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Advanced Graph and Sequence Neural Networks for Molecular Property
  Prediction and Drug Discovery
v1v2v3 (latest)

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

2 December 2020
Zhengyang Wang
Meng Liu
Youzhi Luo
Zhao Xu
Yaochen Xie
Limei Wang
Lei Cai
Q. Qi
Zhuoning Yuan
Tianbao Yang
Shuiwang Ji
ArXiv (abs)PDFHTML

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

42 / 42 papers shown
DACTYL: Diverse Adversarial Corpus of Texts Yielded from Large Language Models
DACTYL: Diverse Adversarial Corpus of Texts Yielded from Large Language Models
Shantanu Thorat
Andrew Caines
235
0
0
01 Aug 2025
Multi-Level Fusion Graph Neural Network for Molecule Property Prediction
Multi-Level Fusion Graph Neural Network for Molecule Property Prediction
XiaYu Liu
Chao Fan
Yang Liu
Hou-biao Li
AI4CE
197
1
0
04 Jul 2025
Adapting Differential Molecular Representation with Hierarchical Prompts
  for Multi-label Property Prediction
Adapting Differential Molecular Representation with Hierarchical Prompts for Multi-label Property Prediction
Linjia Kang
Songhua Zhou
Shuyan Fang
Shichao Liu
Wen Zhang
AI4CE
422
5
0
29 May 2024
Single-loop Stochastic Algorithms for Difference of Max-Structured
  Weakly Convex Functions
Single-loop Stochastic Algorithms for Difference of Max-Structured Weakly Convex Functions
Quanqi Hu
Qi Qi
Zhaosong Lu
Tianbao Yang
534
4
0
28 May 2024
Impact of Domain Knowledge and Multi-Modality on Intelligent Molecular
  Property Prediction: A Systematic Survey
Impact of Domain Knowledge and Multi-Modality on Intelligent Molecular Property Prediction: A Systematic SurveyBig Data Mining and Analytics (BDMA), 2024
Taojie Kuang
Pengfei Liu
Zhixiang Ren
AI4CE
330
14
0
11 Feb 2024
Advancing Explainable AI Toward Human-Like Intelligence: Forging the
  Path to Artificial Brain
Advancing Explainable AI Toward Human-Like Intelligence: Forging the Path to Artificial Brain
Yongchen Zhou
Richard Jiang
367
7
0
07 Feb 2024
ADA-GNN: Atom-Distance-Angle Graph Neural Network for Crystal Material
  Property Prediction
ADA-GNN: Atom-Distance-Angle Graph Neural Network for Crystal Material Property Prediction
Jiao Huang
Qianli Xing
Jinglong Ji
Bo Yang
166
4
0
22 Jan 2024
PerCNet: Periodic Complete Representation for Crystal Graphs
PerCNet: Periodic Complete Representation for Crystal GraphsNeural Networks (Neural Netw.), 2023
Jiao Huang
Qianli Xing
Jinglong Ji
Bo Yang
308
4
0
03 Dec 2023
LLM-Prop: Predicting Physical And Electronic Properties Of Crystalline
  Solids From Their Text Descriptions
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
335
40
0
21 Oct 2023
Efficient Approximations of Complete Interatomic Potentials for Crystal
  Property Prediction
Efficient Approximations of Complete Interatomic Potentials for Crystal Property PredictionInternational Conference on Machine Learning (ICML), 2023
Yu-Ching Lin
Keqiang Yan
Youzhi Luo
Lu Dong
Xiaoning Qian
Shuiwang Ji
826
50
0
12 Jun 2023
Efficient and Equivariant Graph Networks for Predicting Quantum
  Hamiltonian
Efficient and Equivariant Graph Networks for Predicting Quantum HamiltonianInternational Conference on Machine Learning (ICML), 2023
Haiyang Yu
Zhao Xu
X. Qian
Xiaoning Qian
Shuiwang Ji
312
50
0
08 Jun 2023
LibAUC: A Deep Learning Library for X-Risk Optimization
LibAUC: A Deep Learning Library for X-Risk OptimizationKnowledge Discovery and Data Mining (KDD), 2023
Zhuoning Yuan
Dixian Zhu
Zimeng Qiu
Gang Li
Xuanhui Wang
Tianbao Yang
BDL
254
21
0
05 Jun 2023
AUC Optimization from Multiple Unlabeled Datasets
AUC Optimization from Multiple Unlabeled DatasetsAAAI Conference on Artificial Intelligence (AAAI), 2023
Zheng Xie
Yu Liu
Ming Li
445
2
0
