def check_transformer_pickle(name, Transformer):
X, y = make_blobs(n_samples=30, centers=[[0, 0, 0], [1, 1, 1]],
random_state=0, n_features=2, cluster_std=0.1)
n_samples, n_features = X.shape
X = StandardScaler().fit_transform(X)
X -= X.min()
# catch deprecation warnings
with warnings.catch_warnings(record=True):
transformer = Transformer()
if not hasattr(transformer, 'transform'):
return
set_random_state(transformer)
set_fast_parameters(transformer)
# fit
if name in CROSS_DECOMPOSITION:
random_state = np.random.RandomState(seed=12345)
y_ = np.vstack([y, 2 * y + random_state.randint(2, size=len(y))])
y_ = y_.T
else:
y_ = y
transformer.fit(X, y_)
X_pred = transformer.fit(X, y_).transform(X)
pickled_transformer = pickle.dumps(transformer)
unpickled_transformer = pickle.loads(pickled_transformer)
pickled_X_pred = unpickled_transformer.transform(X)
assert_array_almost_equal(pickled_X_pred, X_pred)
def check_classifiers_classes(name, Classifier):
X, y = make_blobs(n_samples=30, random_state=0, cluster_std=0.1)
X, y = shuffle(X, y, random_state=7)
X = StandardScaler().fit_transform(X)
# We need to make sure that we have non negative data, for things
# like NMF
X -= X.min() - .1
y_names = np.array(["one", "two", "three"])[y]
for y_names in [y_names, y_names.astype('O')]:
if name in ["LabelPropagation", "LabelSpreading"]:
# TODO some complication with -1 label
y_ = y
else:
y_ = y_names
classes = np.unique(y_)
# catch deprecation warnings
with warnings.catch_warnings(record=True):
classifier = Classifier()
if name == 'BernoulliNB':
classifier.set_params(binarize=X.mean())
set_fast_parameters(classifier)
# fit
classifier.fit(X, y_)
y_pred = classifier.predict(X)
# training set performance
assert_array_equal(np.unique(y_), np.unique(y_pred))
if np.any(classifier.classes_ != classes):
print("Unexpected classes_ attribute for %r: "
"expected %s, got %s" %
(classifier, classes, classifier.classes_))
def test_thresholded_scorers():
"""Test scorers that take thresholds."""
X, y = make_blobs(random_state=0, centers=2)
X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=0)
clf = LogisticRegression(random_state=0)
clf.fit(X_train, y_train)
score1 = SCORERS['roc_auc'](clf, X_test, y_test)
score2 = roc_auc_score(y_test, clf.decision_function(X_test))
score3 = roc_auc_score(y_test, clf.predict_proba(X_test)[:, 1])
assert_almost_equal(score1, score2)
assert_almost_equal(score1, score3)
logscore = SCORERS['log_loss'](clf, X_test, y_test)
logloss = log_loss(y_test, clf.predict_proba(X_test))
assert_almost_equal(-logscore, logloss)
# same for an estimator without decision_function
clf = DecisionTreeClassifier()
clf.fit(X_train, y_train)
score1 = SCORERS['roc_auc'](clf, X_test, y_test)
score2 = roc_auc_score(y_test, clf.predict_proba(X_test)[:, 1])
assert_almost_equal(score1, score2)
# Test that an exception is raised on more than two classes
X, y = make_blobs(random_state=0, centers=3)
X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=0)
clf.fit(X_train, y_train)
assert_raises(ValueError, SCORERS['roc_auc'], clf, X_test, y_test)
def test_fit_uuu():
n_samples1 = 10000
n_features = 5
centers1 = np.array([[10, 5, 1, -5, -10],
[-10, -5, -1, 5, 10]])
cluster_std1 = np.array([[1.0, 2.0, 3.0, 4.0, 5.0],
[5.0, 4.0, 3.0, 2.0, 1.0]])
X1, y1 = make_blobs(n_features=n_features,
n_samples=n_samples1,
centers=centers1,
cluster_std=cluster_std1)
n_samples2 = 5000
centers2 = np.array([[10, 5, 1, -5, -10]])
cluster_std2 = np.array([[1.0, 2.0, 3.0, 4.0, 5.0]])
X2, y2 = make_blobs(n_features=n_features,
n_samples=n_samples2,
centers=centers2,
cluster_std=cluster_std2)
X = np.vstack((X1, X2))
model = mixture.PGMM(covariance_type='UUU', n_components=2, n_pc=3)
model.fit(X)
assert_array_almost_equal(np.sum(model.means_, 0), np.sum(centers1, 0), decimal=0)
assert_array_almost_equal(np.sort(model.weights_), np.array([0.333, 0.666]), decimal=1)
assert_equal(model.means_.shape, np.array([2, n_features]))
assert_equal(model.weights_.shape, np.array([2]))
assert_equal(model.noise_.shape, np.array([2, n_features]))
assert_equal(model.principal_subspace_.shape, np.array([2, n_features, 3]))
assert_equal(model.covars_.shape, np.array([2, n_features, n_features]))
logging.info('TestFitUUU: OK')
def test_check_is_fitted():
# Check is ValueError raised when non estimator instance passed
assert_raises(ValueError, check_is_fitted, ARDRegression, "coef_")
assert_raises(TypeError, check_is_fitted, "SVR", "support_")
ard = ARDRegression()
svr = SVR()
try:
assert_raises(NotFittedError, check_is_fitted, ard, "coef_")
assert_raises(NotFittedError, check_is_fitted, svr, "support_")
except ValueError:
assert False, "check_is_fitted failed with ValueError"
# NotFittedError is a subclass of both ValueError and AttributeError
try:
check_is_fitted(ard, "coef_", "Random message %(name)s, %(name)s")
except ValueError as e:
assert_equal(str(e), "Random message ARDRegression, ARDRegression")
try:
check_is_fitted(svr, "support_", "Another message %(name)s, %(name)s")
except AttributeError as e:
assert_equal(str(e), "Another message SVR, SVR")
ard.fit(*make_blobs())
svr.fit(*make_blobs())
assert_equal(None, check_is_fitted(ard, "coef_"))
assert_equal(None, check_is_fitted(svr, "support_"))
def show_dbscan():
"""
simulate 1 month of normal hourly room percentage data followed by an anomalous percentage
the normal data is bimodal following most peoples activity patterns in which there is routinely a weekday
percentage and a weekend percentage. 1 day in which the person spends a large amount of time in the bathroom
is simulated
"""
# simulate normal hourly data
weekday = ([0.05, 0.95], 0.05) #bath, bed
weekend = ([0.3, 0.7], 0.1)
roomperwd, truelabelswd = make_blobs(n_samples=23, centers=weekday[0],
cluster_std=weekday[1], random_state=0)
roomperwe, truelabelswe = make_blobs(n_samples=8, centers=weekend[0],
cluster_std=weekend[1], random_state=0)
# combine modes
roompers = np.vstack((roomperwd, roomperwe))
# make positive and sum to one to simulate valid distribution
for i in range(roompers.shape[0]):
for j in range(roompers.shape[1]):
if roompers[i, j] < 0:
roompers[i, j] = 0
roompersnorm = normalize(roompers, norm='l1')
# simulate anomaly on most recent day where don't leave bedroom
roompersnorm[-1, :] = np.array([0.8, 0.2])
# detect outliers
roompersdetector = HourlyRoomPercentageAnomalyDetection(roompersnorm, eps=0.3, min_samples=3)
labels = roompersdetector.scale_and_proximity_cluster(eps=0.3, min_samples=3)
# plot results
plt.figure()
seenflag1 = False; seenflag2 = False; seenflag3 = False;
for i, label in enumerate(labels):
if label == 0:
if seenflag1:
plt.plot(roompersnorm[i][0], roompersnorm[i][1], 'ro')
else:
plt.plot(roompersnorm[i][0], roompersnorm[i][1], 'ro', label='Cluster 1')
seenflag1 = True
elif label == 1:
if seenflag2:
plt.plot(roompersnorm[i][0], roompersnorm[i][1], 'kx')
else:
plt.plot(roompersnorm[i][0], roompersnorm[i][1], 'kx', label='Cluster 2')
seenflag2 = True
elif label == -1:
if seenflag3:
plt.plot(roompersnorm[i][0], roompersnorm[i][1], 'b^')
else:
plt.plot(roompersnorm[i][0], roompersnorm[i][1], 'b^', label='Outlier')
seenflag3 = True
plt.legend(loc='lower left')
plt.axis([0, 1, 0, 1])
plt.show()
def test_calibration_multiclass():
"""Test calibration for multiclass """
# test multi-class setting with classifier that implements
# only decision function
clf = LinearSVC()
X, y_idx = make_blobs(n_samples=100, n_features=2, random_state=42,
centers=3, cluster_std=3.0)
# Use categorical labels to check that CalibratedClassifierCV supports
# them correctly
target_names = np.array(['a', 'b', 'c'])
y = target_names[y_idx]
X_train, y_train = X[::2], y[::2]
X_test, y_test = X[1::2], y[1::2]
clf.fit(X_train, y_train)
for method in ['isotonic', 'sigmoid']:
cal_clf = CalibratedClassifierCV(clf, method=method, cv=2)
cal_clf.fit(X_train, y_train)
probas = cal_clf.predict_proba(X_test)
assert_array_almost_equal(np.sum(probas, axis=1), np.ones(len(X_test)))
# Check that log-loss of calibrated classifier is smaller than
# log-loss of naively turned OvR decision function to probabilities
# via softmax
def softmax(y_pred):
e = np.exp(-y_pred)
return e / e.sum(axis=1).reshape(-1, 1)
uncalibrated_log_loss = \
log_loss(y_test, softmax(clf.decision_function(X_test)))
calibrated_log_loss = log_loss(y_test, probas)
assert_greater_equal(uncalibrated_log_loss, calibrated_log_loss)
# Test that calibration of a multiclass classifier decreases log-loss
# for RandomForestClassifier
X, y = make_blobs(n_samples=100, n_features=2, random_state=42,
cluster_std=3.0)
X_train, y_train = X[::2], y[::2]
X_test, y_test = X[1::2], y[1::2]
clf = RandomForestClassifier(n_estimators=10, random_state=42)
clf.fit(X_train, y_train)
clf_probs = clf.predict_proba(X_test)
loss = log_loss(y_test, clf_probs)
for method in ['isotonic', 'sigmoid']:
cal_clf = CalibratedClassifierCV(clf, method=method, cv=3)
cal_clf.fit(X_train, y_train)
cal_clf_probs = cal_clf.predict_proba(X_test)
cal_loss = log_loss(y_test, cal_clf_probs)
assert_greater(loss, cal_loss)
def test_thresholded_scorers():
