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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 1 new columns ({'KRAS_status'}) and 1 missing columns ({'EGFR_status'}).
This happened while the csv dataset builder was generating data using
hf://datasets/Eswar1885/tcga-luad-provgigapath-embeddings/labels/kras_labels.csv (at revision 1e8751d6f782e8043718085dea899c7d5e9338c9), ['hf://datasets/Eswar1885/tcga-luad-provgigapath-embeddings@1e8751d6f782e8043718085dea899c7d5e9338c9/labels/egfr_labels.csv', 'hf://datasets/Eswar1885/tcga-luad-provgigapath-embeddings@1e8751d6f782e8043718085dea899c7d5e9338c9/labels/kras_labels.csv', 'hf://datasets/Eswar1885/tcga-luad-provgigapath-embeddings@1e8751d6f782e8043718085dea899c7d5e9338c9/labels/task_a_pds_labels.csv', 'hf://datasets/Eswar1885/tcga-luad-provgigapath-embeddings@1e8751d6f782e8043718085dea899c7d5e9338c9/labels/task_b_pds_regression_labels.csv', 'hf://datasets/Eswar1885/tcga-luad-provgigapath-embeddings@1e8751d6f782e8043718085dea899c7d5e9338c9/labels/tasks/egfr.csv', 'hf://datasets/Eswar1885/tcga-luad-provgigapath-embeddings@1e8751d6f782e8043718085dea899c7d5e9338c9/labels/tasks/kras.csv', 'hf://datasets/Eswar1885/tcga-luad-provgigapath-embeddings@1e8751d6f782e8043718085dea899c7d5e9338c9/labels/tasks/pds_binary.csv', 'hf://datasets/Eswar1885/tcga-luad-provgigapath-embeddings@1e8751d6f782e8043718085dea899c7d5e9338c9/labels/tasks/tasks_summary.csv', 'hf://datasets/Eswar1885/tcga-luad-provgigapath-embeddings@1e8751d6f782e8043718085dea899c7d5e9338c9/labels/tasks/tp53.csv', 'hf://datasets/Eswar1885/tcga-luad-provgigapath-embeddings@1e8751d6f782e8043718085dea899c7d5e9338c9/labels/tp53_labels.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 1837, 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 2369, in table_cast
return cast_table_to_schema(table, schema)
File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2297, in cast_table_to_schema
raise CastError(
...<3 lines>...
)
datasets.table.CastError: Couldn't cast
patient_barcode: string
KRAS_status: string
-- schema metadata --
pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 531
to
{'patient_barcode': Value('string'), 'EGFR_status': 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 1683, 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 1839, 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 1 new columns ({'KRAS_status'}) and 1 missing columns ({'EGFR_status'}).
This happened while the csv dataset builder was generating data using
hf://datasets/Eswar1885/tcga-luad-provgigapath-embeddings/labels/kras_labels.csv (at revision 1e8751d6f782e8043718085dea899c7d5e9338c9), ['hf://datasets/Eswar1885/tcga-luad-provgigapath-embeddings@1e8751d6f782e8043718085dea899c7d5e9338c9/labels/egfr_labels.csv', 'hf://datasets/Eswar1885/tcga-luad-provgigapath-embeddings@1e8751d6f782e8043718085dea899c7d5e9338c9/labels/kras_labels.csv', 'hf://datasets/Eswar1885/tcga-luad-provgigapath-embeddings@1e8751d6f782e8043718085dea899c7d5e9338c9/labels/task_a_pds_labels.csv', 'hf://datasets/Eswar1885/tcga-luad-provgigapath-embeddings@1e8751d6f782e8043718085dea899c7d5e9338c9/labels/task_b_pds_regression_labels.csv', 'hf://datasets/Eswar1885/tcga-luad-provgigapath-embeddings@1e8751d6f782e8043718085dea899c7d5e9338c9/labels/tasks/egfr.csv', 'hf://datasets/Eswar1885/tcga-luad-provgigapath-embeddings@1e8751d6f782e8043718085dea899c7d5e9338c9/labels/tasks/kras.csv', 'hf://datasets/Eswar1885/tcga-luad-provgigapath-embeddings@1e8751d6f782e8043718085dea899c7d5e9338c9/labels/tasks/pds_binary.csv', 'hf://datasets/Eswar1885/tcga-luad-provgigapath-embeddings@1e8751d6f782e8043718085dea899c7d5e9338c9/labels/tasks/tasks_summary.csv', 'hf://datasets/Eswar1885/tcga-luad-provgigapath-embeddings@1e8751d6f782e8043718085dea899c7d5e9338c9/labels/tasks/tp53.csv', 'hf://datasets/Eswar1885/tcga-luad-provgigapath-embeddings@1e8751d6f782e8043718085dea899c7d5e9338c9/labels/tp53_labels.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.
