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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-6065', 'MB-4732', 'MB-4934', 'MB-4827', 'MB-0462', 'MB-0310', 'MB-0193', 'MB-0485', 'MB-5226', 'MB-5060', 'MB-5050', 'MB-5295', 'MB-0139', 'MB-4484', 'MB-5559', 'MB-5635', 'MB-5206', 'MB-2724', 'MB-7113', 'MB-4961', 'MB-5452', 'MB-3122', 'MB-6337', 'MB-0150', 'MB-7241', 'MB-5208', 'MB-6204', 'MB-0482', 'MB-4866', 'MB-4809', 'MB-6302', 'MB-3606', 'MB-3297', 'MB-3266', 'MB-4871', 'MB-2844', 'MB-7267', 'MB-5154', 'MB-0140', 'MB-5626', 'MB-7000', 'MB-0367', 'MB-4622', 'MB-3008', 'MB-0341', 'MB-6359', 'MB-0486', 'MB-5605', 'MB-5520', 'MB-5601', 'MB-5011', 'MB-0426', 'MB-0438', 'MB-0436', 'MB-3088', 'MB-4127', 'MB-4935', 'MB-7162', 'MB-0583', 'MB-0198', 'MB-5058', 'MB-0340', 'MB-4692', 'MB-7118', 'MB-5123', 'MB-7100', 'MB-5066', 'MB-0590', 'MB-3500', 'MB-0290', 'MB-6113', 'MB-2823', 'MB-3437', 'MB-2900', 'MB-0174', 'MB-4867', 'MB-7161', 'MB-5290', 'MB-6152', 'MB-4673', 'MB-4966', 'MB-4289', 'MB-5397', 'MB-4120', 'MB-4012', 'MB-5453', 'MB-6108', 'MB-5270', 'MB-5490', 'MB-0906', 'MB-6223', 'MB-0164', 'MB-0109', 'MB-4139', 'MB-0513', 'MB-5428', 'MB-0451', 'MB-4764', 'MB-5434', 'MB-2686', 'MB-3211', 'MB-5107', 'MB-4999', 'MB-6131', 'MB-4618', 'MB-7127', 'MB-4785', 'MB-5231', 'MB-6016', 'MB-5470', 'MB-4881', 'MB-0591', 'MB-5511', 'MB-0328', 'MB-5277', 'MB-6305', 'MB-3528', 'MB-6022', 'MB-0514', 'MB-5275', 'MB-3105', 'MB-5188', 'MB-2848', 'MB-5410', 'MB-4529', 'MB-0526', 'MB-0649', 'MB-0308', 'MB-3412', 'MB-4758', 'MB-0476', 'MB-4643', 'MB-4661', 'MB-4752', 'MB-7295', 'MB-5238', 'MB
...
04', 'MB-4649', 'MB-2618', 'MB-4719', 'MB-5288', 'MB-5591', 'MB-0446', 'MB-3383', 'MB-6185', 'MB-5567', 'MB-4264', 'MB-0167', 'MB-5161', 'MB-3167', 'MB-0568', 'MB-0469', 'MB-0005', 'MB-6167', 'MB-2854', 'MB-4829', 'MB-3435', 'MB-7123', 'MB-0361', 'MB-5483', 'MB-5525', 'MB-2960', 'MB-5534', 'MB-5332', 'MB-2790', 'MB-4660', 'MB-5101', 'MB-4332', 'MB-5403', 'MB-5145', 'MB-7037', 'MB-4994', 'MB-2850', 'MB-0631', 'MB-7157', 'MB-3711', 'MB-0263', 'MB-3016', 'MB-7039', 'MB-7013', 'MB-6154', 'MB-7128', 'MB-0660', 'MB-0554', 'MB-6248', 'MB-4666', 'MB-2994', 'MB-0623', 'MB-0422', 'MB-6006', 'MB-4792', 'MB-7236', 'MB-5054', 'MB-4599', 'MB-6182', 'MB-0431', 'MB-4790', 'MB-5368', 'MB-6322', 'MB-0506', 'MB-2642', 'MB-5284', 'MB-0284', 'MB-5433', 'MB-4886', 'MB-5164', 'MB-0545', 'MB-5120', 'MB-7232', 'MB-4654', 'MB-2613', 'MB-6047', 'MB-5457', 'MB-2750', 'MB-0101', 'MB-5588', 'MB-0496', 'MB-0318', 'MB-6083', 'MB-5100', 'MB-5421', 'MB-3104', 'MB-5147', 'MB-4723', 'MB-6239', 'MB-4282', 'MB-4671', 'MB-3492', 'MB-5233', 'MB-4969', 'MB-3600', 'MB-4672', 'MB-4735', 'MB-5369', 'MB-0386', 'MB-0497', 'MB-4663', 'MB-4957', 'MB-0056', 'MB-7280', 'MB-4306', 'MB-4018', 'MB-6169', 'MB-6079', 'MB-5395', 'MB-0521', 'MB-3429', 'MB-4744', 'MB-5505', 'MB-6181', 'MB-0359', 'MB-0247', 'MB-6212', 'MB-5580', 'MB-0511', 'MB-4798', 'MB-6208', 'MB-4633', 'MB-4879', 'MB-0584', 'MB-4986', 'MB-7200', 'MB-3295', 'MB-5114', 'MB-4802', 'MB-0242', 'MB-6036', 'MB-3005', 'MB-0532', 'MB-3530', 'MB-4763', 'MB-0570', 'MB-4145'}) and 23 missing columns ({'ER_IHC', 'THREEGENE', 'HISTOLOGICAL_SUBTYPE', 'BREAST_SURGERY', 'CELLULARITY', 'CLAUDIN_SUBTYPE', 'CHEMOTHERAPY', 'LYMPH_NODES_EXAMINED_POSITIVE', 'AGE_AT_DIAGNOSIS', 'HER2_SNP6', 'INFERRED_MENOPAUSAL_STATE', 'RFS_STATUS', 'RADIO_THERAPY', 'NPI', 'INTCLUST', 'OS_MONTHS', 'OS_STATUS', 'COHORT', 'VITAL_STATUS', 'RFS_MONTHS', 'SEX', 'LATERALITY', 'HORMONE_THERAPY'}).
This happened while the csv dataset builder was generating data using
