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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 15 new columns ({'target_seq', 'publication', 'DMS_id', 'DMS_mutant_type', 'DMS_score_type', 'DMS_filename', 'UniProt_ID', 'seq_len', 'PD_relevance', 'protein_name', 'number_mutants', 'source', 'organism', 'gene_name', 'DMS_phenotype'}) and 4 missing columns ({'mutant', 'label', 'review_status', 'significance'}).
This happened while the csv dataset builder was generating data using
hf://datasets/EvanOLeary/LewyGym/reference_files/DMS_substitutions.csv (at revision 35d69690b4985316ffe0c04039591b1719821e39), ['hf://datasets/EvanOLeary/LewyGym@35d69690b4985316ffe0c04039591b1719821e39/pathogenicity/clinvar_gba_missense.csv', 'hf://datasets/EvanOLeary/LewyGym@35d69690b4985316ffe0c04039591b1719821e39/pathogenicity/clinvar_lrrk2_missense.csv', 'hf://datasets/EvanOLeary/LewyGym@35d69690b4985316ffe0c04039591b1719821e39/pathogenicity/clinvar_park7_missense.csv', 'hf://datasets/EvanOLeary/LewyGym@35d69690b4985316ffe0c04039591b1719821e39/pathogenicity/clinvar_pink1_missense.csv', 'hf://datasets/EvanOLeary/LewyGym@35d69690b4985316ffe0c04039591b1719821e39/pathogenicity/clinvar_prkn_missense.csv', 'hf://datasets/EvanOLeary/LewyGym@35d69690b4985316ffe0c04039591b1719821e39/pathogenicity/clinvar_snca_missense.csv', 'hf://datasets/EvanOLeary/LewyGym@35d69690b4985316ffe0c04039591b1719821e39/pathogenicity/clinvar_vps35_missense.csv', 'hf://datasets/EvanOLeary/LewyGym@35d69690b4985316ffe0c04039591b1719821e39/reference_files/DMS_substitutions.csv', 'hf://datasets/EvanOLeary/LewyGym@35d69690b4985316ffe0c04039591b1719821e39/substitutions/SNCA_HUMAN_Newberry_2020.csv', 'hf://datasets/EvanOLeary/LewyGym@35d69690b4985316ffe0c04039591b1719821e39/substitutions/SNCA_HUMAN_Noh_2026_0001pct.csv', 'hf://datasets/EvanOLeary/LewyGym@35d69690b4985316ffe0c04039591b1719821e39/substitutions/SNCA_HUMAN_Noh_2026_001pct.csv', 'hf://datasets/EvanOLeary/LewyGym@35d69690b4985316ffe0c04039591b1719821e39/substitutions/SNCA_HUMAN_Noh_2026_01pct.csv', 'hf://datasets/EvanOLeary/LewyGym@35d69690b4985316ffe0c04039591b1719821e39/substitutions/SNCA_HUMAN_Noh_2026_1pct.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 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
DMS_id: string
UniProt_ID: string
gene_name: string
protein_name: string
organism: string
seq_len: int64
number_mutants: int64
DMS_phenotype: string
DMS_mutant_type: string
DMS_score_type: string
source: string
publication: string
PD_relevance: string
DMS_filename: string
target_seq: string
-- schema metadata --
pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 2089
to
{'mutant': Value('string'), 'label': Value('int64'), 'significance': Value('string'), 'review_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 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 15 new columns ({'target_seq', 'publication', 'DMS_id', 'DMS_mutant_type', 'DMS_score_type', 'DMS_filename', 'UniProt_ID', 'seq_len', 'PD_relevance', 'protein_name', 'number_mutants', 'source', 'organism', 'gene_name', 'DMS_phenotype'}) and 4 missing columns ({'mutant', 'label', 'review_status', 'significance'}).
