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Datasets:
Marcochris
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GraphResidual-data

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Text
Tags:
graph-residual
protein
mutation
ptm
biomedical
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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 6 new columns ({'original_node_index', 'node_id', 'disease_name', 'node_index', 'source', 'disease_id'}) and 2 missing columns ({'src_index', 'dst_index'}).

This happened while the csv dataset builder was generating data using

hf://datasets/Marcochris/GraphResidual-data/initial_data/inductive_graph_residual_extension/datasets/G_train/node_mappings/disease.tsv (at revision 14a33d376cc8bbe7906588d32bf8512d0012163e), ['hf://datasets/Marcochris/GraphResidual-data@14a33d376cc8bbe7906588d32bf8512d0012163e/initial_data/inductive_graph_residual_extension/datasets/G_train/edges/disease__has_mutation__mutation.tsv.gz', 'hf://datasets/Marcochris/GraphResidual-data@14a33d376cc8bbe7906588d32bf8512d0012163e/initial_data/inductive_graph_residual_extension/datasets/G_train/edges/disease__has_protein__protein.tsv.gz', 'hf://datasets/Marcochris/GraphResidual-data@14a33d376cc8bbe7906588d32bf8512d0012163e/initial_data/inductive_graph_residual_extension/datasets/G_train/edges/disease__has_ptm__ptm.tsv.gz', 'hf://datasets/Marcochris/GraphResidual-data@14a33d376cc8bbe7906588d32bf8512d0012163e/initial_data/inductive_graph_residual_extension/datasets/G_train/edges/mutation__on_protein__protein.tsv.gz', 'hf://datasets/Marcochris/GraphResidual-data@14a33d376cc8bbe7906588d32bf8512d0012163e/initial_data/inductive_graph_residual_extension/datasets/G_train/edges/protein__has_ptm__ptm.tsv.gz', 'hf://datasets/Marcochris/GraphResidual-data@14a33d376cc8bbe7906588d32bf8512d0012163e/initial_data/inductive_graph_residual_extension/datasets/G_train/edges/protein__in_pathway__pathway.tsv.gz', 'hf://datasets/Marcochris/GraphResidual-data@14a33d376cc8bbe7906588d32bf8512d0012163e/initial_data/inductive_graph_residual_extension/datasets/G_train/node_mappings/disease.tsv', 'hf://datasets/Marcochris/GraphResidual-data@14a33d376cc8bbe7906588d32bf8512d0012163e/initial_data/inductive_graph_residual_extension/datasets/G_train/node_mappings/mutation.tsv', 'hf://datasets/Marcochris/GraphResidual-data@14a33d376cc8bbe7906588d32bf8512d0012163e/initial_data/inductive_graph_residual_extension/datasets/G_train/node_mappings/pathway.tsv', 'hf://datasets/Marcochris/GraphResidual-data@14a33d376cc8bbe7906588d32bf8512d0012163e/initial_data/inductive_graph_residual_extension/datasets/G_train/node_mappings/protein.tsv', 'hf://datasets/Marcochris/GraphResidual-data@14a33d376cc8bbe7906588d32bf8512d0012163e/initial_data/inductive_graph_residual_extension/datasets/G_train/node_mappings/ptm.tsv', 'hf://datasets/Marcochris/GraphResidual-data@14a33d376cc8bbe7906588d32bf8512d0012163e/initial_data/inductive_graph_residual_extension/datasets/G_train/relation_mappings.tsv']

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 765, 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 773, 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
              node_index: int64
              node_id: string
              disease_id: double
              disease_name: string
              source: string
              original_node_index: int64
              -- schema metadata --
              pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 1004
              to
              {'src_index': Value('int64'), 'dst_index': Value('int64')}
              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 6 new columns ({'original_node_index', 'node_id', 'disease_name', 'node_index', 'source', 'disease_id'}) and 2 missing columns ({'src_index', 'dst_index'}).
              
