Archive for ABC

ACDC versus ABC

Posted in Books, Kids, pictures, Statistics, Travel with tags , , , , , on June 12, 2017 by xi'an

At the Bayes, Fiducial and Frequentist workshop last month, I discussed with the authors of this newly arXived paper, Approximate confidence distribution computing, Suzanne Thornton and Min-ge Xie. Which they abbreviate as ACC and not as ACDC. While I have discussed the notion of confidence distribution in some earlier posts, this paper aims at producing proper frequentist coverage within a likelihood-free setting. Given the proximity with our recent paper on the asymptotics of ABC, as well as with Li and Fearnhead (2016) parallel endeavour, it is difficult (for me) to spot the actual distinction between ACC and ABC given that we also achieve (asymptotically) proper coverage when the limiting ABC distribution is Gaussian, which is the case for a tolerance decreasing quickly enough to zero (in the sample size).

“Inference from the ABC posterior will always be difficult to justify within a Bayesian framework.”

Indeed the ACC setting is eerily similar to ABC apart from the potential of the generating distribution to be data dependent. (Which is fine when considering that the confidence distributions have no Bayesian motivation but are a tool to ensure proper frequentist coverage.) That it is “able to offer theoretical support for ABC” (p.5) is unclear to me, given both this data dependence and the constraints it imposes on the [sampling and algorithmic] setting. Similarly, I do not understand how the authors “are not committing the error of doubly using the data” (p.5) and why they should be concerned about it, standing outside the Bayesian framework. If the prior involves the data as in the Cauchy location example, it literally uses the data [once], followed by an ABC comparison between simulated and actual data, that uses the data [a second time].

“Rather than engaging in a pursuit to define a moving target such as [a range of posterior distributions], ACC maintains a consistently clear frequentist interpretation (…) and thereby offers a consistently cohesive interpretation of likelihood-free methods.”

The frequentist coverage guarantee comes from a bootstrap-like assumption that [with tolerance equal to zero] the distribution of the ABC/ACC/ACDC random parameter around an estimate of the parameter given the summary statistic is identical to the [frequentist] distribution of this estimate around the true parameter [given the true parameter, although this conditioning makes no sense outside a Bayesian framework]. (There must be a typo in the paper when the authors define [p.10] the estimator as minimising the derivative of the density of the summary statistic, while still calling it an MLE.) That this bootstrap-like assumption holds is established (in Theorem 1) under a CLT on this MLE and assumptions on the data-dependent proposal that connect it to the density of the summary statistic. Connection that seem to imply a data-dependence as well as a certain knowledge about this density. What I find most surprising in this derivation is the total absence of conditions or even discussion on the tolerance level which, as we have shown, is paramount to the validation or invalidation of ABC inference. It sounds like the authors of Approximate confidence distribution computing are setting ε equal to zero for those theoretical derivations. While in practice they apply rules [for choosing ε] they do not voice out, but which result in very different acceptance rates for the ACC version they oppose to an ABC version. (In all illustrations, it seems that ε=0.1, which does not make much sense.) All in all, I am thus rather skeptical about the practical implications of the paper in that it seems to achieve confidence guarantees by first assuming proper if implicit choices of summary statistics and parameter generating distribution.

fast ε-free ABC

Posted in Books, Mountains, pictures, Running, Statistics, Travel, University life with tags , , , , , , , , , on June 8, 2017 by xi'an

Last Fall, George Papamakarios and Iain Murray from Edinburgh arXived an ABC paper on fast ε-free inference on simulation models with Bayesian conditional density estimation, paper that I missed. The idea there is to approximate the posterior density by maximising the likelihood associated with a parameterised family of distributions on θ, conditional on the associated x. The data being then the ABC reference table. The family chosen there is a mixture of K Gaussian components, which parameters are then estimated by a (Bayesian) neural network using x as input and θ as output. The parameter values are simulated from an adaptive proposal that aims at approximating the posterior better and better. As in population Monte Carlo, actually. Except for the neural network part, which I fail to understand why it makes a significant improvement when compared with EM solutions. The overall difficulty with this approach is that I do not see a way out of the curse of dimensionality: when the dimension of θ increases, the approximation to the posterior distribution of θ does deteriorate, even in the best of cases, as any other non-parametric resolution. It would have been of (further) interest to see a comparison with a most rudimentary approach, namely the one we proposed based on empirical likelihoods.

efficient acquisition rules for ABC

Posted in pictures, Statistics, University life with tags , , , , , , , , on June 5, 2017 by xi'an

A few weeks ago, Marko Järvenpää, Michael Gutmann, Aki Vehtari and Pekka Marttinen arXived a paper on sampling design for ABC that reminded me of presentations Michael gave at NIPS 2014 and in Banff last February. The main notion is that, when the simulation from the model is hugely expensive, random sampling does not make sense.