This happened while the csv dataset builder was generating data using
hf://datasets/EvanOLeary/LewyGym/reference_files/DMS_substitutions.csv (at revision 35d69690b4985316ffe0c04039591b1719821e39), ['hf://datasets/EvanOLeary/LewyGym@35d69690b4985316ffe0c04039591b1719821e39/pathogenicity/clinvar_gba_missense.csv', 'hf://datasets/EvanOLeary/LewyGym@35d69690b4985316ffe0c04039591b1719821e39/pathogenicity/clinvar_lrrk2_missense.csv', 'hf://datasets/EvanOLeary/LewyGym@35d69690b4985316ffe0c04039591b1719821e39/pathogenicity/clinvar_park7_missense.csv', 'hf://datasets/EvanOLeary/LewyGym@35d69690b4985316ffe0c04039591b1719821e39/pathogenicity/clinvar_pink1_missense.csv', 'hf://datasets/EvanOLeary/LewyGym@35d69690b4985316ffe0c04039591b1719821e39/pathogenicity/clinvar_prkn_missense.csv', 'hf://datasets/EvanOLeary/LewyGym@35d69690b4985316ffe0c04039591b1719821e39/pathogenicity/clinvar_snca_missense.csv', 'hf://datasets/EvanOLeary/LewyGym@35d69690b4985316ffe0c04039591b1719821e39/pathogenicity/clinvar_vps35_missense.csv', 'hf://datasets/EvanOLeary/LewyGym@35d69690b4985316ffe0c04039591b1719821e39/reference_files/DMS_substitutions.csv', 'hf://datasets/EvanOLeary/LewyGym@35d69690b4985316ffe0c04039591b1719821e39/substitutions/SNCA_HUMAN_Newberry_2020.csv', 'hf://datasets/EvanOLeary/LewyGym@35d69690b4985316ffe0c04039591b1719821e39/substitutions/SNCA_HUMAN_Noh_2026_0001pct.csv', 'hf://datasets/EvanOLeary/LewyGym@35d69690b4985316ffe0c04039591b1719821e39/substitutions/SNCA_HUMAN_Noh_2026_001pct.csv', 'hf://datasets/EvanOLeary/LewyGym@35d69690b4985316ffe0c04039591b1719821e39/substitutions/SNCA_HUMAN_Noh_2026_01pct.csv', 'hf://datasets/EvanOLeary/LewyGym@35d69690b4985316ffe0c04039591b1719821e39/substitutions/SNCA_HUMAN_Noh_2026_1pct.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.
mutant string | label int64 | significance string | review_status string |
|---|---|---|---|
P454R | 1 | Pathogenic | no assertion criteria provided |
P454R | 1 | Pathogenic | no assertion criteria provided |
N409S | 1 | Pathogenic/Likely pathogenic; risk factor | criteria provided, multiple submitters, no conflicts |
N409S | 1 | Pathogenic/Likely pathogenic; risk factor | criteria provided, multiple submitters, no conflicts |
R159Q | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
R159Q | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
V433L | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
V433L | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
D448H | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
D448H | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
D448V | 1 | Pathogenic/Likely pathogenic | no assertion criteria provided |
D448V | 1 | Pathogenic/Likely pathogenic | no assertion criteria provided |
R502C | 1 | Pathogenic | criteria provided, multiple submitters, no conflicts |
R502C | 1 | Pathogenic | criteria provided, multiple submitters, no conflicts |
G85E | 1 | Pathogenic | criteria provided, multiple submitters, no conflicts |
G85E | 1 | Pathogenic | criteria provided, multiple submitters, no conflicts |
F255Y | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
F255Y | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
K196Q | 1 | Likely pathogenic | criteria provided, single submitter |
K196Q | 1 | Likely pathogenic | criteria provided, single submitter |
F252I | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
F252I | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
V437F | 1 | Pathogenic | no assertion criteria provided |
V437F | 1 | Pathogenic | no assertion criteria provided |
P328L | 1 | Pathogenic | no assertion criteria provided |
P328L | 1 | Pathogenic | no assertion criteria provided |
T362I | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
T362I | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
P161S | 1 | Likely pathogenic | criteria provided, single submitter |
P161S | 1 | Likely pathogenic | criteria provided, single submitter |
R535H | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
R535H | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
V54L | 1 | Likely pathogenic | criteria provided, single submitter |
V54L | 1 | Likely pathogenic | criteria provided, single submitter |
N227S | 1 | Pathogenic | criteria provided, multiple submitters, no conflicts |
N227S | 1 | Pathogenic | criteria provided, multiple submitters, no conflicts |
F255V | 1 | Pathogenic | no assertion criteria provided |
F255V | 1 | Pathogenic | no assertion criteria provided |
W351C | 1 | Likely pathogenic | criteria provided, single submitter |
W351C | 1 | Likely pathogenic | criteria provided, single submitter |
G364R | 1 | Likely pathogenic | criteria provided, multiple submitters, no conflicts |
G364R | 1 | Likely pathogenic | criteria provided, multiple submitters, no conflicts |
C381G | 1 | Likely pathogenic | criteria provided, single submitter |
C381G | 1 | Likely pathogenic | criteria provided, single submitter |
S403T | 1 | Likely pathogenic | criteria provided, multiple submitters, no conflicts |
S403T | 1 | Likely pathogenic | criteria provided, multiple submitters, no conflicts |
