Skip to main content

Approximate Bayesian Computational Methods for the Inference of Unknown Parameters

  • Chapter
  • First Online:
2017 MATRIX Annals

Part of the book series: MATRIX Book Series ((MXBS,volume 2))

  • 1146 Accesses

Abstract

Recent advances in biology, economics, engineering and physical sciences have generated a large number of mathematical models for describing the dynamics of complex systems. A key step in mathematical modelling is to estimate model parameters in order to realize experimental observations. However, it is difficult to derive the analytical density functions in the Bayesian methods for these mathematical models. During the last decade, approximate Bayesian computation (ABC) has been developed as a major method for the inference of parameters in mathematical models. A number of new methods have been designed to improve the efficiency and accuracy of ABC. Theoretical studies have also been conducted to investigate the convergence property of these methods. In addition, these methods have been applied to a wide range of deterministic and stochastic models. This chapter gives a brief review of the main ABC algorithms and various improvements.

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 119.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 159.99
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

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Aeschbacher, S., Beaumont, M. A., Futschik, A.: A novel approach for choosing summary statistics in approximate Bayesian computation. Genetics 192, 1027–1047 (2012)

    Google Scholar 

  2. Barthelmé, S., Chopin, N.: Expectation propagation for likelihood-free inference. J. Am. Stat. Assoc. 109, 315–333 (2014)

    MathSciNet  MATH  Google Scholar 

  3. Bazin, E., Dawson, K.J., Beaumont, M.A.: Likelihoodfree inference of population structure and local adaptation in a Bayesian hierarchical model. Genetics 185, 587–602 (2010)

    Google Scholar 

  4. Beaumont, M.A.: Adaptive approximate Bayesian computation. Biometrika 96, 983–990 (2009)

    MathSciNet  MATH  Google Scholar 

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

    Google Scholar 

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

    Google Scholar 

  7. Biau, G., Cérou, F., Guyader, A.: New insights into approximate Bayesian computation. Ann. I. H. Poincaré B 51, 376–403 (2015)

    MathSciNet  MATH  Google Scholar 

  8. Blum, M.G.B.: Approximate Bayesian computation: a nonparametric perspective. J. Am. Stat. Assoc. 105, 1178–1187 (2010)

    MathSciNet  MATH  Google Scholar 

  9. Blum, M.G.B.: Regression approaches for approximate Bayesian computation (2017). arXiv:1707.01254v1

    Google Scholar 

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

    MathSciNet  Google Scholar 

  11. 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)

    MathSciNet  MATH  Google Scholar 

  12. Cappé, O., Guillin, A., Marin, J.-M., Robert, C.P.: Population Monte Carlo. J. Comput. Graph. Stat. 13(4), 907–929 (2004)

    MathSciNet  Google Scholar 

  13. Christen, J.A., Fox, C.: Markov chain Monte Carlo using an approximation. J. Comput. Graph. Stat. 14, 795–810 (2005)

    MathSciNet  Google Scholar 

  14. Csilléry, K., Blum, M.G.B., Gaggiotti, O., François, O.: Approximate Bayesian computation (ABC) in practice. Trends Ecol. Evol. 25(7), 410–418 (2010)

    Google Scholar 

  15. Del Moral, P., Doucet, A., Jasra, A.: Sequential Monte Carlo samplers. J. R. Stat. Soc. Ser. B 68, 411–436 (2006)

    MathSciNet  MATH  Google Scholar 

  16. Del Moral, P., Doucet, A, Jasra, A.: An adaptive sequential Monte Carlo method for approximate Bayesian computation. Stat. Comput. 22(5), 1009–1020 (2012)

    MathSciNet  MATH  Google Scholar 

  17. Deng, Z., Tian, T.: A continuous optimization approach for inferring parameters in mathematical models of regulatory networks. BMC Bioinform. 15, 256 (2014)

    Google Scholar 

  18. Drovandi, C.C., Pettitt, A.N.: Estimation of parameters for macroparasite population evolution using approximate Bayesian computation. Biometrics 67(1), 225–233 (2011)

