Meliha Yetişgen, PhD Professor, Biomedical and Health Informatics, University of Washington Adjunct Professor, Department of Linguistics, University of Washington Contact Information: Address: Box 358047 Seattle, WA 98109 Telephone: (206) 685-8224 Email:melihay at uw dot edu Office: South Lake Union - C-237

Bio

Research Interests

• Clinical Natural language processing
• Information retrieval

Research Projects

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

Graduate Students

• Arjun Chakraborty - PhD Student, Biomedical and Health Informatics
• Namu Park - PhD Student, Biomedical and Health Informatics
• Velvin Fu - PhD Student, Biomedical and Health Informatics
• Changyuan (Peter) Qiu - PhD Student, Biomedical and Health Informatics (co-advise with Trevor Cohen)
• Sitong Zhou - PhD Student, Electrical and Computer Engineering (co-advise with Mari Ostendorf)
• Zhaoyi Sun - Phd Student, Biomedical and Health Informatics
• Avery Yu - PhD Student, Biomedical and Health Informatics

Former Students & UW-BioNLP Group Members

• Weipeng Zhou - PhD Student, Biomedical and Health Informatics (2024) - Postdoctoral researcher,Yale University
• Nicholas Dobbins - PhD, Biomedical and Health Informatics (2023) - Assistant Professor, Johns Hopkins University
• Wilson Lau - PhD, Biomedical and Health Informatics (2022)- Principle ML engineering, Truveta
• Grace Turner - MS, Biomedical and Health Informatics (2022)- Software developer, Truveta
• Kevin Lybarger, PhD (Co-advised with Mari Ostendorf). Electrical and Computer Engineering (2020)- Assistant Professor at George Mason University
• Dae Hyun Lee - PhD (Co-advised with Eric Horvitz), Biomedical and Health Informatics (2020) - Applied Research Scientist, Amazon
• Adyasha Maharana - MS, Biomedical and Health Informatics (2017) - PhD Student at University of North Carolina at Chapel Hill
• Wen-wai Yim - PhD, Biomedical and Health Informatics (2016) - Applied Research Scientist at Microsoft Health
• Michael Semanik - MS, Biomedical and Health Informatics (2016) - Assistant Professor at University of Wisconsin, Madison
• Adam Rhine - MA Student, Department of Linguistics
• Prescott Klassen - PhD, Linguistics (Co-advised with Fei Xia) (2016) - Senior Researcher at Philips
• Cosmin Adrian Bejan - Research Assistant Professor in Biomedical and Health Informatics at Vanderbilt University
• Wynona Black - PhD, Biomedical and Health Informatics (Co-advised with John Gennari) - Senior Data Scientist at Oracle
• Nick Flacco - MA, Department of Linguistics - Senior Software Engineer at Snapchat

Teaching

• 2012-present/Spring: NMETH 529 - Database Concepts and Application in Clinical Informatics
• 2012-2022/Winter: NMETH 528 - Computing Fundamentals: From Theory to Application
• 2016/Spring: LING575 : Clinical Natural Language Processing
• 2010/Spring: MEBI591C - Data and Text Mining in Biomedical Informatics

Publications

2025

• Yujuan Velvin Fu, Giridhar Kaushik Ramachandran, Namu Park, Kevin Lybarger, Fei Xia, Ozlem Uzuner, Meliha Yetisgen. BioMistral-NLU: Towards More Generalizable Medical Language Understanding through Instruction Tuning. Under review. Available at: https://arxiv.org/abs/2410.18955 (accepted AMIA SUMMIT)

