Detecting the impact of subject characteristics on machine learning-based diagnostic applications

• Published in: NPJ digital medicine 2019-10, Vol.2 (1), p.99-99, Article 99
• Main Authors: Chaibub Neto, Elias, Pratap, Abhishek, Perumal, Thanneer M., Tummalacherla, Meghasyam, Snyder, Phil, Bot, Brian M., Trister, Andrew D., Friend, Stephen H., Mangravite, Lara, Omberg, Larsson
• Format: Article
• Language: English
• Subjects: 639/705/531; 692/308/2778; Biomedicine; Biotechnology; Digital technology; Health informatics; Machine learning; Medical diagnosis; Medicine; Medicine & Public Health
• ISSN: 2398-6352; 2398-6352
• DOI: 10.1038/s41746-019-0178-x

Collection of high-dimensional, longitudinal digital health data has the potential to support a wide-variety of research and clinical applications including diagnostics and longitudinal health tracking. Algorithms that process these data and inform digital diagnostics are typically developed using training and test sets generated from multiple repeated measures collected across a set of individuals. However, the inclusion of repeated measurements is not always appropriately taken into account in the analytical evaluations of predictive performance. The assignment of repeated measurements from each individual to both the training and the test sets (“record-wise” data split) is a common practice and can lead to massive underestimation of the prediction error due to the presence of “identity confounding.” In essence, these models learn to identify subjects, in addition to diagnostic signal. Here, we present a method that can be used to effectively calculate the amount of identity confounding learned by classifiers developed using a record-wise data split. By applying this method to several real datasets, we demonstrate that identity confounding is a serious issue in digital health studies and that record-wise data splits for machine learning- based applications need to be avoided.