BioLLM mechanisms: Intestine and Pancreas
Collection
Frozen two-tissue datasets, scratch 1-layer Geneformer/scGPT and simple controls, plus full metrics and provenance. • 13 items • Updated
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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 53 new columns ({'compartment_new2', 'probability_class_4', 'annotation_res0.34_new2', 'label_index', 'evaluation_split', 'suspension_type', 'observation_joinid', 'sex', 'is_primary_data', 'assay_ontology_term_id', 'self_reported_ethnicity', 'research_split', 'prediction_index', 'tissue_type', 'development_stage_ontology_term_id', 'epcam_positive', 'source_record_count', 'correct', 'cell_line', 'source_matrix_row', 'self_reported_ethnicity_ontology_term_id', 'probability_class_3', 'probability_class_7', 'development_stage', 'organism', 'vim_positive', 'donor_id', 'prediction_cell_type', 'assay', 'nCount_RNA', 'source_file', 'cell_type', 'sex_ontology_term_id', 'probability_class_2', 'condition_new', 'tissue_ontology_term_id', 'raw_profile_sha256', 'percent.mt', 'cell_type_ontology_term_id', 'source_obs_name', 'source_row', 'tissue', 'nFeature_RNA', 'probability_class_6', 'organism_ontology_term_id', 'probability_class_5', 'cell_id', 'disease', 'source_cell_id', 'disease_ontology_term_id', 'probability_class_0', 'probability_class_1', 'annotation_res0.34_simple2'}) and 9 missing columns ({'mesenchymal stem cell', 'enterocyte', 'neuron', 'goblet cell', 'enteroendocrine cell', 'true_class', 'paneth cell', 'transit amplifying cell', 'myofibroblast cell'}).
This happened while the csv dataset builder was generating data using
hf://datasets/transhumanist-already-exists/experiment-artifacts/pca/intestine/predictions_train.csv (at revision 0507b86589e3075b27dc9728cfd45dee67fbff8a), ['hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/pca/intestine/confusion_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/pca/intestine/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/pca/pancreas/confusion_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/pca/pancreas/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/intestine/baselines/shared_numeric_linear/seed_0/final_epoch_20/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/intestine/baselines/shared_numeric_linear/seed_0/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/intestine/baselines/shared_numeric_mlp128/seed_0/final_epoch_20/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/intestine/baselines/shared_numeric_mlp128/seed_0/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/intestine/geneformer_d1_s0_b128_e20/final_epoch_20/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/intestine/geneformer_d1_s0_b128_e20/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/intestine/scgpt_d1_s0_b128_e20/final_epoch_20/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/intestine/scgpt_d1_s0_b128_e20/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/pancreas/baselines/shared_numeric_linear/seed_0/final_epoch_20/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/pancreas/baselines/shared_numeric_linear/seed_0/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/pancreas/baselines/shared_numeric_mlp128/seed_0/final_epoch_20/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/pancreas/baselines/shared_numeric_mlp128/seed_0/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/pancreas/geneformer_d1_s0_b128_e20/final_epoch_20/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/pancreas/geneformer_d1_s0_b128_e20/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/pancreas/scgpt_d1_s0_b128_e20/final_epoch_20/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/pancreas/scgpt_d1_s0_b128_e20/predictions_train.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
cell_id: string
nCount_RNA: double
nFeature_RNA: int64
percent.mt: double
cell_line: string
epcam_positive: int64
vim_positive: int64
condition_new: string
annotation_res0.34_new2: string
annotation_res0.34_simple2: string
compartment_new2: string
organism_ontology_term_id: string
tissue_ontology_term_id: string
tissue_type: string
assay_ontology_term_id: string
disease_ontology_term_id: string
cell_type_ontology_term_id: string
self_reported_ethnicity_ontology_term_id: string
development_stage_ontology_term_id: string
sex_ontology_term_id: string
suspension_type: string
donor_id: string
is_primary_data: bool
cell_type: string
assay: string
disease: string
organism: string
sex: string
tissue: string
self_reported_ethnicity: string
development_stage: string
observation_joinid: string
source_file: string
source_row: int64
source_obs_name: string
source_cell_id: string
raw_profile_sha256: string
research_split: string
source_record_count: int64
source_matrix_row: int64
label_index: int64
evaluation_split: string
prediction_index: int64
prediction_cell_type: string
correct: bool
probability_class_0: double
probability_class_1: double
probability_class_2: double
probability_class_3: double
probability_class_4: double
probability_class_5: double
probability_class_6: double
probability_class_7: double
-- schema metadata --
pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 7258
to
{'true_class': Value('string'), 'transit amplifying cell': Value('int64'), 'myofibroblast cell': Value('int64'), 'goblet cell': Value('int64'), 'neuron': Value('int64'), 'mesenchymal stem cell': Value('int64'), 'enterocyte': Value('int64'), 'enteroendocrine cell': Value('int64'), 'paneth cell': 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 53 new columns ({'compartment_new2', 'probability_class_4', 'annotation_res0.34_new2', 'label_index', 'evaluation_split', 'suspension_type', 'observation_joinid', 'sex', 'is_primary_data', 'assay_ontology_term_id', 'self_reported_ethnicity', 'research_split', 'prediction_index', 'tissue_type', 'development_stage_ontology_term_id', 'epcam_positive', 'source_record_count', 'correct', 'cell_line', 'source_matrix_row', 'self_reported_ethnicity_ontology_term_id', 'probability_class_3', 'probability_class_7', 'development_stage', 'organism', 'vim_positive', 'donor_id', 'prediction_cell_type', 'assay', 'nCount_RNA', 'source_file', 'cell_type', 'sex_ontology_term_id', 'probability_class_2', 'condition_new', 'tissue_ontology_term_id', 'raw_profile_sha256', 'percent.mt', 'cell_type_ontology_term_id', 'source_obs_name', 'source_row', 'tissue', 'nFeature_RNA', 'probability_class_6', 'organism_ontology_term_id', 'probability_class_5', 'cell_id', 'disease', 'source_cell_id', 'disease_ontology_term_id', 'probability_class_0', 'probability_class_1', 'annotation_res0.34_simple2'}) and 9 missing columns ({'mesenchymal stem cell', 'enterocyte', 'neuron', 'goblet cell', 'enteroendocrine cell', 'true_class', 'paneth cell', 'transit amplifying cell', 'myofibroblast cell'}).
