Meliha Yetisgen-Yildiz

Assistant Professor, Biomedical and Health Informatics, University of Washington
Adjunct Assistant Professor, Department of Linguistics, University of Washington

Contact Information:
Dept. of Medical Education and Biomedical Informatics
University of Washington
Box 357240
Seattle, WA 98195-7240

Telephone: (206) 685-8224
Email:melihay at uw dot edu
Office: I-264

Education

PhD in Information Science, University of Washington
MSc in Computer Engineering, Middle East Technical University
BSc in Computer Engineering, Bilkent University

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.

Teaching

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

Publications

Journal Papers

C.A. Bejan, L. Vanderwende, F. Xia, M. Wurfel, M. Yetisgen-Yildiz. Pneumonia identification using statistical feature selection. To appear in J Am Med Inform Assoc., 2012.
Z. Luo, M. Yetisgen-Yildiz, C. Weng. Dynamic Categorization of Clinical Research Eligibility Criteria by Hierarchical Clustering, Journal of Biomedical Informatics, 2011, 44(6):927-35.
M. Yetisgen-Yildiz and W. Pratt. A New Evaluation Methodology for Literature-Based Discovery. Journal of Biomedical Informatics. Journal of Biomedical Informatics, 2009, 42(4):633-643.
M. Yetisgen-Yildiz and W. Pratt. Using Statistical and Knowledge Based Approaches for Literature-Based Discovery. Journal of Biomedical Informatics, 2006, 39(6):600-611.
I. H. Toroslu and M. Yetisgen-Yildiz. Data Mining in Deductive Databases Using Query Flocks. Expert Systems with Applications, 28(3):395-407, 2005.

Conference & Workshop Papers

F. Xia, M. Yetisgen-Yildiz. Clinical corpus annotation: challenges and strategies. To appear in 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. To appear in Proceedings of the International Conference on Language Resources and Evaluation (LREC), Istanbul, May, 2012.
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. 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, 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.
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.
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.
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.
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.
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.

Book Chapter

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.

Letter

W. Pratt and M. Yetisgen-Yildiz. Response to Validating discovery in literature-based discovery. Journal of Biomedical Informatics, 40(4), pp.450-452, 2007.

Extended Abstracts and Posters

H.L. Evans, M. Yetisgen-Yildiz, C.A. Bejan, K.J. Warner, R.A. Black, R.V. Maier, M. Wurfel. Developing a natural language processing system for screening chest radiographs in trauma patients suspected of having ventilator associated pneumonia. To be presented in National Trauma Institute Meeting, May, 2012.
H.L. Evans, K.J. Warner, R.V. Maier, R.A. Black, M. Yetisgen-Yildiz, C.A. Bejan. Chest X-ray Report Language is Incongruous with Quantitative Results in VAP. To be presented in 32nd Annual Meeting of Surgical Infection Society, April, 2012.
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.
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. 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.
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.

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)

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.