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publications

2015

Zhehuan Zhao, Zhihao Yang, Ling Luo, Hongfei Lin, Jian Wang and Song Gao. Deep neural network based protein-protein interaction extraction from biomedical literature. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2015.
Ling Luo, Yidong Chen, Xiaodong Shi and Jinsong Su. Chinese Idiom Translation Based on Paraphrasing (In Chinese). Journal of Chinese Information Processing, 29(4):166-174, 2015.

2016

Zhehuan Zhao, Zhihao Yang, Ling Luo, Hongfei Lin and Jian Wang. Drug drug interaction extraction from biomedical literature using syntax convolutional neural network. Bioinformatics, Volume 32, Issue 22, Pages 3444–3453, 2016.
Zhehuan Zhao, Zhihao Yang, Ling Luo, Yin Zhang, Lei Wang, Hongfei Lin and Jian Wang. ML-CNN: A novel deep learning based disease named entity recognition architecture. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2016.

2017

Ling Luo, Zhihao Yang, Hongfei Lin and Jian Wang. DUTIR at the BioCreative VI Precision Medicine Track: document triage for identifying PPIs affected by genetic mutations. Proceedings of the BioCreative VI Workshop. 2017: 120-123.
Ling Luo, Pei Yang, Zhihao Yang, Hongfei Lin and Jian Wang. DUTIR at the BioCreative V.5.BeCalm Tasks: A BLSTM-CRF Approach for Biomedical Entity Recognition in Patents. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 2017.
Wei Zheng, Hongfei Lin, Ling Luo, Zhehuan Zhao, Zhengguang Li, Yijia Zhang, Zhihao Yang and Jian Wang. An attention-based effective neural model for drug-drug interactions extraction. BMC Bioinformatic, 18:445, 2017.
Zhehuan Zhao, Zhihao Yang, Ling Luo, Lei Wang, Yin Zhang, Hongfei Lin and Jian Wang. Disease named entity recognition from biomedical literature using a novel convolutional neural network. BMC Medical Genomics, 10(5):73, 2017.

2018

Ling Luo, Zhihao Yang, Lei Wang, Yin Zhang, Hongfei Lin, Jian Wang, Liang Yang, Kan Xu and Yijia Zhang. Protein-Protein Interaction Article Classification: A Knowledge-enriched Self-Attention Convolutional Neural Network Approach. Procceding of 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2018. (Regular Paper)
Ling Luo, Zhihao Yang, Pei Yang, Yin Zhang, Lei Wang, Jian Wang and Hongfei Lin. A neural network approach to chemical and gene/protein entity recognition in patents. Journal of Cheminformatics, 2018, 10:65.
Ling Luo, Zhihao Yang, Hongfei Lin, Jian Wang. Document triage for identifying protein–protein interactions affected by mutations: a neural network ensemble approach. Database, 2018.
Ling Luo, Nan Li, Shuaichi Li, Zhihao Yang and Hongfei Lin. DUTIR at the CCKS-2018 Task1: A Neural Network Ensemble Approach for Chinese Clinical Named Entity Recognition. Proceedings of the Evaluation Tasks at the China Conference on Knowledge Graph and Semantic Computing (CCKS-Tasks 2018), 2018.
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. Bioinformatics, Volume 34, Issue 8, 15 April 2018, Pages 1381–1388.
Qingqing Li, Zhihao Yang, Ling Luo, Lei Wang, Yin Zhang, Hongfei Lin, Jian Wang, Liang Yang, Kan Xu and Yijia Zhang. A multi-task learning based approach to biomedical entity relation extraction. Procceding of 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2018: 680-682.

