gridsearch

Class for GridSearchCV with silhouette score.

MIT License Copyright © 2021-2022, Daniel Nagel All rights reserved.

GridSearchCV(*, similarity, clustering, param_grid, gridsearch_kwargs={})

Bases: GridSearchCV

Class for grid search cross validation.

Parameters:

• similarity (Similarity) –

  Similarity instance setup with constant parameters, see mosaic.Similarity for available parameters. low_memory is not supported.

• clustering (Clustering) –

  Clustering instance setup with constant parameters, see mosaic.Clustering for available parameters.

• param_grid (dict) –

  Dictionary with parameters names (str) as keys and lists of parameter settings to try as values, or list of such dictionaries, in which case the grids spanned by each dictionary in the list are explored.

• gridsearch_kwargs (dict, default: {} ) –

  Dictionary with parameters to be used for sklearn.model_selection.GridSearchCV class. The parameter estimator is not supported and param_grid needs to be passed directly to the class.

Attributes:

• cv_results_ (dict of numpy (masked) ndarrays) –

  A dict with keys as column headers and values as columns.

• best_estimator_ (estimator) –

  Estimator that was chosen by the search, i.e. estimator which gave highest score (or smallest loss if specified) on the left out data.

• best_score_ (float) –

  Mean cross-validated score of the best_estimator.

• best_params_ (dict) –

  Parameter setting that gave the best results on the hold out data.

• best_index_ (int) –

  The index (of the cv_results_ arrays) which corresponds to the best candidate parameter setting.

• n_splits_ (int) –

  The number of cross-validation splits (folds/iterations).

Notes

Check out sklearn.model_selection.GridSearchCV for an overview of all available attributes and more detailed description.

Examples:

>>> import mosaic
>>> # create two correlated data sets
>>> traj = np.array([
...     func(np.linspace(0, 20, 1000))
...     for  func in (
...         np.sin,
...         lambda x: np.sin(x + 0.1),
...         np.cos,
...         lambda x: np.cos(x + 0.1),
...     )
... ]).T
>>> search = mosaic.GridSearchCV(
...     similarity=mosaic.Similarity(),
...     clustering=mosaic.Clustering(),
...     param_grid={'resolution_parameter': [0.05, 0.2]},
... )
>>> search.fit(traj)
GridSearchCV(clustering=Clustering(),
             param_grid={'clust__resolution_parameter': [0.05, 0.2]},
             similarity=Similarity())
>>> search.best_params_
{'clust__resolution_parameter': 0.2}
>>> search.best_estimator_
Pipeline(steps=[('sim', Similarity()),
                ('clust', Clustering(resolution_parameter=0.2))])

Initialize GridSearchCV class.

Source code in src/mosaic/gridsearch.py

@beartype
def __init__(
    self,
    *,
    similarity: Similarity,
    clustering: Clustering,
    param_grid: Dict,
    gridsearch_kwargs: Dict = {},
) -> None:
    """Initialize GridSearchCV class."""
    self.similarity: Similarity = similarity
    self.clustering: Clustering = clustering
    self.gridsearch_kwargs: Dict = gridsearch_kwargs

    if 'estimator' in self.gridsearch_kwargs:
        raise NotImplementedError(
            'Custom estimators are not supported. Please use the '
            'sklearn class GirdSearchCV directly.',
        )

    if 'param_grid' in self.gridsearch_kwargs:
        raise NotImplementedError(
            "Please pass 'param_grid' directly to the the class.",
        )

    if similarity.get_params()['low_memory']:
        raise NotImplementedError(
            "'low_memory' is currently not implemented.",
        )

    if not param_grid:
        raise ValueError(
            'At least a single parameter needs to be provided',
        )

    self.pipeline = Pipeline([
        (self._sim_prefix, self.similarity),
        (self._clust_prefix, self.clustering),
    ])

    self.param_grid: Dict = {}
    for param, values in param_grid.items():
        if param in similarity.get_params():
            self.param_grid[
                f'{self._sim_prefix}__{param}'
            ] = values
        elif param in clustering.get_params():
            self.param_grid[
                f'{self._clust_prefix}__{param}'
            ] = values
        else:
            raise ValueError(
                f"param_grid key '{param}' is not available."
            )

    super().__init__(
        estimator=self.pipeline,
        param_grid=self.param_grid,
        **self.gridsearch_kwargs,
    )

fit(X, y=None)

Clusters the correlation matrix by Leiden clustering on a graph.

Parameters:

• X (ndarray of shape (n_samples, n_features)) –

  Training vector, where n_samples is the number of samples and n_features is the number of features.

• y (Ignored, default: None ) –

  Not used, present for scikit API consistency by convention.

Returns:

• self ( object ) –

  Fitted estimator.

Source code in src/mosaic/gridsearch.py

@beartype
def fit(
    self,
    X: FloatMax2DArray,
    y: Optional[np.ndarray] = None,
):
    """Clusters the correlation matrix by Leiden clustering on a graph.

    Parameters
    ----------
    X : ndarray of shape (n_samples, n_features)
        Training vector, where `n_samples` is the number of samples and
        `n_features` is the number of features.
    y : Ignored
        Not used, present for scikit API consistency by convention.

    Returns
    -------
    self : object
        Fitted estimator.

    """
    return super().fit(X)