Transformer-based named entity recognition for parsing clinical trial eligibility criteria. - Shubo Tian; Arslan Erdengasileng; Xi Yang 015; Yi Guo 005; Yonghui Wu; Jinfeng Zhang; Jiang Bian 001; Zhe He 001 (BCB, 2021)

A PubMedBERT-based Classifier with Data Augmentation Strategy for Detecting Medication Mentions in Tweets. - Qing Han; Shubo Tian; Jinfeng Zhang (CoRR, 2021)

Using Twitter Data Analysis to Understand the Perceptions, Awareness, and Barriers to the Wide Use of Pre-Exposure Prophylaxis in the United States. - Arslan Erdengasileng; Shubo Tian; Sara S. Green; Sylvie Naar; Zhe He 001 (BIBM, 2022)

Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations. - Qingyu Chen 001; Alexis Allot; Robert Leaman; Rezarta Islamaj; Jingcheng Du; Li Fang; Wang Kai; Shuo Xu 001; Yuefu Zhang; Parsa Bagherzadeh; Sabine Bergler; Aakash Bhatnagar; et al. (Database J. Biol. Databases Curation, 2022)

Pre-trained models, data augmentation, and ensemble learning for biomedical information extraction and document classification. - Arslan Erdengasileng; Qing Han; Tingting Zhao; Shubo Tian; Xin Sui; Keqiao Li; Wanjing Wang; Jian Wang; Ting Hu; Feng Pan; Yuan Zhang; Jinfeng Zhang (Database J. Biol. Databases Curation, 2022)

Temporal Subtyping of Alzheimer's Disease Using Medical Conditions Preceding Alzheimer's Disease Onset in Electronic Health Records. - Zhe He 001; Shubo Tian; Arslan Erdengasileng; Neil Charness; Jiang Bian 001 (CoRR, 2022)

Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations. - Qingyu Chen 001; Alexis Allot; Robert Leaman; Rezarta Islamaj Dogan; Jingcheng Du; Li Fang; Wang Kai; Shuo Xu 001; Yuefu Zhang; Parsa Bagherzadeh; Sabine Bergler; Aakash Bhatnagar; et al. (CoRR, 2022)

A Machine-Learning Based Approach for Predicting Older Adults' Adherence to Technology-Based Cognitive Training. - Zhe He 001; Shubo Tian; Ankita Singh; Shayok Chakraborty; Shenghao Zhang; Mia Liza A. Lustria; Neil Charness; Nelson A. Roque; Erin Harrell; Walter R. Boot (Inf. Process. Manag., 2022)

Parsing Clinical Trial Eligibility Criteria for Cohort Query by a Multi-Input Multi-Output Sequence Labeling Model. - Shubo Tian; Pengfei Yin; Hansi Zhang; Arslan Erdengasileng; Jiang Bian 001; Zhe He 001 (BIBM, 2023)

Response to Letter to Editor 'Timely need for navigating the potential and downsides of LLMs in healthcare and biomedicine'. - Shubo Tian; Qiao Jin 001; Zhiyong Lu (Briefings Bioinform., 2024)

Opportunities and challenges for ChatGPT and large language models in biomedicine and health. - Shubo Tian; Qiao Jin 001; Lana Yeganova; Po-Ting Lai; Qingqing Zhu; Xiuying Chen; Yifan Yang 006; Qingyu Chen 001; Won Kim 003; Donald C. Comeau; Rezarta Islamaj; Aadit Kapoor; et al. (Briefings Bioinform., 2024)

Information Retrieval and Classification of Real-Time Multi-Source Hurricane Evacuation Notices. - Tingting Zhao; Shubo Tian; Jordan Daly; Melissa Geiger; Minna Jia; Jinfeng Zhang (CoRR, 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)

Quality of Answers of Generative Large Language Models vs Peer Patients for Interpreting Lab Test Results for Lay Patients: Evaluation Study. - Zhe He 001; Balu Bhasuran; Qiao Jin 001; Shubo Tian; Karim Hanna; Cindy Shavor; Lisbeth Y. Garcia Arguello; Patrick Murray; Zhiyong Lu (CoRR, 2024)

GeneAgent: Self-verification Language Agent for Gene Set Knowledge Discovery using Domain Databases. - Zhizheng Wang; Qiao Jin 001; Chih-Hsuan Wei; Shubo Tian; Po-Ting Lai; Qingqing Zhu; Chi-Ping Day; Christina Ross; Zhiyong Lu (CoRR, 2024)

Demystifying Large Language Models for Medicine: A Primer. - Qiao Jin 001; Nicholas Wan; Robert Leaman; Shubo Tian; Zhizheng Wang; Yifan Yang 006; Zifeng Wang 008; Guangzhi Xiong; Po-Ting Lai; Qingqing Zhu; Benjamin Hou; Maame Sarfo-Gyamfi; et al. (CoRR, 2024)

Large language models in biomedicine and health: current research landscape and future directions. - Zhiyong Lu; Yifan Peng 002; Trevor Cohen; Marzyeh Ghassemi; Chunhua Weng; Shubo Tian (J. Am. Medical Informatics Assoc., 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)

A comprehensive large-scale biomedical knowledge graph for AI-powered data-driven biomedical research. - Yuan Zhang; Xin Sui; Feng Pan; Kaixian Yu; Keqiao Li; Shubo Tian; Arslan Erdengasileng; Qing Han; Wanjing Wang; Jianan Wang; Jian Wang; Donghu Sun; et al. (Nat. Mac. Intell., 2025)

Enhancing Biomedical Relation Extraction with Directionality. - Po-Ting Lai; Chih-Hsuan Wei; Shubo Tian; Robert Leaman; Zhiyong Lu (CoRR, 2025)

Knowledge-guided Contextual Gene Set Analysis Using Large Language Models. - Zhizheng Wang; Chi-Ping Day; Chih-Hsuan Wei; Qiao Jin 001; Robert Leaman; Yifan Yang 006; Shubo Tian; Aodong Qiu; Yin Fang; Qingqing Zhu; Xinghua Lu 001; Zhiyong Lu (CoRR, 2025)