Meliha Yetişgen-Yıldız

Assistant Professor, Biomedical and Health Informatics, University of Washington Adjunct Assistant Professor, Department of Linguistics, University of Washington Contact Information: Dept. of Biomedical Informatics and Medical Education University of Washington Box 357240 Seattle, WA 98195-7240 Telephone: (206) 685-8224 Email:melihay at uw dot edu Office: I-264

Research Interests

• Biomedical text mining
• Statistical natural language processing
• Information retrieval

Research Projects

• Detailed information about my current research projects is available at the Biomedical Language Processing Group webpage.

Graduate Students

• Michael Tepper - PhD Student, Department of Linguistics (Co-advised with Fei Xia)
• Wen-wai Yim - PhD Student, Biomedical and Health Informatics
• Wynona Black - PhD Student, Biomedical and Health Informatics (Co-advised with John Gennari)

Post-doctoral Researcher

• Cosmin Adrian Bejan, Biomedical and Health Informatics

Teaching

• 2013/Winter: NMETH 528 - Computing Fundamentals: From Theory to Application
• 2013/Spring: NMETH529 : Database Concepts and Application in Clinical Informatics
• 2012/Winter: NMETH 528 - Computing Fundamentals: From Theory to Application
• 2012/Spring: NMETH529 : Database Concepts and Application in Clinical Informatics
• 2010/Spring: MEBI591C - Data and Text Mining in Biomedical Informatics

Publications

2013

• L. Vanderwende, F. Xia, M. Yetisgen-Yildiz. Annotating Change of State for Clinical Events. To appear in the Proceedings of The 1st Workshop on EVENTS: Definition, Detection, Coreference, and Representation Workshop of NAACL'2013, 2013.
• M. Tepper, H.L. Evans, F. Xia, M. Yetisgen-Yildiz. Modeling Annotator Rationales with Application to Pneumonia Classification. To appear in the Proceedings of Expanding the Boundaries of Health Informatics Using AI Workshop of AAAI'2013, 2013.
• M. Yetisgen-Yildiz, M.L. Gunn, F. Xia, T.H. Payne. A Text Processing Pipeline to Extract Recommendations from Radiology Reports. J Biomed Inform., 2013;46(2):354-362.
• C.A. Bejan, L. Vanderwende, F. Xia, M. Yetisgen-Yildiz. Assertion modeling and its role in clinical phenotype identification. J Biomed Inform. 2013;46(1):68-74.
• M. Yetisgen-Yildiz, C.A. Bejan, L. Vanderwende, F. Xia, H.L. Evans, M.M. Wurfel. Automated Tools for Phenotype Extraction from Medical Records. Proceedings of the American Medical Informatics Association Clinical Research Informatics Summit (AMIA CRI'13). San Francisco, CA, March, 2013.

2012

• C.A. Bejan, L. Vanderwende, F. Xia, M. Wurfel, M. Yetisgen-Yildiz. Pneumonia identification using statistical feature selection. J Am Med Inform Assoc. 2012;19(5):817-23.
• F. Xia, M. Yetisgen-Yildiz. Clinical corpus annotation: challenges and strategies. Proceedings of Third Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM'2012) of the International Conference on Language Resources and Evaluation (LREC), Istanbul, May, 2012.
• M. Tepper, D. Capurro, F. Xia, L. Vanderwende, M. Yetisgen-Yildiz. Statistical Section Segmentation in Free-Text Clinical Records. Proceedings of the International Conference on Language Resources and Evaluation (LREC), Istanbul, May, 2012.
• C.A. Bejan, L. Vanderwende, M.M. Wurfel, and M. Yetisgen-Yildiz. Assessing Pneumonia Identification from Time-Ordered Narrative Reports. In Proceedings of the American Medical Informatics Association Fall Symposium (AMIA'12). Chicago, IL, November, 2012. M. Tepper, F. Xia, and M. Yetisgen-Yildiz. Smoking Status Detection Across Domains. In Proceedings of the American Medical Informatics Association Fall Symposium (AMIA'12). Chicago, IL, November, 2012.
• J. Huh, M. Yetisgen-Yildiz, A. Hartzler, D. McDonald, A. Park and W. Pratt. Toward Automatic Weaving of Medical Advice with Patient Experiences Using Text Classification. In Proceedings of the American Medical Informatics Association Fall Symposium (AMIA'12). Chicago, IL, November, 2012.

2011

• Z. Luo, M. Yetisgen-Yildiz, C. Weng. Dynamic Categorization of Clinical Research Eligibility Criteria by Hierarchical Clustering, J Biomed Inform. 2011;44(6):927-35.
• M. Yetisgen-Yildiz, B.J. Glavan, F. Xia, L. Vanderwende, M.M. Wurfel. Identifying Patients with Pneumonia from Free-Text Intensive Care Unit Reports. Proceedings of Learning from Unstructured Clinical Text Workshop of ICML'2011. Bellevue, WA, July, 2011.
• M. Yetisgen-Yildiz, M.L. Gunn, F. Xia, T.H. Payne. Automatic Identification of Critical Follow-Up Recommendation Sentences in Radiology Reports. Proceedings of the American Medical Informatics Association Fall Symposium (AMIA'11). Washington D.C. October, 2011.
• M. Yetisgen-Yildiz, B.J. Glavan, F. Xia, L. Vanderwende, M.M. Wurfel. Extraction of Pneumonia Cases from Free-Text Intensive Care Unit Reports. Proceedings of American Medical Informatics Association Fall Symposium (AMIA'2011). Washington, D.C., October, 2011.
• W. Black, E. Horvitz, M. Yetisgen-Yildiz, J.H. Gennari. Exploring Predictive Models of ACS Outcomes with a Longitudinal, Multi-institutional Patient Database. Proceedings of American Medical Informatics Association Fall Symposium (AMIA'2011). Washington, D.C., October, 2011.

