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A fundamental question that shrouds the emergence of massively parallel computing (MPC) platforms is how can the additional power of the MPC paradigm be leveraged to achieve faster algorithms compared to classical parallel models such as…
The index coding problem is concerned with broadcasting encoded information to a collection of receivers in a way that enables each receiver to discover its required data based on its side information, which comprises the data required by…
We give a quasipolynomial time algorithm for the graph matching problem (also known as noisy or robust graph isomorphism) on correlated random graphs. Specifically, for every $\gamma>0$, we give a $n^{O(\log n)}$ time algorithm that given a…
Let $\mathcal{C}$ and $\mathcal{D}$ be hereditary graph classes. Consider the following problem: given a graph $G\in\mathcal{D}$, find a largest, in terms of the number of vertices, induced subgraph of $G$ that belongs to $\mathcal{C}$. We…
Deep learning based molecular graph generation and optimization has recently been attracting attention due to its great potential for de novo drug design. On the one hand, recent models are able to efficiently learn a given graph…
Diameter -- the task of computing the length of a longest shortest path -- is a fundamental graph problem. Assuming the Strong Exponential Time Hypothesis, there is no $O(n^{1.99})$-time algorithm even in sparse graphs [Roditty and…
A planar orthogonal drawing {\Gamma} of a connected planar graph G is a geometric representation of G such that the vertices are drawn as distinct points of the plane, the edges are drawn as chains of horizontal and vertical segments, and…
Determining the interaction strength between proteins and small molecules is key to analyzing their biological function. Quantum-mechanical calculations such as \emph{Density Functional Theory} (DFT) give accurate and theoretically…
Sublinear time algorithms represent a new paradigm in computing, where an algorithm must give some sort of an answer after inspecting only a small portion of the input. The most typical situation where sublinear time algorithms are…
Networks are largely used for modelling and analysing data and relations among them. Recently, it has been shown that the use of a single network may not be the optimal choice, since a single network may misses some aspects. Consequently,…
The simulation of the physical movement of multi-body systems at an atomistic level, with forces calculated from a quantum mechanical description of the electrons, motivates a graph partitioning problem studied in this article. Several…
Subgraph Isomorphism is a very basic graph problem, where given two graphs $G$ and $H$ one is to check whether $G$ is a subgraph of $H$. Despite its simple definition, the Subgraph Isomorphism problem turns out to be very broad, as it…
Computing a shortest path between two nodes in an undirected unweighted graph is among the most basic algorithmic tasks. Breadth first search solves this problem in linear time, which is clearly also a lower bound in the worst case.…
Recent advances in molecular representation learning have produced highly effective encodings of molecules for numerous cheminformatics and bioinformatics tasks. However, extracting general chemical insight while balancing predictive…
Temporal graphs are graphs whose topology is subject to discrete changes over time. Given a static underlying graph $G$, a temporal graph is represented by assigning a set of integer time-labels to every edge $e$ of $G$, indicating the…
Graph transformation formalisms have proven to be suitable tools for the modelling of chemical reactions. They are well established in theoretical studies and increasingly also in practical applications in chemistry. The latter is made…
We present the graph-based molecule software Molassembler for building organic and inorganic molecules. Molassembler provides algorithms for the construction of molecules built from any set of elements from the periodic table. In…
In this paper, we present two main results. First, by only one conjecture (Conjecture 2.9) for recognizing a vertex symmetric graph, which is the hardest task for our problem, we construct an algorithm for finding an isomorphism between two…
We describe algorithms to efficiently compute minimum $(s,t)$-cuts and global minimum cuts of undirected surface-embedded graphs. Given an edge-weighted undirected graph $G$ with $n$ vertices embedded on an orientable surface of genus $g$,…
A subgraph is constructed by using a subset of vertices and edges of a given graph. There exist many graph properties that are hereditary for subgraphs. Hence, researchers from different communities have paid a great deal of attention in…