Principal component analysis is a widely used method for the dimensionality reduction of a given data set in a high-dimensional Euclidean space. Here we define and analyze two analogues of principal component analysis in the setting of tropical geometry. In one approach, we study the Stiefel tropical linear space of fixed dimension closest to the data points in the tropical projective torus; in the other approach, we consider the tropical polytope with a fixed number of vertices closest to the data points. We then give approximative algorithms for both approaches and apply them to phylogenetics, testing the methods on simulated phylogenetic data and on an empirical dataset of Apicomplexa genomes.

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Motivation 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. Results 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. Availability Dataset: http://polytopes.net/Data.tar.gz, Code: http://polytopes.net/tropica_MCMC_codes.tar.gz Supplementary information Supplementary data are available at http://polytopes.net/supplement.pdf.

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We present results on the number of linear regions of the functions that can be represented by artificial feedforward neural networks with maxout units. A rank-k maxout unit is a function computing the maximum of k linear functions. For networks with a single layer of maxout units, the linear regions correspond to the upper vertices of a Minkowski sum of polytopes. We obtain face counting formulas in terms of the intersection posets of tropical hypersurfaces or the number of upper faces of partial Minkowski sums, along with explicit sharp upper bounds for the number of regions for any input dimension, any number of units, and any ranks, in the cases with and without biases. Based on these results we also obtain asymptotically sharp upper bounds for networks with multiple layers.