From Modular Decomposition Trees to Rooted Median Graphs

TL;DR

This paper introduces a method to explain symmetric maps using rooted median graphs, extending modular decomposition trees, with applications in phylogenetics and a linear-time algorithm for construction.

Contribution

It generalizes modular decomposition trees to rooted median graphs for explaining symmetric maps and provides a linear-time algorithm for their construction.

Findings

Every symmetric map can be explained by extended hypercubes and half-grids.

A linear-time algorithm resolves prime vertices to produce explaining median graphs.

Tree-like median graphs have potential applications in phylogenetics.

Abstract

The modular decomposition of a symmetric map $\delta\colon X\times X \to \Upsilon$ (or, equivalently, a set of symmetric binary relations, a 2-structure, or an edge-colored undirected graph) is a natural construction to capture key features of $\delta$ in labeled trees. A map $\delta$ is explained by a vertex-labeled rooted tree $(T,t)$ if the label $\delta(x,y)$ coincides with the label of the last common ancestor of $x$ and $y$ in $T$, i.e., if $\delta(x,y)=t(\mathrm{lca}(x,y))$. Only maps whose modular decomposition does not contain prime nodes, i.e., the symbolic ultrametrics, can be exaplained in this manner. Here we consider rooted median graphs as a generalization to (modular decomposition) trees to explain symmetric maps. We first show that every symmetric map can be explained by "extended" hypercubes and half-grids. We then derive a a linear-time algorithm that stepwisely resolves prime vertices in the modular decomposition tree to obtain a rooted and labeled median graph that explains a given symmetric map $\delta$. We argue that the resulting "tree-like" median graphs may be of use in phylogenetics as a model of evolutionary relationships.