Variational Combinatorial Sequential Monte Carlo for Bayesian Phylogenetics in Hyperbolic Space

Code

• github.com/axchen7/vcsmc
  Officialpytorch★ 0

Abstract

Hyperbolic space naturally encodes hierarchical structures such as phylogenies (binary trees), where inward-bending geodesics reflect paths through least common ancestors, and the exponential growth of neighborhoods mirrors the super-exponential scaling of topologies. This scaling challenge limits the efficiency of Euclidean-based approximate inference methods. Motivated by the geometric connections between trees and hyperbolic space, we develop novel hyperbolic extensions of two sequential search algorithms: Combinatorial and Nested Combinatorial Sequential Monte Carlo (Csmc and Ncsmc). Our approach introduces consistent and unbiased estimators, along with variational inference methods (H-Vcsmc and H-Vncsmc), which outperform their Euclidean counterparts. Empirical results demonstrate improved speed, scalability and performance in high-dimensional phylogenetic inference tasks.

Tasks

Reproductions