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 …

Diffusion models in de novo drug design

A Alakhdar, B Poczos, N Washburn - Journal of Chemical …, 2024 - ACS Publications
Diffusion models have emerged as powerful tools for molecular generation, particularly in
the context of 3D molecular structures. Inspired by nonequilibrium statistical physics, these …

Generative diffusion models on graphs: Methods and applications

C Liu, W Fan, Y Liu, J Li, H Li, H Liu, J Tang… - arXiv preprint arXiv …, 2023 - arxiv.org
Diffusion models, as a novel generative paradigm, have achieved remarkable success in
various image generation tasks such as image inpainting, image-to-text translation, and …

Graphvf: Controllable protein-specific 3d molecule generation with variational flow

F Sun, Z Zhan, H Guo, M Zhang, J Tang - arXiv preprint arXiv:2304.12825, 2023 - arxiv.org
Designing molecules that bind to specific target proteins is a fundamental task in drug
discovery. Recent models leverage geometric constraints to generate ligand molecules that …

Equivariant 3D-Conditional Diffusion Model for De Novo Drug Design

J Zheng, HC Yi, ZH You - IEEE Journal of Biomedical and …, 2024 - ieeexplore.ieee.org
De novo drug design speeds up drug discovery, mitigating its time and cost burdens with
advanced computational methods. Previous work either insufficiently utilized the 3D …