Tree topologies along a tropical line segment

DOI10.1007/S10013-021-00526-3zbMATH Open1485.14118arXiv2104.09022OpenAlexW4206048385WikidataQ114228678 ScholiaQ114228678MaRDI QIDQ2135083FDOQ2135083

Authors: Ruriko Yoshida, Shelby Cox 

Publication date: 4 May 2022

Published in: Vietnam Journal of Mathematics (Search for Journal in Brave)

Abstract: Tropical geometry with the max-plus algebra has been applied to statistical learning models over tree spaces because geometry with the tropical metric over tree spaces has some nice properties such as convexity in terms of the tropical metric. One of the challenges in applications of tropical geometry to tree spaces is the difficulty interpreting outcomes of statistical models with the tropical metric. This paper focuses on combinatorics of tree topologies along a tropical line segment, an intrinsic geodesic with the tropical metric, between two phylogenetic trees over the tree space and we show some properties of a tropical line segment between two trees. Specifically we show that a probability of a tropical line segment of two randomly chosen trees going through the origin (the star tree) is zero if the number of leave is greater than four, and we also show that if two given trees differ only one nearest neighbor interchange (NNI) move, then the tree topology of a tree in the tropical line segment between them is the same tree topology of one of these given two trees with possible zero branch lengths.

Full work available at URL: https://arxiv.org/abs/2104.09022

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zbMATH Keywords

phylogenomicsultrametricsphylogenetic treestree spaces

Mathematics Subject Classification ID

Problems related to evolution (92D15) Trees (05C05) Combinatorial aspects of tropical varieties (14T15) Applications of tropical geometry (14T90)

Cites Work

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Cited In (15)

• An invitation to tropical Alexandrov curvature
• Tropical principal component analysis and its application to phylogenetics
• (5d RG-flow) trees in the tropical rain forest
• Dissimilarity maps on trees and the representation theory of \(\mathrm{SL}_{m}(\mathbb C)\)
• Tropical convexity
• The space of tropically collinear points is shellable
• Title not available (Why is that?)
• Tropical optimal transport and Wasserstein distances
• Classifying tree topology changes along tropical line segments
• Estimating tropical principal components using the Metropolis-Hastings algorithm
• Extreme rays of the \(\ell^\infty\)-nearest ultrametric tropical polytope
• The proportion of trees that are linear
• How to Correctly Prune Tropical Trees
• Convexity in tree spaces
• Tropical geometric variation of tree shapes

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