Lawrence Hunter

Also published as: Lawrence E. Hunter


2019

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CRAFT Shared Tasks 2019 Overview — Integrated Structure, Semantics, and Coreference
William Baumgartner | Michael Bada | Sampo Pyysalo | Manuel R. Ciosici | Negacy Hailu | Harrison Pielke-Lombardo | Michael Regan | Lawrence Hunter
Proceedings of The 5th Workshop on BioNLP Open Shared Tasks

As part of the BioNLP Open Shared Tasks 2019, the CRAFT Shared Tasks 2019 provides a platform to gauge the state of the art for three fundamental language processing tasks — dependency parse construction, coreference resolution, and ontology concept identification — over full-text biomedical articles. The structural annotation task requires the automatic generation of dependency parses for each sentence of an article given only the article text. The coreference resolution task focuses on linking coreferring base noun phrase mentions into chains using the symmetrical and transitive identity relation. The ontology concept annotation task involves the identification of concept mentions within text using the classes of ten distinct ontologies in the biomedical domain, both unmodified and augmented with extension classes. This paper provides an overview of each task, including descriptions of the data provided to participants and the evaluation metrics used, and discusses participant results relative to baseline performances for each of the three tasks.

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)

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)

2011

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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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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

2010

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An Overview of the CRAFT Concept Annotation Guidelines
Michael Bada | Miriam Eckert | Martha Palmer | Lawrence Hunter
Proceedings of the Fourth Linguistic Annotation Workshop

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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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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

2008

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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

2006

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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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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

2000

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Extracting Molecular Binding Relationships from Biomedical Text
Thomas C. Rindflesch | Jayant V. Rajan | Lawrence Hunter
Sixth Applied Natural Language Processing Conference