Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks.

ABSTRACT: Widely applicable, accurate and fast inference methods in phylodynamics are needed to fully profit from the richness of genetic data in uncovering the dynamics of epidemics. Standard methods, including maximum-likelihood and Bayesian approaches, generally rely on complex mathematical formulae and approximations, and do not scale with dataset size. We develop a likelihood-free, simulation-based approach, which combines deep learning with (1) a large set of summary statistics measured on phylogenies or (2) a complete and compact representation of trees, which avoids potential limitations of summary statistics and applies to any phylodynamics model. Our method enables both model selection and estimation of epidemiological parameters from very large phylogenies. We demonstrate its speed and ac

SUBMITTER: Voznica J 

PROVIDER: S-EPMC9258765 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature