Literature DB >> 14663152

Markov chain Monte Carlo without likelihoods.

Paul Marjoram1, John Molitor, Vincent Plagnol, Simon Tavare.   

Abstract

Many stochastic simulation approaches for generating observations from a posterior distribution depend on knowing a likelihood function. However, for many complex probability models, such likelihoods are either impossible or computationally prohibitive to obtain. Here we present a Markov chain Monte Carlo method for generating observations from a posterior distribution without the use of likelihoods. It can also be used in frequentist applications, in particular for maximum-likelihood estimation. The approach is illustrated by an example of ancestral inference in population genetics. A number of open problems are highlighted in the discussion.

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Year:  2003        PMID: 14663152      PMCID: PMC307566          DOI: 10.1073/pnas.0306899100

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  9 in total

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2.  The effects of rate variation on ancestral inference in the coalescent.

Authors:  L Markovtsova; P Marjoram; S Tavaré
Journal:  Genetics       Date:  2000-11       Impact factor: 4.562

3.  The age of a unique event polymorphism.

Authors:  L Markovtsova; P Marjoram; S Tavaré
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4.  Approximate Bayesian computation in population genetics.

Authors:  Mark A Beaumont; Wenyang Zhang; David J Balding
Journal:  Genetics       Date:  2002-12       Impact factor: 4.562

Review 5.  Inching toward reality: an improved likelihood model of sequence evolution.

Authors:  J L Thorne; H Kishino; J Felsenstein
Journal:  J Mol Evol       Date:  1992-01       Impact factor: 2.395

6.  Extensive mitochondrial diversity within a single Amerindian tribe.

Authors:  R H Ward; B L Frazier; K Dew-Jager; S Pääbo
Journal:  Proc Natl Acad Sci U S A       Date:  1991-10-01       Impact factor: 11.205

7.  Inference of population history using a likelihood approach.

Authors:  G Weiss; A von Haeseler
Journal:  Genetics       Date:  1998-07       Impact factor: 4.562

8.  Estimating the age of the common ancestor of a sample of DNA sequences.

Authors:  Y X Fu; W H Li
Journal:  Mol Biol Evol       Date:  1997-02       Impact factor: 16.240

9.  Inferring coalescence times from DNA sequence data.

Authors:  S Tavaré; D J Balding; R C Griffiths; P Donnelly
Journal:  Genetics       Date:  1997-02       Impact factor: 4.562

  9 in total
  183 in total

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Journal:  Am J Hum Genet       Date:  2004-07-12       Impact factor: 11.025

2.  Bayesian posterior distributions without Markov chains.

Authors:  Stephen R Cole; Haitao Chu; Sander Greenland; Ghassan Hamra; David B Richardson
Journal:  Am J Epidemiol       Date:  2012-02-03       Impact factor: 4.897

3.  Population divergence with or without admixture: selecting models using an ABC approach.

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7.  Detecting selection in population trees: the Lewontin and Krakauer test extended.

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8.  Likelihood-free inference of population structure and local adaptation in a Bayesian hierarchical model.

Authors:  Eric Bazin; Kevin J Dawson; Mark A Beaumont
Journal:  Genetics       Date:  2010-04-09       Impact factor: 4.562

9.  Dating primate divergences through an integrated analysis of palaeontological and molecular data.

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10.  Modeling and inference for infectious disease dynamics: a likelihood-based approach.

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