Archive for Monte Carlo Statistical Methods

scalable Monte Carlo for Bayesian learning [book review]

Posted in Books, Statistics, University life with tags , , , , , , , , , , , , , , , , , , , , on September 26, 2025 by xi'an

This book by Paul Fearnhead, Christopher Nemeth, Chris Oates, and Chris Sherlock is part of the IMS Monograph series. And published by Cambridge University Press. It covers most recent developments in MCMC methods, namely stochastic gradient MCMC (Chap. 3), non-reversible MCMC (Chap. 4), continuous-time MCMC (Chap. 5), and assessing and improving MCMC (Chap. 6). I find the book remarkable in its attention to rigour and clarity, without falling into overly technical derivations. It is perfectly suited for a graduate course to students with a solid mathematical background. In short, had I considered a new edition of our Monte Carlo Statistical Methods book to incorporate these advances, I could not done such a good job!

The first chapter provides a quick refresher of the background, from Monte Carlo principles, to Markov chains, SDEs, and the kernel “trick” (which requires a dozen pages of exposition). Nonetheless, it contains side remarks of true interest, including some suggestions I had not previously seen, as for instance an unusual introduction of the HMC algorithm as an underdamped Langevin diffusion. Chapter 2 prolongates this recap by covering reversible MCMC algorithms and the attached optimal scalings. This is done in a particularly friendly presentation that I intend to use in my own course. The HMC section is probably the best coverage I have seen on the topic, including most naturally the leapfrog steps.

Chapter 3 gets into stochastic gradient MCMC as an approximate MCMC, with nice arguments and formal convergence bounds. Again quite efficiently, if focussing almost solely on Gaussian settings (but including a neural network example). Similarly, Chapter 4 provides intuitive (if informal) arguments on the worth of non-reversible algorithms that are well-suited to a textbook of this level. This chapter introduces a PDMP sampler like the discrete bouncy particle sampler.

Chapter 5 is a (nicely) monstrous coverage of continuous time MCMC samplers that reaches very recent advances on PDMPs. The focus is on expressing them as limits, in order to derive mixing rates without extreme mathematical steps. (The chapter even includes a mention to the coordinate sampler that my PhD student Wu Changye derived in 2018!) Again a chapter I plan to use when teaching MCM methods, if possibly skipping some of the 66 pages.

Chapter 6 completes the monograph with a presentation of convergence assessment tools and diagnostics, exploiting the kernel trick, as well as convergence bounds that reflect very recent research in that domain. The conclusive section on optimal weights and optimal thinning will presumably be new to most readers. (Making me wonder if a link can be found with our importance Markov chain construct.)

[Disclaimer about potential self-plagiarism as usual: this post or an edited version will eventually appear in my Books Review section in CHANCE.]

bridging ratio estimators

Posted in Books, Statistics, University life with tags , , , , , , , , , , on June 3, 2025 by xi'an

easily computed marginal likelihoods for multivariate mixture models using the THAMES estimator

Posted in Books, Statistics, University life with tags , , , , , , , , , , , , , , , , , , , , , on May 25, 2025 by xi'an

Martin Metodiev and his coauthor(es)s have produced another paper on the THAMES Monte Carlo method when specifically targetting marginal likelihoods for mixture models. Since this problem has long been a central interest of mine’s and since the method is closely connected with the harmonic mean solution we developed with Darren Wraith in 2009, (and also included in our 2009 survey with Jean-Michel Marin of evidence approximations, published in Frontiers of Statistical Decision Making and Bayesian Analysis for Jim Berger’s 60th birthday), I quickly went into the paper. The core purpose of this paper is to adapt THAMES to a multimodal setting since using an ellipsoidal region as the support of the Uniform reciprocal importance sampling distribution does not make sense for a multimodal target. After reading it a few times, and while some computational aspects remain obscure to me, I am not convinced this brings an adequate answer to the challenge.  Indeed, while the approach borrows directly from Berkhof et al. (2003) that inspired the resolution we proposed, Jeong (Kate) Lee and myself, the issues I have with the current proposal are that

1. the evacuation of earlier methods as not simple or not universal enough is rather disingenuous. For instance, software that do not return (latent) allocation vectors can easily be post-processed. And the current method uses allocation probabilities just the same (in Section 3.3). Similarly, the random shuffling answer to label (lack of) switching proposed by Sylvia Früwirth-Schnatter—which again can be achieved by post-processing—cannot be rejected on the sole basis that the component means (based on the MCMC sample) are all similar. It is furthermore debatable that the current proposal is simple, when involving relabelling à la Stephens, averaging over permutations, selecting over said permutations by constructing a graph over components (section 3.2.1) and  running a quadratic discriminant analysis (section 3.2.2) on the posterior sample, based on an arbitrary Normal representation of the distributions of the clusters, and finally defining a new ordering constraint (section 3.2.3). Computing efforts  required by the respective methods do not appear in the main text.

