arXiv:2510.09159cs.LGcs.AI2025-10被引 4

首个系统性对比EHR数据表示方法的基准,助力临床预测模型选型。

Cross-Representation Benchmarking in Time-Series Electronic Health Records for Clinical Outcome Prediction

  • 构建统一框架,对比时序、事件流与文本流三种数据表示方法。
  • 事件流模型表现最佳,预训练模型在小样本下更具优势。
  • 特征剪枝策略需依临床场景调整:重症用删稀疏特征,长期随访则保留。

电子健康记录(EHR)为临床预测提供了深度学习基础,但最优数据表示方法仍不明确,主要因评估方式不一致。本文首次系统性地构建了跨表示范式的基准,涵盖多变量时间序列、事件流及面向大语言模型(LLM)的文本事件流。该基准在两个不同临床场景中标准化数据处理与评估:使用MIMIC-IV数据集进行重症监护任务(死亡率、表型分类),以及使用EHRSHOT数据集进行长期照护任务(30天再入院、1年胰腺癌)。针对每种范式,评估相应建模范式——时间序列采用Transformer、MLP、LSTM和Retain;事件流采用CLMBR与计数模型;文本流采用8-20B规模的大语言模型。同时分析基于数据缺失情况的特征剪枝影响。实验表明,事件流模型始终表现最优。预训练模型如CLMBR在少样本设置下具有高样本效率,而足够数据下简单计数模型也能具备竞争力。此外,特征选择策略需适配临床场景:在重症任务中剪除稀疏特征可提升性能,而在长期任务中保留这些特征至关重要。研究结果依托统一且可复现的流程,为基于临床背景与数据条件选择合适表示方法提供实用指导。

原文摘要 · Abstract (English)

Electronic Health Records (EHRs) enable deep learning for clinical predictions, but the optimal method for representing patient data remains unclear due to inconsistent evaluation practices. We present the first systematic benchmark to compare EHR representation methods, including multivariate time-series, event streams, and textual event streams for LLMs. This benchmark standardises data curation and evaluation across two distinct clinical settings: the MIMIC-IV dataset for ICU tasks (mortality, phenotyping) and the EHRSHOT dataset for longitudinal care (30-day readmission, 1-year pancreatic cancer). For each paradigm, we evaluate appropriate modelling families--including Transformers, MLP, LSTMs and Retain for time-series, CLMBR and count-based models for event streams, 8-20B LLMs for textual streams--and analyse the impact of feature pruning based on data missingness. Our experiments reveal that event stream models consistently deliver the strongest performance. Pre-trained models like CLMBR are highly sample-efficient in few-shot settings, though simpler count-based models can be competitive given sufficient data. Furthermore, we find that feature selection strategies must be adapted to the clinical setting: pruning sparse features improves ICU predictions, while retaining them is critical for longitudinal tasks. Our results, enabled by a unified and reproducible pipeline, provide practical guidance for selecting EHR representations based on the clinical context and data regime.

EHR建模临床预测事件流基准测试

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