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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 1306 new columns ({'MB-2778', 'MB-4012', 'MB-0120', 'MB-0451', 'MB-4666', 'MB-4578', 'MB-7081', 'MB-6359', 'MB-0198', 'MB-6178', 'MB-4785', 'MB-4626', 'MB-0167', 'MB-7295', 'MB-0249', 'MB-4737', 'MB-0519', 'MB-4692', 'MB-4784', 'MB-2845', 'MB-7185', 'MB-5011', 'MB-5043', 'MB-4749', 'MB-4925', 'MB-4982', 'MB-0487', 'MB-5591', 'MB-3500', 'MB-6085', 'MB-0481', 'MB-0600', 'MB-4881', 'MB-0553', 'MB-5308', 'MB-4416', 'MB-0891', 'MB-0436', 'MB-4119', 'MB-4024', 'MB-7056', 'MB-0438', 'MB-7090', 'MB-0093', 'MB-0284', 'MB-0315', 'MB-5004', 'MB-0202', 'MB-6263', 'MB-5139', 'MB-2629', 'MB-5567', 'MB-4965', 'MB-4707', 'MB-7154', 'MB-4871', 'MB-6184', 'MB-4938', 'MB-7141', 'MB-5226', 'MB-4716', 'MB-5431', 'MB-5347', 'MB-7189', 'MB-3083', 'MB-0142', 'MB-4735', 'MB-0615', 'MB-5455', 'MB-4353', 'MB-7200', 'MB-4708', 'MB-5450', 'MB-5124', 'MB-5412', 'MB-4858', 'MB-5475', 'MB-4643', 'MB-4618', 'MB-5072', 'MB-5163', 'MB-5414', 'MB-2669', 'MB-0270', 'MB-0215', 'MB-5559', 'MB-0526', 'MB-0166', 'MB-5397', 'MB-0660', 'MB-4332', 'MB-6024', 'MB-0305', 'MB-7269', 'MB-4434', 'MB-0134', 'MB-3110', 'MB-6036', 'MB-4710', 'MB-5130', 'MB-7228', 'MB-5267', 'MB-4764', 'MB-4717', 'MB-5425', 'MB-5299', 'MB-2643', 'MB-3567', 'MB-4654', 'MB-2686', 'MB-4968', 'MB-0201', 'MB-7218', 'MB-7130', 'MB-3711', 'MB-7065', 'MB-0162', 'MB-0605', 'MB-0178', 'MB-0410', 'MB-5312', 'MB-5322', 'MB-3088', 'MB-4904', 'MB-0356', 'MB-5013', 'MB-6188', 'MB-3360', 'MB-5565', 'MB-2763', 'MB-5277', 'MB-2919', 'MB-7287', 'MB-3389', 'MB-7054', 'MB-4672', 'MB
...
14', 'MB-4763', 'MB-5470', 'MB-6208', 'MB-5389', 'MB-2952', 'MB-5603', 'MB-5238', 'MB-5395', 'MB-0322', 'MB-6287', 'MB-5498', 'MB-4599', 'MB-5065', 'MB-6160', 'MB-0152', 'MB-3383', 'MB-0155', 'MB-3528', 'MB-0580', 'MB-7292', 'MB-2618', 'MB-7075', 'MB-7072', 'MB-6363', 'MB-5576', 'MB-5497', 'MB-2771', 'MB-0641', 'MB-4098', 'MB-3412', 'MB-6239', 'MB-0303', 'MB-3502', 'MB-3378', 'MB-0174', 'MB-0308', 'MB-7083', 'MB-3490', 'MB-2970', 'MB-5331', 'MB-0221', 'MB-0181', 'MB-5193', 'MB-5101', 'MB-4976', 'MB-0364', 'MB-7014', 'MB-2969', 'MB-7000', 'MB-0368', 'MB-2711', 'MB-5365', 'MB-7104', 'MB-5066', 'MB-4791', 'MB-0434', 'MB-4005', 'MB-0097', 'MB-0506', 'MB-6281', 'MB-2645', 'MB-0584', 'MB-0570', 'MB-5655', 'MB-0482', 'MB-5239', 'MB-3497', 'MB-7032', 'MB-2730', 'MB-3008', 'MB-0222', 'MB-7004', 'MB-0630', 'MB-3510', 'MB-5553', 'MB-7045', 'MB-6092', 'MB-3417', 'MB-5589', 'MB-3298', 'MB-5114', 'MB-7170', 'MB-3871', 'MB-5058', 'MB-5054', 'MB-4870', 'MB-5653', 'MB-7258', 'MB-4145', 'MB-2931', 'MB-2895', 'MB-3046', 'MB-5300', 'MB-0372', 'MB-0151', 'MB-4328', 'MB-5457', 'MB-7066', 'MB-7144', 'MB-4281', 'MB-3344', 'MB-6144', 'MB-2858', 'MB-4801', 'MB-2977', 'MB-4324', 'MB-0203', 'MB-2753', 'MB-5390', 'MB-4897', 'MB-5126', 'MB-7127', 'MB-0121', 'MB-6105', 'MB-5543', 'MB-2960', 'MB-3063', 'MB-3165', 'MB-7226', 'MB-5053', 'MB-4935', 'MB-4839', 'MB-7205', 'MB-4743', 'MB-0466', 'MB-0453', 'MB-4996', 'MB-6211', 'MB-7232', 'MB-6083', 'MB-4141', 'MB-3211', 'MB-0496', 'MB-7244', 'MB-7060', 'MB-5388'}) and 23 missing columns ({'HISTOLOGICAL_SUBTYPE', 'OS_STATUS', 'BREAST_SURGERY', 'VITAL_STATUS', 'INTCLUST', 'AGE_AT_DIAGNOSIS', 'ER_IHC', 'RFS_MONTHS', 'CHEMOTHERAPY', 'INFERRED_MENOPAUSAL_STATE', 'HORMONE_THERAPY', 'NPI', 'RFS_STATUS', 'CLAUDIN_SUBTYPE', 'THREEGENE', 'LATERALITY', 'OS_MONTHS', 'RADIO_THERAPY', 'HER2_SNP6', 'COHORT', 'SEX', 'CELLULARITY', 'LYMPH_NODES_EXAMINED_POSITIVE'}).
