Archive for Monte Carlo Statistical Methods

MCqMC 2014 [day #3]

Posted in pictures, Running, Statistics, Travel, University life, Wines with tags , , , , , , , , , , , , , , , , on April 10, 2014 by xi'an


As the second day at MCqMC 2014, was mostly on multi-level Monte Carlo and quasi-Monte Carlo methods, I did not attend many talks but had a long run in the countryside (even saw a pheasant and a heron), worked at “home” on pressing recruiting evaluations and had a long working session with Pierre Jacob. Plus an evening out sampling (just) a few Belgian beers in the shade of the city hall…

Today was more in my ballpark as there were MCMC talks the whole day! The plenary talk was not about MCMC as Erich Novak presented a survey on the many available results bounding the complexity of approximating an integral based on a fixed number of evaluations of the integrand, some involving the dimension (and its curse), some not, some as fast as √n and some not as fast, all this depending on the regularity and the size of the classes of integrands considered. In some cases, the solution was importance sampling, in other cases, quasi-Monte Carlo, and yet other cases were still unsolved. Then Yves Atchadé gave a new perspective on computing the asymptotic variance in the central limit theorem on Markov chains when truncating the autocovariance, Matti Vihola talked about theoretical orderings of Markov chains that transmuted into the very practical consequence that using more simulations in a pseudo-marginal likelihood approximation improved acceptance rate and asymptotic variances (and this applies to aBC-MCMC as well), Radu Craiu proposed a novel processing of adaptive MCMC by treating various approximations to the true target as food for a multiple-try Metropolis algorithm, and Luca Martino had a go at resuscitating the ARMS algorithm of Gilks and Wild (used for a while in BUGS), although the talk did not dissipate all of my misgivings about the multidimensional version! I had more difficulties following the “Warwick session” which was made of four talks by current or former students from Warwick, although I appreciated the complexity of the results in infinite dimensional settings and novel approximations to diffusion based Metropolis algorithms. No further session this afternoon as the “social” activity was to visit the nearby Stella Artois brewery! This activity made us very social, for certain, even though there was hardly a soul around in this massively automated factory. (Maybe an ‘Og post to come one of those days…)

MCqMC 2014 [day #1]

Posted in pictures, Running, Statistics, Travel, University life with tags , , , , , , , , , on April 9, 2014 by xi'an


As I have been kindly invited to give a talk at MCqMC 2014, here am I. in Leuven, Belgium, for this conference I have never attended before. (I was also invited for MCqMC 2012 in Sydney The talk topics and the attendees’ “sociology” are quite similar to those of the IMACS meeting in Annecy last summer. Namely, rather little on MCMC, particle filters, and other tools familiar in Bayesian computational statistics, but a lot on diffusions and stochastic differential equations and of course quasi-Monte Carlo methods. I thus find myself at a boundary of the conference range and a wee bit lost by some talks, which even titles make little sense to me.

For instance, I have trouble to connect with multi-level Monte Carlo within my own referential. My understanding of the method is one of a control variate version of tempering, namely of using a sequence of approximations to the true target and using rougher approximations as control variates for the finer approximations. But I cannot find on the Web a statistical application of the method outside of diffusions and SDEs, i.e. outside of continuous time processes… Maybe using a particle filter from one approximation to the next, down in terms of roughness, could help.

“Several years ago, Giles (2008) introduced an intriguing multi-level idea to deal with such biased settings that can dramatically improve the rate of convergence and can even, in some settings, achieve the canonical “square root” convergence rate associated with unbiased Monte Carlo.” Rhee and Glynn, 2012

Those were my thoughts before lunchtime. today (namely April 7, 2014). And then, after lunch, Peter Glynn gave his plenary talk that just answered those questions of mine’s!!! Essentially, he showed that formula Pierre Jacob also used in his Bernoulli factory paper to transform a converging-biased-into-an-unbiased estimator, based on a telescopic series representation and a random truncation… This approach is described in a paper with Chang-han Rhee, arXived a few years ago. The talk also covered more recent work (presumably related with Chang-han Rhee’s thesis) extending the above to Markov chains. As explained to me later by Pierre Jacob [of Statisfaction fame!], a regular chain does not converge fast enough to compensate for the explosive behaviour of the correction factor, which is why Rhee and Glynn used instead a backward chain, linking to the exact or perfect samplers of the 1990′s (which origin can be related to a 1992 paper of Asmussen, Glynn and Thorisson). This was certainly the most riveting talk I attended in the past years in that it brought a direct answer to a question I was starting to investigate. And more. I was also wondering how connected it was with our “exact” representation of the stationary distribution (in an Annals of Probability paper with Jim Hobert).   Since we use a stopping rule based on renewal and a geometric waiting time, a somewhat empirical version of the inverse probability found in Peter’s talk. This talk also led me to re-consider a recent discussion we had in my CREST office with Andrew about using square root(ed) importance weights, since one of Peter’s slides exhibited those square roots as optimal. Paradoxically, Peter started the talk by down-playing it, stating there was a single idea therein and a single important slide, making it a perfect after-lunch talk: I wish I had actually had thrice more time to examine each slide! (In the afternoon session, Éric Moulines also gave a thought-provoking talk on particle islands and double bootstrap, a research project I will comment in more detail the day it gets arXived.)

