load_clintox#

skfp.datasets.moleculenet.load_clintox(data_dir: str | PathLike | None = None, as_frame: bool = False, verbose: bool = False, force_update: bool = False) → DataFrame | tuple[list[str], ndarray]#

Load the ClinTox dataset.

The task is to predict drug approval viability, by predicting clinical trial toxicity and final FDA approval status [1]. Both tasks are binary.

Tasks

2

Task type

multitask classification

Total samples

1477

Recommended split

scaffold

Recommended metric

AUROC
Parameters:

  • data_dir ({None, str, path-like}, default=None) – Path to the root data directory. If None, currently set scikit-learn directory is used, by default $HOME/scikit_learn_data.

  • as_frame (bool, default=False) – If True, returns the raw DataFrame with columns “SMILES” and 2 label columns, FDA approval and clinical trial toxicity. Otherwise, returns SMILES as list of strings, and labels as a NumPy array (2D integer array).

  • verbose (bool, default=False) – If True, progress bar will be shown for downloading or loading files.

  • force_update (bool, default=False) – If True, always re-download the dataset from HuggingFace Hub, even if it is already present locally. If False, the dataset is downloaded only if it is not yet available locally.

Returns:

data – Depending on the as_frame argument, one of: - Pandas DataFrame with columns “SMILES” and 2 label columns - tuple of: list of strings (SMILES), NumPy array (labels)

Return type:

pd.DataFrame or tuple(list[str], np.ndarray)

References

Examples

>>> from skfp.datasets.moleculenet import load_clintox
>>> dataset = load_clintox()
>>> dataset  
(['[C@@H]1([C@@H]([C@@H]([C@H]([C@@H]([C@@H]1Cl)Cl)Cl)Cl)Cl)Cl', ..., 'S=[Se]=S'], array([[1, 0],
   [1, 0],
   [1, 0],
   ...,
   [1, 0],
   [1, 0],
   [1, 0]]))

>>> dataset = load_clintox(as_frame=True)
>>> dataset.head() 
                                                  SMILES  FDA_APPROVED  CT_TOX
0  [C@@H]1([C@@H]([C@@H]([C@H]([C@@H]([C@@H]1Cl)C...             1       0
1  [C@H]([C@@H]([C@@H](C(=O)[O-])O)O)([C@H](C(=O)...             1       0
2  [H]/[NH+]=C(/C1=CC(=O)/C(=C\C=c2ccc(=C([NH3+])...             1       0
3  [H]/[NH+]=C(\N)/c1ccc(cc1)OCCCCCOc2ccc(cc2)/C(...             1       0
4                                 [N+](=O)([O-])[O-]             1       0