Archive for Approximate Bayesian computation

variational approximation to empirical likelihood ABC

Posted in Statistics with tags , , , , , , , , , , , , , , , , , , on October 1, 2021 by xi'an

Sanjay Chaudhuri and his colleagues from Singapore arXived last year a paper on a novel version of empirical likelihood ABC that I hadn’t yet found time to read. This proposal connects with our own, published with Kerrie Mengersen and Pierre Pudlo in 2013 in PNAS. It is presented as an attempt at approximating the posterior distribution based on a vector of (summary) statistics, the variational approximation (or information projection) appearing in the construction of the sampling distribution of the observed summary. (Along with a weird eyed-g symbol! I checked inside the original LaTeX file and it happens to be a mathbbmtt g, that is, the typewriter version of a blackboard computer modern g…) Which writes as an entropic correction of the true posterior distribution (in Theorem 1).

“First, the true log-joint density of the observed summary, the summaries of the i.i.d. replicates and the parameter have to be estimated. Second, we need to estimate the expectation of the above log-joint density with respect to the distribution of the data generating process. Finally, the differential entropy of the data generating density needs to be estimated from the m replicates…”

The density of the observed summary is estimated by empirical likelihood, but I do not understand the reasoning behind the moment condition used in this empirical likelihood. Indeed the moment made of the difference between the observed summaries and the observed ones is zero iff the true value of the parameter is used in the simulation. I also fail to understand the connection with our SAME procedure (Doucet, Godsill & X, 2002), in that the empirical likelihood is based on a sample made of pairs (observed,generated) where the observed part is repeated m times, indeed, but not with the intent of approximating a marginal likelihood estimator… The notion of using the actual data instead of the true expectation (i.e. as a unbiased estimator) at the true parameter value is appealing as it avoids specifying the exact (or analytical) value of this expectation (as in our approach), but I am missing the justification for the extension to any parameter value. Unless one uses an ancillary statistic, which does not sound pertinent… The differential entropy is estimated by a Kozachenko-Leonenko estimator implying k-nearest neighbours.

“The proposed empirical likelihood estimates weights by matching the moments of g(X¹), , g(X) with that of
g(X), without requiring a direct relationship with the parameter. (…) the constraints used in the construction of the empirical likelihood are based on the identity in (7), which can only be satisfied when θ = θ⁰. “

Although I am feeling like missing one argument, the later part of the paper seems to comfort my impression, as quoted above. Meaning that the approximation will fare well only in the vicinity of the true parameter. Which makes it untrustworthy for model choice purposes, I believe. (The paper uses the g-and-k benchmark without exploiting Pierre Jacob’s package that allows for exact MCMC implementation.)

what a party!

Posted in pictures, Statistics, Travel, University life, Wines with tags , , , , , , , , , , , , , , on September 13, 2021 by xi'an

We ended up having a terrific b’day party last Thursday after noon, with about 30 friends listening in Institut Henri Poincaré to Florence, Pierre, and Sylvia giving lectures on my favourite themes, namely ABC, MCMC, and mixture inference. Incl. subtle allusions to my many idiosyncrasies in three different flavours!  And a limited number of anecdotes, incl. the unavoidable Cancún glasses disaster! We later headed to a small Ethiopian restaurant located on the other side of the Panthéon, rue de l’Ecole Polytechnique (rather than on the nearby rue Laplace!), which was going to be too tiny for us, especially in these COVID times, until the sky cleared up and the restaurant set enough tables in the small street to enjoy their injeras and wots till almost midnight. The most exciting episode of the evening came when someone tried to steal some of our bags that had been stored in a back room and when Tony spotted the outlier and chased him till the thief dropped the bags..! Thanks to Tony for saving the evening and our computers!!! To Éric, Jean-Michel and Judith for organising this 9/9 event (after twisting my arm just a wee bit). And to all my friends who joined the party, some from far away…

ISBA 2021.3

Posted in Kids, Mountains, pictures, Running, Statistics, Travel, University life, Wines with tags , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , on July 1, 2021 by xi'an

Now on the third day which again started early with a 100% local j-ISBA session. (After a group run to and around Mont Puget, my first real run since 2020!!!) With a second round of talks by junior researchers from master to postdoc level. Again well-attended. A talk about Bayesian non-parametric sequential taxinomy by Alessandro Zito used the BayesANT acronym, which reminded me of the new vave group Adam and the Ants I was listening to forty years ago, in case they need a song as well as a logo! (Note that BayesANT is also used for a robot using Bayesian optimisation!) And more generally a wide variety in the themes. Thanks to the j-organisers of this 100% live session!

The next session was on PDMPs, which I helped organise, with Manon Michel speaking from Marseille, exploiting the symmetry around the gradient, which is distribution-free! Then, remotely, Kengo Kamatani, speaking from Tokyo, who expanded the high-dimensional scaling limit to the Zig-Zag sampler, exhibiting an argument against small refreshment rates, and Murray Pollock, from Newcastle, who exposed quite clearly the working principles of the Restore algorithm, including why coupling from the past was available in this setting. A well-attended session despite the early hour (in the USA).

Another session of interest for me [which I attended by myself as everyone else was at lunch in CIRM!] was the contributed C16 on variational and scalable inference that included a talk on hierarchical Monte Carlo fusion (with my friends Gareth and Murray as co-authors), Darren’s call to adopt functional programming in order to save Bayesian computing from extinction, normalising flows for modularisation, and Dennis’ adversarial solutions for Bayesian design, avoiding the computation of the evidence.

Wes Johnson’s lecture was about stories with setting prior distributions based on experts’ opinions. Which reminded me of the short paper Kaniav Kamary and myself wrote about ten years ago, in response to a paper on the topic in the American Statistician. And could not understand the discrepancy between two Bayes factors based on Normal versus Cauchy priors, until I was told they were mistakenly used repeatedly.

Rushing out of dinner, I attended both the non-parametric session (live with Marta and Antonio!) and the high-dimension computational session on Bayesian model choice (mute!). A bit of a schizophrenic moment, but allowing to get a rough picture in both areas. At once. Including an adaptive MCMC scheme for selecting models by Jim Griffin. Which could be run directly over the model space. With my ever-going wondering at the meaning of neighbour models.

ISBA 20.2.21

Posted in Kids, Mountains, pictures, Running, Statistics, Travel, University life, Wines with tags , , , , , , , , , , , , , , , , , , , , , , , , , , , on June 30, 2021 by xi'an

A second day which started earlier and more smoothly with a 100% local j-ISBA session. (Not counting the invigorating swim in Morgiou!) With talks by junior researchers from master to postdoc level, as this ISBA mirror meeting was primarily designed for them, so that they could all present their work, towards gaining more visibility for their research and facilitating more interactions with the participants. CIRM also insisted on this aspect of the workshop, which was well-attended.

I alas had to skip the poster session [and the joys of gather.town] despite skipping lunch [BND], due to organisational constraints. Then attended the Approximate Bayesian computation section, including one talk by Geoff Nicholls on confidence estimation for ABC, following upon the talk given by Kate last evening. And one by Florian Maire on learning the bound in accept-reject algorithms on the go, as in Caffo et al. (2002), which I found quite exciting and opening new possibilities, esp. if the Markov chain thus produced can be recycled towards unbiasedness without getting the constant right! For instance, by Rao-Blackwellisation, multiple mixtures, black box importance sampling, whatever. (This also reminded me of the earlier Goffinet et al. 1996.)

Followed by another Bayesian (modeling and) computation session. With my old friend Peter Müller talking about mixture inference with dependent priors (and a saturated colour scheme!), Matteo Ruggieri [who could not make it to CIRM!] on computable Bayesian inference for HMMs. Providing an impressive improvement upon particle filters for approximating the evidence. Also bringing the most realistic Chinese restaurant with conveyor belt! And Ming Yuan Zhou using optimal transport to define distance between distributions. With two different conditional distributions depending on which marginal is first fixed. And a connection with GANs (of course!).

And it was great to watch and listen to my friend Alicia Carriquiry talking on forensic statistics and the case for (or not?!) Bayes factors. And remembering Dennis Lindley. And my friend Jim Berger on frequentism versus Bayes! Consistency seems innocuous as most Bayes procedures are. Empirical coverage is another kind of consistency, isn’t it?

A remark I made when re-typing the program for CIRM is that there are surprisingly few talks about COVID-19 overall, maybe due to the program being mostly set for ISBA 2020 in Kunming. Maybe because we are more cautious than the competition…?!

And, at last, despite a higher density of boars around the CIRM facilities, no one got hurt yesterday! Unless one counts the impact of the French defeat at the Euro 2021 on the football fans here…

ISBA 2021.1

Posted in Kids, Mountains, pictures, Running, Statistics, Travel, University life, Wines with tags , , , , , , , , , , , , , , , , , , on June 29, 2021 by xi'an

An infinite (mixture) session was truly the first one I could attend on Day 1, as a heap of unexpected last minute issues kept me busy or on hedge for the beginning of the day (if not preventing me from a dawn dip in Calanque de Morgiou). Using the CIRM video system for zoom talked required more preparation than I had thought and we made it barely in time for the first session, while I had to store zoom links for all speakers present in Luminy.  Plus allocate sessions to the rooms provided by CIRM, twice since there was a mishap with the other workshop present at CIRM. And reassuring speakers, made anxious by the absence of a clear schedule. Chairing the second ABC session was also a tense moment, from checking every speaker could connect and share slides, to ensuring they kept on schedule (and they did on both!, ta’), to checking for questions at the end. Spotting a possible connection between Takuo Mastubara’s Stein’s approximation for in the ABC setup and a related paper by Liu and Lee I had read just a few days ago. Alas, it was too early to relax as an inverter in the CIRM room burned and led to a local power failure. Fortunately this was restored prior to the mixture session! (As several boars were spotted on the campus yesternight, I hope no tragic encounter happens before the end of the meeting!!!) So the mixture session proposed new visions on infering K, the number of components, some of which reminded me of… my first talk at CIRM where I was trying to get rid of empty components at each MCMC step, albeit in a much more rudimentary way obviously. And later had the wonderful surprise of hearing Xiao-Li’s lecture start by an excerpt from Car Talk, the hilarious Sunday morning radio talk-show about the art of used car maintenance on National Public Radio (NPR) that George Casella could not miss (and where a letter he wrote them about a mistaken probability computation was mentioned!). The final session of the day was an invited ABC session I chaired (after being exfiltrated from the CIRM dinner table!) with Kate Lee, Ryan Giordano, and Julien Stoehr as speakers. Besides Julien’s talk on our Gibbs-ABC paper, both other talks shared a concern with the frequentist properties of the ABC posterior, either to be used as a control tool or as a faster assessment of the variability of the (Monte Carlo) ABC output.

%d bloggers like this: