Deep neural network based protein-protein interaction extraction from biomedical literature. - Zhehuan Zhao; Zhihao Yang; Ling Luo 001; Hongfei Lin; Jian Wang 021; Song Gao (BIBM, 2015)

ML-CNN: A novel deep learning based disease named entity recognition architecture. - Zhehuan Zhao; Zhihao Yang; Ling Luo 001; Yin Zhang 009; Lei Wang 085; Hongfei Lin; Jian Wang 021 (BIBM, 2016)

Drug drug interaction extraction from biomedical literature using syntax convolutional neural network. - Zhehuan Zhao; Zhihao Yang; Ling Luo 001; Hongfei Lin; Jian Wang 021 (Bioinform., 2016)

An attention-based effective neural model for drug-drug interactions extraction. - Wei Zheng 003; Hongfei Lin; Ling Luo 001; Zhehuan Zhao; Zhengguang Li; Yijia Zhang 001; Zhihao Yang; Jian Wang 021 (BMC Bioinform., 2017)

A multi-task learning based approach to biomedical entity relation extraction. - Qingqing Li; Zhihao Yang; Ling Luo 001; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021; Liang Yang 003; Kan Xu; Yijia Zhang 001 (BIBM, 2018)

HMNPPID: A Database of Protein-protein Interactions Associated with Human Malignant Neoplasms. - Qingqing Li; Zhihao Yang; Zhehuan Zhao; Ling Luo 001; Zhiheng Li 004; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021; Yijia Zhang 001 (BIBM, 2018)

Protein-Protein Interaction Article Classification: A Knowledge-enriched Self-Attention Convolutional Neural Network Approach. - Ling Luo 001; Zhihao Yang; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021; Liang Yang 003; Kan Xu; Yijia Zhang 001 (BIBM, 2018)

DUTIR at the CCKS-2018 Task1: A Neural Network Ensemble Approach for Chinese Clinical Named Entity Recognition. - Ling Luo 001; Nan Li; Shuaichi Li; Zhihao Yang; Hongfei Lin (CCKS Tasks, 2018)

Document triage for identifying protein-protein interactions affected by mutations: a neural network ensemble approach. - Ling Luo 001; Zhihao Yang; Hongfei Lin; Jian Wang 021 (Database J. Biol. Databases Curation, 2018)

An attention-based BiLSTM-CRF approach to document-level chemical named entity recognition. - Ling Luo 001; Zhihao Yang; Pei Yang; Yin Zhang 009; Lei Wang 085; Hongfei Lin; Jian Wang 021 (Bioinform., 2018)

A neural network approach to chemical and gene/protein entity recognition in patents. - Ling Luo 001; Zhihao Yang; Pei Yang; Yin Zhang 009; Lei Wang 085; Jian Wang 021; Hongfei Lin (J. Cheminformatics, 2018)

DUTIR at TREC 2019: Precision Medicine Track. - Jingkun Feng; Zhihao Yang; Zhiqiang Liu; Ling Luo 001; Hongfei Lin; Jian Wang 021 (TREC, 2019)

A Deep Learning Approach With Deep Contextualized Word Representations for Chemical-Protein Interaction Extraction From Biomedical Literature. - Cong Sun 004; Zhihao Yang; Ling Luo 001; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021 (IEEE Access, 2019)

Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. - Rezarta Islamaj Dogan; Sun Kim; Andrew Chatr-aryamontri; Chih-Hsuan Wei; Donald C. Comeau; Rui Antunes 002; Sérgio Matos; Qingyu Chen 001; Aparna Elangovan; Nagesh C. Panyam; Karin Verspoor; Hongfang Liu; et al. (Database J. Biol. Databases Curation, 2019)

KeSACNN: a protein-protein interaction article classification approach based on deep neural network. - Ling Luo 001; Zhihao Yang; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021 (Int. J. Data Min. Bioinform., 2019)

Exploiting sequence labeling framework to extract document-level relations from biomedical texts. - Zhiheng Li 004; Zhihao Yang; Yang Xiang 003; Ling Luo 001; Yuanyuan Sun 002; Hongfei Lin (BMC Bioinform., 2020)

Artificial Intelligence (AI) in Action: Addressing the COVID-19 Pandemic with Natural Language Processing (NLP). - Qingyu Chen 001; Robert Leaman; Alexis Allot; Ling Luo 001; Chih-Hsuan Wei; Shankai Yan; Zhiyong Lu (CoRR, 2020)

Exploiting adversarial transfer learning for adverse drug reaction detection from texts. - Zhiheng Li 004; Zhihao Yang; Ling Luo 001; Yang Xiang 003; Hongfei Lin (J. Biomed. Informatics, 2020)

A neural network-based joint learning approach for biomedical entity and relation extraction from biomedical literature. - Ling Luo 001; Zhihao Yang; Mingyu Cao; Lei Wang 085; Yin Zhang 009; Hongfei Lin (J. Biomed. Informatics, 2020)

KGHC: a knowledge graph for hepatocellular carcinoma. - Nan Li; Zhihao Yang; Ling Luo 001; Lei Wang 085; Yin Zhang 009; Hongfei Lin; Jian Wang 021 (BMC Medical Informatics Decis. Mak., 2020)

PhenoTagger: a hybrid method for phenotype concept recognition using human phenotype ontology. - Ling Luo 001; Shankai Yan; Po-Ting Lai; Daniel Veltri; Andrew J. Oler; Sandhya Xirasagar; Rajarshi Ghosh; Morgan Similuk; Peter N. Robinson; Zhiyong Lu (Bioinform., 2021)

LitSuggest: a web-based system for literature recommendation and curation using machine learning. - Alexis Allot; Kyubum Lee; Qingyu Chen 001; Ling Luo 001; Zhiyong Lu (Nucleic Acids Res., 2021)

BioRED: A Comprehensive Biomedical Relation Extraction Dataset. - Ling Luo 001; Po-Ting Lai; Chih-Hsuan Wei; Cecilia N. Arighi; Zhiyong Lu (AMIA, 2022)

PhenoGene: Disease-gene prioritization using graph embedding on patient phenotypic profiles. - Shankai Yan; Ling Luo 001; Li Fang; Daniel Veltri; Andrew J. Oler; Rajarshi Ghosh; Chih-Hsuan Wei; Morgan Similuk; Kai Wang; Zhiyong Lu (AMIA, 2022)

BioRED: a rich biomedical relation extraction dataset. - Ling Luo 001; Po-Ting Lai; Chih-Hsuan Wei; Cecilia N. Arighi; Zhiyong Lu (Briefings Bioinform., 2022)

Assigning species information to corresponding genes by a sequence labeling framework. - Ling Luo 001; Chih-Hsuan Wei; Po-Ting Lai; Qingyu Chen 001; Rezarta Islamaj; Zhiyong Lu (Database J. Biol. Databases Curation, 2022)

A sequence labeling framework for extracting drug-protein relations from biomedical literature. - Ling Luo 001; Po-Ting Lai; Chih-Hsuan Wei; Zhiyong Lu (Database J. Biol. Databases Curation, 2022)

PhenoRerank: A re-ranking model for phenotypic concept recognition pre-trained on human phenotype ontology. - Shankai Yan; Ling Luo 001; Po-Ting Lai; Daniel Veltri; Andrew J. Oler; Sandhya Xirasagar; Rajarshi Ghosh; Morgan Similuk; Peter N. Robinson; Zhiyong Lu (J. Biomed. Informatics, 2022)

Joint Biomedical Entity and Relation Extraction Based on Triple Region Vertices. - Yuqi Liu; Zhihao Yang; Jinzhong Ning; Zhijun Wang; Ling Luo 001; Lei Wang 085; Yin Zhang 009; Wei Liu; Hongfei Lin; Jian Wang 021 (BIBM, 2023)

