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Yaoyun Zhang, PhD

Assistant Professor

Yaoyun Zhang, PhD, joined SBMI as an assistant professor in November of 2017. Prior to starting her faculty appointment, Yaoyun served as both a research scientist (from 2015 to 2017) and a postdoc research fellow (from 2013 to 2015) working with Professor Hua Xu, PhD on several grant funded research projects here at SBMI. Dr. Zhang’s research interests include natural language processing, machine learning, and text mining. Her recent research efforts are devoted to computational applications of mental health.

Contact

 [email protected]
Phone: 713-500-3900


Staff Support

 Yukiko Bryson
Phone: 713-500-3992


Education

  • PhD, 2012, Computer Application Technology, Harbin Institute of Technology, Harbin, China
  • MS, 2007, Computer Application Technology, Harbin Institute of Technology, Harbin, China
  • BS, 2005, Computer Science and Technology, Harbin University of Science and Technology, Harbin, China

Areas of Expertise

  • Natural Language Processing
  • Machine Learning
  • Text Mining

Funding

Current Grants:

  • R01AI130460-01 (NIH/NIAID) | Cui Tao (PI) | 02/01/2017 - 01/31/2022
    Title: Dynamic Learning For Post-Vaccine Event Prediction Using Temporal Information In VAERS
    This project will develop a novel framework to extract and accurately interpret the temporal information contained in the narratives through informatics approaches, and to develop prediction models for risk of severe AEs.
    Role: Co-Investigator
  • U01HG009454? (NIH/ NHGRI) | Cui Tao (PI) | 09/28/2016 - 07/31/2019
    Title: Metadata Applications on Informed Content to Facilitate Biorepository Data Regulation and Sharing
    This proposed study will focus on (1) developing a standard conforming metadata ontology to formally represent the informed consent domain; and (2) an automatic tool to semantically annotate informed consent documents to facilitate biorepository data regulation, sharing, and decision support.
    Role: Co-Investigator

Completed Grants:

  • R1307 (CPRIT) |  Hua Xu (PI) | 03/01/2013 – 02/28/2018
    Title: CPRIT Rising Stars Award
    This study is to develop novel informatics approaches to facilitate large-scale drug-repurposing studies for identifying potential cancer therapeutic agents by using Electronic Health Records (EHRs) data. The hypothesis is that EHRs can be used to detect new indications of existing drugs for cancer therapy in a very efficient way, with the help of advanced informatics methods.
    Role: Co-Investigator

Peer Reviewed Articles – Journal

    1. Zhang Y, Zhang O, Wu Y, Lee HJ, Xu J, Xu H, Roberts K. Psychiatric symptom recognition without labeled data using distributional representations of phrases and on-line knowledge. Journal of biomedical informatics. 2017 Nov 1;75:S129-37.
    2. Lee HJ, Wu Y, Zhang Y, Xu J, Xu H, Roberts K. A hybrid approach to automatic de-identification of psychiatric notes. Journal of biomedical informatics. 2017 Nov 1;75:S19-27.
    3. Zhang Y, Xu J, Chen H, Wang J, Wu Y, Manu P, Xu H. Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning. Database: The Journal of Biological Databases and Curation. 2016. doi: 10.1093/database/baw049.
    4. Xu J, Lee H-J, Zeng J, Wu Y, Zhang Y, Huang L, Johnson A, Holla V, Bailey M, Cohen T, Meric-Bernstam F, Bernstam V, Xu H. Extracting Genetic Alteration Information for Personalized Cancer Therapy from ClinicalTrials.gov. J Am Med Inform Assoc. 2016;23(4):750-757.
    5. Xu J, Wu Y, Zhang Y, Wang J, Lee H-J, Xu H. CD-REST: a system for extracting chemical-induced disease relation in literature. Database: The Journal of Biological Databases and Curation. 2016;2016:baw036. doi:10.1093/database/baw036.
    6. Zhang Y, Wu H, Du J, Xu J, Wang J, Tao C, Li L and Xu H. Extracting Drug-Enzyme Relation from Literature as Evidence for Drug Drug Interaction. J Biomed Semantics. 2016; 7: 11.
    7. Zhang Y, Wu H, Xu J, Wang J, Soysal E, Li L and Xu H. Leveraging Syntactic and Semantic Graph Kernels to Extract Pharmacokinetic Drug Drug Interactions from Biomedical Literature. BMC Syst Biol. 2016 Aug 26;10 Suppl 3:67.doi: 10.1186/s12918-016-0311-2.
    8. Zhang Y, Tang B, Jiang M, Wang J, Xu H. Domain Adaptation for Semantic Role labeling of Clinical Text. Journal of the American Medical Informatics Association. 2015.
    9. Tang B, Feng Y, Wang X, Wu Y, Zhang Y, Jiang M, Wang J, Xu H. A Comparison of Conditional Random Fields and Structured Support Vector Machines for Chemical Entity Recognition in Biomedical Literature. Journal of Cheminformatics. 2014
    10. Hou Y, Zhang Y, Wang X, Chen Q, Wang Y. Recognition and Retrieval of Time-sensitive Question in Chinese QA System. Journal of Computer Research and Development. 2013(12): 2612-262
    11. Fan S, Wang X, Zhang Y. Real Environment Oriented Question Analyzing. Acta Electronic Sinica. 2010, vol. 38, no.5.
    12. Fan S, Wang X, Wang X, Zhang Y. A new question analysis approach for community question answering system. International Journal of Asian Language Processing. 19(3), 95-108, 2009.
    13. Zhang Y, Wang X, Fan S. Expanding User Intention by Type Similarity of Complex Questions. Proceedings of Chinese Information Retrieval Conference. Bejing, China. October 15-16 2008. Journal of Computational Information Systems. 2009, vol. 5, no.3.

