Yonghui Wu,
Associate Professor & Director Of Natural Language Processing
Department:
MD-HOBI-BIOMED INFORMATICS
Business Phone:
(352) 294-8436
Business Email:
yonghui.wu@ufl.edu
About Yonghui Wu
Dr. Yonghui Wu is an Associate Professor with Tenure in the College of Medicine, Department of Health Outcomes & Biomedical Informatics at the University of Florida. He also serves as the Director of Natural Language Processing (NLP) at UF Clinical and Translational Science Institute (CTSI) and OneFlorida Clinical Research Consortium. Dr. Wu’s research interests include natural language processing (NLP), machine learning, computational drug repurposing, and applications of artificial intelligence (AI) technologies to electronic health records for clinical and translational research. He has published over 80 peer-reviewed papers and has been the principal investigator for grants from the National Institutes of Health (NIH) and Patient-Centered Outcomes Research Institute.
Dr. Wu received his Ph.D. from the Harbin Institute of Technology, School of Computer Science with a focus on natural language processing. Then, he entered medical informatics research with a motivation to help improve the quality of healthcare delivery and the safety of patients. He has Biomedical informatics training at Vanderbilt University and the University of Texas Health Science Center at Houston.
Accomplishments
Top-ranked (#2) ”end-to-end system” to identify medications, adverse druge events and their relations
2018
·
2018 N2C2 challenge
Top-ranked (#3) ”medications and adverse drug events concepts recognition” system
2018
·
2017 MADE challenge
One of the best articles from the literature in the Natural Language Process- ing subfield of medical informatics
2017
·
International Medical Informatics Association (IMIA)
Best performed ”chemical-induced disease relation extraction” system
2015
·
015 BioCreative V open challenge
Top-ranked (#1) clinical abbreviation disambiguation system
2014
·
2013 ShARe/CLEF eHealth Shared Tasks in Clinical NLP
Finalist of best paper award (Co-first author), AMIA Translational Bioinformat- ics Summit
2012
·
AMIA
Top-ranked (#1) “temporal relation extraction” system
2012
·
2012 i2b2 Clinical NLP challenge
Teaching Profile
Courses Taught
2019-2021
GMS6803 Data Science for Clinical Research
2019-2021,2023
GMS6856 Introduction to Biomedical Natural Language Processing
Research Profile
Open Researcher and Contributor ID (ORCID)
0000-0002-6780-6135
Publications
2024
Combining Federated Machine Learning and Qualitative Methods to Investigate Novel Pediatric Asthma Subtypes: Protocol for a Mixed Methods Study
JMIR Research Protocols.
13
[DOI] 10.2196/57981.
[PMID] 38976313.
2024
Generative large language models are all-purpose text analytics engines: text-to-text learning is all your need
Journal of the American Medical Informatics Association.
31(9):1892-1903
[DOI] 10.1093/jamia/ocae078.
[PMID] 38630580.
2024
Identifying social determinants of health from clinical narratives: A study of performance, documentation ratio, and potential bias
Journal of Biomedical Informatics.
153
[DOI] 10.1016/j.jbi.2024.104642.
[PMID] 38621641.
2024
Large language models as decision aids in neuro-oncology: a review of shared decision-making applications
Journal of Cancer Research and Clinical Oncology.
150(3)
[DOI] 10.1007/s00432-024-05673-x.
[PMID] 38503921.
2024
Model tuning or prompt Tuning? a study of large language models for clinical concept and relation extraction
Journal of Biomedical Informatics.
153
[DOI] 10.1016/j.jbi.2024.104630.
[PMID] 38548007.
2023
A study of generative large language model for medical research and healthcare
npj Digital Medicine.
6(1)
[DOI] 10.1038/s41746-023-00958-w.
[PMID] 37973919.
2023
Assess the documentation of cognitive tests and biomarkers in electronic health records via natural language processing for Alzheimer’s disease and related dementias.
International journal of medical informatics.
170
[DOI] 10.1016/j.ijmedinf.2022.104973.
[PMID] 36577203.
2023
Clinical concept and relation extraction using prompt-based machine reading comprehension
Journal of the American Medical Informatics Association.
30(9):1486-1493
[DOI] 10.1093/jamia/ocad107.
[PMID] 37316988.
2023
Clinical Prediction Models for Hospital-Induced Delirium Using Structured and Unstructured Electronic Health Record Data: Protocol for a Development and Validation Study
JMIR Research Protocols.
12
[DOI] 10.2196/48521.
[PMID] 37943599.
