ArticleBioinformatics advances2024
CAFA-evaluator: a Python tool for benchmarking ontological classification methods.
Article in Bioinformatics advances, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- GPCR-GO: Relation-aware graph learning for predicting Gene Ontology terms of G protein-coupled receptors.PLoS computational biology · 2026Article
- On the state of protein function prediction: a report on the fourth CAFA challenge.bioRxiv : the preprint server for biology · 2026Article
- LAFA: A Framework for Reproducible Longitudinal Assessment of Protein Function Annotation Models.ArXiv · 2026Article
- Advances in Protein Function Prediction from the Fifth CAFA Challenge.bioRxiv : the preprint server for biology · 2026Article
- A unified multimodal model for generalizable zero-shot and supervised protein function prediction.Bioinformatics (Oxford, England) · 2026Article
- Critical assessment in the age of AI: challenges and opportunities for computational biology.Bioinformatics advances · 2026Article
- LAFA: a framework for reproducible longitudinal assessment of protein function annotation models.Bioinformatics advances · 2026Article
- Comparative Assessment of Protein Large Language Models for Enzyme Commission Number Prediction.BMC bioinformatics · 2025Article
- Learning maximally spanning representations improves protein function annotation.bioRxiv : the preprint server for biology · 2025Article
- Deep learning methods for protein function prediction.Proteomics · 2025Review
- Hayai-Annotation: A functional gene prediction tool that integrates orthologs and gene ontology for network analysis in plant species.Computational and structural biotechnology journal · 2025Article
- ProtFun: a protein function prediction model using graph attention networks with a protein large language model.Bioinformatics advances · 2025Article
- Improving protein function prediction by learning and integrating representations of protein sequences and function labels.Bioinformatics advances · 2024Article
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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. Availability and implementation: https://pypi.org/project/cafaeval.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.