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基于转换器模型的临床记录中药物提及和药物变更事件的检测。

Detection of Medication Mentions and Medication Change Events in Clinical Notes Using Transformer-Based Models.

机构信息

Department of Biomedical Informatics, School of Medicine, Emory University, Atlanta, United States.

出版信息

Stud Health Technol Inform. 2024 Jan 25;310:685-689. doi: 10.3233/SHTI231052.

Abstract

In this paper, we address the related tasks of medication extraction, event classification, and context classification from clinical text. The data for the tasks were obtained from the National Natural Language Processing (NLP) Clinical Challenges (n2c2) Track 1. We developed a named entity recognition (NER) model based on BioClinicalBERT and applied a dictionary-based fuzzy matching mechanism to identify the medication mentions in clinical notes. We developed a unified model architecture for event classification and context classification. The model used two pre-trained models-BioClinicalBERT and RoBERTa to predict the class, separately. Additionally, we applied an ensemble mechanism to combine the predictions of BioClinicalBERT and RoBERTa. For event classification, our best model achieved 0.926 micro-averaged F1-score, 5% higher than the baseline model. The shared task released the data in different stages during the evaluation phase. Our system consistently ranked among the top 10 for Releases 1 and 2.

摘要

在本文中,我们解决了从临床文本中提取药物、事件分类和上下文分类的相关任务。这些任务的数据来自国家自然语言处理(NLP)临床挑战(n2c2)赛道 1。我们开发了一个基于 BioClinicalBERT 的命名实体识别(NER)模型,并应用基于字典的模糊匹配机制来识别临床记录中的药物提及。我们为事件分类和上下文分类开发了一个统一的模型架构。该模型使用两个预训练模型-BioClinicalBERT 和 RoBERTa 分别预测类别。此外,我们应用了集成机制来结合 BioClinicalBERT 和 RoBERTa 的预测结果。对于事件分类,我们最好的模型在微平均 F1 分数上达到了 0.926,比基线模型高出 5%。共享任务在评估阶段的不同阶段发布数据。我们的系统在发布 1 和发布 2 中始终排在前 10 名。

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