Kevin Bretonnel Cohen
Director, Biomedical Text Mining Group
Computational Bioscience Program
University of Colorado School of Medicine

Office: RC-1 S. Room L18-6102
Phone: 303-916-2417
E-mail: Kevin.Cohen@gmail.com

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Publications

2016

  • Karën Fort, Gilles Adda, and K. Bretonnel Cohen (2016) Éthique et traitement automatique des langues et de la parole: entre truismes et tabous. Traitement Automatique des Langues, Volume 57.
  • K. Bretonnel Cohen, Jingbo Xia, Christophe Roeder, and Lawrence E. Hunter (to appear, May 2016) Reproducibility in natural language processing: A case study of two R libraries for mining PubMed/MEDLINE. Workshop on Research Results Reproducibility and Resources Citation in Science and Technology of Language, LREC 2016.
  • John P. Pestian, Michael Sorter, Brian Connolly, Kevin Bretonnel Cohen, Cheryl McCullumsmith, Jeffry T. Gee, Louis-Philippe Morency, Stefan Scherer, and Lesley Rohlfs (2016) A machine learning approach to identifying the thought markers of suicidal subjects: a prospective multi-center trial. Suicide and life-threatening behavior.
  • K. Bretonnel Cohen, Arrick Lanfranchi, Miji Joo-young Choi, Michael Bada, William A. Baumgartner Jr., Natalya Panteleyeva, Karin Verspoor, Martha Palmer, and Lawrence E. Hunter (accepted) Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles. BMC Bioinformatics.
  • K. Bretonnel Cohen, Karen Fort, Gilles Adda, Dimeji Farri, and Sophia Zhou (2016) Ethical issues in corpus linguistics and annotation: Pay per HIT does not affect effective hourly rate for linguistic resource development on Amazon Mechanical Turk. ETHI-CA 2016: Ethics In Corpus Collection, Annotation & Application, LREC 2016.
  • Christopher S. Funk, Kevin Bretonnel Cohen, Lawrence E. Hunter, and Karin M. Verspoor (2016) Gene Ontology synonym generation rules lead to increased performance in biomedical concept recognition. Journal of Biomedical Semantics 7(1):52.
  • Kevin Bretonnel Cohen, Benjamin Glass, Hansel M. Greiner, Katherine Holland-Bouley, Shannon Standridge, Ravindra Arya, Robert Faist, Diego Morita, Francesco Mangano, Brian Connolly, Tracy Glauser and John Pestian (2016) Methodological Issues in Predicting Pediatric Epilepsy Surgery Candidates Through Natural Language Processing and Machine Learning. Biomedical Informatics Insights 2016:8, 11-18.
  • Aurélie Névéol, Cyril Grouin, Kevin Bretonnel Cohen, and Aude Robert (2016) Replicability of research in biomedical natural language processing: A pilot evaluation for a coding task. Health Text Mining and Information Analysis, pp. 78-84.
  • Aurélie Névéol, K. Bretonnel Cohen, Cyril Grouin, Thierry Hamon, Thomas Lavergne, Liadh Kelly, Lorraine Goeuriot, Grégoire Rey, Aude Robert, Xavier Tannier, and Pierre Zweigenbaum (2016) Clinical information extraction at the CLEF eHealth evaluation lab 2016. Proceedings of CLEF eHealth 2016.
  • Lynette Hirschman, Karën Fort, Stephanie Boué, Nikos Kyrpides, Rezarta Islamaj Dogan, and Kevin Bretonnel Cohen (2016) Crowdsourcing and curation: perspectives from biology and natural language processing. DATABASE: The Journal of Biological Databases and Curation, doi: 10.1093/database/baw115.
  • K. Bretonnel Cohen, William A. Baumgartner Jr., and Irina P. Temnikova (2016) SuperCAT: The (new and improved) Corpus Analysis Toolkit. Language Resources and Evaluation Conference.

