Archive for Gibbs sampler

mostly Monte Carlo [13/03]

Posted in Statistics, Travel, University life with tags , , , , , , , , , , , , , , , , , , on March 10, 2026 by xi'an

A new episode of our mostly Monte Carlo seminar, very soon coming near you (if in Paris):

On Friday 13/02/26, from 3-5pm at PariSanté Campus

15h00: Pierre Del Moral (INRIA, Bordeaux)

On the Kantorovich contraction of Markov semigroup

We present a novel operator theoretic framework to study the contraction properties of Markov semigroups with respect to a general class of Kantorovich semi-distances, which notably includes Wasserstein distances. This rather simple contraction cost framework combines standard Lyapunov techniques with local contraction conditions. Our results can be applied to both discrete time and continuous time Markov semigroups, and we illustrate their wide applicability in the context of (i) Markov transitions on models with boundary states, including bounded domains with entrance boundaries, (ii) operator products of a Markov kernel and its adjoint, including two-block-type Gibbs samplers, (iii) iterated random functions and (iv) diffusion models, including overdampted Langevin diffusion with convex at infinity potentials.

16h00: Bob Carpenter (Flatiron Institute, New York)

GIST, WALNUTS, and Continuous Nutpie: mass-matrix and step-size adaptation for Hamiltonian Monte Carlo

I will introduce Gibbs self tuning (GIST), our new technique for coupling tuning parameters and conditionally Gibbs-sampling them per iteration in Hamiltonian Monte Carlo. Then I will turn to the within-orbit adaptive NUTS (WALNUTS) sampler, which adapts the step size every leapfrog step in order to conserve the Hamiltonian. Empirical evaluations on varying multi-scale target distributions, including Neal’s funnel and the Stock-Watson stochastic volatility time-series model, demonstrate that WALNUTS achieves substantial improvements in sampling efficiency and robustness. I will review the Nutpie mass-matrix adaptation scheme, which is designed to minimize Fisher divergence by estimating the mass matrix as the geometric midpoint (aka barycenter) between the inverse covariance of the draws and the covariance of the scores of the draws. Then I will describe a continuously adapting version that adapts per iteration by continuously discounting the past rather than updating in fixed blocks. I will also show how the Adam optimizer outperforms dual averaging for step-size adaptation. I will conclude by considering a lock-free multi-threading implementation that automatically monitors adaptation and sampling for convergence for automatic stopping.

mixture models [book review]

Posted in Books, Statistics, University life with tags , , , , , , , , , , , , , , , , , , , , , , , on August 14, 2024 by xi'an

Strangely enough, I became aware of this new book on mixtures through one of these annoying emails “Your work has been cited n times this week“… Mixture Models (Parametric, Semiparametric, and New Directions) by Weixin Yao and Sijia Wang got published by CRC Press earlier this year, within the Monographs on Statistics and Applied Probability green series (#175), and covers across 380 pages most aspects of mixture (and hidden Markov) estimation, if with strong emphasis on maximum likelihood estimation, while the new directions are unsurprisingly those pursued by the authors, namely robust and semi-parametric estimation, as well as model selection by testing.

An early warning about this book review is that I co-edited a Handbook of Mixture Analysis with my friends Sylvia Früwirth-Schnatter and Gilles Celeux a few years ago. I am therefore biased in what I would have included in a new book on the topic, the more because I find the available literature already plentiful, even though the early (1984) book of Titterington et al. that was my entry to the field may have become an historical reference. For instance, Finite Mixtures by McLachlan and Peel (2000) remains relevant, with similar emphasis on maximum likelihood and the EM algorithm, while Sylvia’s Finite Mixture and Markov Switching Models is still a reference to this day.

And an additional warning on me not being a massive fan of semi- and non-parametric estimation in this setting…

Preliminaries that may explain my limited enthusiasm about the book and its limited originality. Not that I found significant errors there (even though “improper priors [do not always] yield improper posteriors” [p.145] as we demonstrated in several papers), however, I had trouble with the uneven pace adopted by the authors that often skim some topics of importance while spending an inconsiderate amount of space on less relevant once. Some items get many bibliographical references, while others do not. For instance, EM receives a lion’s share (see, e..g, Sections 6.6 and 6.7). Or the 12 pages of proof in Chapter 10. Declination of sections into mixtures, mixtures of regressions, multivariate mixtures, hidden Markov models, and so on feels somewhat repetitive. This is particularly the case for the “mixture regression models” chapter.

The book also contains Bayesian entries, with a first introduction (p.105) in the discrete data chapter that precedes the short Bayesian chapter #4 (p.145), the same issue arising for related algorithms like Gibbs (p.107) that “estimate properties of the joint posterior” and MCMC (p.112). Which sort of erases the specificity of a Bayesian approach by reducing it to one item in the toolbox (with the wrong stress on MAP estimates). In this Bayesian chapter, MCMC validation is handled for discrete state spaces while applied in general spaces. The focus is mostly on relabelling for the following label switching chapter, albeit a large collection of methods are compared if not mentioned.

Handing an unknown number of components by hypothesis testing is supported in the next short chapter, although very little is said about reversible jump MCMC. And there is no general discussion on the consistency of these tests, in particular with bootstrap. Or at least on the regularity conditions they request. An puzzling paradox (p.191) is the existence of an unbounded Fisher information of an exponential mixture

\pi\mathcal Exp(1)+(1-\pi)\mathcal Exp(2)

when the weight π is the parameter (and close to 1).

High-dimensional mixtures in Chapter 8 are mostly handled by linear projections in smaller subspaces, which is natural given that they preserve the mixture structure but open a Pandora box of a wide range of proposed methods, again with little comparison available. Except in the R final section opposing several R functions on the same dataset (if unconclusively).

The semi-parametric chapters mention Dirichlet process priors, albeit briefly, but fail to relate to the recent works on using these when inferring about the number of components. Or failing to do so. There is also a very limited connection pointed out with machine learning but little can be gathered from the three page presentation (pp.308-310). These chapters also have significant overlap with the review paper of Xiang et al. (2019) in Statistical Science.

Most chapters end up with an R section, which usually reads as a quick demo of a related R package, like BayesLCA or our own mixtool. Hence not massively helpful beyond pointers to these packages. The numerical illustrations also are unevenly distributed between chapters, from nothing at all to four pages of small font tables on an MSE comparison between more or less robust approaches undertaken by Yu et al. (2020).

The above thus explains why I am not particularly excited about this bibliographical addition to the analysis of mixtures. It does offer a reference for researchers in the field by adding recent references and approaches to the existing books mentioned above, but I could not recommend it as a textbook (as suggested on p.xiii).

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

scalability of Metropolis-within-Gibbs schemes

Posted in Books, Statistics, University life with tags , , , , , , on July 17, 2024 by xi'an

My friends Filipo Ascolani, Gareth Roberts, and Giacomo Zanella recently arXived a paper on the scalability (in the dimension) of Gibbs and Metropolis-within-Gibbs sampling schemes. Which is celebrating a sort of return of the Gibbs sampler as a dimension resistant device (when compared with other solutions), witness the following extract:

“….we provide bounds on the approximate conductance of a generic coordinate-wise scheme in terms of the corresponding quantity for the Gibbs sampler. Working with the approximate version of the conductance is crucial for our purposes and subsequent applications. The general theory naturally applies to Metropolis-within-Gibbs schemes, such as those targeting conditionally log-concave distributions. In the second part, we analyze performances of coordinate-wise samplers for relevant statistical applications, combining the bounds discussed above with specific model properties, statistical asymptotics and some novel auxiliary results on approximate conductances and perturbation of Markov operators. Much emphasis is placed on coordinate-wise schemes for generic two-levels hierarchical models with non-conjugate likelihood for which we are able to prove dimension-free behaviour of total variation mixing times, under warm and feasible starts.” F. Ascolani, G.O. Roberts, and G. Zanella

Here, M -warm starts meaning a starting measure bounded by the target, i.e., not too far in the tails, while conductance Φ is a measure related with the probability that the Markov chain exits an arbitrary set A in one step, given that it starts from the target π restricted to A. The paper quantifies the loss of efficiency incurred by substituting an exact Gibbs update with a π¹-invariant one, e.g. M-within-G, that is

\Phi_s(P)\ge\min_i\kappa(P_i, X)\Phi_s(G)

following from

G_i(\partial A)\ge P_i(\partial A)\ge \kappa_i(P_i, X)G_i(\partial A)

In the (rather unrealistic) case of an independent Metropolis-within-Gibbs proposal enjoying an upper bound M on the Radon-Nykodym derivative between target and kernel, the conductance of Metropolis-within-Gibbs is at least one M-th of the conductance of Gibbs, ie a constant slowdown relative to exact Gibbs if the dimensionality is fixed but arbitrary.

The paper further studies a hierarchical Bayes model when the number J of groups goes to infinity and only top (of the hierarchy) parameter is of interest. In that setting, only two requirements need be satisfied for the Metropolis-within-Gibbs kernel P to mix fast: namely that the Gibbs kernel G mixes fast and  that the conditional conductance of P around true ψ is good enough. A further point of relevance is the demonstrated O(J) computational cost, ie the Metropolis-within-Gibbs algorithm with kernel P produces a sample with ϵ-accuracy in TV distance with O(J) cost when initialized from a warm start, a better magnitude than alternatives like the Metropolis-Adjusted Langevin (MALA) and the Hamiltonian Monte Carlo (HMC) algorithms. When checking for connections with other papers, I came across the nearly completed book by Sinho Chewi on long-concave sampling, which seems to be exploring similar ground.

 

biXarre, biXarre

Posted in Books, Statistics with tags , , , , , on May 2, 2024 by xi'an

inference with insufficient statistics #2

Posted in Books, Kids, Statistics with tags , , , , , , , on December 28, 2023 by xi'an

Another X validated question of some interest: how to infer about the parameters of a model when only given a fraction 1-α of the order statistics. For instance, the (1-α)n largest observations. On a primary level, the answer is somewhat obvious since the joint density of these observations is available in closed form. At another level, it brings out the fact that the distribution of the unobserved part of the sample given the observed one only depends on the smallest observed order statistic ς (which is thus sufficient in that sense) and ends up being the original distribution truncated at ς, which allows for a closed form EM implementation. Which is also interesting given that the moments of a Normal order statistic are not available in closed form. This reminded me of the insufficient Gibbs paper we wrote with Antoine and Robin a few months ago, except for the available likelihood. And provided fodder for the final exam of my introductory mathematical statistics course at Paris Dauphine.