2023
The role of health system penetration rate in estimating the prevalence of type 1 diabetes in children and adolescents using electronic health records
Journal of the American Medical Informatics Association.
31(1):165-173
[DOI] 10.1093/jamia/ocad194.
[PMID] 37812771.
2022
A large language model for electronic health records
npj Digital Medicine.
5(1)
[DOI] 10.1038/s41746-022-00742-2.
[PMID] 36572766.
2022
Barriers and Facilitators of Obtaining Social Determinants of Health of Patients With Cancer Through the Electronic Health Record Using Natural Language Processing Technology: Qualitative Feasibility Study With Stakeholder Interviews
JMIR Formative Research.
6(12)
[DOI] 10.2196/43059.
[PMID] 36574288.
2022
Identify diabetic retinopathy-related clinical concepts and their attributes using transformer-based natural language processing methods.
BMC medical informatics and decision making.
22(Suppl 3)
[DOI] 10.1186/s12911-022-01996-2.
[PMID] 36167551.
2022
Machine learning algorithms for predicting direct-acting antiviral treatment failure in chronic hepatitis C: An HCV-TARGET analysis.
Hepatology (Baltimore, Md.).
76(2):483-491
[DOI] 10.1002/hep.32347.
[PMID] 35034373.
2022
Noninvasive Diagnosis of Nonalcoholic Steatohepatitis and Advanced Liver Fibrosis Using Machine Learning Methods: Comparative Study With Existing Quantitative Risk Scores
JMIR Medical Informatics.
10(6)
[DOI] 10.2196/36997.
[PMID] 35666557.
2022
Procedural complications associated with invasive diagnostic procedures after lung cancer screening with low-dose computed tomography.
Lung cancer (Amsterdam, Netherlands).
165:141-144
[DOI] 10.1016/j.lungcan.2021.12.020.
[PMID] 35124410.
2020
Assessing mental health signals among sexual and gender minorities using Twitter data.
Health informatics journal.
26(2):765-786
[DOI] 10.1177/1460458219839621.
[PMID] 30969146.
2020
Assessing the practice of data quality evaluation in a national clinical data research network through a systematic scoping review in the era of real-world data.
Journal of the American Medical Informatics Association : JAMIA.
27(12):1999-2010
[DOI] 10.1093/jamia/ocaa245.
[PMID] 33166397.
2020
Clinical concept extraction using transformers.
Journal of the American Medical Informatics Association : JAMIA.
27(12):1935-1942
[DOI] 10.1093/jamia/ocaa189.
[PMID] 33120431.
2020
Extracting Family History of Patients From Clinical Narratives: Exploring an End-to-End Solution With Deep Learning Models
JMIR Medical Informatics.
8(12)
[DOI] 10.2196/22982.
[PMID] 33320104.
2020
Identification of important factors in an inpatient fall risk prediction model to improve the quality of care using EHR and electronic administrative data: A machine-learning approach.
International journal of medical informatics.
143
[DOI] 10.1016/j.ijmedinf.2020.104272.
[PMID] 32980667.
2020
Identifying relations of medications with adverse drug events using recurrent convolutional neural networks and gradient boosting.
Journal of the American Medical Informatics Association : JAMIA.
27(1):65-72
[DOI] 10.1093/jamia/ocz144.
[PMID] 31504605.
2020
International Classification of Diseases, Tenth Revision, Clinical Modification social determinants of health codes are poorly used in electronic health records.
Medicine.
99(52)
[DOI] 10.1097/MD.0000000000023818.
[PMID] 33350768.
2020
Measurement of Semantic Textual Similarity in Clinical Texts: Comparison of Transformer-Based Models
JMIR Medical Informatics.
8(11)
[DOI] 10.2196/19735.
[PMID] 33226350.
2019
A Study of Deep Learning Methods for De-identification of Clinical Notes at Cross Institute Settings.
IEEE International Conference on Healthcare Informatics. IEEE International Conference on Healthcare Informatics.
2019
[DOI] 10.1109/ICHI.2019.8904544.
[PMID] 31879734.
2019
Applying a deep learning-based sequence labeling approach to detect attributes of medical concepts in clinical text.
BMC medical informatics and decision making.
19(Suppl 5)
[DOI] 10.1186/s12911-019-0937-2.
[PMID] 31801529.
2019
Detect Attributes of Medical Concepts via Sequence Labeling.
IEEE International Conference on Healthcare Informatics. IEEE International Conference on Healthcare Informatics.