2024

• Yujuan Fu, Ozlem Uzuner, Meliha Yetisgen, Fei Xia. Does Data Contamination Detection Work (Well) for LLMs? A Survey and Evaluation on Detection Assumptions. Under Review. Available at: https://arxiv.org/abs/2410.18966
• Yujuan Velvin Fu, Giridhar Kaushik Ramachandran, Namu Park, Kevin Lybarger, Fei Xia, Ozlem Uzuner, Meliha Yetisgen. BioMistral-NLU: Towards More Generalizable Medical Language Understanding through Instruction Tuning. Under review. Available at: https://arxiv.org/abs/2410.18955
• Fu YV, Ramachandran GK, Halwani A, McInnes BT, Xia F, Lybarger K, Yetisgen M, Uzuner Ö. CACER: Clinical concept Annotations for Cancer Events and Relations. J Am Med Inform Assoc. 2024 Nov 1;31(11):2583-2594. doi: 10.1093/jamia/ocae231. PMID: 39225779; PMCID: PMC11491616.
• Yujuan Fu, Giridhar Kaushik Ramachandran, Nicholas J. Dobbins, Namu Park, Michael Leu, Abby R. Rosenberg, Kevin Lybarger, Fei Xia, Özlem Uzuner, and Meliha Yetisgen. 2024. Extracting Social Determinants of Health from Pediatric Patient Notes Using Large Language Models: Novel Corpus and Methods. In Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024), pages 7045–7056, Torino, Italia. ELRA and ICCL. (Distinguished paper award)
• Namu Park, Kevin Lybarger, Giridhar Kaushik Ramachandran, Spencer Lewis, Aashka Damani, Özlem Uzuner, Martin Gunn, and Meliha Yetisgen. 2024. A Novel Corpus of Annotated Medical Imaging Reports and Information Extraction Results Using BERT-based Language Models. In Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024), pages 1280–1292, Torino, Italia. ELRA and ICCL.
• Chung P, Fong CT, Walters AM, Aghaeepour N, Yetisgen M, O'Reilly-Shah VN. Large Language Model Capabilities in Perioperative Risk Prediction and Prognostication. JAMA Surg. 2024 Aug 1;159(8):928-937. doi: 10.1001/jamasurg.2024.1621. PMID: 38837145; PMCID: PMC11154375.
• Sahoo SS, Plasek JM, Xu H, Uzuner Ö, Cohen T, Yetisgen M, Liu H, Meystre S, Wang Y. Large language models for biomedicine: foundations, opportunities, challenges, and best practices. J Am Med Inform Assoc. 2024 Apr 24:ocae074. doi: 10.1093/jamia/ocae074. Epub ahead of print. PMID: 38657567.
• Gao Y, Mahajan D, Uzuner Ö, Yetisgen M. Clinical natural language processing for secondary uses. J Biomed Inform. 2024 Feb;150:104596. doi: 10.1016/j.jbi.2024.104596.
• Gomez F, Danos AM, Del Fiol G, Madabhushi A, Tiwari P, McMichael JF, Bakas S, Bian J, Davatzikos C, Fertig EJ, Kalpathy-Cramer J, Kenney J, Savova GK, Yetisgen M, Van Allen EM, Warner JL, Prior F, Griffith M, Griffith OL. A New Era of Data-Driven Cancer Research and Care: Opportunities and Challenges. Cancer Discov. 2024 Oct 4;14(10):1774-1778. doi: 10.1158/2159-8290.CD-24-1130. PMID: 39363742; PMCID: PMC11463721.
• Sahoo SS, Plasek JM, Xu H, Uzuner Ö, Cohen T, Yetisgen M, Liu H, Meystre S, Wang Y. Large language models for biomedicine: foundations, opportunities, challenges, and best practices. J Am Med Inform Assoc. 2024 Sep 1;31(9):2114-2124. doi: 10.1093/jamia/ocae074. PMID: 38657567; PMCID: PMC11339493.
• Wen-wai Yim, Asma Ben Abacha, Yujuan Fu, Zhaoyi Sun, Fei Xia, Meliha Yetisgen, and Martin Krallinger. 2024. Overview of the MEDIQA-M3G 2024 Shared Task on Multilingual Multimodal Medical Answer Generation. In Proceedings of the 6th Clinical Natural Language Processing Workshop, pages 581–589, Mexico City, Mexico. Association for Computational Linguistics.
• Asma Ben Abacha, Wen-wai Yim, Yujuan Fu, Zhaoyi Sun, Fei Xia, and Meliha Yetisgen. 2024. Overview of the MEDIQA-CORR 2024 Shared Task on Medical Error Detection and Correction. In Proceedings of the 6th Clinical Natural Language Processing Workshop, pages 596–603, Mexico City, Mexico. Association for Computational Linguistics.
• Brian Hur, Lucy Lu Wang, Laura Hardefeldt, and Meliha Yetisgen. 2024. Is That the Right Dose? Investigating Generative Language Model Performance on Veterinary Prescription Text Analysis. In Proceedings of the 23rd Workshop on Biomedical Natural Language Processing, pages 390–397, Bangkok, Thailand. Association for Computational Linguistics.
• Wen-wai Yim, Yujuan Fu, Asma Ben Abacha, and Meliha Yetisgen. 2024. To Err Is Human, How about Medical Large Language Models? Comparing Pre-trained Language Models for Medical Assessment Errors and Reliability. In Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024), pages 16211–16223, Torino, Italia. ELRA and ICCL.

2023

• Yim W, Fu Y, Abacha AB, Snider N, Lin T, Yetisgen M. ACI-BENCH: a Novel Ambient Clinical Intelligence Dataset for Benchmarking Automatic Visit Note Generation. Accepted to Nature - Scientific Data.
• Dobbins N, Han B, Zhou W, Lan K, Kim N, Harrington R, Uzuner O, Yetisgen M. LeafAI: query generator for clinical cohort discovery rivaling a human programmer. Accepted to JAMIA.
• Ding X, Sheng Z, Yetisgen M, Pakhomov S, Cohen T. Backdoor Adjustment of Confounding by Provenance for Robust Text Classification of Multi-institutional Clinical Notes. Accepted to AMIA Annual Conference.
• Fu V, Ramachandran GK, Dorvall N, Stiles E, Raub S, Lybarger K, McInnes B, Yetisgen M, Uzuner O. Domain Adaptation for Clinical Relation Extraction. Accepted to AMIA Annual Symposium.
• Abacha AB, Yim W, Adams GT, Snider N, Yetisgen M. Overview of the MEDIQA-Chat 2023 Shared Tasks on the Summarization & Generation of Doctor-Patient Conversations. Accepted to 2023 ACL Clinical NLP workshop.
• Ramanchandran G, Fu V, Han B, Lybarger K, Uzuner O, Yetisgen M. Prompt-based Extraction of Social Determinants of Health Using Few-shot Learning. Accepted to 2023 ACL Clinical NLP workshop.
• Zhou S, Yetisgen M, Ostendorf M. Building blocks for complex tasks: Robust generative event extraction for radiology reports under domain shifts. Accepted to 2023 ACL Clinical NLP workshop.
• Zhou S, Lybarger K, Yetisgen M, Ostendorf M. Generalizing through Forgetting -- Domain Generalization for Symptom Event Extraction in Clinical Notes. arxiv link (Accepted 2023 AMIA Summit)
• Lybarger K, Bear Don't Walk OJ, Yetisgen M, Uzuner Ö. Advancements in extracting social determinants of health information from narrative text. J Am Med Inform Assoc. 2023 Jul 19;30(8):1363-1366.
• Lybarger K, Yetisgen M, Uzuner O. The 2022 n2c2/UW Shared Task on Extracting Social Determinants of Health. arxiv link (Accepted JAMIA)
• Lybarger K, Dobbins NJ, Long R, Singh A, Wedgeworth P, Uzuner Ö, Yetisgen M. Leveraging natural language processing to augment structured social determinants of health data in the electronic health record. J Am Med Inform Assoc. 2023 May 2:ocad073. arxiv link (Accepted JAMIA)
• Ramachandran GK, Lybarger K, Liu Y, Mahajan D, Liang JJ, Tsou CH, Yetisgen M, Uzuner Ö. Extracting medication changes in clinical narratives using pre-trained language models. J Biomed Inform. 2023 Mar;139:104302. arxiv link (Under review JBI)
• Zhou W, Yetisgen M, Afshar M, Gao Y, Savova G, Miller TA. Improving model transferability for clinical note section classification models using continued pretraining. J Am Med Inform Assoc. 2023 Dec 22;31(1):89-97. doi: 10.1093/jamia/ocad190. PMID: 37725927;
• Chung P, Fong CT, Walters AM, Yetisgen M, O'Reilly-Shah VN. Prediction of American Society of Anesthesiologists Physical Status Classification from preoperative clinical text narratives using natural language processing. BMC Anesthesiol. 2023 Sep 4;23(1):296. doi: 10.1186/s12871-023-02248-0. PMID: 37667258; PMCID: PMC10476287.

