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The dataset generation failed
Error code: DatasetGenerationError
Exception: CastError
Message: Couldn't cast
input_ids: list<item: int16>
child 0, item: int16
soma_joinid: int64
dataset_id: string
assay: string
assay_ontology_term_id: string
cell_type: string
cell_type_ontology_term_id: string
development_stage: string
development_stage_ontology_term_id: string
disease: string
disease_ontology_term_id: string
donor_id: string
is_primary_data: bool
self_reported_ethnicity: string
self_reported_ethnicity_ontology_term_id: string
sex: string
sex_ontology_term_id: string
suspension_type: string
tissue: string
tissue_ontology_term_id: string
tissue_general: string
tissue_general_ontology_term_id: string
fulltext: string
length: int64
-- schema metadata --
huggingface: '{"info": {"features": {"input_ids": {"feature": {"dtype": "' + 1412
to
{'indices': Value(dtype='uint64', id=None)}
because column names don't match
Traceback: Traceback (most recent call last):
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1855, in _prepare_split_single
for _, table in generator:
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 690, in wrapped
for item in generator(*args, **kwargs):
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/packaged_modules/arrow/arrow.py", line 76, in _generate_tables
yield f"{file_idx}_{batch_idx}", self._cast_table(pa_table)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/packaged_modules/arrow/arrow.py", line 59, in _cast_table
pa_table = table_cast(pa_table, self.info.features.arrow_schema)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2293, in table_cast
return cast_table_to_schema(table, schema)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2241, in cast_table_to_schema
raise CastError(
datasets.table.CastError: Couldn't cast
input_ids: list<item: int16>
child 0, item: int16
soma_joinid: int64
dataset_id: string
assay: string
assay_ontology_term_id: string
cell_type: string
cell_type_ontology_term_id: string
development_stage: string
development_stage_ontology_term_id: string
disease: string
disease_ontology_term_id: string
donor_id: string
is_primary_data: bool
self_reported_ethnicity: string
self_reported_ethnicity_ontology_term_id: string
sex: string
sex_ontology_term_id: string
suspension_type: string
tissue: string
tissue_ontology_term_id: string
tissue_general: string
tissue_general_ontology_term_id: string
fulltext: string
length: int64
-- schema metadata --
huggingface: '{"info": {"features": {"input_ids": {"feature": {"dtype": "' + 1412
to
{'indices': Value(dtype='uint64', id=None)}
because column names don't match
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1431, in compute_config_parquet_and_info_response
parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet(
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 992, in stream_convert_to_parquet
builder._prepare_split(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1742, in _prepare_split
for job_id, done, content in self._prepare_split_single(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1898, in _prepare_split_single
raise DatasetGenerationError("An error occurred while generating the dataset") from e
datasets.exceptions.DatasetGenerationError: An error occurred while generating the datasetNeed help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
indices
uint64 |
|---|
14,340,059
|
14,340,561
|
14,341,066
|
14,341,098
|
14,342,958
|
14,344,068
|
14,344,243
|
14,344,463
|
14,344,508
|
14,344,540
|
14,344,713
|
14,344,771
|
14,345,335
|
14,345,590
|
14,345,618
|
14,345,787
|
14,345,906
|
14,346,285
|
14,346,421
|
14,346,457
|
14,359,356
|
14,359,545
|
14,359,691
|
14,359,789
|
14,360,037
|
14,360,358
|
14,360,415
|
14,360,665
|
14,360,679
|
14,360,779
|
14,360,960
|
14,361,108
|
14,361,150
|
14,361,175
|
14,361,485
|
14,361,722
|
14,361,786
|
14,361,906
|
14,361,934
|
14,362,102
|
14,362,139
|
14,362,215
|
14,362,229
|
14,362,281
|
14,362,313
|
14,362,325
|
14,362,386
|
14,362,445
|
14,362,511
|
14,362,546
|
14,362,592
|
14,362,597
|
14,362,622
|
14,362,690
|
14,362,730
|
14,362,793
|
14,362,812
|
14,362,834
|
14,362,837
|
14,362,949
|
14,362,951
|
14,362,959
|
14,362,977
|
14,362,989
|
14,363,030
|
14,363,122
|
14,363,134
|
14,363,157
|
14,363,158
|
14,363,213
|
14,363,255
|
14,363,261
|
14,363,327
|
14,363,408
|
14,363,429
|
14,363,473
|
14,363,564
|
14,363,583
|
14,363,634
|
14,363,635
|
14,363,639
|
14,363,666
|
14,363,723
|
14,363,733
|
14,363,765
|
14,363,790
|
14,363,798
|
14,363,827
|
14,363,831
|
14,363,848
|
14,363,899
|
14,363,900
|
14,364,015
|
14,364,122
|
14,364,125
|
14,364,149
|
14,364,172
|
14,364,173
|
14,364,187
|
14,364,226
|
End of preview.
The dataset scLibrary is the pre-training dataset used by the LangCell model.
You can use git-lfs to download sclibrary.dataset from this repository, and then use the following code to load the data:
from datasets import load_from_disk
sclibrary=load_from_disk("/path/to/sclibrary.dataset")
Model github: https://github.com/PharMolix/LangCell
Paper: https://arxiv.org/abs/2405.06708
Citation
If you find scLibrary helpful to your research, please consider giving our Github repository a 🌟star and 📎citing the following article. Thank you for your support!
@misc{zhao2024langcell,
title={LangCell: Language-Cell Pre-training for Cell Identity Understanding},
author={Suyuan Zhao and Jiahuan Zhang and Yizhen Luo and Yushuai Wu and Zaiqing Nie},
year={2024},
eprint={2405.06708},
archivePrefix={arXiv},
primaryClass={q-bio.GN}
}
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