This happened while the csv dataset builder was generating data using
hf://datasets/huseyincavus/flexynesis-datasets/brca_metabric_processed/train/cna.csv (at revision 69b9b84b0f230dd3a6c8d347599ca8470ac82ed3), [/tmp/hf-datasets-cache/medium/datasets/92917345236671-config-parquet-and-info-huseyincavus-flexynesis-d-d8c38db6/hub/datasets--huseyincavus--flexynesis-datasets/snapshots/69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/brca_metabric_processed/train/clin.csv (origin=hf://datasets/huseyincavus/flexynesis-datasets@69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/brca_metabric_processed/train/clin.csv), /tmp/hf-datasets-cache/medium/datasets/92917345236671-config-parquet-and-info-huseyincavus-flexynesis-d-d8c38db6/hub/datasets--huseyincavus--flexynesis-datasets/snapshots/69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/brca_metabric_processed/train/cna.csv (origin=hf://datasets/huseyincavus/flexynesis-datasets@69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/brca_metabric_processed/train/cna.csv), /tmp/hf-datasets-cache/medium/datasets/92917345236671-config-parquet-and-info-huseyincavus-flexynesis-d-d8c38db6/hub/datasets--huseyincavus--flexynesis-datasets/snapshots/69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/brca_metabric_processed/train/gex.csv (origin=hf://datasets/huseyincavus/flexynesis-datasets@69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/brca_metabric_processed/train/gex.csv), /tmp/hf-datasets-cache/medium/datasets/92917345236671-config-parquet-and-info-huseyincavus-flexynesis-d-d8c38db6/hub/datasets--huseyincavus--flexynesis-datasets/snapshots/69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/brca_metabric_processed/train/mut.csv (origin=hf://datasets/huseyincavus/flexynesis-datasets@69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/brca_metabric_processed/train/mut.csv), /tmp/hf-datasets-cache/medium/datasets/92917345236671-config-parquet-and-info-huseyincavus-flexynesis-d-d8c38db6/hub/datasets--huseyincavus--flexynesis-datasets/snapshots/69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/dataset1/train/clin.csv (origin=hf://datasets/huseyincavus/flexynesis-datasets@69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/dataset1/train/clin.csv), /tmp/hf-datasets-cache/medium/datasets/92917345236671-config-parquet-and-info-huseyincavus-flexynesis-d-d8c38db6/hub/datasets--huseyincavus--flexynesis-datasets/snapshots/69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/dataset1/train/cnv.csv (origin=hf://datasets/huseyincavus/flexynesis-datasets@69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/dataset1/train/cnv.csv), /tmp/hf-datasets-cache/medium/datasets/92917345236671-config-parquet-and-info-huseyincavus-flexynesis-d-d8c38db6/hub/datasets--huseyincavus--flexynesis-datasets/snapshots/69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/dataset1/train/gex.csv (origin=hf://datasets/huseyincavus/flexynesis-datasets@69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/dataset1/train/gex.csv), /tmp/hf-datasets-cache/medium/datasets/92917345236671-config-parquet-and-info-huseyincavus-flexynesis-d-d8c38db6/hub/datasets--huseyincavus--flexynesis-datasets/snapshots/69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/dataset2/train/clin.csv (origin=hf://datasets/huseyincavus/flexynesis-datasets@69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/dataset2/train/clin.csv), /tmp/hf-datasets-cache/medium/datasets/92917345236671-config-parquet-and-info-huseyincavus-flexynesis-d-d8c38db6/hub/datasets--huseyincavus--flexynesis-datasets/snapshots/69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/dataset2/train/gex.csv (origin=hf://datasets/huseyincavus/flexynesis-datasets@69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/dataset2/train/gex.csv), /tmp/hf-datasets-cache/medium/datasets/92917345236671-config-parquet-and-info-huseyincavus-flexynesis-d-d8c38db6/hub/datasets--huseyincavus--flexynesis-datasets/snapshots/69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/dataset2/train/meth.csv (origin=hf://datasets/huseyincavus/flexynesis-datasets@69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/dataset2/train/meth.csv), /tmp/hf-datasets-cache/medium/datasets/92917345236671-config-parquet-and-info-huseyincavus-flexynesis-d-d8c38db6/hub/datasets--huseyincavus--flexynesis-datasets/snapshots/69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/lgggbm_tcga_pub_processed/train/clin.csv (origin=hf://datasets/huseyincavus/flexynesis-datasets@69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/lgggbm_tcga_pub_processed/train/clin.csv), /tmp/hf-datasets-cache/medium/datasets/92917345236671-config-parquet-and-info-huseyincavus-flexynesis-d-d8c38db6/hub/datasets--huseyincavus--flexynesis-datasets/snapshots/69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/lgggbm_tcga_pub_processed/train/cna.csv (origin=hf://datasets/huseyincavus/flexynesis-datasets@69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/lgggbm_tcga_pub_processed/train/cna.csv), /tmp/hf-datasets-cache/medium/datasets/92917345236671-config-parquet-and-info-huseyincavus-flexynesis-d-d8c38db6/hub/datasets--huseyincavus--flexynesis-datasets/snapshots/69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/lgggbm_tcga_pub_processed/train/mut.csv (origin=hf://datasets/huseyincavus/flexynesis-datasets@69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/lgggbm_tcga_pub_processed/train/mut.csv), /tmp/hf-datasets-cache/medium/datasets/92917345236671-config-parquet-and-info-huseyincavus-flexynesis-d-d8c38db6/hub/datasets--huseyincavus--flexynesis-datasets/snapshots/69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/singlecell_bonemarrow/train/ADT.csv (origin=hf://datasets/huseyincavus/flexynesis-datasets@69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/singlecell_bonemarrow/train/ADT.csv), /tmp/hf-datasets-cache/medium/datasets/92917345236671-config-parquet-and-info-huseyincavus-flexynesis-d-d8c38db6/hub/datasets--huseyincavus--flexynesis-datasets/snapshots/69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/singlecell_bonemarrow/train/RNA.csv (origin=hf://datasets/huseyincavus/flexynesis-datasets@69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/singlecell_bonemarrow/train/RNA.csv), /tmp/hf-datasets-cache/medium/datasets/92917345236671-config-parquet-and-info-huseyincavus-flexynesis-d-d8c38db6/hub/datasets--huseyincavus--flexynesis-datasets/snapshots/69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/singlecell_bonemarrow/train/clin.csv (origin=hf://datasets/huseyincavus/flexynesis-datasets@69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/singlecell_bonemarrow/train/clin.csv)]
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 "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1800, in _prepare_split_single
writer.write_table(table)
File "/usr/local/lib/python3.12/site-packages/datasets/arrow_writer.py", line 765, in write_table
self._write_table(pa_table, writer_batch_size=writer_batch_size)
File "/usr/local/lib/python3.12/site-packages/datasets/arrow_writer.py", line 773, in _write_table
pa_table = table_cast(pa_table, self._schema)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2321, in table_cast
return cast_table_to_schema(table, schema)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2249, in cast_table_to_schema
raise CastError(
datasets.table.CastError: Couldn't cast
MB-2960: int64
MB-0511: int64
MB-5204: int64
MB-5074: int64
MB-5322: int64
MB-5193: int64
MB-3277: int64
MB-0134: int64
MB-5171: int64
MB-5434: int64
MB-0097: int64
MB-0571: int64
MB-6337: int64
MB-0303: int64
MB-3211: int64
MB-6185: int64
MB-0641: int64
MB-4710: int64
MB-5427: int64
MB-3063: int64
MB-5408: int64
MB-4758: int64
MB-4881: int64
MB-3181: int64
MB-6156: int64
MB-5294: int64
MB-4651: int64
MB-0426: int64
MB-5453: int64
MB-2750: int64
MB-5428: int64
MB-7288: int64
MB-5211: int64
MB-0482: int64
MB-0637: int64
MB-0501: int64
MB-7044: int64
MB-5421: int64
MB-4598: int64
MB-4859: int64
MB-0269: int64
MB-7014: int64
MB-5505: int64
MB-0350: int64
MB-6154: int64
MB-0383: int64
MB-2795: int64
MB-5520: int64
MB-4862: int64
MB-3871: int64
MB-4785: int64
MB-5347: int64
MB-4741: int64
MB-3235: int64
MB-0429: int64
MB-0611: int64
MB-0245: int64
MB-5549: int64
MB-4944: int64
MB-0590: int64
MB-5599: int64
MB-4235: int64
MB-4925: int64
MB-3530: int64
MB-3360: int64
MB-0121: int64
MB-2834: int64
MB-0112: int64
MB-7232: int64
MB-0207: int64
MB-7295: int64
MB-0221: int64
MB-4888: int64
MB-5475: int64
MB-7067: int64
MB-0172: int64
MB-4855: int64
MB-6101: int64
MB-6214: int64
MB-4004: int64
MB-0062: int64
MB-5525: int64
MB-7143: int64
MB-5351: int64
MB-4897: int64
MB-5471: int64
MB-4869: int64
MB-7025: int64
MB-7038: int64
MB-0178: int64
MB-4730: int64
MB-0516: int64
MB-7015: int64
MB-5529: int64
MB-4794: int64
MB-0479: int64
MB-0273: int64
MB-4880: int64
MB-6254: int64
MB-0204: int64
...
