Equivariant Energy-Guided SDE for Inverse Molecular Design

30 September 2022

Jun Zhu

Papers citing "Equivariant Energy-Guided SDE for Inverse Molecular Design"

50 / 50 papers shown

Title
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 28 0 0 08 Apr 2025
Towards Unified Latent Space for 3D Molecular Latent Diffusion Modeling Yanchen Luo Zhiyuan Liu Yi Zhao Sihang Li Kenji Kawaguchi Tat-Seng Chua X. Wang MedIm 59 0 0 19 Mar 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 45 0 0 18 Mar 2025
Siamese Foundation Models for Crystal Structure Prediction Liming Wu Wenbing Huang Rui Jiao Jianxing Huang Liwei Liu ... Hao Sun Yang Liu F. Sun Yuxiang Ren J. Wen 50 0 0 13 Mar 2025
NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation Zhiyuan Liu Yanchen Luo Han Huang Enzhi Zhang Sihang Li Junfeng Fang Yaorui Shi X. Wang Kenji Kawaguchi Tat-Seng Chua 100 3 0 18 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 64 1 0 04 Feb 2025
Unified Guidance for Geometry-Conditioned Molecular Generation Sirine Ayadi Leon Hetzel Johanna Sommer Fabian J. Theis Stephan Günnemann 30 0 0 05 Jan 2025
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 29 4 0 01 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
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 38 5 0 14 Oct 2024
Chemistry-Inspired Diffusion with Non-Differentiable Guidance Yuchen Shen Chenhao Zhang Sijie Fu Chenghui Zhou Newell Washburn Barnabás Póczos 50 0 0 09 Oct 2024
Text-guided Diffusion Model for 3D Molecule Generation Yanchen Luo Junfeng Fang Sihang Li Zhiyuan Liu Jiancan Wu An Zhang Wenjie Du Xiang Wang 29 6 0 04 Oct 2024
TFG: Unified Training-Free Guidance for Diffusion Models Haotian Ye Haowei Lin Jiaqi Han Minkai Xu Sheng Liu Yitao Liang Jianzhu Ma James Zou Stefano Ermon 31 13 0 24 Sep 2024
Spiking Diffusion Models Jiahang Cao Hanzhong Guo Ziqing Wang Deming Zhou Hao Cheng Qiang Zhang Renjing Xu DiffM 40 2 0 29 Aug 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
General Binding Affinity Guidance for Diffusion Models in Structure-Based Drug Design Yue Jian Curtis Wu Danny Reidenbach Aditi S. Krishnapriyan 34 1 0 24 Jun 2024
Lift Your Molecules: Molecular Graph Generation in Latent Euclidean Space Mohamed Amine Ketata Nicholas Gao Johanna Sommer Tom Wollschlager Stephan Günnemann DiffM 36 1 0 15 Jun 2024
$Diffusion Models in $\textit{De Novo}$ Drug Design$ Diffusion Models in $\textit{De Novo}$ Drug Design Amira Alakhdar Barnabás Póczos Newell Washburn MedIm 36 13 0 07 Jun 2024
TAGMol: Target-Aware Gradient-guided Molecule Generation Vineeth Dorna Subhalingam D Keshav Kolluru Shreshth Tuli Mrityunjay Singh Saurabh Singal N. M. A. Krishnan Sayan Ranu 32 2 0 03 Jun 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
Diffusion-Driven Domain Adaptation for Generating 3D Molecules Haokai Hong Wanyu Lin Kay Chen Tan DiffM 37 2 0 01 Apr 2024
Stabilizing Policy Gradients for Stochastic Differential Equations via Consistency with Perturbation Process Xiangxin Zhou Liang Wang Yichi Zhou DiffM 21 4 0 07 Mar 2024
Rethinking Specificity in SBDD: Leveraging Delta Score and Energy-Guided Diffusion Bowen Gao Minsi Ren Yuyan Ni Yanwen Huang Bo Qiang Zhiming Ma Wei-Ying Ma Yanyan Lan 32 4 0 04 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 34 20 0 01 Mar 2024
Extended Flow Matching: a Method of Conditional Generation with Generalized Continuity Equation Noboru Isobe Masanori Koyama Jinzhe Zhang Kohei Hayashi Kenji Fukumizu 37 10 0 29 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
The Blessing of Randomness: SDE Beats ODE in General Diffusion-based Image Editing Shen Nie Hanzhong Guo Cheng Lu Yuhao Zhou Chenyu Zheng Chongxuan Li DiffM 19 37 0 02 Nov 2023
