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Within biology, it is of interest to construct DNA complexes of a certain shape. These complexes can be represented through graph theory, using edges to model strands of DNA joined at junctions, represented by vertices. Because guided…
Branched molecules of deoxyribonucleic acid (DNA) can self-assemble into nanostructures through complementary cohesive strand base pairing. The production of DNA nanostructures is valuable in targeted drug delivery and biomolecular…
NP-hard problems such as the maximum clique or minimum vertex cover problems, two of Karp's 21 NP-hard problems, have several applications in computational chemistry, biochemistry and computer network security. Adiabatic quantum annealers…
In the Edge Coloring problem, we are given an undirected graph $G$ with $n$ vertices and $m$ edges, and are tasked with finding the smallest positive integer $k$ so that the edges of $G$ can be assigned $k$ colors in such a way that no two…
We study the rainbow matching (RM) problem: given an edge-colored graph, find a maximum matching with at most one edge of each color. Rainbow matchings correspond to stable sets in the \emph{augmented} graph $H$ obtained from the line graph…
The $\lambda$-backbone coloring of the graph $G$ with backbone $H$ is a graph-coloring problem in which we are given a graph $G$ and a subgraph $H$, and we want to assign colors to vertices in such a way that the endpoints of every edge…
A linearly ordered (LO) $k$-colouring of a hypergraph is a colouring of its vertices with colours $1, \dots, k$ such that each edge contains a unique maximal colour. Deciding whether an input hypergraph admits LO $k$-colouring with a fixed…
The problem of computing all maximal induced subgraphs of a graph G that have a graph property P, also called the maximal P-subgraphs problem, is considered. This problem is studied for hereditary, connected-hereditary and rooted-hereditary…
Approximate random $k$-colouring of a graph $G$ is a well studied problem in computer science and statistical physics. It amounts to constructing a $k$-colouring of $G$ which is distributed close to {\em Gibbs distribution} in polynomial…
Many exact search algorithms for NP-hard graph problems adopt the old Davis-Putman branch-and-reduce paradigm. The performance of these algorithms often suffers from the increasing number of graph modifications, such as vertex/edge…
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…
Determinantal Point Processes (DPPs) are a widely used probabilistic model for negatively correlated sets. DPPs have been successfully employed in Machine Learning applications to select a diverse, yet representative subset of data. In…
Many variations of the classical graph coloring model have been intensively studied due to their multiple applications; scheduling problems and aircraft assignments, for instance, motivate the robust coloring problem. This model gets to…
We aim to find orientations of mixed graphs optimizing the total reachability, a problem that has applications in causality and biology. For given a digraph $D$, we use $P(D)$ for the set of ordered pairs of distinct vertices in $V(D)$ and…
We reduce the problem of finding an augmenting path in a general graph to a reachability problem in a directed bipartite graph. A slight modification of depth-first search leads to an algorithm for finding such paths. Although this setting…
A code design problem for memory devises with restricted state transitions is formulated as a combinatorial optimization problem that is called a subgraph domatic partition (subDP) problem. If any neighbor set of a given state transition…
We consider the graph $k$-colouring problem encoded as a set of polynomial equations in the standard way over $0/1$-valued variables. We prove that there are bounded-degree graphs that do not have legal $k$-colourings but for which the…
Subgraph matching is a core task in graph analytics, widely used in domains such as biology, finance, and social networks. Existing top-k diversified methods typically focus on maximizing vertex coverage, but often return results in the…
We study the problem of coloring a given graph using a small number of colors in several well-established models of computation for big data. These include the data streaming model, the general graph query model, the massively parallel…
Finding maximum-cardinality matchings in undirected graphs is arguably one of the most central graph problems. For general m-edge and n-vertex graphs, it is well-known to be solvable in $O(m \sqrt{n})$ time. We develop a linear-time…