Archive for population Monte Carlo

parallel adaptive importance sampling

Posted in Statistics with tags , , , , , on August 30, 2016 by xi'an

Following Paul Russell’s talk at MCqMC 2016, I took a look at his recently arXived paper. In the plane to Sydney. The pseudo-code representation of the method is identical to our population Monte Carlo algorithm as is the suggestion to approximate the posterior by a mixture, but one novel aspect is to use Reich’s ensemble transportation at the resampling stage, in order to maximise the correlation between the original and the resampled versions of the particle systems. (As in our later versions of PMC, the authors also use as importance denominator the entire mixture rather than conditioning on the selected last-step particle.)

“The output of the resampling algorithm gives us a set of evenly weighted samples that we believe represents the target distribution well”

I disagree with this statement: Reweighting does not improve the quality of the posterior approximation, since it introduces more variability. If the original sample is found missing in its adequation to the target, so is the resampled one. Worse, by producing a sample with equal weights, this step may give a false impression of adequate representation…

Another unclear point in the pape relates to tuning the parameters of the mixture importance sampler. The paper discusses tuning these parameters during a burn-in stage, referring to “due to the constraints on adaptive MCMC algorithms”, which indeed is only pertinent for MCMC algorithms, since importance sampling can be constantly modified while remaining valid. This was a major point for advocating PMC. I am thus unsure what the authors mean by a burn-in period in such a context. Actually, I am also unsure on how they use effective sample size to select the new value of the importance parameter, e.g., the variance β in a random walk mixture: the effective sample size involves this variance implicitly through the realised sample hence changing β means changing the realised sample… This seems too costly to contemplate so I wonder at the way Figure 4.2 is produced.

“A popular approach for adaptive MCMC algorithms is to view the scaling parameter as a random variable which we can sample during the course of the MCMC iterations.”

While this is indeed an attractive notion [that I played with in the early days of adaptive MCMC, with the short-lived notion of cyber-parameters], I do not think it is of much help in optimising an MCMC algorithm, since the scaling parameter need be optimised, resulting into a time-inhomogeneous target. A more appropriate tool is thus stochastic optimisation à la Robbins-Monro, as exemplified in Andrieu and Moulines (2006). The paper however remains unclear as to how the scales are updated (see e.g. Section 4.2).

“Ideally, we would like to use a resampling algorithm which is not prohibitively costly for moderately or large sized ensembles, which preserves the mean of the samples, and which makes it much harder for the new samples to forget a significant region in the density.”

The paper also misses on the developments of the early 2000’s about more sophisticated resampling steps, especially Paul Fearnhead’s contributions (see also Nicolas Chopin’s thesis). There exist valid resampling methods that require a single uniform (0,1) to be drawn, rather than m. The proposed method has a flavour similar to systematic resampling, but I wonder at the validity of returning values that are averages of earlier simulations, since this modifies their distribution into ones with slimmer tails. (And it is parameterisation dependent.) Producing xi with probability pi is not the same as returning the average of the pixi‘s.

MCqMC 2016 [#4]

Posted in Mountains, pictures, Running, Statistics, Travel, University life with tags , , , , , , , , , , , , , , on August 21, 2016 by xi'an

In his plenary talk this morning, Arnaud Doucet discussed the application of pseudo-marginal techniques to the latent variable models he has been investigating for many years. And its limiting behaviour towards efficiency, with the idea of introducing correlation in the estimation of the likelihood ratio. Reducing complexity from O(T²) to O(T√T). With the very surprising conclusion that the correlation must go to 1 at a precise rate to get this reduction, since perfect correlation would induce a bias. A massive piece of work, indeed!

The next session of the morning was another instance of conflicting talks and I hoped from one room to the next to listen to Hani Doss’s empirical Bayes estimation with intractable constants (where maybe SAME could be of interest), Youssef Marzouk’s transport maps for MCMC, which sounds like an attractive idea provided the construction of the map remains manageable, and Paul Russel’s adaptive importance sampling that somehow sounded connected with our population Monte Carlo approach. (With the additional step of considering transform maps.)