    MathSciNet  MATH  Google Scholar 

  19. Fearnhead, P., Prangle, D.: Constructing summary statistics for approximate Bayesian computation: semi-automatic approximate Bayesian computation. J. R. Stat. Soc. Ser. B 74, 419–474 (2012)

    MathSciNet  Google Scholar 

  20. Gelman, A., Carlin, J.B., Stern, H.S., Rubin, D.B.: Bayesian Data Analysis. Chapman and Hall/CRC Press, London (2003)

    MATH  Google Scholar 

  21. Goel, G., Chou, I.C., Voit, E.O.: System estimation from metabolic time-series data. Bioinformatics 24(21), 2505–2511 (2008)

    Google Scholar 

  22. Green, P.J., Łatuszyński, K., Pereyra, M., Robert, C.P.: Bayesian computation: a summary of the current state, and samples backwards and forwards. Stat. Comput. 25, 835–862 (2015)

    MathSciNet  MATH  Google Scholar 

  23. Johnson, R., Kirk, P., Stumpf, M.P.H.: SYSBIONS: nested sampling for systems biology. Bioinformatics 31(4), 604–605 (2015)

    Google Scholar 

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

    Google Scholar 

  25. Kousathanas, A., Leuenberger, C., Helfer, J., Quinodoz, M., Foll, M., Wegmann, D.: Likelihood-free inference in high-dimensional models. Genetics 203, 893–904 (2016)

    Google Scholar 

  26. Kypraios, T., Neal, P., Prangle, D.: A tutorial introduction to Bayesian inference for stochastic epidemic models using approximate Bayesian computation. Math. Biosci. 287, 42–53 (2016)

    MathSciNet  MATH  Google Scholar 

  27. Lenormand, M., Jabot, F., Deffuant, G.: Adaptive approximate Bayesian computation for complex models. Comput Stat. 28(6), 2777–2796 (2013)

    MathSciNet  MATH  Google Scholar 

  28. Li, J., Nott, D.J., Fan, Y., Sisson, S.A.: Extending approximate Bayesian computation methods to high dimensions via a Gaussian copula model. Comput. Stat. Data Anal. 106, 77–89 (2017)

    MathSciNet  MATH  Google Scholar 

  29. Liepe, J., et al.: A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation. Nat. Protoc. 9(2), 439–456 (2014)

    Google Scholar 

  30. Lillacci, G., Khammash, M.: Parameter estimation and model selection in computational biology. PLoS Comput. Biol. 6(3), e1000696 (2010)

    MathSciNet  MATH  Google Scholar 

  31. Lintusaari, J., Gutmann, M., Dutta, R., Kaski, S., Corander, J.: Fundamentals and recent developments in approximate Bayesian computation. Syst. Biol. 66(1), e66–e82 (2017)

    Google Scholar 

  32. Marin, J.-M., Pudlo, P., Robert, C.P., Ryder, R.J.: Approximate Bayesian computational methods. Stat. Comput. 22, 1167–1180 (2012)

    MathSciNet  MATH  Google Scholar 

  33. Marjoram, P., Molitor, J., Plagnol, V., Tavaré, S.: Markov chain Monte Carlo without likelihoods. Proc. Natl. Acad. Sci. U. S. A. 100(26), 15324–15328 (2003)

    Google Scholar 

  34. Nott, D.J., Fan, Y., Marshall, L., Sisson, S.A.: Approximate Bayesian computation and Bayes’s linear analysis: toward high-dimensional ABC. J. Comput. Graph. Stat. 23(1), 65–86 (2014)

    MathSciNet  Google Scholar 

  35. Nunes, M.A., Balding, D.J.: On optimal selection of summary statistics for approximate Bayesian computation. Stat. Appl. Genet. Mol. Biol. 9, Article 34 (2010)

    MathSciNet  MATH  Google Scholar 

  36. Nunes, M.A., Prangle, D.: abctools: an R package for tuning approximate Bayesian computation analyses. R J. 7(2), 189–205 (2015)

