IDEAS home Printed from https://ideas.repec.org/a/eee/csdana/v124y2018icp277-297.html
   My bibliography  Save this article

Optimal Bayesian design for discriminating between models with intractable likelihoods in epidemiology

Author

Listed:
  • Dehideniya, Mahasen B.
  • Drovandi, Christopher C.
  • McGree, James M.

Abstract

A methodology is proposed to derive Bayesian experimental designs for discriminating between rival epidemiological models with computationally intractable likelihoods. Methods from approximate Bayesian computation are used to facilitate inference in this setting, and an efficient implementation of this inference framework for approximating the expectation of utility functions is proposed. Three utility functions for model discrimination are considered, and the performance each utility is explored in designing experiments for discriminating between three epidemiological models; the death model, the Susceptible–Infected model, and the Susceptible–Exposed–Infected model. The challenge of efficiently locating optimal designs is addressed by an adaptation of the coordinate exchange algorithm which exploits parallel computational architectures.

Suggested Citation

  • Dehideniya, Mahasen B. & Drovandi, Christopher C. & McGree, James M., 2018. "Optimal Bayesian design for discriminating between models with intractable likelihoods in epidemiology," Computational Statistics & Data Analysis, Elsevier, vol. 124(C), pages 277-297.
    • Handle: RePEc:eee:csdana:v:124:y:2018:i:c:p:277-297
    DOI: 10.1016/j.csda.2018.03.004
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0167947318300525
    Download Restriction: Full text for ScienceDirect subscribers only.
    File URL: https://libkey.io/10.1016/j.csda.2018.03.004?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Ryan, Elizabeth G. & Drovandi, Christopher C. & Thompson, M. Helen & Pettitt, Anthony N., 2014. "Towards Bayesian experimental design for nonlinear models that require a large number of sampling times," Computational Statistics & Data Analysis, Elsevier, vol. 70(C), pages 45-60.
    2. Woods, David C. & McGree, James M. & Lewis, Susan M., 2017. "Model selection via Bayesian information capacity designs for generalised linear models," Computational Statistics & Data Analysis, Elsevier, vol. 113(C), pages 226-238.
    3. Simon Barthelmé & Nicolas Chopin, 2014. "Expectation Propagation for Likelihood-Free Inference," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 109(505), pages 315-333, March.
    4. Elizabeth G. Ryan & Christopher C. Drovandi & James M. McGree & Anthony N. Pettitt, 2016. "A Review of Modern Computational Algorithms for Bayesian Optimal Design," International Statistical Review, International Statistical Institute, vol. 84(1), pages 128-154, April.
    5. Simon N. Wood, 2010. "Statistical inference for noisy nonlinear ecological dynamic systems," Nature, Nature, vol. 466(7310), pages 1102-1104, August.
    6. Muller, Werner G & Ponce de Leon, Antonio C M, 1996. "Optimal Design of an Experiment in Economics," Economic Journal, Royal Economic Society, vol. 106(434), pages 122-127, January.
    7. McGree, J.M., 2017. "Developments of the total entropy utility function for the dual purpose of model discrimination and parameter estimation in Bayesian design," Computational Statistics & Data Analysis, Elsevier, vol. 113(C), pages 207-225.
    8. Jonathan R. Stroud & Peter Müller & Gary L. Rosner, 2001. "Optimal sampling times in population pharmacokinetic studies," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 50(3), pages 345-359.
    9. Xing Ju Lee & Christopher C. Drovandi & Anthony N. Pettitt, 2015. "Model choice problems using approximate Bayesian computation with applications to pathogen transmission data sets," Biometrics, The International Biometric Society, vol. 71(1), pages 198-207, March.
    10. Alex R. Cook & Gavin J. Gibson & Christopher A. Gilligan, 2008. "Optimal Observation Times in Experimental Epidemic Processes," Biometrics, The International Biometric Society, vol. 64(3), pages 860-868, September.
    11. Christopher C. Drovandi & Anthony N. Pettitt, 2013. "Bayesian Experimental Design for Models with Intractable Likelihoods," Biometrics, The International Biometric Society, vol. 69(4), pages 937-948, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Ryan, Elizabeth G. & Drovandi, Christopher C. & Pettitt, Anthony N., 2015. "Simulation-based fully Bayesian experimental design for mixed effects models," Computational Statistics & Data Analysis, Elsevier, vol. 92(C), pages 26-39.
    2. Elizabeth G. Ryan & Christopher C. Drovandi & James M. McGree & Anthony N. Pettitt, 2016. "A Review of Modern Computational Algorithms for Bayesian Optimal Design," International Statistical Review, International Statistical Institute, vol. 84(1), pages 128-154, April.