An interesting item of information I got from the final announcements at MCqMC 2016 just before heading to Monash, Melbourne, is that MCqMC 2018 will take place in the city of Rennes, Brittany, on July 2-6. Not only it is a nice location on its own, but it is most conveniently located in space and time to attend ISBA 2018 in Edinburgh the week after! Just moving from one Celtic city to another Celtic city. Along with other planned satellite workshops, this occurrence should make ISBA 2018 more attractive [if need be!] for participants from oversea.

multiple try Metropolis

Posted in Books, Statistics, University life with tags , , , , , , on February 18, 2016 by xi'an

martinLuca Martino and Francisco Louzada recently wrote a paper in Computational Statistics about some difficulties with the multiple try Metropolis algorithm. This version of Metropolis by Liu et al. (2000) makes several proposals in parallel and picks one among them by multinomial sampling where the weights are proportional to the corresponding importance weights. This is followed by a Metropolis acceptance step that requires simulating the same number of proposed moves from the selected value. While this is necessary to achieve detailed balance, this mixture of MCMC and importance sampling is inefficient in that it simulates a large number of particles and ends up using only one of them. By comparison, a particle filter for the same setting would propagate all N particles along iterations and only resamples occasionaly when the ESS is getting too small. (I also wonder if the method could be seen as a special kind of pseudo-marginal approach, given that the acceptance ratio is an empirical average with expectation the missing normalising constan [as I later realised the authors had pointed out!]… In which case efficiency comparisons by Christophe Andrieu and Matti Vihola could prove useful.)

The issue raised by Martino and Louzada is that the estimator of the normalising constant can be poor at times, especially when the chain is in low regions of the target, and hence get the chain stuck. The above graph illustrates this setting in the paper. However, the reason for the failure is mostly that the proposal distribution is inappropriate for the purpose of approximating the normalising constant, i.e., that importance sampling does not converge in this situation, since otherwise the average of the importance weights should a.s. converge to the normalising constant. And the method should not worsen when increasing the number of proposals at a given stage. (The solution proposed by the authors to have a random number of proposals seems unlikely to solve the issue in a generic situation. Changing the proposals towards different tail behaviours as in population Monte Carlo is more akin to defensive sampling and thus more likely to avoid trapping states. Interestingly, the authors eventually resort to a mixture denominator in the importance sampler following AMIS.)

multiple importance sampling

Posted in Books, Statistics, University life with tags , , , , , , , , on November 20, 2015 by xi'an

“Within this unified context, it is possible to interpret that all the MIS algorithms draw samples from a equal-weighted mixture distribution obtained from the set of available proposal pdfs.”

In a very special (important?!) week for importance sampling!, Elvira et al. arXived a paper about generalized multiple importance sampling. The setting is the same as in earlier papers by Veach and Gibas (1995) or Owen and Zhou (2000) [and in our AMIS paper], namely a collection of importance functions and of simulations from those functions. However, there is no adaptivity for the construction of the importance functions and no Markov (MCMC) dependence on the generation of the simulations.

“One of the goals of this paper is to provide the practitioner with solid theoretical results about the superiority of some specific MIS schemes.”

One first part deals with the fact that a random point taken from the conjunction of those samples is distributed from the equiweighted mixture. Which was a fact I had much appreciated when reading Owen and Zhou (2000). From there, the authors discuss the various choices of importance weighting. Meaning the different degrees of Rao-Blackwellisation that can be applied to the sample. As we discovered in our population Monte Carlo research [which is well-referred within this paper], conditioning too much leads to useless adaptivity. Again a sort of epiphany for me, in that a whole family of importance functions could be used for the same target expectation and the very same simulated value: it all depends on the degree of conditioning employed for the construction of the importance function. To get around the annoying fact that self-normalised estimators are never unbiased, the authors borrow Liu’s (2000) notion of proper importance sampling estimators, where the ratio of the expectations is returning the right quantity. (Which amounts to recover the correct normalising constant(s), I believe.) They then introduce five (5!) different possible importance weights that all produce proper estimators. However, those weights correspond to different sampling schemes, so do not apply to the same sample. In other words, they are not recycling weights as in AMIS. And do not cover the adaptive cases where the weights and parameters of the different proposals change along iterations. Unsurprisingly, the smallest variance estimator is the one based on sampling without replacement and an importance weight made of the entire mixture. But this result does not apply for the self-normalised version, whose variance remains intractable.

I find this survey of existing and non-existing multiple importance methods quite relevant and a must-read for my students (and beyond!). My reservations (for reservations there must be!) are that the study stops short of pushing further the optimisation. Indeed, the available importance functions are not equivalent in terms of the target and hence weighting them equally is sub-efficient. The adaptive part of the paper broaches upon this issue but does not conclude.

trip to München

Posted in Mountains, Statistics, Travel, University life, Wines with tags , , , , , , , , , , , , , on October 19, 2015 by xi'an