2. the handling of the label switching issue—the reason why Larry Wasserman saw mixtures at the same magnitude of evil as tequila!—is problematic for several reasons. My position (since at least 2000!) on the matter is that the proper posterior sample must exhibit label switching and come close to symmetry among the “components”. The label switching problem (section 3.1) is rather when the MCMC sample does not “switch their labels”. The relabelling approach (e.g., à la Stephens) allows for a differentiation between components, to some extent, which helps with computing basic posterior moments for point estimation or for the calibration of the support of the Uniform reciprocal importance sampling distribution, but the use of any relabelling procedure is tampering with the original MCMC sample and thus bound to impact the distribution of the resulting relabelled sample. Furthermore, relabelling depends on the value of G, whereas the actual number of (significant) modes in the posterior is also connected with the (partial) fit of the data to the model, meaning the creation of further modes than those linked with relabelling. Especially when the model is misspecified. Incidentally, the symmetrised version of THAMES (5) does not require relabelling. Neither does the Bayes factor. In addition, the experiment section (4.1.2) mentions that bridge sampling is biased by a factor of G!, which comes as a surprise to me since I associated this factor with the call to Sid Chib’s formula in the absence of label switching, i.e. when the MCMC sample was stuck on a mode, as exposed by Radford Neal in 1999. Is it because bridge sampling is applied to the relabelled sample? It is also surprising that the gap appears in the simulated datasets (Fig.3) and not in the real ones (Fig.5).

3. the (legitimate) purpose of using marginal likelihoods for selecting the number G of components is weakened by the intrusion of alternate proposals to assess G from the data, like the criterion of overlap (section 3.2.1), which instead aims at the number of clusters, with an elimination of “empty components” that should either remain a possibility (within a regular mixture model) or be evacuated with a different modelling (à la Diebolt & Robert, or à la Wasserman). This overlapping criterion is further used in the discriminant analysis that only applies to “non-overlapping components” of the mixture (section 3.2.3)—at which point I got lost in the reordering and simplification of the computation of THAMES (but got reminded of the results of Agostino Nobile in the 2000’s, with whom I used to discuss a lot in my yearly visit to the University of Glasgow).

4. several mentions are made of the other estimators being biased, which is indeed the case for bridge sampling (if not necessarily for importance sampling), but not necessarily a central issue, while the original generalised harmonic proposal by Gelfand and Dey (1994) and thus THAMES produce an unbiased estimator of the inverse of the evidence (thus neither of the evidence nor of the log-evidence). However, in the paper, the volume of the support of the Uniform reciprocal importance sampling distribution is estimated by a basic Monte Carlo coverage probability in (3), which induces the same type of bias as the other methods.

Monte Carlo [exam]

Posted in Kids, pictures, R, Statistics, University life with tags , , , , , , , , , , , , , , , , , on January 22, 2025 by xi'an

My final exam for the Monte Carlo course I taught last semester proved too much of a challenge for my fourth year students, despite being rather elementary and centred on accept-reject algorithms and importance/bridge sampling. One of the problems was a decomposition of the truncated Normal simulation method proposed by Marsaglia in 1963, found on X Validated!, which I had posted on the course Teams forum (and discussed on the ‘Og!). Obviously overlooked by the students as hardly anyone solved the central question… Quite a disappointment (and more exams to grade for the resit exam in June!)

webinar on Monte Carlo Methods

Posted in Books, Statistics, University life with tags , , , , , , , , , , , , on October 7, 2024 by xi'an


Hey, there is a new international Monte Carlo webinar starting this semester! Taking place at 8:30 am PT, 11:30 am ET (which currently set it at 16:30 in Tórshavn time and 17:30 in Longyearbyen time!). The first speakers on the list are

  1. Persi Diaconis (who gave a talk last week)
  2. Mike Giles (tomorrow!)
  3. Art Owen (on quasi-Monte Carlo)
  4. Gareth O Roberts (Warwick)

Enjoy!