Publications

Selected Recent Publications

AI for Science

• Yin Fang, Qiang Zhang, Ningyu Zhang, Zhuo Chen, Xiang Zhuang, Xin Shao, Xiaohui Fan, Huajun Chen*.Knowledge graph-enhanced molecular contrastive learning with functional prompt. Nature Machine Intelligence. 2023.
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• Zeyuan Wang, Qiang Zhang, Shuang-Wei HU, Haoran Yu, Xurui Jin, Zhichen Gong, Huajun Chen*. Multi-level Protein Structure Pre-training via Prompt Learning. International Conference on Learning Representations(ICLR). 2023.
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• Xiang Zhuang, Qiang Zhang, Bin Wu, Keyan Ding, Yin Fang, Huajun Chen*. Graph Sampling-based Meta-Learning for Molecular Property Prediction. International Joint Conference on Artificial Intelligenc(IJCAI). 2023.
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• Jie Liao , Jingyang Qian , Yin Fang , Zhuo Chen , Xiang Zhuang , Ningyu Zhang , Xin Shao , Yining Hu , Penghui Yang , Junyun Cheng , Yang Hu , Lingqi Yu , Haihong Yang , Jinlu Zhang , Xiaoyan Lu , Li Shao , Dan Wu , Yue Gao , Huajun Chen*, Xiaohui Fan*. De novo analysis of bulk RNA-seq data at spatially resolved single-cell resolution. Nature Communications. 2022.
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• Xin Shao , Chengyu Li , Haihong Yang , Xiaoyan Lu , Jie Liao , Penghui Yang , Huajun Chen*, Xiao Xu，Xiaohui Fan. Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data with SpaTalk. Nature Communications. 2022.
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• Ningyu Zhang, Zhen Bi, Xiaozhuan Liang, Siyuan Cheng, Haosen Hong, Shumin Deng, Qiang Zhang, Jiazhang Lian, Huajun Chen*. OntoProtein: Protein Pretraining With Gene Ontology Embedding. Tenth International Conference on Learning Representations(ICLR). 2022.
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• Yin Fang, Qiang Zhang, Haihong Yang, Xiang Zhuang, Shumin Deng, Wen Zhang, Ming Qin, Zhuo Chen, Xiaohui Fan, Huajun Chen*. Molecular Contrastive Learning with Chemical Element Knowledge Graph. Association for the Advancement of Artificial Intelligence(AAAI). 2022.
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• Xin Shao, Haihong Yang, Xiang Zhuang, Jie Liao, Huajun Chen*, Xiaohui Fan*. scDeepSort: a Pre-trained Cell-type Annotation Method for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network. Nucleic Acids Research. 2021.
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KG & NLP

• Jiaoyan Chen, Yuxia Geng, Zhuo Chen, Jeff Z. Pan, Yuan He, Wen Zhang, Ian Horrocks and Huajun Chen*. Zero-shot and Few-shot Learning with Knowledge Graphs: A Comprehensive Survey. Proceedings of the IEEE. 2023.
  

• Mingyang Chen, Wen Zhang, Yuxia Geng, Zezhong Xu, Jeff Z. Pan, Huajun Chen*. Generalizing to Unseen Elements: A Survey on Knowledge Extrapolation for Knowledge Graphs. International Joint Conference on Artificial Intelligence(IJCAI). 2023.
  

• Ningyu Zhang, Lei Li, Xiang Chen, Xiaozhuan Liang, Shumin Deng, Huajun Chen*. Multimodal Analogical Reasoning over Knowledge Graphs. International Conference on Learning Representations(ICLR). 2023.
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• Wen Zhang, Yushan Zhu, Mingyang Chen, Yuxia Geng, Yufeng Huang, Yajing Xu, Wenting Song, Huajun Chen*. KGTransformer: Structure Pre-training and Prompt Tuning for Knowledge Graph Transfer. Proceedings of the ACM Web Conference(WWW). 2022.
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• Shuofei Qiao, Yixin Ou, Ningyu Zhang, Xiang Chen, Yunzhi Yao, Shumin Deng, Chuanqi Tan, Fei Huang, Huajun Chen*. Reasoning with Language Model Prompting: A Survey.** Annual Meeting of the Association for Computational Linguistics(ACL)**. 2023.
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• Yunzhi Yao, Shengyu Mao, Xiang Chen, Shumin Deng, Ningyu Zhang, Xi Chen and Huajun Chen*. Schema-aware Reference as Prompt Improves Data-Efficient Knowledge Graph Construction. Special Interest Group on Information Retrieval (SIGIR). 2023.
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• Mingyang Chen,Wen Zhang,Zhen Yao, Yushan Zhu, Yang Gao,Jeff Z. Pan,Huajun Chen*. Entity-Agnostic Representation Learning for Parameter-Efficient Knowledge Graph Embedding. Thirty-Seventh AAAI Conference on Artificial Intelligence(AAAI). 2023.
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• Zhen Yao，Wen Zhang，Mingyang Chen,Yufeng Huang,Yi Yang,Huajun Chen. Analogical Inference Enhanced Knowledge Graph Embedding. Thirty-Seventh AAAI Conference on Artificial Intelligence(AAAI). 2023.
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• Yuxia Geng,Jiaoyan Chen,Wen Zhang,Jeff Z. Pan, Mingyang Chen,Song Jiang, Huajun Chen*. Relational Message Passing for Fully Inductive Knowledge Graph Completion. International Conference On Data Engineering(ICDE). 2023.
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• Zezhong Xu, Wen Zhang, Peng Ye, Hui Chen, Huajun Chen*. Neural-Symbolic Entangled Framework for Complex Query Answering. Thirty-Sixth Conference on Neural Information Processing Systems(NeurIPS). 2023.
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• Xiang Chen, Lei Li, Ningyu Zhang, Xiaozhuan Liang, Shumin Deng, Chuanqi Tan, Fei Huang, Luo Si, Huajun Chen*. Decoupling Knowledge from Memorization: Retrieval-augmented Prompt Learning. Thirty-Sixth Conference on Neural Information Processing Systems(NeurIPS). 2022.
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• Yuxia Geng，Jiaoyan Chen，Wen Zhang，Zhuo Chen，Jeff Z. Pan，Feiyu Xiong，Huajun Chen*. Disentangled Ontology Embedding for Zero-shot Learning. ACM SIGKDD Conference on Knowledge Discovery and Data Mining(KDD). 2022.
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• Lingbing Guo，Zequn Sun，Mingyang Chen，Wei Hu，Qiang Zhang，Huajun Chen*. Understanding and Improving Knowledge Graph Embedding for Entity Alignment. International Conference on Machine Learning (ICML). 2022.
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• Mingyang Chen,Wen Zhang,Zhen Yao,Fei Huang,Huajun Chen*. Meta-Learning Based Knowledge Extrapolation for Knowledge Graphs in the Federated Setting. The 31st International Joint Conference on Artificial Intelligence (IJCAI) . 2022.
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• Ningyu Zhang, Luoqiu Li, Xiang Chen, Shumin Deng, Zhen Bi, Chuanqi Tan, Fei Huang, Huajun Chen*. Differentiable Prompt Makes Pre-trained Language Models Better Few-shot Learners. Tenth International Conference on Learning Representations(ICLR). 2022.
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• Xiang Chen, Ningyu Zhang, Xin Xie, Shumin Deng, Yunzhi Yao, Chuanqi Tan, Fei Huang, Luo Si and Huajun Chen*. KnowPrompt: Knowledge-aware Prompt-tuning with Synergistic Optimization for Relation Extraction. Proceedings of the ACM Web Conference(WWW). 2022.
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