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We present an automatic data-driven machine learning (ML) approach for the development, evaluation and interpretation of deep neural networks (DNNs) for turbulence closures and demonstrate their usage in the context of cold-flow large-eddy simulation (LES) of the four-stroke Darmstadt engine using an open-source compressible multi-dimensional CFD solver OFICE, in a hybrid PDE-ML framework. Rather than explicitly using canonical formulations of closure terms, these DNNs robustly discover the functional relationships between the large-scale features of the resolved flow (cell Re, strain and rotation rate tensors etc.) obtained by solving the Navier Stokes to the small-scale unresolved terms. Experimentally validated high-fidelity LES solutions of the engine at different crank angles are utilized as the ground truth to train the DNN based closure models.