Beyond deep reinforcement learning: A tutorial on generative diffusion models in network optimization

H Du, R Zhang, Y Liu, J Wang, Y Lin, Z Li… - arXiv preprint arXiv …, 2023 - arxiv.org
Generative Diffusion Models (GDMs) have emerged as a transformative force in the realm of
Generative Artificial Intelligence (GAI), demonstrating their versatility and efficacy across a …

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 …

Midi: Mixed graph and 3d denoising diffusion for molecule generation

C Vignac, N Osman, L Toni, P Frossard - Joint European Conference on …, 2023 - Springer
This work introduces MiDi, a novel diffusion model for jointly generating molecular graphs
and their corresponding 3D atom arrangements. Unlike existing methods that rely on …

Mudiff: Unified diffusion for complete molecule generation

C Hua, S Luan, M Xu, Z Ying, J Fu… - Learning on Graphs …, 2024 - proceedings.mlr.press
Molecule generation is a very important practical problem, with uses in drug discovery and
material design, and AI methods promise to provide useful solutions. However, existing …

On the design fundamentals of diffusion models: A survey

Z Chang, GA Koulieris, HPH Shum - arXiv preprint arXiv:2306.04542, 2023 - arxiv.org
Diffusion models are generative models, which gradually add and remove noise to learn the
underlying distribution of training data for data generation. The components of diffusion …

Generative flows on discrete state-spaces: Enabling multimodal flows with applications to protein co-design

A Campbell, J Yim, R Barzilay, T Rainforth… - arXiv preprint arXiv …, 2024 - arxiv.org
Combining discrete and continuous data is an important capability for generative models.
We present Discrete Flow Models (DFMs), a new flow-based model of discrete data that …

ScaffoldGVAE: scaffold generation and hopping of drug molecules via a variational autoencoder based on multi-view graph neural networks

C Hu, S Li, C Yang, J Chen, Y Xiong, G Fan… - Journal of …, 2023 - Springer
In recent years, drug design has been revolutionized by the application of deep learning
techniques, and molecule generation is a crucial aspect of this transformation. However …

An equivariant generative framework for molecular graph-structure co-design

Z Zhang, Q Liu, CK Lee, CY Hsieh, E Chen - Chemical Science, 2023 - pubs.rsc.org
Designing molecules with desirable physiochemical properties and functionalities is a long-
standing challenge in chemistry, material science, and drug discovery. Recently, machine …

Enhancing Deep Reinforcement Learning: A Tutorial on Generative Diffusion Models in Network Optimization

H Du, R Zhang, Y Liu, J Wang, Y Lin… - … Surveys & Tutorials, 2024 - ieeexplore.ieee.org
Generative Diffusion Models (GDMs) have emerged as a transformative force in the realm of
Generative Artificial Intelligence (GenAI), demonstrating their versatility and efficacy across …

KGDiff: towards explainable target-aware molecule generation with knowledge guidance

H Qian, W Huang, S Tu, L Xu - Briefings in Bioinformatics, 2024 - academic.oup.com
Designing 3D molecules with high binding affinity for specific protein targets is crucial in
drug design. One challenge is that the atomic interaction between molecules and proteins in …