2022

• Zigman Suchsland M, Kowalski L, Burkhardt HA, Prado MG, Kessler LG, Yetisgen M, Au MA, Stephens KA, Farjah F, Schleyer AM, Walter FM, Neal RD, Lybarger K, Thompson CA, Achkar MA, Sarma EA, Turner G, Thompson M. How Timely Is Diagnosis of Lung Cancer? Cohort Study of Individuals with Lung Cancer Presenting in Ambulatory Care in the United States. Cancers (Basel). 2022 Nov 23;14(23):5756. doi: 10.3390/cancers14235756.
• Dobbins N, Mullen T, Uzuner O, Yetisgen M. The Leaf Clinical Trials Corpus: a new resource for query generation from clinical trial eligibility criteria. Nature - Scientific Data, 9, 490 (2022). Available at: https://arxiv.org/abs/2207.13757.
• Lau W, Lybarger K, Gunn ML, Yetisgen M. Event-based clinical findings extraction from radiology reports with pre-trained language model. Accepted - Journal of Digital Imaging. Available at: https://arxiv.org/abs/2112.13512.
• Lybarger K, Damani A, Gunn ML, Uzuner O, Yetisgen M. Extracting Radiological Findings with Normalized Anatomical Information Using a Span-based BERT Relation Extraction Model. AMIA Informatics Summit, 2022. Available at: http://arxiv.org/abs/2108.09211..

2021

• Lybarger K, Mabrey L, Thau M, Bhatraju PK, Wurfel M, Yetisgen M.Identifying ARDS using the Hierarchical Attention Network with Sentence Objectives Framework. Available at: https://arxiv.org/abs/2103.06352.
• Lau W, Altonen L, Gunn, M, Yetisgen M. Automatic Assignment of Radiology Examination Protocols Using Pre-trained Language Models with Knowledge Distillation. Available at: https://arxiv.org/abs/2009.00694.
• Lybarger K, Ostendorf M, Thompson M, Yetisgen M. Extracting COVID-19 diagnoses and symptoms from clinical text: A new annotated corpus and neural event extraction framework. Available at: https://arxiv.org/abs/2012.00974.
• Lee K, Dobbins NJ, McInnes B, Yetisgen M, Uzuner O. Transferability of Neural Network-based De-identification Systems. Available at: https://arxiv.org/abs/2102.08517.
• Lybarger K, Ostendorf M, Yetisgen M. Annotating Social Determinants of Health Using Active Learning and Characterizing Determinants Using Neural Event Extraction. J Biomed Inform. 2020 Dec 5:103631. doi: 10.1016/j.jbi.2020.103631. Epub ahead of print. Available at: https://arxiv.org/abs/2004.05438.
• Barry P, Henry S, Yetisgen M, McInnes B, Uzuner O. Jointly Learning Clinical Entities and Relations with Contextual Language Models and Explicit Context. Available at: https://arxiv.org/abs/2102.11031. (Abstract)
• Dobbins NJ, Lee K, Uzuner O, Yetisgen M. Performance of Automatic De-identification Across Different Note Types. In AMIA Summit Proceedings, 2021. Available at: https://arxiv.org/abs/2102.11032. (Abstract)
• Burkhardt HA, Dobbins N, Mollis B, Au M, Ma PK, Yetisgen M, Singh A, Thompson M, Stephens KA. Extracting COVID-19 Related Symptoms from EHR Data: A Comparison of Three Methods. In Proceedings of AMIA 2021 Joint Summits on Translational Science. 2021. (Abstract)

