Related papers: Finding Largest Common Substructures of Molecules …
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…
A (unit) disk graph is the intersection graph of closed (unit) disks in the plane. Almost three decades ago, an elegant polynomial-time algorithm was found for \textsc{Maximum Clique} on unit disk graphs [Clark, Colbourn, Johnson; Discrete…
We present quantum algorithms for the following graph problems: finding a maximal bipartite matching in time O(n sqrt{m+n} log n), finding a maximal non-bipartite matching in time O(n^2 (sqrt{m/n} + log n) log n), and finding a maximal flow…
Given a graph $G$, the maximal induced subgraphs problem asks to enumerate all maximal induced subgraphs of $G$ that belong to a certain hereditary graph class. While its optimization version, known as the minimum vertex deletion problem in…
Designing new molecules with a set of predefined properties is a core problem in modern drug discovery and development. There is a growing need for de-novo design methods that would address this problem. We present MolecularRNN, the graph…
In this paper, we show that given a weighted, directed planar graph $G$, and any $\epsilon >0$, there exists a polynomial time and $O(n^{\frac{1}{2}+\epsilon})$ space algorithm that computes the shortest path between two fixed vertices in…
Given a connected undirected weighted graph, we are concerned with problems related to partitioning the graph. First of all we look for the closest disconnected graph (the minimum cut problem), here with respect to the Euclidean norm. We…
In this work, we propose a novel approach for subgraph matching, the problem of finding a given query graph in a large source graph, based on the fused Gromov-Wasserstein distance. We formulate the subgraph matching problem as a partial…
Proteins perform much of the work in living organisms, and consequently the development of efficient computational methods for protein representation is essential for advancing large-scale biological research. Most current approaches…
In the past decades for more and more graph classes the Graph Isomorphism Problem was shown to be solvable in polynomial time. An interesting family of graph classes arises from intersection graphs of geometric objects. In this work we show…
We consider the problem of generating uniformly random partitions of the vertex set of a graph such that every piece induces a connected subgraph. For the case where we want to have partitions with linearly many pieces of bounded size, we…
Classification and regression in which the inputs are graphs of arbitrary size and shape have been paid attention in various fields such as computational chemistry and bioinformatics. Subgraph indicators are often used as the most…
Vertex splitting replaces a vertex by two copies and partitions its incident edges amongst the copies. This problem has been studied as a graph editing operation to achieve desired properties with as few splits as possible, most often…
We study a variant of the subgraph isomorphism problem that is of high interest to the quantum computing community. Our results give an algorithm to perform pattern matching in quantum circuits for many patterns simultaneously,…
Graph neural networks (GNNs) have been used extensively for addressing problems in drug design and discovery. Both ligand and target molecules are represented as graphs with node and edge features encoding information about atomic elements…
This paper addresses the problem of finding the densest $k$-vertex subgraph in an arbitrary graph. This problem is NP-hard and has important applications in social network analysis, fraud detection, recommendation systems, and…
Designing molecules with specific properties is a long-lasting research problem and is central to advancing crucial domains such as drug discovery and material science. Recent advances in deep graph generative models treat molecule design…
In this paper we present an efficiently scaling quantum algorithm which finds the size of the maximum common edge subgraph for a pair of arbitrary graphs and thus provides a meaningful measure of graph similarity. The algorithm makes use of…
Partitioning a graph into blocks of "roughly equal" weight while cutting only few edges is a fundamental problem in computer science with a wide range of applications. In particular, the problem is a building block in applications that…
The Outerplanar Diameter Improvement problem asks, given a graph $G$ and an integer $D$, whether it is possible to add edges to $G$ in a way that the resulting graph is outerplanar and has diameter at most $D$. We provide a dynamic…