Related papers: Tree Topologies along a Tropical Line Segment
The space of phylogenetic trees arises naturally in tropical geometry as the tropical Grassmannian. Tropical geometry therefore suggests a natural notion of a tropical path between two trees, given by a tropical line segment in the tropical…
We study the behavior of phylogenetic tree shapes in the tropical geometric interpretation of tree space. Tree shapes are formally referred to as tree topologies; a tree topology can also be thought of as a tree combinatorial type, which is…
Phylogenetic trees are the fundamental mathematical representation of evolutionary processes in biology. They are also objects of interest in pure mathematics, such as algebraic geometry and combinatorics, due to their discrete geometry.…
Tropical Geometry and Mathematical Morphology share the same max-plus and min-plus semiring arithmetic and matrix algebra. In this chapter we summarize some of their main ideas and common (geometric and algebraic) structure, generalize and…
We study the geometry of metrics and convexity structures on the space of phylogenetic trees, which is here realized as the tropical linear space of all \ ultrametrics. The ${\rm CAT}(0)$-metric of Billera-Holmes-Vogtman arises from the…
Much evidence from biological theory and empirical data indicates that, gene tree, phylogenetic trees reconstructed from different genes (loci), do not have to have exactly the same tree topologies. Such incongruence between gene trees…
Classification of gene trees is an important task both in the analysis of multi-locus phylogenetic data, and assessment of the convergence of Markov Chain Monte Carlo (MCMC) analyses used in Bayesian phylogenetic tree reconstruction. The…
We discuss a notion of convergence for binary trees that is based on subtree sizes. In analogy to recent developments in the theory of graphs, posets and permutations we investigate some general aspects of the topology, such as a…
When we apply comparative phylogenetic analyses to genome data, it is a well-known problem and challenge that some of given species (or taxa) often have missing genes. In such a case, we have to impute a missing part of a gene tree from a…
We study tree metrics that can be realized as a mixture of two star tree metrics. We prove that the only trees admitting such a decomposition are the ones coming from a tree with at most one internal edge, and whose weight satisfies certain…
The problem of comparing probability distributions is at the heart of many tasks in statistics and machine learning. Established comparison methods treat the standard setting that the distributions are supported in the same space. Recently,…
In the last few years there has been a growing interest towards methods for statistical inference and learning based on computational geometry and, notably, tropical geometry, that is, the study of algebraic varieties over the min-plus…
In this paper, we present a flexible and probabilistic framework for tracking topological features in time-varying scalar fields using merge trees and partial optimal transport. Merge trees are topological descriptors that record the…
Abstractly, tropical hyperelliptic curves are metric graphs that admit a two-to-one harmonic morphism to a tree. They also appear as embedded tropical curves in the plane arising from triangulations of polygons with all interior lattice…
We investigate the tree gonality of a genus-$g$ metric graph, defined as the minimum degree of a tropical morphism from any tropical modification of the metric graph to a metric tree. We give a combinatorial constructive proof that this…
In order to conduct a statistical analysis on a given set of phylogenetic gene trees, we often use a distance measure between two trees. In a statistical distance-based method to analyze discordance between gene trees, it is a key to decide…
Deep neural networks show great success when input vectors are in an Euclidean space. However, those classical neural networks show a poor performance when inputs are phylogenetic trees, which can be written as vectors in the tropical…
We introduce tropical dual numbers as an extension of tropical semiring. By this innovation, one can work with honest ideals, instead of congruences, and recover the Euclidean topology on affine tropical spaces similar to Zariski's approach…
Tropical mathematics redefines the rules of arithmetic by replacing addition with taking a maximum, and by replacing multiplication with addition. After briefly discussing a tropical version of linear algebra, we study polynomials build…
We investigate location problems whose optimum lies in the tropical convex hull of the input points. Firstly, we study geodesically star-convex sets under the asymmetric tropical distance and introduce the class of tropically quasiconvex…