Archive for population Monte Carlo

ABC by QMC

Posted in Books, Kids, Statistics, University life with tags , , , , , , , , , , on November 5, 2018 by xi'an

A paper by Alexander Buchholz (CREST) and Nicolas Chopin (CREST) on quasi-Monte Carlo methods for ABC is going to appear in the Journal of Computational and Graphical Statistics. I had missed the opportunity when it was posted on arXiv and only became aware of the paper’s contents when I reviewed Alexander’s thesis for the doctoral school. The fact that the parameters are simulated (in ABC) from a prior that is quite generally a standard distribution while the pseudo-observations are simulated from a complex distribution (associated with the intractability of the likelihood function) means that the use of quasi-Monte Carlo sequences is in general only possible for the first part.

The ABC context studied there is close to the original version of ABC rejection scheme [as opposed to SMC and importance versions], the main difference standing with the use of M pseudo-observations instead of one (of the same size as the initial data). This repeated version has been discussed and abandoned in a strict Monte Carlo framework in favor of M=1 as it increases the overall variance, but the paper uses this version to show that the multiplication of pseudo-observations in a quasi-Monte Carlo framework does not increase the variance of the estimator. (Since the variance apparently remains constant when taking into account the generation time of the pseudo-data, we can however dispute the interest of this multiplication, except to produce a constant variance estimator, for some targets, or to be used for convergence assessment.) L The article also covers the bias correction solution of Lee and Latuszyǹski (2014).

Due to the simultaneous presence of pseudo-random and quasi-random sequences in the approximations, the authors use the notion of mixed sequences, for which they extend a one-dimension central limit theorem. The paper focus on the estimation of Z(ε), the normalization constant of the ABC density, ie the predictive probability of accepting a simulation which can be estimated at a speed of O(N⁻¹) where N is the number of QMC simulations, is a wee bit puzzling as I cannot figure the relevance of this constant (function of ε), especially since the result does not seem to generalize directly to other ABC estimators.

A second half of the paper considers a sequential version of ABC, as in ABC-SMC and ABC-PMC, where the proposal distribution is there  based on a Normal mixture with a small number of components, estimated from the (particle) sample of the previous iteration. Even though efficient techniques for estimating this mixture are available, this innovative step requires a calculation time that should be taken into account in the comparisons. The construction of a decreasing sequence of tolerances ε seems also pushed beyond and below what a sequential approach like that of Del Moral, Doucet and Jasra (2012) would produce, it seems with the justification to always prefer the lower tolerances. This is not necessarily the case, as recent articles by Li and Fearnhead (2018a, 2018b) and ours have shown (Frazier et al., 2018). Overall, since ABC methods are large consumers of simulation, it is interesting to see how the contribution of QMC sequences results in the reduction of variance and to hope to see appropriate packages added for standard distributions. However, since the most consuming part of the algorithm is due to the simulation of the pseudo-data, in most cases, it would seem that the most relevant focus should be on QMC add-ons on this part, which may be feasible for models with a huge number of standard auxiliary variables as for instance in population evolution.

efficient adaptive importance sampling

Posted in Books, Statistics with tags , , , , , , , on June 22, 2018 by xi'an

Bernard Delyon and François Portier just recently arXived a paper on population or evolutionary importance sampling, pointed out to me by Víctor Elvira. Changing the proposal or importance sampler at each iteration. And averaging the estimates across iterations, but also mentioning AMIS. While drawing a distinction that I do not understand, since the simulation cost remains the same, while improving the variance of the resulting estimator. (But the paper points out later that their martingale technique of proof does not apply in this AMIS case.) Some interesting features of the paper are that

  • convergence occurs when the total number of simulations grows to infinity, which is the most reasonable scale for assessing the worth of the method;
  • some optimality in the oracle sense is established for the method;
  • an improvement is found by eliminating outliers and favouring update rate over simulation rate (at a constant cost). Unsurprisingly, the optimal weight of the t-th estimator is given by its inverse variance (with eqn (13) missing an inversion step). Although it relies on the normalised versions of the target and proposal densities, since it assumes the expectation of the ratio is equal to one.

