MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation

17 February 2023

Papers citing "MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation"

49 / 49 papers shown

Title
Pharmacophore-Conditioned Diffusion Model for Ligand-Based De Novo Drug Design Amira Alakhdar Barnabás Póczos Newell Washburn 19 0 0 15 May 2025
GEOM-Drugs Revisited: Toward More Chemically Accurate Benchmarks for 3D Molecule Generation Filipp Nikitin Ian Dunn D. Koes Olexandr Isayev 118 0 0 30 Apr 2025
Clifford Group Equivariant Diffusion Models for 3D Molecular Generation Cong Liu Sharvaree P. Vadgama David Ruhe Erik J Bekkers Patrick Forré DiffM 22 0 0 22 Apr 2025
FLOWR: Flow Matching for Structure-Aware De Novo, Interaction- and Fragment-Based Ligand Generation Julian Cremer Ross Irwin Alessandro Tibot J. Janet Simon Olsson Djork-Arné Clevert 35 0 0 14 Apr 2025
Towards Unified Latent Space for 3D Molecular Latent Diffusion Modeling Yanchen Luo Zhiyuan Liu Yi Zhao Sihang Li Kenji Kawaguchi Tat-Seng Chua X. Wang MedIm 64 0 0 19 Mar 2025
A Reinforcement Learning-Driven Transformer GAN for Molecular Generation Chen Li Huidong Tang Ye Zhu Yoshihiro Yamanishi AI4CE 41 0 0 17 Mar 2025
Straight-Line Diffusion Model for Efficient 3D Molecular Generation Yuyan Ni Shikun Feng Haohan Chi Bowen Zheng Huan-ang Gao Wei-Ying Ma Zhi-Ming Ma Yanyan Lan DiffM 71 2 0 04 Mar 2025
NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation Zhiyuan Liu Yanchen Luo Han Huang Enzhi Zhang Sihang Li Junfeng Fang Yaorui Shi X. Wang Kenji Kawaguchi Tat-Seng Chua 100 3 0 18 Feb 2025
Score-based 3D molecule generation with neural fields Matthieu Kirchmeyer Pedro H. O. Pinheiro Saeed Saremi DiffM 45 0 0 15 Jan 2025
Unified Guidance for Geometry-Conditioned Molecular Generation Sirine Ayadi Leon Hetzel Johanna Sommer Fabian J. Theis Stephan Günnemann 30 0 0 05 Jan 2025
Exploring Discrete Flow Matching for 3D De Novo Molecule Generation Ian Dunn D. Koes 92 4 0 25 Nov 2024
LayerDAG: A Layerwise Autoregressive Diffusion Model for Directed Acyclic Graph Generation Mufei Li Viraj Shitole Eli Chien Changhai Man Zhaodong Wang Srinivas Sridharan Ying Zhang Tushar Krishna P. Li 37 0 0 04 Nov 2024
UniGEM: A Unified Approach to Generation and Property Prediction for Molecules Shikun Feng Yuyan Ni Yan Lu Zhi-Ming Ma Wei-Ying Ma Yanyan Lan 38 5 0 14 Oct 2024
Geometric Representation Condition Improves Equivariant Molecule Generation Zian Li Cai Zhou Xiyuan Wang Xingang Peng Muhan Zhang 45 1 0 04 Oct 2024
Geometry Informed Tokenization of Molecules for Language Model Generation Xiner Li Limei Wang Youzhi Luo Carl N. Edwards Shurui Gui Yuchao Lin Heng Ji Shuiwang Ji 29 6 0 19 Aug 2024
3D Vessel Graph Generation Using Denoising Diffusion Chinmay Prabhakar Suprosanna Shit Fabio Musio Kaiyuan Yang Tamaz Amiranashvili Johannes C. Paetzold Hongwei Bran Li Bjoern H. Menze DiffM MedIm 52 2 0 08 Jul 2024
NEBULA: Neural Empirical Bayes Under Latent Representations for Efficient and Controllable Design of Molecular Libraries E. Nowara Pedro H. O. Pinheiro Sai Pooja Mahajan Omar Mahmood Andrew Watkins Saeed Saremi Michael R. Maser BDL DiffM 40 2 0 03 Jul 2024
Generative Modelling of Structurally Constrained Graphs Manuel Madeira Clément Vignac D. Thanou Pascal Frossard DiffM 51 0 0 25 Jun 2024
Cometh: A continuous-time discrete-state graph diffusion model Antoine Siraudin Fragkiskos D. Malliaros Christopher Morris 31 3 0 10 Jun 2024
Response Matching for generating materials and molecules Bingqing Cheng DiffM 27 1 0 15 May 2024
Structure-based drug design by denoising voxel grids Pedro H. O. Pinheiro Arian R. Jamasb Omar Mahmood Vishnu Sresht Saeed Saremi DiffM 34 8 0 07 May 2024
Mixed Continuous and Categorical Flow Matching for 3D De Novo Molecule Generation Ian Dunn D. Koes BDL DiffM 44 11 0 30 Apr 2024
ControlMol: Adding Substruture Control To Molecule Diffusion Models Zhengyang Qi Zijing Liu Jiying Zhang He Cao Yu Li 40 2 0 22 Apr 2024
