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Licensed Unlicensed Requires Authentication Published by De Gruyter May 6, 2013

Approximate Bayesian computation (ABC) gives exact results under the assumption of model error

  • Richard David Wilkinson EMAIL logo

Abstract

Approximate Bayesian computation (ABC) or likelihood-free inference algorithms are used to find approximations to posterior distributions without making explicit use of the likelihood function, depending instead on simulation of sample data sets from the model. In this paper we show that under the assumption of the existence of a uniform additive model error term, ABC algorithms give exact results when sufficient summaries are used. This interpretation allows the approximation made in many previous application papers to be understood, and should guide the choice of metric and tolerance in future work. ABC algorithms can be generalized by replacing the 0–1 cut-off with an acceptance probability that varies with the distance of the simulated data from the observed data. The acceptance density gives the distribution of the error term, enabling the uniform error usually used to be replaced by a general distribution. This generalization can also be applied to approximate Markov chain Monte Carlo algorithms. In light of this work, ABC algorithms can be seen as calibration techniques for implicit stochastic models, inferring parameter values in light of the computer model, data, prior beliefs about the parameter values, and any measurement or model errors.


Corresponding author: Richard David Wilkinson, University of Nottingham – School of Mathematical Sciences, University Park Nottingham, Nottinghamshire NG7 2RD, UK

I would like to thank Professor Paul Blackwell for his suggestion that the metric in the ABC algorithm might have a probabilistic interpretation. I would also like to thank Professor Simon Tavaré, Professor Tony O’Hagan, and Dr Jeremy Oakley for useful discussions on an early draft of the manuscript.

References

Barnes, C. P., S. Filippi M. P. H. Stumpf and T. Thorne (2012): “Considerate approaches to constructing summary statistics for ABC model selection,” Stat. Comput., 22, 1181–1197.Search in Google Scholar

Beaumont, M. A., J. M. Cornuet, J. M. Marin and C. P. Robert (2009): “Adaptivity for ABC algorithms: the ABC-PMC,” Biometrika, 96, 983–990.10.1093/biomet/asp052Search in Google Scholar

Beaumont, M. A., W. Zhang and D. J. Balding (2002): “Approximate Bayesian computatation in population genetics,” Genetics, 162, 2025–2035.10.1093/genetics/162.4.2025Search in Google Scholar PubMed PubMed Central

Blum, M. and V. Tran (2010): “HIV with contact tracing: a case study in approximate Bayesian computation,” Biostatistics, 11, 644–660.10.1093/biostatistics/kxq022Search in Google Scholar PubMed

Campbell, K. (2006): “Statistical calibration of computer simulations,” Reliab. Eng. Syst. Safe., 91, 1358–1363.Search in Google Scholar

Cornuet, J.-M., F. Santos, M. A. Beaumont, C. P. Robert, J.-M. Marin, D. J. Balding, T. Guillemaud and A. Estoup (2008): “Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation,” Bioinformatics, 24, 2713–2719.10.1093/bioinformatics/btn514Search in Google Scholar PubMed PubMed Central

Del Moral, P., A. Doucet and A. Jasra (2012): “An adaptive sequential Monte Carlo method for approximate Bayesian computation,” Stat. Comput., 22, 1009–1020.Search in Google Scholar

Didelot, X., R. G. Everitt, A. M. Johansen and D. J. Lawson (2011): “Likelihood-free estimation of model evidence,” Bayesian analysis, 6, 49–76.10.1214/11-BA602Search in Google Scholar

Diggle, P. J. and R. J. Gratton (1984): “Monte Carlo methods of inference for implicit statistical models,” J. R. Statist. Soc. B, 46, 193–227.Search in Google Scholar

Drovandi, C. C., A. N. Pettitt and M. J. Faddy (2011): “Approximate Bayesian computation using indirect inference,” J. R. Stat. Soc. Ser. C, 60, 317–337.Search in Google Scholar

Fearnhead, P. and D. Prangle (2012): “Constructing summary statistics for approximate Bayesian computation: semi-automatic approximate Bayesian computation,” J. Roy. Stat. Soc. Ser. B, 74, 419–474.Search in Google Scholar

Foll, M., M.A. Beaumont and O.Gaggiotti (2008): “An approximate Bayesian computation approach to overcome biases that arise when using amplifed fragment length polymorphism markers to study population structure,” Genetics, 179, 927–939.10.1534/genetics.107.084541Search in Google Scholar PubMed PubMed Central

Goldstein, M. and J. Rougier (2009): “Reified Bayesian modelling and inference for physical systems,” J. Stat. Plan. Infer., 139, 1221–1239.Search in Google Scholar

Hamilton, G., M. Currat, N. Ray, G. Heckel, M. A. Beaumont and L. Excoffier (2005): “Bayesian estimation of recent migration rates after a spatial expansion,” Genetics, 170, 409–417.10.1534/genetics.104.034199Search in Google Scholar PubMed PubMed Central

