Skip to main content

Approximate Bayesian Computation: A Survey on Recent Results

  • Conference paper
  • First Online:
Monte Carlo and Quasi-Monte Carlo Methods

Part of the book series: Springer Proceedings in Mathematics & Statistics ((PROMS,volume 163))

Abstract

Approximate Bayesian Computation (ABC) methods have become a “mainstream” statistical technique in the past decade, following the realisation by statisticians that they are a special type of non-parametric inference. In this survey of ABC methods, we focus on the recent literature, building on the previous survey of Marin et al. Stat Comput 21(2):279–291, 2011, [39]. Given the importance of model choice in the applications of ABC, and the associated difficulties in its implementation, we also give emphasis to this aspect of ABC techniques.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Notes

  1. 1.

    As detailed below, the distance may depend solely on an insufficient statistic \(S(\varvec{x})\) and hence not be a distance from a formal perspective, while introduction a second level of approximation to the ABC scheme.

  2. 2.

    Or, more accurately, posterior-to-prior.

References

  1. Allingham, D., King, R., Mengersen, K.: Bayesian estimation of quantile distributions. Stat. Comput. 19, 189–201 (2009)

    Article  MathSciNet  Google Scholar 

  2. Andrieu, C., Roberts, G.: The pseudo-marginal approach for efficient Monte Carlo computations. Ann. Stat. 37(2), 697–725 (2009)

    Article  MathSciNet  MATH  Google Scholar 

  3. Beaumont, M.: Approximate Bayesian computation in evolution and ecology. Annu. Rev. Ecol. Evol. Syst. 41, 379–406 (2010)

    Article  Google Scholar 

  4. Beaumont, M., Cornuet, J.-M., Marin, J.-M., Robert, C.: Adaptive approximate Bayesian computation. Biometrika 96(4), 983–990 (2009)

    Article  MathSciNet  MATH  Google Scholar 

  5. Beaumont, M., Nielsen, R., Robert, C., Hey, J., Gaggiotti, O., Knowles, L., Estoup, A., Mahesh, P., Coranders, J., Hickerson, M., Sisson, S., Fagundes, N., Chikhi, L., Beerli, P., Vitalis, R., Cornuet, J.-M., Huelsenbeck, J., Foll, M., Yang, Z., Rousset, F., Balding, D., Excoffier, L.: In defense of model-based inference in phylogeography. Mol. Ecol. 19(3), 436–446 (2010)

    Article  Google Scholar 

  6. Beaumont, M., Zhang, W., Balding, D.: Approximate Bayesian computation in population genetics. Genetics 162, 2025–2035 (2002)

    Google Scholar 

  7. Belle, E., Benazzo, A., Ghirotto, S., Colonna, V., Barbujani, G.: Comparing models on the genealogical relationships among Neandertal, Cro-Magnoid and modern Europeans by serial coalescent simulations. Heredity 102(3), 218–225 (2008)

    Article  Google Scholar 

  8. Berger, J., Fienberg, S., Raftery, A., Robert, C.: Incoherent phylogeographic inference. Proc. Natl. Acad. Sci. 107(41), E57 (2010)

    Article  Google Scholar 

  9. Biau, G., Cérou, F., Guyader, A.: New insights into approximate Bayesian computation. Annales de l’IHP (Probab. Stat.) 51, 376–403 (2015)

    MathSciNet  MATH  Google Scholar 

  10. Blum, M.: Approximate Bayesian computation: a non-parametric perspective. J. Am. Stat. Assoc. 105(491), 1178–1187 (2010)

    Article  MATH  Google Scholar 

  11. Blum, M., François, O.: Non-linear regression models for approximate Bayesian computation. Stat. Comput. 20, 63–73 (2010)

    Article  MathSciNet  Google Scholar 

  12. Blum, M.G.B., Nunes, M.A., Prangle, D., Sisson, S.A.: A comparative review of dimension reduction methods in approximate Bayesian computation. Stat. Sci. 28(2), 189–208 (2013)

    Article  MathSciNet  MATH  Google Scholar 

  13. Bollerslev, T., Chou, R., Kroner, K.: ARCH modeling in finance. A review of the theory and empirical evidence. J. Econom. 52, 5–59 (1992)

    Article  MATH  Google Scholar 

  14. Calvet, C., Czellar, V.: Accurate methods for approximate Bayesian computation filtering. J. Econom. (2014, to appear)

    Google Scholar 

  15. Cornuet, J.-M., Ravigné, V., Estoup, A.: Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0). BMC Bioinform. 11, 401 (2010)