# Test scorers that take thresholds.
X, y = make_blobs(random_state=0, centers=2)
X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=0)
clf = LogisticRegression(random_state=0)
clf.fit(X_train, y_train)
score1 = get_scorer('roc_auc')(clf, X_test, y_test)
score2 = roc_auc_score(y_test, clf.decision_function(X_test))
score3 = roc_auc_score(y_test, clf.predict_proba(X_test)[:, 1])
assert_almost_equal(score1, score2)
assert_almost_equal(score1, score3)
logscore = get_scorer('neg_log_loss')(clf, X_test, y_test)
logloss = log_loss(y_test, clf.predict_proba(X_test))
assert_almost_equal(-logscore, logloss)
# same for an estimator without decision_function
clf = DecisionTreeClassifier()
clf.fit(X_train, y_train)
score1 = get_scorer('roc_auc')(clf, X_test, y_test)
score2 = roc_auc_score(y_test, clf.predict_proba(X_test)[:, 1])
assert_almost_equal(score1, score2)
# test with a regressor (no decision_function)
reg = DecisionTreeRegressor()
reg.fit(X_train, y_train)
score1 = get_scorer('roc_auc')(reg, X_test, y_test)
score2 = roc_auc_score(y_test, reg.predict(X_test))
assert_almost_equal(score1, score2)
# Test that an exception is raised on more than two classes
X, y = make_blobs(random_state=0, centers=3)
X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=0)
clf.fit(X_train, y_train)
with pytest.raises(ValueError, match="multiclass format is not supported"):
get_scorer('roc_auc')(clf, X_test, y_test)
# test error is raised with a single class present in model
# (predict_proba shape is not suitable for binary auc)
X, y = make_blobs(random_state=0, centers=2)
X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=0)
clf = DecisionTreeClassifier()
clf.fit(X_train, np.zeros_like(y_train))
with pytest.raises(ValueError, match="need classifier with two classes"):
get_scorer('roc_auc')(clf, X_test, y_test)
# for proba scorers
with pytest.raises(ValueError, match="need classifier with two classes"):
get_scorer('neg_log_loss')(clf, X_test, y_test)
def check_clustering(name, Alg):
X, y = make_blobs(n_samples=50, random_state=1)
X, y = shuffle(X, y, random_state=7)
X = StandardScaler().fit_transform(X)
n_samples, n_features = X.shape
# catch deprecation and neighbors warnings
with warnings.catch_warnings(record=True):
alg = Alg()
set_fast_parameters(alg)
if hasattr(alg, "n_clusters"):
alg.set_params(n_clusters=3)
set_random_state(alg)
if name == 'AffinityPropagation':
alg.set_params(preference=-100)
alg.set_params(max_iter=100)
# fit
alg.fit(X)
# with lists
alg.fit(X.tolist())
assert_equal(alg.labels_.shape, (n_samples,))
pred = alg.labels_
assert_greater(adjusted_rand_score(pred, y), 0.4)
# fit another time with ``fit_predict`` and compare results
if name is 'SpectralClustering':
# there is no way to make Spectral clustering deterministic :(
return
set_random_state(alg)
with warnings.catch_warnings(record=True):
pred2 = alg.fit_predict(X)
assert_array_equal(pred, pred2)
def test_compute_class_weight_invariance():
# Test that results with class_weight="balanced" is invariant wrt
# class imbalance if the number of samples is identical.
# The test uses a balanced two class dataset with 100 datapoints.
# It creates three versions, one where class 1 is duplicated
# resulting in 150 points of class 1 and 50 of class 0,
# one where there are 50 points in class 1 and 150 in class 0,
# and one where there are 100 points of each class (this one is balanced
# again).
# With balancing class weights, all three should give the same model.
X, y = make_blobs(centers=2, random_state=0)
# create dataset where class 1 is duplicated twice
X_1 = np.vstack([X] + [X[y == 1]] * 2)
y_1 = np.hstack([y] + [y[y == 1]] * 2)
# create dataset where class 0 is duplicated twice
X_0 = np.vstack([X] + [X[y == 0]] * 2)
y_0 = np.hstack([y] + [y[y == 0]] * 2)
# duplicate everything
X_ = np.vstack([X] * 2)
y_ = np.hstack([y] * 2)
# results should be identical
logreg1 = LogisticRegression(class_weight="balanced").fit(X_1, y_1)
logreg0 = LogisticRegression(class_weight="balanced").fit(X_0, y_0)
logreg = LogisticRegression(class_weight="balanced").fit(X_, y_)
assert_array_almost_equal(logreg1.coef_, logreg0.coef_)
assert_array_almost_equal(logreg.coef_, logreg0.coef_)
def check_pipeline_consistency(name, Estimator):
if name in ('CCA', 'LocallyLinearEmbedding', 'KernelPCA') and _is_32bit():
# Those transformers yield non-deterministic output when executed on
# a 32bit Python. The same transformers are stable on 64bit Python.
# FIXME: try to isolate a minimalistic reproduction case only depending
# scipy and/or maybe generate a test dataset that does not
# cause such unstable behaviors.
msg = name + ' is non deterministic on 32bit Python'
raise SkipTest(msg)
# check that make_pipeline(est) gives same score as est
X, y = make_blobs(n_samples=30, centers=[[0, 0, 0], [1, 1, 1]],
random_state=0, n_features=2, cluster_std=0.1)
X -= X.min()
y = multioutput_estimator_convert_y_2d(name, y)
estimator = Estimator()
set_fast_parameters(estimator)
set_random_state(estimator)
pipeline = make_pipeline(estimator)
estimator.fit(X, y)
pipeline.fit(X, y)
funcs = ["score", "fit_transform"]
for func_name in funcs:
func = getattr(estimator, func_name, None)
if func is not None:
func_pipeline = getattr(pipeline, func_name)
result = func(X, y)
result_pipe = func_pipeline(X, y)
assert_array_almost_equal(result, result_pipe)
def check_estimators_overwrite_params(name, Estimator):
X, y = make_blobs(random_state=0, n_samples=9)
y = multioutput_estimator_convert_y_2d(name, y)
# some want non-negative input
X -= X.min()
with warnings.catch_warnings(record=True):
# catch deprecation warnings
estimator = Estimator()
if name == 'MiniBatchDictLearning' or name == 'MiniBatchSparsePCA':
# FIXME
# for MiniBatchDictLearning and MiniBatchSparsePCA
estimator.batch_size = 1
set_fast_parameters(estimator)
set_random_state(estimator)
params = estimator.get_params()
estimator.fit(X, y)
new_params = estimator.get_params()
for k, v in params.items():
assert_false(np.any(new_params[k] != v),
"Estimator %s changes its parameter %s"
" from %s to %s during fit."
