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Equivariant Diffusion for Molecule Generation in 3D

31 March 2022

Emiel Hoogeboom

Victor Garcia Satorras

Papers citing "Equivariant Diffusion for Molecule Generation in 3D"

50 / 404 papers shown

Title
Generative Uncertainty in Diffusion Models Metod Jazbec Eliot Wong-Toi Guoxuan Xia Dan Zhang Eric T. Nalisnick Stephan Mandt DiffM 127 1 0 28 Feb 2025
Towards Hierarchical Rectified Flow Yichi Zhang Yici Yan Alex Schwing Zhizhen Zhao 121 2 0 24 Feb 2025
Value Gradient Sampler: Sampling as Sequential Decision Making Sangwoong Yoon Himchan Hwang Hyeokju Jeong Dong Kyu Shin Che-Sang Park Sehee Kwon Frank C. Park 139 0 0 18 Feb 2025
NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation Zhiyuan Liu Yanchen Luo Han Huang Enzhi Zhang Changhao Nai Sihang Li Yaorui Shi Xiang Wang Kenji Kawaguchi Tat-Seng Chua 190 4 0 18 Feb 2025
Survey on Recent Progress of AI for Chemistry: Methods, Applications, and Opportunities Ding Hu Pengxiang Hua Zhen Huang 250 0 0 09 Feb 2025
Generating 3D Binding Molecules Using Shape-Conditioned Diffusion Models with Guidance Ziqi Chen Bo Peng Tianhua Zhai Daniel Adu-Ampratwum Xia Ning 143 1 0 09 Feb 2025
Training-Free Constrained Generation With Stable Diffusion Models Stefano Zampini Jacob K Christopher Luca Oneto Davide Anguita Ferdinando Fioretto 101 2 0 08 Feb 2025
SymmCD: Symmetry-Preserving Crystal Generation with Diffusion Models Daniel Levy Siba Smarak Panigrahi Sékou-Oumar Kaba Qiang Zhu Kin Long Kelvin Lee Mikhail Galkin Santiago Miret Siamak Ravanbakhsh 555 15 0 05 Feb 2025
A Periodic Bayesian Flow for Material Generation Hanlin Wu Yuxuan Song Jingjing Gong Ziyao Cao Y. Ouyang Jianbing Zhang Hao Zhou Wei-Ying Ma Jingjing Liu DiffM 149 3 0 04 Feb 2025
Score-based 3D molecule generation with neural fields Matthieu Kirchmeyer Pedro H. O. Pinheiro Saeed Saremi DiffM 121 2 0 15 Jan 2025
Unified Guidance for Geometry-Conditioned Molecular Generation Sirine Ayadi Leon Hetzel Johanna Sommer Fabian J. Theis Stephan Günnemann 100 1 0 05 Jan 2025
Text2Data: Low-Resource Data Generation with Textual Control Shiyu Wang Yihao Feng Tian Lan Ning Yu Yu Bai Ran Xu Han Wang Caiming Xiong Siyang Song DiffM 152 0 0 03 Jan 2025
S-Diff: An Anisotropic Diffusion Model for Collaborative Filtering in Spectral Domain Rui Xia Yanhua Cheng Yongxiang Tang Xiaocheng Liu Xialong Liu Lisong Wang Peng Jiang DiffM 104 1 0 03 Jan 2025
Rethinking Addressing in Language Models via Contexualized Equivariant Positional Encoding Jiajun Zhu Peihao Wang Ruisi Cai Jason D. Lee Pan Li Ziyi Wang KELM 112 1 0 03 Jan 2025
TrojFlow: Flow Models are Natural Targets for Trojan Attacks Zhengyang Qi Xiaohua Xu AAML 148 0 0 21 Dec 2024
EquiFlow: Equivariant Conditional Flow Matching with Optimal Transport for 3D Molecular Conformation Prediction Qingwen Tian Yuxin Xu Yixuan Yang Zhen Wang Ziqi Liu Pengju Yan Xiaolin Li 116 1 0 15 Dec 2024
ArtFormer: Controllable Generation of Diverse 3D Articulated Objects Jiayi Su Youhe Feng Zheng Li Jinhua Song Yangfan He Botao Ren Botian Xu AI4CE 156 3 0 10 Dec 2024
Efficient Diversity-Preserving Diffusion Alignment via Gradient-Informed GFlowNets Zhen Liu Tim Z. Xiao Weiyang Liu Yoshua Bengio Dinghuai Zhang 252 6 0 10 Dec 2024
LMDM:Latent Molecular Diffusion Model For 3D Molecule Generation Xiang Chen DiffM 116 0 0 05 Dec 2024
Generative modeling assisted simulation of measurement-altered quantum criticality Yuchen Zhu Molei Tao Yuebo Jin Xie Chen 103 1 0 02 Dec 2024
Hierarchical VAE with a Diffusion-based VampPrior Anna Kuzina Jakub M. Tomczak DiffM TPM BDL 119 3 0 02 Dec 2024
Rectified Flow For Structure Based Drug Design Daiheng Zhang Chengyue Gong Qiang Liu DiffM 115 0 0 02 Dec 2024
Schedule On the Fly: Diffusion Time Prediction for Faster and Better Image Generation Zilyu Ye Zhiyang Chen Tiancheng Li Zemin Huang Weijian Luo Guo-Jun Qi DiffM 132 6 0 02 Dec 2024
Vertical Validation: Evaluating Implicit Generative Models for Graphs on Thin Support Regions Mai Elkady Thu Bui Bruno Ribeiro David I. Inouye 110 0 0 20 Nov 2024
