A two-stage model for unified sentence- and document-level biomedical event extraction

Biomedical event extraction, a cornerstone of information extraction, has increasingly attracted attention within the biomedical research community. Moreover, it is a highly complex task, which not only deals with many sub-tasks but also involves nested events. Currently, the research on biomedical event extraction, whether pipelined model or joint method, needs to be processed for each sub-task. The process of processing each sub-task one by one lead to the degradation of event extraction performance. In addition, most studies focus on extracting sentence-level events and ignore cross-sentence event information. To solve these problems, we simplify the process of event extraction, reduce the processing steps, and combine the two sub-tasks of relation extraction and argument combination as one sub-task. In addition, we consider document-level event extraction, which not only extracts cross-sentence events but also considers broader context information. Experimental results indicate that our novel approach outperforms prior studies. Additionally, the document-level event extraction model attains the top performance on the BioNLP’11 test data and achieves near-leading performance on the BioNLP’13 test data.