DICE: Data-Efficient Clinical Event Extraction with Generative Models

Abstract

Event extraction in the clinical domain is an under-explored research area. The lack of training data in addition to the high volume of domain-specific jargon that includes long entities with vague boundaries make the task especially challenging. In this paper, we introduce DICE, a robust and data-efficient generative model for clinical event extraction. DICE frames event extraction as a conditional generation problem and utilizes descriptions provided by domain experts to boost the performance under low-resource settings. Furthermore, DICE learns to locate and bound biomedical mentions with an auxiliary mention identification task trained jointly with event extraction tasks to leverage inter-task dependencies and further incorporates the identified mentions as trigger and argument candidates for their respective tasks. We also introduce MACCROBAT-EE, the first clinical event extraction dataset with event argument annotation. Our experiments demonstrate the robustness of DICE under low data settings for the clinical domain and the benefits of incorporating flexible joint training and mention markers into generative approaches.

Publication
arXiv