def test_abod(self):
clf = ABOD(contamination=0.05)
clf.fit(self.X_train)
assert_equal(len(clf.decision_scores), self.X_train.shape[0])
# invert the scores
pred_scores = clf.decision_function(self.X_test) * -1
assert_equal(pred_scores.shape[0], self.X_test.shape[0])
assert_equal(clf.predict(self.X_test).shape[0],
self.X_test.shape[0])
assert_greater(roc_auc_score(self.y_test, pred_scores), 0.5)
def fast_abod_pyod_once(X_nor,
X_test,
y_test,
n_neighbors,
contamination=0.05):
fastABOD = ABOD(n_neighbors=n_neighbors,
contamination=contamination,
method='fast')
X_train = X_nor.astype(float).values.copy()
fastABOD.fit(X_train)
## now threshold is determined
y_pred = fastABOD.predict(X_test)
scoreTable = fastABOD.decision_function(X_test)
#print(scoreTable)
scoreTable = np.nan_to_num(scoreTable, copy=True)
## confusion matrix
tn, fp, fn, tp = confusion_matrix(y_test, y_pred).ravel()
tpr = tp / (tp + fn)
fpr = fp / (tn + fp)
#tprW[trail] = tpr
#fprW[trail] = fpr
tprW = tpr
fprW = fpr
# Auc score
auc = roc_auc_score(y_test, scoreTable)
#print(tpr, fpr)
#print(auc)
return tprW, fprW, auc, scoreTable
class TestFastABOD(unittest.TestCase):
def setUp(self):
self.n_train = 100
self.n_test = 50
self.contamination = 0.1
self.roc_floor = 0.6
self.X_train, self.y_train, self.X_test, self.y_test = generate_data(
n_train=self.n_train,
n_test=self.n_test,
contamination=self.contamination,
random_state=42)
self.clf = ABOD(contamination=self.contamination)
self.clf.fit(self.X_train)
def test_sklearn_estimator(self):
check_estimator(self.clf)
def test_parameters(self):
assert_true(
hasattr(self.clf, 'decision_scores_')
and self.clf.decision_scores_ is not None)
assert_true(
hasattr(self.clf, 'labels_') and self.clf.labels_ is not None)
assert_true(
hasattr(self.clf, 'threshold_')
and self.clf.threshold_ is not None)
assert_true(hasattr(self.clf, '_mu') and self.clf._mu is not None)
assert_true(
hasattr(self.clf, '_sigma') and self.clf._sigma is not None)
assert_true(hasattr(self.clf, 'tree_') and self.clf.tree_ is not None)
def test_train_scores(self):
assert_equal(len(self.clf.decision_scores_), self.X_train.shape[0])
def test_prediction_scores(self):
pred_scores = self.clf.decision_function(self.X_test)
# check score shapes
assert_equal(pred_scores.shape[0], self.X_test.shape[0])
# check performance
assert_greater(roc_auc_score(self.y_test, pred_scores), self.roc_floor)
def test_prediction_labels(self):
pred_labels = self.clf.predict(self.X_test)
assert_equal(pred_labels.shape, self.y_test.shape)
def test_prediction_proba(self):
pred_proba = self.clf.predict_proba(self.X_test)
assert_greater_equal(pred_proba.min(), 0)
assert_less_equal(pred_proba.max(), 1)
def test_prediction_proba_linear(self):
pred_proba = self.clf.predict_proba(self.X_test, method='linear')
assert_greater_equal(pred_proba.min(), 0)
assert_less_equal(pred_proba.max(), 1)
def test_prediction_proba_unify(self):
pred_proba = self.clf.predict_proba(self.X_test, method='unify')
assert_greater_equal(pred_proba.min(), 0)
assert_less_equal(pred_proba.max(), 1)
def test_prediction_proba_parameter(self):
with assert_raises(ValueError):
self.clf.predict_proba(self.X_test, method='something')
def test_fit_predict(self):
pred_labels = self.clf.fit_predict(self.X_train)
assert_equal(pred_labels.shape, self.y_train.shape)
def test_fit_predict_score(self):
self.clf.fit_predict_score(self.X_test, self.y_test)
