Archive for Monte Carlo Statistical Methods

retrospective Monte Carlo

Posted in pictures, Running, Statistics, Travel, University life with tags , , , , , , , , , , on July 12, 2016 by xi'an

the pond in front of the Zeeman building, University of Warwick, July 01, 2014The past week I spent in Warwick ended up with a workshop on retrospective Monte Carlo, which covered exact sampling, debiasing, Bernoulli factory problems and multi-level Monte Carlo, a definitely exciting package! (Not to mention opportunities to go climbing with some participants.) In particular, several talks focussed on the debiasing technique of Rhee and Glynn (2012) [inspired from von Neumann and Ulam, and already discussed in several posts here]. Including results in functional spaces, as demonstrated by a multifaceted talk by Sergios Agapiou who merged debiasing, deburning, and perfect sampling.

From a general perspective on unbiasing, while there exist sufficient conditions to ensure finite variance and aim at an optimal version, I feel a broader perspective should be adopted towards comparing those estimators with biased versions that take less time to compute. In a diffusion context, Chang-han Rhee presented a detailed argument as to why his debiasing solution achieves a O(√n) convergence rate in opposition the regular discretised diffusion, but multi-level Monte Carlo also achieves this convergence speed. We had a nice discussion about this point at the break, with my slow understanding that continuous time processes had much much stronger reasons for sticking to unbiasedness. At the poster session, I had the nice surprise of reading a poster on the penalty method I discussed the same morning! Used for subsampling when scaling MCMC.

On the second day, Gareth Roberts talked about the Zig-Zag algorithm (which reminded me of the cigarette paper brand). This method has connections with slice sampling but it is a continuous time method which, in dimension one, means running a constant velocity particle that starts at a uniform value between 0 and the maximum density value and proceeds horizontally until it hits the boundary, at which time it moves to another uniform. Roughly. More specifically, this approach uses piecewise deterministic Markov processes, with a radically new approach to simulating complex targets based on continuous time simulation. With computing times that [counter-intuitively] do not increase with the sample size.

Mark Huber gave another exciting talk around the Bernoulli factory problem, connecting with perfect simulation and demonstrating this is not solely a formal Monte Carlo problem! Some earlier posts here have discussed papers on that problem, but I was unaware of the results bounding [from below] the expected number of steps to simulate B(f(p)) from a (p,1-p) coin. If not of the open questions surrounding B(2p). The talk was also great in that it centred on recursion and included a fundamental theorem of perfect sampling! Not that surprising given Mark’s recent book on the topic, but exhilarating nonetheless!!!

The final talk of the second day was given by Peter Glynn, with connections with Chang-han Rhee’s talk the previous day, but with a different twist. In particular, Peter showed out to achieve perfect or exact estimation rather than perfect or exact simulation by a fabulous trick: perfect sampling is better understood through the construction of random functions φ¹, φ², … such that X²=φ¹(X¹), X³=φ²(X²), … Hence,


which helps in constructing coupling strategies. However, since the φ’s are usually iid, the above is generally distributed like


which seems pretty similar but offers a much better concentration as t grows. Cutting the function composition is then feasible towards producing unbiased estimators and more efficient. (I realise this is not a particularly clear explanation of the idea, detailed in an arXival I somewhat missed. When seen this way, Y would seem much more expensive to compute [than X].)

the penalty method

Posted in Statistics, University life with tags , , , , , , , , , , on July 7, 2016 by xi'an

“In this paper we will make conceptually simple generalization of Metropolis algorithm, by adjusting the acceptance ratio formula so that the transition probabilities are unaffected by the fluctuations in the estimate of [the acceptance ratio]…”

Last Friday, in Paris-Dauphine, my PhD student Changye Wu showed me a paper of Ceperley and Dewing entitled the penalty method for random walks with uncertain energies. Of which I was unaware of (and which alas pre-dated a recent advance made by Changye).  Despite its physics connections, the paper is actually about estimating a Metropolis-Hastings acceptance ratio and correcting the Metropolis-Hastings move for this estimation. While there is no generic solution to this problem, assuming that the logarithm of the acceptance ratio estimate is Gaussian around the true log acceptance ratio (and hence unbiased) leads to a log-normal correction for the acceptance probability.

“Unfortunately there is a serious complication: the variance needed in the noise penalty is also unknown.”

Even when the Gaussian assumption is acceptable, there is a further issue with this approach, namely that it also depends on an unknown variance term. And replacing it with an estimate induces further bias. So it may be that this method has not met with many followers because of those two penalising factors. Despite precluding the pseudo-marginal approach of Mark Beaumont (2003) by a few years, with the later estimating separately numerator and denominator in the Metropolis-Hastings acceptance ratio. And hence being applicable in a much wider collection of cases. Although I wonder if some generic approaches like path sampling or the exchange algorithm could be applied on a generic basis… [I just realised the title could be confusing in relation with the current football competition!]

simple, scalable and accurate posterior interval estimation

Posted in Statistics with tags , , , , , , , on July 6, 2016 by xi'an

“There is a lack of simple and scalable algorithms for uncertainty quantification.”

