Archive for bootstrap likelihood

stratified ABC [One World ABC webinar]

Posted in Books, Statistics, University life with tags , , , , , , , , on May 15, 2020 by xi'an

The third episode of the One World ABC seminar (Season 1!) was kindly delivered by Umberto Picchini on Stratified sampling and bootstrapping for ABC which I already if briefly discussed after BayesComp 2020. Which sounds like a million years ago… His introduction on the importance of estimating the likelihood using a kernel, while 600% justified wrt his talk, made the One World ABC seminar sounds almost like groundhog day!  The central argument is in the computational gain brought by simulating a single θ dependent [expensive] dataset followed by [cheaper] bootstrap replicates. Which turns de fact into bootstrapping the summary statistics.

If I understand correctly, the post-stratification approach of Art Owen (2013?, I cannot find the reference) corrects a misrepresentation of mine. Indeed, defining a partition with unknown probability weights seemed to me to annihilate the appeal of stratification, because the Bernoulli variance of the estimated probabilities brought back the same variability as the mother estimator. But with bootstrap, this requires only two simulations, one for the weights and one for the target. And further allows for a larger ABC tolerance in fine. Free lunch?!

The speaker in two weeks (21 May or Ascension Thursday!) is my friend and co-author Gael Martin from Monash University, who will speak on Focused Bayesian prediction, at quite a late time down under..!

BayesComp’20

Posted in Books, pictures, Statistics, Travel, University life with tags , , , , , , , , , , , , , , , , , , , , , on January 10, 2020 by xi'an

First, I really have to congratulate my friend Jim Hobert for a great organisation of the meeting adopting my favourite minimalist principles (no name tag, no “goodies” apart from the conference schedule, no official talks). Without any pretense at objectivity, I also appreciated very much the range of topics and the sweet frustration of having to choose between two or three sessions each time. Here are some notes taken during some talks (with no implicit implication for the talks no mentioned, re. above frustration! as well as very short nights making sudden lapse in concentration highly likely).

On Day 1, Paul Fearnhead’s inaugural plenary talk was on continuous time Monte Carlo methods, mostly bouncy particle and zig-zag samplers, with a detailed explanation on the simulation of the switching times which likely brought the audience up to speed even if they had never heard of them. And an opening on PDMPs used as equivalents to reversible jump MCMC, reminding me of the continuous time (point process) solutions of Matthew Stephens for mixture inference (and of Preston, Ripley, Møller).

The same morn I heard of highly efficient techniques to handle very large matrices and p>n variables selections by Akihiko Nishimura and Ruth Baker on a delayed acceptance ABC, using a cheap proxy model. Somewhat different from indirect inference. I found the reliance on ESS somewhat puzzling given the intractability of the likelihood (and the low reliability of the frequency estimate) and the lack of connection with the “real” posterior. At the same ABC session, Umberto Picchini spoke on a joint work with Richard Everitt (Warwick) on linking ABC and pseudo-marginal MCMC by bootstrap. Actually, the notion of ABC likelihood was already proposed as pseudo-marginal ABC by Anthony Lee, Christophe Andrieu and Arnaud Doucet in the discussion of Fearnhead and Prangle (2012) but I wonder at the focus of being unbiased when the quantity is not the truth, i.e. the “real” likelihood. It would seem more appropriate to attempt better kernel estimates on the distribution of the summary itself. The same session also involved David Frazier who linked our work on ABC for misspecified models and an on-going investigation of synthetic likelihood.

Later, there was a surprise occurrence of the Bernoulli factory in a talk by Radu Herbei on Gaussian process priors with accept-reject algorithms, leading to exact MCMC, although the computing implementation remains uncertain. And several discussions during the poster session, incl. one on the planning of a 2021 workshop in Oaxaca centred on objective Bayes advances as we received acceptance of our proposal by BIRS today!

On Day 2, David Blei gave a plenary introduction to variational Bayes inference and latent Dirichlet allocations, somewhat too introductory for my taste although other participants enjoyed this exposition. He also mentioned a recent JASA paper on the frequentist consistency of variational Bayes that I should check. Speaking later with PhD students, they really enjoyed this opening on an area they did not know that well.

A talk by Kengo Kamatani (whom I visited last summer) on improved ergodicity rates for heavy tailed targets and Crank-NIcholson modifications to the random walk proposal (which uses an AR(1) representation instead of the random walk). With the clever idea of adding the scale of the proposal as an extra parameter with a prior of its own. Gaining one order of magnitude in the convergence speed (i.e. from d to 1 and from d² to d, where d is the dimension), which is quite impressive (and just published in JAP).Veronica Rockova linked Bayesian variable selection and machine learning via ABC, with conditions on the prior for model consistency. And a novel approach using part of the data to learn an ABC partial posterior, which reminded me of the partial  Bayes factors of the 1990’s although it is presumably unrelated. And a replacement of the original rejection ABC via multi-armed bandits, where each variable is represented by an arm, called ABC Bayesian forests. Recalling the simulation trick behind Thompson’s approach, reproduced for the inclusion or exclusion of variates and producing a fixed estimate for the (marginal) inclusion probabilities, which makes it sound like a prior-feeback form of empirical Bayes. Followed by a talk of Gregor Kastner on MCMC handling of large time series with specific priors and a massive number of parameters.

