Yonghui Wu,
Director Of Natural Language Processing & Assistant Professor
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
Teaching Profile
Courses Taught
2019-2021
GMS6803 Data Science for Clinical Research
2019-2021
GMS6856 Introduction to Biomedical Natural Language Processing
Research Profile
Open Researcher and Contributor ID (ORCID)
0000-0002-6780-6135
Publications
2022
Machine learning algorithms for predicting direct-acting antiviral treatment failure in chronic hepatitis C: An HCV-TARGET analysis.
Hepatology (Baltimore, Md.).
[DOI] 10.1002/hep.32347.
[PMID] 35034373.
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.
Extracting Family History of Patients From Clinical Narratives: Exploring an End-to-End Solution With Deep Learning Models (Preprint)
.
[DOI] 10.2196/preprints.22982.
Measurement of Semantic Textual Similarity in Clinical Texts: Comparison of Transformer-Based Models (Preprint)
.
[DOI] 10.2196/preprints.19735.
Grants
Jan 2022
ACTIVE
OneFlorida+ Phase 3 Clinical Research Network
Role: Co-Investigator
Funding: PATIENT-CENTERED OUTCOMES RES INST
Dec 2021
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 NY
via NATL INST OF HLTH NIA
Jul 2021
ACTIVE
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 NY
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
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
– Nov 2021
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
Contact Details
Phones:
- Business:
- (352) 294-8436
Emails:
- Business:
- yonghui.wu@ufl.edu
Addresses:
- Business Mailing:
-
PO Box 100177
GAINESVILLE FL 32610 - Business Street:
-
2004 MOWRY RD
GAINESVILLE FL 32610