Improving alfalfa nitrogen estimation with canopy structural priors from DSSAT–PROSAIL and UAV hyperspectral data

Accurate estimation of nitrogen (N) concentration in alfalfa ( Medicago sativa L .) supports forage quality assessment and harvest scheduling. Empirical remote sensing models often overfit because of confounding effects of three-dimensional canopy structure. Incorporating structural parameters can stabilize biochemical inversions, but concurrent in situ morphological measurements are difficult to acquire at scale. We developed the Morphology-Aware Latent Embedding Network (MALENet), a hybrid framework integrating physiological and morphological mechanisms with hyperspectral data. The Decision Support System for Agrotechnology Transfer (DSSAT), coupled with the PROSAIL radiative transfer model, generated a structurally rich synthetic hyperspectral prior. A convolutional neural network (CNN) with a Squeeze-and-Excitation (SE) attention mechanism, was pre-trained on these data to distill ecophysiological knowledge into a dense latent representation. This mechanistically derived embedding was then fused with empirical hyperspectral measurements collected under diverse field conditions. Evaluation using multi-year field quadrats in the Hexi Corridor showed improved predictive performance ( R² = 0.71, RMSE = 0.30%) relative to conventional machine learning and deep learning models (LASSO-ANN: R² = 0.61; CNN: R² = 0.66). Feature attribution indicated that MALENet used near-infrared multiple scattering (58.3% attribution) as a structural proxy to calibrate nitrogen concentration retrieval against the confounding effects of canopy architecture. Despite constraints imposed by sample size and PROSAIL's 1D canopy assumption, these findings demonstrate the potential of physically guided deep learning to use structural information for agricultural trait retrieval in precision forage management.