Speeding Up MCMC by Delayed Acceptance and Data Subsampling

The complexity of the Metropolis-Hastings (MH) algorithm arises from the requirement of a likelihood evaluation for the full data set in each iteration. Payne and Mallick (2015) propose to speed up the algorithm by a delayed acceptance approach where the acceptance decision proceeds in two stages. In the first stage, an estimate of the likelihood based on a random subsample determines if it is likely that the draw will be accepted and, if so, the second stage uses the full data likelihood to decide upon final acceptance. Evaluating the full data likelihood is thus avoided for draws that are unlikely to be accepted. We propose a more precise likelihood estimator which incorporates auxiliary information about the full data likelihood while only operating on a sparse set of the data. We prove that the resulting delayed acceptance MH is more efficient compared to that of Payne and Mallick (2015). The caveat of this approach is that the full data set needs to be evaluated in the second stage. We therefore propose to substitute this evaluation by an estimate and construct a state-dependent approximation thereof to use in the first stage. This results in an algorithm that (i) can use a smaller subsample m by leveraging on recent advances in Pseudo-Marginal MH (PMMH) and (ii) is provably within $O(m^{-2})$ of the true posterior.Comment: Accepted for publication in Journal of Computational and Graphical Statistic

Speeding up MCMC by Efficient Data Subsampling

We propose Subsampling MCMC, a Markov Chain Monte Carlo (MCMC) framework where the likelihood function for n observations is estimated from a random subset of m observations. We introduce a general and highly efficient unbiased estimator of the log-likelihood based on control variates obtained from clustering the data. The cost of computing the log-likelihood estimator is much smaller than that of the full log-likelihood used by standard MCMC. The likelihood estimate is bias-corrected and used in two correlated pseudo-marginal algorithms to sample from a perturbed posterior, for which we derive the asymptotic error with respect to n and m, respectively. A practical estimator of the error is proposed and we show that the error is negligible even for a very small m in our applications. We demonstrate that Subsampling MCMC is substantially more efficient than standard MCMC in terms of sampling efficiency for a given computational budget, and that it outperforms other subsampling methods for MCMC proposed in the literature