Peng Chen, Jian Wang, Hongfei Lin, Di Zhao, Zhihao Yang. Few-shot biomedical named entity recognition via knowledge-guided instance generation and prompt contrastive learning [J]. Bioinformatics, 2023, 39(8): btad496.[paper][code]
Peng Chen, Jian Wang, Hongfei Lin, Yijia Zhang, Zhihao Yang. Knowledge Adaptive Multi-way Matching Network for Biomedical Named Entity Recognition via Machine Reading Comprehension [J]. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2023, 20(3): 2101-2111. [paper][code]
Jinzhong Ning, Zhihao Yang, Yuanyuan Sun, Zhizheng Wang, Hongfei Lin. OD-RTE: A One-Stage Object Detection Framework for Relational Triple Extraction [C]. In Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics (ACL), Volume 1: Long Papers, 2023, 11120-11135. [paper][code]
Jinzhong Ning, Zhihao Yang, Zhizheng Wang, Yuanyuan Sun, Hongfei Lin. ODEE: A One-Stage Object Detection Framework for Overlapping and Nested Event Extraction [C]. In Proceedings of the Thirty-Second International Joint Conference on Artificial Intelligence (IJCAI), Main Track, 2023, 5170-5178. [paper][code]
Yingwen Zhao, Zhihao Yang, Yongkai Hong, Yumeng Yang, Lei Wang, Yin Zhang, Hongfei Lin, and Jian Wang. Protein Function Prediction with Functional and Topological Knowledge of Gene Ontology [J]. IEEE Transactions on NanoBioscience, 2023, 22(4): 755 - 762. [paper][code]
Yunzhi Qiu, Xiaokun Zhang, Weiwei Wang, Tongxuan Zhang, Bo Xu and Hongfei Lin. KESDT: knowledge enhanced shallow and deep Transformer for detecting adverse drug reactions [C]. In Natural Language Processing and Chinese Computing (NLPCC), 2023, 14303: 601-613. [paper]
2022
Yingwen Zhao, Zhihao Yang, Yongkai Hong, Lei Wang, Yin Zhang, Hongfei Lin, and Jian Wang. Improving Protein Function Prediction by Adaptively Fusing Information From Protein Sequences and Biomedical Literature [J]. IEEE Journal of Biomedical and Health Informatics, 2022, 27(2): 1140-1148. [paper][code]
Jinzhong Ning, Zhihao Yang, Zhizheng Wang, Yuanyuan Sun, Hongfei Lin, Jian Wang. Two Languages Are Better than One: Bilingual Enhancement for Chinese Named Entity Recognition [C]. In Proceedings of the 29th International Conference on Computational Linguistics (COLING), 2022, 2024-2033. [paper]
Jinzhong Ning, Jiru Li, Zhihao Yang, Yuanyuan Sun, Lei Wang, Yin Zhang, Hongfei Lin, Jian Wang. BioNER-CFEM: Biomedical Named Entity Recognition Based on Character Feature Enhancement with Multimodal Method [C]. In IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2022, 787-790. [paper]
Yan Zhang, Jiru Li, Zhihao Yang, Hongfei Lin, Jian Wang. Location-Guided Token Pair Tagger for Joint Biomedical Entity and Relation Extraction [C]. In IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2022, 666-67[paper]
Peng Chen, Jian Wang, Hongfei Lin, Yichen Wang, Di Zhao, Yijia Zhang. Syntactic Type-aware Graph Attention Network for Drug-drug Interactions and their Adverse Effects Extraction [C]. In IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2022, 404-409. [paper][code]
Kaiyuan Shi, Shaowu Zhang, Haifeng Liu, Yijia Zhang, Hongfei Lin. MGEDR: A Molecular Graph Encoder for Drug Recommendation [C]. In Natural Language Processing and Chinese Computing (NLPCC), 2022, 13552: 98-109. [paper]
Yingwen Zhao, Zhihao Yang, Yongkai Hong, Lei Wang, Yin Zhang, Hongfei Lin, and Jian Wang. Adaptive Multi-view Graph Convolutional Network for Gene Ontology Annotations of Proteins[C]. In IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2022, 90-93. [paper][code]
Dinghao Pan, Zhihao Yang, Haixin Tan, Jiangming Wu and Hongfei Lin. Dialogue Topic Extraction as Sentence Sequence Labeling [C]. In Natural Language Processing and Chinese Computing (NLPCC), 2022, 13552: 252-262. [paper]
Early Selected Publications
Peng Chen, Jian Wang, Hongfei Lin, Yijia Zhang, Zhihao Yang, Di Zhao, Hui Ma. Co-attentive span network with multi-task learning for biomedical named entity recognition [C]. In IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2021, 649–652. [paper][code]
Ling Luo, Zhihao Yang, Mingyu Cao, Lei Wang, Yin Zhang and Hongfei Lin. A neural network-based joint learning approach for biomedical entity and relation extraction from biomedical literature [J]. Journal of Biomedical Informatics, 2020, 103: 103384. [paper]
Ling Luo, Zhihao Yang, Yawen Song, Nan Li and Hongfei Lin. Chinese Clinical Named Entity Recognition Based on Stroke ELMo and Multi-Task Learning [J]. Chinese Journal of Computers, 2020, 43(10): 1943-1957. (In Chinese) [paper]
Ling Luo, Zhihao Yang, Pei Yang, Yin Zhang, Lei Wang, Hongfei Lin and Jian Wang. An attention-based BiLSTM-CRF approach to document-level chemical named entity recognition [J]. Bioinformatics, 2018, 34(8): 1381–1388. [paper]
Zhehuan Zhao, Zhihao Yang, Ling Luo, Hongfei Lin, Jian Wang. Drug drug interaction extraction from biomedical literature using syntax convolutional neural network [J]. Bioinformatics, 2016, 32(22): 3444-3453. [paper]