K. Bretonnel Cohen

K. Bretonnel Cohen, Xuan Qin, Jin-Dong Kim, 2018, 2018 11th International Congress on Image and Signal Processing, BioMedical Engineering and Informatics (CISP-BMEI).

Erratum to: Replicability and reproducibility of research results for human language technology: introducing an LRE special section

Piek T. J. M. Vossen, K. Bretonnel Cohen, Nicoletta Calzolari, 2017, Lang. Resour. Evaluation.

Inter-Annotator Agreement and the Upper Limit on Machine Performance: Evidence from Biomedical Natural Language Processing

K. Bretonnel Cohen, Mayla Boguslav, K. Cohen, 2017, MedInfo.

Combining Heterogenous Data for Prediction of Disease Related and Pharmacogenes

K. Bretonnel Cohen, Lawrence Hunter, Christopher S. Funk, 2013, Pacific Symposium on Biocomputing.

Proceedings of the Workshop on BioNLP 2007: Biological, Translational, and Clinical Language Processing

K. Bretonnel Cohen, Carol Friedman, Lynette Hirschman, 2007 .

Natural Language Processing and Systems Biology

K. Bretonnel Cohen, Lawrence Hunter, K. Cohen, 2004, Artificial Intelligence Methods And Tools For Systems Biology.

Manual curation is not sufficient for annotation of genomic databases

K. Bretonnel Cohen, Lawrence Hunter, William A. Baumgartner, 2007, ISMB/ECCB.

Software Engineering, Testing, and Quality Assurance for Natural Language Processing

K. Bretonnel Cohen, Bob Carpenter, 2008 .

New Challenges For NLP Frameworks Programme

K. Bretonnel Cohen, Karin M. Verspoor, Christophe Roeder, 2010 .

Recognizing Sublanguages in Scientific Journal Articles through Closure Properties

K. Bretonnel Cohen, Irina P. Temnikova, 2013, BioNLP@ACL.

Overview of the BioCreative III Workshop

Zhiyong Lu, K. Bretonnel Cohen, Alfonso Valencia, 2011, BMC Bioinformatics.

Evaluation of Lexical Methods for Detecting Relationships Between Concepts from Multiple Ontologies

Zhiyong Lu, K. Bretonnel Cohen, Helen L. Johnson, 2006, Pacific Symposium on Biocomputing.

The Curative Power of Medical Data

K. Bretonnel Cohen, Diana Trandabat, Jingbo Xia, 2018, JCDL.

A nonparametric Bayesian method of translating machine learning scores to probabilities in clinical decision support

K. Bretonnel Cohen, John Pestian, Ulya Bayram, 2017, BMC Bioinformatics.

BioCreative-2012 Virtual Issue

Zhiyong Lu, K. Bretonnel Cohen, Alfonso Valencia, 2012, Database J. Biol. Databases Curation.

BioNLP

K. Bretonnel Cohen, 2007, Handbook of Natural Language Processing.

Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters

K. Bretonnel Cohen, Karin M. Verspoor, Christophe Roeder, 2014, BMC Bioinformatics.

Current issues in biomedical text mining and natural language processing

K. Bretonnel Cohen, Wendy W. Chapman, W. Chapman, 2009, J. Biomed. Informatics.

Assessing the similarity of surface linguistic features related to epilepsy across pediatric hospitals

K. Bretonnel Cohen, John Pestian, Pawel Matykiewicz, 2014, J. Am. Medical Informatics Assoc..

The state of the art in text mining and natural language processing for pharmacogenomics

K. Bretonnel Cohen, Russ B. Altman, Adrien Coulet, 2012, J. Biomed. Informatics.

CLEF eHealth 2017 Multilingual Information Extraction task Overview: ICD10 Coding of Death Certificates in English and French

K. Bretonnel Cohen, Pierre Zweigenbaum, Cyril Grouin, 2017, CLEF.

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task

Jeyakumar Natarajan, Zhiyong Lu, K. Bretonnel Cohen, 2013, Database J. Biol. Databases Curation.

