Prediction of diabetic kidney disease risk using machine learning models: a population-based cohort study of Asian adults

Abstract

Background: Machine learning (ML) techniques improve disease prediction by identifying the most relevant features in multi-dimensional data. We compared the accuracy of ML algorithms for predicting incident diabetic kidney disease (DKD). Methods: We utilized longitudinal data from 1365 Chinese, Malay and Indian participants aged 40-80 years with diabetes but free of DKD who participated in the baseline and 6-year follow-up visit of the Singapore Epidemiology of Eye Diseases Study (2004-2017). Incident DKD (11.9%) was defined as an estimated glomerular filtration rate (eGFR) <60 mL/min/1.73m2 with at least 25% decrease in eGFR at follow-up from baseline. 339 features including participant characteristics, retinal imaging, genetic and blood metabolites were used as predictors. Performances of several ML models were compared to each other and to logic regression (LR) model based on established features of DKD (age, sex, ethnicity, duration of diabetes, systolic blood pressure, HbA1c, and body mass index) using area under the receiver operating characteristic curve (AUC). Results: ML model, Elastic Net (EN) had the best AUC (95% confidence interval) of 0.851 (0.847-0.856), which was 7.0% relatively higher than by LR 0.795 (0.790-0.801). Sensitivity and specificity of EN were 88.2% and 65.9% vs. 73.0% and 72.8% by LR. The top-15 predictors included age, ethnicity, antidiabetic medication, hypertension, diabetic retinopathy, systolic blood pressure, HbA1c, eGFR and metabolites related to lipids, lipoproteins, fatty acids and ketone bodies. Conclusions: Our results showed ML together with feature selection improves prediction accuracy of DKD risk in an asymptomatic stable population and identifies novel risk factors including metabolites.