Archive for MCMC

Pre-processing for approximate Bayesian computation in image analysis

Posted in R, Statistics, University life with tags , , , , , , , , , , , , , on March 21, 2014 by xi'an

ridge6With Matt Moores and Kerrie Mengersen, from QUT, we wrote this short paper just in time for the MCMSki IV Special Issue of Statistics & Computing. And arXived it, as well. The global idea is to cut down on the cost of running an ABC experiment by removing the simulation of a humongous state-space vector, as in Potts and hidden Potts model, and replacing it by an approximate simulation of the 1-d sufficient (summary) statistics. In that case, we used a division of the 1-d parameter interval to simulate the distribution of the sufficient statistic for each of those parameter values and to compute the expectation and variance of the sufficient statistic. Then the conditional distribution of the sufficient statistic is approximated by a Gaussian with these two parameters. And those Gaussian approximations substitute for the true distributions within an ABC-SMC algorithm à la Del Moral, Doucet and Jasra (2012).


Across 20 125 × 125 pixels simulated images, Matt’s algorithm took an average of 21 minutes per image for between 39 and 70 SMC iterations, while resorting to pseudo-data and deriving the genuine sufficient statistic took an average of 46.5 hours for 44 to 85 SMC iterations. On a realistic Landsat image, with a total of 978,380 pixels, the precomputation of the mapping function took 50 minutes, while the total CPU time on 16 parallel threads was 10 hours 38 minutes. By comparison, it took 97 hours for 10,000 MCMC iterations on this image, with a poor effective sample size of 390 values. Regular SMC-ABC algorithms cannot handle this scale: It takes 89 hours to perform a single SMC iteration! (Note that path sampling also operates in this framework, thanks to the same precomputation: in that case it took 2.5 hours for 10⁵ iterations, with an effective sample size of 10⁴…)

Since my student’s paper on Seaman et al (2012) got promptly rejected by TAS for quoting too extensively from my post, we decided to include me as an extra author and submitted the paper to this special issue as well.

Advances in Scalable Bayesian Computation [group photo]

Posted in Kids, Mountains, pictures, Statistics, Travel, University life with tags , , , , , , , , on March 8, 2014 by xi'an

Nonlinear Time Series just appeared

Posted in Books, R, Statistics, University life with tags , , , , , , , , , , , , , , , on February 26, 2014 by xi'an

My friends Randal Douc and Éric Moulines just published this new time series book with David Stoffer. (David also wrote Time Series Analysis and its Applications with Robert Shumway a year ago.) The books reflects well on the research of Randal and Éric over the past decade, namely convergence results on Markov chains for validating both inference in nonlinear time series and algorithms applied to those objects. The later includes MCMC, pMCMC, sequential Monte Carlo, particle filters, and the EM algorithm. While I am too close to the authors to write a balanced review for CHANCE (the book is under review by another researcher, before you ask!), I think this is an important book that reflects the state of the art in the rigorous study of those models. Obviously, the mathematical rigour advocated by the authors makes Nonlinear Time Series a rather advanced book (despite the authors’ reassuring statement that “nothing excessively deep is used”) more adequate for PhD students and researchers than starting graduates (and definitely not advised for self-study), but the availability of the R code (on the highly personal page of David Stoffer) comes to balance the mathematical bent of the book in the first and third parts. A great reference book!

evaluating stochastic algorithms

Posted in Books, R, Statistics, University life with tags , , , , , , , , on February 20, 2014 by xi'an

Reinaldo sent me this email a long while ago

Could you recommend me a nice reference about 
measures to evaluate stochastic algorithms (in 
particular focus in approximating posterior 

and I hope he is still reading the ‘Og, despite my lack of prompt reply! I procrastinated and procrastinated in answering this question as I did not have a ready reply… We have indeed seen (almost suffered from!) a flow of MCMC convergence diagnostics in the 90′s.  And then it dried out. Maybe because of the impossibility to be “really” sure, unless running one’s MCMC much longer than “necessary to reach” stationarity and convergence. The heat of the dispute between the “single chain school” of Geyer (1992, Statistical Science) and the “multiple chain school” of Gelman and Rubin (1992, Statistical Science) has since long evaporated. My feeling is that people (still) run their MCMC samplers several times and check for coherence between the outcomes. Possibly using different kernels on parallel threads. At best, but rarely, they run (one or another form of) tempering to identify the modal zones of the target. And instances where non-trivial control variates are available are fairly rare. Hence, a non-sequitur reply at the MCMC level. As there is no automated tool available, in my opinion. (Even though I did not check the latest versions of BUGS.)

As it happened, Didier Chauveau from Orléans gave today a talk at Big’MC on convergence assessment based on entropy estimation, a joint work with Pierre Vandekerkhove. He mentioned SamplerCompare which is an R package that appeared in 2010. Soon to come is their own EntropyMCMC package, using parallel simulation. And k-nearest neighbour estimation.

If I re-interpret the question as focussed on ABC algorithms, it gets both more delicate and easier. Easy because each ABC distribution is different. So there is no reason to look at the unreachable original target. Delicate because there are several parameters to calibrate (tolerance, choice of summary, …) on top of the number of MCMC simulations. In DIYABC, the outcome is always made of the superposition of several runs to check for stability (or lack thereof). But this tells us nothing about the distance to the true original target. The obvious but impractical answer is to use some basic bootstrapping, as it is generally much too costly.

finite mixture models [book review]

Posted in Books, Kids, Statistics, University life with tags , , , , , , , , , , , on February 17, 2014 by xi'an

Here is a review of Finite Mixture Models (2000) by Geoff McLachlan & David Peel that I wrote aeons ago (circa 1999), supposedly for JASA, which lost first the files and second the will to publish it. As I was working with my student today, I mentioned the book to her and decided to publish it here, if only because I think the book deserved a positive review, even after all those years! (Since then, Sylvia Frühwirth-Schnatter published Finite Mixture and Markov Switching Models (2004), which is closer to my perspective on the topic and that I would more naturally recommend.)

Mixture modeling, that is, the use of weighted sums of standard distributions as in

\sum_{i=1}^k p_i f({\mathbf y};{\mathbf \theta}_i)\,,

is a widespread and increasingly used technique to overcome the rigidity of standard parametric distributions such as f(y;θ), while retaining a parametric nature, as exposed in the introduction of my JASA review to Böhning’s (1998) book on non-parametric mixture estimation (Robert, 2000). This review pointed out that, while there are many books available on the topic of mixture estimation, the unsurpassed reference remained the book by Titterington, Smith and Makov (1985)  [hereafter TSM]. I also suggested that a new edition of TSM would be quite timely, given the methodological and computational advances that took place in the past 15 years: while it remains unclear whether or not this new edition will ever take place, the book by McLachlan and Peel gives an enjoyable and fairly exhaustive update on the topic, incorporating the most recent advances on mixtures and some related models.

Geoff McLachlan has been a major actor in the field for at least 25 years, through papers, software—the book concludes with a review of existing software—and books: McLachlan (1992), McLachlan and Basford (1988), and McLachlan and Krishnan (1997). I refer the reader to Lindsay (1989) for a review of the second book, which is a forerunner of, and has much in common with, the present book. Continue reading


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