Fragment-based pretraining and finetuning on molecular graphs

KD Luong, AK Singh - Advances in Neural Information …, 2024 - proceedings.neurips.cc
Property prediction on molecular graphs is an important application of Graph Neural
Networks (GNNs). Recently, unlabeled molecular data has become abundant, which …

Motif-based graph self-supervised learning for molecular property prediction

Z Zhang, Q Liu, H Wang, C Lu… - Advances in Neural …, 2021 - proceedings.neurips.cc
Predicting molecular properties with data-driven methods has drawn much attention in
recent years. Particularly, Graph Neural Networks (GNNs) have demonstrated remarkable …

Molcpt: Molecule continuous prompt tuning to generalize molecular representation learning

C Diao, K Zhou, Z Liu, X Huang, X Hu - arXiv preprint arXiv:2212.10614, 2022 - arxiv.org
Molecular representation learning is crucial for the problem of molecular property prediction,
where graph neural networks (GNNs) serve as an effective solution due to their structure …

ASGN: An active semi-supervised graph neural network for molecular property prediction

Z Hao, C Lu, Z Huang, H Wang, Z Hu, Q Liu… - Proceedings of the 26th …, 2020 - dl.acm.org
Molecular property prediction (eg, energy) is an essential problem in chemistry and biology.
Unfortunately, many supervised learning methods usually suffer from the problem of scarce …

Graph neural networks pretraining through inherent supervision for molecular property prediction

R Benjamin, U Singer, K Radinsky - Proceedings of the 31st ACM …, 2022 - dl.acm.org
Recent global events have emphasized the importance of accelerating the drug discovery
process. A way to deal with the issue is to use machine learning to increase the rate at which …

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 …

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 …

Motif-aware attribute masking for molecular graph pre-training

E Inae, G Liu, M Jiang - arXiv preprint arXiv:2309.04589, 2023 - arxiv.org
Attribute reconstruction is used to predict node or edge features in the pre-training of graph
neural networks. Given a large number of molecules, they learn to capture structural …

Molecule generation by principal subgraph mining and assembling

X Kong, W Huang, Z Tan, Y Liu - Advances in Neural …, 2022 - proceedings.neurips.cc
Molecule generation is central to a variety of applications. Current attention has been paid to
approaching the generation task as subgraph prediction and assembling. Nevertheless …

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 …