% (name, k, v, new_params[k]))
def separable_demo():
""" Generate a linearly-separable dataset D, train a linear SVM on
D, then output the resulting decision boundary on a figure.
"""
from sklearn.datasets import make_blobs
X, y = make_blobs(n_samples=200, n_features=2,
centers=((0,0), (4, 4)),
cluster_std=1.0)
plot_data(X, y)
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.25)
svc = svm.SVC(class_weight='auto')
param_grid = {'kernel': ['linear'],
'C': [1e0, 1e1, 1e2, 1e3, 1e4]}
strat_2fold = StratifiedKFold(y_train, k=2)
print " Parameters to be chosen through cross validation:"
for name, vals in param_grid.iteritems():
if name != 'kernel':
print " {0}: {1}".format(name, vals)
clf = GridSearchCV(svc, param_grid, n_jobs=1, cv=strat_2fold)
clf.fit(X_train, y_train)
print "== Best Parameters:", clf.best_params_
y_pred = clf.predict(X_test)
acc = len(np.where(y_pred == y_test)[0]) / float(len(y_pred))
print "== Accuracy:", acc
print classification_report(y_test, y_pred)
plot_svm(clf.best_estimator_, X, y, X_test, y_test,
title="SVM Decision Boundary, Linear Kernel ({0} accuracy, C={1})".format(acc, clf.best_params_['C']))
def check_class_weight_classifiers(name, Classifier):
if name == "NuSVC":
# the sparse version has a parameter that doesn't do anything
raise SkipTest
if name.endswith("NB"):
# NaiveBayes classifiers have a somewhat different interface.
# FIXME SOON!
raise SkipTest
for n_centers in [2, 3]:
# create a very noisy dataset
X, y = make_blobs(centers=n_centers, random_state=0, cluster_std=20)
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=.5,
random_state=0)
n_centers = len(np.unique(y_train))
if n_centers == 2:
class_weight = {0: 1000, 1: 0.0001}
else:
class_weight = {0: 1000, 1: 0.0001, 2: 0.0001}
with warnings.catch_warnings(record=True):
classifier = Classifier(class_weight=class_weight)
if hasattr(classifier, "n_iter"):
classifier.set_params(n_iter=100)
if hasattr(classifier, "min_weight_fraction_leaf"):
classifier.set_params(min_weight_fraction_leaf=0.01)
set_random_state(classifier)
classifier.fit(X_train, y_train)
y_pred = classifier.predict(X_test)
assert_greater(np.mean(y_pred == 0), 0.89)
def test_transformers_data_not_an_array():
# test if transformers do something sensible on training set
# also test all shapes / shape errors
transformers = all_estimators(type_filter='transformer')
X, y = make_blobs(n_samples=30, centers=[[0, 0, 0], [1, 1, 1]],
random_state=0, n_features=2, cluster_std=0.1)
X = StandardScaler().fit_transform(X)
# We need to make sure that we have non negative data, for things
# like NMF
X -= X.min() - .1
for name, Transformer in transformers:
# XXX: some transformers are transforming the input
# data. This is a bug that we'll fix later. Right now we copy
# the data each time
this_X = NotAnArray(X.copy())
this_y = NotAnArray(np.asarray(y))
if name in dont_test:
continue
# these don't actually fit the data:
if name in ['AdditiveChi2Sampler', 'Binarizer', 'Normalizer']:
continue
# And these wan't multivariate output
if name in ('PLSCanonical', 'PLSRegression', 'CCA', 'PLSSVD'):
continue
yield check_transformer, name, Transformer, this_X, this_y
def test_class_weight_classifiers():
# test that class_weight works and that the semantics are consistent
classifiers = all_estimators(type_filter="classifier")
with warnings.catch_warnings(record=True):
classifiers = [c for c in classifiers if "class_weight" in c[1]().get_params().keys()]
for n_centers in [2, 3]:
# create a very noisy dataset
X, y = make_blobs(centers=n_centers, random_state=0, cluster_std=20)
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.5, random_state=0)
for name, Classifier in classifiers:
if name == "NuSVC":
# the sparse version has a parameter that doesn't do anything
continue
if name.endswith("NB"):
# NaiveBayes classifiers have a somewhat different interface.
# FIXME SOON!
continue
if n_centers == 2:
class_weight = {0: 1000, 1: 0.0001}
else:
class_weight = {0: 1000, 1: 0.0001, 2: 0.0001}
with warnings.catch_warnings(record=True):
classifier = Classifier(class_weight=class_weight)
if hasattr(classifier, "n_iter"):
classifier.set_params(n_iter=100)
set_random_state(classifier)
classifier.fit(X_train, y_train)
y_pred = classifier.predict(X_test)
assert_greater(np.mean(y_pred == 0), 0.9)
def test_decision_function_shape_two_class():
for n_classes in [2, 3]:
X, y = make_blobs(centers=n_classes, random_state=0)
for estimator in [svm.SVC, svm.NuSVC]:
clf = OneVsRestClassifier(estimator(
decision_function_shape="ovr")).fit(X, y)
assert_equal(len(clf.predict(X)), len(y))
def test_classifiers_classes():
# test if classifiers can cope with non-consecutive classes
classifiers = all_estimators(type_filter='classifier')
X, y = make_blobs(random_state=12345)
X, y = shuffle(X, y, random_state=7)
X = StandardScaler().fit_transform(X)
y = 2 * y + 1
classes = np.unique(y)
# TODO: make work with next line :)
#y = y.astype(np.str)
for name, Clf in classifiers:
if Clf in dont_test:
continue
if Clf in [MultinomialNB, BernoulliNB]:
# TODO also test these!
continue
# catch deprecation warnings
with warnings.catch_warnings(record=True):
clf = Clf()
# fit
clf.fit(X, y)
y_pred = clf.predict(X)
# training set performance
assert_array_equal(np.unique(y), np.unique(y_pred))
assert_greater(zero_one_score(y, y_pred), 0.78,
"accuracy of %s not greater than 0.78" % str(Clf))
assert_array_equal(
clf.classes_, classes,
"Unexpected classes_ attribute for %r" % clf)
def check_estimators_overwrite_params(name, Estimator):
X, y = make_blobs(random_state=0, n_samples=9)
y = multioutput_estimator_convert_y_2d(name, y)
# some want non-negative input
X -= X.min()
with warnings.catch_warnings(record=True):
# catch deprecation warnings
estimator = Estimator()
set_fast_parameters(estimator)
set_random_state(estimator)
# Make a physical copy of the orginal estimator parameters before fitting.
params = estimator.get_params()
original_params = deepcopy(params)
# Fit the model
estimator.fit(X, y)
# Compare the state of the model parameters with the original parameters
new_params = estimator.get_params()
for param_name, original_value in original_params.items():
new_value = new_params[param_name]
# We should never change or mutate the internal state of input
# parameters by default. To check this we use the joblib.hash function
# that introspects recursively any subobjects to compute a checksum.
# The only exception to this rule of immutable constructor parameters
# is possible RandomState instance but in this check we explicitly
# fixed the random_state params recursively to be integer seeds.
assert_equal(hash(new_value), hash(original_value),
"Estimator %s should not change or mutate "
" the parameter %s from %s to %s during fit."
