| --- |
| license: apache-2.0 |
| task_categories: |
| - feature-extraction |
| - text-classification |
| tags: |
| - protein |
| - bioinformatics |
| - embeddings |
| - conformal-prediction |
| size_categories: |
| - 1M<n<10M |
| --- |
| |
| # Conformal Protein Retrieval - Data Files |
|
|
| This dataset contains the large data files required to run the [Conformal Protein Retrieval Gradio Space](https://huggingface.co/spaces/LoocasGoose/cpr). |
|
|
| ## Contents |
|
|
| ### 📊 Lookup Databases |
|
|
| **UniProt Database:** |
| - `data/lookup_embeddings.npy` - Pre-embedded UniProt protein sequences (Protein-Vec embeddings) |
| - `data/lookup_embeddings_meta_data.tsv` - Metadata for UniProt proteins (Entry, Pfam, Protein names) |
|
|
| **SCOPE Database:** |
| - `data/lookup/scope_lookup_embeddings.npy` - Pre-embedded SCOPE protein domain sequences |
| - `data/lookup/scope_lookup.fasta` - FASTA metadata for SCOPE proteins |
|
|
| ### 🎯 Conformal Prediction Files |
|
|
| - `results/fdr_thresholds.csv` - Precomputed FDR (False Discovery Rate) thresholds |
| - `results/fnr_thresholds.csv` - Precomputed FNR (False Negative Rate) thresholds |
| - `results/calibration_probs.csv` - Calibration probabilities for Venn-Abers prediction |
|
|
| ### 🧬 Protein-Vec Model |
|
|
| - `protein_vec_models/protein_vec.ckpt` - Main Protein-Vec model checkpoint |
| - `protein_vec_models/protein_vec_params.json` - Model configuration |
| - `protein_vec_models/*.py` - Model architecture code files |
|
|
| ## Usage |
|
|
| These files are automatically loaded by the Gradio Space application. To use them locally: |
|
|
| ```python |
| from huggingface_hub import hf_hub_download |
| import numpy as np |
| |
| # Download a specific file |
| embedding_file = hf_hub_download( |
| repo_id="LoocasGoose/cpr_data", |
| filename="data/lookup_embeddings.npy", |
| repo_type="dataset" |
| ) |
| |
| # Load the embeddings |
| embeddings = np.load(embedding_file) |
| ``` |
|
|
| ## Citation |
|
|
| If you use these data files, please cite the original paper: |
|
|
| ```bibtex |
| @article{boger2025functional, |
| title={Functional protein mining with conformal guarantees}, |
| author={Boger, Ron S and Chithrananda, Seyone and Angelopoulos, Anastasios N and Yoon, Peter H and Jordan, Michael I and Doudna, Jennifer A}, |
| journal={Nature Communications}, |
| volume={16}, |
| number={1}, |
| pages={85}, |
| year={2025}, |
| publisher={Nature Publishing Group UK London} |
| } |
| ``` |
|
|
| ## License |
|
|
| Apache 2.0 |
|
|
| ## Source |
|
|
| Original data from: [Zenodo](https://zenodo.org/records/14272215) |
|
|
|
|
