Archive for ESS

BayesComp’20

Posted in Books, pictures, Statistics, Travel, University life with tags , , , , , , , , , , , , , , , , , , , , , on January 10, 2020 by xi'an

First, I really have to congratulate my friend Jim Hobert for a great organisation of the meeting adopting my favourite minimalist principles (no name tag, no “goodies” apart from the conference schedule, no official talks). Without any pretense at objectivity, I also appreciated very much the range of topics and the sweet frustration of having to choose between two or three sessions each time. Here are some notes taken during some talks (with no implicit implication for the talks no mentioned, re. above frustration! as well as very short nights making sudden lapse in concentration highly likely).

On Day 1, Paul Fearnhead’s inaugural plenary talk was on continuous time Monte Carlo methods, mostly bouncy particle and zig-zag samplers, with a detailed explanation on the simulation of the switching times which likely brought the audience up to speed even if they had never heard of them. And an opening on PDMPs used as equivalents to reversible jump MCMC, reminding me of the continuous time (point process) solutions of Matthew Stephens for mixture inference (and of Preston, Ripley, Møller).

The same morn I heard of highly efficient techniques to handle very large matrices and p>n variables selections by Akihiko Nishimura and Ruth Baker on a delayed acceptance ABC, using a cheap proxy model. Somewhat different from indirect inference. I found the reliance on ESS somewhat puzzling given the intractability of the likelihood (and the low reliability of the frequency estimate) and the lack of connection with the “real” posterior. At the same ABC session, Umberto Picchini spoke on a joint work with Richard Everitt (Warwick) on linking ABC and pseudo-marginal MCMC by bootstrap. Actually, the notion of ABC likelihood was already proposed as pseudo-marginal ABC by Anthony Lee, Christophe Andrieu and Arnaud Doucet in the discussion of Fearnhead and Prangle (2012) but I wonder at the focus of being unbiased when the quantity is not the truth, i.e. the “real” likelihood. It would seem more appropriate to attempt better kernel estimates on the distribution of the summary itself. The same session also involved David Frazier who linked our work on ABC for misspecified models and an on-going investigation of synthetic likelihood.

Later, there was a surprise occurrence of the Bernoulli factory in a talk by Radu Herbei on Gaussian process priors with accept-reject algorithms, leading to exact MCMC, although the computing implementation remains uncertain. And several discussions during the poster session, incl. one on the planning of a 2021 workshop in Oaxaca centred on objective Bayes advances as we received acceptance of our proposal by BIRS today!

On Day 2, David Blei gave a plenary introduction to variational Bayes inference and latent Dirichlet allocations, somewhat too introductory for my taste although other participants enjoyed this exposition. He also mentioned a recent JASA paper on the frequentist consistency of variational Bayes that I should check. Speaking later with PhD students, they really enjoyed this opening on an area they did not know that well.

A talk by Kengo Kamatani (whom I visited last summer) on improved ergodicity rates for heavy tailed targets and Crank-NIcholson modifications to the random walk proposal (which uses an AR(1) representation instead of the random walk). With the clever idea of adding the scale of the proposal as an extra parameter with a prior of its own. Gaining one order of magnitude in the convergence speed (i.e. from d to 1 and from d² to d, where d is the dimension), which is quite impressive (and just published in JAP).Veronica Rockova linked Bayesian variable selection and machine learning via ABC, with conditions on the prior for model consistency. And a novel approach using part of the data to learn an ABC partial posterior, which reminded me of the partial  Bayes factors of the 1990’s although it is presumably unrelated. And a replacement of the original rejection ABC via multi-armed bandits, where each variable is represented by an arm, called ABC Bayesian forests. Recalling the simulation trick behind Thompson’s approach, reproduced for the inclusion or exclusion of variates and producing a fixed estimate for the (marginal) inclusion probabilities, which makes it sound like a prior-feeback form of empirical Bayes. Followed by a talk of Gregor Kastner on MCMC handling of large time series with specific priors and a massive number of parameters.

The afternoon also had a wealth of exciting talks and missed opportunities (in the other sessions!). Which ended up with a strong if unintended French bias since I listened to Christophe Andrieu, Gabriel Stolz, Umut Simsekli, and Manon Michel on different continuous time processes, with Umut linking GANs, multidimensional optimal transport, sliced-Wasserstein, generative models, and new stochastic differential equations. Manon Michel gave a highly intuitive talk on creating non-reversibility, getting rid of refreshment rates in PDMPs to kill any form of reversibility.

dynamic nested sampling for stars

Posted in Books, pictures, Statistics, Travel with tags , , , , , , , , , , , , , , , , , on April 12, 2019 by xi'an

In the sequel of earlier nested sampling packages, like MultiNest, Joshua Speagle has written a new package called dynesty that manages dynamic nested sampling, primarily intended for astronomical applications. Which is the field where nested sampling is the most popular. One of the first remarks in the paper is that nested sampling can be more easily implemented by using a Uniform reparameterisation of the prior, that is, a reparameterisation that turns the prior into a Uniform over the unit hypercube. Which means in fine that the prior distribution can be generated from a fixed vector of uniforms and known transforms. Maybe not such an issue given that this is the prior after all.  The author considers this makes sampling under the likelihood constraint a much simpler problem but it all depends in the end on the concentration of the likelihood within the unit hypercube. And on the ability to reach the higher likelihood slices. I did not see any special trick when looking at the documentation, but reflected on the fundamental connection between nested sampling and this ability. As in the original proposal by John Skilling (2006), the slice volumes are “estimated” by simulated Beta order statistics, with no connection with the actual sequence of simulation or the problem at hand. We did point out our incomprehension for such a scheme in our Biometrika paper with Nicolas Chopin. As in earlier versions, the algorithm attempts at visualising the slices by different bounding techniques, before proceeding to explore the bounded regions by several exploration algorithms, including HMC.

