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Ye Ye, PhD
- Adjunct Professor of Biomedical Informatics (2025–Present)
- Assistant Professor of Biomedical Informatics (2022–2025)
Department of Biomedical Informatics (DBMI) | University of Pittsburgh School of Medicine
Biography
Dr. Ye Ye is a biomedical informatician whose research focuses on transfer learning, public health surveillance, and the application of machine learning to clinical and epidemiological data. She earned her PhD in Intelligent Systems from the University of Pittsburgh in 2018 and completed postdoctoral training at DBMI under Drs. Michael Becich, Michael Wagner, and Gregory Cooper. She served as a tenure-track Assistant Professor at DBMI from May 2022 through April 2025, with a secondary appointment at the Clinical and Translational Science Institute.
Research Interests
Dr. Ye’s research addresses a fundamental challenge in health informatics: machine-learned models developed in one healthcare system often underperform when applied elsewhere. She develops transfer learning frameworks that enable robust sharing of models and knowledge across heterogeneous institutions, benefiting public health surveillance (particularly for infectious diseases), readmission prediction, and clinical AI generalizability. She also investigates near-real-time active surveillance approaches using NLP-driven case detection systems derived from electronic medical records.
Specialties
- Transfer Learning for Clinical and Epidemiological Models
- Public Health Surveillance and Disease Case Detection
- Natural Language Processing in Clinical Settings
- Bayesian Networks and Deep Learning
- Readmission Risk Prediction
Education & Training
- B.Med., Preventive MedicinePeking University Health Science Center, Beijing, China2006
- M.S., Epidemiology and Health StatisticsPeking University School of Public Health, Beijing, China2009
- M.S.P.H., Public Health InformaticsEmory University, Atlanta, GA2011
- Ph.D., Intelligent SystemsUniversity of Pittsburgh School of Computing and Information, Pittsburgh, PA2018
- Postdoctoral Associate, Biomedical InformaticsUniversity of Pittsburgh (Mentors: Becich, Wagner, Cooper), Pittsburgh, PA2019–2022
Awards & Distinctions
- University of Pittsburgh Innovator AwardUniversity of Pittsburgh2016
- Andrew Mellon FellowshipUniversity of Pittsburgh2017–2018
- Best Student Paper, 2nd PlaceDBMI Training Program2014, 2017
- Distinguished Poster AwardAMIA Annual Symposium2014, 2015
- Doctoral Dissertation Award FinalistAmerican Medical Informatics Association2019
Representative Publications
Aronis JM, Ye Y, Espino J, et al. A Bayesian System to Detect and Track Outbreaks of Influenza-Like Illnesses Including Novel Diseases. JMIR Public Health Surveill 10:e57349, 2024.
Gao Y, Mazurek JM, Li Y, et al. Industry, occupation, and exposure history of mesothelioma patients in the US National Mesothelioma Virtual Bank. Environ Res 230:115085, 2023.
Bernstam EV, Shireman PK, Meric-Bernstam F, et al. Artificial intelligence in clinical and translational science: Successes, challenges and opportunities. Clin Transl Sci 15(2):309–321, 2022.
Ye Y, Barapatre S, Davis MK, et al. Open-source Software Sustainability Models. J Med Internet Res 23(12):e20028, 2021.
Ye Y, Wagner MM, Cooper GF, et al. A study of the transferability of influenza case detection systems between two large healthcare systems. PLoS One 12(4):e0174970, 2017.
Research Grants
| Grant / Funding Agency | Role | Grant Number | Years |
|---|---|---|---|
| Transfer Learning to Improve the Reusability of Computable Biomedical Knowledge NIH/NLM | PI | R00LM013383 | 2022–2025 |
| Automated Surveillance of Overlapping Outbreaks and New Outbreak Diseases NIH/NLM | Co-I | R01LM013509 | 2022–2025 |
| National Mesothelioma Virtual Bank CDC | Researcher | U24 OH009077 | 2021–2026 |
| Models of Infectious Disease Agent Study (MIDAS) Coordination Center NIH | Researcher | R24GM153920 | 2024–2029 |
Trainees
| Trainee | Degree Program / Role & Years |
|---|---|
| Yuhe Gao | Master's Student Researcher, Information Science | 2022–Present |
| Yiming Sun | PhD Student Researcher, School of Engineering | 2023–Present |
| Yuelyu Ji | Master's Student Researcher, Information Science | 2022–2023 |
| Runxue Bao | PhD Student Researcher, School of Engineering | 2022 |