Note that this class will be held in 411 West Hall, coinciding with the statistics graduate student seminar.
Reading: King, Lin & Ionides (2025). Exact phylodynamic likelihood via structured Markov genealogy processes. ArXiv:2405.17032. https://doi.org/10.48550/arXiv.2405.17032.
This work generalizes King, Lin & Ionides (2022) to allow for population structure in the infected individuals. Theorems 1 of KLI25 is analogous to Theorem 2 of KLI22. Subsequent results show how to write likelihoods as solutions to filter equations. Then, Appendix B obtains some relevant results for this class of filter equations and relates these to a particle filter algorithm.
The math is extensive, so don’t expect to get it all quickly! Focus on the main ideas. What scientific questions can be asked and answered using these methods that go beyond last week’s paper (Vaughan & Stadle, 2025).
As before, you can get your class participation credit by submitting ahead of class, in writing, a few sentences describing (i) something you got out of reading this paper; (ii) something you got stuck on trying to understand. You can email this to ionides@umich.edu and kingaa@umich.edu with subject “700 participation”.
Note that each class is graded with one point for attendance and one for participation.