The afternoon also had a wealth of exciting talks and missed opportunities (in the other sessions!). Which ended up with a strong if unintended French bias since I listened to Christophe Andrieu, Gabriel Stolz, Umut Simsekli, and Manon Michel on different continuous time processes, with Umut linking GANs, multidimensional optimal transport, sliced-Wasserstein, generative models, and new stochastic differential equations. Manon Michel gave a highly intuitive talk on creating non-reversibility, getting rid of refreshment rates in PDMPs to kill any form of reversibility.

bootstrap(ed) likelihood for ABC

Posted in pictures, Statistics with tags , , , , , , , , on November 6, 2015 by xi'an

AmstabcThis recently arXived paper by Weixuan Zhu , Juan Miguel Marín, and Fabrizio Leisen proposes an alternative to our empirical likelihood ABC paper of 2013, or BCel. Besides the mostly personal appeal for me to report on a Juan Miguel Marín working [in Madrid] on ABC topics, along my friend Jean-Michel Marin!, this paper is another entry on ABC that connects with yet another statistical perspective, namely bootstrap. The proposal, called BCbl, is based on a reference paper by Davison, Hinkley and Worton (1992) which defines a bootstrap likelihood, a notion that relies on a double-bootstrap step to produce a non-parametric estimate of the distribution of a given estimator of the parameter θ. This estimate includes a smooth curve-fitting algorithm step, for which little description is available from the current paper. The bootstrap non-parametric substitute then plays the role of the actual likelihood, with no correction for the substitution just as in our BCel. Both approaches are convergent, with Monte Carlo simulations exhibiting similar or even identical convergence speeds although [unsurprisingly!] no deep theory is available on the comparative advantage.

An important issue from my perspective is that, while the empirical likelihood approach relies on a choice of identifying constraints that strongly impact the numerical value of the likelihood approximation, the bootstrap version starts directly from a subjectively chosen estimator of θ, which may also impact the numerical value of the likelihood approximation. In some ABC settings, finding a primary estimator of θ may be a real issue or a computational burden. Except when using a preliminary ABC step as in semi-automatic ABC. This would be an interesting crash-test for the BCbl proposal! (This would not necessarily increase the computational cost by a large amount.) In addition, I am not sure the method easily extends to larger collections of summary statistics as those used in ABC, in particular because it necessarily relies on non-parametric estimates, only operating in small enough dimensions where smooth curve-fitting algorithms can be used. Critically, the paper only processes examples with a few parameters.

The comparisons between BCel and BCbl that are produced in the paper show some gain towards BCbl. Obviously, it depends on the respective calibrations of the non-parametric methods and of regular ABC, as well as on the available computing time. I find the population genetic example somewhat puzzling: The paper refers to our composite likelihood to set the moment equations. Since this is a pseudo-likelihood, I wonder how the authors do select their parameter estimates in the double-bootstrap experiment. And for the Ising model, it is not straightforward to conceive of a bootstrap algorithm on an Ising model: (a) how does one subsample pixels and (b) what are the validity guarantees for the estimation procedure.

a bootstrap likelihood approach to Bayesian computation

Posted in Books, R, Statistics, University life with tags , , , , , , , , on October 16, 2014 by xi'an

This paper by Weixuan Zhu, Juan Miguel Marín [from Carlos III in Madrid, not to be confused with Jean-Michel Marin, from Montpellier!], and Fabrizio Leisen proposes an alternative to our 2013 PNAS paper with Kerrie Mengersen and Pierre Pudlo on empirical likelihood ABC, or BCel. The alternative is based on Davison, Hinkley and Worton’s (1992) bootstrap likelihood, which relies on a double-bootstrap to produce a non-parametric estimate of the distribution of a given estimator of the parameter θ. Including a smooth curve-fitting algorithm step, for which not much description is available from the paper.

“…in contrast with the empirical likelihood method, the bootstrap likelihood doesn’t require any set of subjective constrains taking advantage from the bootstrap methodology. This makes the algorithm an automatic and reliable procedure where only a few parameters need to be specified.”

The spirit is indeed quite similar to ours in that a non-parametric substitute plays the role of the actual likelihood, with no correction for the substitution. Both approaches are convergent, with similar or identical convergence speeds. While the empirical likelihood relies on a choice of parameter identifying constraints, the bootstrap version starts directly from the [subjectively] chosen estimator of θ. For it indeed needs to be chosen. And computed.

“Another benefit of using the bootstrap likelihood (…) is that the construction of bootstrap likelihood could be done once and not at every iteration as the empirical likelihood. This leads to significant improvement in the computing time when different priors are compared.”

This is an improvement that could apply to the empirical likelihood approach, as well, once a large enough collection of likelihood values has been gathered. But only in small enough dimensions where smooth curve-fitting algorithms can operate. The same criticism applying to the derivation of a non-parametric density estimate for the distribution of the estimator of θ. Critically, the paper only processes examples with a few parameters.

In the comparisons between BCel and BCbl that are produced in the paper, the gain is indeed towards BCbl. Since this paper is mostly based on examples and illustrations, not unlike ours, I would like to see more details on the calibration of the non-parametric methods and of regular ABC, as well as on the computing time. And the variability of both methods on more than a single Monte Carlo experiment.

I am however uncertain as to how the authors process the population genetic example. They refer to the composite likelihood used in our paper to set the moment equations. Since this is not the true likelihood, how do the authors select their parameter estimates in the double-bootstrap experiment? The inclusion of Crakel’s and Flegal’s (2013) bivariate Beta, is somewhat superfluous as this example sounds to me like an artificial setting.

In the case of the Ising model, maybe the pre-processing step in our paper with Matt Moores could be compared with the other algorithms. In terms of BCbl, how does the bootstrap operate on an Ising model, i.e. (a) how does one subsample pixels and (b)what are the validity guarantees?

A test that would be of interest is to start from a standard ABC solution and use this solution as the reference estimator of θ, then proceeding to apply BCbl for that estimator. Given that the reference table would have to be produced only once, this would not necessarily increase the computational cost by a large amount…