hf://datasets/huseyincavus/flexynesis-datasets/brca_metabric_processed/train/cna.csv (at revision 41de0b87bb3b2bc8971c6b0042d95b9b1da406d2), ['hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/brca_metabric_processed/train/clin.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/brca_metabric_processed/train/cna.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/brca_metabric_processed/train/gex.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/brca_metabric_processed/train/mut.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/ccle_vs_gdsc/train/clin.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/ccle_vs_gdsc/train/cnv.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/ccle_vs_gdsc/train/mutation.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/ccle_vs_gdsc/train/rna.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/dataset1/train/clin.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/dataset1/train/cnv.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/dataset1/train/gex.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/dataset2/train/clin.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/dataset2/train/gex.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/dataset2/train/meth.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/depmap_gene_dependency/train/clin.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/depmap_gene_dependency/train/crispr.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/depmap_gene_dependency/train/describeProt.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/depmap_gene_dependency/train/gex.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/depmap_gene_dependency/train/protTrans.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/lgggbm_tcga_pub_processed/train/clin.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/lgggbm_tcga_pub_processed/train/cna.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/lgggbm_tcga_pub_processed/train/mut.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/neuroblastoma_target_vs_depmap/train/clin.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/neuroblastoma_target_vs_depmap/train/gex.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/panGI_msi/train/clin.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/panGI_msi/train/gex.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/panGI_msi/train/meth.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/singlecell_bonemarrow/train/ADT.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/singlecell_bonemarrow/train/RNA.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/singlecell_bonemarrow/train/clin.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/tcga_cancertype/train/clin.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/tcga_cancertype/train/gex.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/tcga_cancertype/train/meth.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/tcga_to_ccle/train/clin.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/tcga_to_ccle/train/cna.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/tcga_to_ccle/train/gex.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/python3.14/site-packages/datasets/builder.py", line 1848, in _prepare_split_single
writer.write_table(table)
~~~~~~~~~~~~~~~~~~^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/arrow_writer.py", line 784, in write_table
self._write_table(pa_table, writer_batch_size=writer_batch_size)
~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/arrow_writer.py", line 795, in _write_table
pa_table = table_cast(pa_table, self._schema)
File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2378, in table_cast
return cast_table_to_schema(table, schema)
File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2306, in cast_table_to_schema
raise CastError(
...<3 lines>...
)
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' + 145340
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 1369, in compute_config_parquet_and_info_response
parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet(
~~~~~~~~~~~~~~~~~~~~~~~~~^
builder, max_dataset_size_bytes=max_dataset_size_bytes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 948, in stream_convert_to_parquet
builder._prepare_split(split_generator=splits_generators[split], file_format="parquet")
~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1694, in _prepare_split
for job_id, done, content in self._prepare_split_single(
~~~~~~~~~~~~~~~~~~~~~~~~~~^
gen_kwargs=gen_kwargs, job_id=job_id, **_prepare_split_args
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
):
^
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1850, in _prepare_split_single
raise DatasetGenerationCastError.from_cast_error(
...<4 lines>...
)
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-6065', 'MB-4732', 'MB-4934', 'MB-4827', 'MB-0462', 'MB-0310', 'MB-0193', 'MB-0485', 'MB-5226', 'MB-5060', 'MB-5050', 'MB-5295', 'MB-0139', 'MB-4484', 'MB-5559', 'MB-5635', 'MB-5206', 'MB-2724', 'MB-7113', 'MB-4961', 'MB-5452', 'MB-3122', 'MB-6337', 'MB-0150', 'MB-7241', 'MB-5208', 'MB-6204', 'MB-0482', 'MB-4866', 'MB-4809', 'MB-6302', 'MB-3606', 'MB-3297', 'MB-3266', 'MB-4871', 'MB-2844', 'MB-7267', 'MB-5154', 'MB-0140', 'MB-5626', 'MB-7000', 'MB-0367', 'MB-4622', 'MB-3008', 'MB-0341', 'MB-6359', 'MB-0486', 'MB-5605', 'MB-5520', 'MB-5601', 'MB-5011', 'MB-0426', 'MB-0438', 'MB-0436', 'MB-3088', 'MB-4127', 'MB-4935', 'MB-7162', 'MB-0583', 'MB-0198', 'MB-5058', 'MB-0340', 'MB-4692', 'MB-7118', 'MB-5123', 'MB-7100', 'MB-5066', 'MB-0590', 'MB-3500', 'MB-0290', 'MB-6113', 'MB-2823', 'MB-3437', 'MB-2900', 'MB-0174', 'MB-4867', 'MB-7161', 'MB-5290', 'MB-6152', 'MB-4673', 'MB-4966', 'MB-4289', 'MB-5397', 'MB-4120', 'MB-4012', 'MB-5453', 'MB-6108', 'MB-5270', 'MB-5490', 'MB-0906', 'MB-6223', 'MB-0164', 'MB-0109', 'MB-4139', 'MB-0513', 'MB-5428', 'MB-0451', 'MB-4764', 'MB-5434', 'MB-2686', 'MB-3211', 'MB-5107', 'MB-4999', 'MB-6131', 'MB-4618', 'MB-7127', 'MB-4785', 'MB-5231', 'MB-6016', 'MB-5470', 'MB-4881', 'MB-0591', 'MB-5511', 'MB-0328', 'MB-5277', 'MB-6305', 'MB-3528', 'MB-6022', 'MB-0514', 'MB-5275', 'MB-3105', 'MB-5188', 'MB-2848', 'MB-5410', 'MB-4529', 'MB-0526', 'MB-0649', 'MB-0308', 'MB-3412', 'MB-4758', 'MB-0476', 'MB-4643', 'MB-4661', 'MB-4752', 'MB-7295', 'MB-5238', 'MB
...
04', 'MB-4649', 'MB-2618', 'MB-4719', 'MB-5288', 'MB-5591', 'MB-0446', 'MB-3383', 'MB-6185', 'MB-5567', 'MB-4264', 'MB-0167', 'MB-5161', 'MB-3167', 'MB-0568', 'MB-0469', 'MB-0005', 'MB-6167', 'MB-2854', 'MB-4829', 'MB-3435', 'MB-7123', 'MB-0361', 'MB-5483', 'MB-5525', 'MB-2960', 'MB-5534', 'MB-5332', 'MB-2790', 'MB-4660', 'MB-5101', 'MB-4332', 'MB-5403', 'MB-5145', 'MB-7037', 'MB-4994', 'MB-2850', 'MB-0631', 'MB-7157', 'MB-3711', 'MB-0263', 'MB-3016', 'MB-7039', 'MB-7013', 'MB-6154', 'MB-7128', 'MB-0660', 'MB-0554', 'MB-6248', 'MB-4666', 'MB-2994', 'MB-0623', 'MB-0422', 'MB-6006', 'MB-4792', 'MB-7236', 'MB-5054', 'MB-4599', 'MB-6182', 'MB-0431', 'MB-4790', 'MB-5368', 'MB-6322', 'MB-0506', 'MB-2642', 'MB-5284', 'MB-0284', 'MB-5433', 'MB-4886', 'MB-5164', 'MB-0545', 'MB-5120', 'MB-7232', 'MB-4654', 'MB-2613', 'MB-6047', 'MB-5457', 'MB-2750', 'MB-0101', 'MB-5588', 'MB-0496', 'MB-0318', 'MB-6083', 'MB-5100', 'MB-5421', 'MB-3104', 'MB-5147', 'MB-4723', 'MB-6239', 'MB-4282', 'MB-4671', 'MB-3492', 'MB-5233', 'MB-4969', 'MB-3600', 'MB-4672', 'MB-4735', 'MB-5369', 'MB-0386', 'MB-0497', 'MB-4663', 'MB-4957', 'MB-0056', 'MB-7280', 'MB-4306', 'MB-4018', 'MB-6169', 'MB-6079', 'MB-5395', 'MB-0521', 'MB-3429', 'MB-4744', 'MB-5505', 'MB-6181', 'MB-0359', 'MB-0247', 'MB-6212', 'MB-5580', 'MB-0511', 'MB-4798', 'MB-6208', 'MB-4633', 'MB-4879', 'MB-0584', 'MB-4986', 'MB-7200', 'MB-3295', 'MB-5114', 'MB-4802', 'MB-0242', 'MB-6036', 'MB-3005', 'MB-0532', 'MB-3530', 'MB-4763', 'MB-0570', 'MB-4145'}) and 23 missing columns ({'ER_IHC', 'THREEGENE', 'HISTOLOGICAL_SUBTYPE', 'BREAST_SURGERY', 'CELLULARITY', 'CLAUDIN_SUBTYPE', 'CHEMOTHERAPY', 'LYMPH_NODES_EXAMINED_POSITIVE', 'AGE_AT_DIAGNOSIS', 'HER2_SNP6', 'INFERRED_MENOPAUSAL_STATE', 'RFS_STATUS', 'RADIO_THERAPY', 'NPI', 'INTCLUST', 'OS_MONTHS', 'OS_STATUS', 'COHORT', 'VITAL_STATUS', 'RFS_MONTHS', 'SEX', 'LATERALITY', 'HORMONE_THERAPY'}).
This happened while the csv dataset builder was generating data using
hf://datasets/huseyincavus/flexynesis-datasets/brca_metabric_processed/train/cna.csv (at revision 41de0b87bb3b2bc8971c6b0042d95b9b1da406d2), ['hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/brca_metabric_processed/train/clin.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/brca_metabric_processed/train/cna.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/brca_metabric_processed/train/gex.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/brca_metabric_processed/train/mut.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/ccle_vs_gdsc/train/clin.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/ccle_vs_gdsc/train/cnv.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/ccle_vs_gdsc/train/mutation.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/ccle_vs_gdsc/train/rna.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/dataset1/train/clin.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/dataset1/train/cnv.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/dataset1/train/gex.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/dataset2/train/clin.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/dataset2/train/gex.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/dataset2/train/meth.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/depmap_gene_dependency/train/clin.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/depmap_gene_dependency/train/crispr.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/depmap_gene_dependency/train/describeProt.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/depmap_gene_dependency/train/gex.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/depmap_gene_dependency/train/protTrans.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/lgggbm_tcga_pub_processed/train/clin.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/lgggbm_tcga_pub_processed/train/cna.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/lgggbm_tcga_pub_processed/train/mut.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/neuroblastoma_target_vs_depmap/train/clin.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/neuroblastoma_target_vs_depmap/train/gex.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/panGI_msi/train/clin.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/panGI_msi/train/gex.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/panGI_msi/train/meth.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/singlecell_bonemarrow/train/ADT.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/singlecell_bonemarrow/train/RNA.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/singlecell_bonemarrow/train/clin.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/tcga_cancertype/train/clin.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/tcga_cancertype/train/gex.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/tcga_cancertype/train/meth.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/tcga_to_ccle/train/clin.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/tcga_to_ccle/train/cna.csv', 'hf://datasets/huseyincavus/flexynesis-datasets@41de0b87bb3b2bc8971c6b0042d95b9b1da406d2/tcga_to_ccle/train/gex.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.
Flexynesis Benchmark Datasets
Part of the Flexynesis: Deep Learning for Bulk Multi-Omics Data Integration collection.
This repository provides processed, standardized multi-omics benchmark cohorts for precision oncology and deep learning data integration, covering bulk RNA-seq, DNA methylation, copy number alterations (CNA/CNV), somatic mutations, and CRISPR dependency screens.
Benchmark Cohorts
| Dataset key | Biology | Modalities | Samples / Info | Task types available |
|---|---|---|---|---|
tcga_cancertype |
Pan-cancer cohort across 21 TCGA cancer types | gex, meth, clin |
100 samples / type | Multi-class cancer type classification |
depmap_gene_dependency |
Gene dependency prediction in human cancer cell lines | crispr, gex, describeProt, protTrans |
Cell lines | Regression, gene dependency |
panGI_msi |
Gastrointestinal & gynecological cancers (MSI) | gex, meth, clin |
7 TCGA cohorts | Binary classification (MSI-H vs MSS) |
ccle_vs_gdsc |
Cross-study cancer drug response (CCLE vs GDSC2) | rna, cnv, mutation, clin |
Pan-cancer cell lines | Regression (drug IC50 response) |
tcga_to_ccle |
Translation from TCGA tumors to CCLE cell lines | gex, cna, mut, clin |
Lung, glioma, breast | Cross-domain transfer & classification |
neuroblastoma_target_vs_depmap |
Pediatric neuroblastoma (TARGET vs DepMap) | gex, clin |
Patient vs cell line | Classification, domain adaptation |
singlecell_bonemarrow |
Bone marrow single-cell CITE-Seq | RNA, ADT, clin |
~10K cells | Cell type classification |
brca_metabric_processed |
Breast cancer (METABRIC cohort) | gex, cna, clin |
~1985 samples | Classification, survival |
lgggbm_tcga_pub_processed |
Brain tumors: LGG + GBM (TCGA) | mut, cna, clin |
794 samples | Classification, survival |
dataset1 & dataset2 |
Drug response & MSI benchmark subsets | gex, cnv, meth |
Cell lines & tumors | Regression & classification |
parquet & csv |
HGNC gene, CpG & UniProt mapping tables | Gene identifier tables | Full human genome | Identifier mapping |
Original Source & License
- Official Source: BIMSBbioinfo/flexynesis_manuscript & Flexynesis Toolkit
- Zenodo Archive: DOI: 10.5281/zenodo.16442998
- License: Creative Commons Attribution 4.0 International (
cc-by-4.0) - Official Publication: Nature Communications (2025) 16:63688
Citation
If you use this dataset in your research or project, please cite:
@article{Uyar2025Flexynesis,
title={Flexynesis: a deep learning toolkit for bulk multi-omics data integration for precision oncology and beyond},
author={Uyar, Bora and others and Akalin, Altuna},
journal={Nature Communications},
year={2025},
doi={10.1038/s41467-025-63688-5}
}
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