Datasets:

sunweiwei
/

ai4sci-virtual-cell-zeroshot-data

Error code:   StreamingRowsError
Exception:    CastError
Message:      Couldn't cast
context: string
n_basal_cells: int64
n_requests: int64
n_response_cells: int64
note: string
perturbation_type: string
n_genes: int64
chemistry: string
context_id: string
to
{'chemistry': Value('string'), 'context_id': Value('string'), 'n_basal_cells': Value('int64'), 'n_genes': Value('int64'), 'n_requests': Value('int64'), 'perturbation_type': Value('string')}
because column names don't match
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/src/worker/utils.py", line 147, in get_rows_or_raise
                  return get_rows(
                      dataset=dataset,
                  ...<4 lines>...
                      column_names=column_names,
                  )
                File "/src/libs/libcommon/src/libcommon/utils.py", line 272, in decorator
                  return func(*args, **kwargs)
                File "/src/services/worker/src/worker/utils.py", line 127, in get_rows
                  rows_plus_one = list(itertools.islice(safe_iter(ds, dataset=dataset), rows_max_number + 1))
                File "/src/services/worker/src/worker/utils.py", line 483, in safe_iter
                  yield from ds.decode(False) if ds.features else ds
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2840, in __iter__
                  for key, example in ex_iterable:
                                      ^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2373, in __iter__
                  for key, pa_table in self._iter_arrow():
                                       ~~~~~~~~~~~~~~~~^^
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2398, in _iter_arrow
                  for key, pa_table in self.ex_iterable._iter_arrow():
                                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 536, in _iter_arrow
                  for key, pa_table in iterator:
                                       ^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 419, in _iter_arrow
                  for key, pa_table in self.generate_tables_fn(**gen_kwags):
                                       ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/json/json.py", line 343, in _generate_tables
                  self._cast_table(pa_table, json_field_paths=json_field_paths),
                  ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/json/json.py", line 132, in _cast_table
                  pa_table = table_cast(pa_table, self.info.features.arrow_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
              context: string
              n_basal_cells: int64
              n_requests: int64
              n_response_cells: int64
              note: string
              perturbation_type: string
              n_genes: int64
              chemistry: string
              context_id: string
              to
              {'chemistry': Value('string'), 'context_id': Value('string'), 'n_basal_cells': Value('int64'), 'n_genes': Value('int64'), 'n_requests': Value('int64'), 'perturbation_type': Value('string')}
              because column names don't match

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ai4sci virtual-cell-zeroshot — release v1

Prepared data for the virtual-cell-zeroshot task: predict single-cell CRISPRi knockdown responses in cellular contexts a model has never seen perturbed (the Arc Virtual Cell Challenge 2026 zero-shot setting), rebuilt from public data.

dev/        what the agent sees (mount read-only at /workspace/data)
  train/{k562,jurkat,hct116,hek293t}/   cells.h5ad, pseudobulk.h5ad, se_embeddings.npy, dev_split/
  test/{ctx_near,ctx_mid,ctx_far}/public/   basal.h5ad, requests.jsonl, context.json
  priors/     ESM-2 gene embeddings, GO annotations, DepMap gene effects (training lines)
  manifest.json, splits.json, gene_panel.csv, gene_panel_intersection.json
private/    grader only: responses of the test contexts, request subsets/strata, cached no-effect + DE tables
manifest.json

dev/se600m/ is not included: fetch SE-600M (se600m_epoch16.ckpt, config.yaml, protein_embeddings.pt, licences) from arcinstitute/SE-600M at revision 5a9a80f into dev/se600m/ (the task's materialize.sh / fetch_release.sh do this).

Schemas, split design, sampling caps and QC: the task's environment/data/README.md. Every source file, size and SHA-256: manifest.json.

Sources and licences

Derived (harmonised, subsampled, re-split) from: Replogle et al. 2022 (Figshare 20029387, CC BY 4.0); Nadig et al. 2025 (GEO GSE264667); X-Atlas/Orion, Xaira Therapeutics (HF Xaira-Therapeutics/X-Atlas-Orion @ 53a5bc98, CC BY-NC-SA 4.0 — the hct116/hek293t trees inherit that licence: non-commercial, share-alike, attribution); Arc Institute Virtual Cell Challenge 2025 H1 hESC data (Arc VCC data terms); DepMap 24Q4 (CC BY 4.0); Gene Ontology annotations (CC BY 4.0). Please cite the original datasets.

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