Figure 2: Overall performance evaluation.
From: A large-scale evaluation of computational protein function prediction
(a,b) The maximum F-measure for the top-performing methods for Molecular Function ontology (a) and Biological Process ontology (b). All panels show the top ten participating methods in each category as well as the BLAST and Naive baseline methods. Note that 33 models outperformed BLAST in the Molecular Function category, whereas 26 models outperformed BLAST in the Biological Process category (cutoff scores below which methods were excluded from the panels were 0.468 and 0.300 for the Molecular Function and Biological Process categories, respectively). In the Molecular Function category, proteins with “protein binding” as their only leaf term were excluded from the analysis because the protein binding term was not considered informative (results that include those proteins are presented in Supplementary Fig. 3). A perfect predictor would be characterized with Fmax = 1. Confidence intervals (95%) were determined using bootstrapping with n = 10,000 iterations on the set of target sequences. For cases in which a principal investigator participated in multiple teams, only the results of the best-scoring method are presented.
