An Algorithm that Learns What‘s in a Name
Machine Learning - Special issue on natural language learning
A maximum entropy approach to named entity recognition
A maximum entropy approach to named entity recognition
Extracting the names of genes and gene products with a hidden Markov model
COLING '00 Proceedings of the 18th conference on Computational linguistics - Volume 1
Named entity recognition using an HMM-based chunk tagger
ACL '02 Proceedings of the 40th Annual Meeting on Association for Computational Linguistics
Comparison between tagged corpora for the named entity task
WCC '00 Proceedings of the workshop on Comparing corpora - Volume 9
Tuning support vector machines for biomedical named entity recognition
BioMed '02 Proceedings of the ACL-02 workshop on Natural language processing in the biomedical domain - Volume 3
Use of support vector machines in extended named entity recognition
COLING-02 proceedings of the 6th conference on Natural language learning - Volume 20
The GENIA corpus: an annotated research abstract corpus in molecular biology domain
HLT '02 Proceedings of the second international conference on Human Language Technology Research
Biomedical named entity recognition using two-phase model based on SVMs
Journal of Biomedical Informatics - Special issue: Named entity recognition in biomedicine
Use of morphological analysis in protein name recognition
Journal of Biomedical Informatics - Special issue: Named entity recognition in biomedicine
Term identification in the biomedical literature
Journal of Biomedical Informatics - Special issue: Named entity recognition in biomedicine
Multi-criteria-based active learning for named entity recognition
ACL '04 Proceedings of the 42nd Annual Meeting on Association for Computational Linguistics
An NP-cluster based approach to coreference resolution
COLING '04 Proceedings of the 20th international conference on Computational Linguistics
Journal of Biomedical Informatics
Experimental Study on a Two Phase Method for Biomedical Named Entity Recognition
IEICE - Transactions on Information and Systems
Recognizing names in biomedical texts using hidden Markov model and SVM plus sigmoid
JNLPBA '04 Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications
Adapting an NER-system for German to the biomedical domain
JNLPBA '04 Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications
Exploring deep knowledge resources in biomedical name recognition
JNLPBA '04 Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications
An unsupervised method for extracting domain-specific affixes in biological literature
BioNLP '07 Proceedings of the Workshop on BioNLP 2007: Biological, Translational, and Clinical Language Processing
Recognising nested named entities in biomedical text
BioNLP '07 Proceedings of the Workshop on BioNLP 2007: Biological, Translational, and Clinical Language Processing
Feature selection techniques for maximum entropy based biomedical named entity recognition
Journal of Biomedical Informatics
Nested named entity recognition
EMNLP '09 Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing: Volume 1 - Volume 1
Automatic extraction of kinetic information from biochemical literatures
FSKD'09 Proceedings of the 6th international conference on Fuzzy systems and knowledge discovery - Volume 5
A composite kernel for named entity recognition
Pattern Recognition Letters
Journal of Biomedical Informatics
Ontology learning from biomedical natural language documents using UMLS
Expert Systems with Applications: An International Journal
Improving noun phrase coreference resolution by matching strings
IJCNLP'04 Proceedings of the First international joint conference on Natural Language Processing
Boosting performance of gene mention tagging system by hybrid methods
Journal of Biomedical Informatics
CICLing'10 Proceedings of the 11th international conference on Computational Linguistics and Intelligent Text Processing
BioOntoVerb: A top level ontology based framework to populate biomedical ontologies from texts
Knowledge-Based Systems
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In this paper, we explore how to adapt a general Hidden Markov Model-based named entity recognizer effectively to biomedical domain. We integrate various features, including simple deterministic features, morphological features, POS features and semantic trigger features, to capture various evidences especially for biomedical named entity and evaluate their contributions. We also present a simple algorithm to solve the abbreviation problem and a rule-based method to deal with the cascaded phenomena in biomedical domain. Our experiments on GENIA V3.0 and GENIA V1.1 achieve the 66.1 and 62.5 F-measure respectively, which outperform the previous best published results by 8.1 F-measure when using the same training and testing data.