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Datasets:
AIBIC
/
MLOmics

Tags:
omics
bioinformatics
License:
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The full dataset viewer is not available (click to read why). Only showing a preview of the rows.
The dataset generation failed because of a cast error
Error code:   DatasetGenerationCastError
Exception:    DatasetGenerationCastError
Message:      An error occurred while generating the dataset

All the data files must have the same columns, but at some point there are 1 new columns ({'Label'}) and 672 missing columns ({'TCGA.AR.A0U2.01', 'TCGA.E9.A1RB.01', 'TCGA.D8.A1X8.01', 'TCGA.PL.A8LZ.01', 'TCGA.E2.A1BC.01', 'TCGA.E9.A1N3.01', 'TCGA.D8.A1JB.01', 'TCGA.A2.A0T5.01', 'TCGA.A2.A0YM.01', 'TCGA.3C.AALK.01', 'TCGA.BH.A0DP.01', 'TCGA.AR.A24Z.01', 'TCGA.BH.A6R8.01', 'TCGA.D8.A27W.01', 'TCGA.AQ.A04H.01', 'TCGA.D8.A1Y0.01', 'TCGA.EW.A1P5.01', 'TCGA.BH.A0H3.01', 'TCGA.BH.A0W5.01', 'TCGA.E2.A576.01', 'TCGA.GM.A3XL.01', 'TCGA.E9.A3X8.01', 'TCGA.E9.A248.01', 'TCGA.A7.A5ZX.01', 'TCGA.D8.A27H.01', 'TCGA.AO.A125.01', 'TCGA.AR.A2LE.01', 'TCGA.GM.A3NW.01', 'TCGA.A2.A25F.01', 'TCGA.BH.A1EV.01', 'TCGA.BH.A1FU.01', 'TCGA.D8.A27T.01', 'TCGA.AO.A0JE.01', 'TCGA.OL.A5RV.01', 'TCGA.E9.A1NE.01', 'TCGA.AR.A24P.01', 'TCGA.PE.A5DC.01', 'TCGA.E2.A9RU.01', 'TCGA.A2.A0CK.01', 'TCGA.S3.AA10.01', 'TCGA.S3.A6ZG.01', 'TCGA.D8.A27G.01', 'TCGA.AO.A03N.01', 'TCGA.A2.A0T0.01', 'TCGA.OL.A5DA.01', 'TCGA.WT.AB41.01', 'TCGA.A2.A0T6.01', 'TCGA.BH.A0W3.01', 'TCGA.A7.A26G.01', 'TCGA.AN.A0XV.01', 'TCGA.AC.A2FG.01', 'TCGA.EW.A1PA.01', 'TCGA.LD.A9QF.01', 'TCGA.WT.AB44.01', 'TCGA.EW.A2FR.01', 'TCGA.C8.A1HG.01', 'TCGA.D8.A1J9.01', 'TCGA.BH.A8G0.01', 'TCGA.D8.A27F.01', 'TCGA.GM.A2D9.01', 'TCGA.UL.AAZ6.01', 'TCGA.AR.A0U3.01', 'TCGA.D8.A1XB.01', 'TCGA.C8.A1HJ.01', 'TCGA.AR.A1AN.01', 'TCGA.C8.A27B.01', 'TCGA.AC.A23C.01', 'TCGA.GM.A2DH.01', 'TCGA.S3.AA15.01', 'TCGA.EW.A1OX.01', 'TCGA.BH.A203.01', 'TCGA.OL.A66J.01', 'TCGA.C8.A278.01', 'TCGA.AC.A3OD.01', 'TCGA.A2.A4S1.01', 'TCGA.A2.A0ST.01', 'TCGA.AC.A3YI.01', 'TCGA.GI.A2C8.01', 'TCGA.S3.A6ZH.01'
...
'TCGA.E9.A1RF.01', 'TCGA.E9.A22H.01', 'TCGA.LL.A740.01', 'TCGA.BH.A0BM.01', 'TCGA.E9.A1R5.01', 'TCGA.LD.A74U.01', 'TCGA.AR.A0TR.01', 'TCGA.D8.A1XA.01', 'TCGA.OL.A6VO.01', 'TCGA.A2.A0T7.01', 'TCGA.A2.A3Y0.01', 'TCGA.AO.A0JG.01', 'TCGA.AR.A0TP.01', 'TCGA.C8.A1HM.01', 'TCGA.A7.A5ZV.01', 'TCGA.A2.A25D.01', 'TCGA.E9.A22B.01', 'TCGA.E9.A1R6.01', 'TCGA.EW.A1IY.01', 'TCGA.BH.A0HP.01', 'TCGA.B6.A0RE.01', 'TCGA.E9.A295.01', 'TCGA.A2.A4S2.01', 'TCGA.E2.A15K.01', 'TCGA.LL.A73Y.01', 'TCGA.C8.A26X.01', 'TCGA.BH.A0DH.01', 'TCGA.E2.A1LI.01', 'TCGA.A7.A2KD.01', 'TCGA.OL.A6VQ.01', 'TCGA.A2.A0YC.01', 'TCGA.A1.A0SG.01', 'TCGA.AC.A2FK.01', 'TCGA.C8.A1HI.01', 'TCGA.BH.A0DS.01', 'TCGA.XX.A89A.01', 'TCGA.GM.A4E0.01', 'TCGA.E9.A6HE.01', 'TCGA.E9.A1R4.01', 'TCGA.PE.A5DE.01', 'TCGA.AR.A24N.01', 'TCGA.OL.A97C.01', 'TCGA.A1.A0SQ.01', 'TCGA.E9.A24A.01', 'TCGA.E2.A1IK.01', 'TCGA.AQ.A7U7.01', 'TCGA.OL.A66I.01', 'TCGA.BH.A0H9.01', 'TCGA.BH.A209.01', 'TCGA.B6.A0RL.01', 'TCGA.E2.A1IO.01', 'TCGA.BH.A0H0.01', 'TCGA.AR.A1AS.01', 'TCGA.LL.A5YL.01', 'TCGA.BH.A0BZ.01', 'TCGA.B6.A401.01', 'TCGA.D8.A1XW.01', 'TCGA.AO.A03M.01', 'TCGA.E9.A1R7.01', 'TCGA.EW.A1J1.01', 'TCGA.LL.A5YM.01', 'TCGA.D8.A27I.01', 'TCGA.A2.A0YT.01', 'TCGA.C8.A8HQ.01', 'TCGA.A7.A3RF.01', 'TCGA.AC.A8OQ.01', 'TCGA.D8.A3Z6.01', 'TCGA.EW.A2FV.01', 'TCGA.D8.A1JU.01', 'TCGA.A2.A25E.01', 'TCGA.E9.A243.01', 'TCGA.A1.A0SJ.01', 'TCGA.B6.A409.01', 'TCGA.D8.A1JS.01', 'TCGA.A2.A3XW.01', 'TCGA.E9.A245.01', 'TCGA.E9.A1ND.01', 'TCGA.E2.A10C.01', 'TCGA.AR.A1AP.01'}).

This happened while the csv dataset builder was generating data using

hf://datasets/AIBIC/MLOmics/Main_Dataset/Classification_datasets/GS-BRCA/Aligned/BRCA_label_num.csv (at revision d7c2239504dcf817ee9f33a693f9617d614eef67)

Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1871, in _prepare_split_single
                  writer.write_table(table)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 643, in write_table
                  pa_table = table_cast(pa_table, self._schema)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2293, in table_cast
                  return cast_table_to_schema(table, schema)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2241, in cast_table_to_schema
                  raise CastError(
              datasets.table.CastError: Couldn't cast
              Label: int64
              -- schema metadata --
              pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 368
              to
              {'Unnamed: 0': Value(dtype='string', id=None), 'TCGA.3C.AAAU.01': Value(dtype='float64', id=None), 'TCGA.3C.AALI.01': Value(dtype='float64', id=None), 'TCGA.3C.AALJ.01': Value(dtype='float64', id=None), 'TCGA.3C.AALK.01': Value(dtype='float64', id=None), 'TCGA.5L.AAT0.01': Value(dtype='float64', id=None), 'TCGA.5T.A9QA.01': Value(dtype='float64', id=None), 'TCGA.A1.A0SB.01': Value(dtype='float64', id=None), 'TCGA.A1.A0SE.01': Value(dtype='float64', id=None), 'TCGA.A1.A0SF.01': Value(dtype='float64', id=None), 'TCGA.A1.A0SG.01': Value(dtype='float64', id=None), 'TCGA.A1.A0SH.01': Value(dtype='float64', id=None), 'TCGA.A1.A0SI.01': Value(dtype='float64', id=None), 'TCGA.A1.A0SJ.01': Value(dtype='float64', id=None), 'TCGA.A1.A0SK.01': Value(dtype='float64', id=None), 'TCGA.A1.A0SO.01': Value(dtype='float64', id=None), 'TCGA.A1.A0SP.01': Value(dtype='float64', id=None), 'TCGA.A1.A0SQ.01': Value(dtype='float64', id=None), 'TCGA.A2.A04R.01': Value(dtype='float64', id=None), 'TCGA.A2.A0CK.01': Value(dtype='float64', id=None), 'TCGA.A2.A0CR.01': Value(dtype='float64', id=None), 'TCGA.A2.A0CT.01': Value(dtype='float64', id=None), 'TCGA.A2.A0EN.01': Value(dtype='float64', id=None), 'TCGA.A2.A0EP.01': Value(dtype='float64', id=None), 'TCGA.A2.A0EU.01': Value(dtype='float64', id=None), 'TCGA.A2.A0ST.01': Value(dtype='float64', id=None), 'TCGA.A2.A0SU.01': Value(dtype='float64', id=None), 'TCGA.A2.A0SV.01': Value(dtype='float64', id=None), 'TCGA.A2.A0SW.01': Value(dtype='float64', id=None
              ...
              L.A6VR.01': Value(dtype='float64', id=None), 'TCGA.OL.A97C.01': Value(dtype='float64', id=None), 'TCGA.PE.A5DC.01': Value(dtype='float64', id=None), 'TCGA.PE.A5DD.01': Value(dtype='float64', id=None), 'TCGA.PE.A5DE.01': Value(dtype='float64', id=None), 'TCGA.PL.A8LV.01': Value(dtype='float64', id=None), 'TCGA.PL.A8LX.01': Value(dtype='float64', id=None), 'TCGA.PL.A8LY.01': Value(dtype='float64', id=None), 'TCGA.PL.A8LZ.01': Value(dtype='float64', id=None), 'TCGA.S3.A6ZF.01': Value(dtype='float64', id=None), 'TCGA.S3.A6ZG.01': Value(dtype='float64', id=None), 'TCGA.S3.A6ZH.01': Value(dtype='float64', id=None), 'TCGA.S3.AA0Z.01': Value(dtype='float64', id=None), 'TCGA.S3.AA10.01': Value(dtype='float64', id=None), 'TCGA.S3.AA11.01': Value(dtype='float64', id=None), 'TCGA.S3.AA12.01': Value(dtype='float64', id=None), 'TCGA.S3.AA14.01': Value(dtype='float64', id=None), 'TCGA.S3.AA15.01': Value(dtype='float64', id=None), 'TCGA.S3.AA17.01': Value(dtype='float64', id=None), 'TCGA.UL.AAZ6.01': Value(dtype='float64', id=None), 'TCGA.UU.A93S.01': Value(dtype='float64', id=None), 'TCGA.V7.A7HQ.01': Value(dtype='float64', id=None), 'TCGA.W8.A86G.01': Value(dtype='float64', id=None), 'TCGA.WT.AB41.01': Value(dtype='float64', id=None), 'TCGA.WT.AB44.01': Value(dtype='float64', id=None), 'TCGA.XX.A899.01': Value(dtype='float64', id=None), 'TCGA.XX.A89A.01': Value(dtype='float64', id=None), 'TCGA.Z7.A8R5.01': Value(dtype='float64', id=None), 'TCGA.Z7.A8R6.01': Value(dtype='float64', id=None)}
              because column names don't match
              
              During handling of the above exception, another exception occurred:
              
              Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1428, in compute_config_parquet_and_info_response
                  parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet(
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 989, in stream_convert_to_parquet
                  builder._prepare_split(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1742, in _prepare_split
                  for job_id, done, content in self._prepare_split_single(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1873, in _prepare_split_single
                  raise DatasetGenerationCastError.from_cast_error(
              datasets.exceptions.DatasetGenerationCastError: An error occurred while generating the dataset
              
              All the data files must have the same columns, but at some point there are 1 new columns ({'Label'}) and 672 missing columns ({'TCGA.AR.A0U2.01', 'TCGA.E9.A1RB.01', 'TCGA.D8.A1X8.01', 'TCGA.PL.A8LZ.01', 'TCGA.E2.A1BC.01', 'TCGA.E9.A1N3.01', 'TCGA.D8.A1JB.01', 'TCGA.A2.A0T5.01', 'TCGA.A2.A0YM.01', 'TCGA.3C.AALK.01', 'TCGA.BH.A0DP.01', 'TCGA.AR.A24Z.01', 'TCGA.BH.A6R8.01', 'TCGA.D8.A27W.01', 'TCGA.AQ.A04H.01', 'TCGA.D8.A1Y0.01', 'TCGA.EW.A1P5.01', 'TCGA.BH.A0H3.01', 'TCGA.BH.A0W5.01', 'TCGA.E2.A576.01', 'TCGA.GM.A3XL.01', 'TCGA.E9.A3X8.01', 'TCGA.E9.A248.01', 'TCGA.A7.A5ZX.01', 'TCGA.D8.A27H.01', 'TCGA.AO.A125.01', 'TCGA.AR.A2LE.01', 'TCGA.GM.A3NW.01', 'TCGA.A2.A25F.01', 'TCGA.BH.A1EV.01', 'TCGA.BH.A1FU.01', 'TCGA.D8.A27T.01', 'TCGA.AO.A0JE.01', 'TCGA.OL.A5RV.01', 'TCGA.E9.A1NE.01', 'TCGA.AR.A24P.01', 'TCGA.PE.A5DC.01', 'TCGA.E2.A9RU.01', 'TCGA.A2.A0CK.01', 'TCGA.S3.AA10.01', 'TCGA.S3.A6ZG.01', 'TCGA.D8.A27G.01', 'TCGA.AO.A03N.01', 'TCGA.A2.A0T0.01', 'TCGA.OL.A5DA.01', 'TCGA.WT.AB41.01', 'TCGA.A2.A0T6.01', 'TCGA.BH.A0W3.01', 'TCGA.A7.A26G.01', 'TCGA.AN.A0XV.01', 'TCGA.AC.A2FG.01', 'TCGA.EW.A1PA.01', 'TCGA.LD.A9QF.01', 'TCGA.WT.AB44.01', 'TCGA.EW.A2FR.01', 'TCGA.C8.A1HG.01', 'TCGA.D8.A1J9.01', 'TCGA.BH.A8G0.01', 'TCGA.D8.A27F.01', 'TCGA.GM.A2D9.01', 'TCGA.UL.AAZ6.01', 'TCGA.AR.A0U3.01', 'TCGA.D8.A1XB.01', 'TCGA.C8.A1HJ.01', 'TCGA.AR.A1AN.01', 'TCGA.C8.A27B.01', 'TCGA.AC.A23C.01', 'TCGA.GM.A2DH.01', 'TCGA.S3.AA15.01', 'TCGA.EW.A1OX.01', 'TCGA.BH.A203.01', 'TCGA.OL.A66J.01', 'TCGA.C8.A278.01', 'TCGA.AC.A3OD.01', 'TCGA.A2.A4S1.01', 'TCGA.A2.A0ST.01', 'TCGA.AC.A3YI.01', 'TCGA.GI.A2C8.01', 'TCGA.S3.A6ZH.01'