% (name, param_name, original_value, new_value))
def test_sag_pobj_matches_logistic_regression():
"""tests if the sag pobj matches log reg"""
n_samples = 100
alpha = 1.0
max_iter = 20
X, y = make_blobs(n_samples=n_samples, centers=2, random_state=0,
cluster_std=0.1)
clf1 = LogisticRegression(solver='sag', fit_intercept=False, tol=.0000001,
C=1. / alpha / n_samples, max_iter=max_iter,
random_state=10)
clf2 = clone(clf1)
clf3 = LogisticRegression(fit_intercept=False, tol=.0000001,
C=1. / alpha / n_samples, max_iter=max_iter,
random_state=10)
clf1.fit(X, y)
clf2.fit(sp.csr_matrix(X), y)
clf3.fit(X, y)
pobj1 = get_pobj(clf1.coef_, alpha, X, y, log_loss)
pobj2 = get_pobj(clf2.coef_, alpha, X, y, log_loss)
pobj3 = get_pobj(clf3.coef_, alpha, X, y, log_loss)
assert_array_almost_equal(pobj1, pobj2, decimal=4)
assert_array_almost_equal(pobj2, pobj3, decimal=4)
assert_array_almost_equal(pobj3, pobj1, decimal=4)
def test_multiclass_classifier_class_weight():
"""tests multiclass with classweights for each class"""
alpha = .1
n_samples = 20
tol = .00001
max_iter = 50
class_weight = {0: .45, 1: .55, 2: .75}
fit_intercept = True
X, y = make_blobs(n_samples=n_samples, centers=3, random_state=0,
cluster_std=0.1)
step_size = get_step_size(X, alpha, fit_intercept, classification=True)
classes = np.unique(y)
clf1 = LogisticRegression(solver='sag', C=1. / alpha / n_samples,
max_iter=max_iter, tol=tol, random_state=77,
fit_intercept=fit_intercept,
class_weight=class_weight)
clf2 = clone(clf1)
clf1.fit(X, y)
clf2.fit(sp.csr_matrix(X), y)
le = LabelEncoder()
class_weight_ = compute_class_weight(class_weight, np.unique(y), y)
sample_weight = class_weight_[le.fit_transform(y)]
coef1 = []
intercept1 = []
coef2 = []
intercept2 = []
for cl in classes:
y_encoded = np.ones(n_samples)
y_encoded[y != cl] = -1
spweights1, spintercept1 = sag_sparse(X, y_encoded, step_size, alpha,
n_iter=max_iter, dloss=log_dloss,
sample_weight=sample_weight)
spweights2, spintercept2 = sag_sparse(X, y_encoded, step_size, alpha,
n_iter=max_iter, dloss=log_dloss,
sample_weight=sample_weight,
sparse=True)
coef1.append(spweights1)
intercept1.append(spintercept1)
coef2.append(spweights2)
intercept2.append(spintercept2)
coef1 = np.vstack(coef1)
intercept1 = np.array(intercept1)
coef2 = np.vstack(coef2)
intercept2 = np.array(intercept2)
for i, cl in enumerate(classes):
assert_array_almost_equal(clf1.coef_[i].ravel(),
coef1[i].ravel(),
decimal=2)
assert_almost_equal(clf1.intercept_[i], intercept1[i], decimal=1)
assert_array_almost_equal(clf2.coef_[i].ravel(),
coef2[i].ravel(),
decimal=2)
assert_almost_equal(clf2.intercept_[i], intercept2[i], decimal=1)
def test_grid_search_correct_score_results():
# test that correct scores are used
n_splits = 3
clf = LinearSVC(random_state=0)
X, y = make_blobs(random_state=0, centers=2)
Cs = [.1, 1, 10]
for score in ['f1', 'roc_auc']:
grid_search = GridSearchCV(clf, {'C': Cs}, scoring=score, cv=n_splits)
results = grid_search.fit(X, y).cv_results_
# Test scorer names
result_keys = list(results.keys())
expected_keys = (("mean_test_score", "rank_test_score") +
tuple("split%d_test_score" % cv_i
for cv_i in range(n_splits)))
assert_true(all(in1d(expected_keys, result_keys)))
cv = StratifiedKFold(n_splits=n_splits)
n_splits = grid_search.n_splits_
for candidate_i, C in enumerate(Cs):
clf.set_params(C=C)
cv_scores = np.array(
list(grid_search.cv_results_['split%d_test_score'
% s][candidate_i]
for s in range(n_splits)))
for i, (train, test) in enumerate(cv.split(X, y)):
clf.fit(X[train], y[train])
if score == "f1":
correct_score = f1_score(y[test], clf.predict(X[test]))
elif score == "roc_auc":
dec = clf.decision_function(X[test])
correct_score = roc_auc_score(y[test], dec)
assert_almost_equal(correct_score, cv_scores[i])
def plot_scaling():
X, y = make_blobs(n_samples=50, centers=2, random_state=4, cluster_std=1)
X += 3
plt.figure(figsize=(15, 8))
main_ax = plt.subplot2grid((2, 4), (0, 0), rowspan=2, colspan=2)
main_ax.scatter(X[:, 0], X[:, 1], c=y, cmap=cm2, s=60)
maxx = np.abs(X[:, 0]).max()
maxy = np.abs(X[:, 1]).max()
main_ax.set_xlim(-maxx + 1, maxx + 1)
main_ax.set_ylim(-maxy + 1, maxy + 1)
main_ax.set_title("Original Data")
other_axes = [plt.subplot2grid((2, 4), (i, j)) for j in range(2, 4) for i in range(2)]
for ax, scaler in zip(other_axes, [StandardScaler(), RobustScaler(),
MinMaxScaler(), Normalizer(norm='l2')]):
X_ = scaler.fit_transform(X)
ax.scatter(X_[:, 0], X_[:, 1], c=y, cmap=cm2, s=60)
ax.set_xlim(-2, 2)
ax.set_ylim(-2, 2)
ax.set_title(type(scaler).__name__)
other_axes.append(main_ax)
for ax in other_axes:
ax.spines['left'].set_position('center')
ax.spines['right'].set_color('none')
ax.spines['bottom'].set_position('center')
ax.spines['top'].set_color('none')
ax.xaxis.set_ticks_position('bottom')
ax.yaxis.set_ticks_position('left')
def test_verbose_boolean():
# checks that the output for the verbose output is the same
# for the flag values '1' and 'True'
# simple 3 cluster dataset
X, y = make_blobs(random_state=1)
for Model in [DPGMM, VBGMM]:
dpgmm_bool = Model(n_components=10, random_state=1, alpha=20,
n_iter=50, verbose=True)
dpgmm_int = Model(n_components=10, random_state=1, alpha=20,
n_iter=50, verbose=1)
old_stdout = sys.stdout
sys.stdout = StringIO()
try:
# generate output with the boolean flag
dpgmm_bool.fit(X)
verbose_output = sys.stdout
verbose_output.seek(0)
bool_output = verbose_output.readline()
# generate output with the int flag
dpgmm_int.fit(X)
verbose_output = sys.stdout
verbose_output.seek(0)
int_output = verbose_output.readline()
assert_equal(bool_output, int_output)
finally:
sys.stdout = old_stdout
def test_decision_function_shape():
# check that decision_function_shape='ovr' gives
# correct shape and is consistent with predict
clf = svm.SVC(kernel='linear', C=0.1,
decision_function_shape='ovr').fit(iris.data, iris.target)
dec = clf.decision_function(iris.data)
assert_equal(dec.shape, (len(iris.data), 3))
assert_array_equal(clf.predict(iris.data), np.argmax(dec, axis=1))
# with five classes:
X, y = make_blobs(n_samples=80, centers=5, random_state=0)
X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=0)
clf = svm.SVC(kernel='linear', C=0.1,
decision_function_shape='ovr').fit(X_train, y_train)
dec = clf.decision_function(X_test)
assert_equal(dec.shape, (len(X_test), 5))
assert_array_equal(clf.predict(X_test), np.argmax(dec, axis=1))
# check shape of ovo_decition_function=True
clf = svm.SVC(kernel='linear', C=0.1,
decision_function_shape='ovo').fit(X_train, y_train)
dec = clf.decision_function(X_train)
assert_equal(dec.shape, (len(X_train), 10))
# check deprecation warning
clf = svm.SVC(kernel='linear', C=0.1).fit(X_train, y_train)
msg = "change the shape of the decision function"
dec = assert_warns_message(ChangedBehaviorWarning, msg,
clf.decision_function, X_train)
assert_equal(dec.shape, (len(X_train), 10))
def single_calc(n_sample):
#n_sample = 1000
n_feature = 2
cluster_std = 0.5
center = 2
#for n_sample in [10, 50, 100, 500, 1000, 5000, 10000]:
pts, labels = datasets.make_blobs(n_samples=n_sample, n_features=n_feature, cluster_std=cluster_std, centers=center)
start = timer()
tri = Tri(pts)
end = timer()
tri_time = end - start
print(tri_time)
#tri_res = compare_labels(labels, tri.labels)
start = timer()
auto = Autoclust(pts)
end = timer()
auto_time = end - start
print(auto_time)
#auto_res = compare_labels(labels, auto.labels)
res_dict = {'tri': tri_time, 'auto': auto_time, 'samples': n_sample}
with open('times', 'a') as f:
print(res_dict, file=f)
def test_vbgmm_no_modify_alpha():
alpha = 2.
