🍩 Database of Original & Non-Theoretical Uses of Topology

1. Tree Decomposition of Reeb Graphs, Parametrized Complexity, and Applications to Phylogenetics (2020)

   Anastasios Stefanou

   Abstract

   Inspired by the interval decomposition of persistence modules and the extended Newick format of phylogenetic networks, we show that, inside the larger category of partially ordered Reeb graphs, every Reeb graph with n leaves and first Betti number s, can be identified with a coproduct of at most \$\$2\textasciicircums\$\$2s partially ordered trees with \$\$(n + s)\$\$(n+s) leaves. Reeb graphs are therefore classified up to isomorphism by their tree-decomposition. An implication of this result, is that the isomorphism problem for Reeb graphs is fixed parameter tractable when the parameter is the first Betti number. We propose partially ordered Reeb graphs as a model for time consistent phylogenetic networks and propose a certain Hausdorff distance as a metric on these structures.

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   • Biology
   • Phylogenetics
   • Tree
   • Hausdorff distance
   • Reeb graph