Publications

Content

[2026] [2025] [2024] [2023] [2022] [Early]

2026

  1. Junliang Liu, Ling Luo, Dinghao Pan, Yiyang Kang, Yuanyuan Sun, Hongfei Lin, Lejing Yu, Huan Zhuang. BioRENLI: enhancing large language models for biomedical relation extraction through preference-aligned natural language inference [J]. Health Information Science and Systems, 2025, 14(74). [paper].

2025

  1. Chao Liu, Ling Luo, Tengxiao Lv, Huan Zhuang, Lejing Yu, Jian Wang, Hongfei Lin. FocusMed: A Large Language Model-based Framework for Enhancing Medical Question Summarization with Focus Identification [C]. 2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Wuhan, China, 2025, 2568-2573. [paper].
  2. Tengxiao Lv, Ling Luo, Juntao Li, Yanhua Wang, Yuchen Pan, Chao Liu, Yanan Wang, Yan Jiang, Huiyi Lv, Yuanyuan Sun, Jian Wang, Hongfei Lin. A Unified Biomedical Named Entity Recognition Framework with Large Language Models [C]. 2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Wuhan, China, 2025, 3913-3916. [paper].
  3. Juntao Li, Haobin Yuan, Ling Luo, Tengxiao Lv, Yan Jiang, Fan Wang, Ping Zhang, Huiyi Lv, Jian Wang, Yuanyuan Sun, Hongfei Lin. Overview of chip 2025 shared task 2: discharge medication recommendation for metabolic diseases based on Chinese electronic health records [C]. China Health Information Processing Conference (CHIP2025), 2025, 477-489. [paper]
  4. Tengxiao Lv, Juntao Li, Chao Liu, Yiyang Kang, Ling Luo, Yuanyuan Sun, Hongfei Lin. DUTIR at SemEval-2025 Task 10: A Large Language Model-based Approach for Entity Framing in Online News [C]. Proceedings of the 19th International Workshop on Semantic Evaluation (SemEval-2025), 2025, 174-179. [paper]
  5. Yumeng Yang, Hongfei Lin, Zhihao Yang, Yijia Zhang, Di Zhao, Ling Luo. LCDL: Classification of ICD codes based on disease label co-occurrence dependency and LongFormer with medical knowledge [J]. Artificial Intelligence in Medicine, 2025, 160: 103041. [paper]

2024

  1. Ling Luo, Jinzhong Ning, Yingwen Zhao, et al. Taiyi: a bilingual fine-tuned large language model for diverse biomedical tasks [J]. Journal of the American Medical Informatics Association, February 2024, btad310. [paper][code]
  2. Peng Chen, Jian Wang, Ling Luo, Hongfei Lin, Zhihao Yang. Learning to explain is a good biomedical few-shot learner [J]. Bioinformatics, 2024, 40(10): btae589. [paper]
  3. Jiewei Qi, Ling Luo, Zhihao Yang, Jian Wang, Huiwei Zhou, Hongfei Lin. An Improved Method for Phenotype Concept Recognition Using Rich HPO Information [C]. 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Lisbon, Portugal, 2024, 1135-1140. [paper].
  4. Yongle Kong, Zhihao Yang, Ling Luo, Zeyuan Ding, Lei Wang, Wei Liu, Yin Zhang, Bo Xu, Jian Wang, Yuanyuan Sun, Zhehuan Zhao, Hongfei Lin. Document Embeddings Enhance Biomedical Retrieval-Augmented Generation [C]. 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Lisbon, Portugal, 2024, 962-967. [paper].
  5. Jiru Li, Yuanyuan Sun, Zhihao Yang, Ling Luo, Lei Wang, Wei Liu, Yin Zhang, Bo Xu, Jian Wang, Yumeng Yang, Zhehuan Zhao, Hongfei Lin. Biomedical Document-level Relation Extraction with Coreference and Anaphor Graphs [C]. 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Lisbon, Portugal, 2024, 982-987. [paper].
  6. Zeyuan Ding, Zhihao Yang, Ling Luo, Yuanyuan Sun, Hongfei Lin. From Retrieval to Generation: A Simple and Unified Generative Model for End-to-End Task-Oriented Dialogue [C]. Proceedings of the AAAI Conference on Artificial Intelligence, 38(16), 2024, 17907-17914. [paper]
  7. Jinzhong Ning, Yuanyuan Sun, Bo Xu, Zhihao Yang, Ling Luo, Hongfei Lin. Breaking the Boundaries: A Unified Framework for Chinese Named Entity Recognition Across Text and Speech [C]. In Findings of the Association for Computational Linguistics: EMNLP 2024, pages 1250–1260, Miami, Florida, USA. Association for Computational Linguistics. [paper]

2023

  1. 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]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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

  1. 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]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. 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

  1. 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]
  2. 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]
  3. 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]
  4. 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]
  5. 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]