Archive for variational Bayes methods

automatic variational ABC

Posted in pictures, Statistics with tags , , , , , , , , , , on July 8, 2016 by xi'an

Amster11“Stochastic Variational inference is an appealing alternative to the inefficient sampling approaches commonly used in ABC.”

Moreno et al. [including Ted Meeds and Max Welling] recently arXived a paper merging variational inference and ABC. The argument for turning variational is computational speedup. The traditional (in variational inference) divergence decomposition of the log-marginal likelihood is replaced by an ABC version, parameterised in terms of intrinsic generators (i.e., generators that do not depend on cyber-parameters, like the U(0,1) or the N(0,1) generators). Or simulation code in the authors’ terms. Which leads to the automatic aspect of the approach. In the paper the derivation of the gradient is indeed automated.

“One issue is that even assuming that the ABC likelihood is an unbiased estimator of the true likelihood (which it is not), taking the log introduces a bias, so that we now have a biased estimate of the lower bound and thus biased gradients.”

I wonder how much of an issue this is, since we consider the variational lower bound. To be optimised in terms of the parameters of the variational posterior. Indeed, the endpoint of the analysis is to provide an optimal variational approximation, which remains an approximation whether or not the likelihood estimator is unbiased. A more “severe” limitation may be in the inversion constraint, since it seems to eliminate Beta or Gamma distributions. (Even though calling qbeta(runif(1),a,b) definitely is achievable… And not rejected by a Kolmogorov-Smirnov test.)

Incidentally, I discovered through the paper the existence of the Kumaraswamy distribution, which main appeal seems to be the ability to produce a closed-form quantile function, while bearing some resemblance with the Beta distribution. (Another arXival by Baltasar Trancón y Widemann studies some connections between those, but does not tell how to select the parameters to optimise the similarity.)

Michael Jordan’s seminar in Paris next week

Posted in Statistics, University life with tags , , , , , on June 3, 2016 by xi'an

Next week, on June 7, at 4pm, Michael will give a seminar at INRIA, rue du Charolais, Paris 12 (map). Here is the abstract:

A Variational Perspective on Accelerated Methods in Optimization

Accelerated gradient methods play a central role in optimization,achieving optimal rates in many settings. While many generalizations and extensions of Nesterov’s original acceleration method have been proposed,it is not yet clear what is the natural scope of the acceleration concept.In this paper, we study accelerated methods from a continuous-time perspective. We show that there is a Lagrangian functional that we call the Bregman Lagrangian which generates a large class of accelerated methods in continuous time, including (but not limited to) accelerated gradient descent, its non-Euclidean extension, and accelerated higher-order gradient methods. We show that the continuous-time limit of all of these methods correspond to travelling the same curve in space time at different speeds, and in this sense the continuous-time setting is the natural one for understanding acceleration.  Moreover, from this perspective, Nesterov’s technique and many of its generalizations can be viewed as a systematic way to go from the continuous-time curves generated by the Bregman Lagrangian to a family of discrete-time accelerated algorithms. [Joint work with Andre Wibisono and Ashia Wilson.]

(Interested readers need to register to attend the lecture.)

variational Bayes for variable selection

Posted in Books, Statistics, University life with tags , , , , , , , on March 30, 2016 by xi'an

Lake Agnes, Canadian Rockies, July 2007Xichen Huang, Jin Wang and Feng Liang have recently arXived a paper where they rely on variational Bayes in conjunction with a spike-and-slab prior modelling. This actually stems from an earlier paper by Carbonetto and Stephens (2012), the difference being in the implementation of the method, which is less Gibbs-like for the current paper. The approach is not fully Bayesian in that, not only an approximate (variational) representation is used for the parameters of interest (regression coefficient and presence-absence indicators) but also the nuisance parameters are replaced with MAPs. The variational approximation on the regression parameters is an independent product of spike-and-slab distributions. The authors show the approximate approach is consistent in both frequentist and Bayesian terms (under identifiability assumptions). The method is undoubtedly faster than MCMC since it shares many features with EM but I still wonder at the Bayesian interpretability of the outcome, which writes out as a product of estimated spike-and-slab mixtures. First, the weights in the mixtures are estimated by EM, hence fixed. Second, the fact that the variational approximation is a product is confusing in that the posterior distribution on the regression coefficients is unlikely to produce posterior independence.