When updating the proposal or importance distribution, the authors consider a parametric family with the update in the parameter being driven by moment or generalised moment matching, or Kullback reduction as in our population Monte Carlo paper. The interesting technical aspects of the paper include the use of martingale and empirical risk arguments. All in all, quite a pleasant surprise to see some follow-up to our work on that topic, more than 10 years later.

MCMC with multiple tries

Posted in Books, pictures, Statistics, University life with tags , , , , , , , , , on April 5, 2018 by xi'an

Earlier this year, Luca Martino wrote and arXived a review on multiple try MCMC. As its name suggests, the starting point of this algorithm is to propose N potential moves simultaneously instead of one, possibly according to N different proposal (conditional) densities, and to select one by a normalised importance sampling weight. The move is accepted by a Metropolis-Hastings step based on the ratio of the normalisation constants [at the current and at the one-before-current stages]. Besides the cost of computing the summation and generating the different variates, this method also faces the drawback of requiring N-1 supplementary simulations that are only used for achieving detailed balance and computing a backward summation of importance weights. (A first section of the review is dedicated to independent Metropolis-Hastings proposals, q(θ), which make life simpler, but are less realistic in my opinion since some prior knowledge or experimentation is necessary to build a relevant distribution q(θ).) An alternative covered in the survey is ensemble Monte Carlo (Neal, 2011), which produces a whole sample at each iteration, with target the product of the initial targets. This reminded me of our pinball sampler, which aimed at producing a spread-out sample while keeping the marginal correct. Although the motivation sounds closer to a particle sampler. Especially with this associated notion of an empirical approximation of the target. The next part of the review is about delayed rejection, which is a natural alternative approach to speeding up MCMC by considering several possibilities, if sequentially. Started in Antonietta Mira‘s 1999 PhD thesis. The difficulty with this approach is that the acceptance probability gets increasingly complex as the number of delays grows, which may annihilate its appeal relative to simultaneous multiple tries.

the invasion of the stochastic gradients

Posted in Statistics with tags , , , , , , , , , on May 10, 2017 by xi'an

Within the same day, I spotted three submissions to arXiv involving stochastic gradient descent, that I briefly browsed on my trip back from Wales:

  1. Stochastic Gradient Descent as Approximate Bayesian inference, by Mandt, Hoffman, and Blei, where this technique is used as a type of variational Bayes method, where the minimum Kullback-Leibler distance to the true posterior can be achieved. Rephrasing the [scalable] MCMC algorithm of Welling and Teh (2011) as such an approximation.
  2. Further and stronger analogy between sampling and optimization: Langevin Monte Carlo and gradient descent, by Arnak Dalalyan, which establishes a convergence of the uncorrected Langevin algorithm to the right target distribution in the sense of the Wasserstein distance. (Uncorrected in the sense that there is no Metropolis step, meaning this is a Euler approximation.) With an extension to the noisy version, when the gradient is approximated eg by subsampling. The connection with stochastic gradient descent is thus tenuous, but Arnak explains the somewhat disappointing rate of convergence as being in agreement with optimisation rates.
  3. Stein variational adaptive importance sampling, by Jun Han and Qiang Liu, which relates to our population Monte Carlo algorithm, but as a non-parametric version, using RKHS to represent the transforms of the particles at each iteration. The sampling method follows two threads of particles, one that is used to estimate the transform by a stochastic gradient update, and another one that is used for estimation purposes as in a regular population Monte Carlo approach. Deconstructing into those threads allows for conditional independence that makes convergence easier to establish. (A problem we also hit when working on the AMIS algorithm.)