2019
[DOI] 10.1109/ICHI.2019.8904714.
[PMID] 32537570.
2019
Evaluation of Machine-Learning Algorithms for Predicting Opioid Overdose Risk Among Medicare Beneficiaries With Opioid Prescriptions.
JAMA network open.
2(3)
[DOI] 10.1001/jamanetworkopen.2019.0968.
[PMID] 30901048.
2019
Time-sensitive clinical concept embeddings learned from large electronic health records.
BMC medical informatics and decision making.
19(Suppl 2)
[DOI] 10.1186/s12911-019-0766-3.
[PMID] 30961579.
2018
A study of generalizability of recurrent neural network-based predictive models for heart failure onset risk using a large and heterogeneous EHR data set
Journal of Biomedical Informatics.
84:11-16
[DOI] 10.1016/j.jbi.2018.06.011.
[PMID] 29908902.
2018
Association of Hemoglobin A1c Levels With Use of Sulfonylureas, Dipeptidyl Peptidase 4 Inhibitors, and Thiazolidinediones in Patients With Type 2 Diabetes Treated With Metformin: Analysis From the Observational Health Data Sciences and Informatics Initiative.
JAMA network open.
1(4)
[DOI] 10.1001/jamanetworkopen.2018.1755.
[PMID] 30646124.
Grants
Jul 2024
ACTIVE
Cost effective Clinical Information Extraction using Large Language Models through Prompt-tuning
Role: Principal Investigator
Funding: SELFIIE CORPORATION
Jul 2024
ACTIVE
AI-based Clinical decision support to idenTify wOmeN for HIV testing and PrEP in Florida (ACTION-HIV)
Role: Co-Investigator
Funding: NATL INST OF HLTH NIMH
Sep 2023
ACTIVE
Assessing performance of a Hepatitis C Emergency Department (HepC-END) Screening Tool
Role: Co-Investigator
Funding: NATL INST OF HLTH NIDA
Sep 2023
ACTIVE
Identifying pediatric asthma subtypes using novel privacy-preserving federated machine learning methods
Role: Co-Investigator
Funding: NATL INST OF HLTH NHLBI
Sep 2023
ACTIVE
An end-to-end informatics framework to study Multiple Chronic Conditions (MCC)s impact on Alzheimers disease using harmonized electronic health records
Role: Co-Investigator
Funding: UNIV OF TEXAS HLTH SCI CTR AT HOUSTON
via NATL INST OF HLTH NIA
Sep 2023
– Jan 2024
ACTS (AD Clinical Trial Simulation): Developing Advanced Informatics Approaches for an Alzheimer's Disease Clinical Trial Simulation System
Role: Co-Investigator
Funding: UNIV OF TEXAS HLTH SCI CTR AT HOUSTON
via NATL INST OF HLTH NIA
Jul 2023
ACTIVE
Advancing Precision Lung Cancer Surveillance and Outcomes in Diverse Populations (PLuS2)
Role: Co-Investigator
Funding: NATL INST OF HLTH NCI
Jul 2023
ACTIVE
De-implementation of inappropriate thyroid ultrasound
Role: Co-Investigator
Funding: MAYO CLINIC
via NATL INST OF HLTH NCI
Apr 2023
ACTIVE
Artificial Intelligence and Counterfactually Actionable Responses to End HIV (AICARE-HIV)
Role: Co-Investigator
Funding: NATL INST OF HLTH NIAID
Mar 2023
ACTIVE
Utilizing Data from the Electronic Health Record to Understand the Progression Pathway of Alzheimers Disease and Related Dementias
Role: Co-Investigator
Funding: FL DEPT OF HLTH ED ETHEL MOORE ALZHEIMER
Feb 2023
ACTIVE
Eligibility criteria design for Alzheimers trials with real-world data and explainable AI
Role: Co-Investigator
Funding: WEILL MED COLLEGE OF CORNELL UNIV
via NATL INST OF HLTH NIA
Mar 2022
ACTIVE
Computational Drug Repurposing for AD/ADRD with Integrative Analysis of Real-World Data and Biomedical Knowledge
Role: Co-Investigator
Funding: WEILL MED COLLEGE OF CORNELL UNIV
via NATL INST OF HLTH NIA
Jan 2022
ACTIVE
OneFlorida+ Phase 3 Clinical Research Network
Role: Co-Investigator
Funding: PATIENT-CENTERED OUTCOMES RES INST
Oct 2021
– May 2023
RESEARCHING COVID TO ENHANCE RECOVERY (RECOVER) INITIATIVE
