A control system is configured to operate a multiple-input system to achieve an optimal value for a performance variable of the multiple-input system. The control system includes a mapper configured to generate a mapping from a first number of manipulated variables to a second number of latent variables. The second number is smaller than the first number and each of the latent variables includes a linear combination of the manipulated variables. The control system also includes an extremum-seeking controller configured to receive the performance variable from the multiple-input system as a feedback and modulate values of the second number of latent variables to drive the performance variable to the optimal value. The mapper is further configured to use the mapping to translate modulated values of the second number of latent variables to modulated values of the first number of manipulated variables and provide the modulated values of the first number of manipulated variables to the multiple-input system.