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The gene family-free framework for comparative genomics aims at developing methods for gene order analysis that do not require prior gene family assignment, but work directly on a sequence similarity multipartite graph. We present a model…
Base polytopes of polymatroids, also known as generalized permutohedra, are polytopes whose edges are parallel to a vector of the form $\mathbf{e}_i - \mathbf{e}_j$. We consider the following computational problem: Given two vertices of a…
Near ubiquitous mobile computing has led to intense interest in dynamic graph theory. This provides a new and challenging setting for algorithmics and complexity theory. For any graph-based problem, the rapid evolution of a (possibly…
We study the computational complexity of routing multiple objects through a network in such a way that only few collisions occur: Given a graph $G$ with two distinct terminal vertices and two positive integers $p$ and $k$, the question is…
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 the Minimum Clique Routing Problem on Cycles \textsc{MCRPC} we are given a cycle together with a set of demands (weighted origin-destination pairs) and the goal is to route all the pairs minimizing the maximum weighted clique of the…
We introduce a new -as far as we know- problem, according to which we are asked to match sequences of two digits in matrices having entries among those two digits (but others too) and prove that this problem is NP-complete
In this paper, we prove that the MaxCut problem is NP-complete on permutation graphs, settling a long-standing open problem that appeared in the 1985 column of the "Ongoing Guide to NP-completeness" by David S. Johnson.
Checking whether a system of linear equations is consistent is a basic computational problem with ubiquitous applications. When dealing with inconsistent systems, one may seek an assignment that minimizes the number of unsatisfied…
Consider a problem where we are given a bipartite graph H with vertices arranged on two horizontal lines in the plane, such that the two sets of vertices placed on the two lines form a bipartition of H. We additionally require that H admits…
Betweenness centrality ranks the importance of nodes by their participation in all shortest paths of the network. Therefore computing exact betweenness values is impractical in large networks. For static networks, approximation based on…
Sequence alignment is a cornerstone technique in computational biology for assessing similarities and differences among biological sequences. A key variant, sequence-to-graph alignment, plays a crucial role in effectively capturing genetic…
The Maximum Betweenness Centrality problem (MBC) can be defined as follows. Given a graph find a $k$-element node set $C$ that maximizes the probability of detecting communication between a pair of nodes $s$ and $t$ chosen uniformly at…
We study the complexity of classical constraint satisfaction problems on a 2D grid. Specifically, we consider the complexity of function versions of such problems, with the additional restriction that the constraints are translationally…
Motivated by comparative genomics, Chen et al. [9] introduced the Maximum Duo-preservation String Mapping (MDSM) problem in which we are given two strings $s_1$ and $s_2$ from the same alphabet and the goal is to find a mapping $\pi$…
In recent years, Graph Neural Networks (GNNs) have achieved remarkable success in many graph mining tasks. However, scaling them to large graphs is challenging due to the high computational and storage costs of repeated feature propagation…
We propose a consistent polynomial-time method for the unseeded node matching problem for networks with smooth underlying structures. Despite widely conjectured by the research community that the structured graph matching problem to be…
Given a weighted graph $G$ with $n$ vertices and $m$ edges, and a positive integer $p$, the Hamiltonian $p$-median problem consists in finding $p$ cycles of minimum total weight such that each vertex of $G$ is in exactly one cycle. We…
Combinatorial reconfiguration is a growing research field studying problems on the transformability between a pair of solutions of a search problem. We consider the approximability of optimization variants of reconfiguration problems; e.g.,…
Crossing minimization is one of the central problems in graph drawing. Recently, there has been an increased interest in the problem of minimizing crossings between paths in drawings of graphs. This is the metro-line crossing minimization…