3 papers
q-bio.PE2025
Assessing the Validity of the Fixed Tree Topology Assumption in Phylodynamic Inference
Mathieu Fourment, Jiansi Gao, Marc A Suchard +1
Fixed tree topologies are widely used in phylodynamic analyses to reduce computational burden, yet the consequences of this assumption remain insufficiently understood. Here, we sy…
q-bio.PE2024
Torchtree: flexible phylogenetic model development and inference using PyTorch
Mathieu Fourment, Matthew Macaulay, Christiaan J Swanepoel +3
Bayesian inference has predominantly relied on the Markov chain Monte Carlo (MCMC) algorithm for many years. However, MCMC is computationally laborious, especially for complex phyl…
q-bio.PE2023
Differentiable Phylogenetics via Hyperbolic Embeddings with Dodonaphy
Matthew Macaulay, Mathieu Fourment
Motivation: Navigating the high dimensional space of discrete trees for phylogenetics presents a challenging problem for tree optimisation. To address this, hyperbolic embeddings o…