An effective self-supervised framework for learning expressive molecular global representations to drug discovery

P Li, J Wang, Y Qiao, H Chen, Y Yu… - Briefings in …, 2021 - academic.oup.com
How to produce expressive molecular representations is a fundamental challenge in
artificial intelligence-driven drug discovery. Graph neural network (GNN) has emerged as a …

Self-supervised graph transformer on large-scale molecular data

Y Rong, Y Bian, T Xu, W Xie, Y Wei… - Advances in neural …, 2020 - proceedings.neurips.cc
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 …

A knowledge-guided pre-training framework for improving molecular representation learning

H Li, R Zhang, Y Min, D Ma, D Zhao, J Zeng - Nature Communications, 2023 - nature.com
Learning effective molecular feature representation to facilitate molecular property prediction
is of great significance for drug discovery. Recently, there has been a surge of interest in pre …

Interpretable chirality-aware graph neural network for quantitative structure activity relationship modeling in drug discovery

YL Liu, Y Wang, O Vu, R Moretti… - Proceedings of the …, 2023 - ojs.aaai.org
In computer-aided drug discovery, quantitative structure activity relation models are trained
to predict biological activity from chemical structure. Despite the recent success of applying …

Pushing the boundaries of molecular representation for drug discovery with the graph attention mechanism

Z Xiong, D Wang, X Liu, F Zhong, X Wan… - Journal of medicinal …, 2019 - ACS Publications
Hunting for chemicals with favorable pharmacological, toxicological, and pharmacokinetic
properties remains a formidable challenge for drug discovery. Deep learning provides us …

Hierarchical molecular graph self-supervised learning for property prediction

X Zang, X Zhao, B Tang - Communications Chemistry, 2023 - nature.com
Molecular graph representation learning has shown considerable strength in molecular
analysis and drug discovery. Due to the difficulty of obtaining molecular property labels, pre …

ReLMole: Molecular representation learning based on two-level graph similarities

Z Ji, R Shi, J Lu, F Li, Y Yang - Journal of Chemical Information …, 2022 - ACS Publications
Molecular representation is a critical part of various prediction tasks for physicochemical
properties of molecules and drug design. As graph notations are common in expressing the …

Learning graph-level representation for drug discovery

J Li, D Cai, X He - arXiv preprint arXiv:1709.03741, 2017 - arxiv.org
Predicating macroscopic influences of drugs on human body, like efficacy and toxicity, is a
central problem of small-molecule based drug discovery. Molecules can be represented as …

Graphaf: a flow-based autoregressive model for molecular graph generation

C Shi, M Xu, Z Zhu, W Zhang, M Zhang… - arXiv preprint arXiv …, 2020 - arxiv.org
Molecular graph generation is a fundamental problem for drug discovery and has been
attracting growing attention. The problem is challenging since it requires not only generating …

Path-augmented graph transformer network

B Chen, R Barzilay, T Jaakkola - arXiv preprint arXiv:1905.12712, 2019 - arxiv.org
Much of the recent work on learning molecular representations has been based on Graph
Convolution Networks (GCN). These models rely on local aggregation operations and can …