Climate-Informed and Explainable Imbalance-Aware Machine Learning for Rift Valley Fever Outbreak Prediction in Kenya

Rift Valley fever (RVF) is a vector-borne zoonotic disease whose occurrence is strongly associated with climatic and environmental conditions, making data-driven approaches potentially valuable for epidemiological surveillance and risk assessment. Using a publicly available historical dataset comprising 180,288 monthly observations from geographically defined administrative units across Kenya between 1981 and 2010, this study investigates machine learning (ML) for the retrospective classification of reported RVF occurrence from contemporaneous climatic, environmental, topographic, and seasonal predictors under an extremely imbalanced classification setting. The dataset provides broad geographic coverage across Kenya over a 30-year historical period; however, because the outcome reflects reported events in historical surveillance records, it is not assumed to constitute a formally population-representative national sample or to capture all underlying RVF transmission. Each observation represents a geographic unit and observation month, and the response indicates whether an RVF event was reported during that corresponding period. Therefore, the present analysis should be interpreted as contemporaneous outbreak classification rather than as a fixed-horizon prospective forecast. Thirteen classifiers representing distinct learning paradigms were systematically evaluated: Logistic Regression, Linear Discriminant Analysis, K-Nearest Neighbors, Classification and Regression Tree, Naive Bayes, Support Vector Machine, Weighted Logistic Regression, XGBoost, LightGBM, CatBoost, Balanced Random Forest, EasyEnsemble, and RUSBoost. Model performance was assessed before and after SMOTENC-based rebalancing using overall and class-specific metrics, including accuracy, precision, sensitivity, specificity, F1-score, ROC–AUC, and precision–recall-based measures. Under the retrospective stratified hold-out benchmark, XGBoost, CatBoost, Balanced Random Forest, and LightGBM achieved ROC–AUC values of 0.9176, 0.9175, 0.9114, and 0.9062, respectively. Balanced Random Forest attained the highest outbreak sensitivity (0.8851), although at the cost of very low precision, illustrating that high rare-event detection can generate a substantial false-alert burden in surveillance settings. SMOTENC produced strongly model-dependent effects: it increased outbreak sensitivity for XGBoost, LightGBM, CatBoost, KNN, CART, and RUSBoost, but substantially reduced sensitivity for Balanced Random Forest and EasyEnsemble. SHAP-based interpretability analysis indicated that month, rainfall, and slope were among the most influential predictors and further showed that class rebalancing can alter the distribution of feature contributions. Overall, the findings demonstrate that modeling reported RVF occurrence under severe class imbalance requires joint evaluation of minority-class detection, false-positive behavior, discrimination, and model interpretability rather than overall accuracy alone. The present results establish a retrospective classification benchmark for climate-informed RVF risk assessment, but they should not be interpreted as an autonomous outbreak-warning system. Translation into prospective early-warning prediction will require an explicit forecasting horizon, predictors constructed exclusively from information available before the target period, temporally and geographically independent validation, and decision thresholds evaluated against an operationally acceptable false-alert burden.