Abstract
Complex models typically involve intractable likelihood functions which, from a Bayesian perspective, lead to intractable posterior distributions. In this context, Approximate Bayesian computation (ABC) methods can be used in order to obtain a valid posterior approximation. However, when simulation from the model is computationally demanding, then the ABC approach may be cumbersome. We discuss an alternative method, where the intractable likelihood is approximated by a quasi-likelihood calculated through an algorithm that is reminiscent of the ABC. The proposed approximation method requires less computational effort than ABC. An extension to multiparameter models is also considered and the method is illustrated by several examples.
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References
Adimari, G., Ventura, L.: Quasi-profile log likelihoods for unbiased estimating functions. Ann. Instit. Stat. Math. 54, 235–244 (2002)
Barndorff-Nielsen, O.: Quasi profile and directed likelihoods from estimating functions. Ann. Instit. Stat. Math. 47, 461–464 (1995)
Bellio, R., Greco, L., Ventura, L.: Modified quasi-profile likelihoods from estimating functions. J. Stat. Plan. Inf. 138, 3059–3068 (2008)
Biau, G., Cérou, F., Guyader, A.: New insights into approximate Bayesian computation (2013). arXiv:preprint arXiv:1207.6461v2
Blum, M.G.B., François, O.: Non-linear regression models for approximate Bayesian computation. Stat. Comput. 20, 63–73 (2010)
Blum, M.G.B., Tran, V.: Hiv with contact tracing: a case study in approximate Bayesian computation. Biostatistics 11, 644–660 (2010)
Blum, M.G.B., Nunes, M., Prangle, D., Sisson, S.A.: A comparative review of dimension reduction methods in approximate Bayesian computation. Stat. Sci. 28(2), 135–281 (2013)
Bortot, P., Coles, S.G., Sisson, S.A.: Inference for stereological extremes. J. Amer. Stat. Assoc. 102, 84–92 (2007)
Cornuet, J., Santos, F., Beaumont, M., Robert, C.P., Marin, J.M., Balding, D., Guillemaud, T., Estoup, A.: Inferring population history with diy abc: a user-friendly approach to approximate Bayesian computation. Bioinformatics 24, 2713–2719 (2008)
Desmond, A.: Optimal estimating functions, quasi-likelihood and statistical modelling. J. Stat. Plan. Inf. 60, 77–104 (1997)
Faisai, M., Futschick, A., Hussain, I.: A new approach to choose acceptance cutoff for approximate Bayesian computation. J. Appl. Stat. 40(4), 862–869 (2013)
Faraway, J.J.: Extending the Linear Model with R. Springer, New York (2006)
Fearnhead, P., Prangle, D.: Constructing summary statistics for approximate Bayesian computation: semi-automatic approximate Bayesian computation. J. Roy. Stat. Soc. Ser. B 74, 419–474 (2012)
Foll, M., Beaumont, M., Gaggiotti, O.: An approximate Bayesian computation approach to overcome biases that arise when using amplified fragment length polymorphism markers to study population structure. Genetics 179, 927–939 (2008)
Greco, L., Racugno, W., Ventura, L.: Robust likelihood functions in bayesian inference. J. Stat. Plan. Inf. 138, 1258–1270 (2008)
Hamilton, G., Currat, M., Ray, N., Heckel, G., Beaumont, M., Excoffier, L.: Bayesian estimation of recent migration rates after a spatial expansion. Genetics 170, 409–417 (2005)
Heggland, K., Frigessi, A.: Estimating functions in indirect inference. J. Roy. Stat. Soc. 66, 447–462(2004)
Heyde, C.: Quasi-Likelihood and Its Application: A General Approach to Optimal Parameter Estimation. Springer Verlag, Berlin (1997)
Jørgensen, B., Knudsen, S.: Parameter orthogonality and bias adjustment for estimating functions. Scand. J. Stat. 31, 93–114 (2004)
Liang, K., Zeger, S.: Inference based on estimating functions in the presence of nuisance parameters. Stat. Sci. 10, 158–173 (1995)
Lin, L.: Quasi Bayesian likelihood. Stat. Methodol. 3, 444–455 (2006)
Marjoram, P., Molitor, J., Plagnol, V., Tavare, S.: Markov chain monte carlo without likelihoods. Proc. Natl. Acad. Sci. USA 100, 15324–15328 (2003)
McCullagh, P.: Quasi-likelihood and estimating functions. In: Hinkley, D., Reid, N., Snell, E. (eds.) Statistical Theory and Modelling, pp. 265–286. Chapman and Hall, London (1991)
Mengersen, K., Pudlo, P., Robert, C.: Approximate Bayesian computation via empirical likelihood. Proc. Natl. Acad. Sci. 110(4), 1321–1326 (2013). doi:10.1073/pnas.1208827110
Owen, A.: Empirical Likelihood, vol. 92. Chapman & Hall, Boca Raton (2001)
Pace, L., Salvan, A.: Principles of Statistical Inference. World Scientific, Singapore (1997)
Prangle, D., Blum, M. G. B., Popovic, G., Sisson, S.A.: Diagnostic tools of approximate Bayesian computation using the coverage property (2013). arXiv:preprint arXiv:1301.3166
Ratmann, O., Andrieu, C., Wiuf, C., Richardson, S.: Model criticism based on likelihood-free inference, with an application to protein network evolution. Proc. Natl. Acad. Sci. USA 106, 10576–10581 (2009)
Ratmann, O., Jørgensen, O., Hinkley, T., Stumpf, M., Richardson, S., Wiuf, C.: Using likelihood-free inference to compare evolutionary dynamics of the protein networks of H. pylori and P. falciparum. PLoS Comput. Biol. 3, 2266–2276 (2007)
Ruli, E., Sartori, N., Ventura, L.: Approximate Bayesian computation with composite score functions. (2013). arXiv:1311.7286v1
Severini, T.: Modified estimating functions. Biometrika 89, 333–343 (2002)
Siegmund, K., Marjoram, P., Shibata, D.: Modeling dna methylation in a population of cancer cells. Stat. Appl. Gen. Mol. Biol. 7, 1–21 (2008)
Stone, C.: Additive regression and other nonparametric models. Ann. Stat. 13, 689–705 (1985)
Tanaka, M., Francis, A., Luciani, F., Sisson, S.: Using approximate Bayesian computation to estimate tuberculosis transmission parameters from genotype data. Genetics 173, 1511–1520 (2006)
Tavaré, S., Balding, D.J., Griffiths, R.C., Donnelly, P.: Inferring coalescence times from dna sequence data. Genetics 145, 505–518 (1997)
Ventura, L., Cabras, S., Racugno, W.: Default prior distributions from quasi- and quasi-profile likelihoods. J. Stat. Plan. Inf. 140, 2937–2942 (2010)
Wang, M., Hanfelt, J.: Adjusted profile estimating function. Biometrika 90, 845–858 (2003)
Acknowledgments
Maria Eugenia Castellanos was partially supported by Ministerio de Ciencia e Innovación grant MTM2010-19528 and the visiting professor program of the Regione Autonoma della Sardegna. Stefano Cabras has been partially supported by Ministerio de Ciencia e Innovación grant ECO2012-38442, RYC-2012-11455 and Erlis Ruli were partially supported by Ministero dell’Istruzione, dell’Univesità e della Ricerca of Italy.
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Cabras, S., Castellanos, M.E. & Ruli, E. A Quasi likelihood approximation of posterior distributions for likelihood-intractable complex models. METRON 72, 153–167 (2014). https://doi.org/10.1007/s40300-014-0040-5
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DOI: https://doi.org/10.1007/s40300-014-0040-5