8 citations · 21 across the 6 of their papers we have counts for
7 papers
Many-core algorithms for high-dimensional gradients on phylogenetic trees
Karthik Gangavarapu, Xiang Ji, Guy Baele +4
The rapid growth in genomic pathogen data spurs the need for efficient inference techniques, such as Hamiltonian Monte Carlo (HMC) in a Bayesian framework, to estimate parameters o…
TreeFlow: probabilistic modelling and automatic differentiation for phylogenetics
Christiaan Swanepoel, Mathieu Fourment, Xiang Ji +4
Probabilistic modelling frameworks are powerful tools for statistical modelling and inference. They are not immediately generalizable to phylogenetic problems due to the particular…
Automatic differentiation is no panacea for phylogenetic gradient computation
Mathieu Fourment, Christiaan J. Swanepoel, Jared G. Galloway +4
Gradients of probabilistic model likelihoods with respect to their parameters are essential for modern computational statistics and machine learning. These calculations are readily…
Fidelity of Hyperbolic Space for Bayesian Phylogenetic Inference
Matthew Macaulay, Aaron E. Darling, Mathieu Fourment
Bayesian inference for phylogenetics is a gold standard for computing distributions of phylogenies. It faces the challenging problem of. moving throughout the high-dimensional spac…
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…
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…
A surrogate function for one-dimensional phylogenetic likelihoods
Brian C. Claywell, Vu C. Dinh, Connor O. McCoy +1
Phylogenetics has seen an steady increase in substitution model complexity, which requires increasing amounts of computational power to compute likelihoods. This model complexity m…