Evaluating and combining biomedical named entity recognition systems

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

Volumn , Issue , 2007, Pages 199-206

  Vlachos, Andreas ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

HIDDEN MARKOV MODELS; PETROLEUM RESERVOIR EVALUATION; SYNTACTICS;

AUTOMATICALLY GENERATED; BIOMEDICAL NAMED ENTITY RECOGNITION; CONDITIONAL RANDOM FIELD; SYNTACTIC PARSING;

TRANSLATION (LANGUAGES);

EID: 84907259669     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.3115/1572392.1572430     Document Type: Conference Paper

References (25)

1. Sophia Ananiadou and John McNaught, editors. 2006. Text Mining in Biology and Biomedicine. Artech House, Inc.
2. Christian Blaschke, Lynette Hirschman, and Alexander Yeh, editors. 2004. Proceedings of the BioCreative Workshop, Granada, March.
3. Ted Briscoe, John Carroll, and Rebecca Watson. 2006. The second release of the RASP system. In Proceedings of the COLING/ACL 2006 Interactive Presentation Sessions.
4. Ann Copestake, Peter Corbett, Peter Murray-Rust, CJ Rupp, Advaith Siddharthan, Simone Teufel, and Ben Waldron. 2006. An architecture for language processing for scientific texts. In Proceedings of the UK e-Science All Hands Meeting 2006.
5. Radu Florian, Abe Ittycheriah, Hongyan Jing, and Tong Zhang. 2003. Named entity recognition through classifier combination. In Walter Daelemans and Miles Osborne, editors, Proceedings of CoNLL-2003, pages 168–171. Edmonton, Canada.
6. C. Gasperin, N. Karamanis, and R. Seal. 2007. Annotation of anaphoric relations in biomedical full-text articles using a domain-relevant scheme. In Proceedings of DAARC.
7. Caroline Gasperin. 2006. Semi-supervised anaphora resolution in biomedical texts. In Proceedings of BioNLP in HLT-NAACL, pages 96–103.
8. Lynette Hirschman, Marc Colosimo, Alexander Morgan, and Alexander Yeh. 2005. Overview of biocreative task 1b: normalized gene lists. BMC Bioinformatics.
9. J. Kim, T. Ohta, Y. Tsuruoka, Y. Tateisi, and N. Collier, editors. 2004. Proceedings of JNLPBA, Geneva.
10. Martin Krallinger and Lynette Hirschman, editors. 2007. Proceedings of the Second BioCreative Challenge Evaluation Workshop, Madrid, April.
11. Trausti Kristjansson, Aron Culotta, Paul Viola, and Andrew McCallum. 2004. Interactive information extraction with constrained conditional random fields.
12. J. D. Lafferty, A. McCallum, and F. C. N. Pereira. 2001. Conditional random fields: Probabilistic models for segmenting and labeling sequence data. In Proceedings of ICML 2001, pages 282–289.
13. Andrew Kachites McCallum. 2002. Mallet: A machine learning for language toolkit. http://mallet.cs.umass.edu.
14. A. Mikheev, M. Moens, and C. Grover. 1999. Named entity recognition without gazetteers.
15. A. A. Morgan, L. Hirschman, M. Colosimo, A. S. Yeh, and J. B. Colombe. 2004. Gene name identification and normalization using a model organism database. J. of Biomedical Informatics, 37(6):396–410.
16. L. R. Rabiner. 1990. A tutorial on hidden markov models and selected apllications in speech recognition. In A. Waibel and K.-F. Lee, editors, Readings in Speech Recognition, pages 267–296. Kaufmann, San Mateo, CA.
17. Burr Settles. 2004. Biomedical Named Entity Recognition Using Conditional Random Fields and Novel Feature Sets. Proceedings of the Joint Workshop on Natural Language Processing in Biomedicine and its Applications.
18. D. Shen, J. Zhang, J. Su, G. Zhou, and C. L. Tan. 2004. Multi-criteria-based active learning for named entity recongition. In Proceedings of ACL 2004, Barcelona.
19. Christian Siefkes. 2006. A comparison of tagging strategies for statistical information extraction. In Proceedings of the Human Language Technology Conference of the NAACL, Companion Volume: Short Papers, pages 149–152, New York City, USA, June. Association for Computational Linguistics.
20. Charles Sutton and Andrew McCallum. 2006. An introduction to conditional random fields for relational learning. In Lise Getoor and Ben Taskar, editors, Introduction to Statistical Relational Learning. MIT Press.
21. Erik F. Tjong Kim Sang and Fien De Meulder. 2003. Introduction to the conll-2003 shared task: Language-independent named entity recognition. In Walter Daelemans and Miles Osborne, editors, Proceedings of CoNLL-2003, pages 142–147. Edmonton, Canada.
22. A. Vlachos and C. Gasperin. 2006. Bootstrapping and evaluating named entity recognition in the biomedical domain. In Proceedings of BioNLP in HLT-NAACL, pages 138–145.
23. A. Vlachos, C. Gasperin, I. Lewin, and T. Briscoe. 2006. Bootstrapping the recognition and anaphoric linking of named entities in drosophila articles. In Proceedings of PSB 2006.
24. Andreas Vlachos. 2007. Tackling the BioCreative2 Gene Mention task with Conditional Random Fields and Syntactic Parsing. In Proceedings of the Second BioCreative Challenge Evaluation Workshop.
25. Ian H. Witten and Timothy C. Bell. 1991. The zero-frequency problem: Estimating the probabilities of novel events in adaptive text compression. IEEE Transactions on Information Theory, 37(4):1085–1094.