Parallel processing of independent Metropolis-Hastings algorithms

October 11, 2010

(This article was first published on Xi'an's Og » R, and kindly contributed to R-bloggers)

With Pierre Jacob, my PhD student, and Murray Smith, from National Institute of Water and Atmospheric Research, Wellington, who actually started us on this project at the last and latest Valencia meeting, we have completed a paper on using parallel computing in independent Metropolis-Hastings algorithms. The paper is arXived and the abstract goes as follows:

In this paper, we consider the implications of the fact that parallel raw-power can be exploited by a generic
Metropolis–Hastings algorithm if the proposed values are independent. In particular, we present improvements to the
independent Metropolis–Hastings algorithm that significantly decrease the variance of any estimator derived from the
MCMC output, for a null computing cost since those improvements are based on a fixed number of target density
evaluations. Furthermore, the techniques developed in this paper do not jeopardize the Markovian convergence properties of the algorithm,
since they are based on the Rao–Blackwell principles of Gelfand and Smith (1990), already exploited in Casella and Robert 91996), Atchadé and Perron (2005) and Douc and Robert (2010). We illustrate those improvement both on a toy normal example and on a classical
probit regression model but insist on the fact that they are universally applicable.

I am quite excited about the results in this paper, which took advantage of (a) older works of mine on Rao-Blackwellisation, (b) Murray’s interests in costly likelihoods, and (c) our mutual excitement when hearing about GPU parallel possibilities from Chris Holmes’ talk in Valencia. (As well as directions drafted in an exciting session in Vancouver!) The (free) gains over standard independent Metropolis-Hastings estimates are equivalent to using importance sampling gains, while keeping the Markov structure of the original chain. Given that 100 or more parallel threads can be enhanced from current GPU cards, this is clearly a field with much potential! The graph below

gives the variance improvements brought by three Rao-Blackwell estimates taking advantage of parallelisation over the initial MCMC estimate (first entry) with the importance sampling estimate (last entry) using only 10 parallel threads.

Filed under: R, Statistics, University life Tagged: Chris Holmes, cloud computing, GPU, importance sampling, JSM 2010, Metropolis-Hastings, parallelisation, Rao-Blackwellisation, Valencia 9

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