Domain-guided Machine Learning for Remotely Sensed In-Season Crop Growth Estimation

Advanced machine learning techniques have been used in remote sensing (RS) applications such as crop mapping and yield prediction, but remain under-utilized for tracking crop progress. In this study, we demonstrate the use of agronomic knowledge of crop growth drivers in a Long Short-Term Memory-based, domain-guided neural network (DgNN) for in-season crop progress estimation. The DgNN uses a branched structure and attention to separate independent crop growth drivers and capture their varying importance throughout the growing season. The DgNN is implemented for corn, using RS data in Iowa for the period 2003-2019, with USDA crop progress reports used as ground truth. State-wide DgNN performance shows significant improvement over sequential and dense-only NN structures, and a widely-used Hidden Markov Model method. The DgNN had a 4.0% higher Nash-Sutfliffe efficiency over all growth stages and 39% more weeks with highest cosine similarity than the next best NN during test years. The DgNN and Sequential NN were more robust during periods of abnormal crop progress, though estimating the Silking-Grainfill transition was difficult for all methods. Finally, Uniform Manifold Approximation and Projection visualizations of layer activations showed how LSTM-based NNs separate crop growth time-series differently from a dense-only structure. Results from this study exhibit both the viability of NNs in crop growth stage estimation (CGSE) and the benefits of using domain knowledge. The DgNN methodology presented here can be extended to provide near-real time CGSE of other crops.