    Google Scholar 

  37. Picchini, U.: Inference for SDE models via approximate Bayesian computation. J. Comput. Graph. Stat. 23(4), 1080–1100 (2014)

    MathSciNet  Google Scholar 

  38. Prangle, D.: Summary statistics in approximate Bayesian computation (2015). arXiv:1512.05633

    Google Scholar 

  39. Prangle, D.: Lazy ABC. Stat. Comput. 26, 171–185 (2016)

    MathSciNet  Google Scholar 

  40. Pritchard, J.K., Seielstad, M.T., Perez-Lezaun, A., Feldman, M.W.: Population growth of human Y chromosomes: a study of Y chromosome microsatellites. Mol. Biol. Evol. 16(12), 1791–1798 (1999)

    Google Scholar 

  41. Robert, C.P.: Approximate Bayesian Computation: A Survey on Recent Results. Monte Carlo and Quasi-Monte Carlo Methods, pp. 185–205. Springer, Cham (2016)

    Google Scholar 

  42. Robert, C.P., Casella, G.: Monte Carlo Statistical Methods. Springer, New York (2004)

    MATH  Google Scholar 

  43. Rubin, D.B.: Bayesianly justifiable and relevant frequency calculations for the applied statistics. Ann. Stat. 12(4), 1151–1172 (1984)

    MATH  Google Scholar 

  44. Sisson, S.A., Fan, Y.: Likelihood-Free MCMC. Handbook of Markov Chain Monte Carlo, pp. 313–335. CRC Press, Boca Raton (2011)

    Google Scholar 

  45. Sisson, S.A., Fan, Y., Tanaka, M.M.: Sequential Monte Carlo without likelihoods. Proc. Natl. Acad. Sci. U. S. A. 104(6), 1760–1765 (2007)

    MathSciNet  MATH  Google Scholar 

  46. Sisson, S.A., Fan, Y., Tanaka, M.M.: Sequential Monte Carlo without likelihoods. Proc. Natl. Acad. Sci. U. S. A. 106(39), 16889 (2009)

    Google Scholar 

  47. Sunnaker, M., et al.: Approximate Bayesian computation. PLoS Comput. Biol. 9(1), e1002803 (2013)

    MathSciNet  Google Scholar 

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

    Google Scholar 

  49. Tian, T., Smith-Miles, K.: Mathematical modeling of GATA-switching for regulating the differentiation of hematopoietic stem cell. BMC Syst. Biol. 8(Suppl 1), S8 (2014)

    Google Scholar 

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

    Google Scholar 

  51. Turner, B.M., Van Zandt, T.: A tutorial on approximate Bayesian computation. J. Math. Psychol. 56(2), 69–85 (2012)

    MathSciNet  MATH  Google Scholar 

  52. Vyshemirsky, V., Girolami, M.: BioBayes: a software package for Bayesian inference in systems biology. Bioinformatics 24(17), 1933–1934 (2008)

    Google Scholar 

  53. Wegmann, D., Leuenberger, C., Excoffier, L.: Efficient approximate Bayesian computation coupled with Markov chain Monte Carlo without likelihood. Genetics 182, 129–141 (2009)

    Google Scholar 

  54. Wilkinson, D.J.: Bayesian methods in bioinformatics and computational systems biology. Brief Bioinform. 8(2), 109–116 (2007)

    Google Scholar 

  55. Wu, Q., Smith-Miles, K., Tian, T.: Approximate Bayesian computation schemes for parameter inference of discrete stochastic models using simulated likelihood density. BMC Bioinform. 15, S3 (2014)

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Tianhai Tian .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Ke, Y., Tian, T. (2019). Approximate Bayesian Computational Methods for the Inference of Unknown Parameters. In: de Gier, J., Praeger, C., Tao, T. (eds) 2017 MATRIX Annals. MATRIX Book Series, vol 2. Springer, Cham. https://doi.org/10.1007/978-3-030-04161-8_45

Download citation

Publish with us

Policies and ethics