Related papers: Complexity of modification problems for best match…
Signed networks, i.e., networks with positive and negative edges, commonly arise in various domains from social media to epidemiology. Modeling signed networks has many practical applications, including the creation of synthetic data sets…
Symmetries found through automorphisms or graph fibrations provide important insights in network analysis. Symmetries identify clusters of robust synchronization in the network which improves the understanding of the functionality of…
Bayesian optimization is a powerful tool to optimize a black-box function, the evaluation of which is time-consuming or costly. In this paper, we propose a new approach to Bayesian optimization called GP-MGC, which maximizes multiscale…
In an edge modification problem, we are asked to modify at most $k$ edges to a given graph to make the graph satisfy a certain property. Depending on the operations allowed, we have the completion problems and the edge deletion problems. A…
The Balanced Connected Subgraph problem (BCS) was recently introduced by Bhore et al. (CALDAM 2019). In this problem, we are given a graph $G$ whose vertices are colored by red or blue. The goal is to find a maximum connected subgraph of…
Parameterized algorithms are a very useful tool for dealing with NP-hard problems on graphs. Yet, to properly utilize parameterized algorithms it is necessary to choose the right parameter based on the type of problem and properties of the…
In this paper we consider a variation of a recoloring problem, called the Color-Fixing. Let us have some non-proper $r$-coloring $\varphi$ of a graph $G$. We investigate the problem of finding a proper $r$-coloring of $G$, which is "the…
Genetic algorithms have played an important role in engineering optimization. Traditional GAs treat each gene separately. However, biophysical studies of gene regulatory networks revealed direct associations between different genes. It…
Recent investigations in computational biology have focused on a family of 2-colored digraphs, called 2-colored best match graphs, which naturally arise from rooted phylogenetic trees. Actually the defining properties of such graphs are…
We consider the problem of exact and inexact matching of weighted undirected graphs, in which a bijective correspondence is sought to minimize a quadratic weight disagreement. This computationally challenging problem is often relaxed as a…
The study of genetic map linearization leads to a combinatorial hard problem, called the {\em minimum breakpoint linearization} (MBL) problem. It is aimed at finding a linearization of a partial order which attains the minimum breakpoint…
An instance of the maximum mixed graph orientation problem consists of a mixed graph and a collection of source-target vertex pairs. The objective is to orient the undirected edges of the graph so as to maximize the number of pairs that…
Matrix Graph Grammars (MGG) is a novel approach to the study of graph dynamics ([15]). In the present contribution we look at MGG as a formal grammar and as a model of computation, which is a necessary step in the more ambitious program of…
Colouring sparse graphs under various restrictions is a theoretical problem of significant practical relevance. Here we consider the problem of maximizing the number of different colours available at the nodes and their neighbourhoods,…
Deciding whether a collection of unrooted trees is compatible is a fundamental problem in phylogenetics. Two different graph-theoretic characterizations of tree compatibility have recently been proposed. In one of these, tree compatibility…
We study the problem of determining whether a given graph~$G=(V,E)$ admits a matching~$M$ whose removal destroys all odd cycles of~$G$ (or equivalently whether~$G-M$ is bipartite). This problem is equivalent to determine whether~$G$ admits…
A vertex of a plane digraph is bimodal if all its incoming edges (and hence all its outgoing edges) are consecutive in the cyclic order around it. A plane digraph is bimodal if all its vertices are bimodal. Bimodality is at the heart of…
Finding an optimal assignment between two sets of objects is a fundamental problem arising in many applications, including the matching of `bag-of-words' representations in natural language processing and computer vision. Solving the…
Let G be a simple connected graph with vertex set V(G) and edge set E(G. Each vertex of V(G) is colored by a color from the set of colors {c_1, c_2,\dots, c_{\alpha}}. We take a subset S of V(G), such that for every vertex v in V(G)\S, at…
The maximum clique problem (MCP) is a fundamental problem in graph theory and in computational complexity. Given a graph G, the problem is that of finding the largest clique (complete subgraph) in G. The MCP has many important applications…