A data-driven method for research trend analysis in a scientific discipline: Application to the journal of biomedical informatics.

Yilu Fang https://orcid.org/0000-0002-2681-1931

Yilu Fang Gongbo Zhang Samir Sanchez Tejada Fangyi Chen Edward H. Shortliffe Vimla L. Patel Mor Peleg Chunhua Weng A data-driven method for research trend analysis in a scientific discipline: Application to the journal of biomedical informatics. 2026 105013 178 J. Biomed. Informatics https://doi.org/10.1016/j.jbi.2026.105013 db/journals/jbi/jbi178.html#FangZTCSPPW26 streams/journals/jbi

Fangyi Chen Gongbo Zhang Yilu Fang Yifan Peng 0002 Chunhua Weng Semi-supervised learning from small annotated data and large unlabeled data for fine-grained Participants, Intervention, Comparison, and Outcomes entity recognition. 555-565 2025 32 J. Am. Medical Informatics Assoc. 3 https://doi.org/10.1093/jamia/ocae326 db/journals/jamia/jamia32.html#ChenZFPW25 streams/journals/jamia

Yilu Fang Gongbo Zhang Fangyi Chen George Hripcsak Yifan Peng 0002 Patrick B. Ryan Chunhua Weng CLEAR: A vision to support clinical evidence lifecycle with continuous learning. 104884 2025 169 J. Biomed. Informatics https://doi.org/10.1016/j.jbi.2025.104884 db/journals/jbi/jbi169.html#FangZCHPRW25 streams/journals/jbi

Yilun Liang Gongbo Zhang Edward Sun Betina Idnay Yilu Fang Fangyi Chen Casey N. Ta Yifan Peng 0002 Chunhua Weng Scalable scientific interest profiling using large language models. 104949 2025 172 J. Biomed. Informatics https://doi.org/10.1016/j.jbi.2025.104949 db/journals/jbi/jbi172.html#LiangZSIFCTPW25 streams/journals/jbi

Yilu Fang Jordan G. Nestor Casey N. Ta Jerard Z. Kneifati-Hayek Chunhua Weng A method for characterizing disease progression from acute kidney injury to chronic kidney disease. 104956 2025 172 J. Biomed. Informatics https://doi.org/10.1016/j.jbi.2025.104956 db/journals/jbi/jbi172.html#FangNTKW25 streams/journals/jbi

Gongbo Zhang Zihan Xu Qiao Jin 0001 Fangyi Chen Yilu Fang Yi Liu 0059 Justin F. Rousseau Ziyang Xu Zhiyong Lu Chunhua Weng Yifan Peng 0002 Leveraging long context in retrieval augmented language models for medical question answering. 2025 8 npj Digit. Medicine 1 https://doi.org/10.1038/s41746-025-01651-w db/journals/npjdm/npjdm8.html#ZhangXJCFLRXLWP25 streams/journals/npjdm

Yilun Liang Gongbo Zhang Edward Sun Betina Idnay Yilu Fang Fangyi Chen Casey N. Ta Yifan Peng 0002 Chunhua Weng Scalable Scientific Interest Profiling Using Large Language Models. 2025 August abs/2508.15834 CoRR https://doi.org/10.48550/arXiv.2508.15834 db/journals/corr/corr2508.html#abs-2508-15834 streams/journals/corr

Yilu Fang Jordan G. Nestor Casey N. Ta Jerard Z. Kneifati-Hayek Chunhua Weng A Method for Characterizing Disease Progression from Acute Kidney Injury to Chronic Kidney Disease. 2025 November abs/2511.14603 CoRR https://doi.org/10.48550/arXiv.2511.14603 db/journals/corr/corr2511.html#abs-2511-14603 streams/journals/corr

