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We present CAFA-evaluator, a powerful Python program designed to evaluate theperformance of prediction methods on targets with hierarchical conceptdependencies. It generalizes multi-label evaluation to modern ontologies wherethe prediction targets are drawn from a directed acyclic graph and achieveshigh efficiency by leveraging matrix computation and topological sorting. Theprogram requirements include a small number of standard Python libraries,making CAFA-evaluator easy to maintain. The code replicates the CriticalAssessment of protein Function Annotation (CAFA) benchmarking, which evaluatespredictions of the consistent subgraphs in Gene Ontology. Owing to itsreliability and accuracy, the organizers have selected CAFA-evaluator as theofficial CAFA evaluation software.

CAFA-evaluator: A Python Tool for Benchmarking Ontological Classification Methods