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

BACKGROUND: Machine learning (ML) techniques improve disease prediction by identifying the most relevant features in multidimensional 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 y 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/1.73 m(2) with at least 25% decrease in eGFR at follow-up from baseline. A total of 339 features, including participant characteristics, retinal imaging, and genetic and blood metabolites, were used as predictors. Performances of several ML models were compared to each other and to logistic 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% CI) 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 that ML, together with feature selection, improves prediction accuracy of DKD risk in an asymptomatic stable population and identifies novel risk factors, including metabolites. FUNDING: This study was supported by the National Medical Research Council, NMRC/OFLCG/001/2017 and NMRC/HCSAINV/MOH-001019-00. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.