accelerating MCMC via parallel predictive prefetching

Posted in Books, Statistics, University life with tags , , , , , , , , on April 7, 2014 by xi'an

¨The idea is to calculate multiple likelihoods ahead of time (“pre-fetching”), and only use the ones which are needed.” A. Brockwell, 2006

Yet another paper on parallel MCMC, just arXived by Elaine Angelino, Eddie Kohler, Amos Waterland, Margo Seltzer, and Ryan P. Adams. Now,  besides “prefetching” found in the title, I spotted “speculative execution”, “slapdash treatment”, “scheduling decisions” in the very first pages: this paper definitely is far from shying away from using fancy terminology! I actually found the paper rather difficult to read to the point I had to give up my first attempt during an endless university board of governors meeting yesterday. (I also think “prefetching” is awfully painful to type!)

What is “prefetching” then? It refers to a 2006 JCGS paper by Anthony Brockwell. As explained in the above quote from Brockwell, prefetching means computing the 2², 2³, … values of the likelihood that will be needed in 2, 3, … iterations. Running a regular Metropolis-Hastings algorithm then means building a decision tree back to the current iteration and drawing 2,3, … uniform to go down the tree to the appropriate branch. So in the end only one path of the tree is exploited, which does not seem particularly efficient when vanilla Rao-Blackwellisation and recycling could be implemented almost for free.

“Another intriguing possibility, suggested to the author by an anonymous referee, arises in the case where one can guess whether or not acceptance probabilities will be “high” or “low.” In this case, the tree could be made deeper down “high” probability paths and shallower in the “low” probability paths.” A. Brockwell, 2006

The current paper stems from Brockwell’s 2006 final remark, as reproduced above, by those “speculative moves” that considers the reject branch of the prefetching tree more often that not, based on some preliminary or dynamic evaluation of the acceptance rate. Using a fast but close enough approximation to the true target (and a fixed sequence of uniforms) may also produce a “single most likely path on which” prefetched simulations can be run. The basic idea is thus to run simulations and costly likelihood computations on many parallel processors along a prefetched path, path that has been prefetched for its high approximate likelihood. (With of courses cases where this speculative simulation is not helpful because we end up following another path with the genuine target.) The paper actually goes further than the basic idea to avoid spending useless time on paths that will not be chosen, by constructing sequences of approximations for the precomputations. The proposition for the sequence found therein is to subsample the original data and use a normal approximation to the difference of the log (sub-)likelihoods. Even though the authors describe the system implementation of the progressive approximation idea, it remains rather unclear (to me) how the adaptive estimation of the acceptance probability is compatible with the parallelisation idea. Because it seems (to me) that it induces a lot of communication between the cores. Also, the method is advocated mainly for burnin’ (or warmup, to follow Andrew’s terminology!), which seems to remove the need to use exact targets: if the approximation is close enough, the Markov chain will quickly reach a region of interest for the true target and from there there seems to be little speedup in implementing this nonetheless most interesting strategy.

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.

fine-sliced Poisson [a.k.a. sashimi]

Posted in Books, Kids, pictures, R, Running, Statistics, University life with tags , , , , , , , , , on March 20, 2014 by xi'an

As my student Kévin Guimard had not mailed me his own Poisson slice sampler of a Poisson distribution, I could not tell why the code was not working! My earlier post prompted him to do so and a somewhat optimised version is given below:

nsim = 10^4
lambda = 6

max.factorial = function(x,u){
        k = x
        while (parf*u<1){
          k = k + 1
          parf = parf * k
        k = k - (parf*u>1)
        return (k)

x = rep(floor(lambda), nsim)
for (t in 2:nsim){
        v1 = ceiling((log(runif(1))/log(lambda))+x[t-1])

As you can easily check by running the code, it does not work. My student actually majored my MCMC class and he spent quite a while pondering why the code was not working. I did ponder as well for a part of a morning in Warwick, removing causes for exponential or factorial overflows (hence the shape of the code), but not eliciting the issue… (This now sounds like lethal fugu sashimi! ) Before reading any further, can you spot the problem?!

The corrected R code is as follows:

x = rep(lambda, nsim)
for (t in 2:nsim){
        if (length(ranj)>1){
          x[t] = sample(ranj, size = 1)

The culprit is thus the R function sample which simply does not understand Dirac masses and the basics of probability! When running

> sample(150:150,1)
[1] 23

you can clearly see where the problem stands…! Well-documented issue with sample that already caused me woes… Another interesting thing about this slice sampler is that it is awfully slow in exploring the tails. And to converge to the centre from the tails. This is not very pronounced in the above graph with a mean of 6. Moving to 50 makes it more apparent:

slisson5This is due to the poor mixing of the chain, as shown by the raw sequence below, which strives to achieve a single cycle out of 10⁵ iterations! In any case, thanks to Kévin for an interesting morning!



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