25 May 2023
Provable Multi-instance Deep AUC Maximization with Stochastic Pooling
Provable Multi-instance Deep AUC Maximization with Stochastic PoolingInternational Conference on Machine Learning (ICML), 2023
Dixian Zhu
Bokun Wang
Zhi Chen
Yaxing Wang
Milan Sonka
Xiaodong Wu
Tianbao Yang
497
5
0
14 May 2023
A Latent Diffusion Model for Protein Structure Generation
A Latent Diffusion Model for Protein Structure GenerationLOG IN (LOG IN), 2023
Cong Fu
Keqiang Yan
Limei Wang
Wing Yee Au
Michael McThrow
Tao Komikado
Koji Maruhashi
Kanji Uchino
Xiaoning Qian
Shuiwang Ji
DiffM
358
50
0
06 May 2023
3D Molecular Geometry Analysis with 2D Graphs
3D Molecular Geometry Analysis with 2D GraphsSDM (SDM), 2023
Zhao Xu
Yaochen Xie
Youzhi Luo
Xuan Zhang
Xinyi Xu
Meng Liu
Kaleb Dickerson
Cheng Deng
Maho Nakata
Shuiwang Ji
302
2
0
01 May 2023
A new perspective on building efficient and expressive 3D equivariant
  graph neural networks
A new perspective on building efficient and expressive 3D equivariant graph neural networksNeural Information Processing Systems (NeurIPS), 2023
Weitao Du
Yuanqi Du
Limei Wang
Dieqiao Feng
Guifeng Wang
Shuiwang Ji
Daniel Schwalbe-Koda
Zhixin Ma
AI4CE
288
63
0
07 Apr 2023
Graph Neural Networks in Vision-Language Image Understanding: A Survey
Graph Neural Networks in Vision-Language Image Understanding: A SurveyThe Visual Computer (TVC), 2023
Henry Senior
Greg Slabaugh
Shanxin Yuan
Luca Rossi
GNN
365
38
0
07 Mar 2023
Graph Contrastive Learning for Multi-omics Data
Graph Contrastive Learning for Multi-omics Data
Nishant Rajadhyaksha
Aarushi Chitkara
164
9
0
03 Jan 2023
Molecular Joint Representation Learning via Multi-modal Information
Molecular Joint Representation Learning via Multi-modal InformationIEEE/ACM Transactions on Computational Biology & Bioinformatics (TCBB), 2022
Tianyu Wu
Yang Tang
Qiyu Sun
Luolin Xiong
214
24
0
25 Nov 2022
Deep Surrogate Docking: Accelerating Automated Drug Discovery with Graph
  Neural Networks
Deep Surrogate Docking: Accelerating Automated Drug Discovery with Graph Neural Networks
Ryien Hosseini
F. Simini
Austin R. Clyde
A. Ramanathan
321
5
0
04 Nov 2022
Periodic Graph Transformers for Crystal Material Property Prediction
Periodic Graph Transformers for Crystal Material Property PredictionNeural Information Processing Systems (NeurIPS), 2022
Keqiang Yan
Lu Dong
Yu-Ching Lin
Shuiwang Ji
AI4TS
301
134
0
23 Sep 2022
Learning Hierarchical Protein Representations via Complete 3D Graph
  Networks
Learning Hierarchical Protein Representations via Complete 3D Graph NetworksInternational Conference on Learning Representations (ICLR), 2022
Limei Wang
Haoran Liu
Lu Dong
Jerry Kurtin
Shuiwang Ji
GNN
275
88
0
26 Jul 2022
ComENet: Towards Complete and Efficient Message Passing for 3D Molecular
  Graphs
ComENet: Towards Complete and Efficient Message Passing for 3D Molecular GraphsNeural Information Processing Systems (NeurIPS), 2022
Limei Wang
Lu Dong
Yu-Ching Lin
Hao Liu
Shuiwang Ji
GNN
414
120
0
17 Jun 2022
Multi-block Min-max Bilevel Optimization with Applications in Multi-task
  Deep AUC Maximization
Multi-block Min-max Bilevel Optimization with Applications in Multi-task Deep AUC MaximizationNeural Information Processing Systems (NeurIPS), 2022
Quanqi Hu
Yongjian Zhong
Tianbao Yang
453
19
0
01 Jun 2022
AUC Maximization in the Era of Big Data and AI: A Survey
AUC Maximization in the Era of Big Data and AI: A SurveyACM Computing Surveys (ACM CSUR), 2022
Tianbao Yang
Yiming Ying
553
285
0
28 Mar 2022
Benchmarking Deep AUROC Optimization: Loss Functions and Algorithmic
  Choices
Benchmarking Deep AUROC Optimization: Loss Functions and Algorithmic Choices
Dixian Zhu
Xiaodong Wu
Tianbao Yang
318
15
0
27 Mar 2022
