Skip to main content

Improving Approximate Bayesian Computation with Pre-judgment Rule

  • Conference paper
  • First Online:
  • 1211 Accesses

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 1257))

Abstract

Approximate Bayesian Computation (ABC) is a popular approach for Bayesian modeling, when these models exhibit an intractable likelihood. However, during each proposal of ABC, a great number of simulators are required and each simulation is always time-consuming. The overall goal of this work is to avoid inefficient computational cost of ABC. A pre-judgment rule (PJR) is proposed, which mainly aims to judge the acceptance condition using a small fraction of simulators instead of the whole simulators, thus achieving less computational complexity. In addition, it provided a theoretical study of the error bounded caused by PJR Strategy. Finally, the methodology was illustrated with various examples. The empirical results show both the effectiveness and efficiency of PJR compared with the previous methods.

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

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   119.99
Price excludes VAT (USA)
  • Compact, lightweight 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

Learn about institutional subscriptions

Notes

  1. 1.

    \(\rho (\mathbb {S}(x),\mathbb {S}(y))\) is replaced by \(\rho (x,y)\), similar with Step \(\mathbb {C}\)3.

  2. 2.

    E.g., \(\zeta \)-kernel can be chosen as \(\pi _\zeta (x_1\vert x_2) = (1/\sqrt{2\pi }\zeta )\exp (-\Vert x_1-x_2\Vert ^2/2\zeta ^2)\).

  3. 3.

    In Step A2, \(z_0\) is more complex. Checking the acceptance condition is equivalent to judging \(\frac{z}{c} > u\), where c is defined in Eq. 2 and \(u\sim \text {Uniform}(0,1)\).

  4. 4.

    The total variation distance between two distribution P and Q, absolutely continuous w.r.t. measure \(\varOmega \), is defined as \(d_v(P,Q) \triangleq 1/2\int \nolimits _{\theta } \vert f_P(\theta ) - f_Q(\theta ) \vert d\varOmega (\theta )\), where \(f_P(\cdot )\) and \(f_Q(\cdot )\) are their respective densities.

  5. 5.

    Measured in term of number of simulator.

  6. 6.

    Measured in term of TVD with the true posterior distribution.

  7. 7.

    Note that in experiment the total variational distance is estimated empirically owing to the absence of explicit formulae.

References

  1. Ahn, S., Korattikara, A., Welling, M.: Bayesian posterior sampling via stochastic gradient fisher scoring. In: Proceedings of the 29th International Conference on International Conference on Machine Learning, pp. 1771–1778 (2012)

    Google Scholar 

  2. Ahn, S., Shahbaba, B., Welling, M.: Distributed stochastic gradient MCMC. In: Proceedings of the 31st International Conference on Machine Learning (ICML-14), pp. 1044–1052 (2014)

    Google Scholar 

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

    Article  MathSciNet  MATH  Google Scholar 

  4. Barber, S., Voss, J., Webster, M., et al.: The rate of convergence for approximate Bayesian computation. Electron. J. Stat. 9(1), 80–105 (2015)

    Article  MathSciNet  MATH  Google Scholar 

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

    Article  Google Scholar 

  6. Bernton, E., Jacob, P.E., Gerber, M., Robert, C.P.: Approximate Bayesian computation with the Wasserstein distance. J. Roy. Stat. Soc.: Ser. B (Stat. Methodol.) 81(2), 235–269 (2019)

    Article  MathSciNet  MATH  Google Scholar 

  7. Biau, G., Cérou, F., Guyader, A., et al.: New insights into approximate Bayesian computation. In: Annales de l’Institut Henri Poincaré, Probabilités et Statistiques, vol. 51, pp. 376–403. Institut Henri Poincaré (2015)

    Google Scholar 

  8. Blum, M.G., François, O.: Non-linear regression models for approximate Bayesian computation. Stat. Comput. 20(1), 63–73 (2010)

    Article  MathSciNet  Google Scholar 

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

    Article  MathSciNet  MATH  Google Scholar 

  10. Cabras, S., Nueda, M.E.C., Ruli, E., et al.: Approximate Bayesian computation by modelling summary statistics in a quasi-likelihood framework. Bayesian Anal. 10(2), 411–439 (2015)

    Article  MathSciNet  MATH  Google Scholar 

  11. Chen, T., Fox, E., Guestrin, C.: Stochastic gradient Hamiltonian Monte Carlo. In: International Conference on Machine Learning, pp. 1683–1691 (2014)

