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Machine learning (ML) and a nonlinear model predictive controller (NMPC) are used in this paper to minimize the emissions and fuel consumption of a compression ignition engine. In this work machine learning is applied in two methods. In the first application, ML is used to identify a model for implementation in model predictive control optimization problems. In the second application, ML is used as a replacement of the NMPC where the ML controller learns the optimal control action by imitating or mimicking the behavior of the model predictive controller. In this study, a deep recurrent neural network including long-short term memory (LSTM) layers are used to model the emissions and performance of an industrial 4.5 liter 4-cylinder Cummins diesel engine. This model is then used for model predictive controller implementation. Then, a deep learning scheme is deployed to clone the behavior of the developed controller. In the LSTM integration, a novel scheme is used by augmenting hidden and cell states of the network in an NMPC optimization problem. The developed LSTM-NMPC and the imitative NMPC are compared with the Cummins calibrated Engine Control Unit (ECU) model in an experimentally validated engine simulation platform. Results show a significant reduction in Nitrogen Oxides (\nox) emissions and a slight decrease in the injected fuel quantity while maintaining the same load. In addition, the imitative NMPC has a similar performance as the NMPC but with a two orders of magnitude reduction of the computation time.