A paper by Cheng Li , Sanvesh Srivastava, and David Dunson that I had missed and which was pointed out on Andrew’s blog two days ago. As recalled in the very first sentence of the paper, above, the existing scalable MCMC algorithms somewhat fail to account for confidence (credible) intervals. In the sense that handling parallel samples does not naturally produce credible intervals.Since the approach is limited to one-dimensional quantity of interest, ζ=h(θ), the authors of the paper consider the MCMC approximations of the cdf of the said quantity ζ based on the manageable subsets like as many different approximations of the same genuine posterior distribution of that quantity ζ. (Corrected by a power of the likelihood but dependent on the particular subset used for the estimation.) The estimate proposed in the paper is a Wasserstein barycentre of the available estimations, barycentre that is defined as minimising the sum of the Wasserstein distances to all estimates. (Why should this measure be relevant: the different estimates may be of different quality). Interestingly (at least at a computational level), the solution is such that the quantile function of the Wasserstein barycentre is the average of the estimated quantiles functions. (And is there an alternative loss returning the median cdf?) A confidence interval based on the quantile function can then be directly derived. The paper shows that this Wasserstein barycentre converges to the true (marginal) posterior as the sample size m of each sample grows to infinity (and faster than 1/√m), with the strange side-result that the convergence is in 1/√n when the MLE of the global parameter θ is unbiased. Strange to me because unbiasedness is highly dependent on parametrisation while the performances of this estimator should not be, i.e., should be invariant under reparameterisation. Maybe this is due to ζ being a linear transform of θ in the convergence theorem… In any case, I find this question of merging cdf’s from poorly defined approximations to an unknown cdf of the highest interest and look forward any further proposal to this effect!

Statistics & Computing [toc]

Posted in Books, Statistics with tags , , , , on June 29, 2016 by xi'an

The latest [June] issue of Statistics & Computing is full of interesting Bayesian and Monte Carlo entries, some of which are even open access!


control functionals for Monte Carlo integration

Posted in Books, Statistics, University life with tags , , , , , , , , , , , , , on June 28, 2016 by xi'an

img_2451A paper on control variates by Chris Oates, Mark Girolami (Warwick) and Nicolas Chopin (CREST) appeared in a recent issue of Series B. I had read and discussed the paper with them previously and the following is a set of comments I wrote at some stage, to be taken with enough gains of salt since Chris, Mark and Nicolas answered them either orally or in the paper. Note also that I already discussed an earlier version, with comments that are not necessarily coherent with the following ones! [Thanks to the busy softshop this week, I resorted to publish some older drafts, so mileage can vary in the coming days.]

First, it took me quite a while to get over the paper, mostly because I have never worked with reproducible kernel Hilbert spaces (RKHS) before. I looked at some proofs in the appendix and at the whole paper but could not spot anything amiss. It is obviously a major step to uncover a manageable method with a rate that is lower than √n. When I set my PhD student Anne Philippe on the approach via Riemann sums, we were quickly hindered by the dimension issue and could not find a way out. In the first versions of the nested sampling approach, John Skilling had also thought he could get higher convergence rates before realising the Monte Carlo error had not disappeared and hence was keeping the rate at the same √n speed.

The core proof in the paper leading to the 7/12 convergence rate relies on a mathematical result of Sun and Wu (2009) that a certain rate of regularisation of the function of interest leads to an average variance of order 1/6. I have no reason to mistrust the result (and anyway did not check the original paper), but I am still puzzled by the fact that it almost immediately leads to the control variate estimator having a smaller order variance (or at least variability). On average or in probability. (I am also uncertain on the possibility to interpret the boxplot figures as establishing super-√n speed.)

Another thing I cannot truly grasp is how the control functional estimator of (7) can be both a mere linear recombination of individual unbiased estimators of the target expectation and an improvement in the variance rate. I acknowledge that the coefficients of the matrices are functions of the sample simulated from the target density but still…

Another source of inner puzzlement is the choice of the kernel in the paper, which seems too simple to be able to cover all problems despite being used in every illustration there. I see the kernel as centred at zero, which means a central location must be know, decreasing to zero away from this centre, so possibly missing aspects of the integrand that are too far away, and isotonic in the reference norm, which also seems to preclude some settings where the integrand is not that compatible with the geometry.

I am equally nonplussed by the existence of a deterministic bound on the error, although it is not completely deterministic, depending on the values of the reproducible kernel at the points of the sample. Does it imply anything restrictive on the function to be integrated?

A side remark about the use of intractable in the paper is that, given the development of a whole new branch of computational statistics handling likelihoods that cannot be computed at all, intractable should possibly be reserved for such higher complexity models.

