Zhe He (何辙), PhD, FAMIA

[ How to pronounce my name? The pronunciation of "Zhe" is similar to "Geor(gia)" sound. The pronunciation of "He" is like "her" but without the "r" sound (the British accent). ]

Associate Professor (tenured) and MSIT Program Chair, School of Information, Florida State University

Informatics Lead and Team Lead of Biostatistics, Informatics, and Research Design (BIRD) Program of UF-FSU Clinical and Translational Science Award

Associate Professor (courtesy), Department of Behavioral Sciences & Social Medicine, College of Medicine, Florida State University

Associate Professor (courtesy), Department of Computer Science, Florida State University

Director, eHealth Lab, College of Communication and Information, Florida State University

Fellow of the American Medical Informatics Association

Vice Chair (2023- ), Secretary (2020-2022), AMIA Knowledge Discovery and Data Mining Working Group

Address: 271 Shores Building, 142 Collegiate Loop. Tallahassee FL, 32306-2100

Phone: 850.644.5775

Email: zhe.he AT cci DOT fsu DOT edu OR zhe AT fsu DOT edu

[CV] [FSU FEAS CV] [Academic Genealogy] [GitHub] [Google Scholar] [ResearchGate] [NCBI] [OCRID]

Call for Papers:

Implementation of AI and Machine Learning Technologies in Medicine. Frontiers in Medicine (Deadline: November 11, 2022)


I am a tenured Associate Professor in the School of Information (iSchool) at the Florida State University and a Core Affiliate of the Institute for Successful Longevity. I am also holding courtesy appointments with Department of Behavioral Sciences and Social Medicine of College of Medicine and Department of Computer Science. At Florida State, I am the Team Lead and Informatics Lead of Biostatistics, Informatics, and Research Design (BIRD) Program in the UF-FSU Clinical and Translational Science Award. I am an editorial board member of BMC Medical Informatics and Decision Making, BMC Digital Health, and PLOS One.

My research lies at the intersection of Biomedical & Health Informatics, Computers Science, and Information Science. As an interdisciplinary researcher, my main research expertise includes machine learning, natural language processing, knowledge representation, and big data analytics. In FSU iSchool, I lead the eHealth Lab. The overarching goal of my research is to improve population health and advance biomedical research through the collection, analysis, and application of electronic health data from heterogeneous sources. As Principal Investigator, my research has been funded by the National Library of Medicine / NIH, National Institute on Aging / NIH, UF Clinical and Translational Science Insitute, Eli Lilly and Company, Amazon, NVIDIA, FSU Council on Research and Creativity, and Institute for Successful Longevity.

I received my MS from Columbia University in 2009 and BS from Beijing University of Posts and Telecommunications in 2007, both in Computer Science. I received my 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 is centered on quality assurance methodologies for controlled biomedical vocabularies - Unified Medical Language System (UMLS), SNOMED CT, and domain ontologies in BioPortal. Before joining FSU in Fall 2015, I was a Postdoctoral Research Scientist in the Department of Biomedical informatics at Columbia University between 2014 and 2015, working with Dr. Chunhua Weng. In my postdoctoral research, I developed informatics methods to assess the collective population representativeness of clinical studies, with the goal of improving the transparency of study generalizability to the real-world population. I received early promotion to Associate Professor with tenure from FSU in 2020.

I have published over 100 papers in leading biomedical informatics venues including JAMIA, JBI, AIIM, JMIR, AMIA, and MEDINFO. My papers received a number of 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 community, as an Editorial Board Member of PLOS ONE, BMC Medical Informatics and Decision Making, and BMC Digital Health. I am currently Vice Chair (2023- ) (Former Secretary 2020-2022) of AMIA Knowledge Discovery and Data Mining (KDDM) Working Group. I'm a regular reviewer for over 30 prestigious journals including Nature Medicine, Journal of the American Medical Informatics Association (JAMIA), Journal of Biomedical Informatics (JBI), Artificial Intelligence in Medicine. I have also chaired the International Workshop on Semantics-Powered Health Data Analytics (SEPDA) 6 times and served as a PC member in many mainstream conferences including AMIA Annual Symposium, AMIA Informatics Summit, MEDINFO, and BIBM.