Higdon, D., J. Gattiker, B. Williams and M. Rightley (2008): “Computer model calibration using high-dimensional output,” J. Am. Statis. Assoc., 103, 570–583.Search in Google Scholar

Joyce, P. and P. Marjoram (2008): “Approximately sufficient statistics and Bayesian computation,” Stat. Appl. Genet. Mo. B., 7, article 26.Search in Google Scholar

Kass, R. E. and A. E. Raftery (1995): “Bayes factors,” J. Am. Statis. Assoc., 90, 773–795.Search in Google Scholar

Kennedy, M. and A. O’Hagan (2001): “Bayesian calibration of computer models (with discussion),” J. R. Statist. Soc. Ser. B, 63, 425–464.Search in Google Scholar

Liu, J. S. (2001): Monte Carlo Strategies in Scientific Computing, Springer Series in Statistics, New York: Springer.Search in Google Scholar

Marjoram, P., J. Molitor, V. Plagnol and S. Tavaré (2003): “Markov chain Monte Carlo without likelihoods,” Proc. Natl. Acad. Sci. USA, 100, 15324–15328.10.1073/pnas.0306899100Search in Google Scholar PubMed PubMed Central

Murray, I., Z. Ghahramani and D. J. C. MacKay (2006) MCMC for doubly-intractable distributions. In Proceedings of the 22nd Annual Conference on Uncertainty in Artificial Intelligence, UAI.Search in Google Scholar

Nunes, M. A. and D. J. Balding (2010): “On optimal selection of summary statistics for approximate Bayesian computation,” Stat. Appl. Genet. Mo. B., 9, Article 34.Search in Google Scholar

Peters, G., Y. Fan and S. Sisson (2012): “On sequential Monte Carlo, partial rejection control and approximate Bayesian computation,” Stat. Comput., 22, 1209–1222.Search in Google Scholar

Plagnol, V. and S. Tavaré (2004) Approximate Bayesian computation and MCMC. In Niederreiter, H. (Ed.) Proceedings of Monte Carlo and Quasi-Monte Carlo Methods 2002, Springer-Verlag, pp. 99–114.10.1007/978-3-642-18743-8_5Search in Google Scholar

Prangle, D., P. Fearnhead, M. P. Cox, and N. P. French (2013): “Semi-automatic selection of summary statistics for ABC model choice”, arXiv:1302:5624.10.1515/sagmb-2013-0012Search in Google Scholar PubMed

Pritchard, J. K., M. T. Seielstad, A. Perez-Lezaun and M. W. Feldman (1999): “Population growth of human Y chromosomes: a study of Y chromosome microsatellites,” Mol. Biol. Evol., 16, 1791–1798.Search in Google Scholar

Ratmann, O., O. Jorgensen, T. Hinkley, M. Stumpf, S. Richardson and C. Wiuf (2007): “Using likelihood-free inference to compare evolutionary dynamics of the protein networks of H. pylori and P. falciparum,” PLoS Comput. Biol., 3, 2266–2276.Search in Google Scholar

Robert, C. P., J. M. Cornuet, J. M. Marin and N. S. Pillai (2011): “Lack of confidence in approximate Bayesian computation model choice,” Proc. Natl. Acad. Sci. USA, 108, 15112–15117.10.1073/pnas.1102900108Search in Google Scholar PubMed PubMed Central

Siegmund, K.D., P. Marjoram and D. Shibata (2008): “Modeling DNA methylation in apopulation of cancer cells,” Stat. Appl. Genet. Mo. B., 7, article 18.Search in Google Scholar

Sisson, S. A., Y. Fan and M. M. Tanaka (2007): “Sequential Monte Carlo without likelihoods,” Proc. Natl. Acad. Sci. USA, 104, 1760–1765.10.1073/pnas.0607208104Search in Google Scholar PubMed PubMed Central

Sunnaker, M., A. G. Busetto, E. Numminen, J. Corander, M. Foll and C. Dessimoz (2013): “Approximate bayesian computation,” PLoS Comput Biol., 9, e1002803.Search in Google Scholar

Tanaka, M. M., A. R. Francis, F. Luciani and S. A. Sisson (2006): “Using approximate Bayesian computation to estimate tuberculosis transmission parameters from genotype data,” Genetics, 173, 1511–1520.10.1534/genetics.106.055574Search in Google Scholar PubMed PubMed Central

Toni, T., D. Welch, N. Strelkowa, A. Ipsen and M. P. H. Stumpf (2009): “Approximate Bayesian Computation scheme for parameter inference and model selection in dynamical systems,” J. R. Soc. Interface, 6, 187–202.Search in Google Scholar

Wilkinson, R. D. (2007): Bayesian inference of primate divergence times, Ph.D. thesis, University of Cambridge.Search in Google Scholar

Wilkinson, R. and S. Tavaré (2009): “Estimating the primate divergence time using conditioned birth-and-death processes”, Theor. Popul. Biol., 75, 278–285.Search in Google Scholar

Published Online: 2013-05-06

©2013 by Walter de Gruyter Berlin Boston

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