Big Data Methods for Comprehensive Similarity based Risk Prediction

项目摘要 电子健康记录(EHR)提供了关于代表性人群的丰富数据来源，但尚未实现 充分利用，增强临床决策能力。临床决策启动中的常规方法 根据主题知识确定相关生物标记物，然后是详细但 仅使用这些生物标志物进行有限分析。正如目前的科学文献所表明的那样，许多人类 疾病具有复杂的病因学基础，并表现出相关的疾病进展。因此，它是 希望使用全面的患者数据来确定患者的相似性。这项提案的重点是推导出一个 目前完整的患者特征的患者相似度的综合综合评分 可用，包括但不限于：1)人口相似性；2)遗传相似性；3)临床表型 相似性；4)治疗相似性；以及5)曝光组相似性(这里曝光组被定义为所有可用的属性 一个人所处的生活环境)，当一些方面可能重叠并相互作用时。我们 将优化信息融合和基于任务的特征选择，以评估临床患者的相似性 风险预测。因为目前不存在能够提取完整可执行文件的管道 为了实现上述研究目标，我们建议首先提供一个开放的- 基于广泛使用的临床数据标准OMOP的源数据准备管道 (观察性医疗结果伙伴关系)公共数据模型(CMD)5.2版。此外，为了减轻 临床数据中常见的缺失和稀疏性挑战，我们描述了第一次尝试表示 患者遗漏的稀疏临床信息，包括诊断信息、用药数据、 治疗干预，具有固定长度的特征向量(即Patient2Vec)。这个项目有四个具体的 目标。目标1是开发一条临床数据处理流水线，用于协调来自多个 源转换为基于标准的统一数据表示，并评估其效率、互操作性、 和精确度。目标2是利用功能强大的机器学习技术Document2Vec 语言处理文献，创建一个开源的Patient2Vec框架，用于派生 患者信息丰富的数字表示法。目标3是开发一个统一的机器学习临床- 用于优化患者相似性融合的结果预测框架(OptPSF) 使用从Patient2Vec(目标2)导出的患者数字表示的医疗协变量以进行改进 临床风险预测。目标4是评估我们用于预测1)终末期风险的相似性框架 肾脏疾病(ESKD)在普通EHR患者群体中的分布和2)慢性高血压患者的死亡风险 肾病(CKD)。

Project Summary Electronic health records (EHR) provide rich source of data about representative populations and are yet to be fully utilized to enhance clinical decision-making. Conventional approaches in clinical decision-making start with the identification of relevant biomarkers based on subject-matter knowledge, followed by detailed but limited analysis using these biomarkers exclusively. As the current scientific literature indicates, many human disorders share a complex etiological basis and exhibit correlated disease progression. Therefore, it is desirable to use comprehensive patient data for patient similarity. This proposal focuses on deriving a comprehensive and integrated score of patient similarity from complete patient characteristics currently available, including but not limited to 1) demographic similarity; 2) genetic similarity; 3) clinical phenotype similarity; 4) treatment similarity; and 5) exposome similarity (here exposome defined as all available attributes of the living environment an individual is exposed to), when some of the aspects may overlap and interact. We will optimize information fusion and task-dependent feature selection for assessing patient similarity for clinical risk prediction. Since currently there does not exist a pipeline that is able to extract executable complete patient determinant data, to achieve the research goal described above, we propose first deliver an open- source data preparation pipeline that is based on a widely used clinical data standard, the OMOP (Observational Medical Outcomes Partnership) Common Data Model (CMD) version 5.2. Moreover, to mitigate common missingness and sparsity challenges in clinical data, we describe the first attempt to represent patients' sparse clinical information with missingness, including diagnosis information, medication data, treatment intervention, with a fixed-length feature vector (i.e. the Patient2Vec). This project has four specific aims. Aim 1 is to develop a clinical data processing pipeline for harmonizing patient information from multiple sources into a standards-based uniformed data representation and to evaluate its efficiency, interoperability, and accuracy. Aim 2 is to leverage a powerful machine learning technique, Document2Vec, from the natural language processing literature, to create an open-source Patient2Vec framework for the derivation of informative numerical representations of patients. Aim 3 is to develop a unified machine learning clinical- outcome-prediction framework for Optimized Patient Similarity Fusion (OptPSF) that integrates traditional medical covariates with the derived numerical patient representations from Patient2Vec (Aim 2) for improved clinical risk prediction. Aim 4 is to evaluate our similarity framework for predicting 1) the risk of end-stage kidney disease (ESKD) in general EHR patient population and 2) the risk of death among patients with chronic kidney disease (CKD).