Archive for Gelman-Rubin statistic

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).

revisiting the Gelman-Rubin diagnostic

Posted in Books, pictures, Statistics, Travel, University life with tags , , , , , , , , , , , , , on January 23, 2019 by xi'an

Just before Xmas, Dootika Vats (Warwick) and Christina Knudson arXived a paper on a re-evaluation of the ultra-popular 1992 Gelman and Rubin MCMC convergence diagnostic. Which compares within-variance and between-variance on parallel chains started from hopefully dispersed initial values. Or equivalently an under-estimating and an over-estimating estimate of the MCMC average. In this paper, the authors take advantage of the variance estimators developed by Galin Jones, James Flegal, Dootika Vats and co-authors, which are batch mean estimators consistently estimating the asymptotic variance. They also discuss the choice of a cut-off on the ratio R of variance estimates, i.e., how close to one need it be? By relating R to the effective sample size (for which we also have reservations), which gives another way of calibrating the cut-off. The main conclusion of the study is that the recommended 1.1 bound is too large for a reasonable proximity to the true value of the Bayes estimator (Disclaimer: The above ABCruise header is unrelated with the paper, apart from its use of the Titanic dataset!)

In fact, I have other difficulties than setting the cut-off point with the original scheme as a way to assess MCMC convergence or lack thereof, among which

  1. its dependence on the parameterisation of the chain and on the estimation of a specific target function
  2. its dependence on the starting distribution which makes the time to convergence not absolutely meaningful
  3. the confusion between getting to stationarity and exploring the whole target
  4. its missing the option to resort to subsampling schemes to attain pseudo-independence or scale time to convergence (albeit see 3. above)
  5. a potential bias brought by the stopping rule.

understanding computational Bayesian statistics: a reply from Bill Bolstad

Posted in Books, R, Statistics, University life with tags , , , , , , , , , , , , , on October 24, 2011 by xi'an

Bill Bolstad wrote a reply to my review of his book Understanding computational Bayesian statistics last week and here it is, unedited except for the first paragraph where he thanks me for the opportunity to respond, “so readers will see that the book has some good features beyond having a “nice cover”.” (!) I simply processed the Word document into an html output and put a Read More bar in the middle as it is fairly detailed. (As indicated at the beginning of my review, I am obviously biased on the topic: thus, I will not comment on the reply, lest we get into an infinite regress!)

The target audience for this book are upper division undergraduate students and first year graduate students in statistics whose prior statistical education has been mostly frequentist based. Many will have knowledge of Bayesian statistics at an introductory level similar to that in my first book, but some will have no previous Bayesian statistics course. Being self-contained, it will also be suitable for statistical practitioners without a background in Bayesian statistics.

The book aims to show that:

  1. Bayesian statistics makes different assumptions from frequentist statistics, and these differences lead to the advantages of the Bayesian approach.
  2. Finding the proportional posterior is easy, however finding the exact posterior distribution is difficult in practice, even numerically, especially for models with many parameters.
  3. Inferences can be based on a (random) sample from the posterior.
  4. There are methods for drawing samples from the incompletely known posterior.
  5. Direct reshaping methods become inefficient for models with large number of parameters.
  6. We can find a Markov chain that has the long-run distribution with the same shape as the posterior. A draw from this chain after it has run a long time can be considered a random draw from the posterior
  7. We have many choices in setting up a Markov chain Monte Carlo. The book shows the things that should be considered, and how problems can be detected from sample output from the chain.
  8. An independent Metropolis-Hastings chain with a suitable heavy-tailed candidate distribution will perform well, particularly for regression type models. The book shows all the details needed to set up such a chain.
  9. The Gibbs sampling algorithm is especially well suited for hierarchical models.

I am satisfied that the book has achieved the goals that I set out above. The title “Understanding Computational Bayesian Statistics” explains what this book is about. I want the reader (who has background in frequentist statistics) to understand how computational Bayesian statistics can be applied to models he/she is familiar with. I keep an up-to-date errata on the book website..The website also contains the computer software used in the book. This includes Minitab macros and R-functions. These were used because because they had good data analysis capabilities that could be used in conjunction with the simulations. The website also contains Fortran executables that are much faster for models containing more parameters, and WinBUGS code for the examples in the book. Continue reading

understanding computational Bayesian statistics

Posted in Books, R, Statistics, University life with tags , , , , , , , , , , , on October 10, 2011 by xi'an

I have just finished reading this book by Bill Bolstad (University of Waikato, New Zealand) which a previous ‘Og post pointed out when it appeared, shortly after our Introducing Monte Carlo Methods with R. My family commented that the cover was nicer than those of my own books, which is true. Before I launch into a review, let me warn the ‘Og reader that, as an author of three books on computational Bayesian statistics, I cannot be very objective on the topic: I do favour the way we approached Bayesian computational methods and, after reading Bolstad’s Understanding computational Bayesian statistics, would still have written the books the way we did. Be warned, thus.

Understanding computational Bayesian statistics is covering the basics of Monte Carlo and (fixed dimension) Markov Chain Monte Carlo methods, with a fair chunk dedicated to prerequisites in Bayesian statistics and Markov chain theory. Even though I have only glanced at the table of contents of Bolstad’s Introduction to Bayesian Statistics [using almost the same nice whirl picture albeit in bronze rather than cobalt], it seems to me that the current book is the continuation of the earlier one, going beyond the Binomial, Poisson, and normal cases, to cover generalised linear models, via MCMC methods. (In this respect, it corresponds to Chapter 4 of Bayesian Core.) The book is associated with Minitab macros and an R package (written by James Curran), Bolstad2, in continuation of Bolstad, written for Introduction to Bayesian Statistics. Overall, the level of the book is such that it should be accessible to undergraduate students, MCMC methods being reduced to Gibbs, random walk and independent Metropolis-Hastings algorithms, and convergence assessments being done via autocorrelation graphs, the Gelman and Rubin (1992) intra-/inter-variance criterion, and a forward coupling device. The illustrative chapters cover logistic regression (Chap. 8), Poisson regression (Chap. 9), and normal hierarchical models (Chap. 10). Again, the overall feeling is that the book should be understandable to undergraduate students, even though it may make MCMC seem easier than it is by sticking to fairly regular models. In a sense, it is more a book of the [roaring MCMC] 90’s in that it does not incorporate advances from 2000 onwards (as seen from the reference list) like adaptive MCMC and the resurgence of importance sampling via particle systems and sequential Monte Carlo.

Continue reading

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