This happened while the csv dataset builder was generating data using
hf://datasets/transhumanist-already-exists/experiment-artifacts/pca/intestine/predictions_train.csv (at revision 0507b86589e3075b27dc9728cfd45dee67fbff8a), ['hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/pca/intestine/confusion_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/pca/intestine/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/pca/pancreas/confusion_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/pca/pancreas/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/intestine/baselines/shared_numeric_linear/seed_0/final_epoch_20/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/intestine/baselines/shared_numeric_linear/seed_0/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/intestine/baselines/shared_numeric_mlp128/seed_0/final_epoch_20/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/intestine/baselines/shared_numeric_mlp128/seed_0/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/intestine/geneformer_d1_s0_b128_e20/final_epoch_20/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/intestine/geneformer_d1_s0_b128_e20/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/intestine/scgpt_d1_s0_b128_e20/final_epoch_20/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/intestine/scgpt_d1_s0_b128_e20/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/pancreas/baselines/shared_numeric_linear/seed_0/final_epoch_20/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/pancreas/baselines/shared_numeric_linear/seed_0/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/pancreas/baselines/shared_numeric_mlp128/seed_0/final_epoch_20/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/pancreas/baselines/shared_numeric_mlp128/seed_0/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/pancreas/geneformer_d1_s0_b128_e20/final_epoch_20/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/pancreas/geneformer_d1_s0_b128_e20/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/pancreas/scgpt_d1_s0_b128_e20/final_epoch_20/predictions_train.csv', 'hf://datasets/transhumanist-already-exists/experiment-artifacts@0507b86589e3075b27dc9728cfd45dee67fbff8a/results/pancreas/scgpt_d1_s0_b128_e20/predictions_train.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.
true_class string | transit amplifying cell int64 | myofibroblast cell int64 | goblet cell int64 | neuron int64 | mesenchymal stem cell int64 | enterocyte int64 | enteroendocrine cell int64 | paneth cell int64 |
|---|---|---|---|---|---|---|---|---|
transit amplifying cell | 579 | 0 | 0 | 0 | 2 | 33 | 0 | 6 |
myofibroblast cell | 0 | 131 | 0 | 0 | 4 | 1 | 0 | 0 |
goblet cell | 3 | 0 | 123 | 0 | 0 | 11 | 1 | 0 |
neuron | 1 | 0 | 0 | 178 | 20 | 0 | 0 | 0 |
mesenchymal stem cell | 5 | 1 | 0 | 1 | 417 | 0 | 0 | 0 |
enterocyte | 18 | 0 | 4 | 0 | 0 | 3,304 | 2 | 11 |
enteroendocrine cell | 1 | 0 | 1 | 0 | 0 | 4 | 117 | 1 |
paneth cell | 7 | 0 | 0 | 0 | 1 | 23 | 0 | 962 |
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End of preview.
experiment-artifacts
Full scientific outputs for the existing two-tissue seed0/batch128/20-epoch scratch experiments: Linear, MLP128, Geneformer1L, scGPT1L and PCA50+5NN controls. Includes train/validation/test predictions CSV+NPZ, full class metrics, training/step/gradient logs and PCA outputs. Best-validation and epoch20 endpoints remain separate.
Datasets: Intestine, Pancreas. This release contains the existing scientific artifacts; no future runs or full pairwise distance intermediates are claimed.
Collection: BioLLM mechanisms.
The private source repository is BogdanDidenko/biollm-mechanisms. Access to that repository requires permission; all files in this HF repository are public.
This release preserves the frozen historical experiment inputs and scientific endpoints. Future matched-initialization 1/2/3-layer panels are planned; their weights are not included. Previously inspected test results are exploratory. Historical 20L/12L models, backup aliases, temporary transfers and pairwise-distance caches are excluded.
Practical GPU experiment plan
Operator runbook and machine checklist: input/replay checks, six diagnostic methods, paired interventions and depth1/2/3 confirmation. The English runbook links implemented scripts, native pinned CPU integration evidence and explicit CUDA verification status. Actual CUDA remains blocked by Runpod402 insufficient balance; no biomedical campaign81 runs was executed.
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