Source code for pyod.models.auto_encoder

# -*- coding: utf-8 -*-
"""Using Auto Encoder with Outlier Detection
# Author: Yue Zhao <>
# License: BSD 2 clause

from __future__ import division
from __future__ import print_function

import numpy as np
from sklearn.preprocessing import StandardScaler
from sklearn.utils import check_array
from sklearn.utils.validation import check_is_fitted

from .base import BaseDetector
from .base_dl import _get_tensorflow_version
from ..utils.stat_models import pairwise_distances_no_broadcast
from ..utils.utility import check_parameter

# if tensorflow 2, import from tf directly
if _get_tensorflow_version() < 200:
    from keras.models import Sequential
    from keras.layers import Dense, Dropout
    from keras.regularizers import l2
    from keras.losses import mean_squared_error
    from tensorflow.keras.models import Sequential
    from tensorflow.keras.layers import Dense, Dropout
    from tensorflow.keras.regularizers import l2
    from tensorflow.keras.losses import mean_squared_error

# noinspection PyUnresolvedReferences,PyPep8Naming,PyTypeChecker
[docs]class AutoEncoder(BaseDetector): """Auto Encoder (AE) is a type of neural networks for learning useful data representations unsupervisedly. Similar to PCA, AE could be used to detect outlying objects in the data by calculating the reconstruction errors. See :cite:`aggarwal2015outlier` Chapter 3 for details. Parameters ---------- hidden_neurons : list, optional (default=[64, 32, 32, 64]) The number of neurons per hidden layers. hidden_activation : str, optional (default='relu') Activation function to use for hidden layers. All hidden layers are forced to use the same type of activation. See output_activation : str, optional (default='sigmoid') Activation function to use for output layer. See loss : str or obj, optional (default=keras.losses.mean_squared_error) String (name of objective function) or objective function. See optimizer : str, optional (default='adam') String (name of optimizer) or optimizer instance. See epochs : int, optional (default=100) Number of epochs to train the model. batch_size : int, optional (default=32) Number of samples per gradient update. dropout_rate : float in (0., 1), optional (default=0.2) The dropout to be used across all layers. l2_regularizer : float in (0., 1), optional (default=0.1) The regularization strength of activity_regularizer applied on each layer. By default, l2 regularizer is used. See validation_size : float in (0., 1), optional (default=0.1) The percentage of data to be used for validation. preprocessing : bool, optional (default=True) If True, apply standardization on the data. verbose : int, optional (default=1) Verbosity mode. - 0 = silent - 1 = progress bar - 2 = one line per epoch. For verbose >= 1, model summary may be printed. random_state : random_state: int, RandomState instance or None, optional (default=None) If int, random_state is the seed used by the random number generator; If RandomState instance, random_state is the random number generator; If None, the random number generator is the RandomState instance used by `np.random`. contamination : float in (0., 0.5), optional (default=0.1) The amount of contamination of the data set, i.e. the proportion of outliers in the data set. When fitting this is used to define the threshold on the decision function. Attributes ---------- encoding_dim_ : int The number of neurons in the encoding layer. compression_rate_ : float The ratio between the original feature and the number of neurons in the encoding layer. model_ : Keras Object The underlying AutoEncoder in Keras. history_: Keras Object The AutoEncoder training history. decision_scores_ : numpy array of shape (n_samples,) The outlier scores of the training data. The higher, the more abnormal. Outliers tend to have higher scores. This value is available once the detector is fitted. threshold_ : float The threshold is based on ``contamination``. It is the ``n_samples * contamination`` most abnormal samples in ``decision_scores_``. The threshold is calculated for generating binary outlier labels. labels_ : int, either 0 or 1 The binary labels of the training data. 0 stands for inliers and 1 for outliers/anomalies. It is generated by applying ``threshold_`` on ``decision_scores_``. """ def __init__(self, hidden_neurons=None, hidden_activation='relu', output_activation='sigmoid', loss=mean_squared_error, optimizer='adam', epochs=100, batch_size=32, dropout_rate=0.2, l2_regularizer=0.1, validation_size=0.1, preprocessing=True, verbose=1, random_state=None, contamination=0.1): super(AutoEncoder, self).