Archive for ABC model choice

SPA 2015 Oxford

Posted in pictures, Statistics, Travel, University life with tags , , , , , , , , , , , , , , , on July 14, 2015 by xi'an

Today I gave a talk on Approximate Bayesian model choice via random forests at the yearly SPA (Stochastic Processes and their Applications) 2015 conference, taking place in Oxford (a nice town near Warwick) this year. In Keble College more precisely. The slides are below and while they are mostly repetitions of earlier slides, there is a not inconsequential novelty in the presentation, namely that I included our most recent and current perspective on ABC model choice. Indeed, when travelling to Montpellier two weeks ago, we realised that there was a way to solve our posterior probability conundrum!

campusDespite the heat wave that rolled all over France that week, we indeed figured out a way to estimate the posterior probability of the selected (MAP) model, way that we had deemed beyond our reach in previous versions of the talk and of the paper. The fact that we could not provide an estimate of this posterior probability and had to rely instead on a posterior expected loss was one of the arguments used by the PNAS reviewers in rejecting the paper. While the posterior expected loss remains a quantity worth approximating and reporting, the idea that stemmed from meeting together in Montpellier is that (i) the posterior probability of the MAP is actually related to another posterior loss, when conditioning on the observed summary statistics and (ii) this loss can be itself estimated via a random forest, since it is another function of the summary statistics. A posteriori, this sounds trivial but we had to have a new look at the problem to realise that using ABC samples was not the only way to produce an estimate of the posterior probability! (We are now working on the revision of the paper for resubmission within a few week… Hopefully before JSM!)

Bureau international des poids et mesures

Posted in Books, Statistics, University life with tags , , , , , , , , , , on June 15, 2015 by xi'an

Today, I am taking part in a meeting in Paris, for an exotic change!, at the Bureau international des poids et mesures (BIPM), which looks after a universal reference for measurements. For instance, here is its definition of the kilogram:

The unit of mass, the kilogram, is the mass of the international prototype of the kilogram kept in air under three bell jars at the BIPM. It is a cylinder made of an alloy for which the mass fraction of platinum is 90 % and the mass fraction of iridium is 10 %.

And the BIPM is thus interested in the uncertainty associated with such measurements. Hence the workshop on measurement uncertainties. Tony O’Hagan will also be giving a talk in a session that opposes frequentist and Bayesian approaches, even though I decided to introduce ABC as it seems to me to be a natural notion for measurement problems (as far as I can tell from my prior on measurement problems).

likelihood-free model choice

Posted in Books, pictures, Statistics, University life, Wines with tags , , , , , , , on March 27, 2015 by xi'an

Jean-Michel Marin, Pierre Pudlo and I just arXived a short review on ABC model choice, first version of a chapter for the incoming Handbook of Approximate Bayesian computation edited by Scott Sisson, Yannan Fan, and Mark Beaumont. Except for a new analysis of a Human evolution scenario, this survey mostly argues for the proposal made in our recent paper on the use of random forests and [also argues] about the lack of reliable approximations to posterior probabilities. (Paper that was rejected by PNAS and that is about to be resubmitted. Hopefully with a more positive outcome.) The conclusion of the survey is  that

The presumably most pessimistic conclusion of this study is that the connections between (i) the true posterior probability of a model, (ii) the ABC version of this probability, and (iii) the random forest version of the above, are at best very loose. This leaves open queries for acceptable approximations of (i), since the posterior predictive error is instead an error assessment for the ABC RF model choice procedure. While a Bayesian quantity that can be computed at little extra cost, it does not necessarily compete with the posterior probability of a model.

reflecting my hope that we can eventually come up with a proper approximation to the “true” posterior probability…

brief stop in Edinburgh

Posted in Mountains, pictures, Statistics, Travel, University life, Wines with tags , , , , , , , , on January 24, 2015 by xi'an