n_components = 3
X, y = make_blobs(random_state=1)
vbgmm = VBGMM(n_components=n_components, alpha=alpha, n_iter=1)
assert_equal(vbgmm.alpha, alpha)
assert_equal(vbgmm.fit(X).alpha_, float(alpha) / n_components)
def test_grid_search_iid():
# test the iid parameter
# noise-free simple 2d-data
X, y = make_blobs(
centers=[[0, 0], [1, 0], [0, 1], [1, 1]], random_state=0, cluster_std=0.1, shuffle=False, n_samples=80
)
# split dataset into two folds that are not iid
# first one contains data of all 4 blobs, second only from two.
mask = np.ones(X.shape[0], dtype=np.bool)
mask[np.where(y == 1)[0][::2]] = 0
mask[np.where(y == 2)[0][::2]] = 0
# this leads to perfect classification on one fold and a score of 1/3 on
# the other
svm = SVC(kernel="linear")
# create "cv" for splits
cv = [[mask, ~mask], [~mask, mask]]
# once with iid=True (default)
grid_search = GridSearchCV(svm, param_grid={"C": [1, 10]}, cv=cv)
grid_search.fit(X, y)
first = grid_search.grid_scores_[0]
assert_equal(first.parameters["C"], 1)
assert_array_almost_equal(first.cv_validation_scores, [1, 1.0 / 3.0])
# for first split, 1/4 of dataset is in test, for second 3/4.
# take weighted average
assert_almost_equal(first.mean_validation_score, 1 * 1.0 / 4.0 + 1.0 / 3.0 * 3.0 / 4.0)
# once with iid=False
grid_search = GridSearchCV(svm, param_grid={"C": [1, 10]}, cv=cv, iid=False)
grid_search.fit(X, y)
first = grid_search.grid_scores_[0]
assert_equal(first.parameters["C"], 1)
# scores are the same as above
assert_array_almost_equal(first.cv_validation_scores, [1, 1.0 / 3.0])
# averaged score is just mean of scores
assert_almost_equal(first.mean_validation_score, np.mean(first.cv_validation_scores))
def check_transformer_general(name, Transformer):
X, y = make_blobs(n_samples=30, centers=[[0, 0, 0], [1, 1, 1]],
random_state=0, n_features=2, cluster_std=0.1)
X = StandardScaler().fit_transform(X)
X -= X.min()
_check_transformer(name, Transformer, X, y)
_check_transformer(name, Transformer, X.tolist(), y.tolist())
def test_search_cv_results_rank_tie_breaking():
X, y = make_blobs(n_samples=50, random_state=42)
# The two C values are close enough to give similar models
# which would result in a tie of their mean cv-scores
param_grid = {'C': [1, 1.001, 0.001]}
grid_search = GridSearchCV(SVC(), param_grid=param_grid)
random_search = RandomizedSearchCV(SVC(), n_iter=3,
param_distributions=param_grid)
for search in (grid_search, random_search):
search.fit(X, y)
results = search.cv_results_
# Check tie breaking strategy -
# Check that there is a tie in the mean scores between
# candidates 1 and 2 alone
assert_almost_equal(results['mean_test_score'][0],
results['mean_test_score'][1])
try:
assert_almost_equal(results['mean_test_score'][1],
results['mean_test_score'][2])
except AssertionError:
pass
# 'min' rank should be assigned to the tied candidates
assert_almost_equal(search.cv_results_['rank_test_score'], [1, 1, 3])
#output1 = np.empty(len(x_input)) #output2 = np.empty(len(x_input)) #for i in range(len(x_input)): # a = A[1,1] # b = (A[1,0] + A[0,1])*x[i] + alpha[1] # c = A[0,0] * x[i]**2 + alpha[0] * x[i] + alpha0 # output1[i], output2[i] = solve_quadratic_eq(a,b,c) # #plt.figure() #plt.scatter(train["Height"], train["Weight"], c=y) #plt.plot(x,output1, label = "first sol") #plt.plot(x,output2, label = "second sol") #plt.legend() #########################################3 X, y = make_blobs(300, 2, centers=2, random_state=100) X[y == 0] = X[y == 0] + 2 X[y == 0] = np.dot(np.array([[0.5, 0.1], [1.2, 1.5]]), X[y == 0].T).T X = X - np.mean(X, axis=0) class1 = X[y == 0] class2 = X[y == 1] prior1 = len(class1) / len(X) prior2 = len(class2) / len(X) cov1 = np.cov(class1.T) cov2 = np.cov(class2.T) #cov1[1,0] = cov1[0,1] = cov2[0,1] = cov2[1,0] = 0 mean1 = np.mean(np.array(class1), axis=0) mean2 = np.mean(np.array(class2), axis=0) A = 0.5 * (np.linalg.inv(cov1) - np.linalg.inv(cov2))
**kwargs)
if __name__ == '__main__':
n_samples = 1000
random_state = 170
transformation = [[0.6, -0.6], [-0.4, 0.8]]
models = [
{
'name':
'Far Blobs',
'X':
datasets.make_blobs(n_samples=n_samples,
centers=25,
random_state=0,
center_box=(-10000, 10000),
cluster_std=50)[0],
},
{
'name':
'Noisy Circles',
'X':
datasets.make_circles(n_samples=n_samples, factor=.5,
noise=.05)[0],
},
{
'name': 'Noisy Moons',
'X': datasets.make_moons(n_samples=n_samples, noise=.05)[0],
},
{
# # Grouping objects by similarity using k-means
# ## K-means clustering using scikit-learn
X, y = make_blobs(n_samples=150,
n_features=2,
centers=3,
cluster_std=0.5,
shuffle=True,
random_state=0)
plt.scatter(X[:, 0], X[:, 1],
c='white', marker='o', edgecolor='black', s=50)
plt.grid()
plt.tight_layout()
#plt.savefig('images/11_01.png', dpi=300)
plt.title("some random data")
plt.show()
plt.show()
# 分类模型随机数据
# X1为样本特征，Y1为样本类别输出， 共400个样本，每个样本2个特征，输出有3个类别，没有冗余特征，每个类别一个簇
X1, Y1 = make_classification(n_samples=400,
n_features=2,
n_redundant=0,
n_clusters_per_class=1,
n_classes=3)
plt.scatter(X1[:, 0], X1[:, 1], marker='o', c=Y1)
plt.show()
# 生成用于聚类的各向同性高斯blobs
# X为样本特征，Y为样本簇类别， 共1000个样本，每个样本2个特征，共3个簇，簇中心在[-1,-1], [1,1], [2,2]， 簇方差分别为[0.4, 0.5, 0.2]
X, y = make_blobs(n_samples=1000,
n_features=2,
centers=[[-1, -1], [1, 1], [2, 2]],
cluster_std=[0.4, 0.5, 0.2])
plt.scatter(X[:, 0], X[:, 1], marker='o', c=y)
plt.show()
# 分组正态分布混合数据
# 生成2维正态分布，生成的数据按分位数分成3组，1000个样本,2个样本特征均值为1和2，协方差系数为2
X1, Y1 = make_gaussian_quantiles(n_samples=1000,
n_features=2,
n_classes=3,
mean=[1, 2],
cov=2)
plt.scatter(X1[:, 0], X1[:, 1], marker='o', c=Y1)
plt.show()
def mejora_semiboost(n=20,
clf=SVC(probability=True),
n_features=5,
n_samples=1000,
ratio_unsampled=0.5,
data_simulation='make_classification',
similarity_kernel='rbf'):
ROC_semiboost = list()
ROC_clf = list()
for i in range(n):
''' SIMULATE SEMI SUPERVISED DATASET '''
if data_simulation == 'make_classification':
X, y = make_classification(n_features=n_features,
n_samples=n_samples,
n_redundant=0,
n_clusters_per_class=1)
elif data_simulation == 'make_blobs':
X, y = make_blobs(n_features=n_features,
centers=2,
n_samples=n_samples)
elif data_simulation == 'make_gaussian_quantiles':
X, y = make_gaussian_quantiles(n_features=n_features,
n_classes=2,
n_samples=n_samples)
elif data_simulation == 'make_moons':
X, y = make_moons(n_samples=n_samples)
elif data_simulation == 'make_circles':
X, y = make_circles(n_samples=n_samples)
else:
print('Unknown data simulation method')
X_train, X_test, y_train, y_test = train_test_split(X,
y,
test_size=0.2,
random_state=42)
labels = np.copy(y_train)
labels[labels == 0] = -1
# create some unlabeled data
random_unlabeled_points = np.random.rand(
len(y_train)) < ratio_unsampled
labels[random_unlabeled_points] = 0
y_train = labels
