**V**ivek Roy, Aixian Tan and James Flegal arXived a new paper, Estimating standard errors for importance sampling estimators with multiple Markov chains, where they obtain a central limit theorem and hence standard error estimates when using several MCMC chains to simulate from a mixture distribution as an importance sampling function. Just before I boarded my plane from Amsterdam to Calgary, which gave me the opportunity to read it completely (along with half a dozen other papers, since it is a long flight!) I first thought it was connecting to our AMIS algorithm (on which convergence Vivek spent a few frustrating weeks when he visited me at the end of his PhD), because of the mixture structure. This is actually altogether different, in that a mixture is made of unnormalised complex enough densities, to act as an importance sampler, and that, due to this complexity, the components can only be simulated via separate MCMC algorithms. Behind this characterisation lurks the challenging problem of estimating multiple normalising constants. The paper adopts the resolution by reverse logistic regression advocated in Charlie Geyer’s famous 1994 unpublished technical report. Beside the technical difficulties in establishing a CLT in this convoluted setup, the notion of mixing importance sampling and different Markov chains is quite appealing, especially in the domain of “tall” data and of splitting the likelihood in several or even many bits, since the mixture contains most of the information provided by the true posterior and can be corrected by an importance sampling step. In this very setting, I also think more adaptive schemes could be found to determine (estimate?!) the optimal weights of the mixture components.

## Archive for MCMC

## importance sampling with multiple MCMC sequences

Posted in Mountains, pictures, Statistics, Travel, University life with tags adaptive MCMC, Ames, AMIS, Amsterdam, Charlie Geyer, importance sampling, Iowa, MCMC, Monte Carlo Statistical Methods, normalising constant, splitting data on October 2, 2015 by xi'an## Je reviendrai à Montréal [NIPS 2015]

Posted in pictures, Statistics, Travel, University life with tags ABC, ABC in Montréal, Approximate Bayesian computation, Bayesian inference, Canada, MCMC, Monte Carlo integration, Monte Carlo Statistical Methods, Montréal, NIPS, NIPS 2015, probabilistic numerics, Québec, Robert Charlebois, scalability on September 30, 2015 by xi'an**I** will be back in Montréal, as the song by Robert Charlebois goes, for the NIPS 2015 meeting there, more precisely for the workshops of December 11 and 12, 2015, on probabilistic numerics and ABC [à Montréal]. I was invited to give the first talk by the organisers of the NIPS workshop on probabilistic numerics, presumably to present a contrapuntal perspective on this mix of Bayesian inference with numerical issues, following my somewhat critical posts on the topic. And I also plan to attend some lectures in the (second) NIPS workshop on ABC methods. Which does not leave much free space for yet another workshop on Approximate Bayesian Inference! The day after, while I am flying back to London, there will be a workshop on scalable Monte Carlo. All workshops are calling for contributed papers to be presented during central poster sessions. To be submitted to abcinmontreal@gmail.com and to probnum@gmail.com and to aabi2015. Before October 16.

Funny enough, I got a joking email from Brad, bemoaning my traitorous participation to the workshop on probabilistic numerics because of its “anti-MCMC” agenda, reflected in the summary:

“Integration is the central numerical operation required for Bayesian machine learning (in the form of marginalization and conditioning). Sampling algorithms still abound in this area, although it has long been known that Monte Carlo methods are fundamentally sub-optimal. The challenges for the development of better performing integration methods are mostly algorithmic. Moreover, recent algorithms have begun to outperform MCMC and its siblings, in wall-clock time, on realistic problems from machine learning.

The workshop will review the existing, by now quite strong, theoretical case against the use of random numbers for integration, discuss recent algorithmic developments, relationships between conceptual approaches, and highlight central research challenges going forward.”

Position that I hope to water down in my talk! In any case,

Je veux revoir le long désert

Des rues qui n’en finissent pas

Qui vont jusqu’au bout de l’hiver

Sans qu’il y ait trace de pas

## SMC 2015

Posted in Statistics, Travel, University life with tags Bayesian computation, coupling, CREST, ENSAE, gender imbalance, MCMC, Monte Carlo Statistical Methods, multiscale, sequential Monte Carlo, SMC 2015, unbiasedness on September 7, 2015 by xi'an**N**icolas Chopin ran a workshop at ENSAE on sequential Monte Carlo the past three days and it was a good opportunity to get a much needed up-to-date on the current trends in the field. Especially given that the meeting was literally downstairs from my office at CREST. And given the top range of researchers presenting their current or past work (in the very amphitheatre where I attended my first statistics lectures, a few dozen years ago!). Since unforeseen events made me miss most of the central day, I will not comment on individual talks, some of which I had already heard in the recent past, but this was a high quality workshop, topped by a superb organisation. (I started wondering why there was no a single female speaker in the program and so few female participants in the audience, then realised this is a field with a massive gender imbalance, which is difficult to explain given the different situation in Bayesian statistics and even in Bayesian computation…) Some key topics I gathered during the talks I could attend–apologies to the other speakers for missing their talk due to those unforeseen events–are *unbiasedness*, which sounds central to the SMC methods [at least those presented there] as opposed to MCMC algorithms, and *local features*, used in different ways like hierarchical decomposition, multiscale, parallelisation, local coupling, &tc., to improve convergence and efficiency…