2019

Ling Luo, Zhihao Yang, Lei Wang, Yin Zhang, Hongfei Lin and Jian Wang. KeSACNN: a protein-protein interaction article classification approach based on deep neural network. International Journal of Data Mining and Bioinformatics, 2019, 22(2): 131-148.
Nan Li, Ling Luo, Zeyuan Ding, Yawen Song, Zhihao Yang and Hongfei Lin. DUTIR at the CCKS-2019 Task1: Improving Chinese Clinical Named Entity Recognition using Stroke ELMo and Transfer Learning. Proceedings of the Evaluation Tasks at the China Conference on Knowledge Graph and Semantic Computing (CCKS-Tasks 2019), 2019.
Yawen Song, Ling Luo, Nan Li, Zeyuan Ding, Zhihao Yang and Hongfei Lin. NER-PS-MS: Medical Attribute Extraction based on Medical Named Entity Recognition. Proceedings of the Evaluation Tasks at the China Conference on Knowledge Graph and Semantic Computing (CCKS-Tasks 2019), 2019.
Cong Sun, Zhihao Yang, Ling Luo, Lei Wang, Yin Zhang, Hongfei Lin and Jian Wang. A Deep Learning Approach With Deep Contextualized Word Representations for Chemical–Protein Interaction Extraction From Biomedical Literature. * IEEE Access*, 2019, 7:151034-151046.
Qingqing Li, Zhihao Yang, Zhehuan Zhao, Ling Luo, Zhiheng Li, Lei Wang, Yin Zhang, Hongfei Lin, Jian Wang and Yijia Zhang. HMNPPID—human malignant neoplasm protein–protein interaction database. Hum Genomics, 2019, 13:44.

2020

Ling Luo, Zhihao Yang, Yawen Song, Nan Li and Hongfei Lin. Chinese Clinical Named Entity Recognition Based on Stroke ELMo and Multi-Task Learning . Chinese Journal of Computers, 2020, 43(10):1943-1957.(In Chinese)
Ling Luo, Shankai Yan, Po-Ting Lai, Daniel Veltri, Andrew Oler, Sandhya Xirasagar, Rajarshi Ghosh, Morgan Similuk, Peter N. Robinson, Zhiyong Lu. A Hybrid Method for Phenotype Concept Recognition using the Human Phenotype Ontology. 28th Conference on Intelligent Systems for Molecular Biology (ISMB 2020), Abstracts (oral and poster), July 2020, online.
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. Journal of Biomedical Informatics, 2020, Volume 103: 103384.
Nan Li, Zhihao Yang, Ling Luo, Lei Wang, Yin Zhang, Hongfei Lin and Jian Wang. KGHC: a knowledge graph for hepatocellular carcinoma. BMC Medical Informatics and Decision Making, 2020, 20:135.
Zhiheng Li, Zhihao Yang, Ling Luo, Yang Xiang and Hongfei Lin. Exploiting Adversarial Transfer Learning for Adverse Drug Reaction Detection from Texts. Journal of Biomedical Informatics, 2020, 106:103431.
Zhiheng Li, Zhihao Yang, Yang Xiang, Ling Luo, Yuanyuan Sun and Hongfei Lin. Exploiting sequence labeling framework to extract document-level relations from biomedical texts. BMC Bioinformatics, 2020, 21: 125.

