Aaron King - Exact phylodynamics via structured Markov genealogy processes скачать в хорошем качестве

Aaron King - Exact phylodynamics via structured Markov genealogy processes

Theoretical Ecology Seminar from the IITE (https://iite.info) by Aaron King (Michigan and Santa Fe) Recorded 12th Nov 2024. Abstract: Phylodynamic inference allows us to extract information on determinants of epidemic dynamics from sampled pathogen genomes. A key problem in phylodynamics has been a mismatch between inference methodology and epidemiological models: the approximations that must be made to perform inference do not align well with the questions of greatest interest. I will describe recent work in which we have obtained exact expressions for phylodynamic likelihoods associated with compartmental models of (almost) arbitrary complexity. To derive these, we first show that to each discretely structured Markov population process there is an associated genealogy process, i.e., a time-evolving tree-valued process defined as the genealogy of all previously sampled individuals. We then deduce exact expressions for the likelihood of an observed genealogy in terms of filter equations. These filter equations can be solved numerically using standard Monte Carlo integration methodology. These results unify and extend existing approaches and broaden the scope of phylodynamic inference methods.