PhylaFlow: Hybrid flow matching in phylogenetic tree space

PhylaFlow is a hybrid flow-matching framework that navigates Billera–Holmes–Vogtmann (BHV) tree space to accelerate Bayesian phylogenetic inference. By learning geodesic paths from random trees to posterior samples, PhylaFlow efficiently initializes MCMC chains, drastically reducing the "burn-in" time. A PhylaFlow-MCMC variant, which guides MrBayes move acceptance, significantly outperforms traditional methods and even existing machine learning baselines for posterior sampling, achieving better results within the same computational budget. The work also explores conditioning on sequence embeddings, aiming for a future phylogenetics foundation model capable of zero-shot inference.