Recognizing names in biomedical texts using mutual information independence model and SVM plus sigmoid》.pdf

International Journal of Medical Informatics (2006) 75, 456—467 Recognizing names in biomedical texts using mutual information independence model and SVM plus sigmoid G.D. Zhou ∗ Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore Received 15 April 2005; received in revised form 30 June 2005; accepted 30 June 2005 KEYWORDS Summary In this paper, we present a biomedical name recognition system, called Biomedical name PowerBioNE. In order to deal with the special phenomena in the biomedical domain, recognition; various evidential features are proposed and integrated through a mutual infor- Mutual information mation independence model (MIIM). In addition, a support vector machine (SVM) independence model; plus sigmoid is proposed to resolve the data sparseness problem in the MIIM. In Support vector machine this way, the data sparseness problem in MIIM-based biomedical name recognition can be resolved effectively and a biomedical name recognition system with bet- ter performance and better portability can be achieved. Finally, we present two post-processing modules to deal with the nested entity name and abbreviation phe- nomena in the biomedical domain to further improve the performance. Evaluation shows that our system achieves F-measures of 69.1 and 71.2 on the 23 classes of GENIA V1.1 and V3.0, respectively. In particular, our system achieves an F-measure of 77.8 on the ‘‘protein’’ class of GENIA V3.0. It also shows that our system outper-