IDEAS home Printed from https://ideas.repec.org/a/eee/csdana/v70y2014icp45-60.html
   My bibliography  Save this article

Towards Bayesian experimental design for nonlinear models that require a large number of sampling times

Author

Listed:
  • Ryan, Elizabeth G.
  • Drovandi, Christopher C.
  • Thompson, M. Helen
  • Pettitt, Anthony N.

Abstract

The use of Bayesian methodologies for solving optimal experimental design problems has increased. Many of these methods have been found to be computationally intensive for design problems that require a large number of design points. A simulation-based approach that can be used to solve optimal design problems in which one is interested in finding a large number of (near) optimal design points for a small number of design variables is presented. The approach involves the use of lower dimensional parameterisations that consist of a few design variables, which generate multiple design points. Using this approach, one simply has to search over a few design variables, rather than searching over a large number of optimal design points, thus providing substantial computational savings. The methodologies are demonstrated on four applications, including the selection of sampling times for pharmacokinetic and heat transfer studies, and involve nonlinear models. Several Bayesian design criteria are also compared and contrasted, as well as several different lower dimensional parameterisation schemes for generating the many design points.

Suggested Citation

  • 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.
    • Handle: RePEc:eee:csdana:v:70:y:2014:i:c:p:45-60
    DOI: 10.1016/j.csda.2013.08.017
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0167947313003149
    Download Restriction: Full text for ScienceDirect subscribers only.
    File URL: https://libkey.io/10.1016/j.csda.2013.08.017?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. Drovandi, Christopher C. & McGree, James M. & Pettitt, Anthony N., 2013. "Sequential Monte Carlo for Bayesian sequentially designed experiments for discrete data," Computational Statistics & Data Analysis, Elsevier, vol. 57(1), pages 320-335.
    2. Peter Müller & Don A. Berry & Andrew P. Grieve & Michael Krams, 2006. "A Bayesian Decision-Theoretic Dose-Finding Trial," Decision Analysis, INFORMS, vol. 3(4), pages 197-207, December.
    3. Concha Bielza & Peter Müller & David Ríos Insua, 1999. "Decision Analysis by Augmented Probability Simulation," Management Science, INFORMS, vol. 45(7), pages 995-1007, July.
    4. 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.
    5. N. Friel & A. N. Pettitt, 2008. "Marginal likelihood estimation via power posteriors," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 70(3), pages 589-607, July.
    6. 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.
    7. 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)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. 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.
    2. 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.
    3. 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.
    4. 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.

    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. 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.
    2. 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.
    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. & 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.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. Jeong Eun Lee & Christian Robert, 2013. "Imortance Sampling Schemes for Evidence Approximation in Mixture Models," Working Papers 2013-42, Center for Research in Economics and Statistics.
    10. Will Penny & Biswa Sengupta, 2016. "Annealed Importance Sampling for Neural Mass Models," PLOS Computational Biology, Public Library of Science, vol. 12(3), pages 1-25, March.
    11. Bielza, Concha & Gómez, Manuel & Shenoy, Prakash P., 2011. "A review of representation issues and modeling challenges with influence diagrams," Omega, Elsevier, vol. 39(3), pages 227-241, June.
    12. Spezia, L. & Cooksley, S.L. & Brewer, M.J. & Donnelly, D. & Tree, A., 2014. "Modelling species abundance in a river by Negative Binomial hidden Markov models," Computational Statistics & Data Analysis, Elsevier, vol. 71(C), pages 599-614.
    13. Ekin, Tahir, 2018. "Integrated maintenance and production planning with endogenous uncertain yield," Reliability Engineering and System Safety, Elsevier, vol. 179(C), pages 52-61.
    14. Vitoratou, Silia & Ntzoufras, Ioannis & Moustaki, Irini, 2016. "Explaining the behavior of joint and marginal Monte Carlo estimators in latent variable models with independence assumptions," LSE Research Online Documents on Economics 57685, London School of Economics and Political Science, LSE Library.
    15. Yijing Li & Prakash P. Shenoy, 2012. "A Framework for Solving Hybrid Influence Diagrams Containing Deterministic Conditional Distributions," Decision Analysis, INFORMS, vol. 9(1), pages 55-75, March.
    16. Spezia, Luigi, 2020. "Bayesian variable selection in non-homogeneous hidden Markov models through an evolutionary Monte Carlo method," Computational Statistics & Data Analysis, Elsevier, vol. 143(C).
    17. AWLP Thilan & P Menéndez & JM McGree, 2023. "Assessing the ability of adaptive designs to capture trends in hard coral cover," Environmetrics, John Wiley & Sons, Ltd., vol. 34(6), September.
    18. Elaine A. Ferguson & Jason Matthiopoulos & Robert H. Insall & Dirk Husmeier, 2017. "Statistical inference of the mechanisms driving collective cell movement," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 66(4), pages 869-890, August.
    19. Tahir Ekin & Stephen Walker & Paul Damien, 2023. "Augmented simulation methods for discrete stochastic optimization with recourse," Annals of Operations Research, Springer, vol. 320(2), pages 771-793, January.
    20. Azriel, David, 2014. "Optimal sequential designs in phase I studies," Computational Statistics & Data Analysis, Elsevier, vol. 71(C), pages 288-297.

    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:70:y:2014:i:c:p:45-60. 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.