An efficient Bayesian inference framework for coalescent-based nonparametric phylodynamics

Shiwei Lan, Julia A. Palacios, Michael Karcher, Vladimir N. Minin, Babak Shahbaba

Research output: Contribution to journalArticlepeer-review

12 Scopus citations

Abstract

Motivation: The field of phylodynamics focuses on the problem of reconstructing population size dynamics over time using current genetic samples taken from the population of interest. This technique has been extensively used in many areas of biology but is particularly useful for studying the spread of quickly evolving infectious diseases agents, e.g. influenza virus. Phylodynamic inference uses a coalescent model that defines a probability density for the genealogy of randomly sampled individuals from the population. When we assume that such a genealogy is known, the coalescent model, equipped with a Gaussian process prior on population size trajectory, allows for nonparametric Bayesian estimation of population size dynamics. Although this approach is quite powerful, large datasets collected during infectious disease surveillance challenge the state-of-the-art of Bayesian phylodynamics and demand inferential methods with relatively low computational cost. Results: To satisfy this demand, we provide a computationally efficient Bayesian inference framework based on Hamiltonian Monte Carlo for coalescent process models. Moreover, we show that by splitting the Hamiltonian function, we can further improve the efficiency of this approach. Using several simulated and real datasets, we show that our method provides accurate estimates of population size dynamics and is substantially faster than alternative methods based on elliptical slice sampler and Metropolis-adjusted Langevin algorithm.

Original languageEnglish (US)
Pages (from-to)3282-3289
Number of pages8
JournalBioinformatics
Volume31
Issue number20
DOIs
StatePublished - Mar 25 2015
Externally publishedYes

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Fingerprint

Dive into the research topics of 'An efficient Bayesian inference framework for coalescent-based nonparametric phylodynamics'. Together they form a unique fingerprint.

Cite this