| A comprehensive survey on deep graph representation learning W Ju, Z Fang, Y Gu, Z Liu, Q Long, Z Qiao, Y Qin, J Shen, F Sun, Z Xiao, ... Neural Networks 173, 106207, 2024 | 346 | 2024 |
| Large language model agent: A survey on methodology, applications and challenges J Luo, W Zhang, Y Yuan, Y Zhao, J Yang, Y Gu, B Wu, B Chen, Z Qiao, ... arXiv preprint arXiv:2503.21460, 2025 | 139* | 2025 |
| Poisoning medical knowledge using large language models J Yang, H Xu, S Mirzoyan, T Chen, Z Liu, Z Liu, W Ju, L Liu, Z Xiao, ... Nature Machine Intelligence 6 (10), 1156-1168, 2024 | 81* | 2024 |
| Towards graph contrastive learning: A survey and beyond W Ju, Y Wang, Y Qin, Z Mao, Z Xiao, J Luo, J Yang, Y Gu, D Wang, ... arXiv preprint arXiv:2405.11868, 2024 | 81 | 2024 |
| Kgnn: Harnessing kernel-based networks for semi-supervised graph classification W Ju, J Yang, M Qu, W Song, J Shen, M Zhang Proceedings of the fifteenth ACM international conference on web search and …, 2022 | 47 | 2022 |
| GHNN: Graph harmonic neural networks for semi-supervised graph-level classification W Ju, X Luo, Z Ma, J Yang, M Deng, M Zhang Neural Networks 151, 70-79, 2022 | 46 | 2022 |
| ESM All-Atom: Multi-Scale Protein Language Model for Unified Molecular Modeling K Zheng, S Long, T Lu, J Yang, X Dai, M Zhang, Z Nie, WY Ma, H Zhou ICML 2024, 0 | 21* | |
| MOL-AE: Auto-Encoder Based Molecular Representation Learning With 3D Cloze Test Objective J Yang, K Zheng, S Long, Z Nie, M Zhang, X Dai, WY Ma, H Zhou ICML 2024, 2024 | 15* | 2024 |
| Smi-editor: Edit-based smiles language model with fragment-level supervision K Zheng, S Liang, J Yang, B Feng, Z Liu, W Ju, Z Xiao, M Zhang arXiv preprint arXiv:2412.05569, 2024 | 8 | 2024 |
| Pathway2text: Dataset and method for biomedical pathway description generation J Yang, Z Liu, M Zhang, S Wang Findings of the Association for Computational Linguistics: NAACL 2022, 1441-1454, 2022 | 3 | 2022 |
| MetaFill: Text Infilling for Meta-Path Generation on Heterogeneous Information Networks Z Liu, K Duan, J Yang, H Xu, M Zhang, S Wang EMNLP 2022, 2022 | 2 | 2022 |
| ExLM: Rethinking the Impact of Tokens in Masked Language Models K Zheng, J Yang, S Liang, B Feng, Z Liu, W Ju, Z Xiao, M Zhang Forty-second International Conference on Machine Learning, 0 | 2* | |
| Artificial intelligence in pathology: advancing large models for scalable applications Z Xiao, B Feng, J Yang, G Sun, Y Shen, S Xu, L Yang, H Xu, M Zhang, ... Annual Review of Biomedical Data Science 8 (1), 149-171, 2025 | 1 | 2025 |
| TowerDNA: Fast and Accurate Graph Retrieval with Dividing, Contrasting and Alignment J Yang, Y Gu, Y Qin, X Luo, Z Xiao, K Zheng, W Ju, XS Hua, M Zhang IEEE Transactions on Knowledge and Data Engineering, 2025 | | 2025 |
