arXiv:2408.06583v1 Announce Type: new
Abstract: Biomedical Event Extraction (BEE) is a critical task that involves modeling complex relationships between fine-grained entities in biomedical text data. However, most existing BEE models rely on classification methods that neglect the label semantics and argument dependency structure within the data. To address these limitations, we propose GenBEE, a generative model enhanced with a structure-aware prefix for biomedical event extraction. GenBEE constructs event prompts that leverage knowledge distilled from large language models (LLMs), thereby incorporating both label semantics and argument dependency relationships. Additionally, GenBEE introduces a structural prefix learning module that generates structure-aware prefixes with structural prompts, enriching the generation process with structural features. Extensive experiments on three benchmark datasets demonstrate the effectiveness of GenBEE and it achieves state-of-the-art performance on the MLEE and GE11 datasets. Furthermore, our analysis shows that the structural prefixes effectively bridge the gap between structural prompts and the representation space of generative models, enabling better integration of event structural information.
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