arXiv:2501.05155cs.CLcs.AI2025-01被引 6

用大模型生成数据并跨文档映射关系,提升生物医学文本的长距离关系抽取效果。

Biomedical Relation Extraction via Adaptive Document-Relation Cross-Mapping and Concept Unique Identifier

  • 通过迭代提示生成关系专用合成数据,缓解标注数据稀缺问题。
  • 设计跨文档-关系交叉映射微调,增强模型跨句推理能力。
  • 利用实体唯一标识符检索增强生成,精准丰富上下文信息,适合医学知识挖掘者。

文档级生物医学关系抽取(Bio-RE)旨在从长篇文献中识别生物实体间的关系,是生物医学文本挖掘的关键任务。现有方法在跨句推理上表现不佳,且常忽略文档不完整性,缺乏外部知识融合,限制了上下文理解。此外,标注数据稀缺也制约模型训练。受大语言模型(LLM)进展启发,本文提出基于自适应文档-关系交叉映射(ADRCM)微调与概念唯一标识符(CUI)检索增强生成(RAG)的框架。首先,设计迭代式关系摘要(IoRs)提示,引导ChatGPT生成特定于生物医学关系的合成数据,以缓解数据不足。其次,提出ADRCM微调方法,建立文档与关系间的跨层映射,强化模型上下文理解与跨句推理能力。最后,在推理阶段引入针对生物医学场景的RAG方法——CUI RAG,以CUI为实体索引缩小检索范围,提升相关上下文的丰富性。在GDA、CDR和BioRED三个数据集上的实验表明,该方法性能达到当前最优水平。

原文摘要 · Abstract (English)

Document-Level Biomedical Relation Extraction (Bio-RE) aims to identify relations between biomedical entities within extensive texts, serving as a crucial subfield of biomedical text mining. Existing Bio-RE methods struggle with cross-sentence inference, which is essential for capturing relations spanning multiple sentences. Moreover, previous methods often overlook the incompleteness of documents and lack the integration of external knowledge, limiting contextual richness. Besides, the scarcity of annotated data further hampers model training. Recent advancements in large language models (LLMs) have inspired us to explore all the above issues for document-level Bio-RE. Specifically, we propose a document-level Bio-RE framework via LLM Adaptive Document-Relation Cross-Mapping (ADRCM) Fine-Tuning and Concept Unique Identifier (CUI) Retrieval-Augmented Generation (RAG). First, we introduce the Iteration-of-REsummary (IoRs) prompt for solving the data scarcity issue. In this way, Bio-RE task-specific synthetic data can be generated by guiding ChatGPT to focus on entity relations and iteratively refining synthetic data. Next, we propose ADRCM fine-tuning, a novel fine-tuning recipe that establishes mappings across different documents and relations, enhancing the model's contextual understanding and cross-sentence inference capabilities. Finally, during the inference, a biomedical-specific RAG approach, named CUI RAG, is designed to leverage CUIs as indexes for entities, narrowing the retrieval scope and enriching the relevant document contexts. Experiments conducted on three Bio-RE datasets (GDA, CDR, and BioRED) demonstrate the state-of-the-art performance of our proposed method by comparing it with other related works.

生物医学关系抽取大模型知识增强

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