self.clf.fit_predict_score(self.X_test,
self.y_test,
scoring='roc_auc_score')
self.clf.fit_predict_score(self.X_test,
self.y_test,
scoring='prc_n_score')
with assert_raises(NotImplementedError):
self.clf.fit_predict_score(self.X_test,
self.y_test,
scoring='something')
def tearDown(self):
pass
class TestABOD(unittest.TestCase):
def setUp(self):
self.n_train = 50
self.n_test = 50
self.contamination = 0.2
self.roc_floor = 0.6
self.X_train, self.y_train, self.X_test, self.y_test = generate_data(
n_train=self.n_train,
n_test=self.n_test,
contamination=self.contamination,
random_state=42)
self.clf = ABOD(contamination=self.contamination, method='default')
self.clf.fit(self.X_train)
def test_sklearn_estimator(self):
check_estimator(self.clf)
def test_parameters(self):
if not hasattr(
self.clf,
'decision_scores_') or self.clf.decision_scores_ is None:
self.assertRaises(AttributeError, 'decision_scores_ is not set')
if not hasattr(self.clf, 'labels_') or self.clf.labels_ is None:
self.assertRaises(AttributeError, 'labels_ is not set')
if not hasattr(self.clf, 'threshold_') or self.clf.threshold_ is None:
self.assertRaises(AttributeError, 'threshold_ is not set')
def test_train_scores(self):
assert_equal(len(self.clf.decision_scores_), self.X_train.shape[0])
def test_prediction_scores(self):
pred_scores = self.clf.decision_function(self.X_test)
# check score shapes
assert_equal(pred_scores.shape[0], self.X_test.shape[0])
# check performance
assert_greater(roc_auc_score(self.y_test, pred_scores), self.roc_floor)
def test_prediction_labels(self):
pred_labels = self.clf.predict(self.X_test)
assert_equal(pred_labels.shape, self.y_test.shape)
def test_prediction_proba(self):
pred_proba = self.clf.predict_proba(self.X_test)
assert_greater_equal(pred_proba.min(), 0)
assert_less_equal(pred_proba.max(), 1)
def test_prediction_proba_linear(self):
pred_proba = self.clf.predict_proba(self.X_test, method='linear')
assert_greater_equal(pred_proba.min(), 0)
assert_less_equal(pred_proba.max(), 1)
def test_prediction_proba_unify(self):
pred_proba = self.clf.predict_proba(self.X_test, method='unify')
assert_greater_equal(pred_proba.min(), 0)
assert_less_equal(pred_proba.max(), 1)
def test_prediction_proba_parameter(self):
with assert_raises(ValueError):
self.clf.predict_proba(self.X_test, method='something')
def test_fit_predict(self):
pred_labels = self.clf.fit_predict(self.X_train)
assert_equal(pred_labels.shape, self.y_train.shape)
def test_fit_predict_score(self):
self.clf.fit_predict_score(self.X_test, self.y_test)
self.clf.fit_predict_score(self.X_test,
self.y_test,
scoring='roc_auc_score')
self.clf.fit_predict_score(self.X_test,
self.y_test,
scoring='prc_n_score')
with assert_raises(NotImplementedError):
self.clf.fit_predict_score(self.X_test,
self.y_test,
scoring='something')
# def test_score(self):
# self.clf.score(self.X_test, self.y_test)
# self.clf.score(self.X_test, self.y_test, scoring='roc_auc_score')
# self.clf.score(self.X_test, self.y_test, scoring='prc_n_score')
# with assert_raises(NotImplementedError):
# self.clf.score(self.X_test, self.y_test, scoring='something')
def test_predict_rank(self):
pred_socres = self.clf.decision_function(self.X_test)
pred_ranks = self.clf._predict_rank(self.X_test)
# assert the order is reserved
assert_allclose(rankdata(pred_ranks), rankdata(pred_socres), atol=3.5)
assert_array_less(pred_ranks, self.X_train.shape[0] + 1)
