用开放信息抽取构建肺癌知识库,提升大模型医学推理能力
Scalable Construction of a Lung Cancer Knowledge Base: Profiling Semantic Reasoning in LLMs
- 通过医学术语表+开源文献提取三元组,自动构建肺癌知识库
- 微调后的T5模型在语义任务中表现更优,ROUGE和BERTScore双提升
- 适合需要低成本高质量医学数据的AI研究者使用
将大语言模型(LLMs)引入生物医学研究,为特定领域推理与知识表示带来新机遇。然而其性能高度依赖训练数据的语义质量。在癌症领域,精准性与可解释性至关重要,因此构建可扩展的结构化知识库对有效微调至关重要。本研究提出一种基于开放信息抽取(OpenIE)的肺癌知识库构建流程:(1) 使用MeSH术语表识别医学概念;(2) 筛选具有宽松许可协议(CC0)的开放获取PubMed文献;(3) 采用OpenIE方法提取(主体,关系,客体)三元组;(4) 通过命名实体识别(NER)增强三元组的生物医学相关性。最终生成的三元组集合构成一个领域专用、大规模且具备噪声感知能力的资源,可用于微调大语言模型。我们评估了在该数据集上微调的T5模型,通过监督语义微调进行测试。与基准相比,使用ROUGE和BERTScore进行的对比评估显示性能显著提升,语义一致性增强,证明了基于OpenIE的数据资源是提升生物医学自然语言处理的可扩展、低成本解决方案。
原文摘要 · Abstract (English)
The integration of Large Language Models (LLMs) into biomedical research offers new opportunities for domainspecific reasoning and knowledge representation. However, their performance depends heavily on the semantic quality of training data. In oncology, where precision and interpretability are vital, scalable methods for constructing structured knowledge bases are essential for effective fine-tuning. This study presents a pipeline for developing a lung cancer knowledge base using Open Information Extraction (OpenIE). The process includes: (1) identifying medical concepts with the MeSH thesaurus; (2) filtering open-access PubMed literature with permissive licenses (CC0); (3) extracting (subject, relation, object) triplets using OpenIE method; and (4) enriching triplet sets with Named Entity Recognition (NER) to ensure biomedical relevance. The resulting triplet sets provide a domain-specific, large-scale, and noise-aware resource for fine-tuning LLMs. We evaluated T5 models finetuned on this dataset through Supervised Semantic Fine-Tuning. Comparative assessments with ROUGE and BERTScore show significantly improved performance and semantic coherence, demonstrating the potential of OpenIE-derived resources as scalable, low-cost solutions for enhancing biomedical NLP.
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