3 papers
stat.CO2023
On the surprising effectiveness of a simple matrix exponential derivative approximation, with application to global SARS-CoV-2
Gustavo Didier, Nathan E. Glatt-Holtz, Andrew J. Holbrook +2
The continuous-time Markov chain (CTMC) is the mathematical workhorse of evolutionary biology. Learning CTMC model parameters using modern, gradient-based methods requires the deri…
q-bio.PE2018
19 dubious ways to compute the marginal likelihood of a phylogenetic tree topology
Mathieu Fourment, Andrew F. Magee, Chris Whidden +3
The marginal likelihood of a model is a key quantity for assessing the evidence provided by the data in support of a model. The marginal likelihood is the normalizing constant for…
q-bio.PE2018
Systematic Exploration of the High Likelihood Set of Phylogenetic Tree Topologies
Chris Whidden, Brian C. Claywell, Thayer Fisher +3
Bayesian Markov chain Monte Carlo explores tree space slowly, in part because it frequently returns to the same tree topology. An alternative strategy would be to explore tree spac…