Ensemble-Based Imputation for Handling Missing Values in Healthcare Datasets: A Comparative Study of Machine Learning Models

This study addresses the challenge of missing numerical values in healthcare datasets by proposing a Particle Swarm Optimization (PSO)-optimized stacking ensemble model for data imputation. The framework combines Random Forest, XGBoost, and Linear Regression within a stacking architecture, with PSO used to optimize model selection and hyperparameters for improved accuracy. The approach was evaluated on the Breast Cancer Wisconsin and Heart Disease datasets under Missing Completely at Random (MCAR) conditions at 30%, 20%, and 10% missingness levels, using RMSE, MAE, R2, and processing time as performance metrics. Experimental results show that the proposed model consistently outperforms individual learners across all missingness scenarios, achieving an RMSE of 0.0446, MAE of 0.0303, and R2 of 86.56% on the Breast Cancer dataset at 10% MCAR, and an RMSE of 0.1388 with an R2 of 75.19% on the Heart Disease dataset. Compared with a MissForest-based existing approach, the proposed framework demonstrates substantial reductions in imputation error, confirming the effectiveness of combining ensemble learning with evolutionary optimization. Although the PSO-based stacking model incurs higher computational cost, the findings indicate that it provides a robust, accurate, and generalizable solution for numerical data imputation in healthcare applications under varying levels of missingness.