The Morgan::SVM model showed the highest mean values for the three performance metrics and significantly higher values of BA and MCC when compared to all but the RDK::SVM model (at 95% confidence level). F1 score showed the lower differences between models, with the Morgan::SVM having the highest mean value and significantly higher values when compared to all but five models, being RDK::SVM, RDK::GBT, RDK::FNN, RDK::RF and Morgan::k-NN (at 95% confidence level). These results suggested Morgan and RDK fingerprints and the SVM algorithm as the best combinations to derive binary classifiers for the current sets of studied epigenetic targets.