patterns of scalable Bayesian inference

Posted in Books, Statistics, University life with tags , , , , , , , , , , , , on February 24, 2016 by xi'an

Elaine Angelino, Matthew Johnson and Ryan Adams just arXived a massive survey of 118 pages on scalable Bayesian inference, which could have been entitled Bayes for Big Data, as this monograph covers state-of-the-art computational approaches to large and complex data structures. I did not read each and every line of it, but I have already recommended it to my PhD students. Some of its material unsurprisingly draws from the recent survey by Rémi Bardenet et al. (2015) I discussed a while ago. It also relates rather frequently to the somewhat parallel ICML paper of Korattikara et al. (2014). And to the firefly Monte Carlo procedure also discussed previously here.

Chapter 2 provides some standard background on computational techniques, Chapter 3 covers MCMC with data subsets, Chapter 4 gives some entries on MCMC with parallel and distributed architectures, Chapter 5 focus on variational solutions, and Chapter 6 is about open questions and challenges.

“Insisting on zero asymptotic bias from Monte Carlo estimates of expectations may leave us swamped in errors from high variance or transient bias.”

One central theme of the paper is the need for approximate solutions, MCMC being perceived as the exact solution. (Somewhat wrongly in the sense that the product of an MCMC is at best an empirical version of the true posterior, hence endowed with a residual and incompressible variation for a given computing budget.) While Chapter 3 stresses the issue of assessing the distance to the true posterior, it does not dwell at all on computing times and budget, which is arguably a much harder problem. Chapter 4 seems to be more aware of this issue since arguing that “a way to use parallel computing resources is to run multiple sequential MCMC algorithms at once [but that this] does not reduce the transient bias in MCMC estimates of posterior expectations” (p.54). The alternatives are to use either prefetching (which was the central theme of Elaine Angelino’s thesis), asynchronous Gibbs with the new to me (?) Hogwild Gibbs algorithms (connected in Terenin et al.’s recent paper, not quoted in the paper), some versions of consensus Monte Carlo covered in earlier posts, the missing links being in my humble opinion an assessment of the worth of those solutions (in the spirit of “here’s the solution, what was the problem again?”) and once again the computing time issue. Chapter 5 briefly discusses some recent developments in variational mean field approximations, which is farther from my interests and (limited) competence, but which appears as a particular class of approximate models and thus could (and should?) relate to likelihood-free methods. Chapter 6 about the current challenges of the field is presumably the most interesting in this monograph in that it produces open questions and suggests directions for future research. For instance, opposing the long term MCMC error with the short term transient part. Or the issue of comparing different implementations in a practical and timely perspective.

variational consensus Monte Carlo

Posted in Books, Statistics, University life with tags , , , , , , on July 2, 2015 by xi'an

“Unfortunately, the factorization does not make it immediately clear how to aggregate on the level of samples without first having to obtain an estimate of the densities themselves.” (p.2)

The recently arXived variational consensus Monte Carlo is a paper by Maxim Rabinovich, Elaine Angelino, and Michael Jordan that approaches the consensus Monte Carlo principle from a variational perspective. As in the embarrassingly parallel version,  the target is split into a product of K terms, each being interpreted as an unnormalised density and being fed to a different parallel processor. The most natural partition is to break the data into K subsamples and to raise the prior to the power 1/K in each term. While this decomposition makes sense from a storage perspective, since each bit corresponds to a different subsample of the data, it raises the question of the statistical pertinence of splitting the prior and my feelings about it are now more lukewarm than when I commented on the embarrassingly parallel version,  mainly for the reason that it is not reparameterisation invariant—getting different targets if one does the reparameterisation before or after the partition—and hence does not treat the prior as the reference measure it should be. I therefore prefer the version where the same original prior is attached to each part of the partitioned likelihood (and even more the random subsampling approaches discussed in the recent paper of Bardenet, Doucet, and Holmes). Another difficulty with the decomposition is that a product of densities is not a density in most cases (it may even be of infinite mass) and does not offer a natural path to the analysis of samples generated from each term in the product. Nor an explanation as to why those samples should be relevant to construct a sample for the original target.