The Compositional Structure of Gene Ontology Terms

K. Bretonnel Cohen, Lawrence Hunter, Philip V. Ogren, 2003, Pacific Symposium on Biocomputing.

Clinical Information Extraction at the CLEF eHealth Evaluation lab 2016

K. Bretonnel Cohen, Thierry Hamon, Pierre Zweigenbaum, 2016, CLEF.

A critical review of PASBio's argument structures for biomedical verbs

K. Bretonnel Cohen, Lawrence Hunter, K. Cohen, 2006, BMC Bioinformatics.

Closure Properties of Bulgarian Clinical Text

Galia Angelova, K. Bretonnel Cohen, William A. Baumgartner, 2013, RANLP.

Contrast and variability in gene names

K. Bretonnel Cohen, Lawrence Hunter, George K. Acquaah-Mensah, 2002, ACL Workshop on Natural Language Processing in the Biomedical Domain.

Mining FDA drug labels for medical conditions

K. Bretonnel Cohen, Louise Deléger, Anil G. Jegga, 2013, BMC Medical Informatics and Decision Making.

De l'intérêt des ontologies modulaires. Application à la modélisation de la prise en charge de la SLA

Jean Charlet, K. Bretonnel Cohen, Xavier Aimé, 2018, IC.

OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression

Zhiyong Lu, K. Bretonnel Cohen, Helen L. Johnson, 2008, BMC Bioinformatics.

MutationFinder: a high-performance system for extracting point mutation mentions from text

K. Bretonnel Cohen, Lawrence Hunter, William A. Baumgartner, 2007, Bioinform..

TRANSLATING BIOLOGY: TEXT MINING TOOLS THAT WORK – Session Introduction

K. Bretonnel Cohen, Philip E. Bourne, Hong Yu, 2007 .

Test Suite Design for Biomedical Ontology Concept Recognition Systems

K. Bretonnel Cohen, Karin M. Verspoor, Christophe Roeder, 2010, LREC.

Replicability of Research in Biomedical Natural Language Processing: a pilot evaluation for a coding task

K. Bretonnel Cohen, Cyril Grouin, Aurélie Névéol, 2016, Louhi@EMNLP.

Three Dimensions of Reproducibility in Natural Language Processing

K. Bretonnel Cohen, Lawrence Hunter, Pierre Zweigenbaum, 2018, LREC.

MEDA 2020: The Curative Power of Medical Data

K. Bretonnel Cohen, Daniela Gîfu, Jingbo Xia, 2020, JCDL.

Ontology Translation: A Case Study on Translating the Gene Ontology from English to German

K. Bretonnel Cohen, Lawrence Hunter, Negacy D. Hailu, 2014, NLDB.

Writing about Data Science Research for Digital Libraries

K. Bretonnel Cohen, Daniela Gîfu, 2020, JCDL.

Intrinsic Evaluation of Text Mining Tools May Not Predict Performance on Realistic Tasks

K. Bretonnel Cohen, Lawrence Hunter, Philip E. Bourne, 2007, Pacific Symposium on Biocomputing.

NEW FRONTIERS IN BIOMEDICAL TEXT MINING – AN INTRODUCTION

K. Bretonnel Cohen, Pierre Zweigenbaum, Hong Yu, 2006 .

The textual characteristics of traditional and Open Access scientific journals are similar

K. Bretonnel Cohen, Karin M. Verspoor, Lawrence Hunter, 2008, BMC Bioinformatics.

Reviewing Natural Language Processing Research

K. Bretonnel Cohen, Margot Mieskes, Karën Fort, 2020, ACL.

A Modular Ontology for Modeling Service Provision in a Communication Network for Coordination of Care

Jean Charlet, K. Bretonnel Cohen, Xavier Aimé, 2018, MIE.

Workshop Introduction

K. Bretonnel Cohen, Udo Hahn, Nigam H. Shah, 2011, Pacific Symposium on Biocomputing.

Introduction

K. Bretonnel Cohen, Karën Fort, Gilles Adda, 2016, Trait. Autom. des Langues.

BioNLP 2010: Year in review

K. Bretonnel Cohen, Sophia Ananiadou, John Pestian, 2010 .

Generif Quality Assurance as Summary Revision

Zhiyong Lu, K. Bretonnel Cohen, Lawrence Hunter, 2006, Pacific Symposium on Biocomputing.

BioCreative-IV virtual issue

Zhiyong Lu, K. Bretonnel Cohen, Alfonso Valencia, 2014, Database J. Biol. Databases Curation.

