Performance Evaluation of Classification Methods Utilizing Resampling Techniques for Water Quality Prediction on Imbalanced Data
Rahmi Fadhilah, Heri Kuswanto, Dedy Dwi Prastyo · Engineering Technology & Applied Science Research · 2025
Commonly observed challenges in water quality anomaly detection using Machine Learning (ML) classifiers include unbalanced class distribution and missing data. Classifiers trained on such imbalanced datasets often exhibit biased accuracy, favoring the majority class and neglecting the minority class, while incomplete datasets limit the applicability of more complex models and hinder thorough analysis. This research addresses the handling of incomplete data and class imbalance by proposing a robust framework for an ML-based water quality anomaly detection system using several resampling techniques. A comparative study was conducted on six imputation methods for missing data, including Expectation Maximization (EM) and Multiple Imputation by Chained Equations (MICE), alongside three resampling techniques: Random Under Sampling (RUS), Rapidly Converging Gibbs (RACOG) sampler, and RACOG combined with RUS (RACOG-RUS). These methods were evaluated across three classifiers: Random Forest (RF), Extreme Gradient Boosting (XGBoost), and Naïve Bayes (NB). The models were assessed using stratified 5-fold cross-validation and evaluated based on accuracy, Receiver Operating Characteristic Area Under Curve (ROC-AUC), and F1-score. Further experiments incorporated feature selection methods such as Boruta and Mean Decrease Accuracy (MDA) to optimize performance. Results demonstrate that RF combined with RACOG-RUS and EM achieved the highest F1-score of 0.9954, effectively addressing both class imbalance and missing data. Additionally, computational analysis highlights the efficiency of RF when optimized with appropriate hyperparameters.