    Article  Google Scholar 

  16. Cornuet, J.-M., Santos, F., Beaumont, M., Robert, C., Marin, J.-M., Balding, D., Guillemaud, T., Estoup, A.: Inferring population history with DIYABC: a user-friendly approach to approximate Bayesian computation. Bioinformatics 24(23), 2713–2719 (2008)

    Article  Google Scholar 

  17. Dean, T., Singh, S., Jasra, A., Peters, G.: Parameter inference for hidden Markov models with intractable likelihoods. Scand. J. Stat. (2014, to appear)

    Google Scholar 

  18. Didelot, X., Everitt, R., Johansen, A., Lawson, D.: Likelihood-free estimation of model evidence. Bayesian Anal. 6, 48–76 (2011)

    Article  MathSciNet  MATH  Google Scholar 

  19. Diggle, P., Gratton, R.: Monte Carlo methods of inference for implicit statistical models. J. R. Stat. Soc. Ser. B 46, 193–227 (1984)

    MathSciNet  MATH  Google Scholar 

  20. Drovandi, C., Pettitt, A., Fddy, M.: Approximate Bayesian computation using indirect inference. J. R. Stat. Soc. Ser. A 60(3), 503–524 (2011)

    MathSciNet  Google Scholar 

  21. Ehrlich, E., Jasra, A., Kantas, N.: Gradient free parameter estimation for hidden markov models with intractable likelihoods. Method. Comp. Appl. Probab. (2014, to appear)

    Google Scholar 

  22. Excoffier, C., Leuenberger, D., Wegmann, L.: Bayesian computation and model selection in population genetics (2009)

    Google Scholar 

  23. Fagundes, N., Ray, N., Beaumont, M., Neuenschwander, S., Salzano, F., Bonatto, S., Excoffier, L.: Statistical evaluation of alternative models of human evolution. Proc. Natl. Acad. Sci. 104(45), 17614–17619 (2007)

    Article  Google Scholar 

  24. Fearnhead, P., Prangle, D.: Constructing summary statistics for Approximate Bayesian computation: semi-automatic approximate Bayesian computation. J. R. Stat. Soc.: Ser. B (Stat. Method.), 74(3), 419–474. (With discussion)

    Google Scholar 

  25. Ghirotto, S., Mona, S., Benazzo, A., Paparazzo, F., Caramelli, D., Barbujani, G.: Inferring genealogical processes from patterns of bronze-age and modern DNA variation in Sardinia. Mol. Biol. Evol. 27(4), 875–886 (2010)

    Article  Google Scholar 

  26. Gouriéroux, C., Monfort, A.: Simulation Based Econometric Methods. CORE Lecture Series. CORE, Louvain (1995)

    MATH  Google Scholar 

  27. Gouriéroux, C., Monfort, A., Renault, E.: Indirect inference. J. Appl. Econom. 8, 85–118 (1993)

    Article  MATH  Google Scholar 

  28. Grelaud, A., Marin, J.-M., Robert, C., Rodolphe, F., Tally, F.: Likelihood-free methods for model choice in Gibbs random fields. Bayesian Anal. 3(2), 427–442 (2009)

    MathSciNet  Google Scholar 

  29. Guillemaud, T., Beaumont, M., Ciosi, M., Cornuet, J.-M., Estoup, A.: Inferring introduction routes of invasive species using approximate Bayesian computation on microsatellite data. Heredity 104(1), 88–99 (2009)

    Article  Google Scholar 

  30. Jasra, A.: Approximate Bayesian Computation for a Class of Time Series Models. e-prints (2014)

    Google Scholar 

  31. Jasra, A., Kantas, N., Ehrlich, E.: Approximate inference for observation driven time series models with intractable likelihoods. TOMACS (2014, to appear)

    Google Scholar 

  32. Jasra, A., Lee, A., Yau, C., Zhang, X.: The Alive Particle Filter. e-prints (2013)

    Google Scholar 

  33. Jasra, A., Singh, S., Martin, J., McCoy, E.: Filtering via approximate Bayesian computation. Stat. Comp. 22, 1223–1237 (2012)

    Article  MathSciNet  MATH  Google Scholar 

  34. Joyce, P., Marjoram, P.: Approximately sufficient statistics and Bayesian computation. Stat. Appl. Genet. Mol. Biol. 7(1), Article 26 (2008)

