A comprehensive survey on deep graph representation learning

W Ju, Z Fang, Y Gu, Z Liu, Q Long, Z Qiao, Y Qin… - Neural Networks, 2024 - Elsevier
Graph representation learning aims to effectively encode high-dimensional sparse graph-
structured data into low-dimensional dense vectors, which is a fundamental task that has …

Geometric deep learning on molecular representations

K Atz, F Grisoni, G Schneider - Nature Machine Intelligence, 2021 - nature.com
Geometric deep learning (GDL) is based on neural network architectures that incorporate
and process symmetry information. GDL bears promise for molecular modelling applications …

MACE: Higher order equivariant message passing neural networks for fast and accurate force fields

I Batatia, DP Kovacs, G Simm… - Advances in Neural …, 2022 - proceedings.neurips.cc
Creating fast and accurate force fields is a long-standing challenge in computational
chemistry and materials science. Recently, Equivariant Message Passing Neural Networks …

Learning local equivariant representations for large-scale atomistic dynamics

A Musaelian, S Batzner, A Johansson, L Sun… - Nature …, 2023 - nature.com
A simultaneously accurate and computationally efficient parametrization of the potential
energy surface of molecules and materials is a long-standing goal in the natural sciences …

Uni-mol: A universal 3d molecular representation learning framework

G Zhou, Z Gao, Q Ding, H Zheng, H Xu, Z Wei, L Zhang… - 2023 - chemrxiv.org
Molecular representation learning (MRL) has gained tremendous attention due to its critical
role in learning from limited supervised data for applications like drug design. In most MRL …

Pre-training molecular graph representation with 3d geometry

S Liu, H Wang, W Liu, J Lasenby, H Guo… - arXiv preprint arXiv …, 2021 - arxiv.org
Molecular graph representation learning is a fundamental problem in modern drug and
material discovery. Molecular graphs are typically modeled by their 2D topological …

3d infomax improves gnns for molecular property prediction

H Stärk, D Beaini, G Corso, P Tossou… - International …, 2022 - proceedings.mlr.press
Molecular property prediction is one of the fastest-growing applications of deep learning with
critical real-world impacts. Although the 3D molecular graph structure is necessary for …

Equiformer: Equivariant graph attention transformer for 3d atomistic graphs

YL Liao, T Smidt - arXiv preprint arXiv:2206.11990, 2022 - arxiv.org
Despite their widespread success in various domains, Transformer networks have yet to
perform well across datasets in the domain of 3D atomistic graphs such as molecules even …

Protein representation learning by geometric structure pretraining

Z Zhang, M Xu, A Jamasb… - arXiv preprint arXiv …, 2022 - arxiv.org
Learning effective protein representations is critical in a variety of tasks in biology such as
predicting protein function or structure. Existing approaches usually pretrain protein …

The Open Catalyst 2022 (OC22) dataset and challenges for oxide electrocatalysts

R Tran, J Lan, M Shuaibi, BM Wood, S Goyal… - ACS …, 2023 - ACS Publications
The development of machine learning models for electrocatalysts requires a broad set of
training data to enable their use across a wide variety of materials. One class of materials …