__init__(contamination=contamination) self.hidden_neurons = hidden_neurons self.hidden_activation = hidden_activation self.output_activation = output_activation self.loss = loss self.optimizer = optimizer self.epochs = epochs self.batch_size = batch_size self.dropout_rate = dropout_rate self.l2_regularizer = l2_regularizer self.validation_size = validation_size self.preprocessing = preprocessing self.verbose = verbose self.random_state = random_state # default values if self.hidden_neurons is None: self.hidden_neurons = [64, 32, 32, 64] # Verify the network design is valid if not self.hidden_neurons == self.hidden_neurons[::-1]: print(self.hidden_neurons) raise ValueError("Hidden units should be symmetric") self.hidden_neurons_ = self.hidden_neurons check_parameter(dropout_rate, 0, 1, param_name='dropout_rate', include_left=True) def _build_model(self): model = Sequential() # Input layer model.add(Dense( self.hidden_neurons_[0], activation=self.hidden_activation, input_shape=(self.n_features_,), activity_regularizer=l2(self.l2_regularizer))) model.add(Dropout(self.dropout_rate)) # Additional layers for i, hidden_neurons in enumerate(self.hidden_neurons_, 1): model.add(Dense( hidden_neurons, activation=self.hidden_activation, activity_regularizer=l2(self.l2_regularizer))) model.add(Dropout(self.dropout_rate)) # Output layers model.add(Dense(self.n_features_, activation=self.output_activation, activity_regularizer=l2(self.l2_regularizer))) # Compile model model.compile(loss=self.loss, optimizer=self.optimizer) if self.verbose >= 1: print(model.summary()) return model # noinspection PyUnresolvedReferences
[docs] def fit(self, X, y=None): """Fit detector. y is ignored in unsupervised methods. Parameters ---------- X : numpy array of shape (n_samples, n_features) The input samples. y : Ignored Not used, present for API consistency by convention. Returns ------- self : object Fitted estimator. """ # validate inputs X and y (optional) X = check_array(X) self._set_n_classes(y) # Verify and construct the hidden units self.n_samples_, self.n_features_ = X.shape[0], X.shape[1] # Standardize data for better performance if self.preprocessing: self.scaler_ = StandardScaler() X_norm = self.scaler_.fit_transform(X) else: X_norm = np.copy(X) # Shuffle the data for validation as Keras do not shuffling for # Validation Split np.random.shuffle(X_norm) # Validate and complete the number of hidden neurons if np.min(self.hidden_neurons) > self.n_features_: raise ValueError("The number of neurons should not exceed " "the number of features") self.hidden_neurons_.insert(0, self.n_features_) # Calculate the dimension of the encoding layer & compression rate self.encoding_dim_ = np.median(self.hidden_neurons) self.compression_rate_ = self.n_features_ // self.encoding_dim_ # Build AE model & fit with X self.model_ = self._build_model() self.history_ =, X_norm, epochs=self.epochs, batch_size=self.batch_size, shuffle=True, validation_split=self.validation_size, verbose=self.verbose).history # Reverse the operation for consistency self.hidden_neurons_.pop(0) # Predict on X itself and calculate the reconstruction error as # the outlier scores. Noted X_norm was shuffled has to recreate if self.preprocessing: X_norm = self.scaler_.transform(X) else: X_norm = np.copy(X) pred_scores = self.model_.predict(X_norm) self.decision_scores_ = pairwise_distances_no_broadcast(X_norm, pred_scores) self._process_decision_scores() return self
[docs] def decision_function(self, X): """Predict raw anomaly score of X using the fitted detector. The anomaly score of an input sample is computed based on different detector algorithms. For consistency, outliers are assigned with larger anomaly scores. Parameters ---------- X : numpy array of shape (n_samples, n_features) The training input samples. Sparse matrices are accepted only if they are supported by the base estimator. Returns ------- anomaly_scores : numpy array of shape (n_samples,) The anomaly score of the input samples. """ check_is_fitted(self, ['model_', 'history_']) X = check_array(X) if self.preprocessing: X_norm = self.scaler_.transform(X) else: X_norm = np.copy(X) # Predict on X and return the reconstruction errors pred_scores = self.model_.predict(X_norm) return pairwise_distances_no_broadcast(X_norm, pred_scores)