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In this article, we study the problem of finding the longest common separable pattern between several permutations. We give a polynomial-time algorithm when the number of input permutations is fixed and show that the problem is NP-hard for…
Tolerance graphs model interval relations in such a way that intervals can tolerate a certain amount of overlap without being in conflict. In one of the most natural generalizations of tolerance graphs with direct applications in the…
We show that any submodular minimization (SM) problem defined on a linear constraint set with constraints having up to two variables per inequality, are 2-approximable in polynomial time. If the constraints are monotone (the two variables…
Finding the minimum distance of linear codes is an NP-hard problem. Traditionally, this computation has been addressed by means of the design of algorithms that find, by a clever exhaustive search, a linear combination of some generating…
Understanding genetic variation, e.g., through mutations, in organisms is crucial to unravel their effects on the environment and human health. A fundamental characterization can be obtained by solving the haplotype assembly problem, which…
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…
Finding cohesive subgraphs in a network is a well-known problem in graph theory. Several alternative formulations of cohesive subgraph have been proposed, a notable example being $s$-club, which is a subgraph where each vertex is at…
Multiple interval graphs are variants of interval graphs where instead of a single interval, each vertex is assigned a set of intervals on the real line. We study the complexity of the MAXIMUM CLIQUE problem in several classes of multiple…
We introduce Permutation and Structured Perturbation Inference (PSPI), a new problem formulation that abstracts many graph matching tasks that arise in systems biology. PSPI can be viewed as a robust formulation of the permutation inference…
We investigate a variety of problems of finding tours and cycle covers with minimum turn cost. Questions of this type have been studied in the past, with complexity and approximation results as well as open problems dating back to work by…
Genome rearrangements are evolutionary events that shuffle genomic architectures. Most frequent genome rearrangements are reversals, translocations, fusions, and fissions. While there are some more complex genome rearrangements such as…
Graph Neural Networks (GNNs) face two fundamental challenges when scaled to deep architectures: oversmoothing, where node representations converge to indistinguishable vectors, and oversquashing, where information from distant nodes fails…
We study the Parallel Task Scheduling problem $Pm|size_j|C_{\max}$ with a constant number of machines. This problem is known to be strongly NP-complete for each $m \geq 5$, while it is solvable in pseudo-polynomial time for each $m \leq 3$.…
Subgraph isomorphism is a well-known NP-hard problem which is widely used in many applications, such as social network analysis and knowledge graph query. Its performance is often limited by the inherent hardness. Several insightful works…
We investigate the complexity of finding a transformation from a given spanning tree in a graph to another given spanning tree in the same graph via a sequence of edge flips. The exchange property of the matroid bases immediately yields…
The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…
Motivation: Genome rearrangement plays an important role in evolutionary biology and has profound impacts on phenotype in organisms ranging from microbes to humans. The mechanisms for genome rearrangement events remain unclear. Lots of…
The maximum graph bisection problem is a well known graph partition problem. The problem has been proven to be NP-hard. In the maximum graph bisection problem it is required that the set of vertices is divided into two partition with equal…
In the Maximum Independent Set problem we are asked to find a set of pairwise nonadjacent vertices in a given graph with the maximum possible cardinality. In general graphs, this classical problem is known to be NP-hard and hard to…
Codes over permutations under the infinity norm have been recently suggested as a coding scheme for correcting limited-magnitude errors in the rank modulation scheme. Given such a code, we show that a simple relabeling operation, which…