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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…