In 2014, I was inducted into Alpha Epsilon Lambda National Graduate and Professional Honor Society. In 2020, I joined Sigma Xi, the Scientific Research Honor Society. In 2022, I was inducted as a Fellow of the American Medical Informatics Association (FAMIA). I am the recipient of the 2022 Lois Lunin Award from the Association for Information Science and Technology (ASIS&T).

In my spare time, I am interested in photography and traveling. This is my Photography Studio.

Research Interests

  • Artificial Intelligence in Medicine

  • Clinical Trial Generalizability Assessment

  • Biomedical Ontologies and Controlled Vocabularies

  • Consumer Health Language

  • Consumer Information Seeking Behavior

Selected Publications (All Publications)

Clinical Research Informatics

  • 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]

  • Qian Li, Zhe He, Yi Guo, Hansi Zhang, Thomas J George Jr, William Hogan, Neil Charness, Jiang Bian. Assessing the Validity of a a priori Patient-Trial Generalizability Score using Real-world Data from a Large Clinical Data Research Network: A Colorectal Cancer Clinical Trial Case Study. AMIA 2019 Annual Symposium. November 14-18, 2019. Washington DC. pp.1101-1110. PMID: 32308907. PMCID: PMC7153072 (:Co-first authors) (2nd Place of the Student Paper Competition) [PMC]

  • Hansi Zhang, Zhe He, Xing He, Yi Guo, David R. Nelson, François Modave, Yonghui Wu, William Hogan, and Jiang Bian. Computable Eligibility Criteria through Ontology-Driven Data Access: A Case Study of Hepatitis C Virus Trials. Proceedings of AMIA 2018 Annual Symposium. November 3-8, 2018. San Francisco, CA. pp. 1601-1610. (Finalist of the Student Paper Award)

  • 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]

  • Zhe He, Arturo Gonzalez-Izquierdo, Spiros Denaxas, Andrei Sura, Yi Guo, William R. Hogan, Elizabeth Shenkman, Jiang Bian. Comparing and Contrasting A Priori and A Posteriori Generalizability Assessment of Clinical Trials on Type 2 Diabetes Mellitus. Proceedings of AMIA 2017 Annual Symposium. November 4-8, 2017. Washington DC. pp. 849-858. PMID: 29854151. PMCID: PMC5977671. [PDF] [PMC] (Distinguished Paper Award; three awards were selected from 105 accepted paper and 266 paper submissions) [Award Certificate] [Live Picture] [CCI News]

  • Zhe He*, Patrick Ryan, Julia Hoxha, Shuang Wang, Simona Carini, Ida Sim, and Chunhua Weng. Multivariate analysis of the population representativeness of related clinical studies. Journal of Biomedical Informatics. 2016;60:66-76. PMID: 26820188.[ScienceDirect] [PubMed] [PDF]

  • Zhe He, Praveen Chandar, Patrick Ryan, and Chunhua Weng. Simulation-based Evaluation of the Generalizability Index for Study Traits. Proceedings of AMIA 2015 Annual Symposium. November 14-18, 2015. San Francisco, CA. pp.594-602. PMID: 26958194 (Distinguished Paper Award News Article) [PDF] [PubMed]

  • Zhe He, Simona Carini, Ida Sim, and Chunhua Weng. Visual aggregate analysis of eligibility features of clinical trials. Journal of Biomedical Informatics. 2015;54:241-255. PMID: 25615940. [ScienceDirect] [PubMed] [PDF]

  • Zhe He, Simona Carini, Tianyong Hao, Ida Sim, and Chunhua Weng. A Method for Analyzing Commonalities in Clinical Trial Target Populations. Proceedings of AMIA 2014 Annual Symposium (AMIA 2014), November 15 - 19, 2014, Washington D.C. pp.1777-1786. PMID: 25954450. [PubMed] [PDF] [Talk Slides]

Consumer Health Informatics

  • Yu Lu, Laura A. Barrett, Rebecca Lin, Muhammad Amith, Cui Tao, and Zhe He. Understanding Information Needs and Barriers to Accessing Health Information Across All Stages of Pregnancy: A Systematic Review. JMIR Pediatrics and Parenting. 2022;5(1):e32235. doi: 10.2196/32235. PMID: 35188477 [JMIR]

  • 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. Understanding and Bridging the Language and Terminology Gap between Health Professionals and Consumers Using Social Media. Social Web and Health Research: Benefits, Limitations, and Best Practices. In: Bian J., Guo Y., He Z., Hu X. (eds) Social Web and Health Research. Springer, Cham. 2019. pp. 103-121. DOI: 10.1007/978-3-030-14714-3_6. [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]

