao-Blackwellisation consists in averaging over all permutations of the labels while the improvement relies on the elimination of useless permutations, namely those that produce a negligible conditional density in Chib’s (candidate’s) formula. While the improvement implies truncated the overall sum and hence induces a potential bias (which was the concern of one referee), the determination of the irrelevant permutations after relabelling next to a single mode does not appear to cause any bias, while reducing the computational overload. Referees also made us aware of many recent proposals that conduct to different evidence approximations, albeit not directly related with our purpose. (One was Rodrigues and Walker, 2014, discussed and commented in a recent post.)