''' SEMIBOOST SKLEARN STYLE '''
model = SemiBoost.SemiBoostClassifier(base_model=clf)
model.fit(X_train,
y_train,
n_neighbors=3,
n_jobs=10,
max_models=15,
similarity_kernel='rbf',
verbose=False)
ROC_semiboost.append(roc_auc_score(model.predict(X_test), y_test))
''' BASE CLASSIFIER '''
model = clf
XX = X_train[~random_unlabeled_points, ]
yy = y_train[~random_unlabeled_points]
model.fit(XX, yy)
ROC_clf.append(roc_auc_score(model.predict(X_test), y_test))
return (np.mean(np.array(ROC_semiboost) - np.array(ROC_clf)),
np.std(np.array(ROC_semiboost) - np.array(ROC_clf)))
def simulate_normal_clusters(N, ndim, centers=4, center_box=(-8, 8), **kwds):
return make_blobs(N, ndim, centers=centers, center_box=center_box, **kwds)
# K Means Outlier Detection On Make_Blobs DataSet
# Generate a single blob of 100 points
# Identify the five points that are furthest from the centroid
from sklearn.datasets import make_blobs
X, labels = make_blobs(100, centers=1)
# The k means should have a single center for most occassions
from sklearn.cluster import KMeans
kmeans = KMeans(n_clusters=1)
kmeans.fit(X)
KMeans(algorithm='auto',
copy_x=True,
init='k-means++',
max_iter=300,
n_clusters=1,
n_init=10,
n_jobs=1,
precompute_distances='auto',
random_state=None,
tol=0.0001,
verbose=0)
# Visualize the blobs with a scatter plot to see the centroid
import matplotlib.pyplot as plt
f, ax = plt.subplots(figsize=(8, 5))
ax.set_title("Blob")
ax.scatter(X[:, 0], X[:, 1], label='Points')
ax.scatter(kmeans.cluster_centers_[:, 0],
kmeans.cluster_centers_[:, 1],
label='Centroid',
import matplotlib.pyplot as plt
def plot_data(X, y, figsize=None):
if not figsize:
figsize = (8, 6)
plt.figure(figsize=figsize)
plt.plot(X[y==0, 0], X[y==0, 1], 'or', alpha=0.5, label=0)
plt.plot(X[y==1, 0], X[y==1, 1], 'ob', alpha=0.5, label=1)
plt.xlim((min(X[:, 0])-0.1, max(X[:, 0])+0.1))
plt.ylim((min(X[:, 1])-0.1, max(X[:, 1])+0.1))
plt.legend()
X, y = make_blobs(n_samples=500,
n_features=2,
centers=4,
cluster_std=1,
center_box=(-10.0, 10.0),
shuffle=True,
random_state=1)
plot_data(X, y)
kmeans_model = cluster.KMeans(n_clusters=2, random_state=1)
kmeans_model.fit(X)
kmeans_model.cluster_centers_
kmeans_model.labels_
#metrics when target labels are not known
silhouette_avg = metrics.silhouette_score(X,kmeans_model.labels_,metric='euclidean')
print(silhouette_avg)
silhouette_samples = metrics.silhouette_samples(X,kmeans_model.labels_,metric='euclidean')
print(silhouette_samples)
ax.set_xlabel('X')
ax.set_ylabel('Y')
markers = ['o', 'd', '^', 'x', '1', '2', '3', 's']
colors = ['r', 'b', 'g', 'c', 'm', 'k', 'y', '#cccfff']
for i in range(nb_samples):
ax.scatter(X[i, 0], X[i, 1], marker=markers[Y[i]], color=colors[Y[i]])
plt.show()
if __name__ == '__main__':
# Create the dataset
X, Y = make_blobs(n_samples=nb_samples,
n_features=2,
centers=8,
cluster_std=2.0)
# Show the dataset
fig, ax = plt.subplots(1, 1, figsize=(10, 8))
ax.grid()
ax.set_xlabel('X')
ax.set_ylabel('Y')
ax.scatter(X[:, 0], X[:, 1], marker='o', color='b')
plt.show()
# Complete linkage
print('Complete linkage')
ac = AgglomerativeClustering(n_clusters=8, linkage='complete')
rowSums = np.sum(self.affMat, axis=1)
dmax = np.max(rowSums)
D = np.diag(rowSums)
L = (self.affMat + dmax * np.eye(D.shape[0]) - D) / dmax
values, vectors = np.linalg.eig(L)
assert np.all(np.isreal(values))
bigEigInd = np.argsort(-values)
return vectors[:, bigEigInd[:self.n_clusters]]
def apply_constraints(self):
self.affMat[self.ML[:, 0], self.ML[:, 1]] = 1
self.affMat[self.CL[:, 0], self.CL[:, 1]] = 0
if __name__ == '__main__':
Nclusters, N, Nconstraints = (3, 100, 40)
data, labels = ds.make_blobs(n_samples=N, n_features=2, centers=Nclusters)
constraintMat = ConstrainedClustering.make_constraints(
labels,
data=data,
method='mmffqs',
Nconstraints=Nconstraints,
errRate=0)
plt.figure()
ConstrainedClustering.plot_constraints(data, constraintMat)
plt.show()
import matplotlib.pyplot as plt
from sklearn.datasets import make_blobs
from scipy.cluster.hierarchy import dendrogram, ward
X, y = make_blobs(n_samples=12, random_state=0)
linkage_array = ward(X)
dendrogram(linkage_array)
ax = plt.gca()
bounds = ax.get_xbound()
ax.plot(bounds, [7.25, 7.25], '--', c='k')
ax.plot(bounds, [4, 4], '--', c='k')
ax.text(bounds[1], 7.25, ' two clusters', va='center')
ax.text(bounds[1], 4, ' three clusters', va='center')
ax.set_xlabel('Sample index')
ax.set_ylabel('Cluster distance')
plt.show()
import matplotlib.pyplot as plt
from sklearn import cluster, datasets
from sklearn.neighbors import kneighbors_graph
from sklearn.preprocessing import StandardScaler
np.random.seed(0)
# Generate datasets. We choose the size big enough to see the scalability
# of the algorithms, but not too big to avoid too long running times
n_samples = 1500
noisy_circles = datasets.make_circles(n_samples=n_samples,
factor=.5,
noise=.05)
noisy_moons = datasets.make_moons(n_samples=n_samples, noise=.05)
blobs = datasets.make_blobs(n_samples=n_samples, random_state=8)
no_structure = np.random.rand(n_samples, 2), None
colors = np.array([x for x in 'bgrcmykbgrcmykbgrcmykbgrcmyk'])
colors = np.hstack([colors] * 20)
clustering_names = [
'MiniBatchKMeans', 'AffinityPropagation', 'MeanShift',
'SpectralClustering', 'Ward', 'AgglomerativeClustering', 'DBSCAN', 'Birch'
]
plt.figure(figsize=(len(clustering_names) * 2 + 3, 9.5))
plt.subplots_adjust(left=.02,
right=.98,
bottom=.001,
top=.96,
if __name__ == '__main__':
from sklearn.datasets import make_blobs
import matplotlib.pyplot as plt
import numpy as np
import argparse
# argparse.ArgumentParser(prog=None, usage=None, description=None, epilog=None, parents=[], formatter_class=argparse.HelpFormatter, prefix_chars='-', fromfile_prefix_chars=None, argument_default=None, conflict_handler='error', add_help=True, allow_abbrev=True, exit_on_error=True)
parser = argparse.ArgumentParser(description='')
# parser.add_argument(name or flags...[, action][, nargs][, const][, default][, type][, choices][, required][, help][, metavar][, dest])
parser.add_argument('-a', '--arg1')
args = parser.parse_args()
# #############################################################################
# Generate sample data
centers = [[1, 1], [-1, -1], [1, -1]]
X, labels_true = make_blobs(n_samples=750, centers=centers, cluster_std=0.4,
random_state=0)
# #############################################################################
n_clusters, labels, core_samples = DBscan(X)
core_samples_mask = np.zeros_like(labels, dtype=bool)
core_samples_mask[core_samples] = True
# Plot result
unique_labels = set(labels)
colors = [plt.cm.Spectral(each)
for each in np.linspace(0, 1, len(unique_labels))]
for k, col in zip(unique_labels, colors):
if k == -1:
