Related papers: Finding Largest Common Substructures of Molecules …
An \emph{obstacle representation} of a graph consists of a set of polygonal obstacles and a distinct point for each vertex such that two points see each other if and only if the corresponding vertices are adjacent. Obstacle representations…
Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the…
We solve the subgraph isomorphism problem in planar graphs in linear time, for any pattern of constant size. Our results are based on a technique of partitioning the planar graph into pieces of small tree-width, and applying dynamic…
Finding dense substructures in a graph is a fundamental graph mining operation, with applications in bioinformatics, social networks, and visualization to name a few. Yet most standard formulations of this problem (like clique, quasiclique,…
Fan-planar graphs were recently introduced as a generalization of 1-planar graphs. A graph is fan-planar if it can be embedded in the plane, such that each edge that is crossed more than once, is crossed by a bundle of two or more edges…
The family of $(k, \ell)$-sparse graphs, introduced by Lorea, plays a central role in combinatorial optimization and has a wide range of applications, particularly in rigidity theory. A key algorithmic challenge is to compute a…
The enumeration of chemical graphs is an important topic in cheminformatics and bioinformatics, particularly in the discovery of novel drugs. These graphs are typically either tree-like multigraphs or composed of tree-like multigraphs…
Due to their excellent drug-like and pharmacokinetic properties, small molecule drugs are widely used to treat various diseases, making them a critical component of drug discovery. In recent years, with the rapid development of deep…
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…
Hypergraphs, increasingly utilised to model complex and diverse relationships in modern networks, have gained significant attention for representing intricate higher-order interactions. Among various challenges, cohesive subgraph discovery…
The maximal clique problem, to find the maximally sized clique in a given graph, is classically an NP-complete computational problem, which has potential applications ranging from electrical engineering, computational chemistry,…
We study the complexity of the problems of finding, given a graph $G$, a largest induced subgraph of $G$ with all degrees odd (called an odd subgraph), and the smallest number of odd subgraphs that partition $V(G)$. We call these parameters…
We determine the optimum topology of quasi-one dimensional nonlinear optical structures using generalized quantum graph models. Quantum graphs are relational graphs endowed with a metric and a multiparticle Hamiltonian acting on the edges,…
IC-planar graphs are those graphs that admit a drawing where no two crossed edges share an end-vertex and each edge is crossed at most once. They are a proper subfamily of the 1-planar graphs. Given an embedded IC-planar graph $G$ with $n$…
The graph retrieval problem is to search in a large corpus of graphs for ones that are most similar to a query graph. A common consideration for scoring similarity is the maximum common subgraph (MCS) between the query and corpus graphs,…
Recently, deep learning based methods have demonstrated promising results on the graph matching problem, by relying on the descriptive capability of deep features extracted on graph nodes. However, one main limitation with existing deep…
Molecular docking is an essential step in the drug discovery process involving the detection of three-dimensional poses of a ligand inside the active site of the protein. In this paper, we address the Molecular Docking search phase by…
Discovering the underlying structure of a given graph is one of the fundamental goals in graph mining. Given a graph, we can often order vertices in a way that neighboring vertices have a higher probability of being connected to each other.…
We study the design of fixed-parameter algorithms for problems already known to be solvable in polynomial time. The main motivation is to get more efficient algorithms for problems with unattractive polynomial running times. Here, we focus…
We present a factor $14D^2$ approximation algorithm for the minimum linear arrangement problem on series-parallel graphs, where $D$ is the maximum degree in the graph. Given a suitable decomposition of the graph, our algorithm runs in time…