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Computational Methods for Complex Stochastic Systems: A Review of Some Alternatives to MCMC.

Fearnhead, Paul (2008) Computational Methods for Complex Stochastic Systems: A Review of Some Alternatives to MCMC. Statistics and Computing, 18 (2). pp. 151-171. ISSN 0960-3174

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    Abstract

    We consider analysis of complex stochastic models based upon partial information. MCMC and reversible jump MCMC are often the methods of choice for such problems, but in some situations they can be difficult to implement; and suffer from problems such as poor mixing, and the difficulty of diagnosing convergence. Here we review three alternatives to MCMC methods: importance sampling, the forward-backward algorithm, and sequential Monte Carlo (SMC). We discuss how to design good proposal densities for importance sampling, show some of the range of models for which the forward-backward algorithm can be applied, and show how resampling ideas from SMC can be used to improve the efficiency of the other two methods. We demonstrate these methods on a range of examples, including estimating the transition density of a diffusion and of a discrete-state continuous-time Markov chain; inferring structure in population genetics; and segmenting genetic divergence data.

    Item Type: Article
    Journal or Publication Title: Statistics and Computing
    Uncontrolled Keywords: Diffusions ; Forward-Backward Algorithm ; Importance Sampling ; Missing Data ; Particle Filter ; Population Genetics
    Subjects: Q Science > QA Mathematics
    Departments: Faculty of Science and Technology > Mathematics and Statistics
    ID Code: 8331
    Deposited By: Prof Paul Fearnhead
    Deposited On: 18 Apr 2008 10:00
    Refereed?: Yes
    Published?: Published
    Last Modified: 09 Oct 2013 15:42
    Identification Number:
    URI: http://eprints.lancs.ac.uk/id/eprint/8331

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