Joint Biomedical Entity and Relation Extraction with Unified Interaction Maps. - Haixin Tan; Zhihao Yang; Zeyuan Ding; Zhijun Wang; Ling Luo 001; Lei Wang 085; Yin Zhang 009; Wei Liu; Hongfei Lin; Jian Wang 021 (BIBM, 2023)

AIONER: all-in-one scheme-based biomedical named entity recognition using deep learning. - Ling Luo 001; Chih-Hsuan Wei; Po-Ting Lai; Robert Leaman; Qingyu Chen 001; Zhiyong Lu (Bioinform., 2023)

GNorm2: an improved gene name recognition and normalization system. - Chih-Hsuan Wei; Ling Luo 001; Rezarta Islamaj; Po-Ting Lai; Zhiyong Lu (Bioinform., 2023)

BioREx: Improving biomedical relation extraction by leveraging heterogeneous datasets. - Po-Ting Lai; Chih-Hsuan Wei; Ling Luo 001; Qingyu Chen 001; Zhiyong Lu (J. Biomed. Informatics, 2023)

Term-BLAST-like alignment tool for concept recognition in noisy clinical texts. - Tudor Groza; Honghan Wu; Marcel E. Dinger; Daniel Danis; Coleman Hilton; Anita Bagley; Jon R. Davids; Ling Luo 001; Zhiyong Lu; Peter N. Robinson (Bioinform., 2023)

From Retrieval to Generation: A Simple and Unified Generative Model for End-to-End Task-Oriented Dialogue. - Zeyuan Ding; Zhihao Yang; Ling Luo 001; Yuanyuan Sun 002; Hongfei Lin (AAAI, 2024)

Biomedical Event Extraction as Semantic Segmentation. - Liangyu Gao; Zhihao Yang; Jinzhong Ning; Kai Ma; Lei Wang 085; Wei Liu; Yin Zhang 009; Ling Luo 001; Bo Xu 009; Jian Wang 021; Yumeng Yang; Zhehuan Zhao; et al. (BIBM, 2024)

Document-level Biomedical Relation Extraction Based on Relation-guided Entity-level Graphs. - Liangyu Gao; Zhihao Yang; Haixin Tan; Lei Wang 085; Wei Liu; Yin Zhang 009; Ling Luo 001; Bo Xu 009; Jian Wang 021; Yumeng Yang; Zhehuan Zhao; Yuanyuan Sun 002; et al. (BIBM, 2024)

Document Embeddings Enhance Biomedical Retrieval-Augmented Generation. - Yongle Kong; Zhihao Yang; Ling Luo 001; Zeyuan Ding; Lei Wang 085; Wei Liu; Yin Zhang 009; Bo Xu 009; Jian Wang 021; Yuanyuan Sun 002; Zhehuan Zhao; Hongfei Lin (BIBM, 2024)

Biomedical Document-level Relation Extraction with Coreference and Anaphor Graphs. - Jiru Li; Yuanyuan Sun 002; Zhihao Yang; Ling Luo 001; Lei Wang 085; Wei Liu; Yin Zhang 009; Bo Xu 009; Jian Wang 021; Yumeng Yang; Zhehuan Zhao; Hongfei Lin (BIBM, 2024)

An Improved Method for Phenotype Concept Recognition Using Rich HPO Information. - Jiewei Qi; Ling Luo 001; Zhihao Yang; Jian Wang 021; Huiwei Zhou; Hongfei Lin (BIBM, 2024)

Efficient Knowledge Graph Embedding Framework to Alleviate Data Sparsity for Polypharmacy Side Effects Prediction. - Senbo Tu; Zhihao Yang; Lei Wang 085; Wei Liu; Yin Zhang 009; Ling Luo 001; Bo Xu 009; Jian Wang 021; Yumeng Yang; Zhehuan Zhao; Hongfei Lin (BIBM, 2024)

Breaking the Boundaries: A Unified Framework for Chinese Named Entity Recognition Across Text and Speech. - Jinzhong Ning; Yuanyuan Sun 002; Bo Xu 009; Zhihao Yang; Ling Luo 001; Hongfei Lin (EMNLP (Findings), 2024)

