Archive for Gibbs sampling

miXtures on arXiv

Posted in Books, Statistics, University life with tags , , , , , , , , , , , , , , , , , , , , on February 5, 2025 by xi'an

A paper about Bayesian inference on mixtures was posted on arXiv last week, as of 13 Jan 2025.  Fast sampling and model selection for Bayesian mixture models, by M. E. J. Newman is based on the notion that (genuine) parameters of a mixture model can be marginalized out when using conjugate priors. This is something that we pointed out quite a while ago, in a 1999 paper with George and Marty, which was devised in a long ride from Baltimore to Cornell after JSM 1999, and again in the 2002 Series B perfect sampling paper with George, Kerrie and Mike. (Also written in 1999.) And marginal likelihood can furthermore be approximated along this way as discussed in the more recent papers Bayesian Inference on Mixtures of Distributions with Kate, Kerrie & Jean-Michel, as well as Approximating the marginal likelihood in mixture models with Jean-Michel.

“Standard mixture models, as commonly formulated, also suffer from a technical, but important, difficulty: the existence of empty components. In many models (…) the number of observations in a component can be zero. Arguably this is acceptable for a model with a fixed number of components, but when the number of components is a free random variable it causes ambiguity, because a given division of observations into components can be represented in more than one way in the model. For instance, we could divide observations into two components, or we could divide them into three components, one of which is empty. This in turn creates difficulties when estimating the number of components—do we have two components or three?”

A very puzzling perspective, imho, since potentially empty components are inherent to (both finite and infinite) mixture models with connected issues of prohibiting some improper priors (if not all) and non-identifiability, including non-identifiability of the number of empty components (which remains random conditional on the data!), but different numbers of components lead to different models and their comparison is handled straightforwardly by a Bayesian analysis.

The author then proceeds to “prohibit empty components” [as a prior choice ?] as we did in the original (!) Gibbs sampler for mixtures in 1990 (published in 1994 in Series B!), seeking posterior properness, a trick later validated by Larry Wasserman (in again 1999, the year of mixtures!). Who called the construct the combination of a fixed prior and of a pseudo-likelihood, correctly imho (as the data dependent part is not properly normalised by a function of the parameters), rather than a prior choice. (The very one who stated that “mixtures, like tequila, are evil and should be avoided“.)

From there, the modelling is rather standard, with an arbitrary prior on k, number of components, a random partition model that prohibits empty components, even though the constraint could be more stringent depending on the number of parameters of a given component and the degree of improperness of the prior, as in our 1990 Series B paper. (Impropriety is not discussed in the paper.) Bayesian inference on k is based on the simulated (pseudo-)posterior. The choice therein as the estimated clustering is the most frequent partition (consensus clustering), connected to our proposal of (again!) 1999 with Merrilee and Gilles. While the estimated mixture is not explicited. The approach is assessed as running at an O(k) cost, with no parallel in terms of the data size n, even though the examples include a 59,946 dataset. One notable algorithmic trick when moving k is in selecting a component at random first rather than an observation index.

Some minor issues: detailed balance indicated as required for convergence (p14), label switching is called component switching (p5), higher acceptance rate indicated as meaning improved performances (p7)

All about that [Bayes] seminar [24 Jan]

Posted in Books, pictures, Statistics, Travel, University life with tags , , , , , , , , , , , , , , , , , , on January 13, 2025 by xi'an

The next All about that (Bayes) seminar will take place on Friday 24 Jan at SCAI, on the Jussieu campus, with the following talks. (Appearances to the contrary, I was not in the least involved in the program!)

13h30 – 14h30 Joshua Bon (OCEAN, Université Paris Dauphine) – Bayesian score calibration for approximate models

 Scientists continue to develop increasingly complex mechanistic models to reflect their knowledge more realistically. Statistical inference using these models can be challenging since the corresponding likelihood function is often intractable and model simulation may be computationally burdensome. Fortunately, in many of these situations, it is possible to adopt a surrogate model or approximate likelihood function. It may be convenient to conduct Bayesian inference directly with the surrogate, but this can result in bias and poor uncertainty quantification. In this paper (https://arxiv.org/abs/2211.05357) we propose a new method for adjusting approximate posterior samples to reduce bias and produce more accurate uncertainty quantification. We do this by optimizing a transform of the approximate posterior that maximizes a scoring rule. Our approach requires only a (fixed) small number of complex model simulations and is numerically stable. We demonstrate beneficial corrections to several approximate posteriors using our method on several examples of increasing complexity.

