Leakage-Safe Precision-Aware Dual-Branch FT-Transformer for Population-Scale Heart Disease Risk Prediction

Heart disease remains one of the leading causes of mortality worldwide, creating a strong need for reliable population-scale risk prediction models for large-scale screening and preventive monitoring. However, existing machine learning and deep learning approaches often struggle under severe class imbalance, data leakage risks, and unstable precision–recall trade-offs, limiting reliability in population-scale health-monitoring settings. To address these challenges, this study proposes a precision-aware Dual-Branch FT-Transformer framework for cardiovascular risk prediction using the BRFSS-2024 dataset. The proposed architecture separates recall-oriented detection and precision-oriented verification through two specialized prediction heads and integrates them using a lightweight gating mechanism trained strictly within training folds to prevent information leakage and enable controlled error arbitration. Under a strict leakage-safe 5-fold cross-validation protocol, the proposed model achieves an F1-score of 0.43, recall of 0.59, and AUPRC of 0.38 at a fixed threshold of 0.50 while reducing false negatives by more than 50% compared to LightGBM without excessive false positives. Although some baseline models achieve higher AUROC values, the proposed framework demonstrates more balanced and clinically meaningful precision–recall behaviour at operational screening thresholds. Additional evaluation on an independent NHANES cohort under the same leakage-safe re-training protocol further suggests robustness across heterogeneous population-health settings. Overall, the proposed dual-objective learning framework provides a practical and robust approach for imbalanced tabular prediction in population-scale cardiovascular risk assessment.