Source code for immuneML.ml_methods.classifiers.KNN

from sklearn.neighbors import KNeighborsClassifier

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




class KNN(SklearnMethod):
    """
    This is a wrapper of scikit-learn’s KNeighborsClassifier class.
    This ML method creates a distance matrix using the given encoded data. If the encoded data is already a distance
    matrix (for example, when using the :ref:`Distance` or :ref:`CompAIRRDistance` encoders), please use :ref:`PrecomputedKNN` instead.

    Please see the `scikit-learn documentation <https://scikit-learn.org/stable/modules/generated/sklearn.neighbors.KNeighborsClassifier.html>`_
    of KNeighborsClassifier for the parameters.

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

    **YAML specification:**

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

        definitions:
            ml_methods:
                my_knn_method:
                    KNN:
                        # sklearn parameters (same names as in original sklearn class)
                        weights: uniform # always use this setting for weights
                        n_neighbors: [5, 10, 15] # find the optimal number of neighbors
                        # Additional parameter that determines whether to print convergence warnings
                        show_warnings: True
                    # if any of the parameters under KNN 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_knn: KNN

    """

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

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

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



    def get_params(self):
        return self.model.get_params(deep=True)




    def can_predict_proba(self) -> bool:
        return True




    def can_fit_with_example_weights(self) -> bool:
        return False




    def get_compatible_encoders(self):
        from immuneML.encodings.distance_encoding.DistanceEncoder import DistanceEncoder
        from immuneML.encodings.evenness_profile.EvennessProfileEncoder import EvennessProfileEncoder
        from immuneML.encodings.abundance_encoding.SequenceAbundanceEncoder import SequenceAbundanceEncoder
        from immuneML.encodings.abundance_encoding.CompAIRRSequenceAbundanceEncoder import CompAIRRSequenceAbundanceEncoder
        from immuneML.encodings.abundance_encoding.KmerAbundanceEncoder import KmerAbundanceEncoder
        from immuneML.encodings.kmer_frequency.KmerFrequencyEncoder import KmerFrequencyEncoder
        from immuneML.encodings.onehot.OneHotEncoder import OneHotEncoder
        from immuneML.encodings.word2vec.Word2VecEncoder import Word2VecEncoder
        return [KmerFrequencyEncoder, OneHotEncoder, Word2VecEncoder, SequenceAbundanceEncoder,
                CompAIRRSequenceAbundanceEncoder, KmerAbundanceEncoder, EvennessProfileEncoder, DistanceEncoder]




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

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

        doc = update_docs_per_mapping(doc, mapping)
        return doc