Learning Gradient Fields for Molecular Conformation Generation

9 May 2021

Jian Tang

Papers citing "Learning Gradient Fields for Molecular Conformation Generation"

50 / 135 papers shown

Title
PolyConf: Unlocking Polymer Conformation Generation through Hierarchical Generative Models Fanmeng Wang Wentao Guo Qi Ou Hongshuai Wang Haitao Lin Hongteng Xu Zhifeng Gao AI4CE 30 1 0 11 Apr 2025
DMol: A Schedule-Driven Diffusion Model for Highly Efficient and Versatile Molecule Generation Peizhi Niu Yu-Hsiang Wang Vishal Rana Chetan Rupakheti Abhishek Pandey O. Milenkovic 26 0 0 08 Apr 2025
Potential Score Matching: Debiasing Molecular Structure Sampling with Potential Energy Guidance Liya Guo Zun Wang Chang-Shu Liu J. Li Pipi Hu Yi Zhu DiffM 43 0 0 18 Mar 2025
Beyond Atoms: Enhancing Molecular Pretrained Representations with 3D Space Modeling Shuqi Lu Xiaohong Ji Bohang Zhang Lin Yao Siyuan Liu Zhifeng Gao Linfeng Zhang Guolin Ke AI4CE 46 1 0 13 Mar 2025
UniGenX: Unified Generation of Sequence and Structure with Autoregressive Diffusion Gongbo Zhang Y. Li Renqian Luo Pipi Hu Zeru Zhao ... Maik Riechert Li-ming Yuan Lei Chen Haiguang Liu Tao Qin DiffM 42 0 0 09 Mar 2025
Periodic Materials Generation using Text-Guided Joint Diffusion Model Kishalay Das Subhojyoti Khastagir Pawan Goyal Seung-Cheol Lee S. Bhattacharjee Niloy Ganguly DiffM 32 0 0 01 Mar 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 64 1 0 04 Feb 2025
Gradient Networks Shreyas Chaudhari Srinivasa Pranav J. M. F. Moura 50 0 0 28 Jan 2025
Generative Model for Synthesizing Ionizable Lipids: A Monte Carlo Tree Search Approach Jingyi Zhao Yuxuan Ou Austin Tripp Morteza Rasoulianboroujeni José Miguel Hernández-Lobato 62 0 0 01 Dec 2024
Conformation Generation using Transformer Flows Sohil Shah V. Koltun MedIm AI4CE 26 0 0 16 Nov 2024
Diffusion Twigs with Loop Guidance for Conditional Graph Generation Giangiacomo Mercatali Yogesh Verma André Freitas Vikas K. Garg 24 3 0 31 Oct 2024
ET-Flow: Equivariant Flow-Matching for Molecular Conformer Generation Majdi Hassan Nikhil Shenoy Jungyoon Lee Hannes Stärk Stephan Thaler Dominique Beaini 27 6 0 29 Oct 2024
Equivariant Blurring Diffusion for Hierarchical Molecular Conformer Generation Jiwoong Park Yang Shen DiffM 23 0 0 26 Oct 2024
Geometric Trajectory Diffusion Models Jiaqi Han Minkai Xu Aaron Lou Haotian Ye Stefano Ermon DiffM 43 4 0 16 Oct 2024
Hessian-Informed Flow Matching Christopher Iliffe Sprague Arne Elofsson Hossein Azizpour 18 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 30 1 0 14 Oct 2024
VisDiff: SDF-Guided Polygon Generation for Visibility Reconstruction and Recognition Rahul Moorthy Volkan Isler 18 0 0 07 Oct 2024
REBIND: Enhancing ground-state molecular conformation via force-based graph rewiring Taewon Kim Hyunjin Seo Sungsoo Ahn Eunho Yang AI4CE 32 1 0 04 Oct 2024
MBDS: A Multi-Body Dynamics Simulation Dataset for Graph Networks Simulators Sheng Yang Fengge Wu Junsuo Zhao AI4CE 13 0 0 04 Oct 2024
Physics-aligned Schrödinger bridge Zeyu Li Hongkun Dou Shen Fang Wang Han Yue Deng Lijun Yang AI4CE DiffM 28 0 0 26 Sep 2024
Mitigating Exposure Bias in Score-Based Generation of Molecular Conformations Sijia Wang Chen Wang Zhenhao Zhao Jiqiang Zhang Weiran Cai 21 0 0 21 Sep 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
RCDM: Enabling Robustness for Conditional Diffusion Model Weifeng Xu Xiang Zhu Xiaoyong Li AAML 21 0 0 05 Aug 2024
Cross-Domain Graph Data Scaling: A Showcase with Diffusion Models Wenzhuo Tang Haitao Mao Danial Dervovic Ivan Brugere Saumitra Mishra Yuying Xie Jiliang Tang 48 3 0 04 Jun 2024
Sifting through the Noise: A Survey of Diffusion Probabilistic Models and Their Applications to Biomolecules Trevor Norton Debswapna Bhattacharya MedIm DiffM 45 2 0 31 May 2024