assert_array_less(-0.1, pred_ranks)
def test_predict_rank_normalized(self):
pred_socres = self.clf.decision_function(self.X_test)
pred_ranks = self.clf._predict_rank(self.X_test, normalized=True)
# assert the order is reserved
assert_allclose(rankdata(pred_ranks), rankdata(pred_socres), atol=3.5)
assert_array_less(pred_ranks, 1.01)
assert_array_less(-0.1, pred_ranks)
def tearDown(self):
pass
n_test = 100 # number of testing points
X_train, y_train, X_test, y_test = generate_data(
n_train=n_train, n_test=n_test, contamination=contamination)
# train ABOD detector
clf_name = 'ABOD'
clf = ABOD()
clf.fit(X_train)
# get the prediction labels and outlier scores of the training data
y_train_pred = clf.labels_ # binary labels (0: inliers, 1: outliers)
y_train_scores = clf.decision_scores_ # raw outlier scores
# get the prediction on the test data
y_test_pred = clf.predict(X_test) # outlier labels (0 or 1)
y_test_scores = clf.decision_function(X_test) # outlier s`cores
# evaluate and print the results
print("\nOn Training Data:")
evaluate_print(clf_name, y_train, y_train_scores)
print("\nOn Test Data:")
evaluate_print(clf_name, y_test, y_test_scores)
# visualize the results
visualize(clf_name,
X_train,
y_train,
X_test,
y_test,
y_train_pred,
# Generate sample data
X_train, y_train, X_test, y_test = \
generate_data(n_train=n_train,
n_test=n_test,
n_features=2,
contamination=contamination,
random_state=42)
# train ABOD detector
clf_name = 'ABOD'
clf = ABOD()
clf.fit(X_train)
# get the prediction labels and outlier scores of the training data
y_train_pred = clf.labels_ # binary labels (0: inliers, 1: outliers)
y_train_scores = clf.decision_scores_ # raw outlier scores
# get the prediction on the test data
y_test_pred = clf.predict(X_test) # outlier labels (0 or 1)
y_test_scores = clf.decision_function(X_test) # outlier s`cores
# evaluate and print the results
print("\nOn Training Data:")
evaluate_print(clf_name, y_train, y_train_scores)
print("\nOn Test Data:")
evaluate_print(clf_name, y_test, y_test_scores)
# visualize the results
visualize(clf_name, X_train, y_train, X_test, y_test, y_train_pred,
y_test_pred, show_figure=True, save_figure=False)
from pyod.models.abod import ABOD
from pyod.models.auto_encoder import AutoEncoder
from sklearn.decomposition import PCA
from sklearn.preprocessing import RobustScaler
#preprocessing
X_train = on.iloc[:,:]
pca = PCA(n_components = 15)
X_train = pca.fit_transform(X_train)
scale = RobustScaler()
X_train = scale.fit_transform(X_train)
#machine learning model
clf_1 = ABOD(contamination = 0.1, n_neighbors = 100)
clf_1.fit(X_train)
pred_1 = clf_1.predict(X_train)
#output of the ML model
out_1 = []
for i in range(0, len(pred_1)):
if pred_1[i] == 0:
out_1.append('Normal')
else:
out_1.append('Abnormal')
state_1 = pd.DataFrame(out_1, columns = ['Condition'])
state_1 = state_1.loc[state_1['Condition'] == 'Abnormal']
ab_state1 = list(state_1.index.values.tolist())
#Deep Learning model using pyod library
clf_2 = AutoEncoder(hidden_neurons = [15, 64, 32, 64, 15], epochs = 350,
class AngularBasedOutlier(OutlierStream):
def __init__(self, inliers, outliers):
data_total = np.concatenate((inliers, outliers), axis=0)
self.data_total = data_total
self.outliers = outliers
self.inliers = inliers
OutlierStream.__init__(self, inliers, outliers)
#self.model = KNN(contamination=0.045)
