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Treewidth is a useful tool in designing graph algorithms. Although many NP-hard graph problems can be solved in linear time when the input graphs have small treewidth, there are problems which remain hard on graphs of bounded treewidth. In…
Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…
The problems studied in this paper originate from Graph Motif, a problem introduced in 2006 in the context of biological networks. Informally speaking, it consists in deciding if a multiset of colors occurs in a connected subgraph of a…
Graph connectivity and network design problems are among the most fundamental problems in combinatorial optimization. The minimum spanning tree problem, the two edge-connected spanning subgraph problem (2-ECSS) and the tree augmentation…
Phylogenetic networks are important for the study of evolution. The number of methods to find such networks is increasing, but most such methods can only reconstruct small networks. To find bigger networks, one can attempt to combine small…
Given two graphs, the graph matching problem is to align the two vertex sets so as to minimize the number of adjacency disagreements between the two graphs. The seeded graph matching problem is the graph matching problem when we are first…
A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard.…
We study the vertex-cover problem which is an NP-hard optimization problem and a prototypical model exhibiting phase transitions on random graphs, e.g., Erdoes-Renyi (ER) random graphs. These phase transitions coincide with changes of the…
Reciprocal best match graphs (RBMGs) are vertex colored graphs whose vertices represent genes and the colors the species where the genes reside. Edges identify pairs of genes that are most closely related with respect to an underlying…
Subgraph matching is to find all subgraphs in a data graph that are isomorphic to an existing query graph. Subgraph matching is an NP-hard problem, yet has found its applications in many areas. Many learning-based methods have been proposed…
The widely studied edge modification problems ask how to minimally alter a graph to satisfy certain structural properties. In this paper, we introduce and study a new edge modification problem centered around transforming a given graph into…
Computing cohesive subgraphs is a central problem in graph theory. While many formulations of cohesive subgraphs lead to NP-hard problems, finding a densest subgraph can be done in polynomial time. As such, the densest subgraph model has…
Let H be a graph, and let C_H(G) be the number of (subgraph isomorphic) copies of H contained in a graph G. We investigate the fundamental problem of estimating C_H(G). Previous results cover only a few specific instances of this general…
Graph clustering is a challenging pattern recognition problem whose goal is to identify vertex partitions with high intra-group connectivity. This paper investigates a bi-objective problem that maximizes the number of intra-cluster edges of…
In our paper, we consider the following general problems: check feasibility, count the number of feasible solutions, find an optimal solution, and count the number of optimal solutions in $P \cap Z^n$, assuming that $P$ is a polyhedron,…
The Spanning Tree Congestion (STC) problem is the following NP-hard problem: given a graph $G$, construct a spanning tree $T$ of $G$ minimizing its maximum edge congestion where the congestion of an edge $e\in T$ is the number of edges $uv$…
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…
We present the first parameterized analysis of a standard (1+1) Evolutionary Algorithm on a distribution of vertex cover problems. We show that if the planted cover is at most logarithmic, restarting the (1+1) EA every $O(n \log n)$ steps…
The Small Set Expansion Hypothesis (SSEH) is a conjecture which roughly states that it is NP-hard to distinguish between a graph with a small subset of vertices whose edge expansion is almost zero and one in which all small subsets of…
This paper presents a fast and simple new 2-approximation algorithm for minimum weighted vertex cover. The unweighted version of this algorithm is equivalent to a well-known greedy maximal independent set algorithm. We prove that this…