用大模型少样本提取生物医学关系,效果优于传统方法。
Few-Shot Biomedical Relation Extraction with Large Language Models: A Viable Alternative to Supervised Learning?

- 用提示学习让大模型识别实体间关系,支持单次调用批量提取。
- 最佳模型微平均F1达0.44,远超此前少样本结果(0.34)。
- 对罕见关系类型表现更好,适合资源有限的生物医学研究。
生物医学关系抽取(BioRE)是将生物医学文献转化为结构化知识的关键步骤。现有方法多依赖昂贵标注数据的监督模型,限制了其在不同关系类型和领域中的可扩展性与适应性。本文探究基于大语言模型(LLM)的少样本生物医学关系抽取,对比两种任务范式:成对分类(预测单一实体对的关系)与联合生成(一次调用提取多个关系)。在BioREDirect数据集上的实验显示明显的精确率-召回率权衡:成对分类召回率更高,而联合生成更精准且计算效率更高。最佳模型取得0.44的微平均F1,显著优于以往少样本结果(0.34),但仍低于监督基线(0.56)。这一差距主要源于一种定义模糊的关系类型。在宏平均F1下,提示学习方法表现超越监督基线(0.45 vs. 0.38),尤其在稀有关系类型上优势明显。结果表明,大模型在低资源环境下具备生物医学关系抽取潜力,同时强调清晰关系定义的重要性。
原文摘要 · Abstract (English)
Biomedical relation extraction (BioRE) is a key step in transforming biomedical literature into structured knowledge. Most existing approaches rely on supervised models trained on costly annotated datasets, limiting their scalability and adaptability across relation types and domains. We investigate few-shot BioRE using prompt-based learning with large language models (LLMs) and compare two task formulations: pairwise classification, which predicts relations for individual entity pairs, and joint generation, which extracts multiple relations in a single model call. Experiments on the BioREDirect dataset reveal a clear precision-recall trade-off. Pairwise classification achieves higher recall, whereas joint generation is more precise and computationally efficient. The best-performing model achieves a micro-F1 score of 0.44, substantially outperforming previous few-shot results (0.34) while remaining below the supervised baseline (0.56). Much of this gap is attributable to a single ambiguously defined relation type. When evaluated using macro-F1, which better captures performance across relation types in an imbalanced setting, prompt-based approaches outperform the supervised baseline (0.45 vs. 0.38), particularly on rare relation types. These findings highlight the potential of LLMs for BioRE in low-resource settings and underscore the importance of well-defined relation schemas.
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