K. Bretonnel Cohen

Also published as: Kevin B. Cohen, Kevin Bretonnel Cohen, Kevin Cohen


2020

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Reviewing Natural Language Processing Research
Kevin Cohen | Karën Fort | Margot Mieskes | Aurélie Névéol
Proceedings of the 58th Annual Meeting of the Association for Computational Linguistics: Tutorial Abstracts

This tutorial will cover the theory and practice of reviewing research in natural language processing. Heavy reviewing burdens on natural language processing researchers have made it clear that our community needs to increase the size of our pool of potential reviewers. Simultaneously, notable “false negatives”---rejection by our conferences of work that was later shown to be tremendously important after acceptance by other conferences—have raised awareness of the fact that our reviewing practices leave something to be desired. We do not often talk about “false positives” with respect to conference papers, but leaders in the field have noted that we seem to have a publication bias towards papers that report high performance, with perhaps not much else of interest in them. It need not be this way. Reviewing is a learnable skill, and you will learn it here via lectures and a considerable amount of hands-on practice.

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Proceedings of the 19th SIGBioMed Workshop on Biomedical Language Processing
Dina Demner-Fushman | Kevin Bretonnel Cohen | Sophia Ananiadou | Junichi Tsujii
Proceedings of the 19th SIGBioMed Workshop on Biomedical Language Processing

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Proceedings of the 1st Workshop on NLP for COVID-19 at ACL 2020
Karin Verspoor | Kevin Bretonnel Cohen | Mark Dredze | Emilio Ferrara | Jonathan May | Robert Munro | Cecile Paris | Byron Wallace
Proceedings of the 1st Workshop on NLP for COVID-19 at ACL 2020

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Proceedings of the 1st Workshop on NLP for COVID-19 (Part 2) at EMNLP 2020
Karin Verspoor | Kevin Bretonnel Cohen | Michael Conway | Berry de Bruijn | Mark Dredze | Rada Mihalcea | Byron Wallace
Proceedings of the 1st Workshop on NLP for COVID-19 (Part 2) at EMNLP 2020

2019

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Proceedings of the 18th BioNLP Workshop and Shared Task
Dina Demner-Fushman | Kevin Bretonnel Cohen | Sophia Ananiadou | Junichi Tsujii
Proceedings of the 18th BioNLP Workshop and Shared Task

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Community Perspective on Replicability in Natural Language Processing
Margot Mieskes | Karën Fort | Aurélie Névéol | Cyril Grouin | Kevin Cohen
Proceedings of the International Conference on Recent Advances in Natural Language Processing (RANLP 2019)

With recent efforts in drawing attention to the task of replicating and/or reproducing results, for example in the context of COLING 2018 and various LREC workshops, the question arises how the NLP community views the topic of replicability in general. Using a survey, in which we involve members of the NLP community, we investigate how our community perceives this topic, its relevance and options for improvement. Based on over two hundred participants, the survey results confirm earlier observations, that successful reproducibility requires more than having access to code and data. Additionally, the results show that the topic has to be tackled from the authors’, reviewers’ and community’s side.

2018

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Three Dimensions of Reproducibility in Natural Language Processing
K. Bretonnel Cohen | Jingbo Xia | Pierre Zweigenbaum | Tiffany Callahan | Orin Hargraves | Foster Goss | Nancy Ide | Aurélie Névéol | Cyril Grouin | Lawrence E. Hunter
Proceedings of the Eleventh International Conference on Language Resources and Evaluation (LREC 2018)

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Proceedings of the BioNLP 2018 workshop
Dina Demner-Fushman | Kevin Bretonnel Cohen | Sophia Ananiadou | Junichi Tsujii
Proceedings of the BioNLP 2018 workshop

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CRF-LSTM Text Mining Method Unveiling the Pharmacological Mechanism of Off-target Side Effect of Anti-Multiple Myeloma Drugs
Kaiyin Zhou | Sheng Zhang | Xiangyu Meng | Qi Luo | Yuxing Wang | Ke Ding | Yukun Feng | Mo Chen | Kevin Cohen | Jingbo Xia
Proceedings of the BioNLP 2018 workshop

Sequence labeling of biomedical entities, e.g., side effects or phenotypes, was a long-term task in BioNLP and MedNLP communities. Thanks to effects made among these communities, adverse reaction NER has developed dramatically in recent years. As an illuminative application, to achieve knowledge discovery via the combination of the text mining result and bioinformatics idea shed lights on the pharmacological mechanism research.

