Leveraging shortest dependency paths in low-resource biomedical relation extraction

Abstract

Background: Biomedical Relation Extraction (RE) is essential for uncovering complex relationships between biomedical entities within text. However, training RE classifiers is challenging in low-resource biomedical applications with few labeled examples. Methods: We explore the potential of Shortest Dependency Paths (SDPs) to aid biomedical RE, especially in situations with limited labeled examples. In this study, we suggest various approaches to employ SDPs when creating word and sentence representations under supervised, semi-supervised, and in-context-learning settings. Results: Through experiments on three benchmark biomedical text datasets, we find that incorporating SDP-based representations enhances the performance of RE classifiers. The improvement is especially notable when working with small amounts of labeled data. Conclusion: SDPs offer valuable insights into the complex sentence structure found in many biomedical text passages. Our study introduces several straightforward techniques that, as demonstrated experimentally, effectively enhance the accuracy of RE classifiers.