Archive for what you get is what you see

transport, diffusions, and sampling

Posted in pictures, Statistics, Travel, University life with tags , , , , , , , , , , , , , , , , , , , , , , on November 19, 2022 by xi'an

At the Sampling, Transport, and Diffusions workshop at the Flatiron Institute, on Day #2, Marilou Gabrié (École Polytechnique) gave the second introductory lecture on merging sampling and normalising flows targeting the target distribution, when driven by a divergence criterion like KL, that only requires the shape of the target density. I first wondered about ergodicity guarantees in simultaneous MCMC and map training due to the adaptation of the flow but the update of the map only depends on the current particle cloud in (8). From an MCMC perspective, it sounds somewhat paradoxical to see the independent sampler making such an unexpected come-back when considering that no insider information is available about the (complex) posterior to drive the [what-you-get-is-what-you-see] construction of the transport map. However, the proposed approach superposed local (random-walk like) and global (transport) proposals in Algorithm 1.

Qiang Liu followed on learning transport maps, with the  Interesting notion of causalizing a graph by removing intersections (which are impossible for an ODE, as discussed by Eric Vanden-Eijden’s talk yesterday) through  coupling. Which underlies his notion of rectified flows. Possibly connecting with the next lightning talk by Jonathan Weare on spurious modes created by a variational Monte Carlo sampler and the use of stochastic gradient, corrected by (case-dependent?) regularisation.

Then came a whole series of MCMC talks!

Sam Livingstone spoke on Barker’s proposal (an incoming Biometrika paper!) as part of a general class of transforms g of the MH ratio, using jump processes based on a nasty normalising constant related with g (tractable for the original Barker algorithm). I then realised I had missed his StatSci paper on how to speak to statistical physics researchers!

Charles Margossian spoke about using a massive number of short parallel runs (many-short-chain regime) from a recent paper written with Aki,  Andrew, and Lionel Riou-Durand (Warwick) among others. Which brings us back to the challenge of producing convergence diagnostics and precisely the Gelman-Rubin R statistic or its recent nR avatar (with its linear limitations and dependence on parameterisation, as opposed to fuller distributional criteria). The core of the approach is in using blocks of GPUs to improve and speed-up the estimation of the between-chain variance. (D for R².) I still wonder at a waste of simulations / computing power resulting from stopping the runs almost immediately after warm-up is over, since reaching the stationary regime or an approximation thereof should be exploited more efficiently. (Starting from a minimal discrepancy sample would also improve efficiency.)

Lu Zhang also talked on the issue of cutting down warmup, presenting a paper co-authored with Bob, Andrew, and Aki, recommending Laplace / variational approximations for reaching faster high-posterior-density regions, using an algorithm called Pathfinder that relies on ELBO checks to counter poor performances of Laplace approximations. In the spirit of the workshop, it could be profitable to further transform / push-forward the outcome by a transport map.

Yuling Yao (of stacking and Pareto smoothing fame!) gave an original and challenging (in a positive sense) talk on the many ways of bridging densities [linked with the remark he shared with me the day before] and their statistical significance. Questioning our usual reliance on arithmetic or geometric mixtures. Ignoring computational issues, selecting a bridging pattern sounds not different from choosing a parameterised family of embedding distributions. This new typology of models can then be endowed with properties that are more or less appealing. (Occurences of the Hyvärinen score and our mixtestin perspective in the talk!)

Miranda Holmes-Cerfon talked about MCMC on stratification (illustrated by this beautiful picture of nanoparticle random walks). Which means sampling under varying constraints and dimensions with associated densities under the respective Hausdorff measures. This sounds like a perfect setting for reversible jump and in a sense it is, as mentioned in the talks. Except that the moves between manifolds are driven by the proximity to said manifold, helping with a higher acceptance rate, and making the proposals easier to construct since projections (or the reverses) have a physical meaning. (But I could not tell from the talk why the approach was seemingly escaping the symmetry constraint set by Peter Green’s RJMCMC on the reciprocal moves between two given manifolds).

assessing MCMC convergence

Posted in Books, Statistics, University life with tags , , , , , , , , , , , on June 6, 2019 by xi'an

When MCMC became mainstream in the 1990’s, there was a flurry of proposals to check, assess, and even guarantee convergence to the stationary distribution, as discussed in our MCMC book. Along with Chantal Guihenneuc and Kerrie Mengersen, we also maintained for a while a reviewww webpage categorising theses. Niloy Biswas and Pierre Jacob have recently posted a paper where they propose the use of couplings (and unbiased MCMC) towards deriving bounds on different metrics between the target and the current distribution of the Markov chain. Two chains are created from a given kernel and coupled with a lag of L, meaning that after a while, the two chains become one with a time difference of L. (The supplementary material contains many details on how to induce coupling.) The distance to the target can then be bounded by a sum of distances between the two chains until they merge. The above picture from the paper is a comparison a Polya-Urn sampler with several HMC samplers for a logistic target (not involving the Pima Indian dataset!). The larger the lag L the more accurate the bound. But the larger the lag the more expensive the assessment of how many steps are needed to convergence. Especially when considering that the evaluation requires restarting the chains from scratch and rerunning until they couple again, rather than continuing one run which can only brings the chain closer to stationarity and to being distributed from the target. I thus wonder at the possibility of some Rao-Blackwellisation of the simulations used in this assessment (while realising once more than assessing convergence almost inevitably requires another order of magnitude than convergence itself!). Without a clear idea of how to do it… For instance, keeping the values of the chain(s) at the time of coupling is not directly helpful to create a sample from the target since they are not distributed from that target.

[Pierre also wrote a blog post about the paper on Statisfaction that is definitely much clearer and pedagogical than the above.]

did variational Bayes work?

Posted in Books, Statistics with tags , , , , , , , , , on May 2, 2019 by xi'an

An interesting ICML 2018 paper by Yuling Yao, Aki Vehtari, Daniel Simpson, and Andrew Gelman I missed last summer on [the fairly important issue of] assessing the quality or lack thereof of a variational Bayes approximation. In the sense of being near enough from the true posterior. The criterion that they propose in this paper relates to the Pareto smoothed importance sampling technique discussed in an earlier post and which I remember discussing with Andrew when he visited CREST a few years ago. The truncation of the importance weights of prior x likelihood / VB approximation avoids infinite variance issues but induces an unknown amount of bias. The resulting diagnostic is based on the estimation of the Pareto order k. If the true value of k is less than ½, the variance of the associated Pareto distribution is finite. The paper suggests to conclude at the worth of the variational approximation when the estimate of k is less than 0.7, based on the empirical assessment of the earlier paper. The paper also contains a remark on the poor performances of the generalisation of this method to marginal settings, that is, when the importance weight is the ratio of the true and variational marginals for a sub-vector of interest. I find the counter-performances somewhat worrying in that Rao-Blackwellisation arguments make me prefer marginal ratios to joint ratios. It may however be due to a poor approximation of the marginal ratio that reflects on the approximation and not on the ratio itself. A second proposal in the paper focus on solely the point estimate returned by the variational Bayes approximation. Testing that the posterior predictive is well-calibrated. This is less appealing, especially when the authors point out the “dissadvantage is that this diagnostic does not cover the case where the observed data is not well represented by the model.” In other words, misspecified situations. This potential misspecification could presumably be tested by comparing the Pareto fit based on the actual data with a Pareto fit based on simulated data. Among other deficiencies, they point that this is “a local diagnostic that will not detect unseen modes”. In other words, what you get is what you see.

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