ProtFunAgent: Structured Ontology Reasoning for Protein Function Annotation

Anonymous reproducibility artifacts for the NeurIPS 2026 submission: “ProtFunAgent: Structured Ontology Reasoning for Protein Function Annotation” This repository contains the core evaluation, ontology-processing, retrieval, and prompting components used in ProtFunAgent, including: - GO prediction evaluation scripts- Hierarchical ontology evaluation- Ontology-aware decoding and pruning- UniProt ontology processing utilities- Retrieval-augmented homology context generation- Prompt templates used for synthesis and verification- Benchmark evaluation pipeline Included files:- evaluate_go.py- evaluate_go_hier.py- evaluate_text.py- evaluate_all.py- ontology_decode.py- make_go_map.py- uniprot_ontology_v2.py- uniprot_prompts.py- homology_rag.py The repository is provided for anonymous peer-review reproducibility purposes and accompanies the corresponding NeurIPS submission.