Related papers: A general method for common intervals
The interval graph for a set of intervals on a line consists of one vertex for each interval, and an edge for each intersecting pair of intervals. A probe interval graph is a variant that is motivated by an application to genomics, where…
Common intervals have been defined as a modelisation of gene clusters in genomes represented either as permutations or as sequences. Whereas optimal algorithms for finding common intervals in permutations exist even for an arbitrary number…
Interval graphs are intersection graphs of closed intervals of the real-line. The well-known computational problem, called recognition, asks whether an input graph $G$ can be represented by closed intervals, i.e., whether $G$ is an interval…
We introduce the class of interval $H$-graphs, which is the generalization of interval graphs, particularly interval bigraphs. For a fixed graph $H$ with vertices $a_1,a_2,\dots,a_k$, we say that an input graph $G$ with given partition…
In a recent paper, we introduced the simultaneous representation problem (defined for any graph class C) and studied the problem for chordal, comparability and permutation graphs. For interval graphs, the problem is defined as follows. Two…
Common intervals of K permutations over the same set of n elements were firstly investigated by T. Uno and M.Yagiura (Algorithmica, 26:290:309, 2000), who proposed an efficient algorithm to find common intervals when K=2. Several particular…
A simple-triangle graph (also known as a PI graph) is the intersection graph of a family of triangles defined by a point on a horizontal line and an interval on another horizontal line. The recognition problem for simple-triangle graphs was…
A graph $G$ is said to be the intersection of graphs $G_1,G_2,\ldots,G_k$ if $V(G)=V(G_1)=V(G_2)=\cdots=V(G_k)$ and $E(G)=E(G_1)\cap E(G_2)\cap\cdots\cap E(G_k)$. For a graph $G$, $\mathrm{dim}_{COG}(G)$ (resp. $\mathrm{dim}_{TH}(G)$)…
Given a graph $G$, the maximal induced subgraphs problem asks to enumerate all maximal induced subgraphs of $G$ that belong to a certain hereditary graph class. While its optimization version, known as the minimum vertex deletion problem in…
Counting small patterns in a large dataset is a fundamental algorithmic task. The most common version of this task is subgraph/homomorphism counting, wherein we count the number of occurrences of a small pattern graph $H$ in an input graph…
In this paper we explain how to easily compute gene clusters, formalized by classical or generalized nested common or conserved intervals, between a set of K genomes represented as K permutations. A b-nested common (resp. conserved)…
The sets of vertices and edges of an undirected, simple, finite, connected graph $G$ are denoted by $V(G)$ and $E(G)$, respectively. An arbitrary nonempty finite subset of consecutive integers is called an interval. An injective mapping…
Our purpose is to study the family of simple undirected graphs whose toric ideal is a complete intersection from both an algorithmic and a combinatorial point of view. We obtain a polynomial time algorithm that, given a graph $G$, checks…
In ongoing work to define a principled method for syntenic block discovery and structuring, work based on homology-derived constraints and a generalization of common intervals, we faced a fundamental computational problem: how to determine…
The intersection graph of a collection of trapezoids with corner points lying on two parallel lines is called a trapezoid graph. These graphs and their generalizations were applied in various fields, including modeling channel routing…
Interval and proper interval graphs are very well-known graph classes, for which there is a wide literature. As a consequence, some generalizations of interval graphs have been proposed, in which graphs in general are expressed in terms of…
Consider a connected graph $G=(E,V)$ with $N=|V|$ vertices. The main purpose of this paper is to explore the question of uniform sampling of a subtree of $G$ with $n$ nodes, for some $n\leq N$ (the spanning tree case correspond to $n=N$,…
The Induced Disjoint Paths problem is to test whether a graph G with k distinct pairs of vertices (s_i,t_i) contains paths P_1,...,P_k such that P_i connects s_i and t_i for i=1,...,k, and P_i and P_j have neither common vertices nor…
Given a weighted graph $G=(V,E)$ with weight functions $c:E\to \mathbb{R}_+$ and $\pi:V\to \mathbb{R}_+$, and a subset $U\subseteq V$, the normalized cut value for $U$ is defined as the sum of the weights of edges exiting $U$ divided by the…
We unify several seemingly different graph and digraph classes under one umbrella. These classes are all broadly speaking different generalizations of interval graphs, and include, in addition to interval graphs, also adjusted interval…