2017

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BioNLP 2017
Kevin Bretonnel Cohen | Dina Demner-Fushman | Sophia Ananiadou | Junichi Tsujii
BioNLP 2017

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Proceedings of the Biomedical NLP Workshop associated with RANLP 2017
Svetla Boytcheva | Kevin Bretonnel Cohen | Guergana Savova | Galia Angelova
Proceedings of the Biomedical NLP Workshop associated with RANLP 2017

2016

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SuperCAT: The (New and Improved) Corpus Analysis Toolkit
K. Bretonnel Cohen | William A. Baumgartner Jr. | Irina Temnikova
Proceedings of the Tenth International Conference on Language Resources and Evaluation (LREC'16)

This paper reports SuperCAT, a corpus analysis toolkit. It is a radical extension of SubCAT, the Sublanguage Corpus Analysis Toolkit, from sublanguage analysis to corpus analysis in general. The idea behind SuperCAT is that representative corpora have no tendency towards closure―that is, they tend towards infinity. In contrast, non-representative corpora have a tendency towards closure―roughly, finiteness. SuperCAT focuses on general techniques for the quantitative description of the characteristics of any corpus (or other language sample), particularly concerning the characteristics of lexical distributions. Additionally, SuperCAT features a complete re-engineering of the previous SubCAT architecture.

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Proceedings of the 15th Workshop on Biomedical Natural Language Processing
Kevin Bretonnel Cohen | Dina Demner-Fushman | Sophia Ananiadou | Jun-ichi Tsujii
Proceedings of the 15th Workshop on Biomedical Natural Language Processing

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Proceedings of the Fifth Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM2016)
Sophia Ananiadou | Riza Batista-Navarro | Kevin Bretonnel Cohen | Dina Demner-Fushman | Paul Thompson
Proceedings of the Fifth Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM2016)

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Replicability of Research in Biomedical Natural Language Processing: a pilot evaluation for a coding task
Aurélie Névéol | Kevin Cohen | Cyril Grouin | Aude Robert
Proceedings of the Seventh International Workshop on Health Text Mining and Information Analysis

2015

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Proceedings of BioNLP 15
Kevin Bretonnel Cohen | Dina Demner-Fushman | Sophia Ananiadou | Jun-ichi Tsujii
Proceedings of BioNLP 15

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Measuring the readability of medical research journal abstracts
Samuel J. Severance | K. Bretonnel Cohen
Proceedings of BioNLP 15

2014

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Proceedings of BioNLP 2014
Kevin Cohen | Dina Demner-Fushman | Sophia Ananiadou | Jun-ichi Tsujii
Proceedings of BioNLP 2014

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Temporal Expression Recognition for Cell Cycle Phase Concepts in Biomedical Literature
Negacy Hailu | Natalya Panteleyeva | Kevin Cohen
Proceedings of BioNLP 2014

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A repository of semantic types in the MIMIC II database clinical notes
Richard Osborne | Alan Aronson | Kevin Cohen
Proceedings of BioNLP 2014

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Sublanguage Corpus Analysis Toolkit: A tool for assessing the representativeness and sublanguage characteristics of corpora
Irina Temnikova | William A. Baumgartner Jr. | Negacy D. Hailu | Ivelina Nikolova | Tony McEnery | Adam Kilgarriff | Galia Angelova | K. Bretonnel Cohen
Proceedings of the Ninth International Conference on Language Resources and Evaluation (LREC'14)

Sublanguages are varieties of language that form “subsets” of the general language, typically exhibiting particular types of lexical, semantic, and other restrictions and deviance. SubCAT, the Sublanguage Corpus Analysis Toolkit, assesses the representativeness and closure properties of corpora to analyze the extent to which they are either sublanguages, or representative samples of the general language. The current version of SubCAT contains scripts and applications for assessing lexical closure, morphological closure, sentence type closure, over-represented words, and syntactic deviance. Its operation is illustrated with three case studies concerning scientific journal articles, patents, and clinical records. Materials from two language families are analyzed―English (Germanic), and Bulgarian (Slavic). The software is available at sublanguage.sourceforge.net under a liberal Open Source license.

