Biomedical document triage using a hierarchical attention-based capsule network

• Main Authors: Jian Wang, Mengying Li, Qishuai Diao, Hongfei Lin, Zhihao Yang, YiJia Zhang
• Format: Article
• Language: English
• Published: BMC 2020-09-01
• Series: BMC Bioinformatics
• Subjects: Biomedical document triage; Capsule network; Hierarchical attention mechanism; Biomedical literature
• Online Access: http://link.springer.com/article/10.1186/s12859-020-03673-5

Abstract Background Biomedical document triage is the foundation of biomedical information extraction, which is important to precision medicine. Recently, some neural networks-based methods have been proposed to classify biomedical documents automatically. In the biomedical domain, documents are often very long and often contain very complicated sentences. However, the current methods still find it difficult to capture important features across sentences. Results In this paper, we propose a hierarchical attention-based capsule model for biomedical document triage. The proposed model effectively employs hierarchical attention mechanism and capsule networks to capture valuable features across sentences and construct a final latent feature representation for a document. We evaluated our model on three public corpora. Conclusions Experimental results showed that both hierarchical attention mechanism and capsule networks are helpful in biomedical document triage task. Our method proved itself highly competitive or superior compared with other state-of-the-art methods.