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('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)
assert_raises(ValueError, get_scorer('roc_auc'), clf, X_test, y_test)
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 __init__(self, estimator, k_features=1,
forward=True, floating=False,
verbose=0, scoring=None,
cv=5, skip_if_stuck=True, n_jobs=1,
pre_dispatch='2*n_jobs',
clone_estimator=True):
self.estimator = estimator
self.k_features = k_features
self.forward = forward
self.floating = floating
self.pre_dispatch = pre_dispatch
self.scoring = scoring
if isinstance(scoring, str):
self.scorer = get_scorer(scoring)
else:
self.scorer = scoring
self.skip_if_stuck = skip_if_stuck
self.cv = cv
self.n_jobs = n_jobs
self.verbose = verbose
self.named_est = {key: value for key, value in
_name_estimators([self.estimator])}
self.clone_estimator = clone_estimator
if self.clone_estimator:
self.est_ = clone(self.estimator)
else:
self.est_ = self.estimator
self.fitted = False
self.subsets_ = {}
self.interrupted_ = False
# don't mess with this unless testing
self._TESTING_INTERRUPT_MODE = False
def __init__(self, estimator, min_features=1, max_features=1,
print_progress=True, scoring='accuracy',
cv=5, n_jobs=1,
pre_dispatch='2*n_jobs',
clone_estimator=True):
self.estimator = estimator
self.min_features = min_features
self.max_features = max_features
self.pre_dispatch = pre_dispatch
self.scoring = scoring
self.scorer = get_scorer(scoring)
self.cv = cv
self.print_progress = print_progress
self.n_jobs = n_jobs
self.named_est = {key: value for key, value in
_name_estimators([self.estimator])}
self.clone_estimator = clone_estimator
if self.clone_estimator:
self.est_ = clone(self.estimator)
else:
self.est_ = self.estimator
self.fitted = False
self.interrupted_ = False
# don't mess with this unless testing
self._TESTING_INTERRUPT_MODE = False
def clf_bias_var(clf, X, y, n_replicas):
roc_auc_scorer = get_scorer("roc_auc")
# roc_auc_scorer(clf, X_test, y_test)
auc_scores = []
error_scores = []
counts = np.zeros(X.shape[0], dtype = np.float64)
sum_preds = np.zeros(X.shape[0], dtype = np.float64)
for it in xrange(n_replicas):
# generate train sets and test sets
train_indices = np.random.randint(X.shape[0], size = X.shape[0])
# get test sets
in_train = np.unique(train_indices)
mask = np.ones(X.shape[0], dtype = np.bool)
mask[in_train] = False
test_indices = np.arange(X.shape[0])[mask]
clf.fit(X[train_indices], y[train_indices])
auc_scores.append(roc_auc_scorer(clf, X[test_indices], y[test_indices]))
error_scores.append(zero_one_loss(y[test_indices], clf.predict(X[test_indices])))
preds = clf.predict(X)
for index in test_indices:
counts[index] += 1
sum_preds[index] += preds[index]
test_mask = (counts > 0) # indices of samples that have been tested
# print('counts mean: {}'.format(np.mean(counts)))
# print('counts standard derivation: {}'.format(np.std(counts)))
bias, var = bias_var(y[test_mask], sum_preds[test_mask], counts[test_mask], n_replicas)
return auc_scores, error_scores, bias, var
def _make_scorer(scoring):
"""Make scorer.
Parameters
----------
scoring : str | callable
If str, must be compatible with sklearn sklearn's get_scorer.
If callable, function with signature ``score_func(y, y_pred,
**kwargs)``.
Returns
-------
scorer : callable | None
The scorer.
"""
from sklearn.metrics import make_scorer, get_scorer
# If scoring is None (default), the predictions are internally
# generated by estimator.score(). Else, we must first get the
# predictions based on the scorer.
if scoring is None:
return None
elif isinstance(scoring, str):
return get_scorer(scoring)
else:
return make_scorer(scoring)
def __init__(self, estimator, k_features,
forward=True, floating=False,
print_progress=True, scoring='accuracy',
cv=5, skip_if_stuck=True, n_jobs=1,
pre_dispatch='2*n_jobs',
clone_estimator=True):
self.estimator = estimator
self.k_features = k_features
self.forward = forward
self.floating = floating
self.pre_dispatch = pre_dispatch
self.scoring = scoring
self.scorer = get_scorer(scoring)
self.skip_if_stuck = skip_if_stuck
self.cv = cv
self.print_progress = print_progress
self.n_jobs = n_jobs
self.named_est = {key: value for key, value in
_name_estimators([self.estimator])}
self.clone_estimator = clone_estimator
if self.clone_estimator:
self.est_ = clone(self.estimator)
else:
self.est_ = self.estimator
self.fitted = False
def __init__(self,
n_jobs=-1,
offset_scale=1.0,
n_buckets=2,
initial_params=None,
minimizer='BFGS',
basinhopping=False,
scoring='accuracy'):
from numpy import array
self.n_jobs = int(n_jobs)
self.offset_scale = float(offset_scale)
self.n_buckets = int(n_buckets)
if initial_params is None:
#self.initial_offsets_ = [-0.5] * self.n_buckets
pass
else:
self.params = array(initial_params)
#assert(len(self.initial_offsets_) == self.n_buckets)
pass
self.minimizer = minimizer
self.basinhopping = basinhopping
from sklearn.metrics import get_scorer
self.scoring = get_scorer(scoring)
pass
def test_rfecv():
generator = check_random_state(0)
iris = load_iris()
X = np.c_[iris.data, generator.normal(size=(len(iris.data), 6))]
y = list(iris.target) # regression test: list should be supported
# Test using the score function
rfecv = RFECV(estimator=SVC(kernel="linear"), step=1, cv=5)
rfecv.fit(X, y)
# non-regression test for missing worst feature:
assert_equal(len(rfecv.grid_scores_), X.shape[1])
assert_equal(len(rfecv.ranking_), X.shape[1])
X_r = rfecv.transform(X)
# All the noisy variable were filtered out
assert_array_equal(X_r, iris.data)
# same in sparse
rfecv_sparse = RFECV(estimator=SVC(kernel="linear"), step=1, cv=5)
X_sparse = sparse.csr_matrix(X)
rfecv_sparse.fit(X_sparse, y)
X_r_sparse = rfecv_sparse.transform(X_sparse)
assert_array_equal(X_r_sparse.toarray(), iris.data)
# Test using a customized loss function
scoring = make_scorer(zero_one_loss, greater_is_better=False)
rfecv = RFECV(estimator=SVC(kernel="linear"), step=1, cv=5, scoring=scoring)
ignore_warnings(rfecv.fit)(X, y)
X_r = rfecv.transform(X)
assert_array_equal(X_r, iris.data)
# Test using a scorer
scorer = get_scorer("accuracy")
rfecv = RFECV(estimator=SVC(kernel="linear"), step=1, cv=5, scoring=scorer)
rfecv.fit(X, y)
X_r = rfecv.transform(X)
assert_array_equal(X_r, iris.data)
# Test fix on grid_scores
def test_scorer(estimator, X, y):
return 1.0
rfecv = RFECV(estimator=SVC(kernel="linear"), step=1, cv=5, scoring=test_scorer)
rfecv.fit(X, y)
assert_array_equal(rfecv.grid_scores_, np.ones(len(rfecv.grid_scores_)))
# Same as the first two tests, but with step=2
rfecv = RFECV(estimator=SVC(kernel="linear"), step=2, cv=5)
rfecv.fit(X, y)
assert_equal(len(rfecv.grid_scores_), 6)
assert_equal(len(rfecv.ranking_), X.shape[1])
X_r = rfecv.transform(X)
assert_array_equal(X_r, iris.data)
rfecv_sparse = RFECV(estimator=SVC(kernel="linear"), step=2, cv=5)
X_sparse = sparse.csr_matrix(X)
rfecv_sparse.fit(X_sparse, y)
X_r_sparse = rfecv_sparse.transform(X_sparse)
assert_array_equal(X_r_sparse.toarray(), iris.data)
def test_classification_scores():
# Test classification scorers.
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 = LinearSVC(random_state=0)
clf.fit(X_train, y_train)
for prefix, metric in [('f1', f1_score), ('precision', precision_score),
('recall', recall_score),
('jaccard', jaccard_score)]:
score1 = get_scorer('%s_weighted' % prefix)(clf, X_test, y_test)
score2 = metric(y_test, clf.predict(X_test), pos_label=None,
average='weighted')
assert_almost_equal(score1, score2)
score1 = get_scorer('%s_macro' % prefix)(clf, X_test, y_test)
score2 = metric(y_test, clf.predict(X_test), pos_label=None,
average='macro')
assert_almost_equal(score1, score2)
score1 = get_scorer('%s_micro' % prefix)(clf, X_test, y_test)
score2 = metric(y_test, clf.predict(X_test), pos_label=None,
average='micro')
assert_almost_equal(score1, score2)
score1 = get_scorer('%s' % prefix)(clf, X_test, y_test)
score2 = metric(y_test, clf.predict(X_test), pos_label=1)
assert_almost_equal(score1, score2)
# test fbeta score that takes an argument
scorer = make_scorer(fbeta_score, beta=2)
score1 = scorer(clf, X_test, y_test)
score2 = fbeta_score(y_test, clf.predict(X_test), beta=2)
assert_almost_equal(score1, score2)
# test that custom scorer can be pickled
unpickled_scorer = pickle.loads(pickle.dumps(scorer))
score3 = unpickled_scorer(clf, X_test, y_test)
assert_almost_equal(score1, score3)
# smoke test the repr:
repr(fbeta_score)
def test_supervised_cluster_scorers():