## ergodicity of approximate MCMC chains with applications to large datasets

Posted in pictures, Statistics, Travel, University life with tags ABC-MCMC, accelerated ABC, Approximate Bayesian computation, austerity sampling, ergodicity, MCMC, Metropolis-Hastings algorithms, Monte Carlo Statistical Methods, Natesh Pillai, subsampling, Wasserstein distance on August 31, 2015 by xi'an**A**nother arXived paper I read on my way to Warwick! And yet another paper written by my friend Natesh Pillai (and his co-author Aaron Smith, from Ottawa). The goal of the paper is to study the ergodicity and the degree of approximation of the true posterior distribution of approximate MCMC algorithms that recently flourished as an answer to “Big Data” issues… *[Comments below are about the second version of this paper.] *One of the most curious results in the paper is the fact that the approximation may prove better than the original kernel, in terms of computing costs! If asymptotically in the computing cost. There also are acknowledged connections with the approximative MCMC kernel of Pierre Alquier, Neal Friel, Richard Everitt and A Boland, briefly mentioned in an earlier post.

The paper starts with a fairly theoretical part, to follow with an application to austerity sampling *[and, in the earlier version of the paper, to the Hoeffding bounds of Bardenet et al., both discussed earlier on the ‘Og, to exponential random graphs (the paper being rather terse on the description of the subsampling mechanism), to stochastic gradient Langevin dynamics (by Max Welling and Yee-Whye Teh), and to ABC-MCMC]*. The assumptions are about the transition kernels of a reference Markov kernel and of one associated with the approximation, imposing some bounds on the Wasserstein distance between those kernels, K and K’. Results being generic, there is no constraint as to how K is chosen or on how K’ is derived from K. Except in Lemma 3.6 and in the application section, where the same proposal kernel L is used for both Metropolis-Hastings algorithms K and K’. While I understand this makes for an easier coupling of the kernels, this also sounds like a restriction to me in that modifying the target begs for a similar modification in the proposal, if only because the tails they are a-changin’…

**I**n the case of subsampling the likelihood to gain computation time (as discussed by Korattikara et al. and by Bardenet et al.), the austerity algorithm as described in Algorithm 2 is surprising as the average of the sampled data log-densities and the log-transform of the remainder of the Metropolis-Hastings probability, which seem unrelated, are compared until they are close enough. I also find hard to derive from the different approximation theorems bounding exceedance probabilities a rule to decide on the subsampling rate as a function of the overall sample size and of the computing cost. (As a side if general remark, I remain somewhat reserved about the subsampling idea, given that it requires the entire dataset to be available at every iteration. This makes parallel implementations rather difficult to contemplate.)

## JSM 2015 [day #4]

Posted in pictures, Running, Statistics, Travel, University life with tags ASA, bag of little bootstraps, consistency, harmonic mean estimator, JSM 2015, Langevin diffusion, Langevin MCMC algorithm, latent variable, marginal likelihood, MCMC, Monte Carlo Statistical Methods, MrBayes, philogenic trees, R.A. Fisher, Seattle, soectral clustering, spectral gap, STAN, University of Warwick on August 13, 2015 by xi'an**M**y first session today was Markov Chain Monte Carlo for Contemporary Statistical Applications with a heap of interesting directions in MCMC research! Now, without any possible bias (!), I would definitely nominate Murray Pollock (incidentally from Warwick) as the winner for best slides, funniest presentation, and most enjoyable accent! More seriously, the scalable Langevin algorithm he developed with Paul Fearnhead, Adam Johansen, and Gareth Roberts, is quite impressive in avoiding computing costly likelihoods. With of course caveats on which targets it applies to. Murali Haran showed a new proposal to handle high dimension random effect models by a projection trick that reduces the dimension. Natesh Pillai introduced us (or at least me!) to a spectral clustering that allowed for an automated partition of the target space, itself the starting point to his parallel MCMC algorithm. Quite exciting, even though I do not perceive partitions as an ideal solution to this problem. The final talk in the session was Galin Jones’ presentation of consistency results and conditions for multivariate quantities which is a surprisingly unexplored domain. MCMC is still alive and running!

