IDEAS home Printed from https://ideas.repec.org/a/bpj/sagmbi/v15y2016i5p363-379n1.html
   My bibliography  Save this article

Diagnostics for assessing the linear noise and moment closure approximations

Author

Listed:
  • Gillespie Colin S.
  • Golightly Andrew

    (Newcastle University – School of Mathematics and Statistics, Newcastle, United Kingdom of Great Britain and Northern Ireland)

Abstract

Solving the chemical master equation exactly is typically not possible, so instead we must rely on simulation based methods. Unfortunately, drawing exact realisations, results in simulating every reaction that occurs. This will preclude the use of exact simulators for models of any realistic size and so approximate algorithms become important. In this paper we describe a general framework for assessing the accuracy of the linear noise and two moment approximations. By constructing an efficient space filling design over the parameter region of interest, we present a number of useful diagnostic tools that aids modellers in assessing whether the approximation is suitable. In particular, we leverage the normality assumption of the linear noise and moment closure approximations.

Suggested Citation

  • Gillespie Colin S. & Golightly Andrew, 2016. "Diagnostics for assessing the linear noise and moment closure approximations," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 15(5), pages 363-379, October.
    • Handle: RePEc:bpj:sagmbi:v:15:y:2016:i:5:p:363-379:n:1
    DOI: 10.1515/sagmb-2014-0071
    as

    Download full text from publisher

    File URL: https://doi.org/10.1515/sagmb-2014-0071
    Download Restriction: For access to full text, subscription to the journal or payment for the individual article is required.
    File URL: https://libkey.io/10.1515/sagmb-2014-0071?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. Golightly, A. & Wilkinson, D.J., 2008. "Bayesian inference for nonlinear multivariate diffusion models observed with error," Computational Statistics & Data Analysis, Elsevier, vol. 52(3), pages 1674-1693, January.
    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. Aliu, A. Hassan & Abiodun A. A. & Ipinyomi R.A., 2017. "Statistical Inference for Discretely Observed Diffusion Epidemic Models," International Journal of Mathematics Research, Conscientia Beam, vol. 6(1), pages 29-35.
    2. Vilda Purutçuoğlu, 2013. "Inference of the stochastic MAPK pathway by modified diffusion bridge method," Central European Journal of Operations Research, Springer;Slovak Society for Operations Research;Hungarian Operational Research Society;Czech Society for Operations Research;Österr. Gesellschaft für Operations Research (ÖGOR);Slovenian Society Informatika - Section for Operational Research;Croatian Operational Research Society, vol. 21(2), pages 415-429, March.
    3. Christophe Andrieu & Arnaud Doucet & Roman Holenstein, 2010. "Particle Markov chain Monte Carlo methods," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 72(3), pages 269-342, June.
    4. Isambi Mbalawata & Simo Särkkä & Heikki Haario, 2013. "Parameter estimation in stochastic differential equations with Markov chain Monte Carlo and non-linear Kalman filtering," Computational Statistics, Springer, vol. 28(3), pages 1195-1223, June.
    5. Marcin Mider & Paul A. Jenkins & Murray Pollock & Gareth O. Roberts, 2022. "The Computational Cost of Blocking for Sampling Discretely Observed Diffusions," Methodology and Computing in Applied Probability, Springer, vol. 24(4), pages 3007-3027, December.
    6. Golightly, Andrew & Bradley, Emma & Lowe, Tom & Gillespie, Colin S., 2019. "Correlated pseudo-marginal schemes for time-discretised stochastic kinetic models," Computational Statistics & Data Analysis, Elsevier, vol. 136(C), pages 92-107.
    7. Colin S. Gillespie & Andrew Golightly, 2010. "Bayesian inference for generalized stochastic population growth models with application to aphids," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 59(2), pages 341-357, March.
    8. Libo Sun & Chihoon Lee & Jennifer A. Hoeting, 2019. "A penalized simulated maximum likelihood method to estimate parameters for SDEs with measurement error," Computational Statistics, Springer, vol. 34(2), pages 847-863, June.
    9. Huang Xiao, 2013. "Quasi-maximum likelihood estimation of multivariate diffusions," Studies in Nonlinear Dynamics & Econometrics, De Gruyter, vol. 17(2), pages 179-197, April.
    10. Quentin Clairon & Adeline Samson, 2020. "Optimal control for estimation in partially observed elliptic and hypoelliptic linear stochastic differential equations," Statistical Inference for Stochastic Processes, Springer, vol. 23(1), pages 105-127, April.
    11. Yuan Shen & Dan Cornford & Manfred Opper & Cedric Archambeau, 2012. "Variational Markov chain Monte Carlo for Bayesian smoothing of non-linear diffusions," Computational Statistics, Springer, vol. 27(1), pages 149-176, March.
    12. Mogens Bladt & Samuel Finch & Michael Sørensen, 2016. "Simulation of multivariate diffusion bridges," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 78(2), pages 343-369, March.
    13. Matthew M. Graham & Alexandre H. Thiery & Alexandros Beskos, 2022. "Manifold Markov chain Monte Carlo methods for Bayesian inference in diffusion models," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 84(4), pages 1229-1256, September.
    14. Giorgos Sermaidis & Omiros Papaspiliopoulos & Gareth O. Roberts & Alexandros Beskos & Paul Fearnhead, 2013. "Markov Chain Monte Carlo for Exact Inference for Diffusions," Scandinavian Journal of Statistics, Danish Society for Theoretical Statistics;Finnish Statistical Society;Norwegian Statistical Association;Swedish Statistical Association, vol. 40(2), pages 294-321, June.
    15. Paul Fearnhead & Vasilieos Giagos & Chris Sherlock, 2014. "Inference for reaction networks using the linear noise approximation," Biometrics, The International Biometric Society, vol. 70(2), pages 457-466, June.
    16. Peavoy, Daniel & Franzke, Christian L.E. & Roberts, Gareth O., 2015. "Systematic physics constrained parameter estimation of stochastic differential equations," Computational Statistics & Data Analysis, Elsevier, vol. 83(C), pages 182-199.
    17. Sukhmani Sidhu & Kanchan Jain & Suresh Kumar Sharma, 2018. "Bayesian estimation of generalized gamma shared frailty model," Computational Statistics, Springer, vol. 33(1), pages 277-297, March.
    18. Beskos, Alexandros & Kalogeropoulos, Konstantinos & Pazos, Erik, 2013. "Advanced MCMC methods for sampling on diffusion pathspace," Stochastic Processes and their Applications, Elsevier, vol. 123(4), pages 1415-1453.
    19. Dureau, Joseph & Kalogeropoulos, Konstantinos & Baguelin, Marc, 2013. "Capturing the time-varying drivers of an epidemic using stochastic dynamical systems," LSE Research Online Documents on Economics 41749, London School of Economics and Political Science, LSE Library.
    20. Chiarella, Carl & Hung, Hing & T, Thuy-Duong, 2009. "The volatility structure of the fixed income market under the HJM framework: A nonlinear filtering approach," Computational Statistics & Data Analysis, Elsevier, vol. 53(6), pages 2075-2088, April.

    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:bpj:sagmbi:v:15:y:2016:i:5:p:363-379:n:1. 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: Peter Golla (email available below). General contact details of provider: https://www.degruyter.com .

    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.