Archive for Gibbs sampling

interdependent Gibbs samplers

Posted in Books, Statistics, University life with tags , , , , , , on April 27, 2018 by xi'an

Mark Kozdoba and Shie Mannor just arXived a paper on an approach to accelerate a Gibbs sampler. With title “interdependent Gibbs samplers“. In fact, it presents rather strong similarities with our SAME algorithm. More of the same, as Adam Johanssen (Warwick) entitled one of his papers! The paper indeed suggests multiplying replicas of latent variables (e.g., an hidden path for an HMM) in an artificial model. And as in our 2002 paper, with Arnaud Doucet and Simon Godsill, the focus here is on maximum likelihood estimation (of the genuine parameters, not of the latent variables). Along with argument that the resulting pseudo-posterior is akin to a posterior with a powered likelihood. And a link with the EM algorithm. And an HMM application.

“The generative model consist of simply sampling the parameters ,  and then sampling m independent copies of the paths”

If anything this proposal is less appealing than SAME because it aims directly at the powered likelihood, rather than utilising an annealed sequence of powers that allows for a primary exploration of the whole parameter space before entering the trapping vicinity of a mode. Which makes me fail to catch the argument from the authors that this improves Gibbs sampling, as a more acute mode has on the opposite the dangerous feature of preventing visits to other modes. Hence the relevance to resort to some form of annealing.

As already mused upon in earlier posts, I find it most amazing that this technique has been re-discovered so many times, both in statistics and in adjacent fields. The idea of powering the likelihood with independent copies of the latent variables is obviously natural (since a version pops up every other year, always under a different name), but earlier versions should eventually saturate the market!

Gibbs for kidds

Posted in Books, Kids, Statistics, University life with tags , , , , , , , , , , , , , , , on February 12, 2018 by xi'an


A chance (?) question on X validated brought me to re-read Gibbs for Kids, 25 years after it was written (by my close friends George and Ed). The originator of the question had difficulties with the implementation, apparently missing the cyclic pattern of the sampler, as in equations (2.3) and (2.4), and with the convergence, which is only processed for a finite support in the American Statistician paper. The paper [which did not appear in American Statistician under this title!, but inspired an animal bredeer, Dan Gianola, to write a “Gibbs for pigs” presentation in 1993 at the 44th Annual Meeting of the European Association for Animal Production, Aarhus, Denmark!!!] most appropriately only contains toy examples since those can be processed and compared to know stationary measures. This is for instance the case for the auto-exponential model

f(x,y) \propto exp(-xy)

which is only defined as a probability density for a compact support. (The paper does not identify the model as a special case of auto-exponential model, which apparently made the originator of the model, Julian Besag in 1974, unhappy, as George and I found out when visiting Bath, where Julian was spending the final year of his life, many years later.) I use the limiting case all the time in class to point out that a Gibbs sampler can be devised and operate without a stationary probability distribution. However, being picky!, I would like to point out that, contrary, to a comment made in the paper, the Gibbs sampler does not “fail” but on the contrary still “converges” in this case, in the sense that a conditional ergodic theorem applies, i.e., the ratio of the frequencies of visits to two sets A and B with finite measure do converge to the ratio of these measures. For instance, running the Gibbs sampler 10⁶ steps and ckecking for the relative frequencies of x’s in (1,2) and (1,3) gives 0.685, versus log(2)/log(3)=0.63, since 1/x is the stationary measure. One important and influential feature of the paper is to stress that proper conditionals do not imply proper joints. George would work much further on that topic, in particular with his PhD student at the time, my friend Jim Hobert.

With regard to the convergence issue, Gibbs for Kids points out to Schervish and Carlin (1990), which came quite early when considering Gelfand and Smith published their initial paper the very same year, but which also adopts a functional approach to convergence, along the paper’s fixed point perspective, somehow complicating the matter. Later papers by Tierney (1994), Besag (1995), and Mengersen and Tweedie (1996) considerably simplified the answer, which is that irreducibility is a necessary and sufficient condition for convergence. (Incidentally, the reference list includes a technical report of mine’s on latent variable model MCMC implementation that never got published.)

two Parisian talks by Pierre Jacob in January

Posted in pictures, Statistics, University life with tags , , , , , , , , , on December 21, 2017 by xi'an

While back in Paris from Harvard in early January, Pierre Jacob will give two talks on works of his:

January 09, 10:30, séminaire d’Analyse-Probabilités, Université Paris-Dauphine: Unbiased MCMC

Markov chain Monte Carlo (MCMC) methods provide consistent approximations of integrals as the number of iterations goes to infinity. However, MCMC estimators are generally biased after any fixed number of iterations, which complicates both parallel computation and the construction of confidence intervals. We propose to remove this bias by using couplings of Markov chains and a telescopic sum argument, inspired by Glynn & Rhee (2014). The resulting unbiased estimators can be computed independently in parallel, and confidence intervals can be directly constructed from the Central Limit Theorem for i.i.d. variables. We provide practical couplings for important algorithms such as the Metropolis-Hastings and Gibbs samplers. We establish the theoretical validity of the proposed estimators, and study their variances and computational costs. In numerical experiments, including inference in hierarchical models, bimodal or high-dimensional target distributions, logistic regressions with the Pólya-Gamma Gibbs sampler and the Bayesian Lasso, we demonstrate the wide applicability of the proposed methodology as well as its limitations. Finally, we illustrate how the proposed estimators can approximate the “cut” distribution that arises in Bayesian inference for misspecified models.

January 11, 10:30, CREST-ENSAE, Paris-Saclay: Better together? Statistical learning in models made of modules [Warning: Paris-Saclay is not in Paris!]

In modern applications, statisticians are faced with integrating heterogeneous data modalities relevant for an inference or decision problem. It is convenient to use a graphical model to represent the statistical dependencies, via a set of connected “modules”, each relating to a specific data modality, and drawing on specific domain expertise in their development. In principle, given data, the conventional statistical update then allows for coherent uncertainty quantification and information propagation through and across the modules. However, misspecification of any module can contaminate the update of others. In various settings, particularly when certain modules are trusted more than others, practitioners have preferred to avoid learning with the full model in favor of “cut distributions”. In this talk, I will discuss why these modular approaches might be preferable to the full model in misspecified settings, and propose principled criteria to choose between modular and full-model approaches. The question is intertwined with computational difficulties associated with the cut distribution, and new approaches based on recently proposed unbiased MCMC methods will be described.

Long enough after the New Year festivities (if any) to be fully operational for them!

probabilities larger than one…

Posted in Statistics with tags , , , , , , on November 9, 2017 by xi'an

repulsive mixtures

Posted in Books, Statistics with tags , , , , , , , , on April 10, 2017 by xi'an

Fangzheng Xie and Yanxun Xu arXived today a paper on Bayesian repulsive modelling for mixtures. Not that Bayesian modelling is repulsive in any psychological sense, but rather that the components of the mixture are repulsive one against another. The device towards this repulsiveness is to add a penalty term to the original prior such that close means are penalised. (In the spirit of the sugar loaf with water drops represented on the cover of Bayesian Choice that we used in our pinball sampler, repulsiveness being there on the particles of a simulated sample and not on components.) Which means a prior assumption that close covariance matrices are of lesser importance. An interrogation I have has is was why empty components are not excluded as well, but this does not make too much sense in the Dirichlet process formulation of the current paper. And in the finite mixture version the Dirichlet prior on the weights has coefficients less than one.

The paper establishes consistency results for such repulsive priors, both for estimating the distribution itself and the number of components, K, under a collection of assumptions on the distribution, prior, and repulsiveness factors. While I have no mathematical issue with such results, I always wonder at their relevance for a given finite sample from a finite mixture in that they give an impression that the number of components is a perfectly estimable quantity, which it is not (in my opinion!) because of the fluid nature of mixture components and therefore the inevitable impact of prior modelling. (As Larry Wasserman would pound in, mixtures like tequila are evil and should likewise be avoided!)

The implementation of this modelling goes through a “block-collapsed” Gibbs sampler that exploits the latent variable representation (as in our early mixture paper with Jean Diebolt). Which includes the Old Faithful data as an illustration (for which a submission of ours was recently rejected for using too old datasets). And use the logarithm of the conditional predictive ordinate as  an assessment tool, which is a posterior predictive estimated by MCMC, using the data a second time for the fit.

recycling Gibbs auxiliaries [a reply]

Posted in Books, pictures, Statistics, University life with tags , , , , , , , on January 3, 2017 by xi'an

[Here is a reply sent to me by Luca Martino, Victor Elvira, and Gustau Camp-Vallis, after my earlier comments on their paper.]