MB-5425: int64
MB-7205: int64
MB-4024: int64
MB-7087: int64
MB-5260: int64
MB-5431: int64
MB-7231: int64
MB-5004: int64
MB-7216: int64
MB-0386: int64
MB-0352: int64
MB-0626: int64
MB-0144: int64
MB-0580: int64
MB-5646: int64
MB-4757: int64
MB-4822: int64
MB-4739: int64
MB-6141: int64
MB-6302: int64
MB-5298: int64
MB-7176: int64
MB-0398: int64
MB-0180: int64
MB-3060: int64
MB-5417: double
MB-7062: int64
MB-2827: int64
MB-3506: int64
MB-5583: int64
MB-0453: int64
MB-4935: int64
MB-3396: int64
MB-5323: int64
MB-4784: int64
MB-5530: int64
MB-7165: int64
MB-5223: int64
MB-4705: int64
MB-2953: int64
MB-6329: double
MB-2815: int64
MB-7285: int64
MB-2626: int64
MB-4993: int64
MB-7275: int64
MB-5189: int64
MB-0262: int64
MB-4886: int64
MB-5123: int64
MB-5441: int64
MB-5450: int64
MB-2999: int64
MB-7100: int64
MB-4331: int64
MB-4353: int64
MB-5238: int64
MB-3865: int64
MB-3435: int64
MB-3378: int64
MB-5513: int64
MB-4300: int64
MB-5118: int64
MB-0583: int64
MB-0558: int64
MB-0400: int64
MB-6131: int64
MB-0109: int64
MB-4928: int64
MB-0365: int64
MB-0008: double
MB-0640: int64
MB-7283: int64
MB-0353: int64
MB-7266: int64
MB-2747: int64
MB-5470: int64
MB-6189: int64
MB-5559: int64
MB-5575: int64
MB-0579: int64
MB-4899: int64
MB-0584: int64
MB-0361: int64
MB-4801: int64
MB-4670: int64
MB-5365: int64
MB-4283: int64
MB-6082: int64
MB-5073: int64
MB-0657: int64
__index_level_0__: string
-- schema metadata --
pandas: '{"index_columns": ["__index_level_0__"], "column_indexes": [{"na' + 145322
to
{'LYMPH_NODES_EXAMINED_POSITIVE': Value('int64'), 'NPI': Value('float64'), 'CELLULARITY': Value('string'), 'CHEMOTHERAPY': Value('string'), 'COHORT': Value('string'), 'ER_IHC': Value('string'), 'HER2_SNP6': Value('string'), 'HORMONE_THERAPY': Value('string'), 'INFERRED_MENOPAUSAL_STATE': Value('string'), 'SEX': Value('string'), 'INTCLUST': Value('string'), 'AGE_AT_DIAGNOSIS': Value('float64'), 'OS_MONTHS': Value('float64'), 'OS_STATUS': Value('string'), 'CLAUDIN_SUBTYPE': Value('string'), 'THREEGENE': Value('string'), 'VITAL_STATUS': Value('string'), 'LATERALITY': Value('string'), 'RADIO_THERAPY': Value('string'), 'HISTOLOGICAL_SUBTYPE': Value('string'), 'BREAST_SURGERY': Value('string'), 'RFS_STATUS': Value('string'), 'RFS_MONTHS': Value('float64'), '__index_level_0__': Value('string')}
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 1348, 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 980, in convert_to_parquet
builder.download_and_prepare(
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 882, in download_and_prepare
self._download_and_prepare(
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 943, in _download_and_prepare
self._prepare_split(split_generator, **prepare_split_kwargs)
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1646, in _prepare_split
for job_id, done, content in self._prepare_split_single(
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1802, 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 1306 new columns ({'MB-2778', 'MB-4012', 'MB-0120', 'MB-0451', 'MB-4666', 'MB-4578', 'MB-7081', 'MB-6359', 'MB-0198', 'MB-6178', 'MB-4785', 'MB-4626', 'MB-0167', 'MB-7295', 'MB-0249', 'MB-4737', 'MB-0519', 'MB-4692', 'MB-4784', 'MB-2845', 'MB-7185', 'MB-5011', 'MB-5043', 'MB-4749', 'MB-4925', 'MB-4982', 'MB-0487', 'MB-5591', 'MB-3500', 'MB-6085', 'MB-0481', 'MB-0600', 'MB-4881', 'MB-0553', 'MB-5308', 'MB-4416', 'MB-0891', 'MB-0436', 'MB-4119', 'MB-4024', 'MB-7056', 'MB-0438', 'MB-7090', 'MB-0093', 'MB-0284', 'MB-0315', 'MB-5004', 'MB-0202', 'MB-6263', 'MB-5139', 'MB-2629', 'MB-5567', 'MB-4965', 'MB-4707', 'MB-7154', 'MB-4871', 'MB-6184', 'MB-4938', 'MB-7141', 'MB-5226', 'MB-4716', 'MB-5431', 'MB-5347', 'MB-7189', 'MB-3083', 'MB-0142', 'MB-4735', 'MB-0615', 'MB-5455', 'MB-4353', 'MB-7200', 'MB-4708', 'MB-5450', 'MB-5124', 'MB-5412', 'MB-4858', 'MB-5475', 'MB-4643', 'MB-4618', 'MB-5072', 'MB-5163', 'MB-5414', 'MB-2669', 'MB-0270', 'MB-0215', 'MB-5559', 'MB-0526', 'MB-0166', 'MB-5397', 'MB-0660', 'MB-4332', 'MB-6024', 'MB-0305', 'MB-7269', 'MB-4434', 'MB-0134', 'MB-3110', 'MB-6036', 'MB-4710', 'MB-5130', 'MB-7228', 'MB-5267', 'MB-4764', 'MB-4717', 'MB-5425', 'MB-5299', 'MB-2643', 'MB-3567', 'MB-4654', 'MB-2686', 'MB-4968', 'MB-0201', 'MB-7218', 'MB-7130', 'MB-3711', 'MB-7065', 'MB-0162', 'MB-0605', 'MB-0178', 'MB-0410', 'MB-5312', 'MB-5322', 'MB-3088', 'MB-4904', 'MB-0356', 'MB-5013', 'MB-6188', 'MB-3360', 'MB-5565', 'MB-2763', 'MB-5277', 'MB-2919', 'MB-7287', 'MB-3389', 'MB-7054', 'MB-4672', 'MB
...
14', 'MB-4763', 'MB-5470', 'MB-6208', 'MB-5389', 'MB-2952', 'MB-5603', 'MB-5238', 'MB-5395', 'MB-0322', 'MB-6287', 'MB-5498', 'MB-4599', 'MB-5065', 'MB-6160', 'MB-0152', 'MB-3383', 'MB-0155', 'MB-3528', 'MB-0580', 'MB-7292', 'MB-2618', 'MB-7075', 'MB-7072', 'MB-6363', 'MB-5576', 'MB-5497', 'MB-2771', 'MB-0641', 'MB-4098', 'MB-3412', 'MB-6239', 'MB-0303', 'MB-3502', 'MB-3378', 'MB-0174', 'MB-0308', 'MB-7083', 'MB-3490', 'MB-2970', 'MB-5331', 'MB-0221', 'MB-0181', 'MB-5193', 'MB-5101', 'MB-4976', 'MB-0364', 'MB-7014', 'MB-2969', 'MB-7000', 'MB-0368', 'MB-2711', 'MB-5365', 'MB-7104', 'MB-5066', 'MB-4791', 'MB-0434', 'MB-4005', 'MB-0097', 'MB-0506', 'MB-6281', 'MB-2645', 'MB-0584', 'MB-0570', 'MB-5655', 'MB-0482', 'MB-5239', 'MB-3497', 'MB-7032', 'MB-2730', 'MB-3008', 'MB-0222', 'MB-7004', 'MB-0630', 'MB-3510', 'MB-5553', 'MB-7045', 'MB-6092', 'MB-3417', 'MB-5589', 'MB-3298', 'MB-5114', 'MB-7170', 'MB-3871', 'MB-5058', 'MB-5054', 'MB-4870', 'MB-5653', 'MB-7258', 'MB-4145', 'MB-2931', 'MB-2895', 'MB-3046', 'MB-5300', 'MB-0372', 'MB-0151', 'MB-4328', 'MB-5457', 'MB-7066', 'MB-7144', 'MB-4281', 'MB-3344', 'MB-6144', 'MB-2858', 'MB-4801', 'MB-2977', 'MB-4324', 'MB-0203', 'MB-2753', 'MB-5390', 'MB-4897', 'MB-5126', 'MB-7127', 'MB-0121', 'MB-6105', 'MB-5543', 'MB-2960', 'MB-3063', 'MB-3165', 'MB-7226', 'MB-5053', 'MB-4935', 'MB-4839', 'MB-7205', 'MB-4743', 'MB-0466', 'MB-0453', 'MB-4996', 'MB-6211', 'MB-7232', 'MB-6083', 'MB-4141', 'MB-3211', 'MB-0496', 'MB-7244', 'MB-7060', 'MB-5388'}) and 23 missing columns ({'HISTOLOGICAL_SUBTYPE', 'OS_STATUS', 'BREAST_SURGERY', 'VITAL_STATUS', 'INTCLUST', 'AGE_AT_DIAGNOSIS', 'ER_IHC', 'RFS_MONTHS', 'CHEMOTHERAPY', 'INFERRED_MENOPAUSAL_STATE', 'HORMONE_THERAPY', 'NPI', 'RFS_STATUS', 'CLAUDIN_SUBTYPE', 'THREEGENE', 'LATERALITY', 'OS_MONTHS', 'RADIO_THERAPY', 'HER2_SNP6', 'COHORT', 'SEX', 'CELLULARITY', 'LYMPH_NODES_EXAMINED_POSITIVE'}).
