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 …

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 …

Learning attributed graph representations with communicative message passing transformer

J Chen, S Zheng, Y Song, J Rao, Y Yang - arXiv preprint arXiv:2107.08773, 2021 - arxiv.org
Constructing appropriate representations of molecules lies at the core of numerous tasks
such as material science, chemistry and drug designs. Recent researches abstract …

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 …

Molecular contrastive learning of representations via graph neural networks

Y Wang, J Wang, Z Cao… - Nature Machine …, 2022 - nature.com
Molecular machine learning bears promise for efficient molecular property prediction and
drug discovery. However, labelled molecule data can be expensive and time consuming to …

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 …

KPGT: knowledge-guided pre-training of graph transformer for molecular property prediction

H Li, D Zhao, J Zeng - Proceedings of the 28th ACM SIGKDD Conference …, 2022 - dl.acm.org
Designing accurate deep learning models for molecular property prediction plays an
increasingly essential role in drug and material discovery. Recently, due to the scarcity of …

Attending to graph transformers

L Müller, M Galkin, C Morris, L Rampášek - arXiv preprint arXiv …, 2023 - arxiv.org
Recently, transformer architectures for graphs emerged as an alternative to established
techniques for machine learning with graphs, such as (message-passing) graph neural …

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 …

Strategies for pre-training graph neural networks

W Hu, B Liu, J Gomes, M Zitnik, P Liang… - arXiv preprint arXiv …, 2019 - arxiv.org
Many applications of machine learning require a model to make accurate pre-dictions on
test examples that are distributionally different from training ones, while task-specific labels …