An Improved Biomedical Event Trigger Identification Framework Via Modeling Document With Hierarchical Attention

Biomedical event extraction has wide applications in biomedicine field. As a prerequisite step in biomedical event extraction, event trigger identification has attracted growing attention in biomedical research. Although many approaches have been proposed for biomedical event trigger identification, two main challenges still remain for researchers: 1) most of the existing approaches treat each sentence separately in biomedical documents, failing to make full use of the semantics in the global document context; 2) the sparseness of event triggers leads to a serious issue of imbalanced class for trigger identification. In this paper, we propose an end-to-end framework for biomedical event trigger identification which addresses effectively the two mentioned challenges accordingly. Specifically, a hierarchical attention mechanism is used to model the global document context, including the semantic relationships both among words in the same sentence and among sentences in the same document. In addition, an adaptive class weight learning method is proposed to treat the class imbalance issue in biomedical event trigger identification. Experimental results on two commonly used datasets demonstrate the effectiveness of the proposed framework.