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Datasets:
liuganghuggingface
/
InfoAlign-Data

Tasks:
Graph Machine Learning
ArXiv:
Tags:
biology
chemistry
License:
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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 2 new columns ({'pert_id', 'gene_id'}) and 2 missing columns ({'Metadata_mmoles_per_liter', 'cell_bid'}).

This happened while the csv dataset builder was generating data using

/tmp/hf-datasets-cache/medium/datasets/74656290791168-config-parquet-and-info-liuganghuggingface-InfoAl-fea82507/downloads/76a00af91259422aaa92e91a5550f4c0bee4d20fe602d29c07f1d55ecbe3cc33

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 2011, in _prepare_split_single
                  writer.write_table(table)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 585, 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 2302, in table_cast
                  return cast_table_to_schema(table, schema)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2256, in cast_table_to_schema
                  raise CastError(
              datasets.table.CastError: Couldn't cast
              gene_id: string
              mol_id: string
              smiles: string
              inchikey: string
              pert_id: string
              -- schema metadata --
              pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 830
              to
              {'cell_bid': Value(dtype='string', id=None), 'mol_id': Value(dtype='string', id=None), 'smiles': Value(dtype='string', id=None), 'inchikey': Value(dtype='string', id=None), 'Metadata_mmoles_per_liter': 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 1542, 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 1156, in convert_to_parquet
                  builder.download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1027, in download_and_prepare
                  self._download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1122, 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 1882, 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 2013, 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 2 new columns ({'pert_id', 'gene_id'}) and 2 missing columns ({'Metadata_mmoles_per_liter', 'cell_bid'}).
              
              This happened while the csv dataset builder was generating data using
              
              /tmp/hf-datasets-cache/medium/datasets/74656290791168-config-parquet-and-info-liuganghuggingface-InfoAl-fea82507/downloads/76a00af91259422aaa92e91a5550f4c0bee4d20fe602d29c07f1d55ecbe3cc33
              
              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.

