Machine learning-based diagnostic prediction of minimal change disease: model development study

Abstract

Minimal change disease (MCD) is a common cause of nephrotic syndrome. Due to its rapid progression, early detection is essential; however, definitive diagnosis requires invasive kidney biopsy. This study aims to develop non-invasive predictive models for diagnosing MCD by machine learning. We retrospectively collected data on demographic characteristics, blood tests, and urine tests from patients with nephrotic syndrome who underwent kidney biopsy. We applied four machine learning algorithms—TabPFN, LightGBM, Random Forest, and Artificial Neural Network—and logistic regression. We compared their performance using stratified 5-repeated 5-fold cross-validation for the area under the receiver operating characteristic curve (AUROC) and the area under the precision-recall curve (AUPRC). Variable importance was evaluated using the SHapley Additive exPlanations (SHAP) method. A total of 248 patients were included, with 82 cases (33%) were diagnosed with MCD. TabPFN demonstrated the best performance with an AUROC of 0.915 (95% CI 0.896–0.932) and an AUPRC of 0.840 (95% CI 0.807–0.872). The SHAP methods identified C3, total cholesterol, and urine red blood cells as key predictors for TabPFN, consistent with previous reports. Machine learning models could be valuable non-invasive diagnostic tools for MCD.