Director, Institute for Successful Longevity
Professor, School of Information, College of Communication and Information
Professor (courtesy), Department of Computer Science
Professor (courtesy), Department of Behavioral Science and Social Medicine
Professor (courtesy), Department of Statistics
Florida State University
Chair, AMIA Knowledge Discovery and Data Mining Working Group
I am a tenured Full Professor in the School of Information (iSchool) and Director of the Institute for Successful Longevity at Florida State University. I am a biomedical informatician and health data scientist with formal education and training in computer science and biomedical informatics. My research lies at the intersection of Biomedical & Health Informatics, Computer Science, and Information Science. My research expertise includes deep learning, machine learning, natural language processing, ontologies, knowledge representation, and big data analytics.
At FSU, I direct the eHealth Lab. The overarching goal of my research is to improve population health and advance biomedical research through the application of informatics and big data. As Contact PI or Multi-PI, my research has been funded by the National Library of Medicine / NIH, National Institute on Aging / NIH, National Institute of Mental Health / NIH, Agency for Healthcare Research and Quality (AHRQ), UF Clinical and Translational Science Insitute, Eli Lilly and Company, Amazon, NVIDIA, FSU Council on Research and Creativity, and Institute for Successful Longevity. I have served as a PI of an NIA/NIH R01 grant (APPT), an AHRQ R21/R33 grant (LabGenie), an NIMH R21/R33 grant (Youth Learning Health Community), an NLM/NIH R21 grant (pediatric transplantation outcomes prediction), and an NIA/NIH R21 grant (clinical trial generalizability analysis). The total grant award I have received since joining FSU in 2015 exceeds $21 million.
I received an MS from Columbia University in 2009 and a BS from Beijing University of Posts and Telecommunications in 2007, both in Computer Science. I received PhD in Computer Science from New Jersey Institute of Technology in 2014, where I worked with Dr. James Geller and Dr. Yehoshua Perl in the Structural Analysis of Biomedical Ontologies Center (SABOC). My doctoral thesis centers on quality assurance methodologies for controlled biomedical vocabularies - Unified Medical Language System (UMLS), SNOMED CT, and domain ontologies in BioPortal. Before joining FSU in 2015, I was a Postdoctoral Research Scientist in the Department of Biomedical Informatics at Columbia University, working with Dr. Chunhua Weng. In my postdoc research, I developed informatics methods to assess the collective population representativeness of clinical studies to improve the transparency of study generalizability to the real-world population. I received an early promotion to Associate Professor with tenure from FSU in 2020. In 2025, I was again promoted to Full Professor at FSU. During my sabbatical year 2023-2024, I visited the National Center for Biotechnology Information, National Library of Medicine/NIH, where I studied biomedical natural language processing and text engineering using knowledge bases and large language models.
I have published over 130 papers in leading biomedical informatics venues, including JAMIA, JBI, Nature Partner Journal Digital Medicine (npj Digital Medicine), JMIR, AMIA, and MEDINFO. My papers received prestigious recognitions including (1) two Distinguished Paper Awards of AMIA 2015 and AMIA 2017 Annual Symposium (AMIA 2015 paper and AMIA 2017 paper), (2) 2nd Place Best Student Paper Award of AMIA 2019 Annual Symposium, (2) paper selection in "AMIA 2014 Informatics Year In Review" (AMIA 2013 paper), (3) finalists of the Student Paper Award of AMIA 2015 Summit on Clinical Research Informatics and MEDINFO 2015, and (4) paper selection in "Clinical Research Informatics 2016 Year in Review" (JBI 2016 and AMIA 2015 paper)
I have been actively serving the biomedical informatics research community as an Editorial Board Member of the Journal of the American Medical Informatics Association (JAMIA), Journal of Biomedical Informatics (JBI), PLOS ONE, BMC Medical Informatics and Decision Making, BMC Digital Health, Social Science Computer Review, and an Associate Editor of Smart Health (Elsevier) and Journal of Healthcare Informatics Research (JHIR). I am currently the Chair of the AMIA Knowledge Discovery and Data Mining (KDDM) Working Group. I'm a regular reviewer for over 40 prestigious journals, including Nature Medicine, NPJ Digital Medicine (a sister journal of Nature), Journal of the American Medical Informatics Association (JAMIA), JBI, and Artificial Intelligence in Medicine.
