Code and notebooks from Functional protein mining with conformal guarantees (2024). We will share a Zenodo with the preprocessed calibration datasets, embeddings and more shortly, but results are already reproducible through executing the data preparation notebooks in each of the subdirectories before running conformal protein retrieval.
pip install -e .
./protein_conformal: utility functions to creating confidence sets and assigning probabilities to any protein machine learning model for search./scope: experiments pertraining to SCOPe./pfam: notebooks demonstrating how to use our techniques to calibrate false discovery and false negative rates for different pfam classes./ec: experiments pertraining to EC number classification on uniprot./data: scripts and notebooks used to process data./clean_selection: scripts and notebooks used to process data