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Optimizing management practices and selecting the best cultivar for planting play a significant role in increasing agricultural food production and decreasing environmental footprint. In this study, we develop optimization frameworks under uncertainty using conditional value-at-risk in the stochastic programming objective function. We integrate the crop model, APSIM, and a parallel Bayesian optimization algorithm to optimize the management practices and select the best cultivar at different levels of risk aversion. This approach integrates the power of optimization in determining the best decisions and crop model in simulating nature's output corresponding to various decisions. As a case study, we set up the crop model for 25 locations across the US Corn Belt. We optimized the management options (planting date, N fertilizer amount, fertilizing date, and plant density in the farm) and cultivar options (cultivars with different maturity days) three times: a) before, b) at planting and c) after a growing season with known weather. Results indicated that the proposed model produced meaningful connections between weather and optima decisions. Also, we found risk-tolerance farmers get more expected yield than risk-averse ones in wet and non-wet weathers.

We investigate the predictive performance of two novel CNN-DNN machine learning ensemble models in predicting county-level corn yields across the US Corn Belt (12 states). The developed data set is a combination of management, environment, and historical corn yields from 1980-2019. Two scenarios for ensemble creation are considered: homogenous and heterogeneous ensembles. In homogenous ensembles, the base CNN-DNN models are all the same, but they are generated with a bagging procedure to ensure they exhibit a certain level of diversity. Heterogenous ensembles are created from different base CNN-DNN models which share the same architecture but have different levels of depth. Three types of ensemble creation methods were used to create several ensembles for either of the scenarios: Basic Ensemble Method (BEM), Generalized Ensemble Method (GEM), and stacked generalized ensembles. Results indicated that both designed ensemble types (heterogenous and homogenous) outperform the ensembles created from five individual ML models (linear regression, LASSO, random forest, XGBoost, and LightGBM). Furthermore, by introducing improvements over the heterogeneous ensembles, the homogenous ensembles provide the most accurate yield predictions across US Corn Belt states. This model could make 2019 yield predictions with a root mean square error of 866 kg/ha, equivalent to 8.5% relative root mean square, and could successfully explain about 77% of the spatio-temporal variation in the corn grain yields. The significant predictive power of this model can be leveraged for designing a reliable tool for corn yield prediction which will, in turn, assist agronomic decision-makers.

This study investigates whether coupling crop modeling and machine learning (ML) improves corn yield predictions in the US Corn Belt. The main objectives are to explore whether a hybrid approach (crop modeling + ML) would result in better predictions, investigate which combinations of hybrid models provide the most accurate predictions, and determine the features from the crop modeling that are most effective to be integrated with ML for corn yield prediction. Five ML models (linear regression, LASSO, LightGBM, random forest, and XGBoost) and six ensemble models have been designed to address the research question. The results suggest that adding simulation crop model variables (APSIM) as input features to ML models can decrease yield prediction root mean squared error (RMSE) from 7 to 20%. Furthermore, we investigated partial inclusion of APSIM features in the ML prediction models and we found soil moisture related APSIM variables are most influential on the ML predictions followed by crop-related and phenology-related variables. Finally, based on feature importance measure, it has been observed that simulated APSIM average drought stress and average water table depth during the growing season are the most important APSIM inputs to ML. This result indicates that weather information alone is not sufficient and ML models need more hydrological inputs to make improved yield predictions.

The emerge of new technologies to synthesize and analyze big data with high-performance computing, has increased our capacity to more accurately predict crop yields. Recent research has shown that Machine learning (ML) can provide reasonable predictions, faster, and with higher flexibility compared to simulation crop modeling. The earlier the prediction during the growing season the better, but this has not been thoroughly investigated as previous studies considered all data available to predict yields. This paper provides a machine learning based framework to forecast corn yields in three US Corn Belt states (Illinois, Indiana, and Iowa) considering complete and partial in-season weather knowledge. Several ensemble models are designed using blocked sequential procedure to generate out-of-bag predictions. The forecasts are made in county-level scale and aggregated for agricultural district, and state level scales. Results show that ensemble models based on weighted average of the base learners outperform individual models. Specifically, the proposed ensemble model could achieve best prediction accuracy (RRMSE of 7.8%) and least mean bias error (-6.06 bu/acre) compared to other developed models. Comparing our proposed model forecasts with the literature demonstrates the superiority of forecasts made by our proposed ensemble model. Results from the scenario of having partial in-season weather knowledge reveal that decent yield forecasts can be made as early as June 1st. To find the marginal effect of each input feature on the forecasts made by the proposed ensemble model, a methodology is suggested that is the basis for finding feature importance for the ensemble model. The findings suggest that weather features corresponding to weather in weeks 18-24 (May 1st to June 1st) are the most important input features.

Crop yield prediction is extremely challenging due to its dependence on multiple factors such as crop genotype, environmental factors, management practices, and their interactions. This paper presents a deep learning framework using convolutional neural networks (CNN) and recurrent neural networks (RNN) for crop yield prediction based on environmental data and management practices. The proposed CNN-RNN model, along with other popular methods such as random forest (RF), deep fully-connected neural networks (DFNN), and LASSO, was used to forecast corn and soybean yield across the entire Corn Belt (including 13 states) in the United States for years 2016, 2017, and 2018 using historical data. The new model achieved a root-mean-square-error (RMSE) 9% and 8% of their respective average yields, substantially outperforming all other methods that were tested. The CNN-RNN have three salient features that make it a potentially useful method for other crop yield prediction studies. (1) The CNN-RNN model was designed to capture the time dependencies of environmental factors and the genetic improvement of seeds over time without having their genotype information. (2) The model demonstrated the capability to generalize the yield prediction to untested environments without significant drop in the prediction accuracy. (3) Coupled with the backpropagation method, the model could reveal the extent to which weather conditions, accuracy of weather predictions, soil conditions, and management practices were able to explain the variation in the crop yields., Comment: 26 Pages, 14 Figures

Pre-season prediction of crop production outcomes such as grain yields and N losses can provide insights to stakeholders when making decisions. Simulation models can assist in scenario planning, but their use is limited because of data requirements and long run times. Thus, there is a need for more computationally expedient approaches to scale up predictions. We evaluated the potential of five machine learning (ML) algorithms as meta-models for a cropping systems simulator (APSIM) to inform future decision-support tool development. We asked: 1) How well do ML meta-models predict maize yield and N losses using pre-season information? 2) How many data are needed to train ML algorithms to achieve acceptable predictions?; 3) Which input data variables are most important for accurate prediction?; and 4) Do ensembles of ML meta-models improve prediction? The simulated dataset included more than 3 million genotype, environment and management scenarios. Random forests most accurately predicted maize yield and N loss at planting time, with a RRMSE of 14% and 55%, respectively. ML meta-models reasonably reproduced simulated maize yields but not N loss. They also differed in their sensitivities to the size of the training dataset. Across all ML models, yield prediction error decreased by 10-40% as the training dataset increased from 0.5 to 1.8 million data points, whereas N loss prediction error showed no consistent pattern. ML models also differed in their sensitivities to input variables. Averaged across all ML models, weather conditions, soil properties, management information and initial conditions were roughly equally important when predicting yields. Modest prediction improvements resulted from ML ensembles. These results can help accelerate progress in coupling simulation models and ML toward developing dynamic decision support tools for pre-season management.