2020

• Hyun Lee D, Yetisgen M, Vanderwende L, Horvitz E. Predicting Severe Clinical Events by Learning about Life-Saving Actions and Outcomes using Distant Supervision. J Biomed Inform. 2020;107:103425.
• Lau W, Payne TH, Uzuner Ö, Yetisgen M. Extraction and Analysis of Clinically Important Follow-up Recommendations in a Large Radiology Dataset. Proceedings of American Medical Informatics Association Informatics Summit, Houston, TX, 22-26 March, 2020. Available at: Available at: https://arxiv.org/abs/1905.05877.
• Yim W, Yetisgen M, Huang J, and Grossman M. Alignment Annotation for Clinic Visit Dialogue to Clinical Note Sentence Language Generation. In Proceedings of International Conference on Language Resources and Evaluation (LREC), 2020.
• Lybarger K, Ostendorf M, Uzuner O, and Yetisgen M. Automatic identification of social determinants of health from clinical records. in AMIA Annual Symposium Proceedings, 2020. (Abstract)

2019

• Maldonado R, Yetisgen M, and Harabagiu SM. Adversarial Learning of Knowledge Embeddings for the Unified Medical Language System. In Proceedings of AMIA 2019 Joint Summits on Translational Science. San Francisco; 2019.

2018

• Lybarger K, Yetisgen M, Ostendorf M. Using neural multitask learning to extract substance abuse information from clinical notes. In Proceedings of the American Medical Informatics Association Fall Symposium (AMIA'18),San Francisco, 2018.
• Payne TH, Alonso WD, Markiel JA, Lybarger K, Lordon R, Yetisgen M, Zech JM, White AA. Using voice to create inpatient progress notes: Effects on note timeliness, quality, and physician satisfaction. JAMIA Open, ooy036, https://doi.org/10.1093/jamiaopen/ooy036. Published: 12 September 2018
• Lybarger KJ, Ostendorf M, Riskin E, Payne TH, White AA, Yetisgen M. Asynchronous speech recognition impacts physician editing of notes. Appl Clin Inform. 2018 Oct;9(4):782-790. doi: 10.1055/s-0038-1673417. Epub 2018 Oct 17. PMID: 30332689
• Lee DH, Yetisgen M, Horwitz E. Learning about Life-Saving Interventions to Predict the Risk of Acute Organ Failures. In Proceedings of the American Medical Informatics Association Fall Symposium (AMIA'18), San Francisco, 2018. (Abstract)
• Maldonado R, Yetisgen M, and Harabagiu SM. Using Neural Multi-task Learning to Extract Substance Abuse Information from Clinical Notes. In Proceedings of the American Medical Informatics Association Fall Symposium (AMIA'18), San Francisco, 2018. (Abstract)

2017

• Yim W, Kwan S, Yetisgen M. Classifying tumor event attributes in radiology reports. Journal of the Association for Information Science and Technology. v68(11):2662-2674, 2017.
• Yim W, Kwan S, Johnson G, Yetisgen M. Classification of Hepatocellular Carcinoma Stages from Free-text Clinical and Radiology Notes. In Proceedings of the American Medical Informatics Association Fall Symposium (AMIA'17), Washington DC, 2017.
• Lybarger K, Ostendorf M, Yetisgen M. Automatically Detecting Likely Edits in Clinical Notes Created Using Automatic Speech Recognition. In Proceedings of the American Medical Informatics Association Fall Symposium (AMIA'17), Washington DC, 2017.
• Payne TH, Markiel JA, Alonso WD, Lordon R, Lybarger K, Yetisgen M, Zech JM, MS, White AA. Improving Electronic Inpatient Progress Notes Using Voice: Results from the VGEENS Project. Presentation at 2017 AMIA Fall Symposium, Washington, DC, November 5, 2017.
• Yetisgen M, Vanderwende L. Automatic Identification of Substance Abuse from Social History in Clinical Text. In the Proceedings of Artificial Intelligence in Medicine, Vienna, June 2017.
• Yim W, Kwan S, Yetisgen M. Automatic Liver Cancer Stage Prediction From Free-Text Clinical Notes. In Proceedings of AMIA 2017 Joint Summits on Translational Science. San Francisco; 2017.
• Yetisgen M, Vanderwende L. Automatic Identification of Substance Abuse Events from Clinical Text. In Proceedings of AMIA 2017 Joint Summits on Translational Science. San Francisco; 2017. (Abstract)
• Hyun-Lee D, Yetisgen M. Clustering Vital Sign Observations Using Unsupervised Random Forest. In Proceedings of the American Medical Informatics Association Fall Symposium (AMIA'17), Washington DC, 2017. (Abstract)

