Archive for marginal likelihood

THAMES for mixtures, a reply from the authors

Posted in Books, pictures, R, Statistics, University life with tags , , , , , , , , , , , , , , on June 23, 2025 by xi'an

[Here is a reply to my comments on THAMES sent by the first author of the paper, Martin Metodiev. The above replica of the cover of Rivers of London is obviously unrelated with the reply or the original blog, beyond presenting a fantasy map of the Thames!]

Thank you for your review of our article! Adapting your previous work in this field has been a pleasure. Before I respond to your comments, I would like to emphasize that the simplicity of our estimator lies in its simple analytic expression (a truncated harmonic mean of reciprocal unnormalized posterior density values). Indeed, our package “thamesmix” (recently submitted to CRAN!) has a function to compute the marginal likelihood of any mixture model. This function requires only two parameters: the unnormalized log-posterior function (the logarithm of the prior plus the log-likelihood) and the MCMC simulations from the posterior.

Regarding your main comments:

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.”

I could not find an example of post-process simulations on top of MCMC outputs applied to compute these methods. It sounds really interesting, and I would be happy to cite it. Is there a reference that you can recommend?

In any case, the point still stands. Most estimators which we cite with regards to this point do not just need allocation samplers, but also the analytic expressions of the distribution of the allocation vectors or the distribution of the data conditional on these allocation vectors that come with them. I do not think that a closed form of this distribution is available in general.

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.”

The fact that our estimator is invariant to label-switching is indeed the core of our method. The simple Gibbs sampler gets stuck in one mode, and this is why the classical version of bridge sampling is biased by a factor of G! in the simulation setting. As you point out, this is successfully resolved when using fully symmetric bridge sampling in the experiment section. However, the computation cost of this fully symmetric estimator rises super-exponentially with G, so I do not see how it could be evaluated for G=15, where the number of symmetric modes is equal to 15! (over one trillion). One of the main points of our article is that the symmetric THAMES can be evaluated in a feasible amount of time, even in such a high-dimensional multivariate setting.

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”

I would like to point out that these alternate proposals do not in any way impact the definition of the THAMES. It is the simple definition given in Equation (5). They are only used to speed up the computation.

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”

The problem that we see with the classical, non-symmetric bridge sampling method in the setting of mixture models is not simply that it is biased. The problem is that the bias is persistent and often roughly equal to the factor of G! when the MCMC sampler failed to switch between modes. We have not had this experience with the THAMES: it converged even when the MCMC was stuck.

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.

Masterclass in Bayesian Asymptotics, Université Paris Dauphine, 18-22 March 2024

Posted in Books, pictures, Statistics, Travel, University life with tags , , , , , , , , , , , , , , , , , , , , on December 8, 2023 by xi'an

On the week of 18-22 March 2024, Judith Rousseau (Paris Dauphine & Oxford) will teach a Masterclass on Bayesian asymptotics. The masterclass takes place in Paris (on the PariSanté Campus) and consists of morning lectures and afternoon labs. Attendance is free with compulsory registration before 11 March (since the building is not accessible without prior registration).

The plan of the course is as follows

Part I: Parametric models
In this part, well- and mis-specified models will be considered.
– Asymptotic posterior distribution: asymptotic normality of the posterior,  penalization induced by the prior and the Bernstein von – Mises theorem. Regular and nonregular models will be treated.
– marginal likelihood and consistency of Bayes factors/model selection approaches.
– Empirical Bayes methods: asymptotic posterior distribution for parametric empirical Bayes methods.

Part II: Nonparametric and semiparametric models
– Posterior consistency and posterior convergence rates: statistical loss functions using the theory initiated by L. Schwartz and developed by Ghosal and Van der Vaart, results on less standard or well behaved losses.
– semiparametric Bernstein von Mises theorems.
– nonparametric Bernstein von Mises theorems and Uncertainty quantification.
– Stepping away from pure Bayes approaches: generalized Bayes, one step posteriors and cut posteriors.

Natural nested sampling

Posted in Books, Statistics, University life with tags , , , , , , , , , , , on May 28, 2023 by xi'an

“The nested sampling algorithm solves otherwise challenging, high-dimensional integrals by evolving a collection of live points through parameter space. The algorithm was immediately adopted in cosmology because it partially overcomes three of the major difficulties in Markov chain Monte Carlo, the algorithm traditionally used for Bayesian computation. Nested sampling simultaneously returns results for model comparison and parameter inference; successfully solves multimodal problems; and is naturally self-tuning, allowing its immediate application to new challenges.”

I came across a review on nested sampling in Nature Reviews Methods Primers of May 2022, with a large number of contributing authors, some of whom I knew from earlier papers in astrostatistics. As illustrated by the above quote from the introduction, the tone is definitely optimistic about the capacities of the method, reproducing the original argument that the evidence is the posterior expectation of the likelihood L(θ) under the prior. Which representation, while valid, is not translating into a dimension-free methodology since parameters θ still need be simulated.

“Nested sampling lies in a class of algorithms that form a path of bridging distributions and evolves samples along that path. Nested sampling stands out because the path is automatic and smooth — compression along log X by, on average, 1/𝑛at each iteration — and because along the path is compressed through constrained priors, rather than from the prior to the posterior. This was a motivation for nested sampling as it avoids phase transitions — abrupt changes in the bridging distributions — that cause problems for other methods, including path samplers, such as annealing.”

The elephant in the room is eventually processed, namely the simulation from the prior constrained to the likelihood level sets that in my experience (with, e.g., mixture posteriors) proves most time consuming. This stems from the fact that these level sets are notoriously difficult to evaluate from a given sample: all points stand within the set but they hardly provide any indication of the boundaries of saif set… Region sampling requires to construct a region that bounds the likelihood level set, which requires some knowledge of the likelihood variations to have a chance to remain efficient, incl. in cosmological applications, while regular MCMC steps require an increasing number of steps as the constraint gets tighter and tighter. For otherwise it essentially amounts to duplicating a live particle.