This happened while the csv dataset builder was generating data using
hf://datasets/huseyincavus/flexynesis-datasets/brca_metabric_processed/train/cna.csv (at revision 69b9b84b0f230dd3a6c8d347599ca8470ac82ed3), [/tmp/hf-datasets-cache/medium/datasets/92917345236671-config-parquet-and-info-huseyincavus-flexynesis-d-d8c38db6/hub/datasets--huseyincavus--flexynesis-datasets/snapshots/69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/brca_metabric_processed/train/clin.csv (origin=hf://datasets/huseyincavus/flexynesis-datasets@69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/brca_metabric_processed/train/clin.csv), /tmp/hf-datasets-cache/medium/datasets/92917345236671-config-parquet-and-info-huseyincavus-flexynesis-d-d8c38db6/hub/datasets--huseyincavus--flexynesis-datasets/snapshots/69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/brca_metabric_processed/train/cna.csv (origin=hf://datasets/huseyincavus/flexynesis-datasets@69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/brca_metabric_processed/train/cna.csv), /tmp/hf-datasets-cache/medium/datasets/92917345236671-config-parquet-and-info-huseyincavus-flexynesis-d-d8c38db6/hub/datasets--huseyincavus--flexynesis-datasets/snapshots/69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/brca_metabric_processed/train/gex.csv (origin=hf://datasets/huseyincavus/flexynesis-datasets@69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/brca_metabric_processed/train/gex.csv), /tmp/hf-datasets-cache/medium/datasets/92917345236671-config-parquet-and-info-huseyincavus-flexynesis-d-d8c38db6/hub/datasets--huseyincavus--flexynesis-datasets/snapshots/69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/brca_metabric_processed/train/mut.csv (origin=hf://datasets/huseyincavus/flexynesis-datasets@69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/brca_metabric_processed/train/mut.csv), /tmp/hf-datasets-cache/medium/datasets/92917345236671-config-parquet-and-info-huseyincavus-flexynesis-d-d8c38db6/hub/datasets--huseyincavus--flexynesis-datasets/snapshots/69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/dataset1/train/clin.csv (origin=hf://datasets/huseyincavus/flexynesis-datasets@69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/dataset1/train/clin.csv), /tmp/hf-datasets-cache/medium/datasets/92917345236671-config-parquet-and-info-huseyincavus-flexynesis-d-d8c38db6/hub/datasets--huseyincavus--flexynesis-datasets/snapshots/69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/dataset1/train/cnv.csv (origin=hf://datasets/huseyincavus/flexynesis-datasets@69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/dataset1/train/cnv.csv), /tmp/hf-datasets-cache/medium/datasets/92917345236671-config-parquet-and-info-huseyincavus-flexynesis-d-d8c38db6/hub/datasets--huseyincavus--flexynesis-datasets/snapshots/69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/dataset1/train/gex.csv 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/tmp/hf-datasets-cache/medium/datasets/92917345236671-config-parquet-and-info-huseyincavus-flexynesis-d-d8c38db6/hub/datasets--huseyincavus--flexynesis-datasets/snapshots/69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/lgggbm_tcga_pub_processed/train/cna.csv (origin=hf://datasets/huseyincavus/flexynesis-datasets@69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/lgggbm_tcga_pub_processed/train/cna.csv), /tmp/hf-datasets-cache/medium/datasets/92917345236671-config-parquet-and-info-huseyincavus-flexynesis-d-d8c38db6/hub/datasets--huseyincavus--flexynesis-datasets/snapshots/69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/lgggbm_tcga_pub_processed/train/mut.csv (origin=hf://datasets/huseyincavus/flexynesis-datasets@69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/lgggbm_tcga_pub_processed/train/mut.csv), 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/tmp/hf-datasets-cache/medium/datasets/92917345236671-config-parquet-and-info-huseyincavus-flexynesis-d-d8c38db6/hub/datasets--huseyincavus--flexynesis-datasets/snapshots/69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/singlecell_bonemarrow/train/clin.csv (origin=hf://datasets/huseyincavus/flexynesis-datasets@69b9b84b0f230dd3a6c8d347599ca8470ac82ed3/singlecell_bonemarrow/train/clin.csv)]
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.
LYMPH_NODES_EXAMINED_POSITIVE int64 | NPI float64 | CELLULARITY string | CHEMOTHERAPY string | COHORT string | ER_IHC string | HER2_SNP6 string | HORMONE_THERAPY string | INFERRED_MENOPAUSAL_STATE string | SEX string | INTCLUST string | AGE_AT_DIAGNOSIS float64 | OS_MONTHS float64 | OS_STATUS string | CLAUDIN_SUBTYPE string | THREEGENE string | VITAL_STATUS string | LATERALITY string | RADIO_THERAPY string | HISTOLOGICAL_SUBTYPE string | BREAST_SURGERY string | RFS_STATUS string | RFS_MONTHS float64 | __index_level_0__ string |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | 4.05 | Moderate | NO | cohort2 | Positve | NEUTRAL | YES | Post | Female | 6 | 69.67 | 222.2 | 1:DECEASED | LumA | ER+/HER2- Low Prolif | Died of Other Causes | Left | NO | Ductal/NST | MASTECTOMY | 0:Not Recurred | 219.28 | MB-2960 |
0 | 3.062 | Moderate | NO | cohort1 | Positve | NEUTRAL | YES | Post | Female | 3 | 59.84 | 61.7 | 0:LIVING | LumA | ER+/HER2- Low Prolif | Living | Left | YES | Ductal/NST | MASTECTOMY | 0:Not Recurred | 60.89 | MB-0511 |
3 | 2.048 | Moderate | NO | cohort3 | Positve | NEUTRAL | YES | Post | Female | 3 | 76.91 | 191.933333 | 1:DECEASED | LumA | ER+/HER2- Low Prolif | Died of Other Causes | Right | NO | Ductal/NST | BREAST CONSERVING | 1:Recurred | 158.06 | MB-5204 |
0 | 4.05 | High | NO | cohort3 | Positve | NEUTRAL | YES | Post | Female | 3 | 70.59 | 221.6 | 1:DECEASED | LumA | ER+/HER2- High Prolif | Died of Other Causes | Left | YES | Lobular | BREAST CONSERVING | 1:Recurred | 161.97 | MB-5074 |