cell_bid
string
mol_id
string
smiles
string
inchikey
string
Metadata_mmoles_per_liter
float64
cb2
m25219
CNC[C@H]1OCc2cnnn2CCCC(=O)N([C@H](C)CO)C[C@@H]1C
FOLOUAULJSJVDY
4.973595
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m25219
CNC[C@@H]1OCc2cnnn2CCCC(=O)N([C@@H](C)CO)C[C@H]1C
FOLOUAULJSJVDY
4.912934
cb4
m25219
CNC[C@@H]1OCc2cnnn2CCCC(=O)N([C@H](C)CO)C[C@H]1C
FOLOUAULJSJVDY
5.012874
cb16
m13874
C[C@H](CO)N1C[C@H](C)[C@@H](CN(C)C(=O)CCC(F)(F)F)OCc2cn(nn2)CCCC1=O
CMMUKIKJYLMGMW
5.107148
cb17
m13874
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CMMUKIKJYLMGMW
5.034691
cb18
m13874
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CMMUKIKJYLMGMW
4.941934
cb20
m34082
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HEIBNMHSSNMFIU
5.00412
cb21
m34082
C[C@H]1CN([C@@H](C)CO)C(=O)CCCn2cc(nn2)CO[C@@H]1CN(C)C(=O)C1CC1
HEIBNMHSSNMFIU
4.954627
cb28
m104318
CC(C)COC(=O)N(C)C[C@@H]1OCc2cn(nn2)CCCC(=O)N([C@@H](C)CO)C[C@H]1C
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5.000144
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m104318
CC(C)COC(=O)N(C)C[C@H]1OCc2cn(nn2)CCCC(=O)N([C@@H](C)CO)C[C@@H]1C
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5.032085
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CC(C)COC(=O)N(C)C[C@@H]1OCc2cn(nn2)CCCC(=O)N([C@H](C)CO)C[C@H]1C
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5.011832
cb31
m49502
C[C@H](CO)N1C[C@H](C)[C@@H](CN(C)S(=O)(=O)c2ccccc2F)OCc2cn(nn2)CCCC1=O
JYOVEVCXPRGJRX
5.018675
cb32
m49502
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JYOVEVCXPRGJRX
5.006231
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C[C@H]1CN([C@@H](C)CO)C(=O)CCCn2cc(nn2)CO[C@@H]1CN(C)S(=O)(=O)c1ccccc1F
JYOVEVCXPRGJRX
4.977088
cb34
m49502
C[C@@H]1CN([C@H](C)CO)C(=O)CCCn2cc(nn2)CO[C@H]1CN(C)S(=O)(=O)c1ccccc1F
JYOVEVCXPRGJRX
4.931146
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4.915798
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HYHIJLYQTCYSKX
4.963155
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4.984176
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C[C@H](CO)N1C[C@H](C)[C@@H](CN(C)Cc2cccc3c2OCCCO3)OCc2cnnn2CCCC1=O
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5.078081
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5.137466
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cb208
m75157
C/C=C/c1ccc2n(c1=O)C[C@H]1[C@H](CO)[C@@H](C(=O)OC)[C@@H]2N1S(=O)(=O)c1cccc(C)c1.C/C=C\c1ccc2n(c1=O)C[C@H]1[C@H](CO)[C@@H](C(=O)OC)[C@@H]2N1S(=O)(=O)c1cccc(C)c1
OPJCSXFNIRQLBQ
4.970894
cb209
m75157
C/C=C/c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(=O)OC)[C@H]2N1S(=O)(=O)c1cccc(C)c1.C/C=C\c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(=O)OC)[C@H]2N1S(=O)(=O)c1cccc(C)c1
OPJCSXFNIRQLBQ
5.046707
cb210
m33105
C/C=C/c1ccc2n(c1=O)C[C@H]1[C@H](CO)[C@@H](C(O)=NCc3cccc(OC)c3)N[C@@H]21.C/C=C\c1ccc2n(c1=O)C[C@H]1[C@H](CO)[C@@H](C(O)=NCc3cccc(OC)c3)N[C@@H]21
GZTMFBFGJVKLKE
5.004025
cb211
m33105
C/C=C/c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(O)=NCc3cccc(OC)c3)N[C@H]21.C/C=C\c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(O)=NCc3cccc(OC)c3)N[C@H]21
GZTMFBFGJVKLKE
5.003749
cb214
m61000
C/C=C/c1ccc2n(c1=O)C[C@H]1[C@H](CO)[C@@H](C(O)=NC3CCC3)[C@@H]2N1S(=O)(=O)c1cn(C)cn1.C/C=C\c1ccc2n(c1=O)C[C@H]1[C@H](CO)[C@@H](C(O)=NC3CCC3)[C@@H]2N1S(=O)(=O)c1cn(C)cn1
MAYPJGPMDPCVRU
5.013725
cb215
m61000
C/C=C/c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(O)=NC3CCC3)[C@H]2N1S(=O)(=O)c1cn(C)cn1.C/C=C\c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(O)=NC3CCC3)[C@H]2N1S(=O)(=O)c1cn(C)cn1
MAYPJGPMDPCVRU
4.994823
cb216
m65679
C/C=C/c1ccc2n(c1=O)C[C@H]1[C@H](CO)[C@@H](C(=O)N(C)C)[C@@H]2N1C(=O)c1ccc(F)cc1.C/C=C\c1ccc2n(c1=O)C[C@H]1[C@H](CO)[C@@H](C(=O)N(C)C)[C@@H]2N1C(=O)c1ccc(F)cc1
MWRJRRDCKGAZGY
5.025057
cb217
m65679
C/C=C/c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(=O)N(C)C)[C@H]2N1C(=O)c1ccc(F)cc1.C/C=C\c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(=O)N(C)C)[C@H]2N1C(=O)c1ccc(F)cc1
MWRJRRDCKGAZGY
4.997863
cb218
m17434
