Related papers: Matching complexes of trees and applications of th…
Hypergraph is a topological model for networks. In order to study the topology of hypergraphs, the homology of the associated simplicial complexes and the embedded homology have been invented. In this paper, we give some algorithms to…
We study an abstract notion of tree structure which lies at the common core of various tree-like discrete structures commonly used in combinatorics: trees in graphs, order trees, nested subsets of a set, tree-decompositions of graphs and…
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…
Graphs provide an efficient tool for object representation in various computer vision applications. Once graph-based representations are constructed, an important question is how to compare graphs. This problem is often formulated as a…
In this paper, we extend the definition of cohomology associated to monotone graph properties, to encompass twisted functor coefficients. We introduce oriented matchings on graphs, and focus on their (twisted) cohomology groups. We…
Graph classification plays an important role is data mining, and various methods have been developed recently for classifying graphs. In this paper, we propose a novel method for graph classification that is based on homotopy equivalence of…
For a graph $G = (V, E)$, the $\gamma$-graph of $G$, denoted $G(\gamma) = (V(\gamma), E(\gamma))$, is the graph whose vertex set is the collection of minimum dominating sets, or $\gamma$-sets of $G$, and two $\gamma$-sets are adjacent in…
In this article, we discuss the vertex decomposability of three well-studied simplicial complexes associated to forests. In particular, we show that the bounded degree complex of a forest and the complex of directed trees of a multidiforest…
Cartesian tree matching is the problem of finding all substrings of a given text which have the same Cartesian trees as that of a given pattern. So far there is one linear-time solution for Cartesian tree matching, which is based on the KMP…
The matching distance is a computationally tractable topological measure to compare multi-filtered simplicial complexes. We design efficient algorithms for approximating the matching distance of two bi-filtered complexes to any desired…
We present a distributed algorithm to compute the first homology of a simplicial complex. Such algorithms are very useful in topological analysis of sensor networks, such as its coverage properties. We employ spanning trees to compute a…
A geometric graph is a graph whose vertex set is a set of points in the plane and whose edge set contains straight-line segments. A matching in a graph is a subset of edges of the graph with no shared vertices. A matching is called perfect…
Motivated by the question of how macromolecules assemble, the notion of an {\it assembly tree} of a graph is introduced. Given a graph $G$, the paper is concerned with enumerating the number of assembly trees of $G$, a problem that applies…
A suffix tree is a data structure used mainly for pattern matching. It is known that the space complexity of simple suffix trees is quadratic in the length of the string. By a slight modification of the simple suffix trees one gets the…
The tree complex is a simplicial complex defined in recent work of Belk, Lanier, Margalit, and Winarski with natural applications to mapping class groups and complex dynamics. In this article, we connect this setting with the study of…
A monotone drawing of a graph G is a straight-line drawing of G such that every pair of vertices is connected by a path that is monotone with respect to some direction. Trees, as a special class of graphs, have been the focus of several…
Merge trees are a type of topological descriptors that record the connectivity among the sublevel sets of scalar fields. They are among the most widely used topological tools in visualization. In this paper, we are interested in sketching a…
Determining the interaction partners among protein/domain families poses hard computational problems, in particular in the presence of paralogous proteins. Available approaches aim to identify interaction partners among protein/domain…
Best match graphs (BMG) are a key intermediate in graph-based orthology detection and contain a large amount of information on the gene tree. We provide a near-cubic algorithm to determine whether a BMG is binary-explainable, i.e., whether…
For a graph $G=(V,E),$ a matching $M$ is a set of independent edges. The topic of matchings is well studied in graph theory. In this paper many varieties of matchings are discussed.