Related papers: Complexity of Sequence-to-Graph Alignment with Co-…
In the Cluster Editing problem, sometimes known as (unweighted) Correlation Clustering, we must insert and delete a minimum number of edges to achieve a graph in which every connected component is a clique. Owing to its applications in…
Correlation clustering seeks a partition of the vertex set of a given graph/network into groups of closely related, or just close enough, vertices so that elements of different groups are not close to each other. The problem has been…
We explore Cluster Editing and its generalization Correlation Clustering with a new operation called permissive vertex splitting which addresses finding overlapping clusters in the face of uncertain information. We determine that both…
This paper studies the problem of graph-level clustering, which is a novel yet challenging task. This problem is critical in a variety of real-world applications such as protein clustering and genome analysis in bioinformatics. Recent years…
We introduce a dynamic version of the NP-hard graph problem Cluster Editing. The essential point here is to take into account dynamically evolving input graphs: Having a cluster graph (that is, a disjoint union of cliques) that represents a…
The problem of matching a query string to a directed graph, whose vertices are labeled by strings, has application in different fields, from data mining to computational biology. Several variants of the problem have been considered,…
The Cluster Editing problem seeks a transformation of a given undirected graph into a disjoint union of cliques via a minimum number of edge additions or deletions. A multi-parameterized version of the problem is studied, featuring a number…
Covering alignment problems arise from recent developments in genomics; so called pan-genome graphs are replacing reference genomes, and advances in haplotyping enable full content of diploid genomes to be used as basis of sequence…
\Graph similarity computation is an essential task in many real-world graph-related applications such as retrieving the similar drugs given a query chemical compound or finding the user's potential friends from the social network database.…
Editing a graph into a disjoint union of clusters is a standard optimization task in graph-based data clustering. Here, complementing classic work where the clusters shall be cliques, we focus on clusters that shall be 2-clubs, that is,…
We study the computational complexity of the graph modification problems Threshold Editing and Chain Editing, adding and deleting as few edges as possible to transform the input into a threshold (or chain) graph. In this article, we show…
Editing a graph to obtain a disjoint union of s-clubs is one of the models for correlation clustering, which seeks a partition of the vertex set of a graph so that elements of each resulting set are close enough according to some given…
Aligning a sequence to a walk in a labeled graph is a problem of fundamental importance to Computational Biology. For finding a walk in an arbitrary graph with $|E|$ edges that exactly matches a pattern of length $m$, a lower bound based on…
Edge Constrained Vertex Coloring (ECVC) problems are defined on a finite multigraph, their solutions are characterized, and a linear time algorithm is given for solving $N$ ECVCs on the same underlying multigraph. Using ECVC problems we…
Cluster Editing, also known as Correlation Clustering, is a well-studied graph modification problem. In this problem, one is given a graph and the task is to perform up to $k$ edge additions or deletions to transform it into a cluster…
Aligning sequencing reads on graph representations of genomes is an important ingredient of pan-genomics. Such approaches typically find a set of local anchors that indicate plausible matches between substrings of a read to subpaths of the…
Clustering a graph when the clusters can overlap can be seen from three different angles: We may look for cliques that cover the edges of the graph with bounded overlap, we may look to add or delete few edges to uncover the cluster…
In the last few years, graph convolutional networks (GCN) have become a popular research direction in the machine learning community to tackle NP-hard combinatorial optimization problems (COPs) defined on graphs. While the obtained results…
Computing efficiently a robust measure of similarity or dissimilarity between graphs is a major challenge in Pattern Recognition. The Graph Edit Distance (GED) is a flexible measure of dissimilarity between graphs which arises in…
The $H$-Coloring problem is a well-known generalization of the classical NP-complete problem $k$-Coloring where the task is to determine whether an input graph admits a homomorphism to the template graph $H$. This problem has been the…