Archive for Metropolis-Hastings algorithms

Posterior expectation of regularly paved random histograms

Posted in Books, Statistics, University life with tags , , , , , , , , , on October 7, 2013 by xi'an

Today, Raazesh Sainudiin from the University of Canterbury, in Christchurch, New Zealand, gave a seminar at CREST in our BIP (Bayesians in Paris) seminar series. Here is his abstract:

We present a novel method for averaging a sequence of histogram states visited by a Metropolis-Hastings Markov chain whose stationary distribution is the posterior distribution over a dense space of tree-based histograms. The computational efficiency of our posterior mean histogram estimate relies on a statistical data-structure that is sufficient for non-parametric density estimation of massive, multi-dimensional metric data. This data-structure is formalized as statistical regular paving (SRP). A regular paving (RP) is a binary tree obtained by selectively bisecting boxes along their first widest side. SRP augments RP by mutably caching the recursively computable sufficient statistics of the data. The base Markov chain used to propose moves for the Metropolis-Hastings chain is a random walk that data-adaptively prunes and grows the SRP histogram tree. We use a prior distribution based on Catalan numbers and detect convergence heuristically. The L1-consistency of the the initializing strategy over SRP histograms using a data-driven randomized priority queue based on a generalized statistically equivalent blocks principle is proved by bounding the Vapnik-Chervonenkis shatter coefficients of the class of SRP histogram partitions. The performance of our posterior mean SRP histogram is empirically assessed for large sample sizes simulated from several multivariate distributions that belong to the space of SRP histograms.

The paper actually appeared in the special issue of TOMACS Arnaud Doucet and I edited last year. It is coauthored by Dominic Lee, Jennifer Harlow and Gloria Teng. Unfortunately, Raazesh could not connect to our video-projector. Or fortunately as he gave a blackboard talk that turned to be fairly intuitive and interactive.

sticky Metropolis

Posted in Statistics, University life with tags , , , , , , on September 6, 2013 by xi'an

My former student Roberto Casarin and his colleagues wrote (and arXived) a paper entitled Adaptive sticky generalized Metropolis algorithm. The basic idea is to use some of the rejected and past values of the chain to build an adaptive proposal, the criterion for choosing those values being related with the distance at the rejected point between the target and the proposal. In a sense, it gives a reward to surprising points, i.e. points where the proposal does poorly in approximating the target. On top of this, they include a multiple-try strategy where several values are generated from the current proposal and one of them is selected, to be accepted or rejected in a Metropolis step. The learning set may include several of the proposed (and rejected) values. This paper generalises Holden, Hauge and Holden (AoAP, 2009) and extends their proof of stationarity. The authors explore at length (the paper is 63 pages long!) the construction of the adaptive proposal distribution. This construction appears to be quite similar to Gilks’ and Wild’s (1993) ARMS algorithm. Hence, unless I missed a generalisation, it seems to me that the solutions are restricted to unidimensional settings. For instance, the authors propose to implement their algorithm for each complex conditional in a Gibbs sampler, meaning starting from scratch and running a large enough number of iterations to “reach” convergence. I also wonder at the correspondence between this construction and the original assumption of a minorisation condition wrt the target density in the event of an unbounded support. While this paper represents an interesting extension of the automated simulation algorithms of the ARMS type, and while the method is investigated thoroughly by several simulation experiments (in the second half of the paper), I remain somehow circumspect at the possibly of using ASMTM in complex high-dimensional problems as the learning cost soar with the dimension.

i-like[d the] workshop

Posted in Running, Statistics, Travel, University life with tags , , , , , , , , on May 17, 2013 by xi'an

Indeed, I liked the i-like workshop very much. Among the many interesting talks of the past two days (incl. Cristiano Varin’s ranking of Series B as the top influential stat. journal!) , Matti Vihola’s and Nicolas Chopin’s had the strongest impact on me (to the point of scribbling in my notebook). In a joint work with Christophe Andrieu, Matti focussed on evaluating the impact of replacing the target with an unbiased estimate in a Metropolis-Hastings algorithm. In particular, they found necessary and sufficient conditions for keeping geometric and uniform ergodicity. My question (asked by Iain Murray) was whether they had derived ways of selecting the number of terms in the unbiased estimator towards maximal efficiency. I also wonder if optimal reparameterisations can be found in this sense (since unbiased estimators remain unbiased after reparameterisation).