    3. McGree, J.M., 2017. "Developments of the total entropy utility function for the dual purpose of model discrimination and parameter estimation in Bayesian design," Computational Statistics & Data Analysis, Elsevier, vol. 113(C), pages 207-225.
    4. Ryan, Elizabeth G. & Drovandi, Christopher C. & Thompson, M. Helen & Pettitt, Anthony N., 2014. "Towards Bayesian experimental design for nonlinear models that require a large number of sampling times," Computational Statistics & Data Analysis, Elsevier, vol. 70(C), pages 45-60.
    5. Price, David J. & Bean, Nigel G. & Ross, Joshua V. & Tuke, Jonathan, 2018. "An induced natural selection heuristic for finding optimal Bayesian experimental designs," Computational Statistics & Data Analysis, Elsevier, vol. 126(C), pages 112-124.
    6. Gael M. Martin & David T. Frazier & Christian P. Robert, 2020. "Computing Bayes: Bayesian Computation from 1763 to the 21st Century," Monash Econometrics and Business Statistics Working Papers 14/20, Monash University, Department of Econometrics and Business Statistics.
    7. Gael M. Martin & David T. Frazier & Christian P. Robert, 2021. "Approximating Bayes in the 21st Century," Monash Econometrics and Business Statistics Working Papers 24/21, Monash University, Department of Econometrics and Business Statistics.
    8. Jonathan U Harrison & Ruth E Baker, 2020. "An automatic adaptive method to combine summary statistics in approximate Bayesian computation," PLOS ONE, Public Library of Science, vol. 15(8), pages 1-21, August.
    9. Grazzini, Jakob & Richiardi, Matteo G. & Tsionas, Mike, 2017. "Bayesian estimation of agent-based models," Journal of Economic Dynamics and Control, Elsevier, vol. 77(C), pages 26-47.
    10. S. G. J. Senarathne & C. C. Drovandi & J. M. McGree, 2020. "Bayesian sequential design for Copula models," TEST: An Official Journal of the Spanish Society of Statistics and Operations Research, Springer;Sociedad de Estadística e Investigación Operativa, vol. 29(2), pages 454-478, June.
    11. Luis Alvarez & Cristine Pinto & Vladimir Ponczek, 2022. "Homophily in preferences or meetings? Identifying and estimating an iterative network formation model," Papers 2201.06694, arXiv.org, revised Mar 2024.
    12. Li, J. & Nott, D.J. & Fan, Y. & Sisson, S.A., 2017. "Extending approximate Bayesian computation methods to high dimensions via a Gaussian copula model," Computational Statistics & Data Analysis, Elsevier, vol. 106(C), pages 77-89.
    13. Georgia Koppe & Hazem Toutounji & Peter Kirsch & Stefanie Lis & Daniel Durstewitz, 2019. "Identifying nonlinear dynamical systems via generative recurrent neural networks with applications to fMRI," PLOS Computational Biology, Public Library of Science, vol. 15(8), pages 1-35, August.
    14. Forneron, Jean-Jacques & Ng, Serena, 2018. "The ABC of simulation estimation with auxiliary statistics," Journal of Econometrics, Elsevier, vol. 205(1), pages 112-139.
    15. Barde, Sylvain, 2024. "Bayesian estimation of large-scale simulation models with Gaussian process regression surrogates," Computational Statistics & Data Analysis, Elsevier, vol. 196(C).
    16. Niyousha Hosseinichimeh & Hazhir Rahmandad & Mohammad S. Jalali & Andrea K. Wittenborn, 2016. "Estimating the parameters of system dynamics models using indirect inference," System Dynamics Review, System Dynamics Society, vol. 32(2), pages 154-178, April.
    17. David J Price & Alexandre Breuzé & Richard Dybowski & Piero Mastroeni & Olivier Restif, 2017. "An efficient moments-based inference method for within-host bacterial infection dynamics," PLOS Computational Biology, Public Library of Science, vol. 13(11), pages 1-27, November.
    18. Ng'ombe, John, 2019. "Economics of the Greenseeder Hand Planter, Discrete Choice Modeling, and On-Farm Field Experimentation," Thesis Commons jckt7, Center for Open Science.
    19. Henri Pesonen & Umberto Simola & Alvaro Köhn‐Luque & Henri Vuollekoski & Xiaoran Lai & Arnoldo Frigessi & Samuel Kaski & David T. Frazier & Worapree Maneesoonthorn & Gael M. Martin & Jukka Corander, 2023. "ABC of the future," International Statistical Review, International Statistical Institute, vol. 91(2), pages 243-268, August.
    20. Ong, Victor M.-H. & Nott, David J. & Tran, Minh-Ngoc & Sisson, Scott A. & Drovandi, Christopher C., 2018. "Likelihood-free inference in high dimensions with synthetic likelihood," Computational Statistics & Data Analysis, Elsevier, vol. 128(C), pages 271-291.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:eee:csdana:v:124:y:2018:i:c:p:277-297. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Catherine Liu (email available below). General contact details of provider: http://www.elsevier.com/locate/csda .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.