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We study a large family of graph covering problems, whose definitions rely on distances, for graphs of bounded cyclomatic number (that is, the minimum number of edges that need to be removed from the graph to destroy all cycles). These…
The Euclidean distance geometry problem arises in a wide variety of applications, from determining molecular conformations in computational chemistry to localization in sensor networks. When the distance information is incomplete, the…
The qubit routing problem, also known as the swap minimization problem, is a (classical) combinatorial optimization problem that arises in the design of compilers of quantum programs. We study the qubit routing problem from the viewpoint of…
Graph Edit Distance (GED) is defined as the minimum cost transformation of one graph into another and is a widely adopted metric for measuring the dissimilarity between graphs. The major problem of GED is that its computation is NP-hard,…
Given a set of strings over a specified alphabet, identifying a median or consensus string that minimizes the total distance to all input strings is a fundamental data aggregation problem. When the Hamming distance is considered as the…
Betweenness is a well-known centrality measure that ranks the nodes of a network according to their participation in shortest paths. Since an exact computation is prohibitive in large networks, several approximation algorithms have been…
The Surjective Homomorphism problem is to test whether a given graph G called the guest graph allows a vertex-surjective homomorphism to some other given graph H called the host graph. The bijective and injective homomorphism problems can…
Many real-world networks can be modeled as graphs. Finding dense subgraphs is a key problem in graph mining with applications in diverse domains. In this paper, we consider two variants of the densest subgraph problem where multiple graph…
Permutation Pattern Matching (PPM) is the problem of deciding for a given pair of permutations P and T whether the pattern P is contained in the text T. Bose, Buss and Lubiw showed that PPM is NP-complete. In view of this result, it is…
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 $uv$…
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…
We systematically study the computational complexity of a broad class of computational problems in phylogenetic reconstruction. The class contains for example the rooted triple consistency problem, forbidden subtree problems, the quartet…
Permutation Pattern Matching (or PPM) is a decision problem whose input is a pair of permutations $\pi$ and $\tau$, represented as sequences of integers, and the task is to determine whether $\tau$ contains a subsequence order-isomorphic to…
We study the problem of computing a minimum equivalent digraph (also known as the problem of computing a strong transitive reduction) and its maximum objective function variant, with two types of extensions. First, we allow to declare a set…
A matching is said to be disconnected if the saturated vertices induce a disconnected subgraph and induced if the saturated vertices induce a 1-regular graph. The disconnected and induced matching numbers are defined as the maximum…
The 1-median problem (1MP) on undirected weighted graphs seeks to find a facility location minimizing the total weighted distance to all customer nodes. Although the 1MP can be solved exactly by computing the single-source shortest paths…
The last decade brought a significant increase in the amount of data and a variety of new inference methods for reconstructing the detailed evolutionary history of various cancers. This brings the need of designing efficient procedures for…
We show that two important problems that have applications in computational biology are ASP-complete, which implies that, given a solution to a problem, it is NP-complete to decide if another solution exists. We show first that a variation…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
This paper introduces the \emph{$d$-distance matching problem}, in which we are given a bipartite graph $G=(S,T;E)$ with $S=\{s_1,\dots,s_n\}$, a weight function on the edges and an integer $d\in\mathbb Z_+$. The goal is to find a maximum…