Title
DecompOpt: Controllable and Decomposed Diffusion Models for Structure-based Molecular Optimization Xiangxin Zhou Xiwei Cheng Yuwei Yang Yu Bao Liang Wang Quanquan Gu 19 14 0 07 Mar 2024
Stabilizing Policy Gradients for Stochastic Differential Equations via Consistency with Perturbation Process Xiangxin Zhou Liang Wang Yichi Zhou DiffM 16 4 0 07 Mar 2024
DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Design Jiaqi Guan Xiangxin Zhou Yuwei Yang Yu Bao Jian-wei Peng Jianzhu Ma Qiang Liu Liang Wang Quanquan Gu 12 30 0 26 Feb 2024
Classification Diffusion Models: Revitalizing Density Ratio Estimation Shahar Yadin Noam Elata T. Michaeli DiffM 22 1 0 15 Feb 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 33 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 14 24 0 13 Feb 2024
Diffusion-based Graph Generative Methods Hongyang Chen Can Xu Lingyu Zheng Qiang Zhang Xuemin Lin DiffM MedIm 15 0 0 28 Jan 2024
FREED++: Improving RL Agents for Fragment-Based Molecule Generation by Thorough Reproduction Alexander Telepov Artem Tsypin Kuzma Khrabrov Sergey Yakukhnov Pavel Strashnov ... Egor Rumiantsev Daniel Ezhov Manvel Avetisian Olga Popova Artur Kadurin 16 4 0 18 Jan 2024
Binding-Adaptive Diffusion Models for Structure-Based Drug Design Zhilin Huang Ling Yang Zaixi Zhang Xiangxin Zhou Yu Bao Xiawu Zheng Yuwei Yang Yu Wang Wenming Yang DiffM 22 8 0 15 Jan 2024
Vector Field Oriented Diffusion Model for Crystal Material Generation Astrid Klipfel Yael Fregier A. Sayede Zied Bouraoui DiffM 13 4 0 20 Dec 2023
FSscore: A Machine Learning-based Synthetic Feasibility Score Leveraging Human Expertise Rebecca M. Neeser Bruno Correia Philippe Schwaller 11 1 0 20 Dec 2023
Autoregressive fragment-based diffusion for pocket-aware ligand design Mahdi Ghorbani Leo Gendelev Paul Beroza Michael J. Keiser DiffM 12 8 0 15 Dec 2023
Diffusion for Natural Image Matting Yihan Hu Yiheng Lin Wei Wang Yao-Min Zhao Yunchao Wei Humphrey Shi 13 7 0 10 Dec 2023
DiffuseBot: Breeding Soft Robots With Physics-Augmented Generative Diffusion Models Tsun-Hsuan Wang Juntian Zheng Pingchuan Ma Yilun Du Byungchul Kim Andrew Spielberg Josh Tenenbaum Chuang Gan Daniela Rus AI4CE 10 22 0 28 Nov 2023
Accelerating Inference in Molecular Diffusion Models with Latent Representations of Protein Structure Ian Dunn D. Koes DiffM GNN 14 3 0 22 Nov 2023
Generative Marginalization Models Sulin Liu Peter J. Ramadge Ryan P. Adams 15 1 0 19 Oct 2023
Closed-Form Diffusion Models Christopher Scarvelis Haitz Sáez de Ocáriz Borde Justin Solomon DiffM 88 9 0 19 Oct 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 16 4 0 17 Oct 2023
Stochastic interpolants with data-dependent couplings M. S. Albergo Mark Goldstein Nicholas M. Boffi Rajesh Ranganath Eric Vanden-Eijnden OT 15 28 0 05 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 17 24 0 29 Sep 2023
RetroBridge: Modeling Retrosynthesis with Markov Bridges Ilia Igashov Arne Schneuing Marwin H. S. Segler Michael M. Bronstein B. Correia 12 4 0 30 Aug 2023
DiAMoNDBack: Diffusion-denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces Michael S. Jones Kirill Shmilovich Andrew L. Ferguson DiffM 21 12 0 23 Jul 2023
SaGess: Sampling Graph Denoising Diffusion Model for Scalable Graph Generation Stratis Limnios Praveen Selvaraj Mihai Cucuringu Carsten Maple G. Reinert Andrew Elliott DiffM 17 7 0 29 Jun 2023
A Systematic Survey in Geometric Deep Learning for Structure-based Drug Design Zaixin Zhang Jiaxian Yan Qi Liu Enhong Chen Marinka Zitnik 17 1 0 20 Jun 2023