2010

• M. Yetisgen-Yildiz, I. Solti, F. Xia. Using Amazon's Mechanical Turk for Annotating Medical Named Entities. Proceedings of American Medical Informatics Association Fall Symposium (AMIA'2010). Washington, D.C., November, 2010.
• M. Yetisgen-Yildiz, I. Solti, F. Xia, S.R. Halgrim. Preliminary Experiments with Amazon's Mechanical Turk for Annotating Medical Named Entities. Proceedings of Creating Speech and Language Data with Amazon's Mechanical Turk Workshop of NAACL'2010, 2010.
• N. Lawson, K. Eustice, M. Perkowitz, M. Yetisgen-Yildiz. Annotating Large Email Datasets for Named Entity Recognition with Mechanical Turk. Proceedings of Creating Speech and Language Data with Amazon's Mechanical Turk Workshop of NAACL'2010, 2010.

Prior to 2010

• M. Yetisgen-Yildiz and W. Pratt. Evaluation of Literature-Based Discovery Systems. P. Bruza and M. Weeber (eds) Literature-Based Discovery. Springer's series on Information Science and Knowledge Management, 2009.
• M. Yetisgen-Yildiz and W. Pratt. A New Evaluation Methodology for Literature-Based Discovery. J Biomed Inform. 2009 Aug;42(4):633-43.
• M. Yetisgen-Yildiz and W. Pratt. Finding the meaning of medical concept correlations. Proceedings of the American Medical Informatics Association Fall Symposium (AMIA'08). Washington D.C., November, 2008.
• M. Yetisgen-Yildiz and W. Pratt. Extracting the meaning of medical concept correlations. Proceedings of the International Conference on Knowledge Capture (K-Cap'07). Whistler, BC, October, 2007.
• W. Pratt and M. Yetisgen-Yildiz. Response to Validating discovery in literature-based discovery. Journal of Biomedical Informatics, 40(4), pp.450-452, 2007.
• M. Yetisgen-Yildiz and W. Pratt. Using Statistical and Knowledge Based Approaches for Literature-Based Discovery. J Biomed Inform. 2006 Dec;39(6):600-11.
• M. Yetisgen-Yildiz. LitLinker: A System for Searching Potential Discoveries in Biomedical Literature. Proceedings of 29th Annual International ACM SIGIR Conference on Research & Development on Information Retrieval (SIGIR'06) Doctoral Consortium. Seattle, WA, August, 2006.
• M. Skeels, K. Henning, M. Yetisgen-Yildiz, and W. Pratt. Interaction Design for Literature-Based Discovery. Proceedings of the International Conference for Human-Computer Interaction (CHI'05). Portland, April, 2005.
• M. Yetisgen-Yildiz and W. Pratt. Feature Representation and Category Relationship Issues in Medline Document Classification. Proceedings of the American Medical Informatics Association Fall Symposium (AMIA'05). Washington D.C., October, 2005.
• I. H. Toroslu and M. Yetisgen-Yildiz. Data Mining in Deductive Databases Using Query Flocks. Expert Systems with Applications, 28(3):395-407, 2005.
• W. Pratt and M. Yetisgen-Yildiz. LitLinker: Capturing Connections across the Biomedical Literature. Proceedings of the International Conference on Knowledge Capture (K-Cap'03). Florida, October 2003.
• W. Pratt and M. Yetisgen-Yildiz. A Study of Biomedical Concept Identification: MetaMap vs. People. Proceedings of the American Medical Informatics Association Fall Symposium (AMIA'03). Washington D.C. November, 2003.
• I. H. Toroslu and M. Yetisgen. Data Mining in Deductive Databases Using Query Flocks. Proceedings of the 6th Joint Conference on Information Sciences, North Carolina 2002.
• M. Yetisgen and I. H. Toroslu. Data Mining Using Query Flocks with Views. Proceedings of the Database and Expert System Applications, (DEXA 2000). LNCS 1879, pages 720-729, London 2000.

Patents

• M. Yetisgen-Yildiz, R.S. Niculescu, R.E. Rosales, R.B. Rao, and, S. Krishnan. Automated Interpretation and Replacement of Date References in Unstructured Text. (Application ID: US20080154897, Publication Date: June 26, 2008)
• K.F. Eustice, N. Lawson, M. Yetisgen-Yildiz, K. Kawai, M. Perkowitz, P.J. Ferrel, J.D. Lazarus: Social Network Model for Semantic Processing. (Application ID: US 20100030715, Publication Date: Feb, 4 2010)
• M. Perkowitz, K.F. Eustice, M. Yetisgen-Yildiz, K. Kawai: Electronic message prioritization. (Application ID: US 8095613, Publication Date: Jan, 10 2012)

Thesis

• M. Yetisgen-Yildiz, Ph.D. Thesis: Using Statistical and Knowledge Based Approaches for Literature-Based Discovery. University of Washington, 2007.
• M. Yetisgen, M.Sc. Thesis: Data Mining Using Query Flocks with Views. Middle East Technical University, 2000.