A conditional random fields approach to biomedical named entity recognition

Named entity recognition is a fundamental task in biomedical data mining. In this letter, a named entity recognition system based on CRFs (Conditional Random Fields) for biomedical texts is presented. The system makes extensive use of a diverse set of features, including local features, full text features and external resource features. All features incorporated in this system are described in detail, and the impacts of different feature sets on the performance of the system are evaluated. In order to improve the performance of system, post-processing modules are exploited to deal with the abbreviation phenomena, cascaded named entity and boundary errors identification. Evaluation on this system proved that the feature selection has important impact on the system performance, and the post-processing explored has an important contribution on system performance to achieve better results.