Artificial Intelligence in Medicine
Clinical Trial Generalizability
Biomedical Ontologies and Controlled Vocabularies
eHealth Tools for Patient Engagement
Patients' Information Behavior
Large Language Models
Balu Bhasuran, Qiao Jin, Yuzhang Xie, Carl Yang, Karim Hanna, Jennifer Costa, Cindy Shavor, Zhiyong Lu, Zhe He. Preliminary analysis of the impact of lab results on large language model generated differential diagnoses. npj Digital Medicine (A Nature partner journal). 8, 166 (2025). [Link]
Xiaoyu Wang, Haoyong Ouyang, Balu Bhasuran, Xiao Luo, Karim Hanna, Mia Liza A. Lustria, Carl Yang, Zhe He. Lab-AI: Using Retrieval Augmentation to Enhance Language Models for Personalized Lab Test Interpretation in Clinical Medicine. The 13th IEEE International Conference on Healthcare Informatics (ICHI 2025), Calabria, Italy, June 18-21, 2025.
Zhe He, Balu Bhasuran, Qiao Jin, Shubo Tian, Karim Hanna, Cindy Shavor, Lisbeth Garcia Arguello, Patrick Murray, Zhiyong Lu. Quality of Answers of Generative Large Language Models Versus Peer Users for Interpreting Laboratory Test Results for Lay Patients: Evaluation Study. Journal of Medical Internet Research. 2024;26:e56655. doi: 10.2196/56655. PMID: 38630520 [Link]
Clinical Informatics / Clinical Research Informatics
Wenshan Han, Balu Bhasuran, Victorine Muse, Søren Brunak, Lifeng Lin, Karim Hanna, Yu Huang, Jiang Bian, Zhe He. Assessing the Seasonality of Lab Tests Among Patients with Alzheimer's Disease and Related Dementias in OneFlorida Data Trust. AMIA 2024 Annual Symposium. In press.
Zhe He, Shubo Tian, Arslan Erdengasileng, Neil Charness, Jiang Bian. Temporal Subtyping of Alzheimer’s Disease Using Medical Conditions Preceding Alzheimer’s Disease Onset in Electronic Health Records. AMIA 2022 Informatics Summit. 2022; 2022: 226-235. PMID: 35854753. PMCID: PMC92851183 [Link]
Zhe He, *Xiang Tang, *Kelsa Bartley, Xi Yang, Yi Guo, Thomas J. George, Neil Charness, William Hogan, Jiang Bian. Clinical Trial Generalizability Assessment in the Big Data Era: A Review. Clinical and Translational Science. 2020; 13(4): 675-684. DOI: 10.1111/cts.12764. PMID: 32058639. [Link] [PubMed] [Dataset Publication]
Zhe He, Jiang Bian, Henry Carretta, Jiwon Lee, William Hogan, Elizabeth Shenkman, and Neil Charness. Prevalence of Multiple Chronic Conditions Among Older Adults in Florida and the United States: Comparative Analysis of the OneFlorida Data Trust and National Inpatient Sample. Journal of Medical Internet Research. 2018; 20(4): e137. PMID: 29650502. PMCID: PMC5920146. [Link] [PubMed] [PMC]
Consumer Health Informatics
Juan Xie*, Zhe He, Gary Burnett, and Ying Cheng. How do mothers exchange parenting-related information in online communities? A meta-synthesis. Computers in Human Behavior. 2021; 115: 106631 (SSCI, Impact Factor: 5.003) [Free Access Link (till Jan 8, 2020) ]
Yu Lu, Xiao Luo, Zhan Zhang, and Zhe He. Retrieving Lab Test Related Questions from Social QA Sites By Combining Shallow Features and Deep Representations. AMIA 2020 Annual Symposium. November 14-18, 2020. Virtual. pp. 717-726. PMID: 33936453. PMCID: PMC8075538. [medRxiv] [PMC]
*Biyang Yu†, Zhe He†, Aiwen Xing, and Mia Liza Lustria. An Informatics Framework to Assess Consumer Health Language Complexity Differences: Proof-of-Concept Study. Journal of Medical Internet Research. 2020;22(5):e16795. [Link]
Zhe He*, Zhiwei Chen, Sanghee Oh, Jinghui Hou, and Jiang Bian. Enriching consumer health vocabulary through mining a social Q&A site: a similarity-based approach. Journal of Biomedical Informatics. 2017;69:75-85. PMID: 28359728 [PubMed] [ScienceDirect] [PDF]
Explainable AI / Machine Learning for Healthcare
Zhe He, Shubo Tian, Ankita Singh, Shayok Chakraborty, Shenghao Zhang, Mia Liza A. Lustria, Neil Charness, Nelson Roque, Erin Harrell, Walter R. Boot. A Machine-Learning Based Approach for Predicting Older Adults’ Adherence to Technology-Based Cognitive Training. Information Processing and Management. 2022; 59(5): 103034.
