比较多种模型对长病历文本的表示能力,提升患者记录匹配精度
Comparing representations of long clinical texts for the task of patient note-identification
- 用BERT等模型处理长篇病历,结合多级池化策略生成患者级表示
- mean_max池化效果最佳,使患者匹配准确率显著提升
- 结果在MIMIC和尼科尔医院数据上均验证,适用于真实医疗场景
本文研究患者病历识别任务,即准确将匿名临床记录匹配到对应患者(由一组相关记录构成)。该任务广泛应用于重复记录检测与患者相似性分析,需构建稳健的患者级表示。我们对比了层次注意力网络(HAN)、三级层次变换器(HTN)、LongFormer及先进BERT模型在处理中长临床文本上的表现,并评估了均值、最大值及均值-最大值池化策略对词级嵌入聚合为患者级表示的效果,同时考察滑动窗口对模型性能的影响。结果表明,BERT基线模型在处理长文本和捕捉细微患者特征方面优于传统与层级模型;其中,mean_max池化始终表现最优,能有效提取关键临床信息。在MIMIC数据集与尼科尔医院数据仓库上的复现结果验证了方法的泛化能力,凸显嵌入方法与聚合策略对优化患者-病历匹配及患者建模的重要性。
原文摘要 · Abstract (English)
In this paper, we address the challenge of patient-note identification, which involves accurately matching an anonymized clinical note to its corresponding patient, represented by a set of related notes. This task has broad applications, including duplicate records detection and patient similarity analysis, which require robust patient-level representations. We explore various embedding methods, including Hierarchical Attention Networks (HAN), three-level Hierarchical Transformer Networks (HTN), LongFormer, and advanced BERT-based models, focusing on their ability to process mediumto-long clinical texts effectively. Additionally, we evaluate different pooling strategies (mean, max, and mean_max) for aggregating wordlevel embeddings into patient-level representations and we examine the impact of sliding windows on model performance. Our results indicate that BERT-based embeddings outperform traditional and hierarchical models, particularly in processing lengthy clinical notes and capturing nuanced patient representations. Among the pooling strategies, mean_max pooling consistently yields the best results, highlighting its ability to capture critical features from clinical notes. Furthermore, the reproduction of our results on both MIMIC dataset and Necker hospital data warehouse illustrates the generalizability of these approaches to real-world applications, emphasizing the importance of both embedding methods and aggregation strategies in optimizing patient-note identification and enhancing patient-level modeling.
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