C/C=C/c1ccc2n(c1=O)C[C@H]1[C@H](CO)[C@@H](C(O)=NCC)[C@@H]2N1Cc1cccc(Cl)c1.C/C=C\c1ccc2n(c1=O)C[C@H]1[C@H](CO)[C@@H](C(O)=NCC)[C@@H]2N1Cc1cccc(Cl)c1
DDLCGIHGNSZQJS
5.013044
cb219
m17434
C/C=C/c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(O)=NCC)[C@H]2N1Cc1cccc(Cl)c1.C/C=C\c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(O)=NCC)[C@H]2N1Cc1cccc(Cl)c1
DDLCGIHGNSZQJS
5.009739
cb220
m5891
C/C=C/c1ccc2n(c1=O)C[C@H]1[C@H](CO)[C@@H](C(O)=NCC)N(Cc3ccccc3Cl)[C@@H]21.C/C=C\c1ccc2n(c1=O)C[C@H]1[C@H](CO)[C@@H](C(O)=NCC)N(Cc3ccccc3Cl)[C@@H]21
BBJDFTMDCDCETN
4.980708
cb221
m5891
C/C=C/c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(O)=NCC)N(Cc3ccccc3Cl)[C@H]21.C/C=C\c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(O)=NCC)N(Cc3ccccc3Cl)[C@H]21
BBJDFTMDCDCETN
5.044683
cb222
m38021
C/C=C/c1ccc2n(c1=O)C[C@H]1[C@H](CO)[C@@H](C(=O)OC)N(CCc3ccccc3)[C@@H]21.C/C=C\c1ccc2n(c1=O)C[C@H]1[C@H](CO)[C@@H](C(=O)OC)N(CCc3ccccc3)[C@@H]21
HWXVAOXZBVDFCJ
4.999661
cb223
m38021
C/C=C/c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(=O)OC)N(CCc3ccccc3)[C@H]21.C/C=C\c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(=O)OC)N(CCc3ccccc3)[C@H]21
HWXVAOXZBVDFCJ
4.994211
cb224
m115136
C/C=C/c1ccc2n(c1=O)C[C@H]1[C@H](CO)[C@@H](C(O)=NCCc3cn(C)cn3)[C@@H]2N1C(=O)CC.C/C=C\c1ccc2n(c1=O)C[C@H]1[C@H](CO)[C@@H](C(O)=NCCc3cn(C)cn3)[C@@H]2N1C(=O)CC
WMZNZTBMFPTLSB
5.007921
cb225
m115136
C/C=C/c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(O)=NCCc3cn(C)cn3)[C@H]2N1C(=O)CC.C/C=C\c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(O)=NCCc3cn(C)cn3)[C@H]2N1C(=O)CC
WMZNZTBMFPTLSB
5.015007
cb226
m64942
C/C=C/c1ccc2n(c1=O)C[C@H]1[C@H](CO)[C@@H](C(O)=NCC3CCCCC3)[C@@H]2N1C(C)=O.C/C=C\c1ccc2n(c1=O)C[C@H]1[C@H](CO)[C@@H](C(O)=NCC3CCCCC3)[C@@H]2N1C(C)=O
MTFSLJXEIRKOKM
5.013939
cb227
m64942
C/C=C/c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(O)=NCC3CCCCC3)[C@H]2N1C(C)=O.C/C=C\c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(O)=NCC3CCCCC3)[C@H]2N1C(C)=O
MTFSLJXEIRKOKM
5.006081
cb230
m59020
C/C=C/c1ccc2n(c1=O)C[C@H]1[C@H](CO)[C@@H](C(O)=Nc3nccs3)N(Cc3cc(F)ccc3F)[C@@H]21.C/C=C\c1ccc2n(c1=O)C[C@H]1[C@H](CO)[C@@H](C(O)=Nc3nccs3)N(Cc3cc(F)ccc3F)[C@@H]21
LROWCOSISYCRIQ
5.047529
cb231
m59020
C/C=C/c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(O)=Nc3nccs3)N(Cc3cc(F)ccc3F)[C@H]21.C/C=C\c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(O)=Nc3nccs3)N(Cc3cc(F)ccc3F)[C@H]21
LROWCOSISYCRIQ
5.007773
cb232
m84316
C/C=C/c1ccc2n(c1=O)C[C@H]1[C@H](CO)[C@@H](C(O)=NCCC)[C@@H]2N1C(O)=Nc1cc(F)ccc1F.C/C=C\c1ccc2n(c1=O)C[C@H]1[C@H](CO)[C@@H](C(O)=NCCC)[C@@H]2N1C(O)=Nc1cc(F)ccc1F
QFZYXZULAIJTQK
4.993766
cb233
m84316
C/C=C/c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(O)=NCCC)[C@H]2N1C(O)=Nc1cc(F)ccc1F.C/C=C\c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(O)=NCCC)[C@H]2N1C(O)=Nc1cc(F)ccc1F
QFZYXZULAIJTQK
4.998789
cb234
m37932
C/C=C/c1ccc2n(c1=O)C[C@H]1[C@H](CO)[C@@H](C(O)=NC3CCC3)[C@@H]2N1C(=O)c1ccccn1.C/C=C\c1ccc2n(c1=O)C[C@H]1[C@H](CO)[C@@H](C(O)=NC3CCC3)[C@@H]2N1C(=O)c1ccccn1
HWNQSPGDBFKSOQ
5.005149
cb235
m37932
C/C=C/c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(O)=NC3CCC3)[C@H]2N1C(=O)c1ccccn1.C/C=C\c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(O)=NC3CCC3)[C@H]2N1C(=O)c1ccccn1
HWNQSPGDBFKSOQ
5.058564
cb238
m29024
C/C=C/c1ccc2n(c1=O)C[C@H]1[C@H](CO)[C@@H](C(O)=NCc3ccc(F)cc3)[C@@H]2N1CCC.C/C=C\c1ccc2n(c1=O)C[C@H]1[C@H](CO)[C@@H](C(O)=NCc3ccc(F)cc3)[C@@H]2N1CCC
GGIDMMYQUXUKCO
5.034635
cb239
m29024
C/C=C/c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(O)=NCc3ccc(F)cc3)[C@H]2N1CCC.C/C=C\c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(O)=NCc3ccc(F)cc3)[C@H]2N1CCC
GGIDMMYQUXUKCO
5.018146
cb242
m86093
C/C=C/c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(O)=N[C@@H](C)c3ccccc3)[C@H]2N1CC.C/C=C\c1ccc2n(c1=O)C[C@@H]1[C@@H](CO)[C@H](C(O)=N[C@@H](C)c3ccccc3)[C@H]2N1CC
QNYIUHHVJKFROO
4.963266
End of preview.

The dataset for the paper "Learning Molecular Representation in a Cell".

For pretraining: Place the files from pretrain_raw into raw_data/pretrain/raw.

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