Archive for ABC validation

exciting week[s]

Posted in Mountains, pictures, Running, Statistics with tags , , , , , , , , , , , , , , on June 27, 2017 by xi'an

The past week was quite exciting, despite the heat wave that hit Paris and kept me from sleeping and running! First, I made a two-day visit to Jean-Michel Marin in Montpellier, where we discussed the potential Peer Community In Computational Statistics (PCI Comput Stats) with the people behind PCI Evol Biol at INRA, Hopefully taking shape in the coming months! And went one evening through a few vineyards in Saint Christol with Jean-Michel and Arnaud. Including a long chat with the owner of Domaine Coste Moynier. [Whose domain includes the above parcel with views of Pic Saint-Loup.] And last but not least! some work planning about approximate MCMC.

On top of this, we submitted our paper on ABC with Wasserstein distances [to be arXived in an extended version in the coming weeks], our revised paper on ABC consistency thanks to highly constructive and comments from the editorial board, which induced a much improved version in my opinion, and we received a very positive return from JCGS for our paper on weak priors for mixtures! Next week should be exciting as well, with BNP 11 taking place in downtown Paris, at École Normale!!!

Approximate Bayesian computation via sufficient dimension reduction

Posted in Statistics, University life with tags , , , , , on August 26, 2016 by xi'an

“One of our contribution comes from the mathematical analysis of the consequence of conditioning the parameters of interest on consistent statistics and intrinsically inconsistent statistics”

Xiaolong Zhong and Malay Ghosh have just arXived an ABC paper focussing on the convergence of the method. And on the use of sufficient dimension reduction techniques for the construction of summary statistics. I had not heard of this approach before so read the paper with interest. I however regret that the paper does not link with the recent consistency results of Liu and Fearnhead and of Daniel Frazier, Gael Martin, Judith Rousseau and myself. When conditioning upon the MLE [or the posterior mean] as the summary statistic, Theorem 1 states that the Bernstein-von Mises theorem holds, missing a limit in the tolerance ε. And apparently missing conditions on the speed of convergence of this tolerance to zero although the conditioning event involves the true value of the parameter. This makes me wonder at the relevance of the result. The part about partial posteriors and the characterisation of limiting posterior distributions stats with the natural remark that the mean of the summary statistic must identify the whole parameter θ to achieve consistency, a point central to our 2014 JRSS B paper. The authors suggest using a support vector machine to derive the summary statistics, an idea already exploited by Heiko Strathmann et al.. There is no consistency result of relevance for ABC in that second and final part, which ends up rather abruptly. Overall, while the paper contributes to the current reflection on the convergence properties of ABC, the lack of scaling of the tolerance ε calls for further investigations.

Inference for stochastic simulation models by ABC

Posted in Books, Statistics, University life with tags , , , , , on February 13, 2015 by xi'an

Hartig et al. published a while ago (2011) a paper  in Ecology Letters entitled “Statistical inference for stochastic simulation models – theory and application”, which is mostly about ABC. (Florian Hartig pointed out the paper to me in a recent blog comment. about my discussion of the early parts of Guttman and Corander’s paper.) The paper is largely a tutorial and it reminds the reader about related methods like indirect inference and methods of moments. The authors also insist on presenting ABC as a particular case of likelihood approximation, whether non-parametric or parametric. Making connections with pseudo-likelihood and pseudo-marginal approaches. And including a discussion of the possible misfit of the assumed model, handled by an external error model. And also introducing the notion of informal likelihood (which could have been nicely linked with empirical likelihood). A last class of approximations presented therein is called rejection filters and reminds me very much of Ollie Ratman’s papers.

“Our general aim is to find sufficient statistics that are as close to minimal sufficiency as possible.” (p.819)

As in other ABC papers, and as often reported on this blog, I find the stress on sufficiency a wee bit too heavy as those models calling for approximation almost invariably do not allow for any form of useful sufficiency. Hence the mathematical statistics notion of sufficiency is mostly useless in such settings.

“A basic requirement is that the expectation value of the point-wise approximation of p(Sobs|φ) must be unbiased” (p.823)

As stated above the paper is mostly in tutorial mode, for instance explaining what MCMC and SMC methods are. As illustrated by the above figure. There is however a final and interesting discussion section on the impact of estimating the likelihood function at different values of the parameter. However, the authors seem to focus solely on pseudo-marginal results to validate this approximation, hence on unbiasedness, which does not work for most ABC approaches that I know. And for the approximations listed in the survey. Actually, it would be quite beneficial to devise a cheap tool to assess the bias or extra-variation due to the use of approximative techniques like ABC… A sort of 21st Century bootstrap?!

Bayesian optimization for likelihood-free inference of simulator-based statistical models

Posted in Books, Statistics, University life with tags , , , , on January 29, 2015 by xi'an

Michael Gutmann and Jukka Corander arXived this paper two weeks ago. I read part of it (mostly the extended introduction part) on the flight from Edinburgh to Birmingham this morning. I find the reflection it contains on the nature of the ABC approximation quite deep and thought-provoking.  Indeed, the major theme of the paper is to visualise ABC (which is admittedly shorter than “likelihood-free inference of simulator-based statistical models”!) as a regular computational method based on an approximation of the likelihood function at the observed value, yobs. This includes for example Simon Wood’s synthetic likelihood (who incidentally gave a talk on his method while I was in Oxford). As well as non-parametric versions. In both cases, the approximations are based on repeated simulations of pseudo-datasets for a given value of the parameter θ, either to produce an estimation of the mean and covariance of the sampling model as a function of θ or to construct genuine estimates of the likelihood function. As assumed by the authors, this calls for a small dimension θ. This approach actually allows for the inclusion of the synthetic approach as a lower bound on a non-parametric version.

In the case of Wood’s synthetic likelihood, two questions came to me:

  • the estimation of the mean and covariance functions is usually not smooth because new simulations are required for each new value of θ. I wonder how frequent is the case where we can always use the same basic random variates for all values of θ. Because it would then give a smooth version of the above. In the other cases, provided the dimension is manageable, a Gaussian process could be first fitted before using the approximation. Or any other form of regularization.
  • no mention is made [in the current paper] of the impact of the parametrization of the summary statistics. Once again, a Cox transform could be applied to each component of the summary for a better proximity of/to the normal distribution.

When reading about a non-parametric approximation to the likelihood (based on the summaries), the questions I scribbled on the paper were:

  • estimating a complete density when using this estimate at the single point yobs could possibly be superseded by a more efficient approach.
  • the authors study a kernel that is a function of the difference or distance between the summaries and which is maximal at zero. This is indeed rather frequent in the ABC literature, but does it impact the convergence properties of the kernel estimator?
  • the estimation of the tolerance, which happens to be a bandwidth in that case, does not appear to be processed in this paper, which could explain for very low probabilities of acceptance mentioned in the paper.
  • I am lost as to why lower bounds on likelihoods are relevant here. Unless this is intended for ABC maximum likelihood estimation.

Guttmann and Corander also comment on the first point, through the cost of producing a likelihood estimator. They therefore suggest to resort to regression and to avoid regions of low estimated likelihood. And rely on Bayesian optimisation. (Hopefully to be commented later.)