2013

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Proceedings of the IWCS 2013 Workshop on Computational Semantics in Clinical Text (CSCT 2013)
Stephen Wu | Nigam Shah | Kevin Bretonnel Cohen
Proceedings of the IWCS 2013 Workshop on Computational Semantics in Clinical Text (CSCT 2013)

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Proceedings of the 2013 Workshop on Biomedical Natural Language Processing
Kevin Bretonnel Cohen | Dina Demner-Fushman | Sophia Ananiadou | John Pestian | Jun’ichi Tsujii
Proceedings of the 2013 Workshop on Biomedical Natural Language Processing

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Earlier Identification of Epilepsy Surgery Candidates Using Natural Language Processing
Pawel Matykiewicz | Kevin Cohen | Katherine D. Holland | Tracy A. Glauser | Shannon M. Standridge | Karin M. Verspoor | John Pestian
Proceedings of the 2013 Workshop on Biomedical Natural Language Processing

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Recognizing Sublanguages in Scientific Journal Articles through Closure Properties
Irina Temnikova | Kevin Cohen
Proceedings of the 2013 Workshop on Biomedical Natural Language Processing

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Proceedings of the Workshop on NLP for Medicine and Biology associated with RANLP 2013
Guergana Savova | Kevin Bretonnel Cohen | Galia Angelova
Proceedings of the Workshop on NLP for Medicine and Biology associated with RANLP 2013

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Evaluation of SPARQL query generation from natural language questions
K. Bretonnel Cohen | Jin-Dong Kim
Proceedings of the Joint Workshop on NLP&LOD and SWAIE: Semantic Web, Linked Open Data and Information Extraction

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Measuring Closure Properties of Patent Sublanguages
Irina Temnikova | Negacy Hailu | Galia Angelova | K. Bretonnel Cohen
Proceedings of the International Conference Recent Advances in Natural Language Processing RANLP 2013

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Closure Properties of Bulgarian Clinical Text
Irina Temnikova | Ivelina Nikolova | William A. Baumgartner | Galia Angelova | K. Bretonnel Cohen
Proceedings of the International Conference Recent Advances in Natural Language Processing RANLP 2013

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UColorado_SOM: Extraction of Drug-Drug Interactions from Biomedical Text using Knowledge-rich and Knowledge-poor Features
Negacy Hailu | Lawrence E. Hunter | K. Bretonnel Cohen
Second Joint Conference on Lexical and Computational Semantics (*SEM), Volume 2: Proceedings of the Seventh International Workshop on Semantic Evaluation (SemEval 2013)

2012

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BioNLP: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing
Kevin B. Cohen | Dina Demner-Fushman | Sophia Ananiadou | Bonnie Webber | Jun’ichi Tsujii | John Pestian
BioNLP: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing

2011

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Proceedings of BioNLP 2011 Workshop
Kevin Bretonnel Cohen | Dina Demner-Fushman | Sophia Ananiadou | John Pestian | Jun’ichi Tsujii | Bonnie Webber
Proceedings of BioNLP 2011 Workshop

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Fast and simple semantic class assignment for biomedical text
K. Bretonnel Cohen | Thomas Christiansen | William Baumgartner Jr. | Karin Verspoor | Lawrence Hunter
Proceedings of BioNLP 2011 Workshop

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Hypothesis and Evidence Extraction from Full-Text Scientific Journal Articles
Elizabeth White | K. Bretonnel Cohen | Larry Hunter
Proceedings of BioNLP 2011 Workshop

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A scaleable automated quality assurance technique for semantic representations and proposition banks
K. Bretonnel Cohen | Lawrence Hunter | Martha Palmer
Proceedings of the 5th Linguistic Annotation Workshop

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Proceedings of the Second Workshop on Biomedical Natural Language Processing
Guergana Savova | Kevin Bretonnel Cohen | Galia Angelova
Proceedings of the Second Workshop on Biomedical Natural Language Processing

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Assignment of Ontology-based Broad Semantic Classes to Biomedical Text
Kevin Bretonnel Cohen
Proceedings of the Second Workshop on Biomedical Natural Language Processing

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Last Words: Amazon Mechanical Turk: Gold Mine or Coal Mine?
Karën Fort | Gilles Adda | K. Bretonnel Cohen
Computational Linguistics, Volume 37, Issue 2 - June 2011

2010

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Proceedings of the 2010 Workshop on Biomedical Natural Language Processing
K. Bretonnel Cohen | Dina Demner-Fushman | Sophia Ananiadou | John Pestian | Jun’ichi Tsujii | Bonnie Webber
Proceedings of the 2010 Workshop on Biomedical Natural Language Processing