Edinburgh1Yesterday, I was all too briefly in Edinburgh for a few hours, to give a seminar in the School of Mathematics, on the random forests approach to ABC model choice (that was earlier rejected). (The slides are almost surely identical to those used at the NIPS workshop.) One interesting question at the end of the talk was on the potential bias in the posterior predictive expected loss, bias against some model from the collection of models being evaluated for selection. In the sense that the array of summaries used by the random forest could fail to capture features of a particular model and hence discriminate against it. While this is correct, there is no fundamental difference with implementing a posterior probability based on the same summaries. And the posterior predictive expected loss offers the advantage of testing, that is, for representative simulations from each model, of returning the corresponding model prediction error to highlight poor performances on some models. A further discussion over tea led me to ponder whether or not we could expand the use of random forests to Bayesian quantile regression. However, this would imply a monotonicity structure on a collection of random forests, which sounds daunting…

My stay in Edinburgh was quite brief as I drove to the Highlands after the seminar, heading to Fort William, Although the weather was rather ghastly, the traffic was fairly light and I managed to get there unscathed, without hitting any of the deer of Rannoch Mor (saw one dead by the side of the road though…) or the snow banks of the narrow roads along Loch Lubnaig. And, as usual, it still was a pleasant feeling to drive through those places associated with climbs and hikes, Crianlarich, Tyndrum, Bridge of Orchy, and Glencoe. And to get in town early enough to enjoy a quick dinner at The Grog & Gruel, reflecting I must have had half a dozen dinners there with friends (or not) over the years. And drinking a great heather ale to them!

not Bayesian enough?!

Posted in Books, Statistics, University life with tags , , , , , , , on January 23, 2015 by xi'an

Elm tree in the park, Parc de Sceaux, Nov. 22, 2011Our random forest paper was alas rejected last week. Alas because I think the approach is a significant advance in ABC methodology when implemented for model choice, avoiding the delicate selection of summary statistics and the report of shaky posterior probability approximation. Alas also because the referees somewhat missed the point, apparently perceiving random forests as a way to project a large collection of summary statistics on a limited dimensional vector as in the Read Paper of Paul Fearnhead and Dennis Prarngle, while the central point in using random forests is the avoidance of a selection or projection of summary statistics.  They also dismissed ou approach based on the argument that the reduction in error rate brought by random forests over LDA or standard (k-nn) ABC is “marginal”, which indicates a degree of misunderstanding of what the classification error stand for in machine learning: the maximum possible gain in supervised learning with a large number of classes cannot be brought arbitrarily close to zero. Last but not least, the referees did not appreciate why we mostly cannot trust posterior probabilities produced by ABC model choice and hence why the posterior error loss is a valuable and almost inevitable machine learning alternative, dismissing the posterior expected loss as being not Bayesian enough (or at all), for “averaging over hypothetical datasets” (which is a replicate of Jeffreys‘ famous criticism of p-values)! Certainly a first time for me to be rejected based on this argument!

ABC by population annealing

Posted in Statistics, University life with tags , , , , , , , , on January 6, 2015 by xi'an

The paper “Bayesian Parameter Inference and Model Selection by Population Annealing in System Biology” by Yohei Murakami got published in PLoS One last August but I only became aware of it when ResearchGate pointed it out to me [by mentioning one of our ABC papers was quoted there].

“We are recommended to try a number of annealing schedules to check the influence of the schedules on the simulated data (…) As a whole, the simulations with the posterior parameter ensemble could, not only reproduce the data used for parameter inference, but also capture and predict the data which was not used for parameter inference.”

Population annealing is a notion introduced by Y Iba, the very same IBA who introduced the notion of population Monte Carlo that we studied in subsequent papers. It reproduces the setting found in many particle filter papers of a sequence of (annealed or rather tempered) targets ranging from an easy (i.e., almost flat) target to the genuine target, and of an update of a particle set by MCMC moves and reweighing. I actually have trouble perceiving the difference with other sequential Monte Carlo schemes as those exposed in Del Moral, Doucet and Jasra (2006, Series B). And the same is true of the ABC extension covered in this paper. (Where the annealed intermediate targets correspond to larger tolerances.) This sounds like a traditional ABC-SMC algorithm. Without the adaptive scheme on the tolerance ε found e.g. in Del Moral et al., since the sequence is set in advance. [However, the discussion about the implementation includes the above quote that suggests a vague form of cross-validated tolerance construction]. The approximation of the marginal likelihood also sounds standard, the marginal being approximated by the proportion of accepted pseudo-samples. Or more exactly by the sum of the SMC weights at the end of the annealing simulation. This actually raises several questions: (a) this estimator is always between 0 and 1, while the marginal likelihood is not restricted [but this is due to a missing 1/ε in the likelihood estimate that cancels from both numerator and denominator]; (b) seeing the kernel as a non-parametric estimate of the likelihood led me to wonder why different ε could not be used in different models, in that the pseudo-data used for each model under comparison differs. If we were in a genuine non-parametric setting the bandwidth would be derived from the pseudo-data.

