Protein Structure and Sequence Generation with Equivariant Denoising Diffusion Probabilistic Models

26 May 2022

Papers citing "Protein Structure and Sequence Generation with Equivariant Denoising Diffusion Probabilistic Models"

50 / 81 papers shown

Title
Uni-3DAR: Unified 3D Generation and Understanding via Autoregression on Compressed Spatial Tokens Shuqi Lu Haowei Lin Lin Yao Zhifeng Gao Xiaohong Ji W. Elwasif Linfeng Zhang Guolin Ke 48 0 0 20 Mar 2025
Towards More Accurate Personalized Image Generation: Addressing Overfitting and Evaluation Bias Mingxiao Li Tingyu Qu Tinne Tuytelaars Marie-Francine Moens EGVM 46 0 0 09 Mar 2025
Symmetry-Preserving Diffusion Models via Target Symmetrization Vinh Tong Yun Ye Trung-Dung Hoang Anji Liu Guy Van den Broeck Mathias Niepert DiffM 82 0 0 17 Feb 2025
Training-Free Constrained Generation With Stable Diffusion Models Stefano Zampini Jacob K Christopher Luca Oneto Davide Anguita Ferdinando Fioretto 46 0 0 08 Feb 2025
Unified Guidance for Geometry-Conditioned Molecular Generation Sirine Ayadi Leon Hetzel Johanna Sommer Fabian J. Theis Stephan Günnemann 34 0 0 05 Jan 2025
Efficient Antibody Structure Refinement Using Energy-Guided SE(3) Flow Matching Jiying Zhang Zijing Liu Shengyuan Bai He Cao Yu Li Lei Zhang DiffM 37 1 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 35 5 0 21 Oct 2024
Latent Diffusion Models for Controllable RNA Sequence Generation Kaixuan Huang Yukang Yang Kaidi Fu Yanyi Chu Le Cong Mengdi Wang 47 1 0 15 Sep 2024
Evaluating the design space of diffusion-based generative models Yuqing Wang Ye He Molei Tao DiffM 36 5 0 18 Jun 2024
Solving Inverse Problems in Protein Space Using Diffusion-Based Priors A. Levy E. R. Chan Sara Fridovich-Keil Frédéric Poitevin Ellen D. Zhong Gordon Wetzstein DiffM 75 3 0 06 Jun 2024
Full-Atom Peptide Design based on Multi-modal Flow Matching Jiahan Li Chaoran Cheng Zuofan Wu Ruihan Guo Shitong Luo Zhizhou Ren Jian-wei Peng Jianzhu Ma 45 15 0 02 Jun 2024
Robust Optimization in Protein Fitness Landscapes Using Reinforcement Learning in Latent Space Minji Lee L. Vecchietti Hyunkyu Jung Hyun Joo Ro Meeyoung Cha Ho Min Kim 32 5 0 29 May 2024
Out of Many, One: Designing and Scaffolding Proteins at the Scale of the Structural Universe with Genie 2 Yeqing Lin Minji Lee Zhao Zhang Mohammed AlQuraishi DiffM 38 17 0 24 May 2024
Lazy Layers to Make Fine-Tuned Diffusion Models More Traceable Haozhe Liu Wentian Zhang Bing Li Bernard Ghanem Jürgen Schmidhuber DiffM WIGM AAML 33 1 0 01 May 2024
An Overview of Diffusion Models: Applications, Guided Generation, Statistical Rates and Optimization Minshuo Chen Song Mei Jianqing Fan Mengdi Wang VLM MedIm DiffM 37 48 0 11 Apr 2024
Protein Conformation Generation via Force-Guided SE(3) Diffusion Models Yan Wang Lihao Wang Yuning Shen Yiqun Wang Huizhuo Yuan Yue Wu Quanquan Gu DiffM 29 25 0 21 Mar 2024
