Using deep learning to recognize biomedical entities

Abstract

With the rapid growth of the high-throughput biological technology, it brings biomedical big omics' data containing literature and annotated data. Especially, a wealth of relevant information exists in various types of biomedical literature. Text mining has emerged as a potential solution to achieve knowledge for bridging between the free text and structured representation of biomedical information. In this work, we used deep learning to recognize biomedical entities. We obtained 84.0% precision, 69.5% recall, and 76.1% F-score aiming at the GENIA corpus, and obtained 91.3% precision, 91.1% recall, and 91.2% F-score aiming at the BioCreAtIvE II Gene Mention corpus. Experimental results show that our proposed approach is promising for developing biomedical text mining technology in biomedical entity recognition.