2021

Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Zhiyong Lu. Extracting Drug-Protein Interaction using an Ensemble of Biomedical Pre-trained Language Models through Sequence Labeling and Text Classification Techniques. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 2021: 26-30.
Ling Luo, Shankai Yan, Po-Ting Lai, Daniel Veltri, Andrew Oler, Sandhya Xirasagar, Rajarshi Ghosh, Morgan Similuk, Peter N. Robinson, Zhiyong Lu. PhenoTagger: A Hybrid Method for Phenotype Concept Recognition using Human Phenotype Ontology. Bioinformatics, Volume 37, Issue 13, 1 July 2021, Pages 1884–1890.
Qingyu Chen, Robert Leaman, Alexis Allot, Ling Luo, Chih-Hsuan Wei, Shankai Yan, Zhiyong Lu. Artificial Intelligence in Action: Addressing the COVID-19 Pandemic with Natural Language Processing. Annual Review of Biomedical Data Science, 2021, Vol. 4:313-339.
Alexis Allot, Kyubum Lee, Qingyu Chen, Ling Luo, Zhiyong Lu. LitSuggest: A Web-based System for Literature Recommendation and Curation using Machine Learning. Nucleic Acids Research, 2021, Volume 49, Issue W1, 2 July 2021, Pages W352–W358.
Yawen Song, Zhihao Yang, Ling Luo, Lei Wang, Yin Zhang, Hongfei Lin, Jian Wang. Biomedical Mutation Entity Recognition Method Based on Character Convolution Neural Network. Journal of Chinese Information Processing, 2021, 35(5): 63-69. (In Chinese)
Zeyuan Ding, Zhihao Yang, Ling Luo, Lei Wang, Yin Zhang, Hongfei Lin, Jian Wang. Chinese Biomedical Entity Relation Extraction System Based on Deep Learning. Journal of Chinese Information Processing, 2021, 35(5): 70-76. (In Chinese)

2022

Ling Luo*, Po-Ting Lai*, Chih-Hsuan Wei*, Cecilia N Arighi, Zhiyong Lu. BioRED: a rich biomedical relation extraction dataset. Briefings in Bioinformatics, Volume 23, Issue 5, September 2022, bbac282.
Ling Luo*, Chih-Hsuan Wei*, Po-Ting Lai, Qingyu Chen, Rezarta Islamaj, Zhiyong Lu. Assigning species information to corresponding genes by a sequence labeling framework. Database, 2022, Volume 2022: baac090.
Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Zhiyong Lu. A sequence labeling framework for extracting drug–protein relations from biomedical literature. Database, 2022, Volume 2022: baac058.
Ling Luo, Li Fang, Shankai Yan, Daniel Veltri, Andrew Oler, Sandhya Xirasagar, Rajarshi Ghosh, Morgan Similuk, Kai Wang, Zhiyong Lu. AI-aided Genetic Diagnosis and Disease-gene Discovery: Scaling Up and Evaluation of an Automated Deep Phenotyping Algorithm on two External EHR Datasets. AMIA 2022 Informatics Summit AI Showcase, Abstracts (poster), 2022, Chicago.
Travis C. Hyams, Ling Luo, Brionna Hair, Kyubum Lee, Zhiyong Lu, and Daniela Seminara. Machine Learning Approach to Facilitate Knowledge Synthesis at the Intersection of Liver Cancer, Epidemiology, and Health Disparities Research. JCO Clinical Cancer Informatics 2022, 6: e2100129.
Shankai Yan, Ling Luo, Po-Ting Lai, Daniel Veltri, Andrew Oler, Sandhya Xirasagar, Rajarshi Ghosh, Morgan Similuk, Peter N. Robinson, Zhiyong Lu. PhenoRerank: a re-ranking model for phenotypic concept recognition pre-trained on human phenotype ontology. Journal of Biomedical Informatics, 2022, Volume 129: 104059.

2023

Ling Luo*, Chih-Hsuan Wei*, Po-Ting Lai, Robert Leaman, Qingyu Chen, Zhiyong Lu. AIONER: all-in-one scheme-based biomedical named entity recognition using deep learning. Bioinformatics, Volume 39, Issue 5, May 2023, btad310.
Chih-Hsuan Wei*, Ling Luo*, Rezarta Islamaj, Po-Ting Lai, Zhiyong Lu. GNorm2: an improved gene name recognition and normalization system. Bioinformatics, Volume 39, Issue 10, October 2023, btad599.
Po-Ting Lai, Chih-Hsuan Wei, Ling Luo, Qingyu Chen, Zhiyong Lu. BioREx: Improving Biomedical Relation Extraction by Leveraging Heterogeneous Datasets. Journal of Biomedical Informatics, Volume 146, October 2023, 104487.