Archive for ABC

ABC and cosmology

Posted in Books, pictures, Statistics, University life with tags , , , , , , , , , , on May 4, 2015 by xi'an

Two papers appeared on arXiv in the past two days with the similar theme of applying ABC-PMC [one version of which we developed with Mark Beaumont, Jean-Marie Cornuet, and Jean-Michel Marin in 2009] to cosmological problems. (As a further coincidence, I had just started refereeing yet another paper on ABC-PMC in another astronomy problem!) The first paper cosmoabc: Likelihood-free inference via Population Monte Carlo Approximate Bayesian Computation by Ishida et al. [“et al” including Ewan Cameron] proposes a Python ABC-PMC sampler with applications to galaxy clusters catalogues. The paper is primarily a description of the cosmoabc package, including code snapshots. Earlier occurrences of ABC in cosmology are found for instance in this earlier workshop, as well as in Cameron and Pettitt earlier paper. The package offers a way to evaluate the impact of a specific distance, with a 2D-graph demonstrating that the minimum [if not the range] of the simulated distances increases with the parameters getting away from the best parameter values.

“We emphasis [sic] that the choice of the distance function is a crucial step in the design of the ABC algorithm and the reader must check its properties carefully before any ABC implementation is attempted.” E.E.O. Ishida et al.

The second [by one day] paper Approximate Bayesian computation for forward modelling in cosmology by Akeret et al. also proposes a Python ABC-PMC sampler, abcpmc. With fairly similar explanations: maybe both samplers should be compared on a reference dataset. While I first thought the description of the algorithm was rather close to our version, including the choice of the empirical covariance matrix with the factor 2, it appears it is adapted from a tutorial in the Journal of Mathematical Psychology by Turner and van Zandt. One out of many tutorials and surveys on the ABC method, of which I was unaware, but which summarises the pre-2012 developments rather nicely. Except for missing Paul Fearnhead’s and Dennis Prangle’s semi-automatic Read Paper. In the abcpmc paper, the update of the covariance matrix is the one proposed by Sarah Filippi and co-authors, which includes an extra bias term for faraway particles.

“For complex data, it can be difficult or computationally expensive to calculate the distance ρ(x; y) using all the information available in x and y.” Akeret et al.

In both papers, the role of the distance is stressed as being quite important. However, the cosmoabc paper uses an L1 distance [see (2) therein] in a toy example without normalising between mean and variance, while the abcpmc paper suggests using a Mahalanobis distance that turns the d-dimensional problem into a comparison of one-dimensional projections.

extending ABC to high dimensions via Gaussian copula

Posted in Books, pictures, Statistics, Travel, Uncategorized, University life with tags , , , on April 28, 2015 by xi'an

plane2Li, Nott, Fan, and Sisson arXived last week a new paper on ABC methodology that I read on my way to Warwick this morning. The central idea in the paper is (i) to estimate marginal posterior densities for the components of the model parameter by non-parametric means; and (ii) to consider all pairs of components to deduce the correlation matrix R of the Gaussian (pdf) transform of the pairwise rank statistic. From those two low-dimensional estimates, the authors derive a joint Gaussian-copula distribution by using inverse  pdf transforms and the correlation matrix R, to end up with a meta-Gaussian representation

f(\theta)=\dfrac{1}{|R|^{1/2}}\exp\{\eta^\prime(I-R^{-1})\eta/2\}\prod_{i=1}^p g_i(\theta_i)

where the η’s are the Gaussian transforms of the inverse-cdf transforms of the θ’s,that is,


Or rather


given that the g’s are estimated.

This is obviously an approximation of the joint in that, even in the most favourable case when the g’s are perfectly estimated, and thus the components perfectly Gaussian, the joint is not necessarily Gaussian… But it sounds quite interesting, provided the cost of running all those transforms is not overwhelming. For instance, if the g’s are kernel density estimators, they involve sums of possibly a large number of terms.