Betina Ross S. Idnay Jianfang Liu Yilu Fang Alex Hernandez Shivani Kaw Alicia Etwaru Janeth Juarez Padilla Sergio Ozoria Ramirez Karen Marder Chunhua Weng Rebecca Schnall Sociotechnical feasibility of natural language processing-driven tools in clinical trial eligibility prescreening for Alzheimer's disease and related dementias. 1062-1073 2024 31 J. Am. Medical Informatics Assoc. 5 https://doi.org/10.1093/jamia/ocae032 db/journals/jamia/jamia31.html#IdnayLFHKEPRMWS24

Yilu Fang Patrick Ryan Chunhua Weng Knowledge-guided generative artificial intelligence for automated taxonomy learning from drug labels. 2065-2075 2024 31 J. Am. Medical Informatics Assoc. 9 https://doi.org/10.1093/jamia/ocae105 db/journals/jamia/jamia31.html#FangRW24 streams/journals/jamia

Jimyung Park Yilu Fang Casey N. Ta Gongbo Zhang Betina Idnay Fangyi Chen David Feng Rebecca Shyu Emily R. Gordon Matthew E. Spotnitz Chunhua Weng Criteria2Query 3.0: Leveraging generative large language models for clinical trial eligibility query generation. 104649 2024 154 J. Biomed. Informatics https://doi.org/10.1016/j.jbi.2024.104649 db/journals/jbi/jbi154.html#ParkFTZICFSGSW24

Betina Idnay Yilu Fang Edward Stanley Brenda Ruotolo Wendy K. Chung Karen Marder Chunhua Weng Promoting equity in clinical research: The role of social determinants of health. 104663 2024 156 J. Biomed. Informatics https://doi.org/10.1016/j.jbi.2024.104663 db/journals/jbi/jbi156.html#IdnayFSRCMW24

Gongbo Zhang Zihan Xu Qiao Jin 0001 Fangyi Chen Yilu Fang Yi Liu 0059 Justin F. Rousseau Ziyang Xu Zhiyong Lu Chunhua Weng Yifan Peng 0002 A MapReduce Approach to Effectively Utilize Long Context Information in Retrieval Augmented Language Models. 2024 abs/2412.15271 CoRR https://doi.org/10.48550/arXiv.2412.15271 db/journals/corr/corr2412.html#abs-2412-15271 streams/journals/corr

Fangyi Chen Gongbo Zhang Yilu Fang Yifan Peng 0002 Chunhua Weng Semi-Supervised Learning from Small Annotated Data and Large Unlabeled Data for Fine-grained PICO Entity Recognition. 2024 abs/2412.19346 CoRR https://doi.org/10.48550/arXiv.2412.19346 db/journals/corr/corr2412.html#abs-2412-19346 streams/journals/corr

Betina Ross S. Idnay Yilu Fang Caitlin N. Dreisbach Karen Marder Chunhua Weng Rebecca Schnall Clinical research staff perceptions on a natural language processing-driven tool for eligibility prescreening: An iterative usability assessment. 104985 2023 March 171 Int. J. Medical Informatics https://doi.org/10.1016/j.ijmedinf.2023.104985 db/journals/ijmi/ijmi171.html#IdnayFDMWS23

Casey N. Ta Jason E. Zucker Po-Hsiang Chiu Yilu Fang Karthik Natarajan Chunhua Weng Clinical and temporal characterization of COVID-19 subgroups using patient vector embeddings of electronic health records. 256-272 2023 January 30 J. Am. Medical Informatics Assoc. 2 https://doi.org/10.1093/jamia/ocac208 db/journals/jamia/jamia30.html#TaZCFNW23

Yilu Fang Hao Liu 0054 Betina Ross S. Idnay Casey N. Ta Karen Marder Chunhua Weng A data-driven approach to optimizing clinical study eligibility criteria. 104375 2023 June 142 J. Biomed. Informatics https://doi.org/10.1016/j.jbi.2023.104375 db/journals/jbi/jbi142.html#FangLITMW23