              ...
              'TCGA.E9.A1RF.01', 'TCGA.E9.A22H.01', 'TCGA.LL.A740.01', 'TCGA.BH.A0BM.01', 'TCGA.E9.A1R5.01', 'TCGA.LD.A74U.01', 'TCGA.AR.A0TR.01', 'TCGA.D8.A1XA.01', 'TCGA.OL.A6VO.01', 'TCGA.A2.A0T7.01', 'TCGA.A2.A3Y0.01', 'TCGA.AO.A0JG.01', 'TCGA.AR.A0TP.01', 'TCGA.C8.A1HM.01', 'TCGA.A7.A5ZV.01', 'TCGA.A2.A25D.01', 'TCGA.E9.A22B.01', 'TCGA.E9.A1R6.01', 'TCGA.EW.A1IY.01', 'TCGA.BH.A0HP.01', 'TCGA.B6.A0RE.01', 'TCGA.E9.A295.01', 'TCGA.A2.A4S2.01', 'TCGA.E2.A15K.01', 'TCGA.LL.A73Y.01', 'TCGA.C8.A26X.01', 'TCGA.BH.A0DH.01', 'TCGA.E2.A1LI.01', 'TCGA.A7.A2KD.01', 'TCGA.OL.A6VQ.01', 'TCGA.A2.A0YC.01', 'TCGA.A1.A0SG.01', 'TCGA.AC.A2FK.01', 'TCGA.C8.A1HI.01', 'TCGA.BH.A0DS.01', 'TCGA.XX.A89A.01', 'TCGA.GM.A4E0.01', 'TCGA.E9.A6HE.01', 'TCGA.E9.A1R4.01', 'TCGA.PE.A5DE.01', 'TCGA.AR.A24N.01', 'TCGA.OL.A97C.01', 'TCGA.A1.A0SQ.01', 'TCGA.E9.A24A.01', 'TCGA.E2.A1IK.01', 'TCGA.AQ.A7U7.01', 'TCGA.OL.A66I.01', 'TCGA.BH.A0H9.01', 'TCGA.BH.A209.01', 'TCGA.B6.A0RL.01', 'TCGA.E2.A1IO.01', 'TCGA.BH.A0H0.01', 'TCGA.AR.A1AS.01', 'TCGA.LL.A5YL.01', 'TCGA.BH.A0BZ.01', 'TCGA.B6.A401.01', 'TCGA.D8.A1XW.01', 'TCGA.AO.A03M.01', 'TCGA.E9.A1R7.01', 'TCGA.EW.A1J1.01', 'TCGA.LL.A5YM.01', 'TCGA.D8.A27I.01', 'TCGA.A2.A0YT.01', 'TCGA.C8.A8HQ.01', 'TCGA.A7.A3RF.01', 'TCGA.AC.A8OQ.01', 'TCGA.D8.A3Z6.01', 'TCGA.EW.A2FV.01', 'TCGA.D8.A1JU.01', 'TCGA.A2.A25E.01', 'TCGA.E9.A243.01', 'TCGA.A1.A0SJ.01', 'TCGA.B6.A409.01', 'TCGA.D8.A1JS.01', 'TCGA.A2.A3XW.01', 'TCGA.E9.A245.01', 'TCGA.E9.A1ND.01', 'TCGA.E2.A10C.01', 'TCGA.AR.A1AP.01'}).
              
