Semantic Data Augmentation for Few-Shot Biomedical Named Entity Recognition

Abstract

Biomedical Named Entity Recognition (BioNER) aims to identify and classify entities in biomedical text. This task struggles with data scarcity due to limited annotated data. Although data augmentation is effective, existing methods fail to handle the complex semantic mappings on biomedical terminology, which results in the generated samples lacking semantic diversity. In this paper, we propose a data augmentation method to create semantically diverse and coherent training samples for few-shot BioNER. The method utilizes the Unified Medical Language System (UMLS) for entity replacement and combines with a Masked Language Model (MLM) to generate contextually relevant words. Experimental results show that our method improves BioNER performance in few-shot scenarios. Compared to all baseline models, our method achieves an average F1 score improvement of 7.6% and 11.6% on the NCBI and JNLPBA datasets, respectively. Our source code and data are available at https://github.com/ABC8184/SDA