Construction and Optimization of Integrated Yield Prediction Model Based on Phenotypic Characteristics of Rice Grown in Small–Scale Plantations

An intelligent prediction model for rice yield in small-scale cultivation areas can provide precise forecasting results for farmers, rice planting enterprises, and researchers, holding significant importance for agricultural industries and crop science research within small regions. Although machine learning can handle complex nonlinear problems to enhance prediction accuracy, further improvements in models are still needed to accurately predict rice yields in small areas facing complex planting environments, thereby enhancing model performance. This study employs four rice phenotypic traits, namely, panicle angle, panicle length, total branch length, and grain number, along with seven machine learning methods—multiple linear regression, support vector machine, MLP, random forest, GBR, XGBoost, and LightGBM—to construct a yield prediction model group. Subsequently, the top three models with the best performance in individual model predictions are integrated using voting and stacking ensemble methods to obtain the optimal integrated model. Finally, the impact of different rice phenotypic traits on the performance of the stacked ensemble model is explored. Experimental results indicate that the random forest model performs best after individual machine learning modeling, with RMSE, R 2 , and MAPE values of 0.2777, 0.9062, and 17.04%, respectively. After model integration, Stacking–3m demonstrates the best performance, with RMSE, R 2 , and MAPE values of 0.2483, 0.9250, and 6.90%, respectively. Compared to the performance after random forest modeling, the RMSE decreased by 10.58%, R 2 increased by 1.88%, and MAPE decreased by 0.76%, indicating improved model performance after stacking ensemble. The Stacking–3m model, which demonstrated the best comprehensive evaluation metrics, was selected for model validation, and the validation results were satisfactory, with MAE, R 2 , and MAPE values of 8.3384, 0.9285, and 0.2689, respectively. The above research findings demonstrate that this integrated model possesses high practical value and fills a gap in precise yield prediction for small-scale rice cultivation in the Yunnan Plateau region.