1. A method of determining a stage of a disease comprising: (a) processing a biological sample from a subject whose stage of the disease is unknown to obtain high dimensional experimental data selected from the group consisting of gene expression levels, protein expression levels, single nucleotide polymorphisms, or comparative genomic analysis; (b) detecting the presence of a first set of multiple data points or a second set of multiple data points in the high dimensional experimental data, wherein the first set of multiple data points is predictive for the stage of the disease as determined by a trained supervised pattern recognition method, and a second set of multiple data points is predictive for a different stage of the disease as determined by the trained supervised pattern recognition method; and (c) determining whether a subject whose stage of the disease is unknown has the stage of the disease or the different stage of the disease by detecting the presence of said first or second set of multiple data points in data obtained from the biological sample.