Generative models as an emerging paradigm in the chemical sciences

DM Anstine, O Isayev - Journal of the American Chemical Society, 2023 - ACS Publications
Traditional computational approaches to design chemical species are limited by the need to
compute properties for a vast number of candidates, eg, by discriminative modeling …

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 …

Geometric latent diffusion models for 3d molecule generation

M Xu, AS Powers, RO Dror, S Ermon… - International …, 2023 - proceedings.mlr.press
Generative models, especially diffusion models (DMs), have achieved promising results for
generating feature-rich geometries and advancing foundational science problems such as …

Geodiff: A geometric diffusion model for molecular conformation generation

M Xu, L Yu, Y Song, C Shi, S Ermon, J Tang - arxiv preprint arxiv …, 2022 - arxiv.org
Predicting molecular conformations from molecular graphs is a fundamental problem in
cheminformatics and drug discovery. Recently, significant progress has been achieved with …

Equivariant 3D-conditional diffusion model for molecular linker design

I Igashov, H Stärk, C Vignac, A Schneuing… - Nature Machine …, 2024 - nature.com
Fragment-based drug discovery has been an effective paradigm in early-stage drug
development. An open challenge in this area is designing linkers between disconnected …

Equivariant flow matching

L Klein, A Krämer, F Noé - Advances in Neural Information …, 2023 - proceedings.neurips.cc
Normalizing flows are a class of deep generative models that are especially interesting for
modeling probability distributions in physics, where the exact likelihood of flows allows …

Periodic graph transformers for crystal material property prediction

K Yan, Y Liu, Y Lin, S Ji - Advances in Neural Information …, 2022 - proceedings.neurips.cc
We consider representation learning on periodic graphs encoding crystal materials. Different
from regular graphs, periodic graphs consist of a minimum unit cell repeating itself on a …

Diffusion-based molecule generation with informative prior bridges

L Wu, C Gong, X Liu, M Ye… - Advances in Neural …, 2022 - proceedings.neurips.cc
AI-based molecule generation provides a promising approach to a large area of biomedical
sciences and engineering, such as antibody design, hydrolase engineering, or vaccine …

Inverse design of 3d molecular structures with conditional generative neural networks

NWA Gebauer, M Gastegger, SSP Hessmann… - Nature …, 2022 - nature.com
The rational design of molecules with desired properties is a long-standing challenge in
chemistry. Generative neural networks have emerged as a powerful approach to sample …

Crystal diffusion variational autoencoder for periodic material generation

T **e, X Fu, OE Ganea, R Barzilay… - arxiv preprint arxiv …, 2021 - arxiv.org
Generating the periodic structure of stable materials is a long-standing challenge for the
material design community. This task is difficult because stable materials only exist in a low …