Assessment of Software Testing and Quality Assurance in Natural Language Processing Applications and a Linguistically Inspired Approach to Improving It

K. Bretonnel Cohen, Lawrence Hunter, Martha Palmer, 2012, EternalS@ECAI.

Community Perspective on Replicability in Natural Language Processing

K. Bretonnel Cohen, Cyril Grouin, Margot Mieskes, 2019, RANLP.

U-Compare: A modular NLP workflow construction and evaluation system

K. Bretonnel Cohen, Lawrence Hunter, Sophia Ananiadou, 2011, IBM J. Res. Dev..

Text mining and manual curation of chemical-gene-disease networks for the Comparative Toxicogenomics Database (CTD)

K. Bretonnel Cohen, Thomas C. Wiegers, Allan Peter Davis, 2009, BMC Bioinformatics.

Exploring Species-Based Strategies for Gene Normalization

K. Bretonnel Cohen, Helen L. Johnson, Karin M. Verspoor, 2010, IEEE ACM Trans. Comput. Biol. Bioinform..

UColorado_SOM: Extraction of Drug-Drug Interactions from Biomedical Text using Knowledge-rich and Knowledge-poor Features

K. Bretonnel Cohen, Lawrence Hunter, Negacy D. Hailu, 2013, SemEval@NAACL-HLT.

Test suite design for ontology concept recognition systems

K. Bretonnel Cohen, Christophe Roeder, Lawrence Hunter, 2010, LREC 2010.

Training the Next Generation of Quantitative Biologists in the Era of Big Data

K. Bretonnel Cohen, Lawrence Hunter, Jason H. Moore, 2014, Pacific Symposium on Biocomputing.

Refactoring Corpora

K. Bretonnel Cohen, Helen L. Johnson, Lawrence Hunter, 2006, BioNLP@NAACL-HLT.

Software Testing and the Naturally Occurring Data Assumption in Natural Language Processing

K. Bretonnel Cohen, Lawrence Hunter, William A. Baumgartner, 2008, SETQALNLP.

High-precision biological event extraction with a concept recognizer

K. Bretonnel Cohen, Helen L. Johnson, Karin M. Verspoor, 2009, BioNLP@HLT-NAACL.

HIGH‐PRECISION BIOLOGICAL EVENT EXTRACTION: EFFECTS OF SYSTEM AND OF DATA

K. Bretonnel Cohen, Helen L. Johnson, Karin M. Verspoor, 2011, Comput. Intell..

Mining the pharmacogenomics literature - a survey of the state of the art

K. Bretonnel Cohen, Udo Hahn, Nigam H. Shah, 2012, Briefings Bioinform..

Temporal Expression Recognition for Cell Cycle Phase Concepts in Biomedical Literature

K. Bretonnel Cohen, Negacy D. Hailu, Natalya Panteleyeva, 2014, BioNLP@ACL.

Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles

K. Bretonnel Cohen, Karin M. Verspoor, Lawrence Hunter, 2017, BMC Bioinformatics.

Empirical data on corpus design and usage in biomedical natural language processing

K. Bretonnel Cohen, Lawrence Hunter, Philip V. Ogren, 2005, AMIA.

Integrating text mining into high-throughput assay analysis

K. Bretonnel Cohen, 2010, BMC Bioinformatics.

A Resource for Constructing Customized Test Suites for Molecular Biology Entity Identification Systems

K. Bretonnel Cohen, Lawrence Hunter, Shuhei Kinoshita, 2004 .

U-Compare: share and compare text mining tools with UIMA

K. Bretonnel Cohen, Lawrence Hunter, Sophia Ananiadou, 2009, Bioinform..

Proceedings of BioNLP 2014

K. Bretonnel Cohen, Sophia Ananiadou, Jun'ichi Tsujii, 2014, BioNLP@ACL.

Visualization and Language Processing for Supporting Analysis across the Biomedical Literature

K. Bretonnel Cohen, Karin M. Verspoor, Lawrence Hunter, 2010, KES.

Measuring Closure Properties of Patent Sublanguages

Galia Angelova, K. Bretonnel Cohen, Irina P. Temnikova, 2013, RANLP.