self.model = ABOD(n_neighbors=20, contamination=0.2)
def train_model(self, data):
self.model.fit(data)
scores_pred = self.model.decision_function(data) * -1
self.threshold = stats.scoreatpercentile(scores_pred, 100 * 0.10)
def update_model(self, data):
return None
def predict_model(self, data):
return self.model.predict(data)
def summary(self, ground_truth, predictions, is_plot=False):
predictions = list(map(lambda x: 1 if x > 0 else 0, predictions))
print(confusion_matrix(predictions, ground_truth))
print("Acuracia: {}".format(accuracy_score(predictions, ground_truth)))
print("Precision: {}".format(precision_score(predictions,
ground_truth)))
print("Recall: {}".format(recall_score(predictions, ground_truth)))
print("F1: {}".format(f1_score(predictions, ground_truth)))
if is_plot:
self._plot()
def _plot(self):
xx, yy = np.meshgrid(np.linspace(-70, 70, 100),
np.linspace(-70, 70, 100))
Z = self.model.decision_function(np.c_[xx.ravel(), yy.ravel()]) * -1
Z = Z.reshape(xx.shape)
subplot = plt.subplot(1, 1, 1)
subplot.contourf(xx,
yy,
Z,
levels=np.linspace(Z.min(), self.threshold, 7),
cmap=plt.cm.Blues_r)
subplot.contourf(xx,
yy,
Z,
levels=[self.threshold, Z.max()],
colors='orange')
a = subplot.contour(xx,
yy,
Z,
levels=[self.threshold],
linewidths=2,
colors='red')
subplot.contourf(xx,
yy,
Z,
levels=[self.threshold, Z.max()],
colors='orange')
b = subplot.scatter(self.outliers[:, 0],
self.outliers[:, 1],
c='red',
s=12,
edgecolor='k')
c = subplot.scatter(self.inliers[:, 0],
self.inliers[:, 1],
c='white',
s=12,
edgecolor='k')
subplot.axis('tight')
subplot.legend([a.collections[0], b, c],
['Borda da funcao', 'Inliers', 'Outliers'],
loc='lower right')
subplot.set_xlim((-70, 70))
subplot.set_ylim((-70, 70))
plt.suptitle("Angular based outlier detection")
plt.show()
df.loc[df['ground.truth'] == 'anomaly', 'ground.truth'] = 1
df.loc[df['ground.truth'] == 'nominal', 'ground.truth'] = 0
y = df['ground.truth'].values.reshape(-1)
df[['V1', 'V2', 'V3', 'V4', 'V5', 'V6', 'V7']] = scaler.fit_transform(
df[['V1', 'V2', 'V3', 'V4', 'V5', 'V6', 'V7']])
x1 = df['V1'].values.reshape(-1, 1)
x2 = df['V2'].values.reshape(-1, 1)
x3 = df['V3'].values.reshape(-1, 1)
x4 = df['V4'].values.reshape(-1, 1)
x5 = df['V5'].values.reshape(-1, 1)
x6 = df['V6'].values.reshape(-1, 1)
x7 = df['V7'].values.reshape(-1, 1)
x = np.concatenate((x1, x2, x3, x4, x5, x6, x7), axis=1)
abod = ABOD(contamination=outliers_fraction)
abod.fit(x)
y_pred = abod.predict(x)
fpr, tpr, threshold = roc_curve(y, y_pred) ###计算真阳性率和假阳性率
roc_auc = auc(fpr, tpr) ###计算auc的值
lw = 2
ax = fig.add_subplot(3, 3, i)
plt.plot(fpr,
tpr,
color='darkorange',
lw=lw,
label='ROC curve (area = %0.3f)' % roc_auc) ###假正率为横坐标，真正率为纵坐标做曲线
plt.plot([0, 1], [0, 1], color='navy', lw=lw, linestyle='--')
plt.xlim([0.0, 1.0])
plt.ylim([0.0, 1.05])
plt.xlabel('False Positive Rate')
plt.ylabel('True Positive Rate')
plt.title('AUC')
class TestABOD(unittest.TestCase):
def setUp(self):
self.n_train = 50
self.n_test = 50
self.contamination = 0.2
self.roc_floor = 0.6
self.X_train, self.y_train, self.X_test, self.y_test = generate_data(
n_train=self.n_train,
n_test=self.n_test,
contamination=self.contamination)
self.clf = ABOD(contamination=self.contamination, method='default')
self.clf.fit(self.X_train)
def test_sklearn_estimator(self):
check_estimator(self.clf)
def test_parameters(self):
if not hasattr(
self.clf,
'decision_scores_') or self.clf.decision_scores_ is None:
self.assertRaises(AttributeError, 'decision_scores_ is not set')
if not hasattr(self.clf, 'labels_') or self.clf.labels_ is None:
self.assertRaises(AttributeError, 'labels_ is not set')
if not hasattr(self.clf, 'threshold_') or self.clf.threshold_ is None:
self.assertRaises(AttributeError, 'threshold_ is not set')
def test_train_scores(self):
assert_equal(len(self.clf.decision_scores_), self.X_train.shape[0])
def test_prediction_scores(self):
pred_scores = self.clf.decision_function(self.X_test)
# check score shapes
assert_equal(pred_scores.shape[0], self.X_test.shape[0])
# check performance
assert_greater(roc_auc_score(self.y_test, pred_scores), self.roc_floor)
def test_prediction_labels(self):
pred_labels = self.clf.predict(self.X_test)
assert_equal(pred_labels.shape, self.y_test.shape)
def test_prediction_proba(self):
pred_proba = self.clf.predict_proba(self.X_test)
assert_greater_equal(pred_proba.min(), 0)
assert_less_equal(pred_proba.max(), 1)
def test_prediction_proba_linear(self):
pred_proba = self.clf.predict_proba(self.X_test, method='linear')
assert_greater_equal(pred_proba.min(), 0)
assert_less_equal(pred_proba.max(), 1)
def test_prediction_proba_unify(self):
pred_proba = self.clf.predict_proba(self.X_test, method='unify')
assert_greater_equal(pred_proba.min(), 0)
assert_less_equal(pred_proba.max(), 1)
def test_prediction_proba_parameter(self):
with assert_raises(ValueError):
self.clf.predict_proba(self.X_test, method='something')
def test_fit_predict(self):
pred_labels = self.clf.fit_predict(self.X_train)
assert_equal(pred_labels.shape, self.y_train.shape)
def test_evaluate(self):
self.clf.fit_predict_evaluate(self.X_test, self.y_test)
def tearDown(self):
pass
n_train = 200
n_test = 100
X_train, y_train, c_train, X_test, y_test, c_test = generate_data(
n_train=n_train, n_test=n_test, contamination=contamination)
# train a ABOD detector (default version)
clf = ABOD(contamination=contamination, fast_method=False)
clf.fit(X_train)
# get the prediction on the training data
y_train_pred = clf.y_pred
y_train_score = clf.decision_scores * -1
# get the prediction on the test data
y_test_pred = clf.predict(X_test)
y_test_score = clf.decision_function(X_test) * -1
print('Train ROC:{roc}, precision@n:{prn}'.format(
roc=roc_auc_score(y_train, y_train_score),
prn=precision_n_scores(y_train, y_train_score)))
print('Test ROC:{roc}, precision@n:{prn}'.format(
roc=roc_auc_score(y_test, y_test_score),
prn=precision_n_scores(y_test, y_test_score)))
#######################################################################
# Visualizations
# initialize the log directory if it does not exist
pathlib.Path('example_figs').mkdir(parents=True, exist_ok=True)
import numpy as np
import pandas as pd
from scipy import stats
import sys
from pyod.models.abod import ABOD
from pyod.utils.data import generate_data, get_outliers_inliers
data = int(sys.argv[1])
# generate random data with two features
X_train, Y_train = generate_data(n_train=2000, train_only=True, n_features=1)
# store outliers and inliers in different numpy arrays
x_outliers, x_inliers = get_outliers_inliers(X_train, Y_train)
clf = ABOD(contamination=0.1)
clf.fit(X_train)
# prediction of a datapoint category outlier or inlier
y_pred = clf.predict(X_train)
output = clf.predict([[data]])
print(output[0])
with open('anomaly.txt', 'w') as file:
file.write(str(output[0]))