“While probabilistic modelling has been used to accelerate ABC inference, and strategies have been proposed for selecting which parameter to simulate next, little work has focused on trying to quantify the amount of uncertainty in the estimator of the ABC posterior density itself.”

The above question  is obviously interesting, if already considered in the literature for it seems to focus on the Monte Carlo error in ABC, addressed for instance in Fearnhead and Prangle (2012), Li and Fearnhead (2016) and our paper with David Frazier, Gael Martin, and Judith Rousseau. With corresponding conditions on the tolerance and the number of simulations to relegate Monte Carlo error to a secondary level. And the additional remark that the (error free) ABC distribution itself is not the ultimate quantity of interest. Or the equivalent (?) one that ABC is actually an exact Bayesian method on a completed space.

The paper initially confused me for a section on the very general formulation of ABC posterior approximation and error in this approximation. And simulation design for minimising this error. It confused me as it sounded too vague but only for a while as the remaining sections appear to be independent. The operational concept of the paper is to assume that the discrepancy between observed and simulated data, when perceived as a random function of the parameter θ, is a Gaussian process [over the parameter space]. This modelling allows for a prediction of the discrepancy at a new value of θ, which can be chosen as maximising the variance of the likelihood approximation. Or more precisely of the acceptance probability. While the authors report improved estimation of the exact posterior, I find no intuition as to why this should be the case when focussing on the discrepancy, especially because small discrepancies are associated with parameters approximately generated from the posterior.

postprocessing for ABC

Posted in Books, Statistics with tags , , , , on June 1, 2017 by xi'an

Two weeks ago, G.S. Rodrigues, Dennis Prangle and Scott Sisson have recently arXived a paper on recalibrating ABC output to make it correctly calibrated (in the frequentist sense). As in earlier papers, it takes advantage of the fact that the tail posterior probability should be uniformly distributed at the true value of the [simulated] parameter behind the [simulated] data. And as in Prangle et al. (2014), relies on a copula representation. The main notion is that marginals posteriors can be reasonably approximated by non-parametric kernel estimators, which means that an F⁰oF⁻¹ transform can be applied to an ABC reference table in a fully non-parametric extension of Beaumont et al.  (2002). Besides the issue that F is an approximation, I wonder about the computing cost of this approach, given that computing the post-processing transforms comes at a cost of O(pT²) when p is the dimension of the parameter and T the size of the ABC learning set… One question that came to me while discussing the paper with Jean-Michel Marin is why one would use F⁻¹(θ¹|s) instead of directly a uniform U(0,1) since in theory this should be a uniform U(0,1).


Posted in Books, pictures, Statistics, Travel, University life with tags , , , , on May 17, 2017 by xi'an

Ritabrata Dutta, Marcel Schöengens, Jukka-Pekka Onnela, and Antonietta Mira recently put a new ABC software on-line, called ABCpy for ABC with Python. The software aims at  an automated parallelisation of ABC runs, requiring only code to generate from the (generative) model and the choice of summary statistics and of associated distance. Alternatively an approximate likelihood (as in synthetic likelihood) can be used. The tolerance ε is chosen as a percentile of the prior predictive distribution on the distance. The versions of ABC found in ABCpy are

  1. Population Monte Carlo for ABC (PMCABC);
  2. sequential Monte Carlo ABC (ABC-SMC);
  3. replenishment Sequential Monte Carlo ABC (RSMC-ABC);
  4. adaptive Population Monte Carlo ABC (APMCABC);
  5. ABC with subset simulation (ABCsubsim); and
  6. simulated annealing ABC (SABC)

Anto mentioned ABCpy to me while in Harvard last week and I have not tested the program (my only brush with Python being the occasional call to latex2wp for SeriesB’log). And obviously, writing a blog about Monte (Carlo and) Python makes a link to the Monty Pythons irresistible:

talk at Trinity College

Posted in pictures, Statistics, Travel, University life with tags , , , , , , , on May 7, 2017 by xi'an

Tomorrow noon, I will give a talk at Trinity College Dublin on the asymptotic properties of ABC. (Here are the slides from the talk I gave in Berlin last month.)

ABC postdoc in Olso

Posted in Kids, Mountains, pictures, Travel, University life with tags , , , , , , , , on April 26, 2017 by xi'an

Jukka Corander sent me the announcement that he is opening a 3 year postdoctoral position at the University of Oslo, to work with him and his team on ABC projects. This sounds quite an exciting offer, plus gives the nominee the opportunity to live in the most enjoyable city of Oslo for several years in fairly comfy conditions! The deadline is May 31. (If I was at a stage of my career where applying made sense, I would definitely candidate. Not even waiting for the outcome of the French elections on May 7!)