1 | 4.046 | Moderate | NO | cohort3 | Positve | NEUTRAL | YES | Post | Female | 2 | 66.58 | 102.3 | 1:DECEASED | LumA | ER+/HER2- High Prolif | Died of Disease | Right | YES | Mixed | BREAST CONSERVING | 1:Recurred | 66.55 | MB-5322 |
1 | 3.06 | Moderate | NO | cohort3 | Positve | NEUTRAL | YES | Post | Female | 7 | 88.8 | 54.266667 | 1:DECEASED | LumA | ER+/HER2- High Prolif | Died of Other Causes | Left | NO | Ductal/NST | MASTECTOMY | 0:Not Recurred | 53.55 | MB-5193 |
3 | 5.06 | High | YES | cohort2 | Negative | NEUTRAL | NO | Pre | Female | 1 | 29.92 | 32.933333 | 1:DECEASED | Basal | ER-/HER2- | Died of Disease | Left | YES | Ductal/NST | MASTECTOMY | 1:Recurred | 22.11 | MB-3277 |
3 | 5.044 | High | NO | cohort1 | Positve | NEUTRAL | YES | Post | Female | 8 | 73.11 | 12.933333 | 1:DECEASED | LumB | ER+/HER2- High Prolif | Died of Disease | Left | YES | Ductal/NST | MASTECTOMY | 1:Recurred | 11.71 | MB-0134 |
0 | 3.022 | Low | NO | cohort3 | Positve | NEUTRAL | NO | Pre | Female | 4ER+ | 46.79 | 185 | 1:DECEASED | Normal | ER+/HER2- Low Prolif | Died of Disease | Right | YES | Ductal/NST | BREAST CONSERVING | 1:Recurred | 126.02 | MB-5171 |
1 | 5.11 | Low | NO | cohort3 | Positve | NEUTRAL | YES | Post | Female | 9 | 71.07 | 45.166667 | 1:DECEASED | LumB | ER+/HER2- High Prolif | Died of Disease | Left | NO | Ductal/NST | MASTECTOMY | 1:Recurred | 37.53 | MB-5434 |
3 | 5.06 | High | NO | cohort1 | Positve | NEUTRAL | YES | Post | Female | 8 | 78.19 | 98.7 | 0:LIVING | LumA | null | Living | Left | YES | Ductal/NST | MASTECTOMY | 0:Not Recurred | 97.4 | MB-0097 |
0 | 2.04 | Moderate | NO | cohort1 | Positve | NEUTRAL | YES | Post | Female | 7 | 61.79 | 149.866667 | 0:LIVING | LumA | ER+/HER2- High Prolif | Living | Right | YES | Ductal/NST | MASTECTOMY | 0:Not Recurred | 147.89 | MB-0571 |
14 | 6.11 | High | YES | cohort5 | Negative | GAIN | NO | Post | Female | 5 | 58.25 | 110.866667 | 1:DECEASED | Basal | HER2+ | Died of Other Causes | Right | YES | Ductal/NST | MASTECTOMY | 0:Not Recurred | 109.41 | MB-6337 |
0 | 4.022 | Low | NO | cohort1 | Negative | NEUTRAL | YES | Pre | Female | 10 | 47.71 | 60.133333 | 0:LIVING | claudin-low | ER-/HER2- | Living | Left | NO | Ductal/NST | MASTECTOMY | 0:Not Recurred | 59.34 | MB-0303 |
0 | 4.026 | High | NO | cohort2 | Negative | NEUTRAL | YES | Post | Female | 10 | 58.31 | 145.5 | 0:LIVING | Basal | ER-/HER2- | Living | Right | YES | Ductal/NST | BREAST CONSERVING | 0:Not Recurred | 143.59 | MB-3211 |
0 | 2.032 | Low | NO | cohort5 | Positve | NEUTRAL | NO | Post | Female | 3 | 75.44 | 197.733333 | 1:DECEASED | LumA | ER+/HER2- Low Prolif | Died of Other Causes | Right | NO | Mixed | MASTECTOMY | 0:Not Recurred | 195.13 | MB-6185 |
1 | 4.028 | Moderate | NO | cohort1 | Positve | NEUTRAL | YES | Post | Female | 4ER+ | 56.34 | 102.566667 | 0:LIVING | claudin-low | ER+/HER2- Low Prolif | Living | Right | YES | Ductal/NST | BREAST CONSERVING | 0:Not Recurred | 101.22 | MB-0641 |
0 | 4.038 | Moderate | NO | cohort3 | Positve | NEUTRAL | YES | Post | Female | 3 | 77.12 | 57.666667 | 0:LIVING | LumA | ER+/HER2- Low Prolif | Living | Left | NO | Ductal/NST | MASTECTOMY | 0:Not Recurred | 56.91 | MB-4710 |
0 | 3.05 | Moderate | NO | cohort3 | Negative | NEUTRAL | YES | Post | Female | 9 | 83.68 | 155.733333 | 1:DECEASED | Basal | ER-/HER2- | Died of Other Causes | Right | YES | Ductal/NST | BREAST CONSERVING | 0:Not Recurred | 153.68 | MB-5427 |
6 | 6.04 | High | YES | cohort2 | Negative | NEUTRAL | NO | Pre | Female | 10 | 43.51 | 28.566667 | 1:DECEASED | Basal | ER-/HER2- | Died of Disease | Right | YES | Ductal/NST | BREAST CONSERVING | 1:Recurred | 20.95 | MB-3063 |
0 | 3.032 | Moderate | NO | cohort3 | Positve | GAIN | NO | Post | Female | 4ER+ | 65.48 | 101.4 | 0:LIVING | claudin-low | ER-/HER2- | Living | Right | YES | Ductal/NST | BREAST CONSERVING | 0:Not Recurred | 100.07 | MB-5408 |
0 | 4.02 | Moderate | NO | cohort3 | Negative | NEUTRAL | NO | Pre | Female | 10 | 45.77 | 211.933333 | 0:LIVING | Basal | ER-/HER2- | Living | Right | YES | Ductal/NST | BREAST CONSERVING | 0:Not Recurred | 209.14 | MB-4758 |
0 | 4.07 | High | NO | cohort3 | Negative | NEUTRAL | NO | Pre | Female | 10 | 37.05 | 274.2 | 0:LIVING | Basal | ER-/HER2- | Living | Left | YES | Ductal/NST | BREAST CONSERVING | 0:Not Recurred | 270.59 | MB-4881 |
0 | 4.028 | High | NO | cohort2 | Positve | NEUTRAL | YES | Pre | Female | 2 | 43.6 | 178.166667 | 1:DECEASED | LumB | null | Died of Disease | Left | YES | Ductal/NST | MASTECTOMY | 1:Recurred | 48.29 | MB-3181 |
0 | 4.05 | High | NO | cohort5 | Positve | GAIN | NO | Pre | Female | 5 | 49.5 | 58.933333 | 1:DECEASED | Her2 | HER2+ | Died of Disease | Left | NO | Ductal/NST | MASTECTOMY | 1:Recurred | 28.75 | MB-6156 |
14 | 6.198 | Moderate | YES | cohort3 | Negative | NEUTRAL | YES | Pre | Female | 10 | 31.71 | 195.933333 | 0:LIVING | Basal | ER-/HER2- | Living | Right | YES | Ductal/NST | MASTECTOMY | 0:Not Recurred | 193.36 | MB-5294 |
0 | 3.07 | High | NO | cohort3 | Positve | NEUTRAL | NO | Post | Female | 6 | 69.96 | 30.3 | 1:DECEASED | LumB | ER+/HER2- High Prolif | Died of Disease | Left | YES | Ductal/NST | BREAST CONSERVING | 1:Recurred | 17.86 | MB-4651 |
2 | 4.084 | Moderate | YES | cohort1 | Positve | NEUTRAL | YES | Post | Female | 3 | 50.48 | 131.1 | 0:LIVING | Normal | ER+/HER2- Low Prolif | Living | Right | YES | Ductal/NST | MASTECTOMY | 0:Not Recurred | 129.38 | MB-0426 |
3 | 5.06 | Low | YES | cohort3 | Negative | NEUTRAL | NO | Pre | Female | 4ER- | 36.99 | 57.3 | 1:DECEASED | Normal | ER-/HER2- | Died of Disease | Left | YES | Ductal/NST | BREAST CONSERVING | 1:Recurred | 46.28 | MB-5453 |
0 | 2.06 | Moderate | NO | cohort2 | Positve | GAIN | NO | Pre | Female | 8 | 47.48 | 145.433333 | 1:DECEASED | LumA | ER+/HER2- Low Prolif | Died of Other Causes | Right | NO | Mixed | MASTECTOMY | 1:Recurred | 55.26 | MB-2750 |
