论文标题
POPDX：英国生物银行研究中392,246个人的患者表型的自动框架
POPDx: An Automated Framework for Patient Phenotyping across 392,246 Individuals in the UK Biobank Study
论文作者
论文摘要
英国生物银行标准化表型代码的目的与住院的患者有关，但对于在门诊环境中仅接受过治疗的许多患者缺失。我们描述了一种表型识别方法，该方法为所有英国生物库参与者施加了表型代码。材料和方法POPDX（深度推断基于人群的客观表型）是双线性机器学习框架，用于同时估计1,538个表型代码的概率。我们从英国生物库中提取了392,246个人的表型和健康相关信息，以进行POPDX开发和评估。总共将12,803个ICD-10患者的诊断代码转换为1,538个phecodes，作为黄金标准标签。对POPDX框架进行了评估，并将其与自动多型识别的其他可用方法进行了比较。结果POPDX可以预测训练中罕见甚至未观察到的表型。我们证明了22种疾病类别的自动多型识别的实质性改善，及其在识别与每种表型相关的关键流行病学特征方面的应用。结论POPDX有助于为下游研究提供明确定义的队列。这是一种通用方法，可以应用于具有多种数据但不完整的其他生物库。
Objective For the UK Biobank standardized phenotype codes are associated with patients who have been hospitalized but are missing for many patients who have been treated exclusively in an outpatient setting. We describe a method for phenotype recognition that imputes phenotype codes for all UK Biobank participants. Materials and Methods POPDx (Population-based Objective Phenotyping by Deep Extrapolation) is a bilinear machine learning framework for simultaneously estimating the probabilities of 1,538 phenotype codes. We extracted phenotypic and health-related information of 392,246 individuals from the UK Biobank for POPDx development and evaluation. A total of 12,803 ICD-10 diagnosis codes of the patients were converted to 1,538 Phecodes as gold standard labels. The POPDx framework was evaluated and compared to other available methods on automated multi-phenotype recognition. Results POPDx can predict phenotypes that are rare or even unobserved in training. We demonstrate substantial improvement of automated multi-phenotype recognition across 22 disease categories, and its application in identifying key epidemiological features associated with each phenotype. Conclusions POPDx helps provide well-defined cohorts for downstream studies. It is a general purpose method that can be applied to other biobanks with diverse but incomplete data.
