Hi,
For a quick assessment I recommend doing 20 runs for each setting and then averaging the results for the 20 best-of-run models (select "Keep & Append Best Models Only" in the General Settings Tab). Then compare the results across the different values of the parameter you're trying to optimize (for example, the number of genes) and choose the best value. Then repeat for the other settings.
As for the metric, you can use the fitness and/or any of the measures of fit GeneXproTools supports (for example, the Classification Accuracy in classification/logistic regression models or the Correlation Coefficient in regression problems).
Candida Ferreira
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