Archive for parallelisation

automatic adaptation of MCMC algorithms

Posted in pictures, Statistics with tags , , , , , , , on March 4, 2019 by xi'an

“A typical adaptive MCMC sampler will approximately optimize performance given the kind of sampler chosen in the first place, but it will not optimize among the variety of samplers that could have been chosen.”

Last February (2018), Dao Nguyen and five co-authors arXived a paper that I missed. On a new version of adaptive MCMC that aims at selecting a wider range of proposal kernels. Still requiring a by-hand selection of this collection of kernels… Among the points addressed, beyond the theoretical guarantees that the adaptive scheme does not jeopardize convergence to the proper target, are a meta-exploration of the set of combinations of samplers and integration of the computational speed in the assessment of each sampler. Including the very difficulty of assessing mixing. One could deem the index of the proposal as an extra (cyber-)parameter to its generic parameter (like the scale in the random walk), but the discreteness of this index makes the extension more delicate than expected. And justifies the distinction between internal and external parameters. The notion of a worst-mixing dimension is quite appealing and connects with the long-term hope that one could spend the maximum fraction of the sampler runtime over the directions that are poorly mixing, while still keeping the target as should be. The adaptive scheme is illustrated on several realistic models with rather convincing gains in efficiency and time.

The convergence tools are inspired from Roberts and Rosenthal (2007), with an assumption of uniform ergodicity over all kernels considered therein which is both strong and delicate to assess in practical settings. Efficiency is rather unfortunately defined in terms of effective sample size, which is a measure of correlation or lack thereof, but which does not relate to the speed of escape from the basin of attraction of the starting point. I also wonder at the pertinence of the estimation of the effective sample size when the chain is based on different successive kernels, since the lack of correlation may be due to another kernel. Another calibration issue is the internal clock that relates to the average number of iterations required to tune properly a specific kernel, which again may be difficult to assess in a realistic situation. A last query is whether or not this scheme could be compared with an asynchronous (and valid) MCMC approach that exploits parallel capacities of the computer.

more multiple proposal MCMC

Posted in Books, Statistics with tags , , , , , , , on July 26, 2018 by xi'an

Luo and Tjelmeland just arXived a paper on a new version of multiple-try Metropolis Hastings, the addendum being in defining the additional proposed copies via a dependence graph like (a) above, with one version from the target and all others from operational and conditional proposal kernels. Respecting the dependence graph, as in (b). As I did, you may then wonder where both the graph and the conditional do come from. Which reminds me of the pseudo-posteriors of Carlin and Chib (1995), even though this is not terribly connected. Green (1995).) (But not disconnected either since the authors mention But, given the graph, following a Gibbs scheme, one of the 17 nodes is chosen as generated from the target, using the proper conditional on that index [which is purely artificial from the point of view of the original simulation problem!]. As noted above, the graph is an issue, but since it is artificial, it can be devised to either allow for quasi-independence between the proposed values or on the opposite to induce long range dependence, which corresponds to conducting multiple MCMC steps before reaching the end nodes, a feature that is very appealing in my opinion. And reminds me of prefetching. (As I am listening to Nicolas Chopin’s lecture in Warwick at the moment, there also seems to be a connection with pMCMC.) Still, I remain unclear as to the devising of the graph of dependent proposals, as its depth should be somehow connected with the mixing properties of the original proposal. Gains in convergence may thus come at a high cost at the construction stage.

convergences of MCMC and unbiasedness

Posted in pictures, Statistics, University life with tags , , , , , , , , , on January 16, 2018 by xi'an

During his talk on unbiased MCMC in Dauphine today, Pierre Jacob provided a nice illustration of the convergence modes of MCMC algorithms. With the stationary target achieved after 100 Metropolis iterations, while the mean of the target taking much more iterations to be approximated by the empirical average. Plus a nice connection between coupling time and convergence. Convergence to the target.During Pierre’s talk, some simple questions came to mind, from developing an “impatient user version”, as in perfect sampling, in order  to stop chains that run “forever”,  to optimising parallelisation in order to avoid problems of asynchronicity. While the complexity of coupling increases with dimension and the coupling probability goes down, the average coupling time varies but an unexpected figure is that the expected cost per iteration is of 2 simulations, irrespective of the chosen kernels. Pierre also made a connection with optimal transport coupling and stressed that the maximal coupling was for the proposal and not for the target.

patterns of scalable Bayesian inference

Posted in Books, Statistics, University life with tags , , , , , , , , , , , , on February 24, 2016 by xi'an

Elaine Angelino, Matthew Johnson and Ryan Adams just arXived a massive survey of 118 pages on scalable Bayesian inference, which could have been entitled Bayes for Big Data, as this monograph covers state-of-the-art computational approaches to large and complex data structures. I did not read each and every line of it, but I have already recommended it to my PhD students. Some of its material unsurprisingly draws from the recent survey by Rémi Bardenet et al. (2015) I discussed a while ago. It also relates rather frequently to the somewhat parallel ICML paper of Korattikara et al. (2014). And to the firefly Monte Carlo procedure also discussed previously here.

Chapter 2 provides some standard background on computational techniques, Chapter 3 covers MCMC with data subsets, Chapter 4 gives some entries on MCMC with parallel and distributed architectures, Chapter 5 focus on variational solutions, and Chapter 6 is about open questions and challenges.

“Insisting on zero asymptotic bias from Monte Carlo estimates of expectations may leave us swamped in errors from high variance or transient bias.”

One central theme of the paper is the need for approximate solutions, MCMC being perceived as the exact solution. (Somewhat wrongly in the sense that the product of an MCMC is at best an empirical version of the true posterior, hence endowed with a residual and incompressible variation for a given computing budget.) While Chapter 3 stresses the issue of assessing the distance to the true posterior, it does not dwell at all on computing times and budget, which is arguably a much harder problem. Chapter 4 seems to be more aware of this issue since arguing that “a way to use parallel computing resources is to run multiple sequential MCMC algorithms at once [but that this] does not reduce the transient bias in MCMC estimates of posterior expectations” (p.54). The alternatives are to use either prefetching (which was the central theme of Elaine Angelino’s thesis), asynchronous Gibbs with the new to me (?) Hogwild Gibbs algorithms (connected in Terenin et al.’s recent paper, not quoted in the paper), some versions of consensus Monte Carlo covered in earlier posts, the missing links being in my humble opinion an assessment of the worth of those solutions (in the spirit of “here’s the solution, what was the problem again?”) and once again the computing time issue. Chapter 5 briefly discusses some recent developments in variational mean field approximations, which is farther from my interests and (limited) competence, but which appears as a particular class of approximate models and thus could (and should?) relate to likelihood-free methods. Chapter 6 about the current challenges of the field is presumably the most interesting in this monograph in that it produces open questions and suggests directions for future research. For instance, opposing the long term MCMC error with the short term transient part. Or the issue of comparing different implementations in a practical and timely perspective.

new version of abcrf

Posted in R, Statistics, University life with tags , , , , , , on February 12, 2016 by xi'an
fig-tree near Brisbane, Australia, Aug. 18, 2012Version 1.1 of our R library abcrf version 1.1  is now available on CRAN.  Improvements against the earlier version are numerous and substantial. In particular,  calculations of the random forests have been parallelised and, for machines with multiple cores, the computing gain can be enormous. (The package does along with the random forest model choice paper published in Bioinformatics.)