Tropical principal component analysis on the space of ultrametrics

In 2019, Yoshida et al. introduced a notion of tropical principal component analysis (PCA). The output is a tropical polytope with a fixed number of vertices that best fits the data. We here apply tropical PCA to dimension reduction and visualization of data sampled from the space of phylogenetic trees. Our main results are twofold: the existence of a tropical cell decomposition into regions of fixed tree topology and the development of a stochastic optimization method to estimate the tropical PCA 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.