Abstract: A data processing and analysis system, and a method of using the same, for discovering implicit relationships in data. The method is executed in a computer system capable of receiving input data comprised of expert knowledge, empirical data, and user-defined constraints for any application domain. The system and method provide any pre-processing the input data may require, and perform feature selection and extraction on the input data. Further, the system and method generate a graphical representation of the implicit relationships in the input data, indicating relationships between both class variables and feature variables. Also generated is a classifier that provides a semantic and statistical justification of its classification results which further provides: statistical relevancy of the data set, including an indication of the undersampled regions of the data space; a data analysis specific to a desired level of confidence; and a sound decision theoretical foundation for classification thresholding.