L-infinity optimization to linear spaces and phylogenetic trees

DOI10.1137/16M1101027zbMATH Open1362.92050arXiv1702.05127OpenAlexW2613993791WikidataQ57428363 ScholiaQ57428363MaRDI QIDQ5346563FDOQ5346563

Daniel Irving Bernstein, Colby Long

Publication date: 24 May 2017

Published in: SIAM Journal on Discrete Mathematics (Search for Journal in Brave)

Abstract: Given a distance matrix consisting of pairwise distances between species, a distance-based phylogenetic reconstruction method returns a tree metric or equidistant tree metric (ultrametric) that best fits the data. We investigate distance-based phylogenetic reconstruction using the $l^{i}nfty$-metric. In particular, we analyze the set of $l^{i}nfty$-closest ultrametrics and tree metrics to an arbitrary dissimilarity map to determine its dimension and the tree topologies it represents. In the case of ultrametrics, we decompose the space of dissimilarity maps on 3 elements and on 4 elements relative to the tree topologies represented. Our approach is to first address uniqueness issues arising in $l^{i}nfty$-optimization to linear spaces. We show that the $l^{i}nfty$-closest point in a linear space is unique if and only if the underlying matroid of the linear space is uniform. We also give a polyhedral decomposition of $r^m$ based on the dimension of the set of $l^{i}nfty$-closest points in a linear space.

Full work available at URL: https://arxiv.org/abs/1702.05127

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zbMATH Keywords

tree metricultrametricoriented matroidzonotopedistance-based methodssubdominant ultrametric

Mathematics Subject Classification ID

Problems related to evolution (92D15) Oriented matroids in discrete geometry (52C40) Combinatorial aspects of matroids and geometric lattices (05B35)

Cites Work

• Title not available (Why is that?)
• Lectures on Polytopes
• Title not available (Why is that?)
• \(l_\infty\)-approximation via subdominants.
• On the Approximability of Numerical Taxonomy (Fitting Distances by Tree Metrics)
• The Bergman complex of a matroid and phylogenetic trees
• The tropical Grassmannian
• Convexity in Tree Spaces
• Tropical Fermat--Weber Points
• Subdominant matroid ultrametrics

Cited In (6)

• New Gromov-inspired metrics on phylogenetic tree space
• Subdominant matroid ultrametrics
• \(l_\infty\)-approximation via subdominants.
• Tropical Fermat--Weber Points
• L-Infinity Optimization to Bergman Fans of Matroids with an Application to Phylogenetics
• Tropical geometric variation of tree shapes

Uses Software

• Maple

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