The second MCMC session of the morning, Monte Carlo Methods Facing New Challenges in Statistics and Science, was equally diverse, with Lynn Kuo’s talk on the HAWK approach, where we discovered that harmonic mean estimators are still in use, e.g., in MrBayes software employed in phylogenetic inference. The proposal to replace this awful estimator that should never be seen again (!) was rather closely related to an earlier solution of us for marginal likelihood approximation, based there on a partition of the whole space rather than an HPD region in our case… Then, Michael Betancourt brilliantly acted as a proxy for Andrew to present the STAN language, with a flashy trailer he most recently designed. Featuring Andrew as the sole actor. And with great arguments for using it, including the potential to run expectation propagation (as a way of life)*. In fine*, Faming Liang proposed a bootstrap subsampling version of the Metropolis-Hastings algorithm, where the likelihood acknowledging the resulting bias in the limiting distribution.

My first afternoon session was another entry on Statistical Phylogenetics, somewhat continued from yesterday’s session. Making me realised I had not seen a single talk on ABC for the entire meeting! The issues discussed in the session were linked with aligning sequences and comparing many trees. Again in settings where likelihoods can be computed more or less explicitly. Without any expertise in the matter, I wondered at a construction that would turn all trees, like into realizations of a continuous model. For instance by growing one branch at a time while removing the MRCA root… And maybe using a particle like method to grow trees. As an aside, Vladimir Minin told me yesterday night about genetic mutations that could switch on and off phenotypes repeatedly across generations… For instance the ability to glow in the dark for species of deep sea fish.

When stating that I did not see a single talk about ABC, I omitted Steve Fienberg’s Fisher Lecture R.A. Fisher and the Statistical ABCs, keeping the *morceau de choix* for the end! Even though of course Steve did not mention the algorithm! A was for *asymptotics*, or ancilarity, B for *Bayesian* (or biducial??), C for *causation* (or cuffiency???)… Among other germs, I appreciated that Steve mentioned my great-grand father Darmois in connection with exponential families! And the connection with Jon Wellner’s LeCam Lecture from a few days ago. And reminding us that Savage was a Fisher lecturer himself. And that Fisher introduced fiducial distributions quite early. And for defending the Bayesian perspective. Steve also set some challenges like asymptotics for networks, Bayesian model assessment (I liked the notion of stepping out of the model), and randomization when experimenting with networks. And for big data issues. And for personalized medicine, building on his cancer treatment. No trace of the ABC algorithm, obviously, but a wonderful Fisher’s lecture, also most obviously!! Bravo, Steve, keep thriving!!!

## Conditional love [guest post]

Posted in Books, Kids, Statistics, University life with tags Andrei Kolmogorov, axioms of probability, Bayes rule, Bayesian nonparametrics, Bayesian statistics, bootstrap, Bruno de Finetti, Céline Dion, David Draper, Dirichlet process, Edwin Jaynes, exchangeability, extendibility, information, JSM 2015, MCMC, plausibility, Richard Cox, Series B, Stone-Weierstrass, Theory of Probability on August 4, 2015 by xi'an*[When Dan Simpson told me he was reading Terenin’s and Draper’s latest arXival in a nice Bath pub—and not a nice bath tub!—, I asked him for a blog entry and he agreed. Here is his piece, read at your own risk! If you remember to skip the part about Céline Dion, you should enjoy it very much!!!]*

**P**robability has traditionally been described, as per Kolmogorov and his ardent follower Katy Perry, unconditionally. This is, of course, excellent for those of us who really like measure theory, as the maths is identical. Unfortunately mathematical convenience is not necessarily enough and a large part of the applied statistical community is working with Bayesian methods. These are unavoidably conditional and, as such, it is natural to ask if there is a fundamentally conditional basis for probability.

Bruno de Finetti—and later Richard Cox and Edwin Jaynes—considered conditional bases for Bayesian probability that are, unfortunately, incomplete. The critical problem is that they mainly consider finite state spaces and construct finitely additive systems of conditional probability. For a variety of reasons, neither of these restrictions hold much truck in the modern world of statistics.

In a recently arXiv’d paper, Alexander Terenin and David Draper devise a set of axioms that make the Cox-Jaynes system of conditional probability rigorous. Furthermore, they show that the complete set of Kolmogorov axioms (including countable additivity) can be derived as theorems from their axioms by conditioning on the entire sample space.

This is a deep and fundamental paper, which unfortunately means that I most probably do not grasp it’s complexities (especially as, for some reason, I keep reading it in pubs!). However I’m going to have a shot at having some thoughts on it, because I feel like it’s the sort of paper one should have thoughts on. Continue reading