ISBA 2016 [#6]

Posted in Kids, Mountains, pictures, Statistics, Travel, University life, Wines with tags , , , , , , , , , , , , , , on June 19, 2016 by xi'an

Fifth and final day of ISBA 2016, which was as full and intense as the previous ones. (Or even more if taking into account the late evening social activities pursued by most participants.) First thing in the morning, I managed to get very close to a hill top, thanks to the hints provided by Jeff Miller!, and with no further scratches from the nasty local thorn bushes. And I was back with plenty of time for a Bayesian robustness session with great talks. (Session organised by Judith Rousseau whom I crossed while running, rushing to the airport thanks to an Air France last-minute cancellation.) First talk by James Watson (on his paper with Chris Holmes on Kullback neighbourhoods on priors that Judith and I discussed recently in Statistical Science). Then as a contrapunto Peter Grünwald gave a neat geometric motivation for possible misbehaviour of Bayesian inference in non-convex misspecified environments and discussed his SafeBayes resolution that weights down the likelihood. In a sort of PAC-Bayesian way. And Erlis Ruli presented the ABC-R approach he developed with Laura Ventura and Nicola Sartori based on M-estimators and score functions. Making wonder [idly, as usual] whether cumulating different M-estimators would make a difference in the performances of the ABC algorithm.

David Dunson delivered one of the plenary lectures on high-dimensional discrete parameter estimation, including for instance categorical data. This wide-range talk covered many aspects and papers of David’s work, including a use of tensors I had neither seen nor heard of before before. With sparse modelling to resist the combinatoric explosion of contingency tables. However, and you may blame my Gallic pessimistic daemon for this remark, I have trouble to picture the meaning and relevance of a joint distribution on a space of hundreds and hundreds of dimension and similarly the ability to check the adequacy of any modelling in terms of goodness of fit. For instance, to borrow a non-military example from David’s talk, handling genetic data on ACGT sequences to infer its distribution sounds unreasonable unless most of the bases are mono-allelic. And the only way I see to test the realism of a model in this framework would be to engineer realisations of this distribution to observe the outcome, a test that seems neither feasible not desirable. Prediction based on such models may obviously operate satisfactorily without such realism requirements.

My first afternoon session (after the ISBA assembly that announced the location of ISBA 2020 in Yunnan, China!, home of Pu’ Ehr tea) was about accelerated MCMC schemes with talks by Sanvesh Srivastava on divide-and-conquer MCMC using Wasserstein barycentres, already discussed here, Minsuk Shin on a faster stochastic search variable selection which I could not understand, and Alex Beskos on the extension of Giles’ multilevel Monte Carlo to MCMC settings, which sounded worth investigating further even though I did not follow the notion all the way through. After listening to Luke Bornn explaining how to recalibrate grid data for climate science by accounting for correlation (with the fun title of `lost moments’), I rushed to my rental to [help] cook dinner for friends and… the ISBA 2016 conference was over!

ISBA 2016 [#5]

Posted in Mountains, pictures, Running, Statistics, Travel with tags , , , , , , , , , , , , , on June 18, 2016 by xi'an

from above Forte Village, Santa Magherita di Pula, Sardinia, June 17, 2016On Thursday, I started the day by a rather masochist run to the nearby hills, not only because of the very hour but also because, by following rabbit trails that were not intended for my size, I ended up being scratched by thorns and bramble all over!, but also with neat views of the coast around Pula.  From there, it was all downhill [joke]. The first morning talk I attended was by Paul Fearnhead and about efficient change point estimation (which is an NP hard problem or close to). The method relies on dynamic programming [which reminded me of one of my earliest Pascal codes about optimising a dam debit]. From my spectator’s perspective, I wonder[ed] at easier models, from Lasso optimisation to spline modelling followed by testing equality between bits. Later that morning, James Scott delivered the first Bayarri Lecture, created in honour of our friend Susie who passed away between the previous ISBA meeting and this one. James gave an impressive coverage of regularisation through three complex models, with the [hopefully not degraded by my translation] message that we should [as Bayesians] focus on important parts of those models and use non-Bayesian tools like regularisation. I can understand the practical constraints for doing so, but optimisation leads us away from a Bayesian handling of inference problems, by removing the ascertainment of uncertainty…

Later in the afternoon, I took part in the Bayesian foundations session, discussing the shortcomings of the Bayes factor and suggesting the use of mixtures instead. With rebuttals from [friends in] the audience!

This session also included a talk by Victor Peña and Jim Berger analysing and answering the recent criticisms of the Likelihood principle. I am not sure this answer will convince the critics, but I won’t comment further as I now see the debate as resulting from a vague notion of inference in Birnbaum‘s expression of the principle. Jan Hannig gave another foundation talk introducing fiducial distributions (a.k.a., Fisher’s Bayesian mimicry) but failing to provide a foundational argument for replacing Bayesian modelling. (Obviously, I am definitely prejudiced in this regard.)

The last session of the day was sponsored by BayesComp and saw talks by Natesh Pillai, Pierre Jacob, and Eric Xing. Natesh talked about his paper on accelerated MCMC recently published in JASA. Which surprisingly did not get discussed here, but would definitely deserve to be! As hopefully corrected within a few days, when I recoved from conference burnout!!! Pierre Jacob presented a work we are currently completing with Chris Holmes and Lawrence Murray on modularisation, inspired from the cut problem (as exposed by Plummer at MCMski IV in Chamonix). And Eric Xing spoke about embarrassingly parallel solutions, discussed a while ago here.


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