Related papers: Least resolved trees for two-colored best match gr…
The study of genetic map linearization leads to a combinatorial hard problem, called the {\em minimum breakpoint linearization} (MBL) problem. It is aimed at finding a linearization of a partial order which attains the minimum breakpoint…
A graph G is called well-indumatched if all of its maximal induced matchings have the same size. In this paper we characterize all well-indumatched trees. We provide a linear time algorithm to decide if a tree is well-indumatched or not.…
Targeted color-dots with varying shapes and sizes in images are first exhaustively identified, and then their multiscale 2D geometric patterns are extracted for testing spatial uniformness in a progressive fashion. Based on color theory in…
Deciding whether there is a single tree -a supertree- that summarizes the evolutionary information in a collection of unrooted trees is a fundamental problem in phylogenetics. We consider two versions of this question: agreement and…
In this paper, we study the (weighted) bichromatic two-center problem on graphs. The input consists of a graph $G$ of $n$ (weighted) vertices and $m$ edges, and a set $\mathcal{P}$ of pairs of distinct vertices, where no vertex appears in…
A linear graph is a graph whose vertices are totally ordered. Biological and linguistic sequences with interactions among symbols are naturally represented as linear graphs. Examples include protein contact maps, RNA secondary structures…
In a vertex-colored graph $G = (V, E)$, a subset $S \subseteq V$ is said to be consistent if every vertex has a nearest neighbor in $S$ with the same color. The problem of computing a minimum cardinality consistent subset of a graph is…
Let $R$ and $B$ be two disjoint sets of points in the plane where the points of $R$ are colored red and the points of $B$ are colored blue, and let $n=|R\cup B|$. A bichromatic spanning tree is a spanning tree in the complete bipartite…
This paper establishes a bridge between linear logic and mainstream graph theory, building on previous work by Retor\'e (2003). We show that the problem of correctness for MLL+Mix proof nets is equivalent to the problem of uniqueness of a…
A transitive graph is 2-dimensional if it can be represented as the intersection of two linear orders. Such representations make answering of reachability queries trivial, and allow many problems that are NP-hard on arbitrary graphs to be…
In binary jumbled pattern matching we wish to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of size $i$ and has exactly $j$ 1-bits. The problem naturally generalizes to…
Evolutionary scenarios describing the evolution of a family of genes within a collection of species comprise the mapping of the vertices of a gene tree $T$ to vertices and edges of a species tree $S$. The relative timing of the last common…
Many of the commonly used methods for orthology detection start from mutually most similar pairs of genes (reciprocal best hits) as an approximation for evolutionary most closely related pairs of genes (reciprocal best matches). This…
The maximum/minimum bisection problems are, given an edge-weighted graph, to find a bipartition of the vertex set into two sets whose sizes differ by at most one, such that the total weight of edges between the two sets is…
An evolutionary tree is a rooted tree where each internal vertex has at least two children and where the leaves are labeled with distinct symbols representing species. Evolutionary trees are useful for modeling the evolutionary history of…
A signed tree model of a graph $G$ is a compact binary structure consisting of a rooted binary tree whose leaves are bijectively mapped to the vertices of $G$, together with 2-colored edges $xy$, called transversal pairs, interpreted as…
A widely used method for determining the similarity of two labeled trees is to compute a maximum agreement subtree of the two trees. Previous work on this similarity measure is only concerned with the comparison of labeled trees of two…
Deciding whether a collection of unrooted trees is compatible is a fundamental problem in phylogenetics. Two different graph-theoretic characterizations of tree compatibility have recently been proposed. In one of these, tree compatibility…
We define a search problem on trees that closely captures the backtracking behavior of all current practical graph isomorphism algorithms. Given two trees with colored leaves, the goal is to find two leaves of matching color, one in each of…
Attempting to recognize a tree inside a phylogenetic network is a fundamental undertaking in evolutionary analysis. In the last few years, therefore, tree-based phylogenetic networks, which are defined by a spanning tree called a…