Source code for alibi.confidence.trustscore

import logging
import numpy as np
from sklearn.neighbors import KDTree
from sklearn.neighbors import KNeighborsClassifier
from typing import Tuple, Any

logger = logging.getLogger(__name__)

[docs]class TrustScore(object):
[docs] def __init__(self, k_filter: int = 10, alpha: float = 0., filter_type: str = None, leaf_size: int = 40, metric: str = 'euclidean', dist_filter_type: str = 'point') -> None: """ Initialize trust scores. Parameters ---------- k_filter Number of neighbors used during either kNN distance or probability filtering. alpha Fraction of instances to filter out to reduce impact of outliers. filter_type Filter method; either 'distance_knn' or 'probability_knn' leaf_size Number of points at which to switch to brute-force. Affects speed and memory required to build trees. Memory to store the tree scales with n_samples / leaf_size. metric Distance metric used for the tree. See sklearn's DistanceMetric class for a list of available metrics. dist_filter_type Use either the distance to the k-nearest point (dist_filter_type = 'point') or the average distance from the first to the k-nearest point in the data (dist_filter_type = 'mean'). """ self.k_filter = k_filter self.alpha = alpha self.filter = filter_type self.eps = 1e-12 self.leaf_size = leaf_size self.metric = metric self.dist_filter_type = dist_filter_type
[docs] def filter_by_distance_knn(self, X: np.ndarray) -> np.ndarray: """ Filter out instances with low kNN density. Calculate distance to k-nearest point in the data for each instance and remove instances above a cutoff distance. Parameters ---------- X Data Returns ------- Filtered data. """ kdtree = KDTree(X, leaf_size=self.leaf_size, metric=self.metric) knn_r = kdtree.query(X, k=self.k_filter + 1)[0] # distances from 0 to k-nearest points if self.dist_filter_type == 'point': knn_r = knn_r[:, -1] elif self.dist_filter_type == 'mean': knn_r = np.mean(knn_r[:, 1:], axis=1) # exclude distance of instance to itself cutoff_r = np.percentile(knn_r, (1 - self.alpha) * 100) # cutoff distance X_keep = X[np.where(knn_r <= cutoff_r)[0], :] # define instances to keep return X_keep
[docs] def filter_by_probability_knn(self, X: np.ndarray, Y: np.ndarray) -> Tuple[np.ndarray, np.ndarray]: """ Filter out instances with high label disagreement amongst its k nearest neighbors. Parameters ---------- X Data Y Predicted class labels Returns ------- Filtered data and labels. """ if self.k_filter == 1: logger.warning('Number of nearest neighbors used for probability density filtering should ' 'be >1, otherwise the prediction probabilities are either 0 or 1 making ' 'probability filtering useless.') # fit kNN classifier and make predictions on X clf = KNeighborsClassifier(n_neighbors=self.k_filter, leaf_size=self.leaf_size, metric=self.metric), Y) preds_proba = clf.predict_proba(X) # define cutoff and instances to keep preds_max = np.max(preds_proba, axis=1) cutoff_proba = np.percentile(preds_max, self.alpha * 100) # cutoff probability keep_id = np.where(preds_max >= cutoff_proba)[0] # define id's of instances to keep X_keep, Y_keep = X[keep_id, :], Y[keep_id] return X_keep, Y_keep
[docs] def fit(self, X: np.ndarray, Y: np.ndarray, classes: int = None) -> None: """ Build KDTrees for each prediction class. Parameters ---------- X Data Y Target labels, either one-hot encoded or the actual class label. classes Number of prediction classes, needs to be provided if Y equals the predicted class. """ self.classes = classes if classes is not None else Y.shape[1] self.kdtrees = [None] * self.classes # type: Any self.X_kdtree = [None] * self.classes # type: Any # KDTree and kNeighborsClassifier need 2D data if len(X.shape) > 2: logger.warning('Reshaping data from {0} to {1} so k-d trees can ' 'be built.'.format(X.shape, X.reshape(X.shape[0], -1).shape)) X = X.reshape(X.shape[0], -1) # make sure Y represents predicted classes, not one-hot encodings if len(Y.shape) > 1: Y = np.argmax(Y, axis=1) if self.filter == 'probability_knn': X_filter, Y_filter = self.filter_by_probability_knn(X, Y) for c in range(self.classes): if self.filter is None: X_fit = X[np.where(Y == c)[0]] elif self.filter == 'distance_knn': X_fit = self.filter_by_distance_knn(X[np.where(Y == c)[0]]) elif self.filter == 'probability_knn': X_fit = X_filter[np.where(Y_filter == c)[0]] no_x_fit = len(X_fit) == 0 if no_x_fit and len(X[np.where(Y == c)[0]]) == 0: logger.warning('No instances available for class %s', c) elif no_x_fit: logger.warning('Filtered all the instances for class %s. Lower alpha or check data.', c) self.kdtrees[c] = KDTree(X_fit, leaf_size=self.leaf_size, metric=self.metric) # build KDTree for class c self.X_kdtree[c] = X_fit
[docs] def score(self, X: np.ndarray, Y: np.ndarray, k: int = 2, dist_type: str = 'point') \ -> Tuple[np.ndarray, np.ndarray]: """ Calculate trust scores = ratio of distance to closest class other than the predicted class to distance to predicted class. Parameters ---------- X Instances to calculate trust score for. Y Either prediction probabilities for each class or the predicted class. k Number of nearest neighbors used for distance calculation. dist_type Use either the distance to the k-nearest point (dist_type = 'point') or the average distance from the first to the k-nearest point in the data (dist_type = 'mean'). Returns ------- Batch with trust scores and the closest not predicted class. """ # make sure Y represents predicted classes, not probabilities if len(Y.shape) > 1: Y = np.argmax(Y, axis=1) # KDTree needs 2D data if len(X.shape) > 2: logger.warning('Reshaping data from {0} to {1} so k-d trees can ' 'be queried.'.format(X.shape, X.reshape(X.shape[0], -1).shape)) X = X.reshape(X.shape[0], -1) d = np.tile(None, (X.shape[0], self.classes)) # init distance matrix: [nb instances, nb classes] for c in range(self.classes): d_tmp = self.kdtrees[c].query(X, k=k)[0] # get k nearest neighbors for each class if dist_type == 'point': d[:, c] = d_tmp[:, -1] elif dist_type == 'mean': d[:, c] = np.mean(d_tmp, axis=1) sorted_d = np.sort(d, axis=1) # sort distance each instance in batch over classes # get distance to predicted and closest other class and calculate trust score d_to_pred = d[range(d.shape[0]), Y] d_to_closest_not_pred = np.where(sorted_d[:, 0] != d_to_pred, sorted_d[:, 0], sorted_d[:, 1]) trust_score = d_to_closest_not_pred / (d_to_pred + self.eps) # closest not predicted class class_closest_not_pred = np.where(d == d_to_closest_not_pred.reshape(-1, 1))[1] return trust_score, class_closest_not_pred