patient_barcode string | EGFR_status string |
|---|---|
TCGA-05-4244 | EGFR_Wild_Type |
TCGA-05-4245 | EGFR_Wild_Type |
TCGA-05-4249 | EGFR_Wild_Type |
TCGA-05-4250 | EGFR_Wild_Type |
TCGA-05-4382 | EGFR_Mutated |
TCGA-05-4395 | EGFR_Wild_Type |
TCGA-05-4396 | EGFR_Wild_Type |
TCGA-05-4397 | EGFR_Wild_Type |
TCGA-05-4398 | EGFR_Wild_Type |
TCGA-05-4402 | EGFR_Mutated |
TCGA-05-4403 | EGFR_Wild_Type |
TCGA-05-4405 | EGFR_Wild_Type |
TCGA-05-4415 | EGFR_Wild_Type |
TCGA-05-4417 | EGFR_Wild_Type |
TCGA-05-4418 | EGFR_Wild_Type |
TCGA-05-4420 | EGFR_Wild_Type |
TCGA-05-4422 | EGFR_Wild_Type |
TCGA-05-4424 | EGFR_Wild_Type |
TCGA-05-4426 | EGFR_Wild_Type |
TCGA-05-4427 | EGFR_Wild_Type |
TCGA-05-4430 | EGFR_Wild_Type |
TCGA-05-4432 | EGFR_Wild_Type |
TCGA-05-4433 | EGFR_Wild_Type |
TCGA-05-4434 | EGFR_Wild_Type |
TCGA-35-3615 | EGFR_Wild_Type |
TCGA-35-4122 | EGFR_Wild_Type |
TCGA-35-4123 | EGFR_Wild_Type |
TCGA-35-5375 | EGFR_Wild_Type |
TCGA-38-4625 | EGFR_Wild_Type |
TCGA-38-4626 | EGFR_Wild_Type |
TCGA-38-4627 | EGFR_Mutated |
TCGA-38-4628 | EGFR_Mutated |
TCGA-38-4629 | EGFR_Mutated |
TCGA-38-4630 | EGFR_Wild_Type |
TCGA-38-4631 | EGFR_Wild_Type |
TCGA-38-4632 | EGFR_Wild_Type |
TCGA-38-6178 | EGFR_Mutated |
TCGA-38-7271 | EGFR_Wild_Type |
TCGA-38-A44F | EGFR_Wild_Type |
TCGA-44-2655 | EGFR_Wild_Type |
TCGA-44-2656 | EGFR_Wild_Type |
TCGA-44-2657 | EGFR_Wild_Type |
TCGA-44-2659 | EGFR_Wild_Type |
TCGA-44-2661 | EGFR_Mutated |
TCGA-44-2662 | EGFR_Wild_Type |
TCGA-44-2664 | EGFR_Wild_Type |
TCGA-44-2665 | EGFR_Wild_Type |
TCGA-44-2666 | EGFR_Wild_Type |
TCGA-44-2668 | EGFR_Wild_Type |
TCGA-44-3396 | EGFR_Wild_Type |
TCGA-44-3398 | EGFR_Wild_Type |
TCGA-44-3917 | EGFR_Wild_Type |
TCGA-44-3918 | EGFR_Wild_Type |
TCGA-44-3919 | EGFR_Wild_Type |
TCGA-44-4112 | EGFR_Wild_Type |
TCGA-44-5643 | EGFR_Wild_Type |
TCGA-44-5644 | EGFR_Wild_Type |
TCGA-44-5645 | EGFR_Mutated |
TCGA-44-6144 | EGFR_Wild_Type |
TCGA-44-6145 | EGFR_Wild_Type |
TCGA-44-6146 | EGFR_Wild_Type |
TCGA-44-6147 | EGFR_Mutated |
TCGA-44-6148 | EGFR_Wild_Type |
TCGA-44-6774 | EGFR_Wild_Type |
TCGA-44-6775 | EGFR_Wild_Type |
TCGA-44-6776 | EGFR_Wild_Type |
TCGA-44-6777 | EGFR_Wild_Type |
TCGA-44-6778 | EGFR_Wild_Type |
TCGA-44-6779 | EGFR_Wild_Type |
TCGA-44-7659 | EGFR_Wild_Type |
TCGA-44-7660 | EGFR_Wild_Type |
TCGA-44-7661 | EGFR_Wild_Type |
TCGA-44-7662 | EGFR_Wild_Type |
TCGA-44-7667 | EGFR_Wild_Type |
TCGA-44-7669 | EGFR_Wild_Type |