Unified Generative Modeling of 3D Molecules via Bayesian Flow Networks Yuxuan Song Jingjing Gong Yanru Qu Hao Zhou Mingyue Zheng Jingjing Liu Wei-Ying Ma 35 10 0 17 Mar 2024
On Diffusion Process in SE(3)-invariant Space Zihan Zhou Ruiying Liu Jiachen Zheng Xiaoxue Wang Tianshu Yu DiffM 34 1 0 03 Mar 2024
Retrieval-Augmented Generation for AI-Generated Content: A Survey Penghao Zhao Hailin Zhang Qinhan Yu Zhengren Wang Yunteng Geng Fangcheng Fu Ling Yang Wentao Zhang Jie Jiang Bin Cui 3DV 115 228 0 29 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 24 25 0 13 Feb 2024
Constrained Synthesis with Projected Diffusion Models Jacob K Christopher Stephen Baek Ferdinando Fioretto DiffM 49 10 0 05 Feb 2024
Diffusion-based Graph Generative Methods Hongyang Chen Can Xu Lingyu Zheng Qiang Zhang Xuemin Lin DiffM MedIm 29 0 0 28 Jan 2024
ProtAgents: Protein discovery via large language model multi-agent collaborations combining physics and machine learning Alireza Ghafarollahi Markus J. Buehler LLMAG AI4CE 15 23 0 27 Jan 2024
Fixed Point Diffusion Models Xingjian Bai Luke Melas-Kyriazi 18 3 0 16 Jan 2024
Towards Joint Sequence-Structure Generation of Nucleic Acid and Protein Complexes with SE(3)-Discrete Diffusion Alex Morehead Jeffrey A. Ruffolo Aadyot Bhatnagar Ali Madani DiffM 24 9 0 21 Dec 2023
Time Series Diffusion Method: A Denoising Diffusion Probabilistic Model for Vibration Signal Generation H. Yi Lei Hou Yuhong Jin N. A. Saeed Ali Kandil Hao Duan DiffM 31 21 0 13 Dec 2023
Equivariant Flow Matching with Hybrid Probability Transport Yuxuan Song Jingjing Gong Minkai Xu Ziyao Cao Yanyan Lan Stefano Ermon Hao Zhou Wei-Ying Ma DiffM 33 45 0 12 Dec 2023
ForceGen: End-to-end de novo protein generation based on nonlinear mechanical unfolding responses using a protein language diffusion model Bo Ni David L. Kaplan Markus J. Buehler DiffM 33 5 0 16 Oct 2023
Generative artificial intelligence for de novo protein design Adam Winnifrith C. Outeiral Brian L. Hie AI4CE 26 23 0 15 Oct 2023
Functional Geometry Guided Protein Sequence and Backbone Structure Co-Design Justin Dumouchelle Yunlong Zhao Wenxian Shi Yang Yang Lei Li 26 2 0 06 Oct 2023
Joint Design of Protein Sequence and Structure based on Motifs Zhenqiao Song Yunlong Zhao Yufei Song Wenxian Shi Yang Yang Lei Li 3DV DiffM 35 3 0 04 Oct 2023
Ophiuchus: Scalable Modeling of Protein Structures through Hierarchical Coarse-graining SO(3)-Equivariant Autoencoders Allan dos Santos Costa Ilan Mitnikov Mario Geiger Manvitha Ponnapati Tess E. Smidt Joseph Jacobson DiffM 20 3 0 04 Oct 2023
SE(3)-Stochastic Flow Matching for Protein Backbone Generation A. Bose Tara Akhound-Sadegh Guillaume Huguet Kilian Fatras Jarrid Rector-Brooks Cheng-Hao Liu A. Nica Maksym Korablyov Michael M. Bronstein Alexander Tong DiffM 47 74 0 03 Oct 2023
Variations and Relaxations of Normalizing Flows Keegan Kelly Lorena Piedras Sukrit Rao David Samuel Roth BDL 27 0 0 08 Sep 2023
