KDClassifier: A urinary proteomic spectra analysis tool based on machine learning for the classification of kidney diseases

Abstract

Background: We aimed to establish a novel diagnostic model for kidney diseases by combining artificial intelligence with complete mass spectrum information from urinary proteomics.

Methods: We enrolled 134 patients (IgA nephropathy, membranous nephropathy, and diabetic kidney disease) and 68 healthy participants as controls, with a total of 610,102 mass spectra from their urinary proteomic profiles. The training data set (80%) was used to create a diagnostic model using XGBoost, random forest (RF), a support vector machine (SVM), and artificial neural networks (ANNs). The diagnostic accuracy was evaluated using a confusion matrix with a test dataset (20%). We also constructed receiver operating-characteristic, Lorenz, and gain curves to evaluate the diagnostic model.

Results: Compared with the RF, SVM, and ANNs, the modified XGBoost model, called Kidney Disease Classifier (KDClassifier), showed the best performance. The accuracy of the XGBoost diagnostic model was 96.03%. The area under the curve of the extreme gradient boosting (XGBoost) model was 0.952 (95% confidence interval, 0.9307–0.9733). The Kolmogorov-Smirnov (KS) value of the Lorenz curve was 0.8514. The Lorenz and gain curves showed the strong robustness of the developed model.

Conclusion: The KDClassifier achieved high accuracy and robustness and thus provides a potential tool for the classification of kidney diseases.

Keywords: Kidney disease classification, urinary proteomics, machine learning algorithm, diagnosis, artificial intelligence