A relationship between an input, a set-point of a plurality of processes and an output of a corresponding process is learned using machine learning. A regression function is derived for each process based upon historical data. An autoencoder is trained for each process based upon the historical data to form a regularizer and the regression functions and regularizers are merged together into a unified optimization problem. System level optimization is performed using the regression functions and regularizers and a set of optimal set-points of a global optimal solution for operating the processes is determined. An industrial system is operated based on the set of optimal set-points.