Accelerating delayed-acceptance Markov chain Monte Carlo algorithms
Preprint, 2019

Delayed-acceptance Markov chain Monte Carlo (DA-MCMC) samples from a probability distribution via a two-stages version of the Metropolis-Hastings algorithm, by combining the target distribution with a "surrogate" (i.e. an approximate and computationally cheaper version) of said distribution. DA-MCMC accelerates MCMC sampling in complex applications, while still targeting the exact distribution. We design a computationally faster, albeit approximate, DA-MCMC algorithm. We consider parameter inference in a Bayesian setting where a surrogate likelihood function is introduced in the delayed-acceptance scheme. When the evaluation of the likelihood function is computationally intensive, our scheme produces a 2-4 times speed-up, compared to standard DA-MCMC. However, the acceleration is highly problem dependent. Inference results for the standard delayed-acceptance algorithm and our approximated version are similar, indicating that our algorithm can return reliable Bayesian inference. As a computationally intensive case study, we introduce a novel stochastic differential equation model for protein folding data.

stochastic differential equation

protein folding

Gaussian process

Bayesian inference

pseudo marginal MCMC


Umberto Picchini

Samuel Wiqvist

Julie Lyng Forman

Kresten Lindorff-Larsen

Wouter Boomsma


Basic sciences

Subject Categories


Probability Theory and Statistics

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