Datasets:

LoocasGoose
/

cpr_data

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 4

Need 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.

📊 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:

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

Downloads last month: 108