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Yonghui Wu, PhD, MS

Assistant Professor


Yonghui Wu, PhD, MS joined SBMI as a non-tenure track assistant professor focusing on research in January of 2016. Prior to starting his faculty appointment, Wu served as both a research scientist (from 2014 to 2015) and a postdoc research fellow (from 2012 to 2013) working with Professor Hua Xu, PhD on several grant funded research projects here at SBMI. From 2010 to 2012, Wu was a postdoc research fellow at Vanderbilt University in the Department of Biomedical Informatics.

Wu is currently working on a Cancer Prevention & Research Institute of Texas project that focuses on using electronic health records for repurposing existing drugs for cancer treatment. Additionally, Wu is working on a NLM funded research project to explore interactive machine learning methods for clinical natural language processing. Wu’s research interests include natural language processing, machine learning, text/data mining, and pharmacovigilance.

Contact

 [email protected]
Phone: 713-500-3903
Fax: 713-500-3929

Staff Support

 Yukiko Bryson
Phone: 713-500-3992


Education

  • PhD, 2010, Computer Application Technology, Harbin Institute of Technology, Harbin, China
  • MS, 2005, Computer Science and Technology, Harbin Institute of Technology, Harbin, China
  • BS, 2003, Computer Science and Technology, Harbin University of Science and Technology, Harbin, China

Areas of Expertise

  • Natural Language Processing
  • Machine Learning
  • Text/Data Mining
  • Pharmacovigilance

Funding

Current Grants

  • Repurposing Existing Drugs for Cancer Treatment using Electronic Health Records
    CPRIT (Cancer Prevention & Research Institute of Texas, PI – Hua Xu)
    03/01/2013 – 02/28/2018
    Role: Co-Investigator
  • Interactive machine learning methods for clinical natural language processing
    NLM 2R01LM010681-05 (PI – Hua Xu)
    09/29/2014 – 09/28/2018
    Role: Co-Investigator

Completed Grants

  • Real-time Disambiguation of Abbreviations in Clinical Notes
    NLM R01LM010681 (PI – Hua Xu)
    05/31/2010 – 5/30/2013
    Role: Postdoc Research Fellow
  • Informatics and Decision Making in Healthcare SHARP
    National Center for Cognitive SHARP ONC 90TR000401 (PI - Jiajie Zhang), National Center for Cognitive
    Role: Postdoc Research Fellow