2015

2014

2013

2012

  • Karin Verspoor, Kevin Cohen, Arrick Lanfranchi, Colin Warner, Helen L Johnson, Christophe Roeder, Jinho D. Choi, Christopher Funk, Yuriy Malenkiy, Miriam Eckert, Nianwen Xue, William A. Baumgartner, Michael Bada, Martha Palmer, and Lawrence E. Hunter (2012) A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools. BMC Bioinformatics 13:207.
  • Michael Bada, Miriam Eckert, Donald Evans, Kristin Garcia, Krista Shipley, Dmitry Sitnikov, William A Baumgartner, Kevin Cohen, Karin Verspoor, Judith A Blake, and Lawrence E. Hunter (2012) Concept annotation in the CRAFT corpus. BMC Bioinformatics 13:161.
  • Lynette Hirschman, Gully A. P. C Burns, Martin Krallinger, Cecilia Arighi, K. Bretonnel Cohen, Alfonso Valencia, Cathy H. Wu, Andrew Chatr-Aryamontri, Karen G. Dowell, Eva Huala, Analia Lourenco, Robert Nash, Anne-Lise Veuthey, Thomas Wiegers, and Andrew G. Winter (2012) Text mining for the biocuration workflow. DATABASE: The journal of biological databases and curation.
  • K. Bretonnel Cohen, Tom Christiansen, and Lawrence E. Hunter (2011) MetaMap is a superior baseline to a standard document retrieval engine for the task of finding patient cohorts in clinical free text. 20th Text Retrieval Conference.
  • Irina Temnikova and K. Bretonnel Cohen (2012) The Crisis Management Corpus and its application to the study of the crisis management sub-language. Language Resources for Public Security Applications.
  • Adrien Coulet, K. Bretonnel Cohen, and Russ B. Altman (2012) The state of the art in text mining and natural language processing for pharmacogenomics. Journal of Biomedical Informatics 45(5):825-826.
  • John P. Pestian, Pawel Matykiewicz, Michelle Linn-Gust, Brett South, Ozlem Uzuner, Jan Wiebe, K. Bretonnel Cohen, John Hurdle, and Christopher Brew (2012) Sentiment analysis of suicide notes: A shared task. Biomedical Informatics Insights 2012:5 (Suppl. 1) 1-14.
  • Yoshinobu Kano, Jari Bjorne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, K. Bretonnel Cohen, Karin Verspoor, Christophe Roeder, Lawrence E. Hunter, Halil Kilicoglu, Sabine Bergler, Sofie Van Landeghem, Thomas Van Parys, Yves Van de Peer, Makoto Miwa, Sophia Ananiadou, Mariana Neves, Alberto Pascual-Montano, Arzucan Ozgur, Dragomir R. Radev, Sebastian Riedel, Rune Saetre, Hong-Woo Chun, Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, and Jun'ichi Tsujii (2011) U-Compare bio-event meta-service: compatible BioNLP event extraction services. BMC Bioinformatics 12:481.

2011

2010

  • K. Bretonnel Cohen, Helen L. Johnson, Karin Verspoor, Christophe Roeder, and Lawrence E. Hunter (2010) The structural and content aspects of abstracts versus bodies of full text journal articles are different. BMC Bioinformatics 11:492.
  • K. Bretonnel Cohen, Christophe Roeder, William A. Baumgartner Jr., Lawrence Hunter, and Karin Verspoor (2010) Test suite design for biomedical ontology concept recognition systems. Language Resources and Evaluation Conference, pp. 441-446.
  • K. Bretonnel Cohen (2010) Biomedical text mining. Chapter 27 of Handbook of natural language processing, 2nd edition, Nitin Indurkhya and Fred J. Damerau, editors. Write me for uncorrected proofs.
  • Karin Verspoor, Christophe Roeder, Helen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner Jr., and Lawrence Hunter (2010) Exploring species-based strategies for gene normalization. IEEE/ACM Transactions in Computational Biology and Bioinformatics 7(3):462-471.
  • K. Bretonnel Cohen, Arrick Lanfranchi, William Corvey, William A. Baumgartner Jr., Christophe Roeder, Philip V. Ogren, Martha Palmer, and Lawrence Hunter (2010) Annotation of all coreference in biomedical text: Guideline selection and adaptation. BioTxtM 2010: 2nd workshop on building and evaluating resources for biomedical text mining, pp. 37-41.
  • Cartic Ramakrishnan, William A. Baumgartner Jr., Judith A. Blake, Gully A.P.C. Burns, K. Bretonnel Cohen, Harold Drabkin, Janan Eppig, Eduard Hovy, Chun-Nan Hsu, Lawrence E. Hunter, Tommy Ingulfsen, Hiroaki 'Rocky' Onda, Sandeep Pokkunuri, Ellen Riloff, Christophe Roeder, and Karin Verspoor (2010) Building the Scientific Knowledge Mine (SciKnowMine): A community-driven framework for text mining tools in direct service to biocuration. New challenges for NLP frameworks, pp. 9-14.
  • Carsten Goerg, Hannah Tipney, Karin Verspoor, William A. Baumgartner Jr., K. Bretonnel Cohen, John Stasko, and Lawrence E. Hunter (2010) Visualization and language processing for supporting analysis across the biomedical literature. Workshop on 3D visualization of natural language, 14th international conference on knowledge-based and intelligent information and engineering systems.

2009

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This document last modified 01/06/17 09:01.