Related papers: Finding Largest Common Substructures of Molecules …
We present an exact algorithm for computing all common subgraphs with the maximum number of vertices across multiple graphs. Our approach is further extended to handle the connected Maximum Common Subgraph (MCS), identifying the largest…
The complexity of the maximum common connected subgraph problem in partial $k$-trees is still not fully understood. Polynomial-time solutions are known for degree-bounded outerplanar graphs, a subclass of the partial $2$-trees. On the other…
The problem of accelerating drug discovery relies heavily on automatic tools to optimize precursor molecules to afford them with better biochemical properties. Our work in this paper substantially extends prior state-of-the-art on…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
Graph generation techniques are increasingly being adopted for drug discovery. Previous graph generation approaches have utilized relatively small molecular building blocks such as atoms or simple cycles, limiting their effectiveness to…
Graphs are ubiquitous data structures for representing interactions between entities. With an emphasis on the use of graphs to represent chemical molecules, we explore the task of learning to generate graphs that conform to a distribution…
Determining whether two graphs are structurally identical is a fundamental problem with applications spanning mathematics, computer science, chemistry, and network science. Despite decades of study, graph isomorphism remains a challenging…
We study the parameterized complexity of the problems of finding a maximum common (induced) subgraph of two given graphs. Since these problems generalize several NP-complete problems, they are intractable even when parameterized by strongly…
Designing molecular structures with desired chemical properties is an essential task in drug discovery and material design. However, finding molecules with the optimized desired properties is still a challenging task due to combinatorial…
The Subgraph Isomorphism problem asks, given a host graph G on n vertices and a pattern graph P on k vertices, whether G contains a subgraph isomorphic to P. The restriction of this problem to planar graphs has often been considered. After…
Machine learning techniques have recently been adopted in various applications in medicine, biology, chemistry, and material engineering. An important task is to predict the properties of molecules, which serves as the main subroutine in…
Designing a network to learn a molecule structure given its physical/chemical properties is a hard problem, but is useful for drug discovery tasks. In this paper, we incorporate higher-order relational learning of Factor Graphs with strong…
In the area of beyond-planar graphs, i.e. graphs that can be drawn with some local restrictions on the edge crossings, the recognition problem is prominent next to the density question for the different graph classes. For 1-planar graphs,…
Molecule generation is a challenging open problem in cheminformatics. Currently, deep generative approaches addressing the challenge belong to two broad categories, differing in how molecules are represented. One approach encodes molecular…
We view molecular optimization as a graph-to-graph translation problem. The goal is to learn to map from one molecular graph to another with better properties based on an available corpus of paired molecules. Since molecules can be…
In order to define the process of restrosynthesis of a new organic molecule, it is often necessary to be able to draw inspiration from that of a molecule similar to the target one of which we know such a process. To compute such a…
Bidimensionality is the most common technique to design subexponential-time parameterized algorithms on special classes of graphs, particularly planar graphs. The core engine behind it is a combinatorial lemma of Robertson, Seymour and…
In drug discovery, knowledge of the graph structure of chemical compounds is essential. Many thousands of scientific articles in chemistry and pharmaceutical sciences have investigated chemical compounds, but in cases the details of the…
Schietgat, Ramon and Bruynooghe proposed a polynomial-time algorithm for computing a maximum common subgraph under the block-and-bridge preserving subgraph isomorphism (BBP-MCS) for outerplanar graphs. We show that the article contains the…
In the last decade, algorithmic frameworks based on a structural graph parameter called mim-width have been developed to solve generally NP-hard problems. However, it is known that the frameworks cannot be applied to the Clique problem, and…