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For Self-Learning:
java -jar -Xms1700m SelfLearner.jar [trainFile] [testFile] [labelFile] [unlabeledFile] [Alpha] [ClassifierType(randomforest,svm)] [resultFile] [ClassifierModelFile]

For example:
java -jar -Xms1700m SelfLearner.jar train.txt test.txt labels.txt unlabeled-normalized.txt 0.5 randomforest randomforest-result.txt randomforest-classifierModel.txt
java -jar -Xms1700m SelfLearner.jar train.txt test.txt labels.txt unlabeled-normalized.txt 0.5 svm svm-result.txt svm-classifierModel.txt

In the Release folder:
train.txt and test.txt is the gene expressions experiment for breast cancer samples downloaded from GSE20713, unlabeled.txt is the gene expressions experiment for breast cancer samples downloaded from GSE16179 and unlabeled-normalized.txt is unlabeled.txt after applying log2-transformation on the expression values.

To run co-training:
java -jar -Xms2500m CoTraining.jar [trainFile-Side1] [testFile-Side1] [labelFile-Side1] [unlabeledFile-Side1] [trainFile-Side2] [testFile-Side2] [labelFile-Side2] [unlabeledFile-Side2] [MappingFile] [Alpha] [ClassifierType(randomforest,svm)] [resultFile] [ClassifierModelFileSide1] [ClassifierModelFileSide2]

java -jar -Xms2500m CoTraining.jar train-side1.txt test-side1.txt labels-side1.txt unlabeled-side1.txt train-side2.txt test-side2.txt labels-side2.txt unlabeled-side2.txt geneMiRNAs.txt 0.5 randomforest randomforest-result.txt randomforest-classifierSide1.txt randomforest-classifierSide2.txt
java -jar -Xms2500m CoTraining.jar train-side1.txt test-side1.txt labels-side1.txt unlabeled-side1.txt train-side2.txt test-side2.txt labels-side2.txt unlabeled-side2.txt geneMiRNAs.txt 0.5 svm svm-result.txt svm-classifierSide1.txt svm-classifierSide2.txt

In the Release folder:
You can find train, test, unlabeled and labels files for side 1 (genes expressions) and side 2 (miRNAs expressions) for breast cancer samples.