从生物医学BERT模型中嵌入的参数知识中预测药物副作用关系:使用自然语言处理方法进行方法学研究
Woohyuk Jeon1, Minjae Park1, Doyeon An1
1Department of Computer Engineering, College of IT Convergence, Gachon University, AI·Engineering Building, 317A, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do, Seongnam, 13120, Republic of Korea, 82 010-9012-9364, 82 031-750-5333.
JMIR medical informatics
|July 10, 2025
概括
这项研究引入了一种使用生物医学BERT模型来预测未知的药物副作用关系的新方法,其性能优于传统模型. 该方法在管理药物不良反应方面表现出高准确性和实际适用性.
科学领域:
- 生物医学信息学 生物医学信息学
- 自然语言处理自然语言处理.
- 药物监督 药物监督 药物监督
背景情况:
- 药物不良反应 (ADR) 对患者健康构成重大风险.
- 传统的词嵌入模型,如Word2Vec与生物医学文本特异性作斗争.
- 伯特模型显示出有希望的结果,但需要进一步的研究来预测未知的药物副作用关系.
研究的目的:
- 用生物医学BERT模型的参数知识来预测新的药物副作用关系.
- 为了提高预测,利用已知的关系的嵌入向量相似性来提高预测.
- 识别潜在的药物副作用候选者,其因果机制未知.
主要方法:
- 利用来自SIDER数据库的158,096种药物副作用对来创建一个相邻矩阵.
- 计算了药物和副作用词嵌入矢量之间的共弦相似性.
- 计算了8,235,435种药物副作用对的关系得分,并使用曲线下的面积 (AUC) 进行评估.
主要成果:
- 在clagator/biobert_v1.1模型中,AUC达到0.915,超过了Word2Vec (AUC为0.848).
- 在生物医学体上预训练的BERT模型表现优于香草BERT (AUC 0.857).
- 外部验证与FDA不良事件报告系统数据显示高统计意义 (P<.001,OR=4.822).
结论:
- 使用预训练的生物医学语言模型开发了一种用于预测药物副作用关系的新方法.
- 基于BERT的模型优秀地预测药物副作用关系,这是由于上下文理解.
- 该方法证明了预测和管理ADR的实际实用性.
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