Diffusion models: A comprehensive survey of methods and applications

L Yang, Z Zhang, Y Song, S Hong, R Xu, Y Zhao… - ACM Computing …, 2023 - dl.acm.org
Diffusion models have emerged as a powerful new family of deep generative models with
record-breaking performance in many applications, including image synthesis, video …

Geometric deep learning for drug discovery

M Liu, C Li, R Chen, D Cao, X Zeng - Expert Systems with Applications, 2023 - Elsevier
Drug discovery is a time-consuming and expensive process. With the development of
Artificial Intelligence (AI) techniques, molecular Geometric Deep Learning (GDL) has …

Two for one: Diffusion models and force fields for coarse-grained molecular dynamics

M Arts, V Garcia Satorras, CW Huang… - Journal of Chemical …, 2023 - ACS Publications
Coarse-grained (CG) molecular dynamics enables the study of biological processes at
temporal and spatial scales that would be intractable at an atomistic resolution. However …

One transformer can understand both 2d & 3d molecular data

S Luo, T Chen, Y Xu, S Zheng, TY Liu… - The Eleventh …, 2022 - openreview.net
Unlike vision and language data which usually has a unique format, molecules can naturally
be characterized using different chemical formulations. One can view a molecule as a 2D …

[HTML][HTML] Evaluation of the MACE force field architecture: From medicinal chemistry to materials science

DP Kovács, I Batatia, ES Arany… - The Journal of Chemical …, 2023 - pubs.aip.org
The MACE architecture represents the state of the art in the field of machine learning force
fields for a variety of in-domain, extrapolation, and low-data regime tasks. In this paper, we …

Artificial intelligence for science in quantum, atomistic, and continuum systems

X Zhang, L Wang, J Helwig, Y Luo, C Fu, Y Xie… - arXiv preprint arXiv …, 2023 - arxiv.org
Advances in artificial intelligence (AI) are fueling a new paradigm of discoveries in natural
sciences. Today, AI has started to advance natural sciences by improving, accelerating, and …

Equiformerv2: Improved equivariant transformer for scaling to higher-degree representations

YL Liao, B Wood, A Das, T Smidt - arXiv preprint arXiv:2306.12059, 2023 - arxiv.org
Equivariant Transformers such as Equiformer have demonstrated the efficacy of applying
Transformers to the domain of 3D atomistic systems. However, they are still limited to small …

Molecular geometry pretraining with se (3)-invariant denoising distance matching

S Liu, H Guo, J Tang - arXiv preprint arXiv:2206.13602, 2022 - arxiv.org
Molecular representation pretraining is critical in various applications for drug and material
discovery due to the limited number of labeled molecules, and most existing work focuses …

A group symmetric stochastic differential equation model for molecule multi-modal pretraining

S Liu, W Du, ZM Ma, H Guo… - … Conference on Machine …, 2023 - proceedings.mlr.press
Molecule pretraining has quickly become the go-to schema to boost the performance of AI-
based drug discovery. Naturally, molecules can be represented as 2D topological graphs or …

Symmetry-informed geometric representation for molecules, proteins, and crystalline materials

S Liu, Y Li, Z Li, Z Zheng, C Duan… - Advances in neural …, 2024 - proceedings.neurips.cc
Artificial intelligence for scientific discovery has recently generated significant interest within
the machine learning and scientific communities, particularly in the domains of chemistry …