{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/exact-phylodynamic-likelihood-via-structured","title":"Exact phylodynamic likelihood via structured Markov genealogy processes","arxiv_id":"2405.17032","date":"2024-05-27","proceeding":null,"authors":["Aaron A. King","Qianying Lin","Edward L. Ionides"],"abstract":"We consider genealogies arising from a Markov population process in which individuals are categorized into a discrete collection of compartments, with the requirement that individuals within the same compartment are statistically exchangeable. When equipped with a sampling process, each such population process induces a time-evolving tree-valued process defined as the genealogy of all sampled individuals. We provide a construction of this genealogy process and derive exact expressions for the likelihood of an observed genealogy in terms of filter equations. These filter equations can be numerically solved using standard Monte Carlo integration methods. Thus, we obtain statistically efficient likelihood-based inference for essentially arbitrary compartment models based on an observed genealogy of individuals sampled from the population.","url_abs":"https://arxiv.org/abs/2405.17032v2","url_pdf":"https://arxiv.org/pdf/2405.17032v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"exact-phylodynamic-likelihood-via-structured","repo_url":"https://github.com/kingaa/phylopomp","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null},{"paper_slug":"exact-phylodynamic-likelihood-via-structured","repo_url":"https://github.com/kingaa/structured-genealogy-process-paper","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}