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The performance is measured by averaging the classification accuracies of 20 times.
We calculated an importance measure for each feature by averaging the classification accuracies of all five-feature subset models containing the feature.
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We compute the mean accuracy of a pathway by averaging the pathway classification results over all trials, using zero percent accuracy for any trial where a pathway was not represented.
The Average method consists of averaging the classification of all classifiers and choosing the class closest to the average.
Group average accuracy was calculated by averaging the co-registered individual classification accuracy volumes.
Using p-value ranked features, we chose different number of probe sets to compare the mean prediction accuracies for each method by averaging the prediction accuracy of the five classification algorithms decision Tree j48 (J48), RF, NB, SL and SMO.
By averaging the AUC performance of the P classification models induced on the P gene subsets selected by the ranker R i, we can evaluate the effectiveness of that ranker in identifying highly predictive gene sets.
To explore how broadly applicable the method is, we turned to ANNEs in which classification is determined by averaging the individual network outputs (which are logistic functions ranging from 0 to 1 for classification models) and comparing that average to an ensemble threshold.
The "true" accuracy of classification was estimated by averaging the performance of the 2 classifiers for each subject.
When top ranked gene sets from both methods, based on FDR for association and the AUC value for ROC-based classification, were combined by averaging the top gene set ranks, there was a significant overlap between the gene sets ranked by both methods (Spearman rank correlation over all gene sets = 0.96, p-value < 10-16 ; Additional File 6).
The random error was computed by averaging the error of five runs of the complete classification procedure on data with CTB and French labels randomly assigned to samples.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com