              This happened while the csv dataset builder was generating data using
              
              hf://datasets/Marcochris/GraphResidual-data/initial_data/inductive_graph_residual_extension/datasets/G_train/node_mappings/disease.tsv (at revision 14a33d376cc8bbe7906588d32bf8512d0012163e), ['hf://datasets/Marcochris/GraphResidual-data@14a33d376cc8bbe7906588d32bf8512d0012163e/initial_data/inductive_graph_residual_extension/datasets/G_train/edges/disease__has_mutation__mutation.tsv.gz', 'hf://datasets/Marcochris/GraphResidual-data@14a33d376cc8bbe7906588d32bf8512d0012163e/initial_data/inductive_graph_residual_extension/datasets/G_train/edges/disease__has_protein__protein.tsv.gz', 'hf://datasets/Marcochris/GraphResidual-data@14a33d376cc8bbe7906588d32bf8512d0012163e/initial_data/inductive_graph_residual_extension/datasets/G_train/edges/disease__has_ptm__ptm.tsv.gz', 'hf://datasets/Marcochris/GraphResidual-data@14a33d376cc8bbe7906588d32bf8512d0012163e/initial_data/inductive_graph_residual_extension/datasets/G_train/edges/mutation__on_protein__protein.tsv.gz', 'hf://datasets/Marcochris/GraphResidual-data@14a33d376cc8bbe7906588d32bf8512d0012163e/initial_data/inductive_graph_residual_extension/datasets/G_train/edges/protein__has_ptm__ptm.tsv.gz', 'hf://datasets/Marcochris/GraphResidual-data@14a33d376cc8bbe7906588d32bf8512d0012163e/initial_data/inductive_graph_residual_extension/datasets/G_train/edges/protein__in_pathway__pathway.tsv.gz', 'hf://datasets/Marcochris/GraphResidual-data@14a33d376cc8bbe7906588d32bf8512d0012163e/initial_data/inductive_graph_residual_extension/datasets/G_train/node_mappings/disease.tsv', 'hf://datasets/Marcochris/GraphResidual-data@14a33d376cc8bbe7906588d32bf8512d0012163e/initial_data/inductive_graph_residual_extension/datasets/G_train/node_mappings/mutation.tsv', 'hf://datasets/Marcochris/GraphResidual-data@14a33d376cc8bbe7906588d32bf8512d0012163e/initial_data/inductive_graph_residual_extension/datasets/G_train/node_mappings/pathway.tsv', 'hf://datasets/Marcochris/GraphResidual-data@14a33d376cc8bbe7906588d32bf8512d0012163e/initial_data/inductive_graph_residual_extension/datasets/G_train/node_mappings/protein.tsv', 'hf://datasets/Marcochris/GraphResidual-data@14a33d376cc8bbe7906588d32bf8512d0012163e/initial_data/inductive_graph_residual_extension/datasets/G_train/node_mappings/ptm.tsv', 'hf://datasets/Marcochris/GraphResidual-data@14a33d376cc8bbe7906588d32bf8512d0012163e/initial_data/inductive_graph_residual_extension/datasets/G_train/relation_mappings.tsv']
              
              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)

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src_index
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dst_index
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End of preview.

GraphResidual data package

Public research dataset package for the GraphResidual repository. It contains source datasets, derived benchmark tables, processed graph tables, and graph artifacts used by the ESM-2 and AMPLIFY-120M experiments.

Layout

  • data_raw/: source data and model assets used by the released experiments.
  • data_benchmark/: benchmark splits, candidate sets, and audit tables.
  • data_processed/: processed node, edge, and label tables.
  • data_processed_clean/: cleaned processed tables.
  • data_processed_core/: core processed tables and candidate tables.
  • work/graph_core/: compact graph mappings, relations, and graph artifacts.
  • work/graph_full/: full graph node and relation tables.
  • initial_data/root/: additional server-side source resources, including ClinVar, Reactome, UniProt, PTM, GTEx, and final ClinVar tables.
  • initial_data/brca_tcga_pan_can_atlas_2018/: BRCA TCGA PanCanAtlas 2018 molecular and clinical source tables.
  • initial_data/clinvar_strict_rebuild_v1/: strict ClinVar graph nodes, edges, mappings, splits, graph inputs, and removal ledgers.
  • initial_data/clinvar_strict_rebuild_audit/: source manifests and audit tables for the strict ClinVar rebuild.
  • initial_data/inductive_graph_residual_extension/: inductive split data, graph mappings, feature inventories, and related data contracts.
  • initial_data/data_raw_download/, data_raw_partial/, and data_raw_scp/: retained raw-download copies and transfer artifacts.

Exclusions

Images, figures, logs, Python bytecode, cache directories, code snapshots, model checkpoints, embeddings, predictions, and experiment-only output tables are not included in this data package.

Reproducibility and provenance

Use the public code and usage guide in GraphResidual for the expected directory layout and model interfaces. The uploaded data are public; check the original source database terms, licenses, and citation requirements before redistribution or publication.
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