Due to new technology for efficiently generating genome data, machine learning methods are urgently needed to analyze large sets of gene trees over the space of phylogenetic trees. However, the space of phylogenetic trees is not Euclidean, so ordinary machine learning methods cannot be directly applied. In 2019, Yoshida et al. introduced the notion of tropical principal component analysis (PCA), a statistical method for visualization and dimensionality reduction using a tropical polytope with a fixed number of vertices that minimizes the sum of tropical distances between each data point and its tropical projection. However, their work focused on the tropical projective space rather than the space of phylogenetic trees. We focus here on tropical PCA for dimension reduction and visualization over the space of phylogenetic trees.
Our main results are twofold: (1) theoretical interpretations of the tropical principal components over the space of phylogenetic trees, namely, the existence of a tropical cell decomposition into regions of fixed tree topology; and (2) the development of a stochastic optimization method to estimate tropical PCs over the space of phylogenetic trees using a Markov Chain Monte Carlo (MCMC) approach. This method performs well with simulation studies, and it is applied to three empirical datasets: Apicomplexa and African coelacanth genomes as well as sequences of hemagglutinin for influenza from New York.
Dataset: http://polytopes.net/Data.tar.gz, Code: http://polytopes.net/tropica_MCMC_codes.tar.gz.
Supplementary data are available at http://polytopes.net/supplement.pdf.

Published by Oxford University Press 2020.