Datasets:

wanglab
/

rna_evaluation

ArXiv:

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Split (3)

train

The full dataset viewer is not available (click to read why). Only showing a preview of the rows.

The dataset generation failed because of a cast error

Error code:   DatasetGenerationCastError
Exception:    DatasetGenerationCastError
Message:      An error occurred while generating the dataset

All the data files must have the same columns, but at some point there are 1 new columns ({'sequence'}) and 1 missing columns ({'seq'}).

This happened while the csv dataset builder was generating data using

hf://datasets/wanglab/rna_evaluation/modification/train.csv (at revision b7ff57e19fdad17f9917cddca3e089ef56838905)

Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1871, in _prepare_split_single
                  writer.write_table(table)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 623, in write_table
                  pa_table = table_cast(pa_table, self._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
              sequence: string
              label: string
              -- schema metadata --
              pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 489
              to
              {'seq': Value(dtype='string', id=None), 'label': Value(dtype='float64', id=None)}
              because column names don't match
              
              During handling of the above exception, another exception occurred:
              
              Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1438, in compute_config_parquet_and_info_response
                  parquet_operations = convert_to_parquet(builder)
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1050, in convert_to_parquet
                  builder.download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 925, in download_and_prepare
                  self._download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1001, in _download_and_prepare
                  self._prepare_split(split_generator, **prepare_split_kwargs)
                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 1873, in _prepare_split_single
                  raise DatasetGenerationCastError.from_cast_error(
              datasets.exceptions.DatasetGenerationCastError: An error occurred while generating the dataset
              
              All the data files must have the same columns, but at some point there are 1 new columns ({'sequence'}) and 1 missing columns ({'seq'}).
              
              This happened while the csv dataset builder was generating data using
              
              hf://datasets/wanglab/rna_evaluation/modification/train.csv (at revision b7ff57e19fdad17f9917cddca3e089ef56838905)
              
              Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)

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.