When AUC meets DRO: Optimizing Partial AUC for Deep Learning with
  Non-Convex Convergence Guarantee
When AUC meets DRO: Optimizing Partial AUC for Deep Learning with Non-Convex Convergence GuaranteeInternational Conference on Machine Learning (ICML), 2022
Dixian Zhu
Gang Li
Bokun Wang
Xiaodong Wu
Tianbao Yang
726
41
0
01 Mar 2022
Task-Agnostic Graph Explanations
Task-Agnostic Graph ExplanationsNeural Information Processing Systems (NeurIPS), 2022
Yaochen Xie
S. Katariya
Xianfeng Tang
E-Wen Huang
Nikhil S. Rao
Karthik Subbian
Shuiwang Ji
349
33
0
16 Feb 2022
Neighbor2Seq: Deep Learning on Massive Graphs by Transforming Neighbors
  to Sequences
Neighbor2Seq: Deep Learning on Massive Graphs by Transforming Neighbors to SequencesSDM (SDM), 2022
Meng Liu
Shuiwang Ji
GNN
141
4
0
07 Feb 2022
Molecular Representation Learning via Heterogeneous Motif Graph Neural
  Networks
Molecular Representation Learning via Heterogeneous Motif Graph Neural NetworksInternational Conference on Machine Learning (ICML), 2022
Zhaoning Yu
Hongyang Gao
382
56
0
01 Feb 2022
Molecule3D: A Benchmark for Predicting 3D Geometries from Molecular
  Graphs
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
259
47
0
30 Sep 2021
ProcK: Machine Learning for Knowledge-Intensive Processes
ProcK: Machine Learning for Knowledge-Intensive Processes
Tobias Jacobs
Jingyi Yu
J. Gastinger
T. Sztyler
216
1
0
10 Sep 2021
Fast Quantum Property Prediction via Deeper 2D and 3D Graph Networks
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
125
20
0
16 Jun 2021
Stochastic Optimization of Areas Under Precision-Recall Curves with
  Provable Convergence
Stochastic Optimization of Areas Under Precision-Recall Curves with Provable ConvergenceNeural Information Processing Systems (NeurIPS), 2021
Qi Qi
Youzhi Luo
Zhao Xu
Shuiwang Ji
Tianbao Yang
700
68
0
18 Apr 2021
DIG: A Turnkey Library for Diving into Graph Deep Learning Research
DIG: A Turnkey Library for Diving into Graph Deep Learning ResearchJournal of machine learning research (JMLR), 2021
Meng Liu
Youzhi Luo
Limei Wang
Yaochen Xie
Haonan Yuan
...
Haoran Liu
Cong Fu
Bora Oztekin
Xuan Zhang
Shuiwang Ji
GNN
346
133
0
23 Mar 2021
Self-Supervised Learning of Graph Neural Networks: A Unified Review
Self-Supervised Learning of Graph Neural Networks: A Unified ReviewIEEE Transactions on Pattern Analysis and Machine Intelligence (TPAMI), 2021
Yaochen Xie
Zhao Xu
Jingtun Zhang
Zhengyang Wang
Shuiwang Ji
SSL
764
397
0
22 Feb 2021
On Explainability of Graph Neural Networks via Subgraph Explorations
On Explainability of Graph Neural Networks via Subgraph ExplorationsInternational Conference on Machine Learning (ICML), 2021
Hao Yuan
Haiyang Yu
Jie Wang
Kang Li
Shuiwang Ji
FAtt
437
496
0
09 Feb 2021
Spherical Message Passing for 3D Graph Networks
Spherical Message Passing for 3D Graph NetworksInternational Conference on Learning Representations (ICLR), 2021
Lu Dong
Limei Wang
Meng Liu
Xuan Zhang
Bora Oztekin
Shuiwang Ji
GNN
803
250
0
09 Feb 2021
GraphDF: A Discrete Flow Model for Molecular Graph Generation
GraphDF: A Discrete Flow Model for Molecular Graph GenerationInternational Conference on Machine Learning (ICML), 2021
Youzhi Luo
Keqiang Yan
Shuiwang Ji
DRL
606
257
0
01 Feb 2021
GraphEBM: Molecular Graph Generation with Energy-Based Models
GraphEBM: Molecular Graph Generation with Energy-Based Models
Meng Liu
Keqiang Yan
Bora Oztekin
Shuiwang Ji
305
103
0
31 Jan 2021
Benchmarking Graph Neural Networks
Benchmarking Graph Neural NetworksJournal of machine learning research (JMLR), 2023
Vijay Prakash Dwivedi
Chaitanya K. Joshi
Anh Tuan Luu
T. Laurent
Yoshua Bengio
Xavier Bresson
1.6K
1,141
0
02 Mar 2020
1
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