arXiv:2511.11935cs.LG2025-11被引 1

统一多模态电子病历生存分析预处理流程,提升模型可比性。

SurvBench: A Standardised Preprocessing Pipeline for Multi-Modal Electronic Health Record Survival Analysis

  • 基于YAML配置的标准化预处理流水线,覆盖四大数据库与四类数据模态。
  • 训练集内完成归一化与缺失值插补,缺失信息以二值掩码保留。
  • 支持单风险与竞争风险终点,适配跨数据集外部验证,助力公平比较。

深度学习在电子病历(EHR)生存分析中的模型难以横向比较,因其上游预处理步骤(如队列定义、时间离散化、缺失值处理和删失规则)通常未记录且不一致。报告的两种死亡率模型之间差异可能源于这些选择而非建模贡献。本文提出SurvBench,一个开源预处理流水线,将原始PhysioNet数据转化为适用于生存分析的张量。该工具覆盖四个重症监护数据库(MIMIC-IV、eICU、MC-MED、HiRID)和四种输入模态:时序生命体征与检验值、静态人口统计学特征、国际疾病分类(ICD)编码、放射科报告嵌入。所有预处理决策通过YAML配置控制。插补、缩放与特征筛选仅在训练集上拟合,缺失情况以二值掩码形式保留在每项特征张量中。支持单风险终点(院内与ICU死亡率)和竞争风险终点(三类急诊科入院路径,回家出院视为行政删失)。同时提供eICU与MIMIC-IV间标准化跨数据集外部验证支持。SurvBench已公开于https://github.com/munibmesinovic/SurvBench,为未来深度学习EHR生存研究(尤其是新兴多模态方法)提供统一基准。

原文摘要 · Abstract (English)

Deep-learning survival models for electronic health record (EHR) data are hard to compare across papers because the upstream preprocessing step, which includes cohort definition, time discretisation, missingness handling, and censoring rules, is typically undocumented and inconsistent. A reported difference in concordance between two mortality models can therefore reflect any of these choices rather than a modelling contribution. We present SurvBench, an open-source preprocessing pipeline that converts raw PhysioNet exports into model-ready tensors for survival analysis. SurvBench covers four critical-care databases (MIMIC-IV, eICU, MC-MED, HiRID) and four input modalities: time-series vitals and laboratory values, static demographics, International Classification of Diseases (ICD) codes, and radiology report embeddings. Every preprocessing decision is controlled through YAML configuration. Imputation, scaling, and feature filtering are fit on the training fold only. Missingness is recorded as a binary mask alongside each feature tensor. The pipeline handles single-risk endpoints (in-hospital and in-ICU mortality) and competing-risks endpoints (a three-way emergency-department admission pathway, with home discharge treated as administrative censoring). We also provide support for harmonised cross-dataset external validation between eICU and MIMIC-IV. SurvBench is publicly available at https://github.com/munibmesinovic/SurvBench, providing a robust platform that future deep-learning EHR survival work, especially nascent multi-modal approaches, can be measured against under matched preprocessing.

电子病历生存分析多模态预处理

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