Related papers: The Largest Compatible Subset Problem for Phylogen…
Finding optimal matchings in dense graphs is of general interest and of particular importance in social, transportation and biological networks. While developing optimal solutions for various matching problems is important, the running…
We consider a natural generalization of Vertex Cover: the Subset Vertex Cover problem, which is to decide for a graph $G=(V,E)$, a subset $T\subseteq V$ and integer $k$, if $V$ has a subset $S$ of size at most $k$, such that $S$ contains at…
In this paper we present a collection of results pertaining to haplotyping. The first set of results concerns the combinatorial problem of reconstructing haplotypes from incomplete and/or imperfectly sequenced haplotype data. More…
We study a well known noisy model of the graph isomorphism problem. In this model, the goal is to perfectly recover the vertex correspondence between two edge-correlated Erd\H{o}s-R\'{e}nyi random graphs, with an initial seed set of…
In a vertex-colored graph $G = (V, E)$, a subset $S \subseteq V$ is said to be consistent if every vertex has a nearest neighbor in $S$ with the same color. The problem of computing a minimum cardinality consistent subset of a graph is…
A central problem in graph mining is finding dense subgraphs, with several applications in different fields, a notable example being identifying communities. While a lot of effort has been put on the problem of finding a single dense…
In this paper we investigate the colorful components framework, motivated by applications emerging from comparative genomics. The general goal is to remove a collection of edges from an undirected vertex-colored graph $G$ such that in the…
This paper explores combinatorial optimization for problems of max-weight graph matching on multi-partite graphs, which arise in integrating multiple data sources. Entity resolution-the data integration problem of performing noisy joins on…
The CONNECTED VERTEX COVER problem asks for a vertex cover in a graph that induces a connected subgraph. The problem is known to be fixed-parameter tractable (FPT), and is unlikely to have a polynomial sized kernel (under complexity…
In the solution discovery problem for a search problem on graphs, we are given an initial placement of $k$ tokens on the vertices of a graph and asked whether this placement can be transformed into a feasible solution by applying a small…
Tree representations of (sets of) symmetric binary relations, or equivalently edge-colored undirected graphs, are of central interest, e.g.\ in phylogenomics. In this context symbolic ultrametrics play a crucial role. Symbolic ultrametrics…
The Minimum Vertex Cover problem, a classical NP-complete problem, presents significant challenges for exact solution on large graphs. Fixed-Parameter Tractability (FPT) offers a powerful paradigm to address such problems by exploiting a…
A rainbow matching in an edge-colored graph is a matching whose edges have distinct colors. We address the complexity issue of the following problem, \mrbm: Given an edge-colored graph $G$, how large is the largest rainbow matching in $G$?…
Cohesive subgraph discovery in a network is one of the fundamental problems and investigated for several decades. In this paper, we propose the Overlapping Cohesive Subgraphs with Minimum degree (OCSM) problem which combines three key…
We consider the problem of embedding the nodes of a hypergraph into Euclidean space under the assumption that the interactions arose through closeness to unknown hyperedge centres. In this way, we tackle the inverse problem associated with…
Graph matching is a challenging problem with very important applications in a wide range of fields, from image and video analysis to biological and biomedical problems. We propose a robust graph matching algorithm inspired in…
Maximum weight matching is one of the most fundamental combinatorial optimization problems with a wide range of applications in data mining and bioinformatics. Developing distributed weighted matching algorithms is challenging due to the…
Knowledge graphs have emerged as fundamental structures for representing complex relational data across scientific and enterprise domains. However, existing embedding methods face critical limitations when modeling diverse relationship…
This paper shows how to evolve numerically the maximum entropy probability distributions for a given set of constraints, which is a variational calculus problem. An evolutionary algorithm can obtain approximations to some well-known…
A phylogeny describes the evolutionary history of an evolving population. Evolutionary search algorithms can perfectly track the ancestry of candidate solutions, illuminating a population's trajectory through the search space. However,…