One thing that bothers me in the approach, albeit mostly at a conceptual level for I realise the practical appeal is the use of different summary statistics for approximating different uni- and bi-dimensional marginals. This makes for an incoherent joint distribution, again at a conceptual level as I do not see immediate practical consequences… Those local summaries also have to be identified, component by component, which adds another level of computational cost to the approach, even when using a semi-automatic approach as in Fernhead and Prangle (2012). Although the whole algorithm relies on a single reference table.

The examples in the paper are (i) the banana shaped “Gaussian” distribution of Haario et al. (1999) that we used in our PMC papers, with a twist; and (ii) a g-and-k quantile distribution. The twist in the banana (!) is that the banana distribution is the prior associated with the mean of a Gaussian observation. In that case, the meta-Gaussian representation seems to hold almost perfectly, even in p=50 dimensions. (If I remember correctly, the hard part in analysing the banana distribution was reaching the tails, which are extremely elongated in at least one direction.) For the g-and-k quantile distribution, the same holds, even for a regular ABC. What seems to be of further interest would be to exhibit examples where the meta-Gaussian is clearly an approximation. If such cases exist.

scalable Bayesian inference for the inverse temperature of a hidden Potts model

Posted in Books, R, Statistics, University life with tags , , , , , , , , , , , on April 7, 2015 by xi'an

Brisbane, summer 2008Matt Moores, Tony Pettitt, and Kerrie Mengersen arXived a paper yesterday comparing different computational approaches to the processing of hidden Potts models and of the intractable normalising constant in the Potts model. This is a very interesting paper, first because it provides a comprehensive survey of the main methods used in handling this annoying normalising constant Z(β), namely pseudo-likelihood, the exchange algorithm, path sampling (a.k.a., thermal integration), and ABC. A massive simulation experiment with individual simulation times up to 400 hours leads to select path sampling (what else?!) as the (XL) method of choice. Thanks to a pre-computation of the expectation of the sufficient statistic E[S(Z)|β].  I just wonder why the same was not done for ABC, as in the recent Statistics and Computing paper we wrote with Matt and Kerrie. As it happens, I was actually discussing yesterday in Columbia of potential if huge improvements in processing Ising and Potts models by approximating first the distribution of S(X) for some or all β before launching ABC or the exchange algorithm. (In fact, this is a more generic desiderata for all ABC methods that simulating directly if approximately the summary statistics would being huge gains in computing time, thus possible in final precision.) Simulating the distribution of the summary and sufficient Potts statistic S(X) reduces to simulating this distribution with a null correlation, as exploited in Cucala and Marin (2013, JCGS, Special ICMS issue). However, there does not seem to be an efficient way to do so, i.e. without reverting to simulating the entire grid X…

MCMskv, Lenzerheide, Jan. 5-7, 2016

Posted in Kids, Mountains, pictures, R, Statistics, Travel, University life with tags , , , , , , , , , , , , , , , , on March 31, 2015 by xi'an

moonriseFollowing the highly successful [authorised opinion!, from objective sources] MCMski IV, in Chamonix last year, the BayesComp section of ISBA has decided in favour of a two-year period, which means the great item of news that next year we will meet again for MCMski V [or MCMskv for short], this time on the snowy slopes of the Swiss town of Lenzerheide, south of Zürich. The committees are headed by the indefatigable Antonietta Mira and Mark Girolami. The plenary speakers have already been contacted and Steve Scott (Google), Steve Fienberg (CMU), David Dunson (Duke), Krys Latuszynski (Warwick), and Tony Lelièvre (Mines, Paris), have agreed to talk. Similarly, the nine invited sessions have been selected and will include Hamiltonian Monte Carlo,  Algorithms for Intractable Problems (ABC included!), Theory of (Ultra)High-Dimensional Bayesian Computation, Bayesian NonParametrics, Bayesian Econometrics,  Quasi Monte Carlo, Statistics of Deep Learning, Uncertainty Quantification in Mathematical Models, and Biostatistics. There will be afternoon tutorials, including a practical session from the Stan team, tutorials for which call is open, poster sessions, a conference dinner at which we will be entertained by the unstoppable Imposteriors. The Richard Tweedie ski race is back as well, with a pair of Blossom skis for the winner!

As in Chamonix, there will be parallel sessions and hence the scientific committee has issued a call for proposals to organise contributed sessions, tutorials and the presentation of posters on particularly timely and exciting areas of research relevant and of current interest to Bayesian Computation. All proposals should be sent to Mark Girolami directly by May the 4th (be with him!).

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…

importance weighting without importance weights [ABC for bandits?!]

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

I did not read very far in the recent arXival by Neu and Bartók, but I got the impression that it was a version of ABC for bandit problems where the probabilities behind the bandit arms are not available but can be generated. Since the stopping rule found in the “Recurrence weighting for multi-armed bandits” is the generation of an arm equal to the learner’s draw (p.5). Since there is no tolerance there, the method is exact (“unbiased”). As no reference is made to the ABC literature, this may be after all a mere analogy…

light and widely applicable MCMC: approximate Bayesian inference for large datasets

Posted in Books, Statistics, University life, Wines with tags , , , , , , , , , , on March 24, 2015 by xi'an

Florian Maire (whose thesis was discussed in this post), Nial Friel, and Pierre Alquier (all in Dublin at some point) have arXived today a paper with the above title, aimed at quickly analysing large datasets. As reviewed in the early pages of the paper, this proposal follows a growing number of techniques advanced in the past years, like pseudo-marginals, Russian roulette, unbiased likelihood estimators. firefly Monte Carlo, adaptive subsampling, sub-likelihoods, telescoping debiased likelihood version, and even our very own delayed acceptance algorithm. (Which is incorrectly described as restricted to iid data, by the way!)

The lightweight approach is based on an ABC idea of working through a summary statistic that plays the role of a pseudo-sufficient statistic. The main theoretical result in the paper is indeed that, when subsampling in an exponential family, subsamples preserving the sufficient statistics (modulo a rescaling) are optimal in terms of distance to the true posterior. Subsamples are thus weighted in terms of the (transformed) difference between the full data statistic and the subsample statistic, assuming they are both normalised to be comparable. I am quite (positively) intrigued by this idea in that it allows to somewhat compare inference based on two different samples. The weights of the subsets are then used in a pseudo-posterior that treats the subset as an auxiliary variable (and the weight as a substitute to the “missing” likelihood). This may sound a wee bit convoluted (!) but the algorithm description is not yet complete: simulating jointly from this pseudo-target is impossible because of the huge number of possible subsets. The authors thus suggest to run an MCMC scheme targeting this joint distribution, with a proposed move on the set of subsets and a proposed move on the parameter set conditional on whether or not the proposed subset has been accepted.

From an ABC perspective, the difficulty in calibrating the tolerance ε sounds more accute than usual, as the size of the subset comes as an additional computing parameter. Bootstrapping options seem impossible to implement in a large size setting.

An MCMC issue with this proposal is that designing the move across the subset space is both paramount for its convergence properties and lacking in geometric intuition. Indeed, two subsets with similar summary statistics may be very far apart… Funny enough, in the representation of the joint Markov chain, the parameter subchain is secondary if crucial to avoid intractable normalising constants. It is also unclear for me from reading the paper maybe too quickly whether or not the separate moves when switching and when not switching subsets retain the proper balance condition for the pseudo-joint to still be the stationary distribution. The stationarity for the subset Markov chain is straightforward by design, but it is not so for the parameter. In case of switched subset, simulating from the true full conditional given the subset would work, but not simulated  by a fixed number L of MCMC steps.

The lightweight technology therein shows its muscles on an handwritten digit recognition example where it beats regular MCMC by a factor of 10 to 20, using only 100 datapoints instead of the 10⁴ original datapoints. While very nice and realistic, this example may be misleading in that 100 digit realisations may be enough to find a tolerable approximation to the true MAP. I was also intrigued by the processing of the probit example, until I realised the authors had integrated the covariate out and inferred about the mean of that covariate, which means it is not a genuine probit model.


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