Zero Shot Molecular Generation via Similarity Kernels Rokas Elijosius Fabian Zills Ilyes Batatia Sam Walton Norwood D. P. Kovács Christian Holm Gábor Csányi DiffM 41 3 0 13 Feb 2024
A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generation Xiangru Tang Howard Dai Elizabeth Knight Fang Wu Yunyang Li Tianxiao Li Mark B. Gerstein 19 25 0 13 Feb 2024
Diffusion-based Graph Generative Methods Hongyang Chen Can Xu Lingyu Zheng Qiang Zhang Xuemin Lin DiffM MedIm 26 0 0 28 Jan 2024
Geometric-Facilitated Denoising Diffusion Model for 3D Molecule Generation Can Xu Haosen Wang Weigang Wang Pengfei Zheng Hongyang Chen DiffM 41 7 0 05 Jan 2024
Efficient and Scalable Graph Generation through Iterative Local Expansion Andreas Bergmeister Karolis Martinkus Nathanael Perraudin Roger Wattenhofer 21 12 0 14 Dec 2023
STRIDE: Structure-guided Generation for Inverse Design of Molecules Shehtab Zaman D. Akhiyarov Mauricio Araya-Polo Kenneth Chiu 21 1 0 06 Nov 2023
Sparse Training of Discrete Diffusion Models for Graph Generation Yiming Qin Clément Vignac Pascal Frossard 19 12 0 03 Nov 2023
Reflection-Equivariant Diffusion for 3D Structure Determination from Isotopologue Rotational Spectra in Natural Abundance Austin H. Cheng Alston Lo Santiago Miret Brooks H Pate Alán Aspuru-Guzik 26 6 0 17 Oct 2023
Harmonic Self-Conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design Hannes Stärk Bowen Jing Regina Barzilay Tommi Jaakkola 31 25 0 09 Oct 2023
Fast, Expressive SE $(n)$ Equivariant Networks through Weight-Sharing in Position-Orientation Space Erik J. Bekkers Sharvaree P. Vadgama Rob D. Hesselink P. A. V. D. Linden David W. Romero 13 24 0 04 Oct 2023
Navigating the Design Space of Equivariant Diffusion-Based Generative Models for De Novo 3D Molecule Generation Tuan Le Julian Cremer Frank Noé Djork-Arné Clevert Kristof T. Schütt DiffM 27 25 0 29 Sep 2023
3D molecule generation by denoising voxel grids Pedro H. O. Pinheiro Joshua Rackers J. Kleinhenz Michael R. Maser Omar Mahmood Andrew Watkins Stephen Ra Vishnu Sresht Saeed Saremi DiffM 34 20 0 13 Jun 2023
MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generation Xingang Peng Jiaqi Guan Qiang Liu Jianzhu Ma DiffM 33 43 0 11 May 2023
MUDiff: Unified Diffusion for Complete Molecule Generation Chenqing Hua Sitao Luan Minkai Xu Rex Ying Jie Fu Stefano Ermon Doina Precup DiffM 47 34 0 28 Apr 2023
SILVR: Guided Diffusion for Molecule Generation Nicholas T. Runcie A. Mey 19 16 0 21 Apr 2023
An Equivariant Generative Framework for Molecular Graph-Structure Co-Design Zaixin Zhang Qi Liu Cheekong Lee Chang-Yu Hsieh Enhong Chen 15 18 0 12 Apr 2023
Geometry-Complete Diffusion for 3D Molecule Generation and Optimization Alex Morehead Jianlin Cheng DiffM 14 22 0 08 Feb 2023
DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking Gabriele Corso Hannes Stärk Bowen Jing Regina Barzilay Tommi Jaakkola DiffM 139 409 0 04 Oct 2022
Diffusion Models for Graphs Benefit From Discrete State Spaces K. Haefeli Karolis Martinkus Nathanael Perraudin Roger Wattenhofer DiffM 85 52 0 04 Oct 2022
Equivariant Energy-Guided SDE for Inverse Molecular Design Fan Bao Min Zhao Zhongkai Hao Pei‐Yun Li Chongxuan Li Jun Zhu DiffM 187 63 0 30 Sep 2022
Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs Yi-Lun Liao Tess E. Smidt 80 213 0 23 Jun 2022
Pre-training Molecular Graph Representation with 3D Geometry Shengchao Liu Hanchen Wang Weiyang Liu Joan Lasenby Hongyu Guo Jian Tang 117 302 0 07 Oct 2021
Top-N: Equivariant set and graph generation without exchangeability Clément Vignac P. Frossard BDL 63 34 0 05 Oct 2021
Argmax Flows and Multinomial Diffusion: Learning Categorical Distributions Emiel Hoogeboom Didrik Nielsen P. Jaini Patrick Forré Max Welling DiffM 207 394 0 10 Feb 2021
MoleculeNet: A Benchmark for Molecular Machine Learning Zhenqin Wu Bharath Ramsundar Evan N. Feinberg Joseph Gomes C. Geniesse Aneesh S. Pappu K. Leswing Vijay S. Pande OOD 169 1,775 0 02 Mar 2017
Spatial Transformer Networks Max Jaderberg Karen Simonyan Andrew Zisserman Koray Kavukcuoglu 144 7,335 0 05 Jun 2015