Related papers: GraphXForm: Graph transformer for computer-aided m…

The discovery of new molecules based on the original chemical molecule distributions is of great importance in medicine. The graph transformer, with its advantages of high performance and scalability compared to traditional graph networks,…

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…

Graph Transformers have recently attracted attention for molecular property prediction by combining the inductive biases of graph neural networks (GNNs) with the global receptive field of Transformers. However, many existing hybrid…

For several decades, chemical knowledge has been published in written text, and there have been many attempts to make it accessible, for example, by transforming such natural language text to a structured format. Although the discovered…

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…

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…

Transformers, adapted from natural language processing, are emerging as a leading approach for graph representation learning. Contemporary graph transformers often treat nodes or edges as separate tokens. This approach leads to…

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…

The generation of drug-like molecules is crucial for drug design. Existing reinforcement learning (RL) methods often overlook structural information. However, feature engineering-based methods usually merely focus on binding affinity…

The prediction of physicochemical properties from molecular structures is a crucial task for artificial intelligence aided molecular design. A growing number of Graph Neural Networks (GNNs) have been proposed to address this challenge.…

Graph neural networks (GNNs) demonstrate great performance in compound property and activity prediction due to their capability to efficiently learn complex molecular graph structures. However, two main limitations persist including…

Transformer-based models trained on large and general purpose datasets consisting of molecular strings have recently emerged as a powerful tool for successfully modeling various structure-property relations. Inspired by this success, we…

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…

Molecular representation learning methods typically tokenize molecules as individual atoms or use rigid, rule-based fragment decompositions, limiting their ability to capture meaningful chemical substructure context. We introduce…

How to obtain informative representations of molecules is a crucial prerequisite in AI-driven drug design and discovery. Recent researches abstract molecules as graphs and employ Graph Neural Networks (GNNs) for molecular representation…

Molecular modeling, a central topic in quantum mechanics, aims to accurately calculate the properties and simulate the behaviors of molecular systems. The molecular model is governed by physical laws, which impose geometric constraints such…

The success of a specific neural network architecture is closely tied to the dataset and task it tackles; there is no one-size-fits-all solution. Thus, considerable efforts have been made to quickly and accurately estimate the performances…

Constructing appropriate representations of molecules lies at the core of numerous tasks such as material science, chemistry and drug designs. Recent researches abstract molecules as attributed graphs and employ graph neural networks (GNN)…

Recently, deep generative models have revealed itself as a promising way of performing de novo molecule design. However, previous research has focused mainly on generating SMILES strings instead of molecular graphs. Although current graph…

Procuring expressive molecular representations underpins AI-driven molecule design and scientific discovery. The research mainly focuses on atom-level homogeneous molecular graphs, ignoring the rich information in subgraphs or motifs.…