ComENet: Towards Complete and Efficient Message Passing for 3D Molecular Graphs

17 June 2022

Papers citing "ComENet: Towards Complete and Efficient Message Passing for 3D Molecular Graphs"

50 / 53 papers shown

Title
Multi-Modal Molecular Representation Learning via Structure Awareness Rong Yin Ruyue Liu Xiaoshuai Hao Xingrui Zhou Yong-Jin Liu Can Ma Weiping Wang 29 0 0 09 May 2025
RISE: Radius of Influence based Subgraph Extraction for 3D Molecular Graph Explanation J. Qu Wenhan Gao Jiaxing Zhang Xufeng Liu Hua Wei Haibin Ling Yong-Jin Liu AI4CE 57 0 0 04 May 2025
Bidirectional Hierarchical Protein Multi-Modal Representation Learning Xuefeng Liu Songhao Jiang Chih-chan Tien J. Xu Rick L. Stevens 25 0 0 07 Apr 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
Invariant Tokenization of Crystalline Materials for Language Model Enabled Generation Keqiang Yan Xiner Li Hongyi Ling Kenna Ashen Carl N. Edwards ... Marinka Zitnik Heng Ji Xiaofeng Qian X. Qian Shuiwang Ji 35 3 0 28 Feb 2025
Enhancing the Scalability and Applicability of Kohn-Sham Hamiltonians for Molecular Systems Yunyang Li Zaishuo Xia Lin Huang Xinran Wei Han Yang ... Zun Wang Chang-Shu Liu Jia Zhang Bin Shao Mark B. Gerstein 77 0 0 26 Feb 2025
Enhancing Retrosynthesis with Conformer: A Template-Free Method Jiaxi Zhuang Qian Zhang Ying Qian 136 0 0 21 Jan 2025
CrystalX: Ultra-Precision Crystal Structure Resolution and Error Correction Using Deep Learning Kaipeng Zheng Weiran Huang Wanli Ouyang Han-Sen Zhong Y. Li 36 0 0 17 Oct 2024
Are High-Degree Representations Really Unnecessary in Equivariant Graph Neural Networks? Jiacheng Cen Anyi Li Ning Lin Yuxiang Ren Zihe Wang Wenbing Huang 43 2 0 15 Oct 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 31 6 0 19 Aug 2024
FreeCG: Free the Design Space of Clebsch-Gordan Transform for Machine Learning Force Fields Shihao Shao Haoran Geng Zun Wang Qinghua Cui 3DV 40 0 0 02 Jul 2024
On the Expressive Power of Sparse Geometric MPNNs Yonatan Sverdlov Nadav Dym 45 1 0 02 Jul 2024
GeoMFormer: A General Architecture for Geometric Molecular Representation Learning Tianlang Chen Shengjie Luo Di He Shuxin Zheng Tie-Yan Liu Liwei Wang AI4CE 38 5 0 24 Jun 2024
Introducing Diminutive Causal Structure into Graph Representation Learning Hang Gao Peng Qiao Yifan Jin Fengge Wu Jiangmeng Li Changwen Zheng 44 4 0 13 Jun 2024
Equivariance via Minimal Frame Averaging for More Symmetries and Efficiency Yuchao Lin Jacob Helwig Shurui Gui Shuiwang Ji 42 7 0 11 Jun 2024
Infusing Self-Consistency into Density Functional Theory Hamiltonian Prediction via Deep Equilibrium Models Zun Wang Chang-Shu Liu Nianlong Zou He Zhang Xinran Wei Lin Huang Lijun Wu Bin Shao 41 1 0 06 Jun 2024
Medication Recommendation via Dual Molecular Modalities and Multi-Substructure Enhancement Shizhuo Mu Shunpan Liang Xiang Li 40 0 0 30 May 2024
SE3Set: Harnessing equivariant hypergraph neural networks for molecular representation learning Hongfei Wu Lijun Wu Guoqing Liu Zhirong Liu Bin Shao Zun Wang 43 1 0 26 May 2024
NaNa and MiGu: Semantic Data Augmentation Techniques to Enhance Protein Classification in Graph Neural Networks Yi-Shan Lan Pin-Yu Chen Tsung-Yi Ho 27 0 0 21 Mar 2024
Complete and Efficient Graph Transformers for Crystal Material Property Prediction Keqiang Yan Cong Fu Xiaofeng Qian Xiaoning Qian Shuiwang Ji 46 19 0 18 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
On the Completeness of Invariant Geometric Deep Learning Models Zian Li Xiyuan Wang Shijia Kang Muhan Zhang 36 2 0 07 Feb 2024
PerCNet: Periodic Complete Representation for Crystal Graphs Jiao Huang Qianli Xing Jinglong Ji Bo Yang 34 1 0 03 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 38 0 0 28 Nov 2023
