Ok, I figured out how to do this, if that could help someone. Get the source code for SMO.java and add it to your package. Allow imports, if any. Set m_fitLogisticModels to true . Change smo.buildClassifier(train, cl1, cl2, false, -1, -1); to smo.buildClassifier(train, cl1, cl2, true, -1, -1); . And viola! distributionForInstance returns confidence metrics instead of hard 0/1.
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