X divergence for approximate inference

Posted in Statistics with tags , , , , , , , on March 14, 2017 by xi'an

Dieng et al. arXived this morning a new version of their paper on using the Χ divergence for variational inference. The Χ divergence essentially is the expectation of the squared ratio of the target distribution over the approximation, under the approximation. It is somewhat related to Expectation Propagation (EP), which aims at the Kullback-Leibler divergence between the target distribution and the approximation, under the target. And to variational Bayes, which is the same thing just the opposite way! The authors also point a link to our [adaptive] population Monte Carlo paper of 2008. (I wonder at a possible version through Wasserstein distance.)

Some of the arguments in favour of this new version of variational Bayes approximations is that (a) the support of the approximation over-estimates the posterior support; (b) it produces over-dispersed versions; (c) it relates to a well-defined and global objective function; (d) it allows for a sandwich inequality on the model evidence; (e) the function of the [approximation] parameter to be minimised is under the approximation, rather than under the target. The latest allows for a gradient-based optimisation. While one of the applications is on a Bayesian probit model applied to the Pima Indian women dataset [and will thus make James and Nicolas cringe!], the experimental assessment shows lower error rates for this and other benchmarks. Which in my opinion does not tell so much about the original Bayesian approach.

SMC on a sequence of increasing dimension targets

Posted in Statistics with tags , , , , , , , , , on February 15, 2017 by xi'an

mixdirRichard Everitt and co-authors have arXived a preliminary version of a paper entitled Sequential Bayesian inference for mixture models and the coalescent using sequential Monte Carlo samplers with transformations. The central notion is an SMC version of the Carlin & Chib (1995) completion in the comparison of models in different dimensions. Namely to create auxiliary variables for each model in such a way that the dimension of the completed models are all the same. (Reversible jump MCMC à la Peter Green (1995) can also be interpreted this way, even though only relevant bits of the completion are used in the transitions.) I find the paper and the topic most interesting if only because it relates to earlier papers of us on population Monte Carlo. It also brought to my awareness the paper by Karagiannis and Andrieu (2013) on annealed reversible jump MCMC that I had missed at the time it appeared. The current paper exploits this annealed expansion in the devising of the moves. (Sequential Monte Carlo on a sequence of models with increasing dimension has been studied in the past.)

The way the SMC is described in the paper, namely, reweight-subsample-move, does not strike me as the most efficient as I would try to instead move-reweight-subsample, using a relevant move that incorporate the new model and hence enhance the chances of not rejecting.

One central application of the paper is mixture models with an unknown number of components. The SMC approach applied to this problem means creating a new component at each iteration t and moving the existing particles after adding the parameters of the new component. Since using the prior for this new part is unlikely to be at all efficient, a split move as in Richardson and Green (1997) can be considered, which brings back the dreaded Jacobian of RJMCMC into the picture! Here comes an interesting caveat of the method, namely that the split move forces a choice of the split component of the mixture. However, this does not appear as a strong difficulty, solved in the paper by auxiliary [index] variables, but possibly better solved by a mixture representation of the proposal, as in our PMC [population Monte Carlo] papers. Which also develop a family of SMC algorithms, incidentally. We found there that using a mixture representation of the proposal achieves a provable variance reduction.

“This puts a requirement on TSMC that the single transition it makes must be successful.”

As pointed by the authors, the transformation SMC they develop faces the drawback that a given model is only explored once in the algorithm, when moving to the next model. On principle, there would be nothing wrong in including regret steps, retracing earlier models in the light of the current one, since each step is an importance sampling step valid on its own right. But SMC also offers a natural albeit potentially high-varianced approximation to the marginal likelihood, which is quite appealing when comparing with an MCMC outcome. However, it would have been nice to see a comparison with alternative estimates of the marginal in the case of mixtures of distributions. I also wonder at the comparative performances of a dual approach that would be sequential in the number of observations as well, as in Chopin (2004) or our first population Monte Carlo paper (Cappé et al., 2005), since subsamples lead to tempered versions of the target and hence facilitate moves between models, being associated with flatter likelihoods.

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.