Fidelity of hyperbolic space for Bayesian phylogenetic inference

• Main Authors: Darling, A. (Author), Fourment, M. (Author), Macaulay, M. (Author)
• Format: Article
• Language: English
• Published: NLM (Medline) 2023
• Subjects: Bayes theorem; Bayes Theorem; genomics; Genomics; Markov chain; Markov Chains; Monte Carlo method; Monte Carlo Method; phylogeny; Phylogeny; probability; Probability
• Online Access: View Fulltext in Publisher; View in Scopus
• ISBN: 15537358 (ISSN)
• DOI: 10.1371/journal.pcbi.1011084

Bayesian inference for phylogenetics is a gold standard for computing distributions of phylogenies. However, Bayesian phylogenetics faces the challenging computational problem of moving throughout the high-dimensional space of trees. Fortunately, hyperbolic space offers a low dimensional representation of tree-like data. In this paper, we embed genomic sequences as points in hyperbolic space and perform hyperbolic Markov Chain Monte Carlo for Bayesian inference in this space. The posterior probability of an embedding is computed by decoding a neighbour-joining tree from the embedding locations of the sequences. We empirically demonstrate the fidelity of this method on eight data sets. We systematically investigated the effect of embedding dimension and hyperbolic curvature on the performance in these data sets. The sampled posterior distribution recovers the splits and branch lengths to a high degree over a range of curvatures and dimensions. We systematically investigated the effects of the embedding space's curvature and dimension on the Markov Chain's performance, demonstrating the suitability of hyperbolic space for phylogenetic inference. Copyright: © 2023 Macaulay et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.