Amber Stubbs

Publications and presentations

2015

Amber Stubbs and Ozlem Uzuner. “Annotating longitudinal clinical narratives for de-identification.” Journal of Biomedical Informatics, Supplement: i2b2 NLP Proceedings 2014. Accepted; Expected publication 2015

Amber Stubbs, Christopher Kotfila, and Ozlem 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: i2b2 NLP Proceedings 2014. Accepted; Expected publication 2015

Amber Stubbs and Ozlem Uzuner. “Annotating Risk Factors for Heart Disease in Clinical Narratives for Diabetic Patients”. Journal of Biomedical Informatics, Supplement: i2b2 NLP Proceedings 2014. Accepted; Expected publication 2015

Amber Stubbs, Christopher Kotfila, Hua Xu, and Ozlem Uzuner. “Identifying risk factors for heart disease over time: Overview of 2014 i2b2/UTHealth shared task Track 2.” Journal of Biomedical Informatics, Supplement: i2b2 NLP Proceedings 2014. Accepted; Expected publication 2015

Kai Zheng, V.G.Vinod Vydiswaran, Yang Liu, Yue Wang, Amber Stubbs, Ozlem 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: i2b2 NLP Proceedings 2014. Accepted; Expected publication 2015

Amber Stubbs, Ozlem Uzuner, Christopher Kotfila, Ira Goldstein, Peter Szolovits. "Challenges in Synthesizing Surrogate PHI in Narrative EMRs" chapter in Medical Data Privacy Handbook. Editors: Aris Gkoulalas-Divanis, Grigorios Loukides. Springer, November 2015.

Amber Stubbs and Ozlem Uzuner. “Biomedical Annotations: i2b2 de-identification”, chapter in Handbook of Linguistic Annotation. Nancy Ide and James Pustejovsky, eds. Springer. Accepted; anticipated publication 2015.

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. Accepted; anticipated publication in 2015.

2014

Ozlem Uzuner, Meliha Yetisgen and Amber Stubbs. "Biomedical/clinical NLP". International Conference on Computational Linguistics (COLING). Dublin, Ireland. August 23rd, 2014.

2013

Ozlem Uzuner, Amber Stubbs, and Weiyi Sun "Chronology of your health events: Approaches to extracting temporal relations from medical narratives." Editorial. Journal of Biomedical Informatics, Vol. 46, December 2013.

Amber Stubbs. "A Methodology for Using Professional Knowledge in Corpus Annotation". PhD. dissertation. Brandeis University, February 2013.

James Pustejovsky and Amber Stubbs "Natural Language Annotation for Machine Learning." O'Reilly Media. Feb 20, 2013.

2012

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

James Pustejovsky and Amber Stubbs "How to Develop Language Annotations for Machine Learning Algorithms." O'Reilly Webcast series, October 16, 2012. Available for download.

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.

2011

Amber Stubbs. "An Introduction to Corpus Linguistics.". New Media Consortium (NMC) Horizon Connect webinar series, December 15, 2011. (iTunes release date December 21).

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.

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.

2010

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

2007

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