While my train ride to the fabulous De Gaulle airport was so much delayed that I had less than ten minutes from jumping from the carriage to sitting in my plane seat, I handled the run through security and the endless corridors of the airport in the allotted time, and reached Munich in time for my afternoon seminar and several discussions that prolonged into a pleasant dinner of Wiener Schnitzel and Eisbier.  This was very exciting as I met physicists and astrophysicists involved in population Monte Carlo and parallel MCMC and manageable harmonic mean estimates and intractable ABC settings (because simulating the data takes eons!). I wish the afternoon could have been longer. And while this is the third time I come to Munich, I still have not managed to see the centre of town! Or even the nearby mountains. Maybe an unsuspected consequence of the Heisenberg principle…

gradient importance sampling

Posted in Books, pictures, Statistics, University life with tags , , , , , , on July 30, 2015 by xi'an

from my office, La Défense & Bois de Boulogne, Paris, May 15, 2012Ingmar Schuster, who visited Paris-Dauphine last Spring (and is soon to return here as a postdoc funded by Fondation des Sciences Mathématiques de Paris) has arXived last week a paper on gradient importance sampling. In this paper, he builds a sequential importance sampling (or population Monte Carlo) algorithm that exploits the additional information contained in the gradient of the target. The proposal or importance function being essentially the MALA move as its proposal, mixed across the elements of the previous population. When compared with our original PMC mixture of random walk proposals found in e.g. this paper, each term in the mixture thus involves an extra gradient, with a scale factor that decreases to zero as 1/t√t. Ingmar compares his proposal with an adaptive Metropolis, an adaptive MALTa and an HM algorithms, for two mixture distributions and the banana target of Haario et al. (1999) we also used in our paper. As well as a logistic regression. In each case, he finds both a smaller squared error and a smaller bias for the same computing time (evaluated as the number of likelihood evaluations). While we discussed this scheme when he visited, I remain intrigued as to why it works so well when compared with the other solutions. One possible explanation is that the use of the gradient drift is more efficient on a population of particles than on a single Markov chain, provided the population covers all modes of importance on the target surface: the “fatal” attraction of the local model is then much less of an issue…

Bayesian model averaging in astrophysics

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

[A 2013 post that somewhat got lost in a pile of postponed entries and referee’s reports…]

In this review paper, now published in Statistical Analysis and Data Mining 6, 3 (2013), David Parkinson and Andrew R. Liddle go over the (Bayesian) model selection and model averaging perspectives. Their argument in favour of model averaging is that model selection via Bayes factors may simply be too inconclusive to favour one model and only one model. While this is a correct perspective, this is about it for the theoretical background provided therein. The authors then move to the computational aspects and the first difficulty is their approximation (6) to the evidence

P(D|M) = E \approx \frac{1}{n} \sum_{i=1}^n L(\theta_i)Pr(\theta_i)\, ,

where they average the likelihood x prior terms over simulations from the posterior, which does not provide a valid (either unbiased or converging) approximation. They surprisingly fail to account for the huge statistical literature on evidence and Bayes factor approximation, incl. Chen, Shao and Ibrahim (2000). Which covers earlier developments like bridge sampling (Gelman and Meng, 1998).

As often the case in astrophysics, at least since 2007, the authors’ description of nested sampling drifts away from perceiving it as a regular Monte Carlo technique, with the same convergence speed n1/2 as other Monte Carlo techniques and the same dependence on dimension. It is certainly not the only simulation method where the produced “samples, as well as contributing to the evidence integral, can also be used as posterior samples.” The authors then move to “population Monte Carlo [which] is an adaptive form of importance sampling designed to give a good estimate of the evidence”, a particularly restrictive description of a generic adaptive importance sampling method (Cappé et al., 2004). The approximation of the evidence (9) based on PMC also seems invalid:

E \approx \frac{1}{n} \sum_{i=1}^n \dfrac{L(\theta_i)}{q(\theta_i)}\, ,

is missing the prior in the numerator. (The switch from θ in Section 3.1 to X in Section 3.4 is  confusing.) Further, the sentence “PMC gives an unbiased estimator of the evidence in a very small number of such iterations” is misleading in that PMC is unbiased at each iteration. Reversible jump is not described at all (the supposedly higher efficiency of this algorithm is far from guaranteed when facing a small number of models, which is the case here, since the moves between models are governed by a random walk and the acceptance probabilities can be quite low).

The second quite unrelated part of the paper covers published applications in astrophysics. Unrelated because the three different methods exposed in the first part are not compared on the same dataset. Model averaging is obviously based on a computational device that explores the posteriors of the different models under comparison (or, rather, averaging), however no recommendation is found in the paper as to efficiently implement the averaging or anything of the kind. In conclusion, I thus find this review somehow anticlimactic.