Yonghui Wu

Yonghui Wu,

AST PROF

Department: MD-HOBI-BIOMED INFORMATICS
Business Phone: (352) 294-8436
Business Email: yonghui.wu@ufl.edu

About Yonghui Wu

Dr. Wu is an Assistant Professor in the College of Medicine, Department of Health Outcomes & Biomedical Informatics at the University of Florida. Dr. Wu’s research interests include Natural Language Processing (NLP) and Machine Learning. He has published over 60 peer-reviewed papers and has been the principal investigator for a number of grants, including an NLP grant from Patient-Centered Outcomes Research Institute. His research has contributed substantially to clinical and biomedical NLP – including information extraction from clinical notes and biomedical literature, Word Sense Disambiguation (WSD) for ambiguous biomedical terms; predictive modeling for drug adverse reactions and drug new indications (known as drug repurposing); various applications to apply NLP and machine learning to solve clinical and translational problems.

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 (2010-2012) and then University of Texas Health Science Center at Houston (2012-2014).

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

Publications

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. 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
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
Proceedings (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
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.
2019
Detect Attributes of Medical Concepts via Sequence Labeling
Proceedings (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
Identifying relations of medications with adverse drug events using recurrent convolutional neural networks and gradient boosting
Journal of the American Medical Informatics Association. 27(1):65-72 [DOI] 10.1093/jamia/ocz144. [PMID] 31504605.
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

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 NY via NATL INST OF HLTH NIMH
Aug 2020 ACTIVE
The External Exposome and COVID-19 Severity
Role: Co-Investigator
Funding: NATL INST OF HLTH NIEHS
Aug 2020 ACTIVE
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 ACTIVE
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 ACTIVE
Systematic Analysis of Clinical Study Generalizability Assessment Methods with Informatics
Role: Co-Investigator
Funding: FL STATE UNIV via NATL INST OF HLTH NIA

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

Teaching Profile

Courses Taught
2019-2021
GMS6803 Data Science for Clinical Research
2019-2021
GMS6856 Introduction to Biomedical Natural Language Processing

Contact Details

Phones:
Business:
(352) 294-8436
Emails:
Business:
yonghui.wu@ufl.edu