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The exploration of high dimensional gene expression microarray data demands powerful analytical tools. Our data mining software, visual data analyzer (VISDA) for cluster discovery, reveals many distinguishing patterns among gene expression profiles. The model-supported hierarchical data exploration tool has two complementary schemes: discriminatory dimensionality reduction for structure-focused data visualization, and cluster decomposition by probabilistic clustering. Reducing dimensionality generates the visualization of the complete data set at the top level. This data set is then partitioned into subclusters that can consequently be visualized at lower levels and if necessary partitioned again. These approaches produce different visualizations that are compared against known phenotypes from the microarray experiments. For class prediction on cancers using miroarray data, multilayer perceptrons (MLPs) are trained and optimized, whose architecture and parameters are regularized and initialized by weighted Fisher criterion (wFC)-based discriminatory component analysis (DCA). The prediction performance is compared and evaluated via multifold cross-validation.