A stacked ensemble machine learning model for the prediction of pentavalent 3 vaccination dropout in East Africa

Vaccination is critical for reducing childhood mortality, yet completion rates for the third dose of the pentavalent vaccine (Penta 3) in East Africa remain inadequate. This study aims to predict Penta 3 vaccination dropout using a stacking ensemble machine learning model with Demographic and Health Survey (DHS) data. The objective is to identify predictors of dropout and enhance intervention strategies.

The study utilized seven base machine learning algorithms to create a stacked ensemble model with three meta-learners: Random Forest (RF), Generalized Linear Model (GLM), and Extreme Gradient Boosting (XGBoost). The H2O package facilitated the development of base learners and the stacking of super learners. Feature selection (FS) and comparisons were performed using the LASSO and Boruta algorithms. The selected features were one-hot encoded, and ordinal encoding was applied where appropriate. Hyperparameter optimization (HPO) and comparisons were conducted using grid search and random search. Model performance was assessed using five key metrics, including accuracy and the area under the curve (AUC). SHAP (Shapley Additive Explanations) values were used to interpret the model outputs and identify influential predictors. The experimental design was employed to present the results.

Four experiments were conducted to evaluate feature selection and HPO methods. All stacked ensemble models outperformed individual learners, with the XGBoost meta-learner optimized with grid search and LASSO FS achieving the highest performance: 93.9% accuracy and 99.4% AUC. While RF and GLM meta-learners were also evaluated, they were outperformed by the XGBoost meta-learner. SHAP analysis revealed key features influencing Penta 3 dropout, including the place of delivery, decision-making autonomy, the mother's level of earning, and healthcare access. Home delivery increased the risk of dropout, while postnatal care by midwives and health insurance coverage lowered dropout likelihood.

This study provides insights into the factors influencing Penta 3 vaccination dropout in East Africa. To reduce dropout rates, interventions should focus on enhancing maternal livelihood opportunities, improving healthcare access in rural areas, and promoting institutional deliveries.