Publications

Peer Reviewed Articles – Journal

  1. Jun Xu, Hee-Jin Lee, Jia Zeng, Yonghui Wu, Yaoyun Zhang, Liang-Chin Huang, Amber Johnson, Vijaykumar Holla, Ann M. Bailey, Trevor Cohen, Funda Meric-Bernstam, Elmer Bernstam, Hua Xu. Extracting genetic alteration information for personalized cancer therapy from ClinicalTrials.gov. J Am Med Inform Assoc. 2016, in press. [PMCID pending]
  2. Yonghui Wu, Joshua C. Denny, S. Trent Rosenbloom, Randolph A. Miller, Dario A. Giuse, Min Song, Hua Xu. A Preliminary Study of Clinical Abbreviation Disambiguation in Real Time. Appl Clin Inform, 2015. [PMCID PMC4493336]
  3. Yonghui Wu, Min Jiang, Jianbo Lei, Hua Xu. Named Entity Recognition in Chinese Clinical Text Using Deep Neural Network. Studies in health technology and informatics, 2015. [PMCID PMC4624324]
  4. Sun J, Zhao M, Jia P, Wang L, Wu Y, Iverson C, Zhou Y, Bowton E, Roden D, Denny J, Aldrich M, Xu H, Zhao Z. Deciphering signaling pathway networks to understand the molecular mechanisms of metformin. PLoS Computational Biology, 2015. [PMCID PMC4470683]
  5. Buzhou Tang, Yudong Feng, Xiaolong Wang, Yonghui Wu, Yaoyun Zhang, Min Jiang, Jingqi Wang, Hua Xu. A comparison of conditional random fields and structured support vector machines for chemical entity recognition in biomedical literature. J Cheminform, 2015. [PMCID PMC4331698]
  6. Yonghui Wu, Jianbo Lei, Wei-Qi Wei, Buzhou Tang, Joshua C. Denny, S. Trent Rosenbloom, Ran-dolph A. Miller, Dario A. Giuse, Kai Zheng, Hua Xu. Analyzing Differences between Chinese and English Clinical Text: A Cross-Institution Comparison of Discharge Summaries in Two Languages. Stud Health Technology Inform, 2013. [PMID 23920639]
  7. Buzhou Tang, Hongxin Cao, Yonghui Wu, Min Jiang and Hua Xu. Recognizing clinical entities in hospital discharge summaries using Structural Support Vector Machines with word representation features. BMC Medical Informatics and Decision Making 2013; 13(Suppl 1):S1. [PMCID PMC3618243]
  8. Buzhou Tang, Yonghui Wu, Min Jiang, Yukun Chen, Joshua C Denny, Hua Xu. A hybrid system for temporal information extraction from clinical text. J Am Med Inform Assoc 2013 Sep Oct;20(5):828-35. [PMCID PMC3756274]
  9. Yonghui Wu, Mia A Levy, Christine M Micheel, Paul Yeh, Buzhou Tang, Michael J Cantrell, Stacy M Cooreman and Hua Xu. Identifying the status of genetic lesions in cancer clinical trial documents using machine learning. BMC Genomics 2012;13(Suppl 8):S21. [PMCID PMC3535695]
  10. Mei Liu, Yonghui Wu, Yukun Chen, Jingchun Sun, Zhongming Zhao, Xue-wen Chen, Michael Edwin Matheny, Hua Xu. Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs. J Am Med Inform Assoc, 2012 Jun 1;19(e1):e28-e35. [PMCID PMC3392844]
  11. Hua Xu, Yonghui Wu, Noémie Elhadad, Peter D. Stetson, Carol Friedman. A new clustering method for detecting rare senses of abbreviations in clinical notes. J Biomed Inform 2012 Dec;45(6):1075-83. [PMCID PMC3729222]
  12. Jingchun Sun, Yonghui Wu, Hua Xu, and Zhongming Zhao. DTome: a web-based tool for drug target interactome construction BMC Bioinformatics 2012;13(Suppl 9):S7. [PMCID PMC3372450]
  13. Yonghui Wu, Xiaolong Wang, Yuxin Ding, Jun Xu. Adaptive On-line Web Topic Detection Method for Web News Recommendation System. Acta Sinica Electronica 2010;38(11):2620-24.
  14. Yonghui Wu, Yuxin Ding, Xiaolong Wang, and Jun Xu. On-line Hot Topic Recommendation Using Tolerance Rough Set Based Topic Clustering. Journal of Computers 2010:5(4):549-56.

