CAFA-evaluator: a Python tool for benchmarking ontological classification methods

CAFA-evaluator: a Python tool for benchmarking ontological classification methods

We present CAFA-evaluator, a powerful Python program designed to evaluate the performance of prediction methods on targets with hierarchical concept dependencies. It generalizes multi-label evaluation to modern ontologies where the prediction targets are drawn from a directed acyclic graph and achie...

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Veröffentlicht in:Bioinformatics advances 2024, Vol.4 (1), p.vbae043-vbae043
Hauptverfasser: Piovesan, Damiano, Zago, Davide, Joshi, Parnal, De Paolis Kaluza, M Clara, Mehdiabadi, Mahta, Ramola, Rashika, Monzon, Alexander Miguel, Reade, Walter, Friedberg, Iddo, Radivojac, Predrag, Tosatto, Silvio C E
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container_issue 1
container_start_page vbae043
container_title Bioinformatics advances
container_volume 4
creator Piovesan, Damiano
Zago, Davide
Joshi, Parnal
De Paolis Kaluza, M Clara
Mehdiabadi, Mahta
Ramola, Rashika
Monzon, Alexander Miguel
Reade, Walter
Friedberg, Iddo
Radivojac, Predrag
Tosatto, Silvio C E
description We present CAFA-evaluator, a powerful Python program designed to evaluate the performance of prediction methods on targets with hierarchical concept dependencies. It generalizes multi-label evaluation to modern ontologies where the prediction targets are drawn from a directed acyclic graph and achieves high efficiency by leveraging matrix computation and topological sorting. The program requirements include a small number of standard Python libraries, making CAFA-evaluator easy to maintain. The code replicates the Critical Assessment of protein Function Annotation (CAFA) benchmarking, which evaluates predictions of the consistent subgraphs in Gene Ontology. Owing to its reliability and accuracy, the organizers have selected CAFA-evaluator as the official CAFA evaluation software. https://pypi.org/project/cafaeval.
doi_str_mv 10.1093/bioadv/vbae043
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title CAFA-evaluator: a Python tool for benchmarking ontological classification methods
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