Performance of MIPS function prediction using a previously established benchmark dataset. Results are shown for five different methods: Funckenstein (light red); MRF-NB  (black); guilt-by-profiling by the RF method alone (dark red); guilt-by-profiling by the PDT method alone (violet); guilt-by-association by the FL method alone (blue). (a) True positive rate versus false positive rate at different score thresholds. (b) Precision versus recall at prediction score thresholds. MIPS, Munich Information Center for Protein Sequences; MRF, Markov random field; NB, naïve Bayes; PDT, probabilistic decision tree; RF, random forest.