# Black used for noise.
col = [0, 0, 0, 1]
class_member_mask = (labels == k)
xy = X[class_member_mask & core_samples_mask]
'''
@Author： Runsen
@微信公众号： 润森笔记
@博客： https://blog.csdn.net/weixin_44510615
@Date： 2020/5/2
'''
from sklearn import datasets
from sklearn.cluster import KMeans
from sklearn.metrics import adjusted_rand_score, silhouette_score, calinski_harabasz_score
x, y = datasets.make_blobs(400, n_features=2, centers=4, random_state=0)
model = KMeans(n_clusters=4)
model.fit(x)
y_pred = model.predict(x)
print(" 调整兰德系数: " + str(adjusted_rand_score(y, y_pred)))
print(" 轮廓系数: " + str(silhouette_score(x, y_pred)))
print(" CH分数: " + str(calinski_harabasz_score(x, y_pred)))
neptune.stop()
## Explore Results
# Scikit-learn KMeans clustering
## Step 1: Create KMeans object and example data
parameters = {'n_init': 11, 'max_iter': 270}
from sklearn.datasets import make_blobs
from sklearn.cluster import KMeans
km = KMeans(**parameters)
X, y = make_blobs(n_samples=579, n_features=17, centers=7, random_state=28743)
## Step 2: Initialize Neptune
import neptune
neptune.init('shared/sklearn-integration', api_token='ANONYMOUS')
## Step 3: Create an Experiment
neptune.create_experiment(params=parameters,
name='clustering-example',
tags=['KMeans', 'clustering'])
## Step 4: Log KMeans clustering summary
from main import mglearn, train_test_split, plt, np
from sklearn.datasets import make_blobs
from sklearn.cluster import AgglomerativeClustering
from scipy.cluster.hierarchy import dendrogram, ward
X, y = make_blobs(random_state=0, n_samples=12)
linkage_array = ward(X)
dendrogram(linkage_array)
ax = plt.gca()
bounds = ax.get_xbound()
ax.plot(bounds, [7.25, 7.25], '--', c='k')
ax.plot(bounds, [4, 4], '--', c='k')
ax.text(bounds[1], 7.25, 'two clusters', va='center', fontdict={"size": 15})
ax.text(bounds[1], 4, 'three clusters', va='center', fontdict={"size": 15})
# agg = AgglomerativeClustering(n_clusters=3)
# assignment = agg.fit_predict(X)
# mglearn.discrete_scatter(X[:, 0], X[:, 1], assignment)
plt.xlabel("Feature 0")
plt.ylabel("Feature 1")
plt.show()
# plt.show()
RS = 11
name = 'wq_random_project'
target = 'quality'
train = pd.read_csv(f'wine_train.csv')
test = pd.read_csv(f'wine_test.csv')
full = pd.concat([train, test])
y = np.array(train.loc[:, target])
X = np.array(train.drop(target, axis=1))
name = 'gb_random_project'
X, y = make_blobs(centers=6, n_features=2, n_samples=1000, random_state=11)
n_pairs = 100
np.random.seed(RS)
sample_idxs = np.random.choice(range(X.shape[0]),
size=2 * n_pairs,
replace=False)
x_vals = np.array(range(1, X.shape[1] + 1))
y_vals = []
for n_components in x_vals:
print(X.shape[1], '->', n_components)
np.random.seed(RS)
best_mean = np.inf
for rs in np.random.choice(range(1000), size=5, replace=False):
transformer = GaussianRandomProjection(random_state=rs,
n_components=n_components)
ap.add_argument("-a",
"--alpha",
type=float,
default=0.01,
help="learning rate")
ap.add_argument("-b",
"--batch-size",
type=int,
default=32,
help="size of SGD mini-batches")
args = vars(ap.parse_args())
# generate a 2-class classification problem with 1000 data points, where each data point is a 2D feature vector
(X, y) = make_blobs(n_samples=1000,
n_features=2,
centers=2,
cluster_std=1.5,
random_state=1)
y = y.reshape((y.shape[0], 1))
# insert a column of 1's as the last entry in the feature matrix -- this little trick allows us to treat
# the bias as a trainable parameter within the weight matrix
X = np.c_[X, np.ones((X.shape[0]))]
# partition the data into training and testing splits using 50% of
# the data for training and the remaining 50% for testing
(trainX, testX, trainY, testY) = train_test_split(X,
y,
test_size=0.5,
random_state=42)
self.means = np.zeros([self.kk, self.mm])
for n in range(self.nn):
self.means[self.assign[n]] += self.data[n]
for k in range(self.kk):
self.means[k] /= self.count[k]
if __name__ == "__main__":
features, target = make_blobs(n_samples=1000,
n_features=2,
centers=3,
cluster_std=0.5,
shuffle=True,
random_state=1)
#plt.scatter(features[:, 0], features[:, 1], c = target)
#plt.show()
centers = np.array([[2.0, 2.0], [-1.0, -5.0], [-5.0, -1.0]])
model = Kmeans(data=features, means=centers)
plt.scatter(features[:, 0], features[:, 1], c=target)
plt.show()
plt.scatter(features[:, 0], features[:, 1], c=model.assign)
return bool(random.getrandbits(1))
# A cluster generator creates a cluster in the range [-1, 1]. It return a tuple (points, cluster_indices)
cluster_generators = []
cluster_generators.append(
(2, lambda samples: make_circles(n_samples=samples,
noise=random.uniform(0, 0.08),
factor=random.uniform(0.1, 0.4))))
circles = make_circles(n_samples=15,
noise=random.uniform(0, 0.08),
factor=random.uniform(0.1, 0.4))
for i in range(10):
data = make_blobs(50, centers=5)
data = make_moons(n_samples=101, noise=random.uniform(0, 0.08))
data_points = data[0]
if rand_bool():
data_points = -data_points
data_points = rotate_2d(data_points, random.uniform(0, np.pi * 2))
data_points = rescale_data(data_points, [0, 1], [0, 1])
data = (data_points, data[1])
plot_data(data)
# for i in range(10):
# plot_data(cluster_generators[0](40))
# 导入高斯朴素贝叶斯
from sklearn.naive_bayes import GaussianNB
# 导入画图工具
import matplotlib.pyplot as plt
# 导入数据集生成工具
from sklearn.datasets import make_blobs
# 导入数据集拆分工具
from sklearn.model_selection import train_test_split
import numpy as np
# 生成样本数量为500， 分类数为5的数据集
X, y = make_blobs(n_samples=500, centers=5, random_state=8)
# 将数据集拆分成训练集和测试集
X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=8)
# 使用高斯朴素贝叶斯
gnb = GaussianNB()
gnb.fit(X_train, y_train)
print('\n代码运行结果： ')
print('训练集数据得分：{:.3f}'.format(gnb.score(X_train, y_train)))
print('测试及数据得分：{:.3f}'.format(gnb.score(X_test, y_test)))
# 限定横轴与纵轴的最大值
x_min, x_max = X[:, 0].min() - 0.5, X[:, 0].max() + 0.5
y_min, y_max = X[:, 1].min() - 0.5, X[:, 1].max() + 0.5
# 用不同的背景色表示不同的分类
xx, yy = np.meshgrid(np.arange(x_min, x_max, .02),
np.arange(y_min, y_max, .02))
z = gnb.predict(np.c_[(xx.ravel(), yy.ravel())]).reshape(xx.shape)
plt.pcolormesh(xx, yy, z, cmap=plt.cm.Spectral)
def plot_classification(clf=SVC(probability=True),
n_features=2,
n_samples=1000,
ratio_unsampled=0.99,
data_simulation='make_classification'):
''' SIMULATE SEMI SUPERVISED DATASET '''
if data_simulation == 'make_classification':
X, y = make_classification(n_features=n_features,
n_samples=n_samples,
n_redundant=0,
n_clusters_per_class=1)
elif data_simulation == 'make_blobs':
X, y = make_blobs(n_features=n_features,
centers=2,
n_samples=n_samples)
elif data_simulation == 'make_gaussian_quantiles':
X, y = make_gaussian_quantiles(n_features=n_features,
n_classes=2,
n_samples=n_samples)
elif data_simulation == 'make_moons':
X, y = make_moons(n_samples=n_samples)
elif data_simulation == 'make_circles':
X, y = make_circles(n_samples=n_samples)
else:
print('Unknown data simulation method')
X_train, X_test, y_train, y_test = train_test_split(X,
y,
test_size=0.2,
random_state=42)
labels = np.copy(y_train)
labels[labels == 0] = -1
# create some unlabeled data
random_unlabeled_points = np.random.rand(len(y_train)) < ratio_unsampled
labels[random_unlabeled_points] = 0
y_train = labels
''' SEMIBOOST SKLEARN STYLE '''
model = SemiBoost.SemiBoostClassifier(base_model=clf)
model.fit(X_train,
y_train,
n_jobs=10,
max_models=10,
similarity_kernel='rbf',
verbose=False)
''' Plot '''
gs = gridspec.GridSpec(1, 2)