14h30 – 15h30 Giacomo Zanella (Bocconi University) – Entropy contraction of the Gibbs sampler under log-concavity

In this talk I will present recent work (https://arxiv.org/abs/2410.00858) on the non-asymptotic analysis of the Gibbs sampler, a classical and popular MCMC algorithm for sampling. In particular, under the assumption that the probability measure π of interest is strongly log-concave, we show that the random scan Gibbs sampler contracts in relative entropy, and provide a sharp characterization of the associated contraction rate. The result implies that, under appropriate conditions, the number of full evaluations of π required for the Gibbs sampler to converge is independent of the dimension. If time permits, I will also discuss connections and applications of the above results to the problem of zero-order parallel sampling, as well as extensions to Hit-and-Run and Metropolis-within-Gibbs.

Based on joint work with Filippo Ascolani and Hugo Lavenant.

16h00 – 17h00 Paul Bastide (Université Paris Cité) – Goodness of Fit for Bayesian Generative Models with Applications in Population Genetics

In population genetics, inference about intractable likelihood models is common, and simulation methods, including Approximate Bayesian Computation (ABC) and Simulation-Based Inference (SBI), are essential. ABC/SBI methods work by simulating instrumental data sets of the models under study and comparing them with the observed data set y⁰. Advanced machine learning tools are used for tasks such as model selection and parameter inference. The present work focuses on model criticism. This type of analysis, called goodness of fit (GoF), is important for model validation. It can also be used for model pruning when the number of candidates to be considered is excessive, especially in the context where data simulation is expensive. We introduce two new GoF tests based on the local outlier factor (LOF), an indicator that was initially defined for outlier and novelty detection. We test whether y⁰ is distributed from the prior predictive distribution (pre-inference GoF) and whether there is a parameter value such that y⁰ is distributed from the likelihood with that value (post-inference GoF).  We evaluate the performance of our two GoF tests on simulated datasets from three different model settings of varying complexity, and on a dataset of single nucleotide polymorphism (SNP) markers for the evaluation of complex evolutionary scenarios of modern human populations.

Joint work with Guillaume Le Mailloux, Jean-Michel Marin and Arnaud Estoup.

Nice meeting!

Posted in pictures, R, Running, Statistics, Travel, University life with tags , , , , , , , , , , , , , , , , , , , , , , , on December 18, 2024 by xi'an

The ICSDS 2024 meeting in Nice is quite impressive and not primarily because it is in Nice under a beautiful December sun. As other (numerous) IMS meetings I attended (since the initial one in Uppsala in 1990!), the program is of high quality and along topics that are currently moving fast or emerging. From the sessions I attended, e-values are strongly represented, although it remains unclear to me why they should constitute a major departure from p-values, as they stick to hypothesis testing, Type I error, power, and the whole paraphernalia of Neyman-Pearson formalism. If I manage to attend a BIRS workshop on the subject next Summer, I may manage to get a better e-derstanding!The MCMC (only!) session included a presentation by Guanyang Wang that generalised different approximate MCMC schemes into a unified one. And one by Filippo Ascolani on Gibbs beating the competition! I also attended the Bayesian prediction session, where my friends Sonia Petrone and Chris Holmes have presentations on their respective Series B papers. I discussed both on the ‘Og, on 15 March 2023 and 07 November 2022, respectively. This time, I found that both talks had a Bayesian bootstrap flavour, which is not surprising when considering the non-parametric nature of the approach. And they left me wondering at it being protected from overfitting.
My only plenary session was Cynthia Dwork’s on outcome indistinguishability, which, while related to the privacy topics I was topic, remained somewhat obscure as to its purpose. Meaning I have to get through the paper to get a more holistic perspective.
Of course, Nice in Winter is a very nice place, with the waterfront available for running an uninterrupted 15km as we found out with Jérémie Houssineau (at a brisk 4’09” pace I had not planned before starting!) and the sea all for myself (for a dozen minutes before losing digits!). Unfortunately I had to skip the final day due to examinations of the Paris Dauphine MASH master. And miss Stan receiving a student award. But I am looking forward the next iterations of ICSDS. (Not including Copenhagen, Madrid and many many other places in 2025, since ICSDS seemed a most common name for conferences, some presumably predatory! The true location is Sevilla, to keep up with the Mediterranean theme of ICSDS!)

insufficiently out!

Posted in Books, Statistics, University life with tags , , , , , on May 31, 2024 by xi'an

insufficient Gibbs sampling bridges as well!

Posted in Books, Kids, pictures, R, Statistics, University life with tags , , , , , , , , , , , , on March 3, 2024 by xi'an

Antoine Luciano, Robin Ryder and I posted a revised version of our insufficient Gibbs sampler on arXiv last week (along with three other revisions or new deposits of mine’s!), following comments and suggestions from referees. Thanks to this revision, we realised that the evidence based on an (insufficient) statistic was also available for approximation by a Monte Carlo estimate attached to the completed sample simulated by the insufficient sampler. Better, a bridge sampling estimator can be used in the same conditions as when the full data is available! In this new version, we thus revisited toy examples first explored in some of my ABC papers on testing (with insufficient statistics), as illustrated by both graphs on this post.