Yilu Fang Betina Ross S. Idnay Yingcheng Sun Hao Liu 0054 Zhehuan Chen Karen Marder Hua Xu 0001 Rebecca Schnall Chunhua Weng Combining human and machine intelligence for clinical trial eligibility querying. 1161-1171 2022 29 J. Am. Medical Informatics Assoc. 7 https://doi.org/10.1093/jamia/ocac051 https://www.wikidata.org/entity/Q112680606 db/journals/jamia/jamia29.html#FangISLCMXSW22

Betina Ross S. Idnay Yilu Fang Caitlin N. Dreisbach Karen Marder Chunhua Weng Rebecca Schnall Optimizing Clinical Research Eligibility Prescreening: An Iterative Usability Evaluation of an NLP-driven Cohort Identification Tool. 2022 AMIA https://knowledge.amia.org/76677-amia-1.4637602/f008-1.4640715/f008-1.4640716/1056-1.4641368/224-1.4641365 conf/amia/2022 db/conf/amia/amia2022.html#IdnayFDMWS22 Betina Ross S. Idnay Yilu Fang Yingcheng Sun Hao Liu 0054 Zhehuan Chen Rebecca Schnall Chunhua Weng Criteria2Query 2.0: Combining Machine Efficiency and Human Intelligence to Define a More Accurate and Feasible Cohort for Clinical Trial Recruitment. 2022 AMIA https://knowledge.amia.org/76677-amia-1.4637602/f009-1.4640668/f009-1.4640669/344-1.4640694/219-1.4640691 conf/amia/2022 db/conf/amia/amia2022.html#IdnayFSLCSW22 Zhehuan Chen Yilu Fang Hao Liu 0054 Chunhua Weng Data-Driven Modeling of Randomized Controlled Trial Outcomes. 392-396 2022 MIE https://doi.org/10.3233/SHTI220481 conf/mie/2022 db/conf/mie/mie2022.html#ChenFLW22 Yingcheng Sun Jiaqi Tang 0008 Alex Butler Cong Liu 0020 Yilu Fang Chunhua Weng Interactive Similarity-Based Search of Clinical Trials. 309-313 2021 MedInfo https://doi.org/10.3233/SHTI220085 conf/medinfo/2021 db/conf/medinfo/medinfo2021.html#SunTBLFW21 Yilu Fang Jae Hyun Kim Betina Ross S. Idnay Rebeca Aragon Garcia Carmen E. Castillo Yingcheng Sun Hao Liu 0054 Cong Liu 0020 Chi Yuan Chunhua Weng Participatory Design of a Clinical Trial Eligibility Criteria Simplification Method. 984-988 2021 MIE https://doi.org/10.3233/SHTI210325 conf/mie/2021 db/conf/mie/mie2021.html#FangKIGCSLLYW21 Alex Butler Carmen E. Castillo Fangyi Chen Zhehuan Chen Po-Hsiang Chiu Wendy K. Chung Caitlin N. Dreisbach Alicia Etwaru David Feng Rebeca Aragon Garcia Emily R. Gordon Alex Hernandez George Hripcsak Betina Ross S. IdnayBetina Idnay Qiao Jin 0001 Shivani Kaw Jae Hyun Kim Jerard Kneifati-HayekJerard Z. Kneifati-Hayek Yilun Liang Cong Liu 0020 Hao Liu 0054 Jianfang Liu Yi Liu 0059 Zhiyong Lu Karen Marder Karthik Natarajan Jordan G. Nestor Janeth Juarez Padilla Jimyung Park Vimla L. Patel Mor Peleg Yifan Peng 0002 Sergio Ozoria Ramirez Justin F. Rousseau Brenda Ruotolo Patrick Ryan Patrick B. Ryan Rebecca Schnall Edward H. Shortliffe Rebecca Shyu Matthew E. Spotnitz Edward Stanley Edward Sun Yingcheng Sun Casey N. Ta Jiaqi Tang 0008 Samir Sanchez Tejada Chunhua Weng Hua Xu 0001 Zihan Xu Ziyang Xu Chi Yuan Gongbo Zhang Jason Zucker 0001Jason E. Zucker