Discrete-state Continuous-time Diffusion for Graph Generation Zhe Xu Ruizhong Qiu Yuzhong Chen Huiyuan Chen Xiran Fan Menghai Pan Zhichen Zeng Mahashweta Das Hanghang Tong 32 8 0 19 May 2024
G-FARS: Gradient-Field-based Auto-Regressive Sampling for 3D Part Grouping Junfeng Cheng Tania Stathaki 21 1 0 10 May 2024
SubGDiff: A Subgraph Diffusion Model to Improve Molecular Representation Learning Jiying Zhang Zijing Liu Yu Wang Yu Li DiffM 39 1 0 09 May 2024
On Diffusion Process in SE(3)-invariant Space Zihan Zhou Ruiying Liu Jiachen Zheng Xiaoxue Wang Tianshu Yu DiffM 32 1 0 03 Mar 2024
A Survey of Geometric Graph Neural Networks: Data Structures, Models and Applications Jiaqi Han Jiacheng Cen Liming Wu Zongzhao Li Xiangzhe Kong ... Zhewei Wei Deli Zhao Yu Rong Wenbing Huang Wenbing Huang AI4CE 32 20 0 01 Mar 2024
Structure Preserving Diffusion Models Haoye Lu S. Szabados Yaoliang Yu DiffM 59 3 0 29 Feb 2024
Graph Learning with Distributional Edge Layouts Xinjian Zhao Chaolong Ying Tianshu Yu 23 0 0 26 Feb 2024
Structure-Based Drug Design via 3D Molecular Generative Pre-training and Sampling Yuwei Yang Siqi Ouyang Xueyu Hu Mingyue Zheng Hao Zhou Lei Li 32 1 0 22 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
Stable Autonomous Flow Matching Christopher Iliffe Sprague Arne Elofsson Hossein Azizpour 33 1 0 08 Feb 2024
Weisfeiler Leman for Euclidean Equivariant Machine Learning Snir Hordan Tal Amir Nadav Dym 44 5 0 04 Feb 2024
Diffusion-based Graph Generative Methods Hongyang Chen Can Xu Lingyu Zheng Qiang Zhang Xuemin Lin DiffM MedIm 20 0 0 28 Jan 2024
Equivariant Graph Neural Operator for Modeling 3D Dynamics Minkai Xu Jiaqi Han Aaron Lou Jean Kossaifi Arvind Ramanathan Kamyar Azizzadenesheli J. Leskovec Stefano Ermon A. Anandkumar AI4CE 24 16 0 19 Jan 2024
Diffusion-Driven Generative Framework for Molecular Conformation Prediction Bobin Yang Jie Deng Zhenghan Chen Ruoxue Wu DiffM 23 0 0 22 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 21 21 0 13 Dec 2023
SE(3)-Invariant Multiparameter Persistent Homology for Chiral-Sensitive Molecular Property Prediction Andac Demir Francis Prael B. Kiziltan 19 2 0 12 Dec 2023
Molecule Joint Auto-Encoding: Trajectory Pretraining with 2D and 3D Diffusion Weitao Du Jiujiu Chen Xuecang Zhang Zhiming Ma Shengchao Liu DiffM 25 9 0 06 Dec 2023
GlycoNMR: Dataset and benchmarks for NMR chemical shift prediction of carbohydrates with graph neural networks Zizhang Chen R. P. Badman Lachele Foley Robert Woods Pengyu Hong 30 0 0 28 Nov 2023
Swallowing the Bitter Pill: Simplified Scalable Conformer Generation Yuyang Wang Ahmed A. A. Elhag Navdeep Jaitly J. Susskind Miguel Angel Bautista DiffM 27 19 0 27 Nov 2023
Multiparameter Persistent Homology for Molecular Property Prediction Andac Demir B. Kiziltan 22 1 0 17 Nov 2023
Gradual Optimization Learning for Conformational Energy Minimization Artem Tsypin L. Ugadiarov Kuzma Khrabrov Alexander Telepov Egor Rumiantsev Alexey Skrynnik Aleksandr I. Panov Dmitry Vetrov E. Tutubalina Artur Kadurin 24 1 0 05 Nov 2023
Towards equilibrium molecular conformation generation with GFlowNets Alexandra Volokhova Michal Koziarski Alex Hernández-García Cheng-Hao Liu Santiago Miret Pablo Lemos Luca Thiede Zichao Yan Alán Aspuru-Guzik Yoshua Bengio 24 9 0 20 Oct 2023
Particle Guidance: non-I.I.D. Diverse Sampling with Diffusion Models Gabriele Corso Yilun Xu Valentin De Bortoli Regina Barzilay Tommi Jaakkola DiffM 14 20 0 19 Oct 2023
MOFDiff: Coarse-grained Diffusion for Metal-Organic Framework Design Xiang Fu Tian Xie Andrew S. Rosen Tommi Jaakkola Jake A. Smith DiffM 21 9 0 16 Oct 2023
Data-Driven Score-Based Models for Generating Stable Structures with Adaptive Crystal Cells Arsen Sultanov J. Crivello Tabea Rebafka Nataliya Sokolovska DiffM 22 6 0 16 Oct 2023