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Inference in molecular population genetics
Author(s) -
Stephens Matthew,
Donnelly Peter
Publication year - 2000
Publication title -
journal of the royal statistical society: series b (statistical methodology)
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 6.523
H-Index - 137
eISSN - 1467-9868
pISSN - 1369-7412
DOI - 10.1111/1467-9868.00254
Subject(s) - markov chain monte carlo , inference , computer science , exploit , variety (cybernetics) , sampling (signal processing) , population , machine learning , importance sampling , markov chain , monte carlo method , artificial intelligence , mathematics , statistics , bayesian probability , demography , computer security , sociology , computer vision , filter (signal processing)
Full likelihood‐based inference for modern population genetics data presents methodological and computational challenges. The problem is of considerable practical importance and has attracted recent attention, with the development of algorithms based on importance sampling (IS) and Markov chain Monte Carlo (MCMC) sampling. Here we introduce a new IS algorithm. The optimal proposal distribution for these problems can be characterized, and we exploit a detailed analysis of genealogical processes to develop a practicable approximation to it. We compare the new method with existing algorithms on a variety of genetic examples. Our approach substantially outperforms existing IS algorithms, with efficiency typically improved by several orders of magnitude. The new method also compares favourably with existing MCMC methods in some problems, and less favourably in others, suggesting that both IS and MCMC methods have a continuing role to play in this area. We offer insights into the relative advantages of each approach, and we discuss diagnostics in the IS framework.