2016

• W. Yim, S. Kwan, M. Yetisgen. Tumor reference resolution and characteristic extraction in radiology reports for liver cancer stage prediction. Journal of Biomedical Informatics. 2016 Dec;64:179-191.
• W. Yim, M. Yetisgen, W. P. Harris, S Kwan, Natural Language Processing in Oncology: A Review. JAMA Oncology. 2(6):797-804, 2016.
• P. Klassen, F. Xia, M. Yetisgen. Annotating and Detecting Medical Events in Clinical Text. In Proceedings of International Conference on Language Resources and Evaluation (LREC), Portoroz, Slovenia, 2016.
• M. Semanik, M.Yetisgen, A. Pollack. Identification of an Acute Kidney Injury Phenotype from Electronic Health Record Data. In Proceedings of AMIA 2016 Joint Summits on Translational Science, San Francisco, 2016.
• W. Yim, T. Denman, S. Kwan, M. Yetisgen. Tumor information extraction in radiology reports for hepatocellular carcinoma patients. In Proceedings of AMIA 2016 Joint Summits on Translational Science, San Francisco, 2016.
• M. Yetisgen, L. Vanderwende, T. Black, S.D. Mooney, P. Tarchzy-Hornoch. A New Way of Representing Clinical Reports for Rapid Phenotyping. In Proceedings of AMIA 2016 Joint Summits on Translational Science, San Francisco, 2016.
• M. Yetisgen, E. Pellicer, D.R. Crosslin, L. Vanderwende. Automatic Identification of Lifestyle and Environmental Factors from Social History in Clinical Text. In Proceedings of AMIA 2016 Joint Summits on Translational Science, San Francisco, 2016..

2015

• M. Yetisgen, P. Klassen, L. McCarthy, T. Payne, M. Gunn. Annotating Recommendation Sentences in Radiology Reports. In Proceedings of the American Medical Informatics Association Fall Symposium (AMIA'15). San Francisco, November, 2015.
• W. Yim, S. Kwan, G. Johnson, M. Yetisgen. Annotation of Disease Characteristics for Cancer Liver Stage Prediction. In Proceedings of the American Medical Informatics Association Fall Symposium (AMIA'15). San Francisco, November, 2015.
• M. Yetisgen, P. Klassen, L. McCarthy, E. Pellicer, T. Payne, M. Gunn. Annotation of Clinically Important Follow-up Recommendations in Radiology Reports. In Proceedings of Sixth International Workshop on Health Text Mining and Information Analysis of EMNLP'2015, Lisbon, Portugal, September, 2015.
• W. Yim, S. Kwan, M. Yetisgen. In-depth annotation for patient level liver cancer staging. To appear in Proceedings of Sixth International Workshop on Health Text Mining and Information Analysis of EMNLP'2015, Lisbon, Portugal, September, 2015.
• W. Yim, H.L. Evans, M. Yetisgen. Structuring Free-text Microbiology Culture Reports for Secondary Use. In Proceedings of the American Medical Informatics Association Clinical Research Informatics Summit (AMIA CRI'15). San Francisco, CA, March, 2015.
• M. Yetisgen, P. Klassen, P. Tarczy-Hornoch. Automating Data Abstraction with Natural Language Processing in a Surgical Quality Improvement Platform. In Proceedings of the American Medical Informatics Association Clinical Research Informatics Summit (AMIA CRI'15). San Francisco, CA, March, 2015.
• M.L. Gunn, M. Yetisgen, B.E. Lehnert, K. Trovato, C. Hall, S. Dalal, Automating Radiology Quality and Efficiency Measures with Natural Language Processing, Radiological Society of North America 2015 Scientific Assembly and Annual Meeting Nov 29-Dec 4, Chicago IL (Radiographics Invitation)
• M.L. Gunn, B.E. Lehnert; C. Hall, M. Yetisgen, K. Trovato, S. Dalal, Impact of Patient Location and Radiology Subspeciality on Imaging Follow-up Recommendation Rate, Radiological Society of North America 2014 Scientific Assembly and Annual Meeting, December 1, 2015, Chicago IL
• M.L. Gunn, B.E. Lehnert, C. Hall, M. Yetisgen, N.J. Beauchamp, K. Trovato, Use of Conditional Statements in Radiology Follow-Recommendation Sentences: Relationship to Follow Up Compliance, Radiological Society of North America 2015 Scientific Assembly and Annual Meeting, December 1, 2015, Chicago IL

