Amber Stubbs

Publications and presentations

Books

James Pustejovsky and Amber Stubbs. Natural Language Annotation for Machine Learning. O'Reilly Media, November 2012.

Peer-Reviewed Book Chapters

Amber Stubbs, Özlem Uzuner, Christopher Kotfila, Ira Goldstein, Peter Szolovits. "Challenges in Synthesizing Surrogate PHI in Narrative EMRs". Chapter in Medical Data Privacy Handbook. Aris Gkoulalas-Divanis and Grigorios Loukides, eds. Springer, November 2015. doi:10.1007/978-3-319-23633-9

Amber Stubbs and Özlem Uzuner. "Biomedical Annotations: i2b2 de-identification", chapter in Handbook of Linguistic Annotation. Nancy Ide and James Pustejovsky, eds. Springer, 2017. doi:10.1007/978-94-024-0881-2

Anna Rumshisky and Amber Stubbs. "Machine Learning for Higher-Level Linguistic Tasks", chapter in Handbook of Linguistic Annotation. Nancy Ide and James Pustejovsky, eds. Springer, 2017. doi:10.1007/978-94-024-0881-2

Peer-Reviewed Journal Articles

Amber Stubbs, Michele Filannino, Özlem Uzuner. "De-identification of psychiatric intake records: Overview of 2016 CEGS N-GRID Shared Tasks Track 1." Journal of Biomedical Informatics, Supplement: 2016 CEGS/N-GRID. Natural Language Processing Challenge in Clinical Data. 2017. doi: 10.1016/j.jbi.2017.06.011.

Michele Filannino, Amber Stubbs, Özlem Uzuner. "Symptom severity prediction from neuropsychiatric clinical records: Overview of 2016 CEGS N-GRID Shared Tasks Track 2." Journal of Biomedical Informatics, Supplement: 2016 CEGS/N-GRID. Natural Language Processing Challenge in Clinical Data. 2017. doi: 10.1016/j.jbi.2017.04.017.

Amber Stubbs, Özlem Uzuner. "Annotating longitudinal clinical narratives for de-identification: The 2014 i2b2/UTHealth corpus." Journal of Biomedical Informatics, Supplement: 2014 i2b2 Natural Language Processing Challenge in Clinical Data. 2015. doi:10.1016/j.jbi.2015.07.020

Amber Stubbs and Özlem Uzuner. "Annotating Risk Factors for Heart Disease in Clinical Narratives for Diabetic Patients". Journal of Biomedical Informatics, Supplement: 2014 i2b2 Natural Language Processing Challenge in Clinical Data. 2015. doi:10.1016/j.jbi.2015.05.009

Amber Stubbs, Christopher Kotfila, and Özlem Uzuner. "Automated systems for the de-identification of longitudinal clinical narratives: Overview of 2014 i2b2/UTHealth shared task Track 1." Journal of Biomedical Informatics, Supplement: 2014 i2b2 Natural Language Processing Challenge in Clinical Data. 2015. doi:10.1016/j.jbi.2015.06.007

Amber Stubbs, Christopher Kotfila, Hua Xu, and Özlem Uzuner. "Identifying risk factors for heart disease over time: Overview of 2014 i2b2/UTHealth shared task Track 2." Journal of Biomedical Informatics, Supplement: 2014 i2b2 Natural Language Processing Challenge in Clinical Data. 2015. doi:10.1016/j.jbi.2015.07.001

Vishesh Kumar, Amber Stubbs, Stanley Shaw, Özlem Uzuner. "Creation of a new longitudinal corpus of clinical narratives." Journal of Biomedical Informatics, Supplement: 2014 i2b2 Natural Language Processing Challenge in Clinical Data. 2015. doi:10.1016/j.jbi.2015.09.018

Kai Zheng, V.G.Vinod Vydiswaran, Yang Liu, Yue Wang, Amber Stubbs, Özlem Uzuner, Anupama E. Gururaj, Samuel Bayer, John Aberdeen, Anna Rumshisky, Serguei Pakhomov, Hongfang Liu, Hua Xu. "Ease of Adoption of Clinical Natural Language Processing Software: An Evaluation of Five Systems." Journal of Biomedical Informatics, Supplement: 2014 i2b2 Natural Language Processing Challenge in Clinical Data. 2015. doi:10.1016/j.jbi.2015.07.008

Peer-Reviewed Conference Presentations

Jessica M. Parr, Amber Stubbs, Teriyana Cohens, Michelle Medici, Patrice Miller, Peizhu Qian. "Digitizing Incarceration: a Database of Unfreedoms". 2019 Lapidus Center Conference, Schomburg Center, New York City, October 10-12, 2019.

Amber Stubbs. "Developing Specifications for Light Annotation Tasks in the Biomedical Domain." In 2012 Proceedings of the Third Workshop on Building and Evaluating Resources for Biomedical Text Mining, Istanbul, Turkey, May 26, 2012.

James Pustejovsky and Amber Stubbs. "Increasing Informativeness in Temporal Annotation." In 2011 Proceedings of the Linguistic Annotation Workshop V, Association of Computational Linguistics, Portland, Oregon, July 23-24, 2011.

Marc Verhagen, Amber Stubbs, and James Pustejovsky. "Combining Independent Syntactic and Semantic Annotation Schemes." In Proceedings of the Linguistic Annotation Workshop, ACL, Prague, Czech Republic. June, 2007.

Peer-Reviewed Conference Panels

Keith O'Hara, Sven Anderson, David Musicant, Amber Stubbs, Thomas Way. "Team-Teaching with Colleagues in the Arts and Humanities" SIGCSE 2018, Baltimore, MD. https://sigcse2018.sigcse.org/attendees/accepted.html

Peer-Reviewed Poster Presentations

Rebecca Haralson, Katherine Sittig-Boyd, Stephanie Worobey, Amber Stubbs. "Analyzing Health Data in Longitudinal Clinical Narratives." TAPIA 2016.

Jennifer A. Roecklein-Canfield, Deborah Tobiason, Margaret Menzin, Mark Mahoney, Nanette Veilleux, and Amber Stubbs. "Using Synthetic Biology to teach undergraduates the cross-disciplinary and collaborative nature of scientific research." 2015 American Society for Cell Biology (ASCB) Annual Meeting in San Diego, CA, December 12-16, 2015.

Amber Stubbs. "MAE and MAI: Lightweight Annotation and Adjudication Tools". In 2011 Proceedings of the Linguistic Annotation Workshop V, Association of Computational Linguistics, Portland, Oregon, July 23-24, 2011.

Amber Stubbs and James Pustejovsky. "Annotation of Discharge Summaries Based on Selection Criteria." In 2011 Proceedings of AMIA Summit on Clinical Research Informatics, San Francisco, March 9-11, 2011.

Amber Stubbs and Benjamin Harshfield. "Applying the TARSQI toolkit to augment text mining of EHRs." BioNLP '10: Proceedings of the 2010 Workshop on Biomedical Natural Language Processing. July 2010.