Role: Co-Investigator
Funding: WEILL MED COLLEGE OF CORNELL UNIV
via NATL INST OF HLTH NHLBI
Jul 2021
– Oct 2023
Developing and Evaluating a Machine-Learning Opioid Prediction & Risk-Stratification E-Platform (DEMONSTRATE)
Role: Co-Investigator
Funding: NATL INST OF HLTH NIDA
Apr 2021
ACTIVE
Advancing Interdisciplinary Science of Aging through Identification of Iatrogenic Complications: The UF EHR Clinical Data Infrastructure for Enhanced Patient Safety among the Elderly (UF-ECLIPSE)
Role: Co-Investigator
Funding: NATL INST OF HLTH NIA
Apr 2021
ACTIVE
Advancing Drug Repositioning for Alzheimers Disease using Real-world Data
Role: Principal Investigator
Funding: NATL INST OF HLTH NIA
Sep 2020
ACTIVE
Using Real-world Data to Assess the Burden of Diabetes in Children and Adolescents in Florida
Role: Co-Investigator
Funding: CTRS FOR DISEASE CONTROL AND PREVENTION
Sep 2020
ACTIVE
Linking VA and non-VA data to study the risk of suicide in chronic pain patients
Role: Co-Investigator
Funding: WEILL MED COLLEGE OF CORNELL UNIV
via NATL INST OF HLTH NIMH
Aug 2020
– Sep 2021
The External Exposome and COVID-19 Severity
Role: Co-Investigator
Funding: NATL INST OF HLTH NIEHS
Aug 2020
– Jan 2024
Using Electronic Health Records from a Large Clinical Data Research Network to Understand Cancer Burden and Cancer Risks Among Transgender and Gender Nonconforming (TGNC) Individuals
Role: Co-Investigator
Funding: NATL INST OF HLTH NCI
Jul 2020
– Dec 2022
DRPD-ROF2020: Advancing Drug Repositioning for Alzheimers Disease using Electronic Health Records
Role: Principal Investigator
Funding: UF RESEARCH
Apr 2020
– Sep 2020
IBM Task Order – Development of New and Innovative Methods for Automated Reporting for CBER-Regulated Biological Products – FDA Task Order 2, Order # 75F40119F19002
Role: Co-Investigator
Funding: IBM CORP
via US FOOD AND DRUG ADMN
Jan 2020
ACTIVE
Extracting information from clinical narratives for Clinical Outcomes Research
Role: Principal Investigator
Funding: PATIENT-CENTERED OUTCOMES RES INST
Jan 2020
ACTIVE
The benefits and harms of lung cancer screening in Florida
Role: Co-Investigator
Funding: NATL INST OF HLTH NCI
Jan 2020
– Mar 2020
Data Science in Health Informatics Workshop with Deep Learning Winter 2020
Role: Co-Investigator
Funding: *NORTHEASTERN UNIVERSITY OF CHINA
Apr 2019
– Mar 2021
Advancing Interdisciplinary Science of Aging through Identification of Iatrogenic Complications: The UF EHR Clinical Data Infrastructure for Enhanced Patient Safety among the Elderly (UF-ECLIPSE)
Role: Co-Investigator
Funding: NATL INST OF HLTH NIA
Feb 2019
– Feb 2021
Utilizing Data from the Electronic Medical Record to Predict Alzheimers and Dementia Risk
Role: Co-Investigator
Funding: FL DEPT OF HLTH ED ETHEL MOORE ALZHEIMER
Jan 2019
– Nov 2022
Systematic Analysis of Clinical Study Generalizability Assessment Methods with Informatics
Role: Co-Investigator
Funding: FL STATE UNIV
via NATL INST OF HLTH NIA
Jul 2018
– Jun 2024
Southeast Enrollment Center (SEEC)
Role: Co-Project Director/Principal Investigator
Funding: UNIV OF MIAMI
via NATL INST OF HLTH OD
Education
Ph.D. in Computer Application Technology
2010
·
Harbin Institute of Technology
M.S. in Computer Science and Technology
2005
·
Harbin Institute of Technology
B.S. in Computer Science and Technology
2003
·
Harbin University of Science and Technology
Contact Details
Phones:
- Business:
- (352) 294-8436
Emails:
- Business:
- yonghui.wu@ufl.edu
Addresses:
- Business Mailing:
-
PO Box 100147
GAINESVILLE FL 32610 - Business Street:
-
1889 Museum Rd, Suite 7000
GAINESVILLE FL 32611