“As with any sampling method, we strongly advocate that Nested Sampling should not be viewed as being strictly“better” or “worse” than MCMC, but rather as a tool that can be more or less useful in certain problems. There is no “One True Method to Rule Them All”, even though it can be tempting to look for one.”

When introducing the dynamic version, the author lists three drawbacks for the static (original) version. One is the reliance on this transform of a Uniform vector over an hypercube. Another one is that the overall runtime is highly sensitive to the choice the prior. (If simulating from the prior rather than an importance function, as suggested in our paper.) A third one is the issue that nested sampling is impervious to the final goal, evidence approximation versus posterior simulation, i.e., uses a constant rate of prior integration. The dynamic version simply modifies the number of point simulated in each slice. According to the (relative) increase in evidence provided by the current slice, estimated through iterations. This makes nested sampling a sort of inversted Wang-Landau since it sharpens the difference between slices. (The dynamic aspects for estimating the volumes of the slices and the stopping rule may hinder convergence in unclear ways, which is not discussed by the paper.) Among the many examples produced in the paper, a 200 dimension Normal target, which is an interesting object for posterior simulation in that most of the posterior mass rests on a ring away from the maximum of the likelihood. But does not seem to merit a mention in the discussion. Another example of heterogeneous regression favourably compares dynesty with MCMC in terms of ESS (but fails to include an HMC version).

[Breaking News: Although I wrote this post before the exciting first image of the black hole in M87 was made public and hence before I was aware of it, the associated AJL paper points out relying on dynesty for comparing several physical models of the phenomenon by nested sampling.]

 

accelerating HMC by learning the leapfrog scale

Posted in Books, Statistics with tags , , , , , , , , on October 12, 2018 by xi'an

In this new arXiv submission that was part of Changye Wu’s thesis [defended last week],  we try to reduce the high sensitivity of the HMC algorithm to its hand-tuned parameters, namely the step size ε  of the discretisation scheme, the number of steps L of the integrator, and the covariance matrix of the auxiliary variables. By calibrating the number of steps of the Leapfrog integrator towards avoiding both slow mixing chains and wasteful computation costs. We do so by learning from the No-U-Turn Sampler (NUTS) of Hoffman and Gelman (2014) which already automatically tunes both the step size and the number of leapfrogs.

The core idea behind NUTS is to pick the step size via primal-dual averaging in a burn-in (warmup, Andrew would say) phase and to build at each iteration a proposal based on following a locally longest path on a level set of the Hamiltonian. This is achieved by a recursive algorithm that, at each call to the leapfrog integrator, requires to evaluate both the gradient of the target distribution and the Hamiltonianitself. Roughly speaking an iteration of NUTS costs twice as much as regular HMC with the same number of calls to the integrator. Our approach is to learn from NUTS the scale of the leapfrog length and use the resulting empirical distribution of the longest leapfrog path to randomly pick the value of  L at each iteration of an HMC scheme. This obviously preserves the validity of the HMC algorithm.

While a theoretical comparison of the convergence performances of NUTS and this eHMC proposal seem beyond our reach, we ran a series of experiments to evaluate these performances, using as a criterion an ESS value that is calibrated by the evaluation cost of the logarithm of target density function and of its gradient, as this is usually the most costly part of the algorithms. As well as a similarly calibrated expected square jumping distance. Above is one such illustration for a stochastic volatility model, the first axis representing the targeted acceptance probability in the Metropolis step. Some of the gains in either ESS or ESJD are by a factor of ten, which relates to our argument that NUTS somewhat wastes computation effort using a uniformly distributed proposal over the candidate set, instead of being close to its end-points, which automatically reduces the distance between the current position and the proposal.

rethinking the ESS

Posted in Statistics with tags , , , , , , , , , on September 14, 2018 by xi'an

Following Victor Elvira‘s visit to Dauphine, one and a half year ago, where we discussed the many defects of ESS as a default measure of efficiency for importance sampling estimators, and then some more efforts (mostly from Victor!) to formalise these criticisms, Victor, Luca Martino and I wrote a paper on this notion, now arXived. (Victor most kindly attributes the origin of the paper to a 2010 ‘Og post on the topic!) The starting thread of the (re?)analysis of this tool introduced by Kong (1992) is that the ESS used in the literature is an approximation to the “true” ESS, generally unavailable. Approximation that is pretty crude and hence impacts the relevance of using it as the assessment tool for comparing importance sampling methods. In the paper, we re-derive (with the uttermost precision) the resulting approximation and list the many assumptions that [would] validate this approximation. The resulting drawbacks are many, from the absurd property of always being worse than direct sampling, to being independent from the target function and from the sample per se. Since only importance weights matter. This list of issues is not exactly brand new, but we think it is worth signaling given the fact that this approximation has been widely used in the last 25 years, due to its simplicity, as a practical rule of thumb [!] in a wide variety of importance sampling methods. In continuation of the directions drafted in Martino et al. (2017), we also indicate some alternative notions of importance efficiency. Note that this paper does not cover the use of ESS for MCMC algorithms, where it is somewhat more legit, if still too rudimentary to really catch convergence or lack thereof! [Note: I refrained from the post title resinking the ESS…]