“The performance of our algorithm depends critically on the choice of aggregation function family.” (p.5)

Since the variational Bayes approach is a common answer to complex products models, Rabinovich et al. explore the use of variational Bayes techniques to build the consensus distribution out of the separate samples. As in Scott et al., and Neiswanger et al., the simulation from the consensus distribution is a transform of simulations from each of the terms in the product, e.g., a weighted average. Which determines the consensus distribution as a member of an aggregation family defined loosely by a Dirac mass. When the transform is a sum of individual terms, variational Bayes solutions get much easier to find and the authors work under this restriction… In the empirical evaluation of this variational Bayes approach as opposed to the uniform and Gaussian averaging options in Scott et al., it improves upon those, except in a mixture example with a large enough common variance.

In fine, despite the relevance of variational Bayes to improve the consensus approximation, I still remain unconvinced about the use of the product of (pseudo-)densities and the subsequent mix of simulations from those components, for the reason mentioned above and also because the tail behaviour of those components is not related with the tail behaviour of the target. Still, this is a working solution to a real problem and as such is a reference for future works.

Bayesian computation: fore and aft

Posted in Books, Statistics, University life with tags , , , , , , , , , , , , on February 6, 2015 by xi'an

BagneuxWith my friends Peter Green (Bristol), Krzysztof Łatuszyński (Warwick) and Marcello Pereyra (Bristol), we just arXived the first version of “Bayesian computation: a perspective on the current state, and sampling backwards and forwards”, which first title was the title of this post. This is a survey of our own perspective on Bayesian computation, from what occurred in the last 25 years [a  lot!] to what could occur in the near future [a lot as well!]. Submitted to Statistics and Computing towards the special 25th anniversary issue, as announced in an earlier post.. Pulling strength and breadth from each other’s opinion, we have certainly attained more than the sum of our initial respective contributions, but we are welcoming comments about bits and pieces of importance that we miss and even more about promising new directions that are not posted in this survey. (A warning that is should go with most of my surveys is that my input in this paper will not differ by a large margin from ideas expressed here or in previous surveys.)

NIPS 2014

Posted in Kids, pictures, Statistics, Travel, University life with tags , , , , , , , , , , , on December 15, 2014 by xi'an

mugSecond and last day of the NIPS workshops! The collection of topics was quite broad and would have made my choosing an ordeal, except that I was invited to give a talk at the probabilistic programming workshop, solving my dilemma… The first talk by Kathleen Fisher was quite enjoyable in that it gave a conceptual discussion of the motivations for probabilistic languages, drawing an analogy with the early days of computer programming that saw a separation between higher level computer languages and machine programming, with a compiler interface. And calling for a similar separation between the models faced by statistical inference and machine-learning and the corresponding code, if I understood her correctly. This was connected with Frank Wood’s talk of the previous day where he illustrated the concept through a generation of computer codes to approximately generate from standard distributions like Normal or Poisson. Approximately as in ABC, which is why the organisers invited me to talk in this session. However, I was a wee bit lost in the following talks and presumably lost part of my audience during my talk, as I realised later to my dismay when someone told me he had not perceived the distinction between the trees in the random forest procedure and the phylogenetic trees in the population genetic application. Still, while it had for me a sort of Twilight Zone feeling of having stepped in another dimension, attending this workshop was an worthwhile experiment as an eye-opener into a highly different albeit connected field, where code and simulator may take the place of a likelihood function… To the point of defining Hamiltonian Monte Carlo directly on the former, as Vikash Mansinghka showed me at the break.

I completed the day with the final talks in the variational inference workshop, if only to get back on firmer ground! Apart from attending my third talk by Vikash in the conference (but on a completely different topic on variational approximations for discrete particle-ar distributions), a talk by Tim Salimans linked MCMC and variational approximations, using MCMC and HMC to derive variational bounds. (He did not expand on the opposite use of variational approximations to build better proposals.) Overall, I found these two days and my first NIPS conference quite exciting, if somewhat overpowering, with a different atmosphere and a different pace compared with (small or large) statistical meetings. (And a staggering gender imbalance!)