We provide our contribution to the discussion, reporting our experience with the application of Metropolis-within-Gibbs schemes. Since in literature there are miscellaneous opinions, we want to point out the following considerations:

– according to our experience, the use of M>1 steps of the Metropolis-Hastings (MH) method for drawing from each full-conditional (with or without recycling), decreases the MSE of the estimation (see code Ex1-Ex2 and related Figure 7(b) and Figures 8). If the corresponding full conditional is very concentrated, one possible solution is to applied an adaptive or automatic MH for drawing from this full-conditional (it can require the use of M internal steps; see references in Section 3.2).

– Fixing the number of evaluations of the posterior, the comparison between a longer Gibbs chain with a single step of MH and a shorter Gibbs chain with M>1 steps of MH per each full-conditional, is required. Generally, there is no clear winner. The better performance depends on different aspects: the specific scenario, if and adaptive MH is employed or not, if the recycling is applied or not (see Figure 10(a) and the corresponding code Ex2).

The previous considerations are supported/endorsed by several authors (see the references in Section 3.2). In order to highlight the number of controversial opinions about the MH-within-Gibbs implementation, we report a last observation:

– If it is possible to draw directly from the full-conditionals, of course this is the best scenario (this is our belief). Remarkably, as also reported in Chapter 1, page 393 of the book “Monte Carlo Statistical Methods”, C. Robert and Casella, 2004, some authors have found that a “bad” choice of the proposal function in the MH step (i.e., different from the full conditional, or a poor approximation of it) can improve the performance of the MH-within-Gibbs sampler. Namely, they assert that a more “precise” approximation of the full-conditional does not necessarily improve the overall performance. In our opinion, this is possibly due to the fact that the acceptance rate in the MH step (lower than 1) induces an “accidental” random scan of the components of the target pdf in the Gibbs sampler, which can improve the performance in some cases. In our work, for the simplicity, we only focus on the deterministic scan. However, a random scan could be also considered.

recycling Gibbs auxiliaries

Posted in Books, pictures, Statistics, University life with tags , , , , , , , , , , on December 6, 2016 by xi'an

wreck of the S.S. Dicky, Caloundra beach, Qld, Australia, Aug. 19, 2012Luca Martino, Victor Elvira and Gustau Camps-Valls have arXived a paper on recycling for Gibbs sampling. The argument therein is to take advantage of all simulations induced by MCMC simulation for one full conditional, towards improving estimation if not convergence. The context is thus one when Metropolis-within-Gibbs operates, with several (M) iterations of the corresponding Metropolis being run instead of only one (which is still valid from a theoretical perspective). While there are arguments in augmenting those iterations, as recalled in the paper, I am not a big fan of running a fixed number of M of iterations as this does not approximate better the simulation from the exact full conditional and even if this approximation was perfect, the goal remains simulating from the joint distribution. As such, multiplying the number of Metropolis iterations does not necessarily impact the convergence rate, only brings it closer to the standard Gibbs rate. Moreover, the improvement does varies with the chosen component, meaning that the different full conditionals have different characteristics that produce various levels of variance reduction:

  • if the targeted expectation only depends on one component of the Markov chain, multiplying the number of simulations for the other components has no clear impact, except in increasing time;
  • if the corresponding full conditional is very concentrated, repeating simulations should produce quasi-repetitions, and no gain.

The only advantage in computing time that I can see at this stage is when constructing the MCMC sampler for the full proposal is much more costly than repeating MCMC iterations, which are then almost free and contribute to the reduction of the variance of the estimator.

This analysis of MCMC-withing-Gibbs strategies reminds me of a recent X validated question, which was about the proper degree of splitting simulations from a marginal and from a corresponding conditional in the chain rule, the optimal balance being in my opinion dependent on the relative variances of the conditional expectations.

A last point is that recycling in the context of simulation and Monte Carlo methodology makes me immediately think of Rao-Blackwellisation, which is surprisingly absent from the current paperRao-Blackwellisation was introduced in the MCMC literature and to the MCMC community in the first papers of Alan Gelfand and Adrian Smith, in 1990. While this is not always producing a major gain in Monte Carlo variability, it remains a generic way of recycling auxiliary variables as shown, e.g., in the recycling paper we wrote with George Casella in 1996, one of my favourite papers.