A systematic survey in geometric deep learning for structure-based drug design

Z Zhang, J Yan, Q Liu, E Chen, M Zitnik - arXiv preprint arXiv:2306.11768, 2023 - arxiv.org
Structure-based drug design (SBDD) utilizes the three-dimensional geometry of proteins to
identify potential drug candidates. Traditional methods, grounded in physicochemical …

Does invariant graph learning via environment augmentation learn invariance?

Y Chen, Y Bian, K Zhou, B Xie… - Advances in Neural …, 2024 - proceedings.neurips.cc
Invariant graph representation learning aims to learn the invariance among data from
different environments for out-of-distribution generalization on graphs. As the graph …

Delocalized, asynchronous, closed-loop discovery of organic laser emitters

F Strieth-Kalthoff, H Hao, V Rathore, J Derasp… - Science, 2024 - science.org
Contemporary materials discovery requires intricate sequences of synthesis, formulation,
and characterization that often span multiple locations with specialized expertise or …

A Hitchhiker's Guide to Geometric GNNs for 3D Atomic Systems

A Duval, SV Mathis, CK Joshi, V Schmidt… - arXiv preprint arXiv …, 2023 - arxiv.org
Recent advances in computational modelling of atomic systems, spanning molecules,
proteins, and materials, represent them as geometric graphs with atoms embedded as …

Mixtures Recomposition by Neural Nets: A Multidisciplinary Overview

A Nicolle, S Deng, M Ihme… - Journal of Chemical …, 2024 - ACS Publications
Artificial Neural Networks (ANNs) are transforming how we understand chemical mixtures,
providing an expressive view of the chemical space and multiscale processes. Their …

A new perspective on building efficient and expressive 3D equivariant graph neural networks

Y Du, L Wang, D Feng, G Wang, S Ji… - Advances in …, 2024 - proceedings.neurips.cc
Geometric deep learning enables the encoding of physical symmetries in modeling 3D
objects. Despite rapid progress in encoding 3D symmetries into Graph Neural Networks …

Uncovering neural scaling laws in molecular representation learning

D Chen, Y Zhu, J Zhang, Y Du, Z Li… - Advances in …, 2024 - proceedings.neurips.cc
Abstract Molecular Representation Learning (MRL) has emerged as a powerful tool for drug
and materials discovery in a variety of tasks such as virtual screening and inverse design …

Defining a new NLP playground

S Li, C Han, P Yu, C Edwards, M Li, X Wang… - arXiv preprint arXiv …, 2023 - arxiv.org
The recent explosion of performance of large language models (LLMs) has changed the
field of Natural Language Processing (NLP) more abruptly and seismically than any other …

[HTML][HTML] JARVIS-Leaderboard: a large scale benchmark of materials design methods

K Choudhary, D Wines, K Li, KF Garrity… - npj Computational …, 2024 - nature.com
Lack of rigorous reproducibility and validation are significant hurdles for scientific
development across many fields. Materials science, in particular, encompasses a variety of …

Advective diffusion transformers for topological generalization in graph learning

Q Wu, C Yang, K Zeng, F Nie, M Bronstein… - arXiv preprint arXiv …, 2023 - arxiv.org
Graph diffusion equations are intimately related to graph neural networks (GNNs) and have
recently attracted attention as a principled framework for analyzing GNN dynamics …