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Computational inference beyond Kingman's coalescent
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Koskela, Jere, Jenkins, Paul and Spanò, Dario (2015) Computational inference beyond Kingman's coalescent. Journal of Applied Probability, Volume 52 (Number 2). pp. 519-537. ISSN 0021-9002.
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Official URL: http://projecteuclid.org/euclid.jap
Abstract
Full likelihood inference under Kingman's coalescent is a computationally challenging problem to which importance sampling (IS) and the product of approximate conditionals (PAC) method have been applied successfully. Both methods can be expressed in terms of families of intractable conditional sampling distributions (CSDs), and rely on principled approximations for accurate inference. Recently, more general Λ- and Ξ- coalescents have been observed to provide better modelling ts to some genetic data sets. We derive families of approximate CSDs for nite sites Λ- and Ξ-coalescents, and use them to obtain "approximately optimal" IS and PAC algorithms for Λ coalescents, yielding substantial gains in efficiency over existing methods.
Item Type: | Journal Article | ||||||||
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Subjects: | Q Science > QA Mathematics | ||||||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Mathematics Faculty of Science, Engineering and Medicine > Science > Statistics |
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Library of Congress Subject Headings (LCSH): | Inference, Sampling (Statistics), Genetics -- Statistical methods | ||||||||
Journal or Publication Title: | Journal of Applied Probability | ||||||||
Publisher: | Applied Probability Trust | ||||||||
ISSN: | 0021-9002 | ||||||||
Official Date: | June 2015 | ||||||||
Dates: |
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Volume: | Volume 52 | ||||||||
Number: | Number 2 | ||||||||
Number of Pages: | 21 | ||||||||
Page Range: | pp. 519-537 | ||||||||
Status: | Peer Reviewed | ||||||||
Publication Status: | Published | ||||||||
Access rights to Published version: | Restricted or Subscription Access | ||||||||
Date of first compliant deposit: | 26 December 2015 | ||||||||
Date of first compliant Open Access: | 26 December 2015 | ||||||||
Funder: | Engineering and Physical Sciences Research Council (EPSRC) | ||||||||
Grant number: | EP/HO23364/1 (EPSRC) | ||||||||
Open Access Version: |
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