DiffI2I: Efficient Diffusion Model for Image-to-Image Translation Bin Xia Yulun Zhang Shiyin Wang Yitong Wang Xing Wu Yapeng Tian Wenming Yang Radu Timotfe Luc Van Gool DiffM VLM 39 14 0 26 Aug 2023
Predict, Refine, Synthesize: Self-Guiding Diffusion Models for Probabilistic Time Series Forecasting Marcel Kollovieh Abdul Fatir Ansari Michael Bohlke-Schneider Jasper Zschiegner Hao Wang Yuyang Wang DiffM AI4TS 20 44 0 21 Jul 2023
Graph Denoising Diffusion for Inverse Protein Folding Kai Yi Bingxin Zhou Yiqing Shen Pietro Lio' Yu Guang Wang DiffM 16 41 0 29 Jun 2023
Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning Xiangzhe Kong Wen-bing Huang Yang Liu 22 13 0 02 Jun 2023
DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing Yang Zhang Zuobai Zhang Bozitao Zhong Sanchit Misra Jian Tang DiffM 21 33 0 01 Jun 2023
Protein Design with Guided Discrete Diffusion Nate Gruver Samuel Stanton Nathan C. Frey Tim G. J. Rudner I. Hotzel J. Lafrance-Vanasse A. Rajpal Kyunghyun Cho A. Wilson DiffM 42 101 0 31 May 2023
Learning Joint 2D & 3D Diffusion Models for Complete Molecule Generation Han Huang Leilei Sun Bowen Du Weifeng Lv DiffM 26 16 0 21 May 2023
Dirichlet Diffusion Score Model for Biological Sequence Generation P. Avdeyev Chenlai Shi Y.M. Tan Kseniia Dudnyk Jian Zhou DiffM 21 48 0 18 May 2023
CREMP: Conformer-Rotamer Ensembles of Macrocyclic Peptides for Machine Learning Colin A. Grambow Hayley Weir Christian N Cunningham Tommaso Biancalani Kangway V Chuang 23 4 0 14 May 2023
A Latent Diffusion Model for Protein Structure Generation Cong Fu Keqiang Yan Limei Wang Wing Yee Au Michael McThrow Tao Komikado Koji Maruhashi Kanji Uchino Xiaoning Qian Shuiwang Ji DiffM 18 31 0 06 May 2023
Geometric Latent Diffusion Models for 3D Molecule Generation Minkai Xu Alexander Powers R. Dror Stefano Ermon J. Leskovec DiffM AI4CE 55 135 0 02 May 2023
EigenFold: Generative Protein Structure Prediction with Diffusion Models Bowen Jing Ezra Erives Peter Pao-Huang Gabriele Corso Bonnie Berger Tommi Jaakkola DiffM 20 66 0 05 Apr 2023
A Survey on Graph Diffusion Models: Generative AI in Science for Molecule, Protein and Material Mengchun Zhang Maryam Qamar Taegoo Kang Yuna Jung Chenshuang Zhang Sung-Ho Bae Chaoning Zhang DiffM MedIm 36 44 0 04 Apr 2023
DDP: Diffusion Model for Dense Visual Prediction Yuanfeng Ji Zhe Chen Enze Xie Lanqing Hong Xihui Liu Zhaoqiang Liu Tong Lu Zhenguo Li Ping Luo DiffM VLM 47 130 0 30 Mar 2023
DiffTAD: Temporal Action Detection with Proposal Denoising Diffusion Sauradip Nag Xiatian Zhu Jiankang Deng Yi-Zhe Song Tao Xiang DiffM VGen 41 21 0 27 Mar 2023
A Complete Survey on Generative AI (AIGC): Is ChatGPT from GPT-4 to GPT-5 All You Need? Chaoning Zhang Chenshuang Zhang Sheng Zheng Yu Qiao Chenghao Li ... Lik-Hang Lee Yang Yang Heng Tao Shen In So Kweon Choong Seon Hong 85 159 0 21 Mar 2023