    Google Scholar 

  35. Le Gland, F., Oudjane, N.: A Sequential Particle Algorithm that Keeps the Particle System Alive. Lecture Notes in Control and Information Sciences, vol. 337, pp. 351–389. Springer, Berlin (2006)

    MATH  Google Scholar 

  36. Lehmann, E., Casella, G.: Theory of Point Estimation, revised edn. Springer, New York (1998)

    MATH  Google Scholar 

  37. Leuenberger, C., Wegmann, D.: Bayesian computation and model selection without likelihoods. Genetics 184(1), 243–252 (2010)

    Article  Google Scholar 

  38. Marin, J., Pillai, N., Robert, C., Rousseau, J.: Relevant statistics for Bayesian model choice. J. R. Stat. Soc. Ser. B 76(5), 833–859 (2014)

    Article  MathSciNet  Google Scholar 

  39. Marin, J., Pudlo, P., Robert, C., Ryder, R.: Approximate Bayesian computational methods. Stat. Comput. 21(2), 279–291 (2011)

    MathSciNet  Google Scholar 

  40. Martin, G.M., McCabe, B.P.M., Maneesoonthorn, W., Robert, C.P. Approximate Bayesian Computation in State Space Models. e-prints (2014)

    Google Scholar 

  41. Martin, J., Jasra, A., Singh, S., Whiteley, N., Del Moral, P., McCoy, E.: Approximate Bayesian computation for smoothing. Stoch. Anal. Appl. 32(3), (2014)

    Google Scholar 

  42. McKinley, T., Ross, J., Deardon, R., Cook, A.: Simulation-based Bayesian inference for epidemic models. Comput. Stat. Data Anal. 71, 434–447 (2014)

    Article  MathSciNet  Google Scholar 

  43. Mengersen, K., Pudlo, P., Robert, C.: Bayesian computation via empirical likelihood. Proc. Natl. Acad. Sci. 110(4), 1321–1326 (2013)

    Article  Google Scholar 

  44. Owen, A.B.: Empirical likelihood ratio confidence intervals for a single functional. Biometrika 75, 237–249 (1988)

    Article  MathSciNet  MATH  Google Scholar 

  45. Owen, A.B.: Empirical Likelihood. Chapman & Hall, Boca Raton (2001)

    Book  MATH  Google Scholar 

  46. Patin, E., Laval, G., Barreiro, L., Salas, A., Semino, O., Santachiara-Benerecetti, S., Kidd, K., Kidd, J., Van Der Veen, L., Hombert, J., et al.: Inferring the demographic history of African farmers and pygmy hunter-gatherers using a multilocus resequencing data set. PLoS Genet. 5(4), e1000448 (2009)

    Article  Google Scholar 

  47. Prangle, D., Blum, M.G.B., Popovic, G., Sisson, S.A.: Diagnostic tools of approximate Bayesian computation using the coverage property. e-prints (2013)

    Google Scholar 

  48. Pritchard, J., Seielstad, M., Perez-Lezaun, A., Feldman, M.: Population growth of human Y chromosomes: a study of Y chromosome microsatellites. Mol. Biol. Evol. 16, 1791–1798 (1999)

    Article  Google Scholar 

  49. Ramakrishnan, U., Hadly, E.: Using phylochronology to reveal cryptic population histories: review and synthesis of 29 ancient DNA studies. Mol. Ecol. 18(7), 1310–1330 (2009)

    Article  Google Scholar 

  50. Ratmann, O., Andrieu, C., Wiuf, C., Richardson, S.: Reply to Robert et al.: Model criticism informs model choice and model comparison. Proc. Natl. Acad. Sci. 107(3), E6–E7 (2010)

    Article  Google Scholar 

  51. Ratmann, O., Andrieu, C., Wiujf, C., Richardson, S.: Model criticism based on likelihood-free inference, with an application to protein network evolution. Proc. Natl. Acad. Sci. USA 106, 1–6 (2009)

    Article  Google Scholar 

  52. Robert, C.: Discussion of “constructing summary statistics for Approximate Bayesian Computation” by Fernhead, P., Prangle, D., J. R. Stat. Soc. Ser. B, 74(3), 447–448 (2012)

    Google Scholar 

  53. Robert, C., Casella, G.: Monte Carlo Statistical Methods, 2nd edn. Springer, New York (2004)

    Book  MATH  Google Scholar 

  54. Robert, C., Cornuet, J.-M., Marin, J.-M., Pillai, N.: Lack of confidence in ABC model choice. Proc. Natl. Acad. Sci. 108(37), 15112–15117 (2011)