Proceedings of the BioNLP 2009 Workshop

K. Bretonnel Cohen, Sophia Ananiadou, Jun'ichi Tsujii, 2009 .

Semantic Relations in Compound Nouns: Perspectives from Inter-Annotator Agreement

K. Bretonnel Cohen, Lawrence Hunter, Elisabetta Jezek, 2017, MedInfo.

Corpus Design for Biomedical Natural Language Processing

K. Bretonnel Cohen, Lawrence Hunter, Philip V. Ogren, 2005, LBLODMBS@IDMB.

Improving precision in concept normalization

K. Bretonnel Cohen, Lawrence Hunter, William A. Baumgartner, 2018, PSB.

A scaleable automated quality assurance technique for semantic representations and proposition banks

K. Bretonnel Cohen, Lawrence Hunter, Martha Palmer, 2011, Linguistic Annotation Workshop.

Finding GeneRIFs via Gene Ontology Annotations

Zhiyong Lu, K. Bretonnel Cohen, Lawrence Hunter, 2005, Pacific Symposium on Biocomputing.

Crowdsourcing and curation: perspectives from biology and natural language processing

K. Bretonnel Cohen, Lynette Hirschman, Karën Fort, 2016, Database J. Biol. Databases Curation.

Fast and simple semantic class assignment for biomedical text

K. Bretonnel Cohen, Karin M. Verspoor, Lawrence Hunter, 2011, BioNLP@ACL.

Session Introduction

Olivier Bodenreider, K. Bretonnel Cohen, Lynette Hirschman, 2006, Pacific Symposium on Biocomputing.

MetaMap is a Superior Baseline to a Standard Document Retrieval Engine for the Task of Finding Patient Cohorts in Clinical Free Text

K. Bretonnel Cohen, Lawrence Hunter, Tom Christiansen, 2011, TREC.

Sublanguage Corpus Analysis Toolkit: A tool for assessing the representativeness and sublanguage characteristics of corpora

Galia Angelova, K. Bretonnel Cohen, Adam Kilgarriff, 2014, LREC.

Themes in biomedical natural language processing: BioNLP08

K. Bretonnel Cohen, Sophia Ananiadou, Jun'ichi Tsujii, 2008, BMC Bioinformatics.

Replicability and reproducibility of research results for human language technology: introducing an LRE special section

Piek T. J. M. Vossen, K. Bretonnel Cohen, Nicoletta Calzolari, 2017, Lang. Resour. Evaluation.

iProLINK: A Framework for Linking Text Mining with Ontology and Systems Biology

K. Bretonnel Cohen, Hongfang Liu, Alfonso Valencia, 2008, 2008 IEEE International Conference on Bioinformatics and Biomedicine.

Concept Recognition and the TREC Genomics Tasks

K. Bretonnel Cohen, Helen L. Johnson, Lawrence Hunter, 2005, TREC.

A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools

K. Bretonnel Cohen, Helen L. Johnson, Karin M. Verspoor, 2012, BMC Bioinformatics.

A repository of semantic types in the MIMIC II database clinical notes

K. Bretonnel Cohen, Alan R. Aronson, Richard Osborne, 2014, BioNLP@ACL.

Proceedings of the ACL-ISMB Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics@ISMB 2005, Detroit, MI, USA June 24, 2005

K. Bretonnel Cohen, Hagit Shatkay, Christian Blaschke, 2005, LBLODMBS@ISMB.

Concept annotation in the CRAFT corpus

K. Bretonnel Cohen, Karin M. Verspoor, Lawrence Hunter, 2012, BMC Bioinformatics.

Measuring the readability of medical research journal abstracts

K. Bretonnel Cohen, Samuel J. Severance, Samuel J. Severance, 2015, BioNLP@IJCNLP.

Bridging heterogeneous mutation data to enhance disease gene discovery

K. Bretonnel Cohen, Jin-Dong Kim, Yuxing Wang, 2021, Briefings Bioinform..

Sentiment Analysis of Suicide Notes: A Shared Task

K. Bretonnel Cohen, Ozlem Uzuner, John F. Hurdle, 2012, Biomedical informatics insights.

PerspectiveBiomedical Language Processing : What ’ s Beyond PubMed ?

K. Bretonnel Cohen, Lawrence Hunter, K. Cohen, .