TCGA-44-7670 | EGFR_Wild_Type |
TCGA-44-7671 | EGFR_Wild_Type |
TCGA-44-7672 | EGFR_Wild_Type |
TCGA-44-8119 | EGFR_Wild_Type |
TCGA-44-A479 | EGFR_Wild_Type |
TCGA-44-A47A | EGFR_Wild_Type |
TCGA-44-A47B | EGFR_Wild_Type |
TCGA-44-A47F | EGFR_Wild_Type |
TCGA-44-A47G | EGFR_Wild_Type |
TCGA-44-A4SS | EGFR_Wild_Type |
TCGA-44-A4SU | EGFR_Mutated |
TCGA-49-4487 | EGFR_Wild_Type |
TCGA-49-4488 | EGFR_Wild_Type |
TCGA-49-4490 | EGFR_Mutated |
TCGA-49-4494 | EGFR_Mutated |
TCGA-49-4501 | EGFR_Mutated |
TCGA-49-4505 | EGFR_Wild_Type |
TCGA-49-4506 | EGFR_Wild_Type |
TCGA-49-4507 | EGFR_Wild_Type |
TCGA-49-4510 | EGFR_Wild_Type |
TCGA-49-4512 | EGFR_Wild_Type |
TCGA-49-4514 | EGFR_Wild_Type |
TCGA-49-6742 | EGFR_Wild_Type |
TCGA-49-6743 | EGFR_Mutated |
TCGA-49-6744 | EGFR_Wild_Type |
End of preview.
TCGA-LUAD — Prov-GigaPath Tile Embeddings
Pre-extracted 1536-dimensional tile embeddings for TCGA-LUAD diagnostic H&E
whole-slide images, produced with the Prov-GigaPath tile encoder
(prov-gigapath/prov-gigapath). Part of a four-encoder benchmark in which every
model was run on the identical tiles for a fair comparison.
Tiling (identical across all encoders in the study)
- Source: raw TCGA-LUAD
.svs(GDC, open-access diagnostic slides). - 20× / 0.5 microns per pixel, MPP-aware (handles mixed 20×/40× scans).
- 256 × 256 px tiles, non-overlapping, full tissue coverage (Otsu on HSV saturation).
- Prov-GigaPath's official transform (Resize 256 → CenterCrop 224 → ImageNet norm) applied per tile.
Format (per slide, CLAM-compatible)
<slide_id>.h5:
features—(N, 1536)float32coords—(N, 2)int32, level-0 (x, y) of each tile- attrs:
patch_size=256,patch_level=0,target_mpp=0.5,model,embed_dim
slide_id = TCGA barcode + GDC file UUID. Task labels (PDS / TP53 / EGFR / KRAS)
are in labels/ (schema: case_id, slide_id, label).
Cohort
531 slides / 478 patients (diagnostic FFPE, primary tumor).
Attribution & license
- Source model: Prov-GigaPath — Xu et al., A whole-slide foundation model for digital pathology from real-world data, Nature 2024. Model under Apache-2.0.
- These derived embeddings are released under CC-BY-NC 4.0, honoring the model's research-only / non-clinical intent. Not for clinical use.
- Source images: TCGA-LUAD (NIH/GDC), open-access.
Provided for non-commercial academic research. Please cite the Prov-GigaPath paper and TCGA when using these features.
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