import copy
import numpy as np
from sklearn.neighbors import KNeighborsClassifier
from immuneML.ml_methods.SklearnMethod import SklearnMethod
from immuneML.util.ParameterValidator import ParameterValidator
[docs]class TCRdistClassifier(SklearnMethod):
"""
Implementation of a nearest neighbors classifier based on TCR distances as presented in
Dash P, Fiore-Gartland AJ, Hertz T, et al. Quantifiable predictive features define epitope-specific T cell receptor repertoires.
Nature. 2017; 547(7661):89-93. `doi:10.1038/nature22383 <https://www.nature.com/articles/nature22383>`_.
This method is implemented using scikit-learn's KNeighborsClassifier with k determined at runtime from the training dataset size and weights
linearly scaled to decrease with the distance of examples.
Arguments:
percentage (float): percentage of nearest neighbors to consider when determining receptor specificity based on known receptors (between 0 and 1)
show_warnings (bool): whether to show warnings generated by scikit-learn, by default this is True.
YAML specification:
.. indent with spaces
.. code-block:: yaml
my_tcr_method:
TCRdistClassifier:
percentage: 0.1
show_warnings: True
"""
def __init__(self, percentage: float, show_warnings: bool = True):
super().__init__()
ParameterValidator.assert_type_and_value(percentage, float, "TCRdistClassifier", "percentage", min_inclusive=0., max_inclusive=1.)
self.percentage = percentage
self.k = None
self.show_warnings = show_warnings
def _get_ml_model(self, cores_for_training: int = 2, X=None):
# compute k (number of nearest neighbors to consider) given the training dataset size (10% in the paper)
self.k = int(X.shape[0] * self.percentage)
# define function for computing weights which linearly decrease with distance
def weights_func(distances):
for point_dist_i, point_dist in enumerate(distances):
if hasattr(point_dist, '__contains__') and 0. in point_dist:
distances[point_dist_i] = point_dist == 0.
else:
distances[point_dist_i] = point_dist / np.sum(point_dist).astype(float)
# make an object of KNN class with precomputed metric
return KNeighborsClassifier(n_neighbors=self.k, weights=weights_func, metric='precomputed', n_jobs=cores_for_training)
[docs] def get_params(self):
return {**self.model.get_params(deep=True), **copy.deepcopy(vars(self))}
[docs] def can_predict_proba(self) -> bool:
return True
def _get_model_filename(self):
return "tcrdist_classifier"
[docs] def get_compatible_encoders(self):
from immuneML.encodings.distance_encoding.TCRdistEncoder import TCRdistEncoder
return [TCRdistEncoder]