0 | 3.03 | Low | NO | cohort3 | Positve | NEUTRAL | YES | Post | Female | 4ER+ | 55.36 | 150.466667 | 0:LIVING | LumA | ER+/HER2- Low Prolif | Living | Left | YES | Mixed | BREAST CONSERVING | 0:Not Recurred | 148.49 | MB-5428 |
8 | 5.06 | High | NO | cohort4 | Positve | NEUTRAL | YES | Post | Female | 8 | 55.7 | 27.066667 | 1:DECEASED | LumB | ER+/HER2- High Prolif | Died of Disease | null | YES | Ductal/NST | BREAST CONSERVING | 1:Recurred | 9.34 | MB-7288 |
0 | 4.06 | High | NO | cohort3 | Positve | NEUTRAL | YES | Post | Female | 7 | 68.42 | 247.833333 | 1:DECEASED | LumB | ER+/HER2- High Prolif | Died of Other Causes | Right | NO | Ductal/NST | MASTECTOMY | 0:Not Recurred | 244.57 | MB-5211 |
1 | 5.032 | Moderate | YES | cohort1 | Negative | GAIN | NO | Pre | Female | 5 | 39.53 | 24.866667 | 1:DECEASED | Normal | HER2+ | Died of Disease | Right | YES | Ductal/NST | BREAST CONSERVING | 1:Recurred | 15.66 | MB-0482 |
0 | 4.062 | High | NO | cohort1 | Positve | NEUTRAL | YES | Post | Female | 10 | 75.71 | 80.666667 | 0:LIVING | LumB | ER+/HER2- High Prolif | Living | Right | YES | Ductal/NST | MASTECTOMY | 0:Not Recurred | 79.61 | MB-0637 |
0 | 4.042 | Moderate | YES | cohort1 | Positve | GAIN | YES | Pre | Female | 8 | 48.93 | 71.5 | 0:LIVING | LumA | ER+/HER2- Low Prolif | Living | Right | YES | Ductal/NST | BREAST CONSERVING | 0:Not Recurred | 70.56 | MB-0501 |
0 | 3.03 | Low | NO | cohort4 | Positve | NEUTRAL | YES | Post | Female | 4ER+ | 67.24 | 86.833333 | 0:LIVING | claudin-low | ER+/HER2- Low Prolif | Living | Right | YES | Ductal/NST | BREAST CONSERVING | 0:Not Recurred | 85.69 | MB-7044 |
0 | 4.04 | High | NO | cohort3 | Negative | NEUTRAL | NO | Post | Female | 10 | 68 | 194.566667 | 0:LIVING | Basal | ER-/HER2- | Living | Left | YES | Ductal/NST | BREAST CONSERVING | 0:Not Recurred | 192.01 | MB-5421 |
6 | 5.05 | Moderate | NO | cohort3 | Positve | NEUTRAL | YES | Post | Female | 8 | 67.92 | 119.366667 | 1:DECEASED | LumB | null | Died of Disease | Right | YES | Ductal/NST | BREAST CONSERVING | 1:Recurred | 62.53 | MB-4598 |
0 | 3.034 | Low | NO | cohort3 | Positve | NEUTRAL | NO | Post | Female | 4ER+ | 74.29 | 157.8 | 1:DECEASED | claudin-low | ER-/HER2- | Died of Other Causes | Right | YES | Ductal/NST | BREAST CONSERVING | 0:Not Recurred | 155.72 | MB-4859 |
2 | 5.052 | Low | YES | cohort1 | Negative | NEUTRAL | NO | Pre | Female | 4ER- | 45.39 | 22.233333 | 0:LIVING | claudin-low | ER-/HER2- | Living | Right | YES | Ductal/NST | MASTECTOMY | 0:Not Recurred | 21.94 | MB-0269 |
1 | 5.038 | High | NO | cohort4 | Positve | NEUTRAL | YES | Post | Female | 1 | 67.57 | 68.7 | 0:LIVING | Basal | ER+/HER2- High Prolif | Living | Left | YES | Mixed | BREAST CONSERVING | 0:Not Recurred | 67.8 | MB-7014 |
0 | 3.03 | Moderate | NO | cohort3 | Positve | NEUTRAL | NO | Post | Female | 3 | 74.26 | 164.6 | 1:DECEASED | LumB | ER+/HER2- High Prolif | Died of Disease | Left | YES | Mixed | BREAST CONSERVING | 1:Recurred | 33.68 | MB-5505 |
0 | 5.16 | High | NO | cohort1 | Negative | NEUTRAL | NO | Pre | Female | 10 | 49.05 | 46.066667 | 1:DECEASED | Basal | null | Died of Disease | null | NO | Ductal/NST | null | 1:Recurred | 45.46 | MB-0350 |
0 | 3.05 | Moderate | NO | cohort5 | Positve | NEUTRAL | NO | Post | Female | 8 | 71.74 | 195.3 | 0:LIVING | LumB | ER+/HER2- High Prolif | Living | Right | NO | Ductal/NST | MASTECTOMY | 0:Not Recurred | 192.73 | MB-6154 |
0 | 4.038 | High | NO | cohort1 | Positve | NEUTRAL | YES | Post | Female | 1 | 65.02 | 85.733333 | 1:DECEASED | LumB | ER+/HER2- High Prolif | Died of Disease | Left | NO | Ductal/NST | MASTECTOMY | 1:Recurred | 84.61 | MB-0383 |
0 | 3.024 | Moderate | NO | cohort2 | Positve | NEUTRAL | NO | Pre | Female | 1 | 42.07 | 272.1 | 0:LIVING | claudin-low | ER+/HER2- Low Prolif | Living | Right | YES | Ductal/NST | BREAST CONSERVING | 0:Not Recurred | 268.52 | MB-2795 |
4 | 6.05 | High | NO | cohort3 | Positve | NEUTRAL | YES | Pre | Female | 7 | 38.49 | 16.3 | 1:DECEASED | LumA | ER+/HER2- High Prolif | Died of Disease | Left | NO | Mixed | MASTECTOMY | 1:Recurred | 0.82 | MB-5520 |
0 | 4.046 | High | NO | cohort3 | Positve | NEUTRAL | YES | Post | Female | 1 | 64.32 | 187.3 | 0:LIVING | LumB | ER+/HER2- High Prolif | Living | Left | YES | Ductal/NST | BREAST CONSERVING | 0:Not Recurred | 184.84 | MB-4862 |
1 | 4.052 | High | NO | cohort2 | Positve | NEUTRAL | YES | Post | Female | 8 | 62.03 | 172.8 | 1:DECEASED | LumA | ER+/HER2- Low Prolif | Died of Other Causes | Left | NO | Ductal/NST | MASTECTOMY | 0:Not Recurred | 170.53 | MB-3871 |
0 | 3.056 | High | NO | cohort3 | Positve | LOSS | NO | Post | Female | 8 | 75.46 | 121.666667 | 1:DECEASED | LumA | ER+/HER2- Low Prolif | Died of Disease | Left | YES | Ductal/NST | BREAST CONSERVING | 1:Recurred | 64.47 | MB-4785 |
1 | 5.05 | High | NO | cohort3 | Positve | NEUTRAL | YES | Post | Female | 3 | 56.89 | 211.9 | 1:DECEASED | LumB | ER+/HER2- High Prolif | Died of Disease | Left | YES | Ductal/NST | BREAST CONSERVING | 1:Recurred | 167.01 | MB-5347 |
1 | 4.04 | High | NO | cohort3 | Positve | NEUTRAL | YES | Post | Female | 8 | 53.02 | 56.5 | 1:DECEASED | LumB | ER+/HER2- Low Prolif | Died of Disease | Left | NO | Lobular | MASTECTOMY | 1:Recurred | 21.91 | MB-4741 |
0 | 4.034 | Moderate | NO | cohort2 | Positve | GAIN | YES | Post | Female | 5 | 50.66 | 236.133333 | 0:LIVING | LumB | ER+/HER2- High Prolif | Living | Right | YES | Ductal/NST | BREAST CONSERVING | 1:Recurred | 149.21 | MB-3235 |
4 | 6.08 | High | NO | cohort1 | Positve | GAIN | YES | Post | Female | 1 | 78.86 | 74.466667 | 1:DECEASED | LumB | ER+/HER2- High Prolif | Died of Other Causes | Right | YES | Lobular | MASTECTOMY | 0:Not Recurred | 73.49 | MB-0429 |
0 | 4.048 | Low | NO | cohort1 | Positve | GAIN | YES | Post | Female | 9 | 75.65 | 104.533333 | 0:LIVING | LumB | ER+/HER2- High Prolif | Living | Right | NO | Ductal/NST | MASTECTOMY | 0:Not Recurred | 103.16 | MB-0611 |