Peer Reviewed Articles - Conference

    1. Du J, Zhang Y, Tao C, Xu H. A pilot study of mining association between psychiatric stressors and symptoms in tweets. In Bioinformatics and Biomedicine (BIBM), 2017 IEEE International Conference on 2017 Nov 13 (pp. 1254-1257).
    2.  Zhang OR, Zhang Y, Xu J, Roberts K, Zhang XY, Xu H. Interweaving Domain Knowledge and Unsupervised Learning for Psychiatric Stressor Extraction from Clinical Notes. Proceedings of International Conference on Industrial, Engineering and Other Applications of Applied Intelligent Systems 2017 Jun 27 (pp. 396-406). Springer, Cham.
    4. Zhang Y, Jiang M, Wang J, Xu H, Semantic Role Labeling of Clinical Text: Comparing Syntactic Parsers and Features, AMIA 2016.
    5. Lee H, Zhang Y, Xu J, Moon S, Wang J, Wu Y, and Xu H, UTHealth at SemEval-2016 Task 12: an End-to-End System for Temporal Information Extraction from Clinical Notes, Proceedings of the 10th International Workshop on Semantic Evaluation (SemEval-2016), 1292-1297, San Diego, California, June, 2016.
    6. 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
    7. Xu J, Zhang Y, Wang J, Wu Y, Jiang M, Soysal E, and Xu H. UTH-CCB: The Participation of the SemEval 2015 Challenge – Task 14. Proceedings of the 9th International Workshop on Semantic Evaluation (SemEval 2015). Denver, Colorado. 2015:311-314.
    8. 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. Accepted.
    9. 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.
    10. Wu, Y, Xu J, Zhang Y, and Xu H. "Clinical Abbreviation Disambiguation Using Neural Word Embeddings." ACL-IJCNLP 2015 (2015): 171.
    11. Wu,Y, Xu,J, Jiang,M, Zhang, Y, Xu, H. A Study of Neural Word Embeddings for Named Entity Recognition in Clinical Text. American Medical Informatics Association Annual Symposium Proceedings, 2015. Accepted
    12. Zhang Y, Soysal E, Moon S, Wang J, Tao C, Xu H. Integrating Multiple On-line Knowledge Bases for Disease-Lab Test Relation Extraction. 2015 Joint Summits on Translational Science:Summit on Clinical Research Informatics. March 25-27.
    13. Xiang Y, Zhang Y, Zhou X, Wang X, Qin Y. Problematic Situation Analysis and Automatic Recognition for Chinese Online Conversational System. Proceedings of the Third CIPS-SIGHAN Joint Conference on Chinese Language Processing, 43–51, Wuhan, China, October 20-21, 2014.
    14. Zhang Y, Wang J, Tang B, Wu Y, Jiang M, Chen Y, Xu H. UTH_CCB: A Report for SemEval 2014 – Task 7 Analysis of Clinical Text. SemEval 2014, 802–806, Dublin, Ireland, August 23-24, 2014.
    15. Zhang Y, Cohen T, Jiang M, Tang B, Xu H. Evaluation of Vector Space Models for Medical Disorders Information Retrieval. Proceedings of the ShARe/CLEF eHealth Evaluation Lab. Valencia, Spain. September 23-26, 2013.
    16. Zhou X, Hou Y, Wang X, Yuan B, Zhang Y. ICRCS at Intent2: Applying Rough Set and Semantic Relevance for Subtopic Mining. Proceedings of the 10th NTCIR Conference, 176-181, June 18-21, Tokyo, Japan, 2013.
    17. Xiang Y, Zhang Y, Wang X, Qin Y. Grammatical Error Correction using Feature Selection and Confidence Tuning. Proceedings of the 6th International Joint Conference on Natural Language Processing. Nagoya, Japan. 2013 pg. 1067-1071
    18. Xiang Y, Yuan B, Zhang Y, Wang X, Zheng W, Wei C. A Hybrid Model for Grammatical Error Correction. Proceedings of CoNLL-Shared Task. Sofia, Bulgaria. 2013 pg. 115-122
    19. Zhang Y, Xu J, Liu C, Wang X, Xu R, Chen Q. ICRC_HITSZ at RITE: Leveraging Multiple Classifiers Voting for Textual Entailment Recognition. Proceedings of the 9th NTCIR Workshop. Tokyo, Japan. December 6-9, 2011 pg. 325-329
    20. Zhang Y, Wang X, Xu R, Hou Y, Fan S. Diversifying Information Needs in Results of Question Retrieval. Proceedings of the 5th International Joint Conference on Natural Language Processing. Chiang Mai, Thailand. November 8-13, 2011 pg. 1432-1436
    21. Zhang Y, Wang X, Xu R, Tang B. Diversifying Question Recommendations in Community-based Question Answering. Proceedings of 18th International Conference on Neural Information Processing. Shanghai, China. November 14-16, 2011 pg. 177-186
    22. Zhang Y, Wang X, Xu R, Hou Y, Fan S. Analysis of Interactive Question Answering Corpus in Open-ended Restricted Domain. Proceedings of the 11th Chinese Computational Linguistics Conference. Luoyang, China, August 20-22, 2011.
    23. Zhang Y, Wang X, Fan S. CogQTaxo: Modeling Human Cognitive Process with a Three-Dimensional Question Taxonomy. Proceedings of International Workshop on Web Information Processing. Qingdao, China. July 12-13, 2010 pg. 3305-3310
    24. Zhang Y, Wang X, Fan S, Zhang D. Using Question Classification to Model User Intentions of Different Levels. Proceedings of the 2009 IEEE international conference on Systems, Man and Cybernetics. San Antonio, TX, USA. October 11-14, 2009 pg. 1153-1158
    25. Zhang Y, Wang X, Fan S. A Stepwise Detection of Conjunctive Structures in Questions Using Maximum Entropy Model. Proceedings of the Sixth International Conference on Machine Learning and Cybernetics. Hong Kong, China. August 20-23, 2007 pg. 3916-3921