Related papers: Finding Largest Common Substructures of Molecules …
The automatic analysis of chemical literature has immense potential to accelerate the discovery of new materials and drugs. Much of the critical information in patent documents and scientific articles is contained in figures, depicting the…
Tackling molecular optimization problems using conventional computational methods is challenging, because the determination of the optimized configuration is known to be an NP-hard problem. Recently, there has been increasing interest in…
In this paper, we study the Maximum Common Vertex Subgraph problem: Given two input graphs $G_1,G_2$ and a non-negative integer $h$, is there a common subgraph $H$ on at least $h$ vertices such that there is no isolated vertex in $H$. In…
We initiate the study of diameter computation in geometric intersection graphs from the fine-grained complexity perspective. A geometric intersection graph is a graph whose vertices correspond to some shapes in $d$-dimensional Euclidean…
Finding dense subgraphs is a core problem in graph mining with many applications in diverse domains. At the same time many real-world networks vary over time, that is, the dataset can be represented as a sequence of graph snapshots. Hence,…
Deciding whether a given graph has a square root is a classical problem that has been studied extensively both from graph theoretic and from algorithmic perspectives. The problem is NP-complete in general, and consequently substantial…
In this study, we intend to solve a mutual information problem in interacting molecules of any type, such as proteins, nucleic acids, and small molecules. Using machine learning techniques, we accurately predict pairwise interactions, which…
We consider the problem of partitioning a graph into a non-fixed number of non-overlapping subgraphs of maximum density. The density of a partition is the sum of the densities of the subgraphs, where the density of a subgraph is its average…
Problems in scientific computing, such as distributing large sparse matrix operations, have analogous formulations as hypergraph partitioning problems. A hypergraph is a generalization of a traditional graph wherein "hyperedges" may connect…
A locally irregular graph is a graph whose adjacent vertices have distinct degrees, a regular graph is a graph where each vertex has the same degree and a locally regular graph is a graph where for every two adjacent vertices u, v, their…
Molecules have seemed like a natural fit to deep learning's tendency to handle a complex structure through representation learning, given enough data. However, this often continuous representation is not natural for understanding chemical…
Graph isomorphism is an important computer science problem. The problem for the general case is unknown to be in polynomial time. The base algorithm for the general case works in quasi-polynomial time. The solutions in polynomial time for…
We present linear time {\it in-place} algorithms for several basic and fundamental graph problems including the well-known graph search methods (like depth-first search, breadth-first search, maximum cardinality search), connectivity…
An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…
Identifying the connected components of a graph, apart from being a fundamental problem with countless applications, is a key primitive for many other algorithms. In this paper, we consider this problem in parallel settings. Particularly,…
Finding a maximum-cardinality or maximum-weight matching in (edge-weighted) undirected graphs is among the most prominent problems of algorithmic graph theory. For $n$-vertex and $m$-edge graphs, the best known algorithms run in…
Given a dynamic network, where edges appear and disappear over time, we are interested in finding sets of edges that have similar temporal behavior and form a dense subgraph. Formally, we define the problem as the enumeration of the maximal…
The forcing number of a graph with a perfect matching $M$ is the minimum number of edges in $M$ whose endpoints need to be deleted, such that the remaining graph only has a single perfect matching. This number is of great interest in…
(Induced) Subgraph Isomorphism and Maximum Common (Induced) Subgraph are fundamental problems in graph pattern matching and similarity computation. In graphs derived from time-series data or protein structures, a natural total ordering of…
In the Graph Reconstruction (GR) problem, the goal is to recover a hidden graph by utilizing some oracle that provides limited access to the structure of the graph. The interest is in characterizing how strong different oracles are when the…