Advanced Graph and Sequence Neural Networks for Molecular Property Prediction and Drug Discovery

2 December 2020

Papers citing "Advanced Graph and Sequence Neural Networks for Molecular Property Prediction and Drug Discovery"

42 / 42 papers shown

Title
Adapting Differential Molecular Representation with Hierarchical Prompts for Multi-label Property Prediction Linjia Kang Songhua Zhou Shuyan Fang Shichao Liu Wen Zhang AI4CE 46 3 0 29 May 2024
Single-loop Stochastic Algorithms for Difference of Max-Structured Weakly Convex Functions Quanqi Hu Qi Qi Zhaosong Lu Tianbao Yang 34 1 0 28 May 2024
Impact of Domain Knowledge and Multi-Modality on Intelligent Molecular Property Prediction: A Systematic Survey Taojie Kuang Pengfei Liu Zhixiang Ren AI4CE 47 1 0 11 Feb 2024
Advancing Explainable AI Toward Human-Like Intelligence: Forging the Path to Artificial Brain Yongchen Zhou Richard Jiang 24 2 0 07 Feb 2024
ADA-GNN: Atom-Distance-Angle Graph Neural Network for Crystal Material Property Prediction Jiao Huang Qianli Xing Jinglong Ji Bo Yang 25 3 0 22 Jan 2024
PerCNet: Periodic Complete Representation for Crystal Graphs Jiao Huang Qianli Xing Jinglong Ji Bo Yang 34 1 0 03 Dec 2023
LLM-Prop: Predicting Physical And Electronic Properties Of Crystalline Solids From Their Text Descriptions Andre Niyongabo Rubungo Craig Arnold Barry P. Rand Adji Bousso Dieng AI4CE 41 28 0 21 Oct 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
LibAUC: A Deep Learning Library for X-Risk Optimization Zhuoning Yuan Dixian Zhu Zimeng Qiu Gang Li Xuanhui Wang Tianbao Yang BDL 43 16 0 05 Jun 2023
AUC Optimization from Multiple Unlabeled Datasets Zheng Xie Yu Liu Ming Li 67 0 0 25 May 2023
Provable Multi-instance Deep AUC Maximization with Stochastic Pooling Dixian Zhu Bokun Wang Zhi Chen Yaxing Wang Milan Sonka Xiaodong Wu Tianbao Yang 16 3 0 14 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
3D Molecular Geometry Analysis with 2D Graphs Zhao Xu Yaochen Xie Youzhi Luo Xuan Zhang Xinyi Xu Meng Liu Kaleb Dickerson Cheng Deng Maho Nakata Shuiwang Ji 19 1 0 01 May 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 27 33 0 07 Apr 2023
Graph Neural Networks in Vision-Language Image Understanding: A Survey Henry Senior Greg Slabaugh Shanxin Yuan Luca Rossi GNN 33 13 0 07 Mar 2023
Graph Contrastive Learning for Multi-omics Data Nishant Rajadhyaksha Aarushi Chitkara 26 6 0 03 Jan 2023
Molecular Joint Representation Learning via Multi-modal Information Tianyu Wu Yang Tang Qiyu Sun Luolin Xiong 13 14 0 25 Nov 2022
Deep Surrogate Docking: Accelerating Automated Drug Discovery with Graph Neural Networks Ryien Hosseini F. Simini Austin R. Clyde A. Ramanathan 21 5 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
Learning Hierarchical Protein Representations via Complete 3D Graph Networks Limei Wang Haoran Liu Yi Liu Jerry Kurtin Shuiwang Ji GNN 30 55 0 26 Jul 2022
ComENet: Towards Complete and Efficient Message Passing for 3D Molecular Graphs Limei Wang Yi Liu Yu-Ching Lin Hao Liu Shuiwang Ji GNN 38 89 0 17 Jun 2022
Multi-block Min-max Bilevel Optimization with Applications in Multi-task Deep AUC Maximization Quanqi Hu Yongjian Zhong Tianbao Yang 25 16 0 01 Jun 2022
AUC Maximization in the Era of Big Data and AI: A Survey Tianbao Yang Yiming Ying 33 178 0 28 Mar 2022
Benchmarking Deep AUROC Optimization: Loss Functions and Algorithmic Choices Dixian Zhu Xiaodong Wu Tianbao Yang 28 10 0 27 Mar 2022
When AUC meets DRO: Optimizing Partial AUC for Deep Learning with Non-Convex Convergence Guarantee Dixian Zhu Gang Li Bokun Wang Xiaodong Wu Tianbao Yang 17 28 0 01 Mar 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
Neighbor2Seq: Deep Learning on Massive Graphs by Transforming Neighbors to Sequences Meng Liu Shuiwang Ji GNN 22 3 0 07 Feb 2022
Molecular Representation Learning via Heterogeneous Motif Graph Neural Networks Zhaoning Yu Hongyang Gao 31 39 0 01 Feb 2022
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 40 39 0 30 Sep 2021
ProcK: Machine Learning for Knowledge-Intensive Processes Tobias Jacobs Jingyi Yu J. Gastinger T. Sztyler 9 1 0 10 Sep 2021
Fast Quantum Property Prediction via Deeper 2D and 3D Graph Networks Meng Liu Cong Fu Xuan Zhang Limei Wang Yaochen Xie Hao Yuan Youzhi Luo Zhao Xu Shenglong Xu Shuiwang Ji GNN 11 17 0 16 Jun 2021
Stochastic Optimization of Areas Under Precision-Recall Curves with Provable Convergence Qi Qi Youzhi Luo Zhao Xu Shuiwang Ji Tianbao Yang 11 58 0 18 Apr 2021
DIG: A Turnkey Library for Diving into Graph Deep Learning Research Meng Liu Youzhi Luo Limei Wang Yaochen Xie Haonan Yuan ... Haoran Liu Cong Fu Bora Oztekin Xuan Zhang Shuiwang Ji GNN 24 118 0 23 Mar 2021
Self-Supervised Learning of Graph Neural Networks: A Unified Review Yaochen Xie Zhao Xu Jingtun Zhang Zhengyang Wang Shuiwang Ji SSL 21 324 0 22 Feb 2021
On Explainability of Graph Neural Networks via Subgraph Explorations Hao Yuan Haiyang Yu Jie Wang Kang Li Shuiwang Ji FAtt 26 380 0 09 Feb 2021
Spherical Message Passing for 3D Graph Networks Yi Liu Limei Wang Meng Liu Xuan Zhang Bora Oztekin Shuiwang Ji GNN 22 197 0 09 Feb 2021
GraphDF: A Discrete Flow Model for Molecular Graph Generation Youzhi Luo Keqiang Yan Shuiwang Ji DRL 185 187 0 01 Feb 2021
GraphEBM: Molecular Graph Generation with Energy-Based Models Meng Liu Keqiang Yan Bora Oztekin Shuiwang Ji 24 84 0 31 Jan 2021
Benchmarking Graph Neural Networks Vijay Prakash Dwivedi Chaitanya K. Joshi Anh Tuan Luu T. Laurent Yoshua Bengio Xavier Bresson 189 916 0 02 Mar 2020
Junction Tree Variational Autoencoder for Molecular Graph Generation Wengong Jin Regina Barzilay Tommi Jaakkola 224 1,338 0 12 Feb 2018
MoleculeNet: A Benchmark for Molecular Machine Learning Zhenqin Wu Bharath Ramsundar Evan N. Feinberg Joseph Gomes C. Geniesse Aneesh S. Pappu K. Leswing Vijay S. Pande OOD 172 1,778 0 02 Mar 2017