Michael O. Killian, Seyedeh Neelufar Payrovnaziri, Dipankar Gupta, Dev Desai, and Zhe He. Machine learning-based prediction of re-hospitalization in pediatric organ transplantation recipients. JAMIA Open. 2021; 4(1): 1-10.
*Seyedeh Neelufar Payrovnaziri, Zhaoyi Chen, Pablo Rengifo-Moreno, Tim Miller, Jiang Bian, Jonathan H. Chen, Xiuwen Liu, and Zhe He. Explainable artificial intelligence models using real-world electronic health record Data: a systematic scoping review. Journal of the American Medical Informatics Association. 2020; 27(7): 1173-1185. PMID: 32417928. [Free Access Link] [PubMed]
Quality Assurance of Biomedical Terminologies / Ontologies
Ling Zheng†, Zhe He†, Duo Wei, Vipina Keloth, Jung-Wei Fan, Luke Lindemann, Xinxin Zhu, James Cimino, and Yehoshua Perl. A review of auditing techniques for the Unified Medical Language System. Journal of the American Medical Informatics Association. 2020; 27(10): 1625-1638. (†: equal-contribution first authors) [Free Access Link]
Muhammad F. Amith†, Zhe He†, Jiang Bian, Juan Antonio Lossio-Ventura, and Cui Tao*. Assessing the practice of biomedical ontology evaluation: Gaps and opportunities. Journal of Biomedical Informatics. 2018;80:1-13. DOI: 10.1016/j.jbi.2018.02.010. PMID. 29462669. (†: equal-contribution first authors) [FSU CCI News] [ScienceDirect] [PubMed]
Zhe He, James Geller, and Yan Chen. A comparative analysis of the density of the SNOMED CT conceptual content for semantic harmonization. Artificial Intelligence in Medicine. 2015;64(1):29-40. PMID: 25890688. [ScienceDirect] [PDF] (Invited Talk at IHTSDO Implementation SIG Webinar [Slides] [Video]) (#14 Hottest Article April - June 2015)
Zhe He, Christopher Ochs, Ankur Agrawal, Yehoshua Perl, Dimitrios Zeginis, Konstantinos Tarabanis, Gai Elhanan, Michael Halper, Natasha Noy, and James Geller. A Family-Based Framework for Supporting Quality Assurance of Biomedical Ontologies in BioPortal. Proceedings of AMIA 2013 Annual Symposium (AMIA 2013) , November 16 - 20, 2013, Washington D.C. pp. 581-90. PMID: 24551360. [PubMed] [PDF] [Talk Slides] (Featured in "AMIA 2014 Year in Review")
Third Place of the 2024 AMIA Knowledge Discovery and Data Mining Innovation Award, November 2024
Pediatric Best Poster Award of 2024 American Transplant Congress, June 2024
Elected as IEEE Senior Member, October 2023
2022 Lois Lunin Award. the Association for Information Science and Technology (ASIS&T), June 2022
2022 Outstanding Faculty Research Award, College of Communication & Information, Florida State University, April 2022
Best Interdisciplinary Research Award, 2021 Aging and Health Informatics Conference, December 2021
Fellow of American Medical Informatics Association (FAMIA), May 2022.
2021 Faculty Leader/Builder Award, College of Communication & Information, Florida State University, April 2021
Co-advisor and co-first author of the 2nd place paper in the Student Paper Competition, AMIA 2019 Annual Symposium, November 2019
2019 Outstanding Faculty Research Award, College of Communication & Information, Florida State University, April 2019
Advisor and co-author for student finalist in AMIA Informatics Summit Student Paper Competition, March 2019
Distinguished Paper Award of AMIA 2017 Annual Symposium, November 2017 [CCI News]
2017 Outstanding Faculty Research Award, College of Communication & Information, Florida State University, April 2017
Runner Up, Most Interesting Preliminary Results Paper Award, iConference 2016, March 2016
Distinguished Paper Award of AMIA 2015 Annual Symposium, November 2015 [News Article]
MEDINFO 2015 Student Paper Award Nominee, August 2015
AMIA 2015 Summit on Clinical Research Informatics Student Paper Award Nominee, April 2015
Top Poster Award, 2014 Columbia University Postdoc Research and Career Symposium (One of the three awards among over 50 postdoc presenters)
Outstanding Leader Award 2013 - 2014, New Jersey Institute of Technology (One award is given annually)
Distinguished College Graduate of Beijing (10 out of over 400 graduates majored in Computer Science at BUPT )
Delegate of China in the 7th China Synergy Programme for Outstanding Youth (Highly selective 48 college student delegates in mainland China)