3 papers
q-bio.PE2024
Finding high posterior density phylogenies by systematically extending a directed acyclic graph
Chris Jennings-Shaffer, David H Rich, Matthew Macaulay +7
Bayesian phylogenetics typically estimates a posterior distribution, or aspects thereof, using Markov chain Monte Carlo methods. These methods integrate over tree space by applying…
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…