Nicolas’ talk was about particle Gibbs sampling, a joint paper with Sumeet Singh recently arXived. I did not catch the whole detail of their method but/as I got intrigued by a property of Marc Beaumont’s algorithm (the very same algorithm used by Matti & Christophe). Indeed, the notion is that an unbiased estimator of the target distribution can be found in missing variable settings by picking an importance sampling distribution q on those variables. This representation leads to a pseudo-target Metropolis-Hastings algorithm. In the stationary regime, there exists a way to derive an “exact” simulation from the joint posterior on (parameter,latent). All the remaining/rejected latents are then distributed from the proposal q. What I do not see is how this impacts the next MCMC move since it implies generating a new sample of latent variables. I spoke with Nicolas about this over breakfast: the explanation is that this re-generated set of latent variables can be used in the denominator of the Metropolis-Hastings acceptance probability and is validated as a Gibbs step. (Incidentally, it may be seen as a regeneration event as well.)

bike trail from Kenilworth to the University of WarwickFurthermore, I had a terrific run in the rising sun (at 5am) all the way to Kenilworth where I saw a deer, pheasants and plenty of rabbits. (As well as this sculpture that now appears to me as being a wee sexist…)

Dear Sir, I am unable to understand…

Posted in Statistics, University life with tags , , , , , , on January 30, 2013 by xi'an

Here is an email I received a few days ago, similar to many other emails I/we receive on a regular basis:

I am working on Markov Chain Monte Carlo methods as part of my Masters project. I have to estimate mean, variance from a Gaussian mixture using metropolis method.  I came across your paper ‘Bayesian Modelling and Inference on Mixtures of Distributions’. I am unable to understand how to obtain the new sample for mean, variance etc… I am using uniform distribution as proposal distribution. Should it be random numbers for the proposal distribution.
I have been working and trying to understand this for a long time. I would be grateful for any help.

While I felt sorry for the Master student, I consider it is the responsibility of his/her advisor to give her/him the proper directions for understanding the paper. (Given the contents of the email, it sounds as if the student would require proper training in both Bayesian statistics [uniform priors on unbounded parameters?] and simulation [the question about random numbers does not make sense]…) This is what I replied to the student, hopefully in a positive tone.

new typos in Monte Carlo Statistical Methods

Posted in Books, Statistics, University life with tags , , , , , , , , on December 7, 2011 by xi'an

Thanks to Jay Bartroff for pointing out those typos after teaching from Monte Carlo Statistical Methods:

  • On page 52, the gamma Ga(α, β) distribution uses β as a rate parameter while in other places it is a scale parameter, see, e.g. eqn (2.2) [correct, I must say the parameterisation of the gamma distribution is a pain and, while we tried to homogenise the notation with the second parameter being the rate, there are places like this where either the rate convention (as in the exponential distribution) or the scale convention (as in the generation) is the natural one…]
  • Still on page 52, in Example 2.20, truncated normals are said to be discussed after Example 1.5, but they’re not. [There is a mention made of constrained parameters right after but this is rather cryptic!]
  • On page 53, the ratio f/gα following the second displayed eqn is missing some terms [or, rather, the equality sign should be a proportional sign]
  • Still on page 53, in eqn (2.11), the whole expression, rather than the square root, should be divided by 2 [yes, surprising typo given that it was derived correctly in the original paper!]
  • On page 92, the exact constraint is that supp(g) actually needs only contain the intersection of supp(f) and supp(h), such as when approximating tail probabilities [correct if the importance sampling method is only used for a single function h, else the condition stands as is]
  • On page 94, fY does not need that integral in the denominator [correct, we already corrected for the truncation by subtracting 4.5 in the exponential]
  • On page 114, Problem 3.22, ωi is missing a factor of 1/n [correct]
  • On page 218, in Example 6.24, P00=0 [indeed, our remark that Pxx>0 should start with x=1. Note that this does not change the aperiodicity, though]
  • On page 282, the log α after the 2nd displayed equation should be eα [correct, this was pointed out in a previous list of typos, but clearly not corrected in the latest printing!]
  • On page 282, in the 5th displayed equation there are missing factors π(α’|b)/π(α0|b) in rejection probability [actually, no, because, those terms being both proposals and priors, they cancel in the ratio. We could add a sentence to this effect to explain why, though.]
  • On page 634, the reference page for exponential distribution is mistakenly given as 99 [wow, very thorough reading! There is an exponential distribution involved on page 99 but I agree this is not the relevant page…]