Explainable rice yield from Sentinel-1 and Sentinel-2 satellite data for food security

Abstract

Reliable, explainable crop-yield estimates are essential for food-security planning in data-sparse regions. We present a transparent pipeline for district-level (regency) rice yield prediction in Indonesia that fuses Sentinel-1 synthetic aperture radar (SAR), Sentinel-2 normalized difference vegetation index (NDVI), and weather/reanalysis features. The system standardizes inputs per province, fixes a 16-day temporal key, and uses a small, auditable ensemble of tree models (gradient boosting+light gradient-boosting machine (LightGBM)). Trained on ≤2023 data and evaluated on a 2024 temporal hold-out, a joint West Java ∪ South Sulawesi model achieves root mean square error (RMSE)≈0.80 t/ha, mean absolute error (MAE)≈0.48 t/ha, and R-squared (R²)≈0.33 at regency scale. Feature importances and Shapley additive explanations (SHAP) confirm that phenology (NDVI peak, integral, green-up/senescence), SAR backscatter (vertical transmit-vertical receive/vertical transmit-horizontal receive (VV/VH)), and wind/pressure are consistent drivers under monsoon conditions. The workflow supports routine, one-click provincial updates and produces parity maps and error bars for actionable diagnostics. These results demonstrate that combining Sentinel-1, Sentinel-2, and basic meteorology delivers accurate, interpretable, and operational yield signals suited to Indonesia’s food security needs, while providing a clear recipe for scaling to additional provinces.