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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 ({'deltaG_bin'})
This happened while the csv dataset builder was generating data using
hf://datasets/benchang323/protein-stability-prediction/ds23_sm_resampled.csv (at revision 27d61b6f9744887dafc07a0e6286cd2fc5bcc012)
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 "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 2011, in _prepare_split_single
writer.write_table(table)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 585, in write_table
pa_table = table_cast(pa_table, self._schema)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2302, in table_cast
return cast_table_to_schema(table, schema)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2256, in cast_table_to_schema
raise CastError(
datasets.table.CastError: Couldn't cast
aa_seq: string
deltaG: double
deltaG_bin: string
-- schema metadata --
pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 608
to
{'aa_seq': Value(dtype='string', id=None), 'deltaG': Value(dtype='float64', id=None)}
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 1321, in compute_config_parquet_and_info_response
parquet_operations = convert_to_parquet(builder)
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 935, in convert_to_parquet
builder.download_and_prepare(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1027, in download_and_prepare
self._download_and_prepare(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1122, in _download_and_prepare
self._prepare_split(split_generator, **prepare_split_kwargs)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1882, in _prepare_split
for job_id, done, content in self._prepare_split_single(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 2013, in _prepare_split_single
raise DatasetGenerationCastError.from_cast_error(
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 ({'deltaG_bin'})
This happened while the csv dataset builder was generating data using
hf://datasets/benchang323/protein-stability-prediction/ds23_sm_resampled.csv (at revision 27d61b6f9744887dafc07a0e6286cd2fc5bcc012)
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.
aa_seq
string | deltaG
float64 |
|---|---|
DEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.332126 |
DEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.399832 |
DEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.315782 |
DEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.272933 |
DEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 2.570242 |
QEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.242632 |
EEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.247267 |
NEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.269113 |
HEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.234823 |
REVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 2.912039 |
KEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.12028 |
TEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.369761 |
SEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.276337 |
AEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.233088 |
GEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.32706 |
MEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.196261 |
LEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.235052 |
VEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.220933 |
IEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.276756 |
WEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.042762 |
YEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.194362 |
FEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.224659 |
PEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.21814 |
CEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.422593 |
GDEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.402943 |
ADEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.375166 |
EVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.306247 |
DQVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.297488 |
DNVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.173002 |
DHVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.32919 |
DDVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.183969 |
DRVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.093489 |
DKVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.123588 |
DTVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.317149 |
DSVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.375629 |
DAVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.253462 |
DGVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.477708 |
DMVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.29866 |
DLVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.2636 |
DVVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.325464 |
DIVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.396734 |
DWVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.295229 |
DYVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.36378 |
DFVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.346061 |
DPVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.26296 |
DCVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 2.927812 |
DGEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.378574 |
DAEVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.332731 |
DVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.212869 |
DEQTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.403116 |
DEETIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.232111 |
DENTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.45349 |
DEHTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.327405 |
DEDTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.172956 |
DERTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 2.80987 |
DEKTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.082417 |
DETTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.329027 |
DESTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.325467 |
DEATIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.385958 |
DEGTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.213911 |
DEMTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.340012 |
DELTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.275759 |
DEITIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.398047 |
DEWTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.484582 |
DEYTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.438408 |
DEFTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.607592 |
DEPTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.103196 |
DECTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.305179 |
DEGVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.388637 |
DEAVTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.345062 |
DETIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.231035 |
DEVQIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.151092 |
DEVEIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.311263 |
DEVNIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.145644 |
DEVHIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.47328 |
DEVDIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.157398 |
DEVRIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 2.942111 |
DEVKIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 2.942878 |
DEVSIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.134132 |
DEVAIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.14162 |
DEVGIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 2.899337 |
DEVMIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.199847 |
DEVLIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.238591 |
DEVVIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.559234 |
DEVIIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.414189 |
DEVWIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 2.792806 |
DEVYIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.378206 |
DEVFIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.384984 |
DEVPIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 2.918139 |
DEVCIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.164047 |
DEVGTIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.241579 |
DEVATIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.304096 |
DEVIHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 3.333269 |
DEVTQHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 2.522421 |
DEVTEHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 2.562329 |
DEVTNHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 2.513628 |
DEVTHHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 2.469732 |
DEVTDHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 2.532587 |
DEVTRHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 2.348101 |
DEVTKHLGDKTIRVDGLDKELLEILKELARRGADEEELRKEIERWER | 2.438938 |
End of preview.
Protein Stability Prediction Dataset (PSPD)
The Protein Stability Prediction Dataset (PSPD) is a curated collection of protein sequences and their corresponding stability measurements, specifically the Gibbs free energy changes (ΔG) upon mutation. This dataset is designed to facilitate the development and evaluation of computational models for predicting the impact of mutations on protein stability, sourced from existing literature sources.
Dataset Description
The PSPD dataset contains the following key information:
- Amino acid sequences of proteins
- Gibbs free energy changes (ΔG) associated with mutations
- Binned ΔG values for classification tasks
The dataset is curated from multiple protein stability data sources in the existing literature, ensuring a diverse and representative collection of proteins and mutations.
Data Format
The dataset is provided in a CSV format, with each row representing a protein entry. The columns include:
aa_seq: Amino acid sequence of the proteindeltaG: Gibbs free energy change (ΔG) upon mutationdeltaG_bin: Binned ΔG values for classification tasks
Example entry: aa_seq,deltaG,deltaG_bin MKIFVKTLTGKTITLEVEPSDTIENVKAKIQDEEGIPPDQQRLIFAGKKLEDGRTLTDYSIQKESTLHLVLR,8.09999848220399,8 to 9
Data Preparation
The dataset undergoes several preprocessing steps to ensure data quality and consistency:
- Cleaning: Null, duplicate, incomplete, or incorrect entries are removed.
- Extraction: Relevant information (amino acid sequences, ΔG values, binned ΔG values) is extracted.
- Normalization: Quantitative inputs are verified and scaled to conform to standard units and scales.
- Augmentation: The dataset is augmented to address the imbalanced distribution of energy values.
Applications
The PSPD dataset is suitable for various applications in computational biology and protein engineering, including:
- Developing and benchmarking machine learning models for predicting protein stability changes upon mutation
- Investigating the relationship between protein sequence and stability
- Guiding rational protein design and mutagenesis studies
License
The PSPD dataset is released under the MIT license. By using this dataset, you agree to abide by the terms and conditions of the license.
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