Delayed Acceptance ABC-SMC

Approximate Bayesian computation (ABC) is now an established technique for statistical inference used in cases where the likelihood function is computationally expensive or not available. It relies on the use of a~model that is specified in the form of a~simulator, and approximates the likelihood at a~parameter value $\theta$ by simulating auxiliary data sets $x$ and evaluating the distance of $x$ from the true data $y$. However, ABC is not computationally feasible in cases where using the simulator for each $\theta$ is very expensive. This paper investigates this situation in cases where a~cheap, but approximate, simulator is available. The approach is to employ delayed acceptance Markov chain Monte Carlo (MCMC) within an ABC sequential Monte Carlo (SMC) sampler in order to, in a~first stage of the kernel, use the cheap simulator to rule out parts of the parameter space that are not worth exploring, so that the ``true'' simulator is only run (in the second stage of the kernel) where there is a~reasonable chance of accepting proposed values of $\theta$. We show that this approach can be used quite automatically, with few tuning parameters. Applications to stochastic differential equation models and latent doubly intractable distributions are presented.

[1]  Richard G. Everitt,et al.  Likelihood-free estimation of model evidence , 2011 .

[2]  D. Gillespie Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .

[3]  Martina Morris,et al.  ergm: A Package to Fit, Simulate and Diagnose Exponential-Family Models for Networks. , 2008, Journal of statistical software.

[4]  C. Andrieu,et al.  The pseudo-marginal approach for efficient Monte Carlo computations , 2009, 0903.5480.

[5]  D. Lusseau,et al.  The bottlenose dolphin community of Doubtful Sound features a large proportion of long-lasting associations , 2003, Behavioral Ecology and Sociobiology.

[6]  Iain Murray,et al.  Fast $\epsilon$-free Inference of Simulation Models with Bayesian Conditional Density Estimation , 2016 .

[7]  Andrew Golightly,et al.  Adaptive, Delayed-Acceptance MCMC for Targets With Expensive Likelihoods , 2015, 1509.00172.

[8]  Andrew Golightly,et al.  Delayed acceptance particle MCMC for exact inference in stochastic kinetic models , 2014, Stat. Comput..

[9]  Richard G. Everitt,et al.  Bayesian Parameter Estimation for Latent Markov Random Fields and Social Networks , 2012, ArXiv.

[10]  Andrew Golightly,et al.  Delayed acceptance particle MCMC for exact inference in stochastic biochemical network models , 2013 .

[11]  Christian P. Robert,et al.  Accelerating Metropolis-Hastings algorithms: Delayed acceptance with prefetching , 2014, 1406.2660.

[12]  P. Moral,et al.  The Alive Particle Filter and Its Use in Particle Markov Chain Monte Carlo , 2015 .

[13]  Arnaud Doucet,et al.  An adaptive sequential Monte Carlo method for approximate Bayesian computation , 2011, Statistics and Computing.

[14]  Julien Stoehr,et al.  A review on statistical inference methods for discrete Markov random fields , 2017, 1704.03331.

[15]  D. Balding,et al.  Approximate Bayesian computation in population genetics. , 2002, Genetics.

[16]  Mark M. Tanaka,et al.  Sequential Monte Carlo without likelihoods , 2007, Proceedings of the National Academy of Sciences.

[17]  Zoubin Ghahramani,et al.  MCMC for Doubly-intractable Distributions , 2006, UAI.

[18]  Malcolm J. A. Strens Efficient hierarchical MCMC for policy search , 2004, ICML '04.

[19]  M. Feldman,et al.  Population growth of human Y chromosomes: a study of Y chromosome microsatellites. , 1999, Molecular biology and evolution.

[20]  A. M. Johansen,et al.  Towards Automatic Model Comparison: An Adaptive Sequential Monte Carlo Approach , 2013, 1303.3123.

[21]  Richard G. Everitt,et al.  Bayesian model comparison with un-normalised likelihoods , 2015, Stat. Comput..

[22]  Paul Fearnhead,et al.  On the Asymptotic Efficiency of Approximate Bayesian Computation Estimators , 2015, 1506.03481.

[23]  Alberto Caimo,et al.  Bayesian inference for exponential random graph models , 2010, Soc. Networks.

[24]  J. Møller,et al.  An efficient Markov chain Monte Carlo method for distributions with intractable normalising constants , 2006 .

[25]  Darren J. Wilkinson Stochastic Modelling for Systems Biology , 2006 .

[26]  Nial Friel Evidence and Bayes Factor Estimation for Gibbs Random Fields , 2013 .

[27]  Umberto Picchini Inference for SDE Models via Approximate Bayesian Computation , 2012, 1204.5459.

[28]  P. Moral,et al.  Sequential Monte Carlo samplers , 2002, cond-mat/0212648.

[29]  Jun S. Liu,et al.  Sequential Imputations and Bayesian Missing Data Problems , 1994 .

[30]  Dennis Prangle,et al.  Lazy ABC , 2014, Stat. Comput..

[31]  L. Tierney A note on Metropolis-Hastings kernels for general state spaces , 1998 .

[32]  P. Moral,et al.  On adaptive resampling strategies for sequential Monte Carlo methods , 2012, 1203.0464.

[33]  Alice S.A. Johnston,et al.  Calibration and evaluation of individual-based models using Approximate Bayesian Computation , 2015 .

[34]  Umberto Picchini,et al.  Accelerating inference for diffusions observed with measurement error and large sample sizes using approximate Bayesian computation , 2013, 1310.0973.

[35]  C. Fox,et al.  Markov chain Monte Carlo Using an Approximation , 2005 .

[36]  Andrew Golightly,et al.  Efficiency of delayed-acceptance random walk Metropolis algorithms , 2015, The Annals of Statistics.

[37]  C. Robert,et al.  ABC likelihood-free methods for model choice in Gibbs random fields , 2008, 0807.2767.

[38]  C. Robert,et al.  Inference in generative models using the Wasserstein distance , 2017, 1701.05146.

[39]  Richard G. Everitt,et al.  A rare event approach to high-dimensional approximate Bayesian computation , 2016, Statistics and Computing.

[40]  Pierre Del Moral,et al.  Sequential Monte Carlo for rare event estimation , 2012, Stat. Comput..