De novo protein design using geometric vector field networks Weian Mao Muzhi Zhu Zheng Sun Shuaike Shen Lin Yuanbo Wu Hao Chen Chunhua Shen DiffM 33 10 0 18 Oct 2023
MOFDiff: Coarse-grained Diffusion for Metal-Organic Framework Design Xiang Fu Tian Xie Andrew S. Rosen Tommi Jaakkola Jake A. Smith DiffM 42 9 0 16 Oct 2023
AtomSurf : Surface Representation for Learning on Protein Structures Vincent Mallet Souhaib Attaiki M. Ovsjanikov 42 3 0 28 Sep 2023
A Systematic Survey in Geometric Deep Learning for Structure-based Drug Design Zaixin Zhang Jiaxian Yan Qi Liu Enhong Chen Marinka Zitnik 32 1 0 20 Jun 2023
QH9: A Quantum Hamiltonian Prediction Benchmark for QM9 Molecules Haiyang Yu Meng Liu Youzhi Luo A. Strasser X. Qian Xiaoning Qian Shuiwang Ji 15 20 0 15 Jun 2023
Efficient Approximations of Complete Interatomic Potentials for Crystal Property Prediction Yu-Ching Lin Keqiang Yan Youzhi Luo Yi Liu Xiaoning Qian Shuiwang Ji 66 33 0 12 Jun 2023
Efficient and Equivariant Graph Networks for Predicting Quantum Hamiltonian Haiyang Yu Zhao Xu X. Qian Xiaoning Qian Shuiwang Ji 37 24 0 08 Jun 2023
A Score-Based Model for Learning Neural Wavefunctions Xuan Zhang Shenglong Xu Shuiwang Ji DiffM 25 1 0 25 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
FAENet: Frame Averaging Equivariant GNN for Materials Modeling Alexandre Duval Victor Schmidt A. Garcia Santiago Miret Fragkiskos D. Malliaros Yoshua Bengio David Rolnick 34 55 0 28 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 32 33 0 07 Apr 2023
GeoTMI:Predicting quantum chemical property with easy-to-obtain geometry via positional denoising Hyeonsu Kim Jeheon Woo Seonghwan Kim Seokhyun Moon Jun Hyeong Kim Woo Youn Kim AI4CE 42 6 0 28 Mar 2023
Knowledge-augmented Graph Machine Learning for Drug Discovery: A Survey from Precision to Interpretability Zhiqiang Zhong A. Barkova Davide Mottin 24 8 0 16 Feb 2023
Complete Neural Networks for Complete Euclidean Graphs Snir Hordan Tal Amir S. Gortler Nadav Dym 3DPC 29 5 0 31 Jan 2023
On the Expressive Power of Geometric Graph Neural Networks Chaitanya K. Joshi Cristian Bodnar Simon V. Mathis Taco Cohen Pietro Liò 55 83 0 23 Jan 2023
End-to-end AI framework for interpretable prediction of molecular and crystal properties Hyun Park Ruijie Zhu Eliu A. Huerta Santanu Chaudhuri E. Tajkhorshid Donny Cooper AI4CE 22 10 0 21 Dec 2022
Geometry-Complete Perceptron Networks for 3D Molecular Graphs Alex Morehead Jianlin Cheng GNN 3DV AI4CE 29 12 0 04 Nov 2022
Periodic Graph Transformers for Crystal Material Property Prediction Keqiang Yan Yi Liu Yu-Ching Lin Shuiwang Ji AI4TS 88 84 0 23 Sep 2022
Graph Neural Network with Local Frame for Molecular Potential Energy Surface Xiyuan Wang Muhan Zhang 38 9 0 01 Aug 2022
Learning Hierarchical Protein Representations via Complete 3D Graph Networks Limei Wang Haoran Liu Yi Liu Jerry Kurtin Shuiwang Ji GNN 33 55 0 26 Jul 2022
Graph-based Molecular Representation Learning Zhichun Guo Kehan Guo B. Nan Yijun Tian Roshni G. Iyer ... Olaf Wiest Xiangliang Zhang Wei Wang Chuxu Zhang Nitesh V. Chawla AI4CE 22 60 0 08 Jul 2022
Task-Agnostic Graph Explanations Yaochen Xie S. Katariya Xianfeng Tang E-Wen Huang Nikhil S. Rao Karthik Subbian Shuiwang Ji 40 25 0 16 Feb 2022
Learning ground states of quantum Hamiltonians with graph networks Dmitrii Kochkov Tobias Pfaff Alvaro Sanchez-Gonzalez Peter W. Battaglia B. Clark 44 26 0 12 Oct 2021
Geometric Transformers for Protein Interface Contact Prediction Alex Morehead Chen Chen Jianlin Cheng 31 28 0 06 Oct 2021
Molecule3D: A Benchmark for Predicting 3D Geometries from Molecular Graphs Zhao Xu Youzhi Luo Xuan Zhang Xinyi Xu Yaochen Xie Meng Liu Kaleb Dickerson Cheng Deng Maho Nakata Shuiwang Ji 43 39 0 30 Sep 2021
Geometric Deep Learning: Grids, Groups, Graphs, Geodesics, and Gauges M. Bronstein Joan Bruna Taco S. Cohen Petar Velivcković GNN 174 1,106 0 27 Apr 2021