CACER:临床概念 癌症事件和关系的注释
Yujuan Velvin Fu1, Giridhar Kaushik Ramachandran2, Ahmad Halwani3
1Department of Biomedical Informatics & Medical Education, University of Washington, Seattle, WA 98195, United States.
我们开发了临床概念癌症事件和关系注释 (CACER) 语料库,从临床笔记中提取癌症药物和医疗问题关系. 微调的变压器模型实现了高性能,在信息提取任务中表现优于GPT-4.
科学领域:
- 在瘤学中的自然语言处理.
- 生物医学信息学 生物医学信息学
- 临床数据挖掘 临床数据挖掘
背景情况:
- 临床笔记包含非结构化的患者病史,包括医疗问题和处方药之间的关系.
- 提取结构化的语义表示对于理解癌症患者的药物问题关联和症状负担至关重要.
研究的目的:
- 通过从瘤学笔记中提取结构化信息来调查癌症药物及其相关症状负担之间的关系.
- 开发和评估基于变压器的信息提取模型,使用新的注释体.
主要方法:
- 创建了临床概念"癌症事件和关系的注释" (CACER) 库,其中有超过48,000个医学问题和药物事件的注释,以及10,000个关系.
- 开发和评估变压器模型,包括从变压器 (BERT) 的双向编码器表示,微调语言净文本到文本传输变压器 (Flan-T5),大型语言模型MetaAI (Llama3) 和生成预训练变压器-4 (GPT-4) 的变压器模型.
- 使用微调和上下文学习 (ICL) 方法进行模型评估.
主要成果:
- 微调的BERT和Llama3模型在事件提取 (88.2-88.0 F1) 中获得了最高的性能,相当于注释器间协议 (88.4 F1).
- 微调的BERT,Flan-T5和Llama3模型在关系提取方面表现最高 (61.8-65.3 F1).
- 在事件和关系提取任务中,ICL的GPT-4表现最差.
结论:
- 微调模型显著优于ICL的GPT-4,强调了注释数据和模型优化的价值.
- 伯特模型的性能与Llama3相似,这表明在这个特定任务中,更大的语言模型没有显著的优势.
- CACER集体和评估模型为从瘤学临床叙述中提取结构化信息提供了基础.
更多相关视频
07:49Global and Current Research Trends of Single-Cell Sequencing in Cancer: A Bibliometric and Visualization Study
Published on: April 18, 2025
07:47Author Spotlight: Unveiling Transmembrane Protein Family-Related Markers in Gastric Cancer and Implications for Targeted Therapies
Published on: September 15, 2023
相关概念视频
Cancer Survival Analysis
What is Cancer?
Although people have known about cancer for centuries, it was only in 1761 that Giovanni Morgagni of Padua performed a detailed autopsy of...
Cancer-Critical Genes I: Proto-oncogenes
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
Adaptive Mechanisms in Cancer Cells
Some of the advantages that cancer cells have on normal cells include - enhanced ability to divide without terminally differentiating, induce new blood vessel formation,...
Cancer-Critical Genes II: Tumor Suppressor Genes
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
Targeted Cancer Therapies
There are several types of targeted therapies against...
