Predicting rice phenology across China by integrating crop phenology model and machine learning

This study explores the integration of crop phenology models and machine learning approaches for predicting rice phenology across China, to gain a deeper understanding of rice phenology prediction. Multiple approaches were used to predict heading and maturity dates at 337 locations across the main rice growing regions of China from 1981 to 2020, including crop phenology model, machine learning and hybrid model that integrate both approaches. Furthermore, an interpretable machine learning (IML) using SHapley Additive exPlanation (SHAP) was employed to elucidate influence of climatic and varietal factors on uncertainty in crop phenology model predictions. Overall, the hybrid model demonstrated a high accuracy in predicting rice phenology, followed by machine learning and crop phenology models. The best hybrid model, based on a serial structure and the eXtreme Gradient Boosting (XGBoost) algorithm, achieved a root mean square error (RMSE) of 4.65 and 5.72 days and coefficient of determination (R²) values of 0.93 and 0.9 for heading and maturity predictions, respectively. SHAP analysis revealed temperature to be the most influential climate variable affecting phenology predictions, particularly under extreme temperature conditions, while rainfall and solar radiation were found to be less influential. The analysis also highlighted the variable importance of climate across different phenological stages, rice cultivation patterns, and geographic regions, underscoring the notable regionality. The study proposed that a hybrid model using an IML approach would not only improve the accuracy of prediction but also offer a robust framework for leveraging data-driven in crop modeling, providing a valuable tool for refining and advancing the modeling process in rice.