Stealing Training Graphs from Graph Neural Networks Minhua Lin Enyan Dai Junjie Xu Jinyuan Jia Xiang Zhang Suhang Wang DiffM 93 2 0 17 Nov 2024
Enhancing Diffusion Posterior Sampling for Inverse Problems by Integrating Crafted Measurements Shijie Zhou Huaisheng Zhu Rohan Sharma Ruiyi Zhang Kaiyi Ji Kaiyi Ji Changyou Chen 69 0 0 15 Nov 2024
Pathway-Guided Optimization of Deep Generative Molecular Design Models for Cancer Therapy Alif Bin Abdul Qayyum S. Mertins Amanda K. Paulson Nathan M. Urban Byung-Jun Yoon 69 0 0 05 Nov 2024
Conditional Synthesis of 3D Molecules with Time Correction Sampler Hojung Jung Youngrok Park Laura Schmid Jaehyeong Jo Dongkyu Lee Bongsang Kim Se-Young Yun Jinwoo Shin DiffM 101 4 0 01 Nov 2024
Bridging Geometric States via Geometric Diffusion Bridge Shengjie Luo Yixian Xu Di He Shuxin Zheng Tie-Yan Liu Liwei Wang 66 0 0 31 Oct 2024
Diffusion Twigs with Loop Guidance for Conditional Graph Generation Giangiacomo Mercatali Yogesh Verma André Freitas Vikas Garg 92 4 0 31 Oct 2024
Learning Infinitesimal Generators of Continuous Symmetries from Data Gyeonghoon Ko Hyunsu Kim Juho Lee 73 5 0 29 Oct 2024
TurboHopp: Accelerated Molecule Scaffold Hopping with Consistency Models Kiwoong Yoo Owen Oertell Junhyun Lee Sanghoon Lee Jaewoo Kang 73 0 0 28 Oct 2024
Equivariant Blurring Diffusion for Hierarchical Molecular Conformer Generation Jiwoong Park Yang Shen DiffM 98 0 0 26 Oct 2024
Flow Generator Matching Zemin Huang Zhengyang Geng Weijian Luo Guo-Jun Qi 123 11 0 25 Oct 2024
Diff-Instruct++: Training One-step Text-to-image Generator Model to Align with Human Preferences Weijian Luo EGVM 112 9 0 24 Oct 2024
Bio2Token: All-atom tokenization of any biomolecular structure with Mamba Andrew Liu Axel Elaldi Nathan Russell Olivia Viessmann Mamba 132 3 0 24 Oct 2024
Training Free Guided Flow Matching with Optimal Control Luran Wang Chaoran Cheng Yizhen Liao Yanru Qu Ge Liu 116 4 0 23 Oct 2024
One-Step Diffusion Distillation through Score Implicit Matching Weijian Luo Zemin Huang Zhengyang Geng J. Zico Kolter Guo-Jun Qi DiffM 92 21 0 22 Oct 2024
Warped Diffusion: Solving Video Inverse Problems with Image Diffusion Models Giannis Daras Weili Nie Karsten Kreis A. Dimakis Morteza Mardani Nikola B. Kovachki Arash Vahdat DiffM 113 10 0 21 Oct 2024
Predicting time-varying flux and balance in metabolic systems using structured neural-ODE processes Santanu Rathod Pietro Lio Xiao Zhang 19 0 0 18 Oct 2024
Measuring Diversity: Axioms and Challenges Mikhail Mironov Liudmila Prokhorenkova 68 1 0 18 Oct 2024
Beyond Autoregression: Discrete Diffusion for Complex Reasoning and Planning Jiacheng Ye Jiahui Gao Shansan Gong Lin Zheng Xin Jiang Zhiyu Li Dianbo Sui DiffM LRM 180 25 0 18 Oct 2024
The Latent Road to Atoms: Backmapping Coarse-grained Protein Structures with Latent Diffusion Xu Han Yuancheng Sun Kai Chen Kang Liu Qiwei Ye DiffM AI4CE 85 1 0 17 Oct 2024
Text-Guided Multi-Property Molecular Optimization with a Diffusion Language Model Yida Xiong Kun Li Jiameng Chen Hongzhi Zhang Di Lin Shirui Pan Wenbin Hu 112 3 0 17 Oct 2024
Geometric Trajectory Diffusion Models Jiaqi Han Minkai Xu Aaron Lou Haotian Ye Stefano Ermon DiffM 112 5 0 16 Oct 2024
Training Neural Samplers with Reverse Diffusive KL Divergence Wenlin Chen Jiajun He Mingtian Zhang David Barber José Miguel Hernández-Lobato DiffM 132 8 0 16 Oct 2024
Are High-Degree Representations Really Unnecessary in Equivariant Graph Neural Networks? Jiacheng Cen Anyi Li Ning Lin Yuxiang Ren Zihe Wang Wenbing Huang 112 5 0 15 Oct 2024
MF-LAL: Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning Peter Eckmann D. Wu G. Heinzelmann Michael K. Gilson Rose Yu AI4CE 122 0 0 15 Oct 2024
Physical Consistency Bridges Heterogeneous Data in Molecular Multi-Task Learning Yuxuan Ren Dihan Zheng Chang-Shu Liu Peiran Jin Yu Shi Lin Huang Jiyan He Shengjie Luo Tao Qin Tie-Yan Liu AI4CE 101 2 0 14 Oct 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 116 7 0 14 Oct 2024