A tutorial on hidden Markov models and selected applications in speech recognition
Readings in speech recognition
Conditional Random Fields: Probabilistic Models for Segmenting and Labeling Sequence Data
ICML '01 Proceedings of the Eighteenth International Conference on Machine Learning
Gene name identification and normalization using a model organism database
Journal of Biomedical Informatics - Special issue: Named entity recognition in biomedicine
Introduction to the CoNLL-2003 shared task: language-independent named entity recognition
CONLL '03 Proceedings of the seventh conference on Natural language learning at HLT-NAACL 2003 - Volume 4
Named entity recognition through classifier combination
CONLL '03 Proceedings of the seventh conference on Natural language learning at HLT-NAACL 2003 - Volume 4
Text Mining for Biology And Biomedicine
Text Mining for Biology And Biomedicine
Multi-criteria-based active learning for named entity recognition
ACL '04 Proceedings of the 42nd Annual Meeting on Association for Computational Linguistics
The second release of the RASP system
COLING-ACL '06 Proceedings of the COLING/ACL on Interactive presentation sessions
Biomedical named entity recognition using conditional random fields and rich feature sets
JNLPBA '04 Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications
Semi-supervised anaphora resolution in biomedical texts
BioNLP '06 Proceedings of the Workshop on Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis
Bootstrapping and evaluating named entity recognition in the biomedical domain
BioNLP '06 Proceedings of the Workshop on Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis
A comparison of tagging strategies for statistical information extraction
NAACL-Short '06 Proceedings of the Human Language Technology Conference of the NAACL, Companion Volume: Short Papers
An analysis of active learning strategies for sequence labeling tasks
EMNLP '08 Proceedings of the Conference on Empirical Methods in Natural Language Processing
A novel approach to automatic gazetteer generation using Wikipedia
People's Web '09 Proceedings of the 2009 Workshop on The People's Web Meets NLP: Collaboratively Constructed Semantic Resources
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This paper is concerned with the evaluation of biomedical named entity recognition systems. We compare two such systems, one based on a Hidden Markov Model and one based on Conditional Random Fields and syntactic parsing. In our experiments we used automatically generated data as well as manually annotated material, including a new dataset which consists of biomedical full papers. Through our evaluation, we assess the strengths and weaknesses of the systems tested, as well as the datasets themselves in terms of the challenges they present to the systems.