Dataset Viewer
The dataset viewer is not available for this split.
Cannot load the dataset split (in streaming mode) to extract the first rows.
Error code: StreamingRowsError
Exception: CastError
Message: Couldn't cast
anchor_id: string
split: string
weak_evidence: list<item: string>
child 0, item: string
no_interaction: list<item: string>
child 0, item: string
positive_records: int64
records_dropped: int64
records_kept: int64
pool_rows_dropped: int64
V_size: int64
schema_version: int64
pool_member_entries_removed: int64
base_pools_sha256: string
sha256s: struct<negative_pools_validation.jsonl: string, validation.jsonl: string, validation_positive.jsonl: (... 8 chars omitted)
child 0, negative_pools_validation.jsonl: string
child 1, validation.jsonl: string
child 2, validation_positive.jsonl: string
base_validation_sha256: string
pool_rows: int64
target_table_sha256: string
to
{'V_size': Value('int64'), 'base_pools_sha256': Value('string'), 'base_validation_sha256': Value('string'), 'pool_member_entries_removed': Value('int64'), 'pool_rows': Value('int64'), 'pool_rows_dropped': Value('int64'), 'positive_records': Value('int64'), 'records_dropped': Value('int64'), 'records_kept': Value('int64'), 'schema_version': Value('int64'), 'sha256s': {'negative_pools_validation.jsonl': Value('string'), 'validation.jsonl': Value('string'), 'validation_positive.jsonl': Value('string')}, 'target_table_sha256': 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 2951, in __iter__
for key, example in ex_iterable:
^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2461, in __iter__
for key, pa_table in self._iter_arrow():
~~~~~~~~~~~~~~~~^^
File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2486, 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 547, in _iter_arrow
for key, pa_table in iterator:
^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 430, 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
anchor_id: string
split: string
weak_evidence: list<item: string>
child 0, item: string
no_interaction: list<item: string>
child 0, item: string
positive_records: int64
records_dropped: int64
records_kept: int64
pool_rows_dropped: int64
V_size: int64
schema_version: int64
pool_member_entries_removed: int64
base_pools_sha256: string
sha256s: struct<negative_pools_validation.jsonl: string, validation.jsonl: string, validation_positive.jsonl: (... 8 chars omitted)
child 0, negative_pools_validation.jsonl: string
child 1, validation.jsonl: string
child 2, validation_positive.jsonl: string
base_validation_sha256: string
pool_rows: int64
target_table_sha256: string
to
{'V_size': Value('int64'), 'base_pools_sha256': Value('string'), 'base_validation_sha256': Value('string'), 'pool_member_entries_removed': Value('int64'), 'pool_rows': Value('int64'), 'pool_rows_dropped': Value('int64'), 'positive_records': Value('int64'), 'records_dropped': Value('int64'), 'records_kept': Value('int64'), 'schema_version': Value('int64'), 'sha256s': {'negative_pools_validation.jsonl': Value('string'), 'validation.jsonl': Value('string'), 'validation_positive.jsonl': Value('string')}, 'target_table_sha256': Value('string')}
because column names don't matchNeed help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
CDCL research data
This repository contains the fixed data snapshots used by the CDCL GO/PPI and TREC Clinical Trials experiments. Paths are preserved relative to the CDCL code repository root so a downloaded snapshot can be copied into a code checkout. These are research datasets, not clinical decision-support resources.
Contents
dataset/go_ppi/: STRING v12.0 human protein files, the GO ontology (go-basic.obo, release 2026-07-26), human GO annotations (goa_human.gaf.gz, generated 2026-05-21), and independent HuRI/Lit-BM data.preprocess/go_ppi/,preprocess/go_ppi_splits/, andpreprocess/go_ppi_lc/: converted protein/pair views, GO indexes, the fixed protein-disjoint splits and negative pools, and learning-curve fractions.trec-clinical-trials/raw/: the five-part April 27, 2021 ClinicalTrials.gov corpus snapshot distributed for the TREC Clinical Trials track, 2021/2022 topics and relevance judgments, and the 2021 MeSH descriptor fileontology/desc2021.gz.preprocess/trec_ct/,preprocess/trec_ct_splits/,preprocess/trec_ct_lc/, andpreprocess/trec_ct_budget/: converted records, fixed splits, negative pools, learning-curve fractions, and budget arms.embedding_cache/: reusable text-embedding caches and the 2021 MeSH index. These are accelerators; the raw ontology and dataset files are the sources.
The TREC patient topics are synthetic case descriptions, not real EHRs. Maintain the published train/validation/test boundaries when running experiments.
Source attribution and reuse
This repository combines materials with different terms; no single license applies to every file.
- Gene Ontology Consortium ontology and annotations: CC BY 4.0. Cite the consortium and the specific GO release used here. See https://geneontology.org/docs/go-citation-policy/ .
- STRING Consortium v12.0 download files: CC BY 4.0; credit STRING and note that these are human-filtered files. See https://string-db.org/cgi/access?footer_active_subpage=licensing .
- TREC Clinical Trials track topics, judgments, and the April 27, 2021 ClinicalTrials.gov snapshot: credit TREC/NIST and ClinicalTrials.gov. See https://www.trec-cds.org/2021.html and https://www.trec-cds.org/2022.html .
- MeSH 2021 descriptors: National Library of Medicine data. This is the 2021 version, not current MeSH. Credit NLM; do not imply NLM endorsement. Redistribution conditions: https://www.nlm.nih.gov/databases/download/terms_and_conditions_mesh.html .
For reproducibility, keep the dated ontology/corpus snapshots rather than silently replacing them with newer downloads. The included split manifests record counts, seeds, and source hashes.
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