Source code for immuneML.ml_methods.LogisticRegression

from sklearn.linear_model import LogisticRegression as SklearnLogisticRegression

from immuneML.ml_methods.SklearnMethod import SklearnMethod
from scripts.specification_util import update_docs_per_mapping


class LogisticRegression(SklearnMethod):
    """
    This is a wrapper of scikit-learn’s LogisticRegression class. Please see the
    `scikit-learn documentation <https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html>`_
    of LogisticRegression for the parameters.

    Note: if you are interested in plotting the coefficients of the logistic regression model,
    consider running the :ref:`Coefficients` report.

    For usage instructions, check :py:obj:`~immuneML.ml_methods.SklearnMethod.SklearnMethod`.


    YAML specification:

    .. indent with spaces
    .. code-block:: yaml

        my_logistic_regression: # user-defined method name
            LogisticRegression: # name of the ML method
                # sklearn parameters (same names as in original sklearn class)
                penalty: l1 # always use penalty l1
                C: [0.01, 0.1, 1, 10, 100] # find the optimal value for C
                # Additional parameter that determines whether to print convergence warnings
                show_warnings: True
            # if any of the parameters under LogisticRegression is a list and model_selection_cv is True,
            # a grid search will be done over the given parameters, using the number of folds specified in model_selection_n_folds,
            # and the optimal model will be selected
            model_selection_cv: True
            model_selection_n_folds: 5
        # alternative way to define ML method with default values:
        my_default_logistic_regression: LogisticRegression

    """

    default_parameters = {"max_iter": 1000, "solver": "saga"}

    def __init__(self, parameter_grid: dict = None, parameters: dict = None):
        parameters = {**self.default_parameters, **(parameters if parameters is not None else {})}

        if parameter_grid is not None:
            parameter_grid = parameter_grid
        else:
            parameter_grid = {"max_iter": [1000]}

        super(LogisticRegression, self).__init__(parameter_grid=parameter_grid, parameters=parameters)

    def _get_ml_model(self, cores_for_training: int = 2, X=None):
        params = self._parameters.copy()
        params["n_jobs"] = cores_for_training
        return SklearnLogisticRegression(**params)

    def can_predict_proba(self) -> bool:
        return True

    def get_params(self):
        params = self.model.get_params()
        params["coefficients"] = self.model.coef_[0].tolist()
        params["intercept"] = self.model.intercept_.tolist()
        return params

    @staticmethod
    def get_documentation():
        doc = str(LogisticRegression.__doc__)

        mapping = {
            "For usage instructions, check :py:obj:`~immuneML.ml_methods.SklearnMethod.SklearnMethod`.": SklearnMethod.get_usage_documentation(
                "LogisticRegression"),
        }

        doc = update_docs_per_mapping(doc, mapping)
        return doc