seq string	label float64
ACCAACATGTAATTTCCACTCTTGA	-1.781224
TGGTAAAATCTAGGGTTTTTTATAA	-0.275643
CAAAAAGTAGACGCAACATGAAAAA	-1.148226
TGGCCTCGTGGATAGGACATTTGGA	-1.16347
TAATCGGTTCTAAATACGATTAGTG	0.629766
TAAAGAAGAGGTTGATGAGAAACCG	-0.056611
AAGCGGTGAATAACACACAGTAAAG	0.437928
ATCTCTCTAGTACAGATTGTCAATA	0.625944
AGACAGCTAAAACCCTACAAAATAA	0.428996
CCTTCGACGACCCACGTCCGCCTTA	0.066963
CGTTGATCATGGATACTTTTTTACA	-1.431016
GTACGCAAACCATCTCTCGATTTCT	0.385245
GTTACCCCCTACTCCAGCTCATACT	0.106418
TCCAATCTTTTGCACCACCCCTAGG	0.167583
CTCCCTCAACAGGTGCCTCACGCTG	0.448294
AGTAATGAGTTTCGGCATTTCAAAG	0.448709
AGGATTGTGTCGCCAGTTCCACTGA	0.226652
TAATATCATATAGTTCTTCTCCCCT	0.091013
TAGAATCGGAAGGAATAGGATTCTA	0.683043
GATGCTTGCACTCGAGGTCCGTGCA	0.777959
GACACCACGTAAAATCCTAATCAAA	0.722772
TCTATGACTCGTTCGCGTAGAATCA	-0.903231
CAAAATGATAAGATGGACCAAAGAT	0.044779
TGCATGATCTGTAGCATTTGCTGCT	-0.282712
GCATGACCAGCCTGTTTAGATAGAA	-0.8849
AGAAAGATAACAAACCACCCGTATG	0.531101
GACCCCTTTACGCAACCTATTGAAC	0.738194
GCCCCTACACTCTGTTTTTTGATCC	0.462663
GGATAAATAAATCTGAGATCAGAAA	0.576403
CCCTGTTGCCAGCCGCATAATCATC	0.507246
GCAGCACGCTTACAGTCCCTCAGAC	0.588532
CTTTTTCCTTACTCGTGATACTATC	0.354998
GTAAACCCAGATCTAGTTTGACTGT	0.434046
CACGCTGCACACCGAACAGCCCAAA	-0.006064
ACTCCGACACCATCTTCATTACAAT	0.409271
TACATGGAACTGTCCCTTCTTACCG	-0.842205
GACCCTCCTATTATCAACCAAGATA	0.208579
AGAGTGAGAGCGCGACAAATCACTG	0.677526
CCGATTGGCGCCCTTTGGCCGGGAG	0.066205
GAGATGAGAAGTCGTGCGAAATAAC	-1.532364
GTCCTCGCGACAACTGTCCCAAACC	0.290489
TTCTGATCGGTGTTCCTCCGTTCTG	0.488669
TCTAGTCGTTTCTAGCATAGACTATA	0.668242
GCAATGCATCCATTCCAATGCCTACT	-1.191314
ACCTTGCCGCATCCCACTTGCCTGCA	0.458991
CAAACTGGGCCCATTTCTATACCAAT	0.178165
ACGAGAGTAACAGATCCAACCTAAA	0.601949
CCTACGCGGGATGCTCTTTTTTATAG	-1.168753
GATCCAGGAGACAGAAACCATCTACC	0.473869
TCGCAAAGAAGAACCTATTTTAAGA	0.701898
TATAATTACGCTTTTCCGTGTATGG	-0.372049
TCAATTACAGCTCGACTTCCATGATC	0.275457
AAGCCGTTCTTTAAATCCACACATTT	0.283248
AGTCCATCCTCGCGGCCTCACACCA	-0.167843
AGTCCCGTCCTACACGCTCGGTCCG	0.313519
CCCCATATCCGATTATCTGCTGGAC	0.567311
CGTAGTGGCGCAGGACCGTCAATTA	0.373652
CTCTGCTATGCCCCACCACTCAACA	0.512616
ATCCACCAATCCCTACATTCATCTTC	0.511226
GAGAGTGTCGCCGAAGCACAAGCCGA	0.469389
CCTGTCGATCTAGGTCCTATTGTCCG	0.64964
ATTTCTAACTTCTTCTGGCAACGACA	0.506169
ATATACGGCAACACGCCCGAACCAGA	0.211927
CCTCGTTAATCCTTCCCTTGTCTCCC	0.164064
TCCCCGCCACGCCCGGTATCCGACTA	-0.031521
GAAACTCGTGTTTATTCTCGTCGAT	0.704065
AAGAAAACATACAAGTCTGTTCACT	0.629363
GTGTGGAGGTCAACCTCCAAGCCCAC	-0.55043
TCGGCTTTAACCAAACCACAATCAG	0.381884
ACCCTCCCAGTGCTCTTATGTTATT	-0.149688
CATTCTTACCTCTCAACAATACACCT	0.349633
CACCCCCAACACCGGCGATTAGCATG	0.541199
TTCCAAACCGATACCTCCCCGGATG	0.371439
GCAAAGTTCCCCTTTGAACTTCTAC	0.397569
CATTGACTATAATATCACTCAACAAT	0.54906
TTGCTCGATCGCCATTTCACGATAGT	0.56468
TTTCTTCTTGTTTTCTTTCTTCATG	0.637018
GGATTTTTCGAACTGACTTTCCGGG	0.467954
CGTGCGCATCCCGTACACTCCCCGAC	0.349608
CAACCCTAATCTCGGGAATGAATCTG	0.657489
ACTGGGTTTATCCGTGATCTATGCGA	0.669683
CCACCTCACCACCCCCTGCCCCCAC	-0.481141
ACATAGCACTAGCGCCTAGAAGTTG	0.279536
GACCGAAGCCTTGAAAGTGAGTGTA	0.442718
CTTCCCTCCCCTCTTCACTAACAAT	0.237183
TGCCCTAGCCCTCCTCCACCCTCTGC	-0.361143
ACGACAAAACGGGCACAAACTCAAT	0.195673
TTTATCGGTGAAACTCGCAGTCGTAC	0.484793
GCCCTCCGCTCTCCGCAACAAATATA	0.08587
TCTACCCACCTCCGCGATAAGCTGC	0.367422
GTCTGAAGTCCCATATAGCTTTCTTT	0.366798
ACGAACTTGCGTAGAGAGCACCGAA	0.51533
TGCCTCCATTCCGATCCTTGAACGG	-0.849736
AGTAATTAGGTGTAAAGCTACTAGA	0.611746
AAACCTTCCTTAGCCCGGAAAGAACG	0.066533
GTGAACTCTGCATCACACCGTCCTA	0.305046
TAGAACTTTCGAGCAATTCTATAATC	0.589372
AACAAAGAGCTTACAAAAAACTAAA	0.540199
CACTCCCGACAAGAGAGCTCCGATC	0.404448
TGTATACTTCCGGAGATATCCTCTTT	0.9295

End of preview.

YAML Metadata Warning: empty or missing yaml metadata in repo card (https://huggingface.co/docs/hub/datasets-cards)

RNA Evalaution Tasks

Obtained from BEACON: Benchmark for Comprehensive RNA Tasks and Language Models

Tasks

Mean Ribosome Loading
Modification
ncRNA Family
Secondary Structure
Splicing

Citation

If you find this repo useful for your research, please consider citing the paper

@misc{ren2024beacon,
      title={BEACON: Benchmark for Comprehensive RNA Tasks and Language Models}, 
      author={Yuchen Ren and Zhiyuan Chen and Lifeng Qiao and Hongtai Jing and Yuchen Cai and Sheng Xu and Peng Ye and Xinzhu Ma and Siqi Sun and Hongliang Yan and Dong Yuan and Wanli Ouyang and Xihui Liu},
      year={2024},
      eprint={2406.10391},
      archivePrefix={arXiv},
      primaryClass={id='q-bio.QM' full_name='Quantitative Methods' is_active=True alt_name=None in_archive='q-bio' is_general=False description='All experimental, numerical, statistical and mathematical contributions of value to biology'}
}

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