1. A method for controlling a manufacturing apparatus, the method comprising: calculating, by a computer system, a set of predicted output values; obtaining, by the computer system, a prediction model based on a set of input parameters, the set of predicted output values and empirical output values, wherein obtaining the predication model comprises transforming the set of input parameters into transformed input values using a transformation function having a plurality of coefficient values; optimizing, by the computer system, the prediction model by minimizing differences between the set of predicted output values and the empirical output values, wherein minimizing the differences comprises collecting historical information on the set of input parameters and the empirical output values; creating a score function on the collected information; and determining coefficient values that minimize the score function to minimize the difference; and adjusting, by the computer system, the set of input parameters using the optimized prediction model to obtain a set of desired output values to control the manufacturing apparatus.