Abstract: A computer implemented method for modeling and controlling batch or transitional processes is disclosed including collecting, or initiating the collection of measurements on a plurality of process variables. The method may include creating, or initiating the creation of, a latent variable model predictive controller based on the collected measurements. The method further provides for applying or initiating the application of, the model predictive controller to predict and control at least one of the process variables to track a desired trajectory, by operation of at least one computer including one or more computer processors. A related system for implementing the method is disclosed as is a computer program operable with this method.