Efficient Planning with Latent Diffusion Wenhao Li DiffM 38 4 0 30 Sep 2023
Inversion-by-Inversion: Exemplar-based Sketch-to-Photo Synthesis via Stochastic Differential Equations without Training Ximing Xing Chuan Wang Haitao Zhou Zhihao Hu Chongxuan Li Dong Xu Qian Yu DiffM 22 1 0 15 Aug 2023
SDDM: Score-Decomposed Diffusion Models on Manifolds for Unpaired Image-to-Image Translation Shikun Sun Longhui Wei Junliang Xing Jia Jia Qi Tian DiffM 17 13 0 04 Aug 2023
Leveraging Side Information for Ligand Conformation Generation using Diffusion-Based Approaches Nhat-Khang Ngô Truong Son-Hy Yuan Yao DiffM 30 0 0 02 Aug 2023
Crystal Structure Prediction by Joint Equivariant Diffusion Rui Jiao Wen-bing Huang Peijia Lin Jiaqi Han Pin Chen Yutong Lu Yang Liu DiffM 19 59 0 30 Jul 2023
Spiking Denoising Diffusion Probabilistic Models Jiahang Cao Ziqing Wang Hanzhong Guo Haotai Cheng Qiang Zhang Renjing Xu DiffM 22 19 0 29 Jun 2023
Learning Joint 2D & 3D Diffusion Models for Complete Molecule Generation Han Huang Leilei Sun Bowen Du Weifeng Lv DiffM 22 16 0 21 May 2023
Contrastive Energy Prediction for Exact Energy-Guided Diffusion Sampling in Offline Reinforcement Learning Cheng Lu Huayu Chen Jianfei Chen Hang Su Chongxuan Li Jun Zhu DiffM OffRL 19 58 0 25 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 31 44 0 04 Apr 2023
A Closer Look at Parameter-Efficient Tuning in Diffusion Models Chendong Xiang Fan Bao Chongxuan Li Hang Su Jun Zhu DiffM 14 16 0 31 Mar 2023
One Transformer Fits All Distributions in Multi-Modal Diffusion at Scale Fan Bao Shen Nie Kaiwen Xue Chongxuan Li Shiliang Pu Yaole Wang Gang Yue Yue Cao Hang Su Jun Zhu DiffM 204 148 0 12 Mar 2023
Reduce, Reuse, Recycle: Compositional Generation with Energy-Based Diffusion Models and MCMC Yilun Du Conor Durkan Robin Strudel J. Tenenbaum Sander Dieleman Rob Fergus Jascha Narain Sohl-Dickstein Arnaud Doucet Will Grathwohl DiffM 24 130 0 22 Feb 2023
Diffusion Models and Semi-Supervised Learners Benefit Mutually with Few Labels Zebin You Yong Zhong Fan Bao Jiacheng Sun Chongxuan Li Jun Zhu DiffM VLM 201 36 0 21 Feb 2023
MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation Clément Vignac Nagham Osman Laura Toni P. Frossard DiffM 39 50 0 17 Feb 2023
Generative Diffusion Models on Graphs: Methods and Applications C. Liu Wenqi Fan Yunqing Liu Jiatong Li Hang Li Hui Liu Jiliang Tang Qing Li MedIm DiffM 32 58 0 06 Feb 2023
Physics-Informed Machine Learning: A Survey on Problems, Methods and Applications Zhongkai Hao Songming Liu Yichi Zhang Chengyang Ying Yao Feng Hang Su Jun Zhu PINN AI4CE 23 89 0 15 Nov 2022
All are Worth Words: A ViT Backbone for Diffusion Models Fan Bao Shen Nie Kaiwen Xue Yue Cao Chongxuan Li Hang Su Jun Zhu VLM 26 313 0 25 Sep 2022
Keeping it Simple: Language Models can learn Complex Molecular Distributions Daniel Flam-Shepherd Kevin Zhu A. Aspuru‐Guzik 129 142 0 06 Dec 2021
Inverse design of 3d molecular structures with conditional generative neural networks Niklas W. A. Gebauer M. Gastegger Stefaan S. P. Hessmann Klaus-Robert Muller Kristof T. Schütt AI4CE 187 166 0 10 Sep 2021
GraphDF: A Discrete Flow Model for Molecular Graph Generation Youzhi Luo Keqiang Yan Shuiwang Ji DRL 176 187 0 01 Feb 2021
3DMolNet: A Generative Network for Molecular Structures V. Nesterov Mario Wieser Volker Roth AI4CE 162 33 0 08 Oct 2020
Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation Jiaxuan You Bowen Liu Rex Ying Vijay S. Pande J. Leskovec GNN 200 885 0 07 Jun 2018
Junction Tree Variational Autoencoder for Molecular Graph Generation Wengong Jin Regina Barzilay Tommi Jaakkola 224 1,337 0 12 Feb 2018