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Test Suite Design for Biomedical Ontology Concept Recognition Systems
K. Bretonnel Cohen | Christophe Roeder | William A. Baumgartner Jr. | Lawrence E. Hunter | Karin Verspoor
Proceedings of the Seventh International Conference on Language Resources and Evaluation (LREC'10)

Systems that locate mentions of concepts from ontologies in free text are known as ontology concept recognition systems. This paper describes an approach to the evaluation of the workings of ontology concept recognition systems through use of a structured test suite and presents a publicly available test suite for this purpose. It is built using the principles of descriptive linguistic fieldwork and of software testing. More broadly, we also seek to investigate what general principles might inform the construction of such test suites. The test suite was found to be effective in identifying performance errors in an ontology concept recognition system. The system could not recognize 2.1% of all canonical forms and no non-canonical forms at all. Regarding the question of general principles of test suite construction, we compared this test suite to a named entity recognition test suite constructor. We found that they had twenty features in total and that seven were shared between the two models, suggesting that there is a core of feature types that may be applicable to test suite construction for any similar type of application.

2009

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Proceedings of the BioNLP 2009 Workshop
K. Bretonnel Cohen | Dina Demner-Fushman | Sophia Ananiadou | John Pestian | Jun’ichi Tsujii | Bonnie Webber
Proceedings of the BioNLP 2009 Workshop

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High-precision biological event extraction with a concept recognizer
K. Bretonnel Cohen | Karin Verspoor | Helen Johnson | Chris Roeder | Philip Ogren | William Baumgartner | Elizabeth White | Lawrence Hunter
Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task

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Proceedings of the Workshop on Software Engineering, Testing, and Quality Assurance for Natural Language Processing (SETQA-NLP 2009)
Kevin Bretonnel Cohen | Marc Light
Proceedings of the Workshop on Software Engineering, Testing, and Quality Assurance for Natural Language Processing (SETQA-NLP 2009)

2008

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Software Engineering, Testing, and Quality Assurance for Natural Language Processing
K. Bretonnel Cohen | Bob Carpenter
Software Engineering, Testing, and Quality Assurance for Natural Language Processing

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Software Testing and the Naturally Occurring Data Assumption in Natural Language Processing
K. Bretonnel Cohen | William A. Baumgartner Jr. | Lawrence Hunter
Software Engineering, Testing, and Quality Assurance for Natural Language Processing

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Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing
Dina Demner-Fushman | Sophia Ananiadou | Kevin Bretonnel Cohen | John Pestian | Jun’ichi Tsujii | Bonnie Webber
Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing

2007

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BioNLP
K. Bretonnel Cohen
Proceedings of the Human Language Technology Conference of the NAACL, Companion Volume: Tutorial Abstracts

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Biological, translational, and clinical language processing
K. Bretonnel Cohen | Dina Demner-Fushman | Carol Friedman | Lynette Hirschman | John Pestian
Biological, translational, and clinical language processing

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A shared task involving multi-label classification of clinical free text
John P. Pestian | Chris Brew | Pawel Matykiewicz | DJ Hovermale | Neil Johnson | K. Bretonnel Cohen | Wlodzislaw Duch
Biological, translational, and clinical language processing

2006

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Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology
Karin Verspoor | Kevin Bretonnel Cohen | Ben Goertzel | Inderjeet Mani
Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology

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Refactoring Corpora
Helen L. Johnson | William A. Baumgartner Jr. | Martin Krallinger | K. Bretonnel Cohen | Lawrence Hunter
Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology

2005

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Proceedings of the ACL-ISMB Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics
K. Bretonnel Cohen | Lynette Hirschman | Hagit Shatkay | Christian Blaschke
Proceedings of the ACL-ISMB Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics

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Corpus Design for Biomedical Natural Language Processing
K. Bretonnel Cohen | Lynne Fox | Philip V. Ogren | Lawrence Hunter
Proceedings of the ACL-ISMB Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics

2004

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A Resource for Constructing Customized Test Suites for Molecular Biology Entity Identification Systems
K. Bretonnel Cohen | Lorraine Tanabe | Shuhei Kinoshita | Lawrence Hunter
HLT-NAACL 2004 Workshop: Linking Biological Literature, Ontologies and Databases

2002

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Contrast and variability in gene names
K. Bretonnel Cohen | Andrew Dolbey | George Acquaah-Mensah | Lawrence Hunter
Proceedings of the ACL-02 Workshop on Natural Language Processing in the Biomedical Domain