0 | 1.028 | High | NO | cohort1 | Positve | NEUTRAL | YES | Post | Female | 3 | 54.76 | 164.7 | 0:LIVING | LumA | ER+/HER2- Low Prolif | Living | Right | NO | Lobular | BREAST CONSERVING | 0:Not Recurred | 162.53 | MB-0245 |
2 | 4.04 | Moderate | YES | cohort3 | Negative | GAIN | NO | Post | Female | 1 | 54.83 | 88.933333 | 1:DECEASED | Her2 | ER-/HER2- | Died of Disease | Left | YES | Ductal/NST | BREAST CONSERVING | 1:Recurred | 67.93 | MB-5549 |
0 | 3.036 | High | NO | cohort3 | Positve | NEUTRAL | NO | Post | Female | 2 | 77.77 | 237.266667 | 1:DECEASED | LumB | ER+/HER2- High Prolif | Died of Other Causes | Left | YES | Ductal/NST | BREAST CONSERVING | 0:Not Recurred | 234.14 | MB-4944 |
15 | 6.06 | High | YES | cohort1 | Positve | GAIN | YES | Post | Female | 9 | 60.27 | 72.466667 | 1:DECEASED | LumB | ER+/HER2- High Prolif | Died of Other Causes | Right | YES | Ductal/NST | MASTECTOMY | 0:Not Recurred | 71.51 | MB-0590 |
3 | 4.04 | High | NO | cohort3 | Positve | NEUTRAL | YES | Post | Female | 7 | 62.88 | 224.866667 | 0:LIVING | LumA | ER+/HER2- Low Prolif | Living | Right | YES | Ductal/NST | BREAST CONSERVING | 0:Not Recurred | 221.91 | MB-5599 |
0 | 3.04 | Moderate | NO | cohort3 | Positve | NEUTRAL | NO | Post | Female | 10 | 67.46 | 335.733333 | 1:DECEASED | Basal | null | Died of Disease | Right | NO | Ductal/NST | MASTECTOMY | 1:Recurred | 290.89 | MB-4235 |
1 | 4.05 | Moderate | NO | cohort3 | Positve | NEUTRAL | YES | Post | Female | 7 | 76.54 | 102.766667 | 1:DECEASED | LumB | null | Died of Other Causes | Left | NO | Ductal/NST | MASTECTOMY | 0:Not Recurred | 101.41 | MB-4925 |
1 | 4.052 | null | NO | cohort2 | Positve | NEUTRAL | YES | Post | Female | 8 | 70.94 | 112.966667 | 1:DECEASED | Her2 | ER+/HER2- High Prolif | Died of Other Causes | Left | NO | Mixed | MASTECTOMY | 0:Not Recurred | 111.48 | MB-3530 |
0 | 4.056 | High | NO | cohort2 | Positve | GAIN | YES | Pre | Female | 5 | 48.48 | 26.766667 | 1:DECEASED | LumB | HER2+ | Died of Disease | Right | YES | Ductal/NST | BREAST CONSERVING | 1:Recurred | 25.07 | MB-3360 |
6 | 5.06 | Moderate | NO | cohort1 | Positve | NEUTRAL | YES | Post | Female | 8 | 78.73 | 152.2 | 0:LIVING | LumA | ER+/HER2- Low Prolif | Living | Left | YES | Ductal/NST | MASTECTOMY | 0:Not Recurred | 150.2 | MB-0121 |
1 | 4.018 | High | NO | cohort2 | Positve | NEUTRAL | NO | Post | Female | 3 | 56.85 | 153.833333 | 1:DECEASED | Her2 | ER-/HER2- | Died of Other Causes | Left | YES | Ductal/NST | BREAST CONSERVING | 0:Not Recurred | 151.81 | MB-2834 |
14 | 6.3 | High | NO | cohort1 | Positve | NEUTRAL | YES | Post | Female | 3 | 83.89 | 39.166667 | 1:DECEASED | LumA | ER+/HER2- Low Prolif | Died of Disease | Right | YES | Lobular | MASTECTOMY | 1:Recurred | 25.13 | MB-0112 |
0 | 3.00424 | High | NO | cohort4 | Positve | NEUTRAL | NO | Post | Female | 8 | 58.37 | 177.6 | 0:LIVING | LumA | ER+/HER2- Low Prolif | Living | Right | NO | Ductal/NST | MASTECTOMY | 0:Not Recurred | 175.26 | MB-7232 |
2 | 4.056 | High | NO | cohort1 | Positve | GAIN | YES | Pre | Female | 8 | 48.13 | 173.633333 | 0:LIVING | LumA | ER+/HER2- Low Prolif | Living | Left | NO | Mixed | MASTECTOMY | 0:Not Recurred | 171.35 | MB-0207 |
1 | 5.05 | High | NO | cohort4 | Positve | NEUTRAL | YES | Pre | Female | 3 | 43.1 | 196.866667 | 0:LIVING | LumA | ER+/HER2- Low Prolif | Living | Right | YES | Lobular | BREAST CONSERVING | 0:Not Recurred | 194.28 | MB-7295 |
7 | 6.04 | Moderate | NO | cohort1 | Negative | GAIN | NO | Post | Female | 4ER- | 77.72 | 20.2 | 1:DECEASED | Her2 | ER+/HER2- High Prolif | Died of Disease | Left | NO | Ductal/NST | MASTECTOMY | 1:Recurred | 19.93 | MB-0221 |
0 | 4.032 | High | NO | cohort3 | Negative | NEUTRAL | NO | Post | Female | 4ER- | 63.95 | 230.5 | 0:LIVING | claudin-low | ER-/HER2- | Living | Right | YES | Ductal/NST | BREAST CONSERVING | 0:Not Recurred | 227.47 | MB-4888 |
3 | 4.046 | High | NO | cohort3 | Positve | NEUTRAL | YES | Post | Female | 2 | 73.55 | 2.533333 | 1:DECEASED | LumB | ER+/HER2- Low Prolif | Died of Other Causes | Left | NO | Ductal/NST | MASTECTOMY | 0:Not Recurred | 2.5 | MB-5475 |
0 | 3.031 | Low | NO | cohort4 | Negative | GAIN | YES | Post | Female | 5 | 69.64 | 105 | 0:LIVING | Her2 | HER2+ | Living | Left | NO | Ductal/NST | MASTECTOMY | 0:Not Recurred | 103.62 | MB-7067 |
1 | 4.04 | Low | YES | cohort1 | Positve | NEUTRAL | YES | Pre | Female | 3 | 48.11 | 138.1 | 0:LIVING | LumA | ER+/HER2- Low Prolif | Living | Right | YES | Ductal/NST | MASTECTOMY | 0:Not Recurred | 136.28 | MB-0172 |
2 | 5.06 | High | NO | cohort3 | Positve | NEUTRAL | YES | Post | Female | 7 | 74.8 | 41.466667 | 1:DECEASED | LumA | ER+/HER2- Low Prolif | Died of Other Causes | Left | NO | Ductal/NST | MASTECTOMY | 1:Recurred | 31.25 | MB-4855 |
0 | 3.07 | High | NO | cohort5 | Positve | NEUTRAL | NO | Post | Female | 7 | 82.51 | 77.5 | 1:DECEASED | Normal | null | Died of Other Causes | Left | NO | Ductal/NST | MASTECTOMY | 0:Not Recurred | 76.48 | MB-6101 |
1 | 4.04 | High | NO | cohort5 | Positve | NEUTRAL | YES | Post | Female | 3 | 74.43 | 174.5 | 1:DECEASED | LumA | ER+/HER2- Low Prolif | Died of Other Causes | Left | NO | Ductal/NST | MASTECTOMY | 0:Not Recurred | 172.2 | MB-6214 |
0 | 4.03 | High | NO | cohort3 | Positve | NEUTRAL | YES | Post | Female | 9 | 61.16 | 256.866667 | 1:DECEASED | LumB | ER+/HER2- High Prolif | Died of Disease | Left | YES | Ductal/NST | BREAST CONSERVING | 1:Recurred | 253.49 | MB-4004 |
0 | 4.034 | High | YES | cohort1 | Negative | NEUTRAL | NO | Post | Female | 10 | 52.14 | 153.966667 | 0:LIVING | Basal | null | Living | Right | YES | Ductal/NST | MASTECTOMY | 0:Not Recurred | 151.94 | MB-0062 |
0 | 4.056 | Moderate | NO | cohort3 | Positve | NEUTRAL | YES | Post | Female | 7 | 63.2 | 2 | 0:LIVING | LumB | ER+/HER2- High Prolif | Living | Right | YES | Mucinous | BREAST CONSERVING | 0:Not Recurred | 1.97 | MB-5525 |
