Dataset Viewer
The dataset viewer is not available for this split.
Cannot extract the features (columns) for the split 'train' of the config 'default' of the dataset.
Error code: FeaturesError
Exception: ParserError
Message: Error tokenizing data. C error: Expected 3 fields in line 123, saw 4
Traceback: Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/split/first_rows.py", line 228, in compute_first_rows_from_streaming_response
iterable_dataset = iterable_dataset._resolve_features()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 3496, in _resolve_features
features = _infer_features_from_batch(self.with_format(None)._head())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2257, in _head
return next(iter(self.iter(batch_size=n)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2461, in iter
for key, example in iterator:
^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 1952, in __iter__
for key, pa_table in self._iter_arrow():
^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 1974, in _iter_arrow
yield from self.ex_iterable._iter_arrow()
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 503, in _iter_arrow
for key, pa_table in iterator:
^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 350, in _iter_arrow
for key, pa_table in self.generate_tables_fn(**gen_kwags):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/packaged_modules/csv/csv.py", line 190, in _generate_tables
for batch_idx, df in enumerate(csv_file_reader):
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 1843, in __next__
return self.get_chunk()
^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 1985, in get_chunk
return self.read(nrows=size)
^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 1923, in read
) = self._engine.read( # type: ignore[attr-defined]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 234, in read
chunks = self._reader.read_low_memory(nrows)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "pandas/_libs/parsers.pyx", line 850, in pandas._libs.parsers.TextReader.read_low_memory
File "pandas/_libs/parsers.pyx", line 905, in pandas._libs.parsers.TextReader._read_rows
File "pandas/_libs/parsers.pyx", line 874, in pandas._libs.parsers.TextReader._tokenize_rows
File "pandas/_libs/parsers.pyx", line 891, in pandas._libs.parsers.TextReader._check_tokenize_status
File "pandas/_libs/parsers.pyx", line 2061, in pandas._libs.parsers.raise_parser_error
pandas.errors.ParserError: Error tokenizing data. C error: Expected 3 fields in line 123, saw 4Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
Conformal Protein Retrieval - Data Files
This dataset contains the large data files required to run the Conformal Protein Retrieval Gradio Space.
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 sequencesdata/lookup/scope_lookup.fasta- FASTA metadata for SCOPE proteins
🎯 Conformal Prediction Files
results/fdr_thresholds.csv- Precomputed FDR (False Discovery Rate) thresholdsresults/fnr_thresholds.csv- Precomputed FNR (False Negative Rate) thresholdsresults/calibration_probs.csv- Calibration probabilities for Venn-Abers prediction
🧬 Protein-Vec Model
protein_vec_models/protein_vec.ckpt- Main Protein-Vec model checkpointprotein_vec_models/protein_vec_params.json- Model configurationprotein_vec_models/*.py- Model architecture code files
Usage
These files are automatically loaded by the Gradio Space application. To use them locally:
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:
@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
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