Sequential Monte Carlo with transformations.

Richard G Everitt, Richard Culliford, Felipe Medina-Aguayo, Daniel J Wilson
Author Information
  1. Richard G Everitt: 1Department of Statistics, University of Warwick, Coventry, CV4 7AL UK. ORCID
  2. Richard Culliford: 2Department of Mathematics and Statistics, University of Reading, Reading, UK.
  3. Felipe Medina-Aguayo: 2Department of Mathematics and Statistics, University of Reading, Reading, UK.
  4. Daniel J Wilson: 3Nuffield Department of Medicine, University of Oxford, Oxford, UK.

Abstract

This paper examines methodology for performing Bayesian inference sequentially on a sequence of posteriors on spaces of different dimensions. For this, we use sequential Monte Carlo samplers, introducing the innovation of using deterministic transformations to move particles effectively between target distributions with different dimensions. This approach, combined with adaptive methods, yields an extremely flexible and general algorithm for Bayesian model comparison that is suitable for use in applications where the acceptance rate in reversible jump Markov chain Monte Carlo is low. We use this approach on model comparison for mixture models, and for inferring coalescent trees sequentially, as data arrives.

Keywords

References

  1. Syst Biol. 2018 May 1;67(3):503-517 [PMID: 29244177]
  2. Nat Commun. 2014 May 23;5:3956 [PMID: 24853639]
  3. J Mol Evol. 1981;17(6):368-76 [PMID: 7288891]
  4. Syst Biol. 2011 Mar;60(2):150-60 [PMID: 21187451]
  5. Mol Biol Evol. 2011 Jul;28(7):2161-72 [PMID: 21310946]
  6. BMC Evol Biol. 2007 Nov 08;7:214 [PMID: 17996036]
  7. Genetics. 2003 Dec;165(4):2213-33 [PMID: 14704198]
  8. PLoS Genet. 2014 May 15;10(5):e1004342 [PMID: 24831947]
  9. Proc Natl Acad Sci U S A. 2009 Oct 13;106(41):17249-54 [PMID: 19805147]
  10. Mol Biol Evol. 2014 Jul;31(7):1869-79 [PMID: 24714079]
  11. Syst Biol. 2018 May 01;67(3):490-502 [PMID: 29186587]
  12. J Chem Phys. 2011 Feb 7;134(5):054107 [PMID: 21303092]
  13. PLoS Genet. 2012;8(11):e1002967 [PMID: 23166502]

Word Cloud

Created with Highcharts 10.0.0MonteCarloBayesianusemodelcomparisonsequentiallydifferentdimensionstransformationsapproachpaperexaminesmethodologyperforminginferencesequenceposteriorsspacessequentialsamplersintroducinginnovationusingdeterministicmoveparticleseffectivelytargetdistributionscombinedadaptivemethodsyieldsextremelyflexiblegeneralalgorithmsuitableapplicationsacceptanceratereversiblejumpMarkovchainlowmixturemodelsinferringcoalescenttreesdataarrivesSequentialCoalescentTrans-dimensional

Similar Articles

Cited By