0 | 4.068 | High | NO | cohort4 | Negative | GAIN | YES | Post | Female | 5 | 61.38 | 186.366667 | 0:LIVING | Her2 | HER2+ | Living | Left | YES | Ductal/NST | BREAST CONSERVING | 0:Not Recurred | 183.91 | MB-7143 |
0 | 4.004 | Moderate | NO | cohort3 | Positve | GAIN | NO | Pre | Female | 4ER+ | 47.35 | 202.1 | 0:LIVING | Normal | HER2+ | Living | Left | NO | Ductal/NST | MASTECTOMY | 0:Not Recurred | 199.44 | MB-5351 |
0 | 2.002 | Low | NO | cohort3 | Positve | NEUTRAL | NO | Pre | Female | 4ER+ | 40.04 | 197.433333 | 0:LIVING | Normal | ER+/HER2- Low Prolif | Living | Left | NO | Mixed | MASTECTOMY | 0:Not Recurred | 194.84 | MB-4897 |
0 | 4.026 | Moderate | NO | cohort3 | Positve | NEUTRAL | NO | Post | Female | 3 | 67.54 | 185.766667 | 0:LIVING | LumA | ER+/HER2- High Prolif | Living | Right | NO | Ductal/NST | MASTECTOMY | 0:Not Recurred | 183.32 | MB-5471 |
2 | 4.06 | High | NO | cohort3 | Positve | NEUTRAL | YES | Post | Female | 8 | 67.12 | 29.3 | 1:DECEASED | LumA | ER+/HER2- Low Prolif | Died of Disease | Left | NO | Ductal/NST | MASTECTOMY | 1:Recurred | 27.66 | MB-4869 |
0 | 4.026 | High | NO | cohort4 | Negative | NEUTRAL | NO | Post | Female | 4ER- | 65.22 | 80.233333 | 0:LIVING | claudin-low | ER-/HER2- | Living | null | YES | Ductal/NST | BREAST CONSERVING | 0:Not Recurred | 79.18 | MB-7025 |
1 | 5.044 | High | YES | cohort4 | Negative | NEUTRAL | NO | Post | Female | 10 | 57.62 | 81.033333 | 0:LIVING | Basal | ER-/HER2- | Living | Right | YES | Ductal/NST | BREAST CONSERVING | 0:Not Recurred | 79.97 | MB-7038 |
0 | 4.042 | High | NO | cohort1 | Positve | NEUTRAL | YES | Post | Female | 1 | 74.63 | 104.466667 | 1:DECEASED | LumB | null | Died of Disease | Left | YES | Ductal/NST | BREAST CONSERVING | 1:Recurred | 103.09 | MB-0178 |
0 | 4.136 | High | NO | cohort3 | Positve | NEUTRAL | NO | Post | Female | 8 | 51.29 | 131.3 | 1:DECEASED | LumA | ER+/HER2- Low Prolif | Died of Other Causes | Right | NO | Mixed | MASTECTOMY | 0:Not Recurred | 129.57 | MB-4730 |
0 | 4.03 | High | YES | cohort1 | Negative | NEUTRAL | NO | Post | Female | 10 | 62.81 | 114.466667 | 0:LIVING | Basal | ER-/HER2- | Living | Right | YES | Ductal/NST | BREAST CONSERVING | 0:Not Recurred | 112.96 | MB-0516 |
0 | 4.05 | High | NO | cohort4 | Positve | NEUTRAL | YES | Post | Female | 8 | 63.79 | 78.166667 | 0:LIVING | LumB | ER+/HER2- High Prolif | Living | Right | YES | Ductal/NST | BREAST CONSERVING | 0:Not Recurred | 77.14 | MB-7015 |
2 | 5.07 | High | YES | cohort3 | Negative | NEUTRAL | NO | Pre | Female | 10 | 40.21 | 14.8 | 1:DECEASED | Basal | ER-/HER2- | Died of Disease | Left | YES | Ductal/NST | BREAST CONSERVING | 1:Recurred | 10.56 | MB-5529 |
3 | 2.07 | High | NO | cohort3 | Positve | NEUTRAL | YES | Post | Female | 7 | 89 | 45.5 | 1:DECEASED | LumA | ER+/HER2- High Prolif | Died of Other Causes | Left | NO | Ductal/NST | MASTECTOMY | 0:Not Recurred | 44.9 | MB-4794 |
0 | 4.044 | High | YES | cohort1 | Negative | GAIN | YES | Pre | Female | 5 | 33.83 | 132.766667 | 0:LIVING | Her2 | HER2+ | Living | Left | YES | Ductal/NST | MASTECTOMY | 0:Not Recurred | 131.02 | MB-0479 |
3 | 4.05 | Moderate | NO | cohort1 | Positve | NEUTRAL | YES | Post | Female | 8 | 68.66 | 186.533333 | 0:LIVING | LumA | ER+/HER2- Low Prolif | Living | Right | YES | Ductal/NST | MASTECTOMY | 0:Not Recurred | 184.08 | MB-0273 |
0 | 4.054 | High | NO | cohort3 | null | NEUTRAL | NO | Post | Female | 9 | 69.68 | 210.966667 | 0:LIVING | Basal | ER-/HER2- | Living | Right | NO | Ductal/NST | MASTECTOMY | 1:Recurred | 85.26 | MB-4880 |
0 | 3.142 | Moderate | NO | cohort5 | Positve | NEUTRAL | YES | Post | Female | 2 | 78.69 | 60.9 | 1:DECEASED | LumB | ER+/HER2- Low Prolif | Died of Disease | Left | NO | Mucinous | MASTECTOMY | 1:Recurred | 60.1 | MB-6254 |
0 | 2.02 | Moderate | NO | cohort1 | Positve | NEUTRAL | YES | Post | Female | 3 | 79.38 | 24.3 | 1:DECEASED | LumA | ER+/HER2- Low Prolif | Died of Disease | Right | YES | Ductal/NST | BREAST CONSERVING | 1:Recurred | 23.91 | MB-0204 |
End of preview.
YAML Metadata Warning:empty or missing yaml metadata in repo card
Check out the documentation for more information.
Flexynesis Benchmark Datasets
| Dataset key | Biology | Modalities | Samples | Task types available |
|---|---|---|---|---|
dataset1 |
Cancer drug response (CCLE/GDSC cell lines) | gex, cnv |
~950 / 240 | Regression (drug IC50 per compound) |
dataset2 |
Microsatellite instability (MSI) | gex, meth |
~380 / 95 | Binary classification (MSI-H vs MSS) |
lgggbm_tcga_pub_processed |
Brain tumours: LGG + GBM (TCGA) | mut, cna |
556 / 238 | Classification, survival, regression |
brca_metabric |
Breast cancer (METABRIC) | gex, cna |
~1390 / 595 | Classification, survival, regression |
singlecell_bonemarrow |
Bone marrow single-cell RNA | gex |
~7500 / 2500 | Classification, unsupervised |
Note on single-cell data: flexynesis was designed for bulk multi-omics data (patient cohorts, cell lines) — not single-cell RNA-seq. It has no built-in handling for the sparsity, scale, or batch structure typical of scRNA-seq. The singlecell_bonemarrow dataset is included as a benchmark curiosity and works well for supervised cell type classification (where cell type labels are available), but flexynesis is not the right tool for unsupervised single-cell analysis, trajectory inference, or integration of large scRNA-seq atlases. For those tasks, use Scanpy/Seurat/scVI instead. If the user's question is specifically about supervised classification of single-cell data with known labels, it is worth trying.
All datasets hosted at https://bimsbstatic.mdc-berlin.de/akalin/buyar/flexynesis-benchmark-datasets/
Reference: Uyar et al., Nature Communications 2025 — https://doi.org/10.1038/s41467-025-63688-5
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