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 …

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 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 …

Machine learning in preclinical drug discovery

DB Catacutan, J Alexander, A Arnold… - Nature Chemical …, 2024 - nature.com
Drug-discovery and drug-development endeavors are laborious, costly and time consuming.
These programs can take upward of 12 years and cost US $2.5 billion, with a failure rate of …

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 …

Graph neural networks: foundation, frontiers and applications

L Wu, P Cui, J Pei, L Zhao, X Guo - … of the 28th ACM SIGKDD Conference …, 2022 - dl.acm.org
The field of graph neural networks (GNNs) has seen rapid and incredible strides over the
recent years. Graph neural networks, also known as deep learning on graphs, graph …

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 …

Generative models for molecular discovery: Recent advances and challenges

C Bilodeau, W **, T Jaakkola… - Wiley …, 2022 - Wiley Online Library
Abstract Development of new products often relies on the discovery of novel molecules.
While conventional molecular design involves using human expertise to propose …

Self-supervised learning of graph neural networks: A unified review

Y **e, Z Xu, J Zhang, Z Wang… - IEEE transactions on …, 2022 - ieeexplore.ieee.org
Deep models trained in supervised mode have achieved remarkable success on a variety of
tasks. When labeled samples are limited, self-supervised learning (SSL) is emerging as a …

Self-supervised learning: Generative or contrastive

X Liu, F Zhang, Z Hou, L Mian, Z Wang… - IEEE transactions on …, 2021 - ieeexplore.ieee.org
Deep supervised learning has achieved great success in the last decade. However, its
defects of heavy dependence on manual labels and vulnerability to attacks have driven …