Peer Reviewed Articles – Conference

  1. Wu,Y., Xu,J., Jiang,M., Zhang, Y., Xu, H. A Study of Neural Word Embeddings for Named Entity Recognition in Clinical Text. AMIA Annu Symp Proc, 2015, in press.
  2. Yonghui Wu, Jun Xu, Yaoyun Zhang, and Hua Xu. Clinical Abbreviation Disambiguation Using Neural Word Embeddings. ACL-IJCNLP 2015, 2015:171.
  3. Zhang Y, Xu J, Wang J, Wu Y, Parkasam M and Xu H. UTH-CCB@BioCreative V Track 2: Recognizing Chemical Entities in Patents. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop 2015:147-148.
  4. Xu J, Wu Y, Zhang Y, Wang J, Liu R, Wei Q, and Xu H. UTH-CCB@BioCreative V CDR Task: Identifying Chemical-induced Disease Relations in Biomedical Text. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop 2015:254-259.
  5. Xu J, Zhang Y, Wu Y, Wang J, Dong X, and Xu H. Citation Sentiment Analysis in Clinical Trial Papers. AMIA Annu Symp Proc 2015, in press.
  6. Xu J, Zhang Y, Wang J, Wu Y, Jiang M, Soysal E, and Xu H. UTH-CCB: The Participation of the SemEval 2015 Challenge âAS Task 14. Proceedings of the 9th International Workshop on Semantic Evaluation (SemEval 2015) 2015:311-314.
  7. Yonghui Wu, Joshua Denny, S. Trent Rosenbloom, Randolph A. Miller, Dario A. Giuse, Min Song, Hua Xu. A prototype application for real-time recognition and disambiguation of clinical abbreviations . In CIKM, Proceedings of the 7th international workshop on Data and text mining in biomedical informatics (DTMBIO ’13) 2013.
  8. Min Jiang, Yonghui Wu, Anushi Shah, Priyanka Priyanka, Joshua C. Denny, Hua Xu. Extracting and standardizing medication information in clinical text – the MedEx-UIMA system. AMIA Summit on Clinical Research Informatics (CRI), 2014.
  9. Yaoyun Zhang, Jingqi Wang, Buzhou Tang, Yonghui Wu, Min Jiang, Yukun Chen, Hua Xu UTH_CCB: A Report for SemEval 2014âASTask 7 Analysis of Clinical Text. SemEval Proc 2014.
  10. Yonghui Wu, Buzhou Tang, Min Jiang, Sungrim Moon, Joshua C. Denny, Hua Xu. Clinical Acronym/Abbreviation Normalization using a Hybrid Approach. Proceedings of CLEF 2013 Evaluation Labs and Workshop 2013.
  11. Buzhou Tang, Xiaolong Wang, Yonghui Wu, Min Jiang, Jingqi Wang, Hua Xu. Recognizing Chemical Entities in Biomedical Literature using Conditional Random Fields and Structured Support Vector Machines. BioCreative Challenge Evaluation Workshop 2013; 2:70-4.
  12. Buzhou Tang, Yonghui Wu, Min Jiang, and Hua Xu. Recognizing and Encoding Disorder Concepts in Clinical Text using Machine Learning and Vector Space Model. Proceedings of CLEF 2013 Evaluation Labs and Workshop 2013.
  13. Buzhou Tang, Hongxin Cao, Yonghui Wu, Min Jiang, Hua Xu. Clinical Entity Recognition using Structural Support Vector Machines with Rich Features. Proceedings of the ACM sixth international workshop on Data and text mining in biomedical informatics 2012:13-20.
  14. Yonghui Wu, Joshua C. Denny, S. Trent Rosenbloom, Ran-dolph A. Miller, Dario A. Giuse, Hua Xu. A comparative study of current clinical natural language processing systems on handling abbreviations in discharge summaries. AMIA Annu Symp Proc 2012:997-1003.
  15. Yonghui Wu, Mei Liu, W. Jim Zheng, Zhongming Zhao, and Hua Xu. Ranking gene-drug relationships in biomedical literature using latent dirichlet allocation. Pac Symp Biocomput 2012.
  16. Mei Liu, Michael E Matheny, Yonghui Wu, ERM Hinz, Joshua C Denny, Jonathan S Schildcrout, Randolph A Miller, Hua Xu. Detecting Adverse Drug Reactions Using Inpatient Medication Orders and Laboratory Tests Data, IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology (HISB) 2012.
  17. Yonghui Wu, S. Trent Rosenbloom, Joshua C. Denny, Randolph A. Miller, Subramani Mani, Dario A. Giuse, Hua Xu. Detecting Abbreviations in Discharge Summaries using Machine Learning Methods. AMIA Annu Symp Proc 2011:1541-9.
  18. Yonghui Wu, Xiaolong Wang, Yuxin Ding, Jun Xu. Topic based Automatic News Recommendation Using Topic Model and Affinity Propagation. IEEE ICMLC 2010:1299–1304.
  19. Yonghui Wu, Yuxin Ding, Xiaolong Wang, and Jun Xu. A Comparative Study of Topic Models for Topic Clustering of Chinese Web News. IEEE, International Conference on Computer Science and Information Technology 2010.
  20. Yonghui Wu, Yuxin Ding, Xiaolong Wang, and Jun Xu. Topic Detection by Topic Model Induced Distance Using Biased Initiation. Lecture Notes in Computer Science/AST 2010:310-323.
  21. Hongzhi Guo, Qingcai Chen, Xiaolong Wang, Zhiyong Wang, Yonghui Wu. STRank: A SiteRank algorithm using semantic relevance and time frequency. IEEE Systems, Man and Cybernetics 2009:4876-4881.
  22. Jun Xu, Yuxin Ding, Xiaolong Wang, and Yonghui Wu. Genre identification of Chinese finance text using machine learning method. Proceedings of the 2008 IEEE International Conference on Systems, Man, and Cybernetics, Singapore, October 2008.
  23. Yuxin Ding, Xiaolong Wang, Lebin Lin, Qi Zhang, Yonghui Wu. The Design and Implementation of The Crawler-Inar. IEEE ICMLC 2006.