  • Min Sook Park, Zhe He*, Zhiwei Chen, Sanghee Oh, and Jiang Bian. Consumer's Use of UMLS Concepts on Social Media: Diabetes-Related Textual Data Analysis in Blog and Social Q&A Sites. JMIR Medical Informatics. 2016; 4(4):e41. PMID: 27884812 (Park MS and He Z are equal-contribution first authors) [JMIR] [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, Aiwen Xing, Shaeke Salman, Xiuwen Liu, Jiang Bian, and Zhe He. Assessing the Impact of Imputation on the Interpretations of Prediction Models: A Case Study on Mortality Prediction for Patients with Acute Myocardial Infarction. AMIA 2021 Informatics Summit. Virtual. March 22-25, 2021. pp. 465-474. [medRxiv] [AMIA]

  • *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]

  • Shaeke Salman, *Seyedeh Neelufar Payrovnaziri, Xiuwen Liu, Pablo Rengifo-Moreno, and Zhe He. DeepConsensus: Consensus-based Interpretable Deep Neural Networks with Application to Mortality Prediction. 2020 International Joint Conference on Neural Networks (IJCNN 2020). Glasgow, United Kingdom, 2020, pp. 1-8, doi: 10.1109/IJCNN48605.2020.9206678. [Link]

  • Seyedeh Neelufar Payrovnaziri, Laura A. Barrett, Daniel Bis, Jiang Bian, and Zhe He. Enhancing Prediction Models for One-Year Mortality in Patients with Acute Myocardial Infarction and Post Myocardial Infarction Syndrome. MEDINFO 2019. August 26-30, 2019. Lyon, France. Studies in Health Technology and Informatics. 2019 Aug 21;264:273-277. doi: 10.3233/SHTI190226. PMID: 31437928. PMCID: PMC6785831 [IOS Press] [PMC]

  • *Laura A. Barrett, *Seyedeh Neelufar Payrovnaziri, Jiang Bian, and Zhe He. Building Computational Models to Predict One-Year Mortality in ICU Patients with Acute Myocardial Infarction and Post Myocardial Infarction Syndrome. AMIA 2019 Informatics Summit. March 25-28, 2019. San Francisco, CA. pp. 407-416. PMID: 31258994. PMCID: PMC6568097. (Finalist of the Student Paper Award) [Preprint] [AMIA] [PMC] (Media Report)

Quality Assurance of Biomedical Terminologies / Ontologies

Honors and Awards

  • 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

  • Provost's Travel Grant (to present my paper in BIBM 2018), Florida State University, November 2018

  • Granted U.S. Permanent Residency under the category of "Aliens with Extraordinary Ability" (EB-1A), March 2018

  • FSU University-Wide Research Recognition Dinner Invitee, March 2018

  • Provost's Travel Grant (to present my paper in AMIA 2017), Florida State University, November 2017

  • 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

  • Provost's Travel Grant (to present my paper in AMIA 2016), Florida State University, November 2016

  • Amazon Web Services Cloud Credits for Research, December 2016 - November 2017

  • Travel Grant, NSF South Big Data Hub, September 2016

  • Travel Grant, NIH Future Research Leaders Conference, Bethesda, MD, September 2016

  • Planning Grant, Institute for Successful Longevity, May 2016

  • Two Papers Featured in Clinical Research Informatics 2016 Year in Review, March 2016 [Link]

  • Runner Up, Most Interesting Preliminary Results Paper Award, iConference 2016, March 2016

  • Travel Grant, Transatlantic Data Science Workshop, Bethesda, MD March 1-2, 2016

  • Florida State University First Year Assistant Professor Grant, May - August, 2016

  • Distinguished Paper Award of AMIA 2015 Annual Symposium, November 2015 [News Article]

  • Amazon Web Services Education Research Grant Award, December 2015 - November 2016

  • Provost's Travel Grant (to present my paper in AMIA 2015), Florida State University, September 2015

  • MEDINFO 2015 Student Paper Award Nominee, August 2015

  • AMIA 2015 Summit on Clinical Research Informatics Student Paper Award Nominee, April 2015

  • One Paper Featured in the "2014 Informatics Year in Review", November 2014 [Link]

  • 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)