A generative artificial intelligence framework based on a molecular diffusion model for the design of metal-organic frameworks for carbon capture Hyun Park Xiaoli Yan Ruijie Zhu Eliu A. Huerta Santanu Chaudhuri Donny Cooper Ian T. Foster E. Tajkhorshid AI4CE 20 4 0 14 Jun 2023
Multi-objective Molecular Optimization for Opioid Use Disorder Treatment Using Generative Network Complex Hongsong Feng Rui Wang C. Zhan Guo-Wei Wei 11 0 0 13 Jun 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 24 20 0 13 Jun 2023
Nested Diffusion Processes for Anytime Image Generation Noam Elata Bahjat Kawar T. Michaeli Michael Elad DiffM 8 4 0 30 May 2023
Functional-Group-Based Diffusion for Pocket-Specific Molecule Generation and Elaboration Haitao Lin Yufei Huang Haotian Zhang Lirong Wu Siyuan Li Zhiyuan Chen Stan Z. Li DiffM 6 23 0 30 May 2023
Subspace-Configurable Networks Dong Wang O. Saukh Xiaoxi He Lothar Thiele OOD 20 0 0 22 May 2023
Training Diffusion Models with Reinforcement Learning Kevin Black Michael Janner Yilun Du Ilya Kostrikov Sergey Levine EGVM 22 312 0 22 May 2023
GSURE-Based Diffusion Model Training with Corrupted Data Bahjat Kawar Noam Elata T. Michaeli Michael Elad DiffM 16 15 0 22 May 2023
Learning Subpocket Prototypes for Generalizable Structure-based Drug Design Zaixin Zhang Qi Liu 17 34 0 22 May 2023
MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generation Xingang Peng Jiaqi Guan Qiang Liu Jianzhu Ma DiffM 20 33 0 11 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 6 31 0 06 May 2023
Accurate transition state generation with an object-aware equivariant elementary reaction diffusion model Chenru Duan Yuanqi Du Haojun Jia Heather J. Kulik DiffM 14 44 0 12 Apr 2023
A new perspective on building efficient and expressive 3D equivariant graph neural networks Weitao Du Yuanqi Du Limei Wang Dieqiao Feng Guifeng Wang Shuiwang Ji Carla P. Gomes Zhixin Ma AI4CE 13 33 0 07 Apr 2023
EigenFold: Generative Protein Structure Prediction with Diffusion Models Bowen Jing Ezra Erives Peter Pao-Huang Gabriele Corso Bonnie Berger Tommi Jaakkola DiffM 12 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 25 43 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 24 85 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 17 21 0 27 Mar 2023
Restoration-Degradation Beyond Linear Diffusions: A Non-Asymptotic Analysis For DDIM-Type Samplers Sitan Chen Giannis Daras A. Dimakis DiffM 6 62 0 06 Mar 2023
GraphVF: Controllable Protein-Specific 3D Molecule Generation with Variational Flow Fangce Sun Zhihao Zhan Hongyu Guo Ming Zhang Jian Tang 11 6 0 23 Feb 2023
Consistent Diffusion Models: Mitigating Sampling Drift by Learning to be Consistent Giannis Daras Y. Dagan A. Dimakis C. Daskalakis DiffM 17 42 0 17 Feb 2023
MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation Clément Vignac Nagham Osman Laura Toni P. Frossard DiffM 30 49 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 40 22 0 13 Feb 2023
3D Molecular Generation via Virtual Dynamics Shuqi Lu Lin Yao X. Chen Hang Zheng Di He Guolin Ke DiffM 16 7 0 12 Feb 2023
Thermodynamic AI and the fluctuation frontier Patrick J. Coles Collin Szczepanski Denis Melanson Kaelan Donatella Antonio J. Martinez Faris M. Sbahi AI4CE 16 16 0 09 Feb 2023
A Survey on Protein Representation Learning: Retrospect and Prospect Lirong Wu Yu-Feng Huang H. Lin Stan Z. Li AI4TS 10 12 0 31 Dec 2022
Structure-based drug discovery with deep learning Rıza Özçelik D. V. Tilborg José Jiménez-Luna F. Grisoni AI4CE 6 34 0 26 Dec 2022