用于识别和规范连续和不连续的表型提及的生成模型和句子转换器:模型开发和评估
Areej Alhassan1,2, Viktor Schlegel1,3, Monira Aloud2
1Department of Computer Science, School of Engineering, University of Manchester, Manchester, United Kingdom.
JMIR medical informatics
|November 5, 2025
概括
这项研究介绍了DiscHPO,这是一种从临床笔记中提取遗传表型的系统. 它有效地使连续和不连续的提及正常化,改善了个性化医疗保健中的遗传状况表示.
科学领域:
- 生物信息学和计算生物学
- 医疗信息学 医疗信息学
- 遗传学和基因组学 在
背景情况:
- 从临床报告中准确地提取和规范化遗传表型,对于理解遗传病症和推进个性化医疗保健至关重要.
- 在临床文本中识别不连续实体跨度存在挑战,这阻碍了精确的数据解释.
- 异形态学严重依赖于准确的表型表示用于诊断和研究.
研究的目的:
- 开发一个系统 (DiscHPO) 来准确地从临床检查报告中提取和规范化遗传表型.
- 专门解决在异形态评估中识别和规范不连续实体跨度的挑战.
- 通过增强的表型识别,改善个性化医学中遗传疾病的表现.
主要方法:
- 采用了双相管道方法,从跨度命名实体识别 (NER) 的序列到序列模型开始.
- 实体规范化阶段使用句子转换器双编码器进行候选生成,并使用交叉编码器重排列器进行概念选择.
- 该系统在BioCreative VIII共享任务,轨道3的背景下进行了评估.
主要成果:
- 性能最好的规范化模型在测试组件上获得了F1得分0.723,最好的跨度提取模型在测试组件上获得了F1得分0.665.
- 这两种模型的表现都超过了基线方法,证明了在处理连续和不连续跨度时的有效性.
- 在验证组中,该系统在不连续跨度上获得了0.631的F1得分,对不连续跨度的准确匹配.
结论:
- 对实体跨度的准确提取并不总是成功的表型规范化所需的.
- 捕捉基本概念信息的部分提及匹配对于临床实用性来说足够了.
- 在下游临床应用中,DiscHPO系统对需要准确的遗传表型数据的临床应用非常有希望.
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