    Article  Google Scholar 

  55. Robert, C., Mengersen, K., Chen, C.: Model choice versus model criticism. Proc. Natl. Acad. Sci. 107(3), E5 (2010)

    Article  Google Scholar 

  56. Rubin, D.: Bayesianly justifiable and relevant frequency calculations for the applied statistician. Ann. Stat. 12, 1151–1172 (1984)

    Article  MathSciNet  MATH  Google Scholar 

  57. Ruli, E., Sartori, N., Ventura, L.: Approximate Bayesian Computation with composite score functions. e-prints (2013)

    Google Scholar 

  58. Stephens, M., Donnelly, P.: Inference in molecular population genetics. J. R. Stat. Soc.: Ser. B (Stat. Method.) 62(4), 605–635 (2000)

    Article  MathSciNet  MATH  Google Scholar 

  59. Stoehr, J., Pudlo, P., Cucala, L.: Adaptive ABC model choice and geometric summary statistics for hidden Gibbs random fields. Stat. Comput. pp. 1–13 (2014)

    Google Scholar 

  60. Sunnåker, M., Busetto, A., Numminen, E., Corander, J., Foll, M., Dessimoz, C.: Approximate Bayesian computation. PLoS Comput. Biol. 9(1), e1002803 (2013)

    Article  MathSciNet  Google Scholar 

  61. Tanner, M., Wong, W.: The calculation of posterior distributions by data augmentation. J. Am. Stat. Assoc. 82, 528–550 (1987)

    Article  MathSciNet  MATH  Google Scholar 

  62. Tavaré, S., Balding, D., Griffith, R., Donnelly, P.: Inferring coalescence times from DNA sequence data. Genetics 145, 505–518 (1997)

    Google Scholar 

  63. Templeton, A.: Statistical hypothesis testing in intraspecific phylogeography: nested clade phylogeographical analysis vs. approximate Bayesian computation. Mol. Ecol. 18(2), 319–331 (2008)

    Article  MathSciNet  Google Scholar 

  64. Templeton, A.: Coherent and incoherent inference in phylogeography and human evolution. Proc. Natl. Acad. Sci. 107(14), 6376–6381 (2010)

    Article  Google Scholar 

  65. Toni, T., Welch, D., Strelkowa, N., Ipsen, A., Stumpf, M.: Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems. J. R. Soc. Interface 6(31), 187–202 (2009)

    Article  Google Scholar 

  66. van der Vaart, A.: Asymptotic Statistics. Cambridge University Press, Cambridge (1998)

    Book  MATH  Google Scholar 

  67. Verdu, P., Austerlitz, F., Estoup, A., Vitalis, R., Georges, M., Théry, S., Froment, A., Le Bomin, S., Gessain, A., Hombert, J.-M., Van der Veen, L., Quintana-Murci, L., Bahuchet, S., Heyer, E.: Origins and genetic diversity of pygmy hunter-gatherers from Western Central Africa. Curr. Biol. 19(4), 312–318 (2009)

    Article  Google Scholar 

  68. Wegmann, D., Excoffier, L.: Bayesian inference of the demographic history of chimpanzees. Mol. Biol. Evol. 27(6), 1425–1435 (2010)

    Article  Google Scholar 

  69. Wikipedia (2014). Approximate Bayesian computation — Wikipedia, The Free Encyclopedia

    Google Scholar 

  70. Wilkinson, R.L: Approximate Bayesian computation (ABC) gives exact results under the assumption of model error. Technical Report (2008)

    Google Scholar 

  71. Wilkinson, R.: Approximate Bayesian computation (ABC) gives exact results under the assumption of model error. Stat. Appl. Genet. Mol. Biol. 12(2), 129–141 (2013)

    MathSciNet  Google Scholar 

  72. Wilkinson, R.D.: Accelerating ABC methods using Gaussian processes. e-prints (2014)

    Google Scholar 

Download references

Acknowledgments

The author is most grateful to an anonymous referee for her or his help with the syntax and grammar of this survey. He also thanks the organisers of MCqMC 2014 in Leuven for their kind invitation.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Christian P. Robert .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer International Publishing Switzerland

About this paper

Cite this paper

Robert, C.P. (2016). Approximate Bayesian Computation: A Survey on Recent Results. In: Cools, R., Nuyens, D. (eds) Monte Carlo and Quasi-Monte Carlo Methods. Springer Proceedings in Mathematics & Statistics, vol 163. Springer, Cham. https://doi.org/10.1007/978-3-319-33507-0_7

Download citation

Publish with us

Policies and ethics