fig = plt.figure(figsize=(10, 8))
ax = plt.subplot(gs[0, 0])
fig = plot_decision_regions(X=X_test, y=y_test, clf=model, legend=2)
plt.title('SemiBoost')
''' BASE CLASSIFIER '''
basemodel = clf
XX = X_train[~random_unlabeled_points, ]
yy = y_train[~random_unlabeled_points]
basemodel.fit(XX, yy)
''' Plot '''
ax = plt.subplot(gs[0, 1])
fig = plot_decision_regions(X=X_test, y=y_test, clf=basemodel, legend=2)
plt.title('BaseModel')
plt.show()
def __init__(self,
model,
population_size,
n_blobs,
n_features,
home_district_in_position,
iseed=None):
self.model = model
self.roulette_distribution = {}
self.feature_vector = {}
self.vector_to_human = {}
self.vector_to_home = {}
self.vector_to_classroom = {}
self.vector_to_office = {}
self.vector_to_restaurant = {}
self.unit_info_map = self.unit_info_map()
n_vec = population_size
blobs, assignments = make_blobs(
n_samples=n_vec,
n_features=n_features,
centers=n_blobs,
cluster_std=0.1, #1.0
center_box=(-10.0, 10.0),
shuffle=False,
random_state=iseed)
self.n_blobs = n_blobs
self.home_district_in_position = home_district_in_position
self.blob_dict = {}
for vec, assignment in zip(blobs, assignments):
if assignment not in self.blob_dict:
self.blob_dict[assignment] = []
self.blob_dict[assignment].append(vec)
self.vectors = blobs
#self.vectors = KeyedVectors(n_features)
#numlist = range(n_vec)
#self.vectors.add(numlist,blobs[:])
#for i in range(n_vec):
#self.vectors.add_vector(i, blobs[i,:])
#vectors.add_vector(str(i), blobs[i,:])
#print (numlist)
#print(blobs)
#print (self.vectors)
for i in range(n_vec):
#vector1 = self.vectors.get_vector(i)
vector1 = self.vectors[i]
tuple_vec1 = tuple(vector1)
similarities = KeyedVectors.cosine_similarities(
vector1, self.vectors)
#print (distances)
#distances = self.vectors.cosine_similarities(vector1,self.vectors)
#self.roulette_distribution[tuple_vec1] = {}
temp = {}
sum_similarities = (similarities - similarities.min()).sum()
for j in range(n_vec):
if i != j:
vector2 = self.vectors[j]
tuple_vec2 = tuple(vector2)
temp[tuple_vec2] = (similarities[j] -
similarities.min()) / sum_similarities
self.roulette_distribution[tuple_vec1] = dict(
sorted(temp.items(), key=lambda item: -item[1]))
from sklearn.ensemble import RandomForestClassifier
from sklearn.datasets import make_blobs
import matplotlib.pyplot as plt
np.random.seed(123)
X, y = make_blobs(n_samples=1000, n_features=10, centers=5, cluster_std=3)
RFC = RandomForestClassifier(n_estimators=80, oob_score=True)
RFC.fit(X, y)
print("oob_score_", RFC.oob_score_)
_x0 = np.random.randn(10)
sample_gen = GenerativeSampler(model=RFC,
target_class=0,
class_err_prob=1 - RFC.oob_score_,
use_empirical=False)
test = sample_gen.run_chain(n=10, x0=_x0)
# Test that class_err_prob self populates correctly
sample_gen = GenerativeSampler(model=RFC,
X=X,
y=y,
target_class=0,
use_empirical=False)
#assert sample_gen.class_err_prob == 0
print(
"calculated class_err_prob", sample_gen.class_err_prob
) # For RFC this will always be 0 because it's calculated against the training data.
test = sample_gen.run_chain(n=10, x0=_x0)
# test that x0 self populates correctly
#!/usr/bin/python # -*- coding: utf-8 -*- #[email protected] """ 层次聚类 自低向上，初始中，每个点作为一类。 """ print(__doc__) from sklearn.datasets import make_moons, make_circles, make_blobs from sklearn.cluster import AgglomerativeClustering import numpy as np import matplotlib.pyplot as plt centers = [[0, 1], [-1, -1], [1, -1]] X, y = make_blobs(n_samples=1500, random_state=170) trs = [[0.60834549, -0.63667341], [-0.40887718, 0.85253229]] X = np.dot(X, trs) """ 层次聚类 =============== 参数： n_clusters：一个整数，指定分类簇的数量 linkage：一个字符串，用于指定链接算法 ‘ward’：单链接single-linkage，采用dmindmin ‘complete’：全链接complete-linkage算法，采用dmaxdmax ‘average’：均连接average-linkage算法，采用davgdavg affinity：一个字符串或者可调用对象，用于计算距离 """ clt = AgglomerativeClustering(linkage="ward")
import matplotlib.pyplot as plt
import seaborn as sns
from sklearn.datasets import make_blobs
sns.set() # for plot styling
features, labels = make_blobs(n_samples=300,
centers=4,
cluster_std=0.60,
random_state=0)
plt.scatter(features[:, 0], features[:, 1], s=50)
plt.show()
# scatter plot of blobs dataset
from sklearn.datasets import make_blobs
from matplotlib import pyplot
from numpy import where
# generate 2d classification dataset
X, y = make_blobs(n_samples=500,
centers=3,
n_features=2,
cluster_std=2,
random_state=2)
# scatter plot for each class value
for class_value in range(3):
# select indices of points with the class label
row_ix = where(y == class_value)
# scatter plot for points with a different color
pyplot.scatter(X[row_ix, 0], X[row_ix, 1])
# show plot
pyplot.show()
from sklearn.datasets import make_blobs
from sklearn.naive_bayes import GaussianNB
from sklearn.metrics import brier_score_loss
from sklearn.calibration import CalibratedClassifierCV
from sklearn.model_selection import train_test_split
n_samples = 50000
n_bins = 3 # use 3 bins for calibration_curve as we have 3 clusters here
# Generate 3 blobs with 2 classes where the second blob contains
# half positive samples and half negative samples. Probability in this
# blob is therefore 0.5.
centers = [(-5, -5), (0, 0), (5, 5)]
X, y = make_blobs(n_samples=n_samples, centers=centers, shuffle=False,
random_state=42)
y[:n_samples // 2] = 0
y[n_samples // 2:] = 1
sample_weight = np.random.RandomState(42).rand(y.shape[0])
# split train, test for calibration
X_train, X_test, y_train, y_test, sw_train, sw_test = \
train_test_split(X, y, sample_weight, test_size=0.9, random_state=42)
# Gaussian Naive-Bayes with no calibration
clf = GaussianNB()
clf.fit(X_train, y_train) # GaussianNB itself does not support sample-weights
prob_pos_clf = clf.predict_proba(X_test)[:, 1]
# Gaussian Naive-Bayes with isotonic calibration
import matplotlib.colors
from sklearn.cluster import DBSCAN
from sklearn.preprocessing import StandardScaler
def expand(a, b):
d = (b - a) * 0.1
return a - d, b + d
if __name__ == "__main__":
N = 1000
centers = [[1, 2], [-1, -1], [1, -1], [-1, 1]]
data, y = ds.make_blobs(N,
n_features=2,
centers=centers,
cluster_std=[0.5, 0.25, 0.7, 0.5],
random_state=0)
data = StandardScaler().fit_transform(data)
# 数据1的参数：(epsilon, min_sample)
params = ((0.2, 5), (0.2, 10), (0.2, 15), (0.3, 5), (0.3, 10), (0.3, 15))
# 数据2
# t = np.arange(0, 2*np.pi, 0.1)
# data1 = np.vstack((np.cos(t), np.sin(t))).T
# data2 = np.vstack((2*np.cos(t), 2*np.sin(t))).T
# data3 = np.vstack((3*np.cos(t), 3*np.sin(t))).T
# data = np.vstack((data1, data2, data3))
# # # 数据2的参数：(epsilon, min_sample)
# params = ((0.5, 3), (0.5, 5), (0.5, 10), (1., 3), (1., 10), (1., 20))
from sklearn.datasets import make_blobs
from matplotlib import pyplot as plt
import numpy as np
import pandas as pd
from sklearn.model_selection import train_test_split
from sklearn.metrics import confusion_matrix
from sklearn.svm import SVC
X, y = make_blobs(n_samples=125, centers=2, cluster_std=0.60, random_state=0)
X_train, X_test, y_train, y_test = train_test_split(X,
y,
test_size=0.20,
random_state=0)
# plt.scatter(X_train[:, 0], X_train[:, 1], c=y_train, cmap="winter")
# plt.show()
model = SVC(kernel='linear')
history = model.fit(X_train, y_train)
# ax = plt.gca()
# xlim = ax.get_xlim()
# ax.scatter(X_test[:, 0], X_test[:, 1], c=y_test, cmap="winter", marker='s')
# w = model.coef_[0]
# a = -w[0] / w[1]
# xx = np.linspace(xlim[0], xlim[1])
# yy = a * xx - (model.intercept_[0] / w[1])
# plt.plot(xx, yy)
plt.show()