    Google Scholar 

  12. Ding, N., Fang, Y., Babbush, R., Chen, C., Skeel, R.D., Neven, H.: Bayesian sampling using stochastic gradient thermostats. In: Advances in Neural Information Processing Systems, pp. 3203–3211 (2014)

    Google Scholar 

  13. Fearnhead, P., Prangle, D.: Constructing summary statistics for approximate Bayesian computation: semi-automatic approximate Bayesian computation. J. Roy. Stat. Soc.: Ser. B (Stat. Methodol.) 74(3), 419–474 (2012)

    Article  MathSciNet  MATH  Google Scholar 

  14. Fu, T., Luo, L., Zhang, Z.: Quasi-Newton Hamiltonian Monte Carlo. In: Proceedings of the Thirty-Second Conference on Uncertainty in Artificial Intelligence, pp. 212–221 (2016)

    Google Scholar 

  15. Jiang, B., Wu, T.Y., Zheng, C., Wong, W.H.: Learning summary statistic for approximate Bayesian computation via deep neural network. Stat. Sin. 27, 1595–1618 (2017)

    MathSciNet  MATH  Google Scholar 

  16. Korattikara, A., Chen, Y., Welling, M.: Austerity in MCMC land: cutting the metropolis-hastings budget. In: International Conference on Machine Learning, pp. 181–189 (2014)

    Google Scholar 

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

    Google Scholar 

  18. Ma, Y.A., Chen, T., Fox, E.: A complete recipe for stochastic gradient MCMC. In: Advances in Neural Information Processing Systems (2015)

    Google Scholar 

  19. Marin, J.M., Pudlo, P., Robert, C.P., Ryder, R.J.: Approximate Bayesian computational methods. Stat. Comput. 22(6), 1167–1180 (2012)

    Article  MathSciNet  MATH  Google Scholar 

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

    Article  Google Scholar 

  21. Meeds, E., Leenders, R., Welling, M.: Hamiltonian ABC. In: Proceedings of the Thirty-First Conference on Uncertainty in Artificial Intelligence, pp. 582–591 (2015)

    Google Scholar 

  22. Meeds, E., Welling, M.: GPS-ABC: Gaussian process surrogate approximate Bayesian computation. In: Proceedings of the Thirtieth Conference on Uncertainty in Artificial Intelligence, pp. 593–602 (2014)

    Google Scholar 

  23. Meeds, T., Welling, M.: Optimization Monte Carlo: efficient and embarrassingly parallel likelihood-free inference. In: Advances in Neural Information Processing Systems, pp. 2071–2079 (2015)

    Google Scholar 

  24. Mondal, M., Bertranpetit, J., Lao, O.: Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania. Nat. Commun. 10(1), 246 (2019)

    Article  Google Scholar 

  25. 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)

    Article  Google Scholar 

  26. Sisson, S.A., Fan, Y., Beaumont, M.: Handbook of Approximate Bayesian Computation. Chapman and Hall/CRC, New York (2018)

    Book  MATH  Google Scholar 

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

    Article  MathSciNet  Google Scholar 

  28. Welling, M., Teh, Y.W.: Bayesian learning via stochastic gradient Langevin dynamics. In: Proceedings of the 28th International Conference on Machine Learning (ICML-11), pp. 681–688 (2011)

    Google Scholar 

  29. Wilkinson, R.: Accelerating ABC methods using Gaussian processes. In: Artificial Intelligence and Statistics, pp. 1015–1023 (2014)

    Google Scholar 

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

    Article  MathSciNet  Google Scholar 

  31. Wood, S.N.: Statistical inference for noisy nonlinear ecological dynamic systems. Nature 466(7310), 1102–1104 (2010)

    Article  Google Scholar 

Download references

Acknowledgement

This study was funded by Scientific research fund of North University of China (No. XJJ201803).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Gangzhu Qiao .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Nature Singapore Pte Ltd.

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Wang, Y., Yu, X., Qin, P., Chai, R., Qiao, G. (2020). Improving Approximate Bayesian Computation with Pre-judgment Rule. In: Zeng, J., Jing, W., Song, X., Lu, Z. (eds) Data Science. ICPCSEE 2020. Communications in Computer and Information Science, vol 1257. Springer, Singapore. https://doi.org/10.1007/978-981-15-7981-3_15

Download citation

  • DOI: https://doi.org/10.1007/978-981-15-7981-3_15

  • Published:

  • Publisher Name: Springer, Singapore

  • Print ISBN: 978-981-15-7980-6

  • Online ISBN: 978-981-15-7981-3

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics