CAFA-evaluator: A Python Tool for Benchmarking Ontological Classification Methods
| Title: | CAFA-evaluator: A Python Tool for Benchmarking Ontological Classification Methods |
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| Authors: | Piovesan, Damiano, Zago, Davide, Joshi, Parnal, Kaluza, M. Clara De Paolis, Mehdiabadi, Mahta, Ramola, Rashika, Monzon, Alexander Miguel, Reade, Walter, Friedberg, Iddo, Radivojac, Predrag, Tosatto, Silvio C. E. |
| Publication Year: | 2023 |
| Collection: | Computer Science Quantitative Biology |
| Subject Terms: | Quantitative Biology - Quantitative Methods, Computer Science - Performance |
| More Details: | 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. Comment: 5 pages |
| Document Type: | Working Paper |
| DOI: | 10.1093/bioadv/vbae043 |
| Access URL: | http://arxiv.org/abs/2310.06881 |
| Accession Number: | edsarx.2310.06881 |
| Database: | arXiv |
| DOI: | 10.1093/bioadv/vbae043 |
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