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"

31 / 81 papers shown

Title
Restoration-Degradation Beyond Linear Diffusions: A Non-Asymptotic Analysis For DDIM-Type Samplers Sitan Chen Giannis Daras A. Dimakis DiffM 26 62 0 06 Mar 2023
Internal-Coordinate Density Modelling of Protein Structure: Covariance Matters Marloes Arts J. Frellsen Wouter Boomsma 36 0 0 27 Feb 2023
Consistent Diffusion Models: Mitigating Sampling Drift by Learning to be Consistent Giannis Daras Y. Dagan A. Dimakis C. Daskalakis DiffM 38 44 0 17 Feb 2023
Diffusion Models in Bioinformatics: A New Wave of Deep Learning Revolution in Action Zhiye Guo Jian Liu Yanli Wang Mengrui Chen Duolin Wang Dong Xu Jianlin Cheng MedIm AI4CE DiffM 46 22 0 13 Feb 2023
A Text-guided Protein Design Framework Shengchao Liu Yanjing Li Zhuoxinran Li A. Gitter Yutao Zhu ... Arvind Ramanathan Chaowei Xiao Jian Tang Hongyu Guo Anima Anandkumar 70 61 0 09 Feb 2023
Geometry-Complete Diffusion for 3D Molecule Generation and Optimization Alex Morehead Jianlin Cheng DiffM 14 25 0 08 Feb 2023
Generative Diffusion Models on Graphs: Methods and Applications Junfeng Fang Wenqi Fan Yunqing Liu Jiatong Li Hang Li Hui Liu Jiliang Tang Qing Li MedIm DiffM 34 58 0 06 Feb 2023
Data-Efficient Protein 3D Geometric Pretraining via Refinement of Diffused Protein Structure Decoy Yufei Huang Lirong Wu Haitao Lin Jiangbin Zheng Ge Wang Stan Z. Li DiffM 31 14 0 05 Feb 2023
SE(3) diffusion model with application to protein backbone generation Jason Yim Brian L. Trippe Valentin De Bortoli Emile Mathieu Arnaud Doucet Regina Barzilay Tommi Jaakkola DiffM 20 197 0 05 Feb 2023
Generating Novel, Designable, and Diverse Protein Structures by Equivariantly Diffusing Oriented Residue Clouds Yeqing Lin Mohammed AlQuraishi DiffM AI4CE 27 75 0 29 Jan 2023
Pre-Training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction Zuobai Zhang Minghao Xu A. Lozano Vijil Chenthamarakshan Payel Das Jian Tang DiffM 19 19 0 28 Jan 2023
DiffSDS: A language diffusion model for protein backbone inpainting under geometric conditions and constraints Zhangyang Gao Cheng Tan Stan Z. Li DiffM 29 19 0 22 Jan 2023
A Transformer-based Diffusion Probabilistic Model for Heart Rate and Blood Pressure Forecasting in Intensive Care Unit Ping Chang Huayu Li S. Quan Shuyang Lu Shu-Fen Wung Janet Roveda Ao Li DiffM 11 16 0 16 Jan 2023
Diffusion-based Data Augmentation for Skin Disease Classification: Impact Across Original Medical Datasets to Fully Synthetic Images Mohamed Akrout Bálint Gyepesi P. Holló A. Poór Blága Kincso ... J. Kawahara Dekker Slade Latif Abid Máté Kovács I. Fazekas DiffM MedIm 19 60 0 12 Jan 2023
Latent Space Diffusion Models of Cryo-EM Structures Karsten Kreis Tim Dockhorn Zihao Li Ellen D. Zhong DiffM 30 15 0 25 Nov 2022
DiffusionDet: Diffusion Model for Object Detection Shoufa Chen Pei Sun Yibing Song Ping Luo 63 443 0 17 Nov 2022
Diffusion Models for Medical Image Analysis: A Comprehensive Survey A. Kazerouni Ehsan Khodapanah Aghdam Moein Heidari Reza Azad Mohsen Fayyaz I. Hacihaliloglu Dorit Merhof DiffM MedIm 49 358 0 14 Nov 2022
Modeling Temporal Data as Continuous Functions with Stochastic Process Diffusion Marin Bilos Kashif Rasul Anderson Schneider Yuriy Nevmyvaka Stephan Günnemann DiffM 27 32 0 04 Nov 2022
Structure-based Drug Design with Equivariant Diffusion Models Arne Schneuing Yuanqi Du Charles Harris Arian R. Jamasb Ilia Igashov ... Pietro Lió Carla P. Gomes Max Welling Michael M. Bronstein B. Correia DiffM 44 196 0 24 Oct 2022
Protein Sequence and Structure Co-Design with Equivariant Translation Chence Shi Chuanrui Wang Jiarui Lu Bozitao Zhong Jian Tang DiffM 30 47 0 17 Oct 2022
Reprogramming Pretrained Language Models for Antibody Sequence Infilling Igor Melnyk Vijil Chenthamarakshan Pin-Yu Chen Payel Das Amit Dhurandhar Inkit Padhi Devleena Das 33 28 0 05 Oct 2022
Protein structure generation via folding diffusion Kevin E. Wu Kevin Kaichuang Yang Rianne van den Berg James Zou Alex X. Lu Ava P. Amini DiffM 35 192 0 30 Sep 2022
State-specific protein-ligand complex structure prediction with a multi-scale deep generative model Zhuoran Qiao Weili Nie Arash Vahdat Thomas F. Miller Anima Anandkumar DiffM 36 84 0 30 Sep 2022
Graph Neural Networks for Molecules Yuyang Wang Zijie Li A. Farimani GNN AI4CE 45 20 0 12 Sep 2022
A Survey on Generative Diffusion Model Hanqun Cao Cheng Tan Zhangyang Gao Yilun Xu Guangyong Chen Pheng-Ann Heng Stan Z. Li MedIm 37 207 0 06 Sep 2022
Diffusion Models: A Comprehensive Survey of Methods and Applications Ling Yang Zhilong Zhang Yingxia Shao Shenda Hong Runsheng Xu Yue Zhao Wentao Zhang Bin Cui Ming-Hsuan Yang DiffM MedIm 224 1,311 0 02 Sep 2022
Accelerating Material Design with the Generative Toolkit for Scientific Discovery Matteo Manica Jannis Born Joris Cadow Dimitrios Christofidellis A. Dave ... Lauren N. McHugh Alexy Khrabrov Payel Das Seiji Takeda John Smith 22 26 0 08 Jul 2022
Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem Brian L. Trippe Jason Yim D. Tischer D. Baker Tamara Broderick Regina Barzilay Tommi Jaakkola DiffM 16 231 0 08 Jun 2022
Riemannian Score-Based Generative Modelling Valentin De Bortoli Emile Mathieu M. Hutchinson James Thornton Yee Whye Teh Arnaud Doucet DiffM 222 165 0 06 Feb 2022
AlphaDesign: A graph protein design method and benchmark on AlphaFoldDB Zhangyang Gao Cheng Tan Stan Z. Li 152 52 0 01 Feb 2022
Deep Generative Modeling for Protein Design Alexey Strokach Philip M. Kim AI4CE 179 90 0 31 Aug 2021