2014

• M. Yetisgen, P. Klassen, P. Tarczy-Hornoch. Automating Data Abstraction in a Quality Improvement Platform for Surgical and Interventional Procedures. Journal of Generating Evidence and Methods to Improve Patient Outcomes (eGEMs), 2(1), 2014.
• W. Yim, X. Engle, H.L. Evans, M. Yetisgen. A New Corpus for Structured Microbiology Results. In Proceedings of the American Medical Informatics Association Fall Symposium (AMIA'14). Washington DC, November, 2014.
• D. Capurro, M. Yetisgen, E. van Eaton, R. Black, P. Tarczy-Hornoch. Availability of Structured and Unstructured Clinical Data for Comparative Effectiveness Research and Quality Improvement: A Multi-Site Assessment. Journal of Generating Evidence and Methods to Improve Patient Outcomes (eGEMs), 2(1), 2014.
• A. Korhonen, Y. Guo, M. Yetisgen, U. Stenius, M. Narita, P. Lio. Improving Literature-Based Discovery with Text Mining. In Proceedings of 11th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, 2014.
• P. Klassen, F. Xia, L. Vanderwende, M. Yetisgen. Annotating Clinical Events in Text Snippets for Phenotype Detection. In Proceedings of International Conference on Language Resources and Evaluation (LREC). Reykjavik, Iceland, May, 2014.
• M. Yetisgen, P. Klassen, L. Vanderwende, F. Xia. A New Corpus for Clinical Events with Change of State. In Proceedings of the American Medical Informatics Association Clinical Research Informatics Summit (AMIA CRI'14). San Francisco, CA, April, 2014.
• E.S. Lee, C. Fong, R.A. Black, M. Yetisgen. Identifying Infection Phenotype Using an NLP Assertion Classifier on Microbiology Text. In Proceedings of the American Medical Informatics Association Clinical Research Informatics Summit (AMIA CRI'14). San Francisco, CA, April, 2014.
• E.B. Devine, E. van Eaton, A. Devlin, N.D. Yanez, M. Yetisgen-Yildiz, D. Capurro, R. Alfonso-Cristancho, D.R. Flum, P. Tarczy-Hornoch. Preparing electronic clinical data for quality improvement and research: The CERTAIN validation project. eGEMs. 1(1), 2014.

2013

• J. Huh, M. Yetisgen-Yildiz, W. Pratt. Text classification for assisting moderators in online health communities. J Biomed Inform., 2013. In Press. doi:10.1016/j.jbi.2013.08.011.
• C.A. Bejan, L. Vanderwende, H.L. Evans, M.M. Wurfel, M. Yetisgen-Yildiz. On-time clinical phenotype prediction based on narrative reports. Proceedings of the American Medical Informatics Association Fall Symposium (AMIA'13). Washington DC, November, 2013. (Distinguished Paper Award)
• M. Yetisgen-Yildiz, C.A. Bejan, M.M. Wurfel.Identification of Patients with Acute Lung Injury from Free-Text Chest X-ray Reports. Proceeding of BioNLP Workshop of ACL'2013, 2013.
• L. Vanderwende, F. Xia, M. Yetisgen-Yildiz. Annotating Change of State for Clinical Events. 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. 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.