Literature DB >> 17264216

Sequential Monte Carlo without likelihoods.

S A Sisson1, Y Fan, Mark M Tanaka.   

Abstract

Recent new methods in Bayesian simulation have provided ways of evaluating posterior distributions in the presence of analytically or computationally intractable likelihood functions. Despite representing a substantial methodological advance, existing methods based on rejection sampling or Markov chain Monte Carlo can be highly inefficient and accordingly require far more iterations than may be practical to implement. Here we propose a sequential Monte Carlo sampler that convincingly overcomes these inefficiencies. We demonstrate its implementation through an epidemiological study of the transmission rate of tuberculosis.

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Year:  2007        PMID: 17264216      PMCID: PMC1794282          DOI: 10.1073/pnas.0607208104

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


  9 in total

1.  Population growth of human Y chromosomes: a study of Y chromosome microsatellites.

Authors:  J K Pritchard; M T Seielstad; A Perez-Lezaun; M W Feldman
Journal:  Mol Biol Evol       Date:  1999-12       Impact factor: 16.240

2.  Markov chain Monte Carlo without likelihoods.

Authors:  Paul Marjoram; John Molitor; Vincent Plagnol; Simon Tavare
Journal:  Proc Natl Acad Sci U S A       Date:  2003-12-08       Impact factor: 11.205

3.  Approximate Bayesian computation in population genetics.

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

4.  Likelihoods from summary statistics: recent divergence between species.

Authors:  Scotland C Leman; Yuguo Chen; Jason E Stajich; Mohamed A F Noor; Marcy K Uyenoyama
Journal:  Genetics       Date:  2005-09-02       Impact factor: 4.562

5.  Using approximate Bayesian computation to estimate tuberculosis transmission parameters from genotype data.

Authors:  Mark M Tanaka; Andrew R Francis; Fabio Luciani; S A Sisson
Journal:  Genetics       Date:  2006-04-19       Impact factor: 4.562

Review 6.  Modern computational approaches for analysing molecular genetic variation data.

Authors:  Paul Marjoram; Simon Tavaré
Journal:  Nat Rev Genet       Date:  2006-10       Impact factor: 53.242

7.  Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster.

Authors:  Kevin Thornton; Peter Andolfatto
Journal:  Genetics       Date:  2005-11-19       Impact factor: 4.562

8.  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.  The epidemiology of tuberculosis in San Francisco. A population-based study using conventional and molecular methods.

Authors:  P M Small; P C Hopewell; S P Singh; A Paz; J Parsonnet; D C Ruston; G F Schecter; C L Daley; G K Schoolnik
Journal:  N Engl J Med       Date:  1994-06-16       Impact factor: 91.245

  9 in total
  117 in total

1.  Squeeze-and-breathe evolutionary Monte Carlo optimization with local search acceleration and its application to parameter fitting.

Authors:  Mariano Beguerisse-Díaz; Baojun Wang; Radhika Desikan; Mauricio Barahona
Journal:  J R Soc Interface       Date:  2012-01-19       Impact factor: 4.118

2.  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

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

Authors:  Richard D Wilkinson; Michael E Steiper; Christophe Soligo; Robert D Martin; Ziheng Yang; Simon Tavaré
Journal:  Syst Biol       Date:  2010-11-04       Impact factor: 15.683

4.  On the Identifiability of Transmission Dynamic Models for Infectious Diseases.

Authors:  Jarno Lintusaari; Michael U Gutmann; Samuel Kaski; Jukka Corander
Journal:  Genetics       Date:  2016-01-06       Impact factor: 4.562

5.  Efficient approximate Bayesian computation coupled with Markov chain Monte Carlo without likelihood.

Authors:  Daniel Wegmann; Christoph Leuenberger; Laurent Excoffier
Journal:  Genetics       Date:  2009-06-08       Impact factor: 4.562

6.  Approximate bayesian computation without summary statistics: the case of admixture.

Authors:  Vitor C Sousa; Marielle Fritz; Mark A Beaumont; Lounès Chikhi
Journal:  Genetics       Date:  2009-02-02       Impact factor: 4.562

7.  REJECTOR: software for population history inference from genetic data via a rejection algorithm.

Authors:  Matthew J Jobin; Joanna L Mountain
Journal:  Bioinformatics       Date:  2008-10-20       Impact factor: 6.937

8.  Cellular connectomes as arbiters of local circuit models in the cerebral cortex.

Authors:  Emmanuel Klinger; Alessandro Motta; Carsten Marr; Fabian J Theis; Moritz Helmstaedter
Journal:  Nat Commun       Date:  2021-05-13       Impact factor: 14.919

9.  Bayesian computation and model selection without likelihoods.

Authors:  Christoph Leuenberger; Daniel Wegmann
Journal:  Genetics       Date:  2009-09-28       Impact factor: 4.562

10.  A second-order iterated smoothing algorithm.

Authors:  Dao Nguyen; Edward L Ionides
Journal:  Stat Comput       Date:  2016-10-15       Impact factor: 2.559

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