EDNER: Edge Detection for Named Entity Recognition. - Liangyu Gao; Zhihao Yang; Ling Luo 001; Wenfei Liu; Hongfei Lin; Jian Wang 021 (NLPCC (2), 2024)

PubTator 3.0: an AI-powered Literature Resource for Unlocking Biomedical Knowledge. - Chih-Hsuan Wei; Alexis Allot; Po-Ting Lai; Robert Leaman; Shubo Tian; Ling Luo 001; Qiao Jin 001; Zhizheng Wang; Qingyu Chen 001; Zhiyong Lu (CoRR, 2024)

EnzChemRED, a rich enzyme chemistry relation extraction dataset. - Po-Ting Lai; Elisabeth Coudert; Lucila Aimo; Kristian B. Axelsen; Lionel Breuza; Edouard De Castro; Marc Feuermann; Anne Morgat; Lucille Pourcel; Ivo Pedruzzi; Sylvain Poux; Nicole Redaschi; et al. (CoRR, 2024)

Taiyi: a bilingual fine-tuned large language model for diverse biomedical tasks. - Ling Luo 001; Jinzhong Ning; Yingwen Zhao; Zhijun Wang; Zeyuan Ding; Peng Chen; Weiru Fu; Qinyu Han; Guangtao Xu; Yunzhi Qiu; Dinghao Pan; Jiru Li; et al. (J. Am. Medical Informatics Assoc., 2024)

The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII. - Rezarta Islamaj; Po-Ting Lai; Chih-Hsuan Wei; Ling Luo 001; Tiago Melo Almeida; Richard A. A. Jonker; Sofia I R. Conceição; Diana F. Sousa; Cong-Phuoc Phan; Jung-Hsien Chiang; Jiru Li; Dinghao Pan; et al. (Database J. Biol. Databases Curation, 2024)

The biomedical relationship corpus of the BioRED track at the BioCreative VIII challenge and workshop. - Rezarta Islamaj; Chih-Hsuan Wei; Po-Ting Lai; Ling Luo 001; Cathleen Coss; Preeti Gokal Kochar; Nicholas Miliaras; Oleg Rodionov; Keiko Sekiya; Dorothy Trinh; Deborah Whitman; Zhiyong Lu (Database J. Biol. Databases Curation, 2024)

Archive of PubTator 3.0 source code and trained models. - Chih-Hsuan Wei; Alexis Allot; Po-Ting Lai; Robert Leaman; Shubo Tian; Ling Luo 001; Qiao Jin 001; Zhizheng Wang; Qingyu Chen 001; Zhiyong Lu (Zenodo, 2024)

EnzChemRED, a rich enzyme chemistry relation extraction dataset. - Po-Ting Lai; Elisabeth Coudert; Lucila Aimo; Kristian B. Axelsen; Lionel Breuza; Edouard De Castro; Marc Feuermann; Anne Morgat; Lucille Pourcel; Ivo Pedruzzi; Sylvain Poux; Nicole Redaschi; et al. (Zenodo, 2024)

Prototype Tuning: A Meta-Learning Approach for Few-Shot Document-Level Relation Extraction with Large Language Models. - Dinghao Pan; Yuanyuan Sun 002; Bo Xu 009; Jiru Li; Zhihao Yang; Ling Luo 001; Hongfei Lin; Jian Wang 021 (NAACL (Findings), 2025)

LCDL: Classification of ICD codes based on disease label co-occurrence dependency and LongFormer with medical knowledge. - Yumeng Yang; Hongfei Lin; Zhihao Yang; Yijia Zhang 001; Di Zhao 003; Ling Luo 001 (Artif. Intell. Medicine, 2025)

Span-based syntactic feature fusion for aspect sentiment triplet extraction. - Guangtao Xu; Zhihao Yang; Bo Xu 009; Ling Luo 001; Hongfei Lin (Inf. Fusion, 2025)