              This happened while the csv dataset builder was generating data using
              
              hf://datasets/AIBIC/MLOmics/Main_Dataset/Classification_datasets/GS-BRCA/Aligned/BRCA_label_num.csv (at revision d7c2239504dcf817ee9f33a693f9617d614eef67)
              
              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.

Unnamed: 0
string
TCGA.3C.AAAU.01
float64
TCGA.3C.AALI.01
float64
TCGA.3C.AALJ.01
float64
TCGA.3C.AALK.01
float64
TCGA.5L.AAT0.01
float64
TCGA.5T.A9QA.01
float64
TCGA.A1.A0SB.01
float64
TCGA.A1.A0SE.01
float64
TCGA.A1.A0SF.01
float64
TCGA.A1.A0SG.01
float64
TCGA.A1.A0SH.01
float64
TCGA.A1.A0SI.01
float64
TCGA.A1.A0SJ.01
float64
TCGA.A1.A0SK.01
float64
TCGA.A1.A0SO.01
float64
TCGA.A1.A0SP.01
float64
TCGA.A1.A0SQ.01
float64
TCGA.A2.A04R.01
float64
TCGA.A2.A0CK.01
float64
TCGA.A2.A0CR.01
float64
TCGA.A2.A0CT.01
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TCGA.A2.A0EN.01
float64
TCGA.A2.A0EP.01
float64
TCGA.A2.A0EU.01
float64
TCGA.A2.A0ST.01
float64
TCGA.A2.A0SU.01
float64
TCGA.A2.A0SV.01
float64
TCGA.A2.A0SW.01
float64
TCGA.A2.A0SX.01
float64
TCGA.A2.A0SY.01
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TCGA.A2.A0T0.01
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TCGA.A2.A0T1.01
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TCGA.A2.A0T2.01
float64
TCGA.A2.A0T4.01
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TCGA.A2.A0T5.01
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TCGA.A2.A0T6.01
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TCGA.A2.A0T7.01
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TCGA.A2.A0YC.01
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TCGA.A2.A0YD.01
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TCGA.A2.A0YH.01
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TCGA.A2.A0YI.01
float64
TCGA.A2.A0YK.01
float64
TCGA.A2.A0YL.01
float64
TCGA.A2.A0YM.01
float64
TCGA.A2.A0YT.01
float64
TCGA.A2.A1FV.01
float64
TCGA.A2.A1FW.01
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TCGA.A2.A1FX.01
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TCGA.A2.A1FZ.01
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TCGA.A2.A1G0.01
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TCGA.A2.A1G1.01
float64
TCGA.A2.A1G4.01
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TCGA.A2.A1G6.01
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TCGA.A2.A259.01
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TCGA.A2.A25A.01
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TCGA.A2.A25B.01
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TCGA.A2.A25C.01
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TCGA.A2.A25D.01
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TCGA.A2.A25E.01
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TCGA.A2.A25F.01
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TCGA.A2.A3KD.01
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TCGA.A2.A3XU.01
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TCGA.A2.A3XV.01
float64
TCGA.A2.A3XW.01
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TCGA.A2.A3XX.01
float64
TCGA.A2.A3XZ.01
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TCGA.A2.A3Y0.01
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TCGA.A2.A4S1.01
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TCGA.A7.A26H.01
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TCGA.A7.A26I.01
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TCGA.A7.A4SD.01
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TCGA.A7.A4SE.01
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TCGA.A7.A56D.01
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TCGA.A7.A5ZV.01
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TCGA.A7.A5ZW.01
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TCGA.A7.A5ZX.01
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End of preview.

MLOmics: Cancer Multi-Omics Database for Machine Learning

Abstract

Framing the investigation of diverse cancers as a machine learning problem has recently shown significant potential in multi-omics analysis and cancer research. Empowering these successful machine learning models are the high-quality training datasets with sufficient data volume and adequate preprocessing. However, while there exist several public data portals including The Cancer Genome Atlas (TCGA) multi-omics initiative or open-bases such as the LinkedOmics, these databases are not off-the-shelf for existing machine learning models. We propose MLOmics, an open cancer multi-omics database aiming at serving better the development and evaluation of bioinformatics and machine learning models. MLOmics contains 8,314 patient samples covering all 32 cancer types with four omics types, stratified features, and extensive baselines. Complementary support for downstream analysis and bio-knowledge linking are also included to support interdisciplinary analysis.

Data Records

The MLOmic main datasets are now accessible under the Creative Commons 4.0 Attribution (CC-BY-4.0), which supports its use for educational and research purposes. The main datasets presented include all cancer multi-omics datasets corresponding to the various tasks.

Main Datasets

The Main Datasets repository is stored as csv files and is organized into three layers. The first layer contains three files corresponding to three different tasks: Classification_datasets, Clustering_datasets, and Imputation_datasets. The second layer includes files for specific tasks, such as GS-BRCA, ACC, and Imp-BRCA. The third layer contains three files corresponding to different feature scales, i.e., Original, Aligned, and Top. The omics data from different omics sources are stored in the following files: Cancer_miRNA_Feature.csv, Cancer_mRNA_Feature.csv, Cancer_CNV_Feature.csv, and Cancer_Methy_Feature.csv. Here, Cancer represents the cancer type, and Feature indicates the feature scale type.
The ground truth labels are provided in the file Cancer_label_num.csv, where Cancer represents the cancer type.
The patient survival records are stored in the file Cancer_survival.csv.

Code Availability

All code are stored on the cloud in user-friendly formats and are accessible via our GitHub repository (https://github.com/chenzRG/Cancer-Multi-Omics-Benchmark). We provide comprehensive guidelines for utilization. All files are ready for direct loading and analysis using standard Python data packages like Numpy or Pandas. We hope it can lower the barriers to entry for machine learning researchers interested in developing methods for cancer multi-omics data analysis, thereby encouraging rapid progress in the field.

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