Next month, I am taking part in a workshop on sampling & clustering at the Max-Planck-Institut für Physik in Garching, Germany (near München). By giving a three hour introduction to ABC, as I did three years ago in Autrans. Being there and talking with local researchers if the sanitary conditions allow. From my office otherwise. Other speakers include Michael Betancourt on HMC and Johannes Buchner on nested sampling. The remote participation to this MPI workshop is both open and free, but participants must register before 18 September, namely tomorrow.
Archive for HMC
state of the art in sampling & clustering [workshop]
Posted in Books, pictures, Statistics, Travel, University life with tags Autrans, clustering, Garching, Germany, HMC, Max Planck Institute, Max-Planck-Institut für Physik, München, nested sampling, sampling, workshop on September 17, 2020 by xi'antransport Monte Carlo
Posted in Books, pictures, Statistics, Travel with tags ABC, Approximate Bayesian computation, BayesComp 2020, Bayesian computation, Dirichlet mixture priors, Gainesville, Gaspard Monge, Hamiltonian Monte Carlo, HMC, macha tea, Monte Carlo error, normalizing flow, optimal transport, Paul Deheuvels, transportation model, University of Florida on August 31, 2020 by xi'an
Read this recent arXival by Leo Duan (from UF in Gainesville) on transport approaches to approximate Bayesian computation, in connection with normalising flows. The author points out a “lack of flexibility in a large class of normalizing flows” to bring forward his own proposal.
“…we assume the reference (a multivariate uniform distribution) can be written as a mixture of many one-to-one transforms from the posterior”
The transportation problem is turned into defining a joint distribution on (β,θ) such that θ is marginally distributed from the posterior and β is one of an infinite collection of transforms of θ. Which sounds quite different from normalizing flows, to be sure. Reverting the order, if one manages to simulate β from its marginal the resulting θ is one of the transforms. Chosen to be a location-scale modification of β, s⊗β+m. The weights when going from θ to β are logistic transforms with Dirichlet distributed scales. All with parameters to be optimised by minimising the Kullback-Leibler distance between the reference measure on β and its inverse mixture approximation, and resorting to gradient descent. (This may sound a wee bit overwhelming as an approximation strategy and I actually had to make a large cup of strong macha to get over it, but this may be due to the heat wave occurring at the same time!) Drawing θ from this approximation is custom-made straightforward and an MCMC correction can even be added, resulting in an independent Metropolis-Hastings version since the acceptance ratio remains computable. Although this may defeat the whole purpose of the exercise by stalling the chain if the approximation is poor (hence suggesting this last step being used instead as a control.)
The paper also contains a theoretical section that studies the approximation error, going to zero as the number of terms in the mixture, K, goes to infinity. Including a Monte Carlo error in log(n)/n (and incidentally quoting a result from my former HoD at Paris 6, Paul Deheuvels). Numerical experiments show domination or equivalence with some other solutions, e.g. being much faster than HMC, the remaining $1000 question being of course the on-line evaluation of the quality of the approximation.
the buzz about nuzz
Posted in Books, Mountains, pictures, Statistics with tags Hamiltonian Monte Carlo, HMC, Jim Berger, Loch Lomond, MALA, Metropolis-Hastings algorithm, partly deterministic processes, PDMP, Poisson process, Purdue University, root finding, Tom Sellke, Wasserstein distance, Zig-Zag on April 6, 2020 by xi'an
“…expensive in these terms, as for each root, Λ(x(s),v) (at the cost of one epoch) has to be evaluated for each root finding iteration, for each node of the numerical integral“
When using the ZigZag sampler, the main (?) difficulty is in producing velocity switch as the switches are produced as interarrival times of an inhomogeneous Poisson process. When the rate of this process cannot be integrated out in an analytical manner, the only generic approach I know is in using Poisson thinning, obtained by finding an integrable upper bound on this rate, generating from this new process and subsampling. Finding the bound is however far from straightforward and may anyway result in an inefficient sampler. This new paper by Simon Cotter, Thomas House and Filippo Pagani makes several proposals to simplify this simulation, Nuzz standing for numerical ZigZag. Even better (!), their approach is based on what they call the Sellke construction, with Tom Sellke being a probabilist and statistician at Purdue University (trivia: whom I met when spending a postdoctoral year there in 1987-1988) who also wrote a fundamental paper on the opposition between Bayes factors and p-values with Jim Berger.
“We chose as a measure of algorithm performance the largest Kolmogorov-Smirnov (KS) distance between the MCMC sample and true distribution amongst all the marginal distributions.”
The practical trick is rather straightforward in that it sums up as the exponentiation of the inverse cdf method, completed with a numerical resolution of the inversion. Based on the QAGS (Quadrature Adaptive Gauss-Kronrod Singularities) integration routine. In order to save time Kingman’s superposition trick only requires one inversion rather than d, the dimension of the variable of interest. This nuzzled version of ZIgZag can furthermore be interpreted as a PDMP per se. Except that it retains a numerical error, whose impact on convergence is analysed in the paper. In terms of Wasserstein distance between the invariant measures. The paper concludes with a numerical comparison between Nuzz and random walk Metropolis-Hastings, HMC, and manifold MALA, using the number of evaluations of the likelihood as a measure of time requirement. Tuning for Nuzz is described, but not for the competition. Rather dramatically the Nuzz algorithm performs worse than this competition when counting one epoch for each likelihood computation and better when counting one epoch for each integral inversion. Which amounts to perfect inversion, unsurprisingly. As a final remark, all models are more or less Normal, with very smooth level sets, maybe not an ideal range
MCMC, with common misunderstandings
Posted in Books, pictures, R, Statistics, University life with tags ABC, Bayesian computing, computational statistics, Gibbs sampling, Handbook of Computational Statistics and Data Science, HMC, IMS Lawrence D. Brown PhD Student Award, MCMC, PhD thesis, Q&A format, Statistics and Computing, survey, variational Bayes methods on January 27, 2020 by xi'an
As I was asked to write a chapter on MCMC methods for an incoming Handbook of Computational Statistics and Data Science, published by Wiley, rather than cautiously declining!, I decided to recycle the answers I wrote on X validated to what I considered to be the most characteristic misunderstandings about MCMC and other computing methods, using as background the introduction produced by Wu Changye in his PhD thesis. Waiting for the opinion of the editors of the Handbook on this Q&A style. The outcome is certainly lighter than other recent surveys like the one we wrote with Peter Green, Krys Latuszinski, and Marcelo Pereyra, for Statistics and Computing, or the one with Victor Elvira, Nick Tawn, and Changye Wu.
BayesComp 2020 at a glance
Posted in Statistics, Travel, University life with tags ABC, BayesComp 2020, Bayesian computation, Bayesian nonparametrics, conference, Gainesville, Gaussian processes, HMC, ISBA, MCMC, non-reversible diffusion, poster session, reversible Markov chain, simulation, University of Florida, USA, Wasserstein distance on December 18, 2019 by xi'an