“Thus, Bayesian model selection by population annealing is valid.”

The discussion about the use of ABC population annealing somewhat misses the point of using ABC, which is to approximate the genuine posterior distribution, to wit the above quote: that the ABC Bayes factors favour the correct model in the simulation does not tell anything about the degree of approximation wrt the original Bayes factor. [The issue of non-consistent Bayes factors does not apply here as there is no summary statistic applied to the few observations in the data.] Further, the magnitude of the variability of the values of this Bayes factor as ε varies, from 1.3 to 9.6, mostly indicates that the numerical value is difficult to trust. (I also fail to explain the huge jump in Monte Carlo variability from 0.09 to 1.17 in Table 1.) That this form of ABC-SMC improves upon the basic ABC rejection approach is clear. However it needs to build some self-control to avoid arbitrary calibration steps and reduce the instability of the final estimates.

“The weighting function is set to be large value when the observed data and the simulated data are ‘‘close’’, small value when they are ‘‘distant’’, and constant when they are ‘‘equal’’.”

The above quote is somewhat surprising as the estimated likelihood f(xobs|xobs,θ) is naturally constant when xobs=xsim… I also failed to understand how the model intervened in the indicator function used as a default ABC kernel

ABC à Montréal

Posted in Kids, pictures, Running, Statistics, Travel, University life with tags , , , , , , , , , , , , , , , , on December 13, 2014 by xi'an

Montreal1So today was the NIPS 2014 workshop, “ABC in Montréal“, which started with a fantastic talk by Juliane Liepe on some exciting applications of ABC to the migration of immune cells, with the analysis of movies involving those cells acting to heal a damaged fly wing and a cut fish tail. Quite amazing videos, really. (With the great entry line of ‘We have all cut  a finger at some point in our lives’!) The statistical model behind those movies was a random walk on a grid, with different drift and bias features that served as model characteristics. Frank Wood managed to deliver his talk despite a severe case of food poisoning, with a great illustration of probabilistic programming that made me understand (at last!) the very idea of probabilistic programming. And  Vikash Mansinghka presented some applications in image analysis. Those two talks led me to realise why probabilistic programming was so close to ABC, with a programming touch! Hence why I was invited to talk today! Then Dennis Prangle exposed his latest version of lazy ABC, that I have already commented on the ‘Og, somewhat connected with our delayed acceptance algorithm, to the point that maybe something common can stem out of the two notions. Michael Blum ended the day with provocative answers to the provocative question of Ted Meeds as to whether or not machine learning needed ABC (Ans. No!) and whether or not machine learning could help ABC (Ans. ???). With an happily mix-up between mechanistic and phenomenological models that helped generating discussion from the floor.

The posters were also of much interest, with calibration as a distance measure by Michael Guttman, in continuation of the poster he gave at MCMski, Aaron Smith presenting his work with Luke Bornn, Natesh Pillai and Dawn Woodard, on why a single pseudo-sample is enough for ABC efficiency. This gave me the opportunity to discuss with him the apparent contradiction with the result of Kryz Łatunsziński and Anthony Lee about the geometric convergence of ABC-MCMC only attained with a random number of pseudo-samples… And to wonder if there is a geometric versus binomial dilemma in this setting, Namely, whether or not simulating pseudo-samples until one is accepted would be more efficient than just running one and discarding it in case it is too far. So, although the audience was not that large (when compared with the other “ABC in…” and when considering the 2500+ attendees at NIPS over the week!), it was a great day where I learned a lot, did not have a doze during talks (!), [and even had an epiphany of sorts at the treadmill when I realised I just had to take longer steps to reach 16km/h without hyperventilating!] So thanks to my fellow organisers, Neil D Lawrence, Ted Meeds, Max Welling, and Richard Wilkinson for setting the program of that day! And, by the way, where’s the next “ABC in…”?! (Finland, maybe?)

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