R87W | 1 | Pathogenic | criteria provided, multiple submitters, no conflicts |
R87W | 1 | Pathogenic | criteria provided, multiple submitters, no conflicts |
R392G | 1 | Likely pathogenic | criteria provided, single submitter |
R392G | 1 | Likely pathogenic | criteria provided, single submitter |
P440L | 1 | Pathogenic | no assertion criteria provided |
P440L | 1 | Pathogenic | no assertion criteria provided |
H350R | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
H350R | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
R398* | 1 | Pathogenic | criteria provided, multiple submitters, no conflicts |
R398* | 1 | Pathogenic | criteria provided, multiple submitters, no conflicts |
G416S | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
G416S | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
R296Q | 1 | Pathogenic | criteria provided, multiple submitters, no conflicts |
R296Q | 1 | Pathogenic | criteria provided, multiple submitters, no conflicts |
R170L | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
R170L | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
K118N | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
K118N | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
F290L | 1 | Pathogenic | no assertion criteria provided |
F290L | 1 | Pathogenic | no assertion criteria provided |
L410V | 1 | Pathogenic | criteria provided, single submitter |
L410V | 1 | Pathogenic | criteria provided, single submitter |
R502H | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
R502H | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
S235P | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
S235P | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
R159W | 1 | Pathogenic | criteria provided, multiple submitters, no conflicts |
R159W | 1 | Pathogenic | criteria provided, multiple submitters, no conflicts |
V391L | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
V391L | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
V414L | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
V414L | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
L483R | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
L483R | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
R170C | 1 | Pathogenic | criteria provided, multiple submitters, no conflicts |
R170C | 1 | Pathogenic | criteria provided, multiple submitters, no conflicts |
R209C | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
R209C | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
N227K | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
N227K | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
G241R | 1 | Pathogenic | criteria provided, multiple submitters, no conflicts |
G241R | 1 | Pathogenic | criteria provided, multiple submitters, no conflicts |
K13R | 0 | Benign | criteria provided, multiple submitters, no conflicts |
K13R | 0 | Benign | criteria provided, multiple submitters, no conflicts |
I299T | 1 | Likely pathogenic | criteria provided, multiple submitters, no conflicts |
I299T | 1 | Likely pathogenic | criteria provided, multiple submitters, no conflicts |
P426L | 1 | Likely pathogenic | criteria provided, single submitter |
P426L | 1 | Likely pathogenic | criteria provided, single submitter |
R535C | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
R535C | 1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
A487T | 1 | Likely pathogenic | criteria provided, single submitter |
A487T | 1 | Likely pathogenic | criteria provided, single submitter |
I466S | 1 | Likely pathogenic | no assertion criteria provided |
I466S | 1 | Likely pathogenic | no assertion criteria provided |
End of preview.
LewyGym — Parkinson's Disease Protein Variant Effect Benchmark
ProteinGym-compatible variant effect prediction benchmark for Parkinson's disease proteins.
Dataset description
LewyGym provides two benchmark tracks for evaluating protein language models on Parkinson's disease variant effect prediction:
Track 1 — DMS substitution fitness (Spearman metric, ProteinGym-compatible)
- 5 SNCA (alpha-synuclein) deep mutational scanning assays
- 13,560 total variant-score pairs
- Source: MaveDB (CC0)
Track 2 — ClinVar pathogenicity classification (AUROC metric)
- 7 PD genes: LRRK2, GBA, PRKN, PINK1, SNCA, PARK7, VPS35
- 874 classified missense variants (P/LP vs B/LB)
- Source: ClinVar (public domain)
Usage
from datasets import load_dataset
# DMS track
dms = load_dataset("Tyronita/LewyGym", "substitutions")
# columns: mutant, DMS_score, DMS_id, gene, source
# Pathogenicity track
path = load_dataset("Tyronita/LewyGym", "pathogenicity")
# columns: mutant, label (1=pathogenic, 0=benign), gene, significance
Scoring with ESM-2
git clone https://github.com/Tyronita/LewyGym
pip install transformers torch pandas scipy
python score.py --model 650M --assays all
Sources
- Newberry et al. 2020, Nature Chemical Biology — SNCA yeast toxicity DMS
- Noh et al. 2026, Protein Science — SNCA concentration-dependent DMS
- Landrum et al., NAR — ClinVar
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