This study proposes a two-level stacking ensemble framework for Remaining Useful Life (RUL) prediction of turbofan engines, evaluated on the NASA C-MAPSS benchmark using the FD001 and FD003 subsets. The framework integrates four heterogeneous deep learning base learners: Long Short-Term Memory (LSTM), Convolutional Neural Network (CNN), CNN-LSTM, and CNN-GRU, whose out-of-fold predictions are combined by an XGBoost meta-learner to capture complex degradation patterns while mitigating individual model biases. Comprehensive experiments demonstrate that the stacking ensemble achieves superior predictive performance, with Root Mean Square Error (RMSE) of 9.989 and 8.613, Mean Absolute Error (MAE) of 7.081 and 5.195, and R-squared values of 0.899 and 0.906 for FD001 and FD003, respectively. Compared to the best-reported baseline (TCAT: RMSE 11.12 and 11.02), the proposed method achieves RMSE reductions of 10.2 percent and 21.8 percent for FD001 and FD003, respectively. Feature correlation analysis, residual diagnostics, and training convergence curves validate the model's robustness. These findings underscore the efficacy of stacking ensemble methods for prognostics and health management in safety-critical aerospace applications.

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