# Test clustering scorers against gold standard labeling.
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)
km = KMeans(n_clusters=3)
km.fit(X_train)
for name in CLUSTER_SCORERS:
score1 = get_scorer(name)(km, X_test, y_test)
score2 = getattr(cluster_module, name)(y_test, km.predict(X_test))
assert_almost_equal(score1, score2)
def test_regression_scorers():
# Test regression scorers.
diabetes = load_diabetes()
X, y = diabetes.data, diabetes.target
X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=0)
clf = Ridge()
clf.fit(X_train, y_train)
score1 = get_scorer('r2')(clf, X_test, y_test)
score2 = r2_score(y_test, clf.predict(X_test))
assert_almost_equal(score1, score2)
def test_unsupervised_scorers():
# Test clustering scorers against gold standard labeling.
# We don't have any real unsupervised Scorers yet.
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)
km = KMeans(n_clusters=3)
km.fit(X_train)
score1 = get_scorer('adjusted_rand_score')(km, X_test, y_test)
score2 = adjusted_rand_score(y_test, km.predict(X_test))
assert_almost_equal(score1, score2)
def test_unsupervised_scorers():
# Test clustering scorers against gold standard labeling.
# We don't have any real unsupervised Scorers yet.
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)
km = KMeans(n_clusters=3)
km.fit(X_train)
score1 = get_scorer('adjusted_rand_score')(km, X_test, y_test)
score2 = adjusted_rand_score(y_test, km.predict(X_test))
assert_almost_equal(score1, score2)
def test_thresholded_scorers_multilabel_indicator_data():
"""Test that the scorer work with multilabel-indicator format
for multilabel and multi-output multi-class classifier
"""
X, y = make_multilabel_classification(return_indicator=True,
allow_unlabeled=False,
random_state=0)
X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=0)
# Multi-output multi-class predict_proba
clf = DecisionTreeClassifier()
clf.fit(X_train, y_train)
y_proba = clf.predict_proba(X_test)
score1 = get_scorer('roc_auc')(clf, X_test, y_test)
score2 = roc_auc_score(y_test, np.vstack(p[:, -1] for p in y_proba).T)
assert_almost_equal(score1, score2)
# Multi-output multi-class decision_function
# TODO Is there any yet?
clf = DecisionTreeClassifier()
clf.fit(X_train, y_train)
clf._predict_proba = clf.predict_proba
clf.predict_proba = None
clf.decision_function = lambda X: [p[:, 1] for p in clf._predict_proba(X)]
y_proba = clf.decision_function(X_test)
score1 = get_scorer('roc_auc')(clf, X_test, y_test)
score2 = roc_auc_score(y_test, np.vstack(p for p in y_proba).T)
assert_almost_equal(score1, score2)
# Multilabel predict_proba
clf = OneVsRestClassifier(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))
assert_almost_equal(score1, score2)
# Multilabel decision function
clf = OneVsRestClassifier(LinearSVC(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))
assert_almost_equal(score1, score2)
def test_thresholded_scorers_multilabel_indicator_data():
"""Test that the scorer work with multilabel-indicator format
for multilabel and multi-output multi-class classifier
"""
X, y = make_multilabel_classification(return_indicator=True,
allow_unlabeled=False,
random_state=0)
X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=0)
# Multi-output multi-class predict_proba
clf = DecisionTreeClassifier()
clf.fit(X_train, y_train)
y_proba = clf.predict_proba(X_test)
score1 = get_scorer('roc_auc')(clf, X_test, y_test)
score2 = roc_auc_score(y_test, np.vstack(p[:, -1] for p in y_proba).T)
assert_almost_equal(score1, score2)
# Multi-output multi-class decision_function
# TODO Is there any yet?
clf = DecisionTreeClassifier()
clf.fit(X_train, y_train)
clf._predict_proba = clf.predict_proba
clf.predict_proba = None
clf.decision_function = lambda X: [p[:, 1] for p in clf._predict_proba(X)]
y_proba = clf.decision_function(X_test)
score1 = get_scorer('roc_auc')(clf, X_test, y_test)
score2 = roc_auc_score(y_test, np.vstack(p for p in y_proba).T)
assert_almost_equal(score1, score2)
# Multilabel predict_proba
clf = OneVsRestClassifier(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))
assert_almost_equal(score1, score2)
# Multilabel decision function
clf = OneVsRestClassifier(LinearSVC(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))
assert_almost_equal(score1, score2)
def test_regression_scorers():
# Test regression scorers.
diabetes = load_diabetes()
X, y = diabetes.data, diabetes.target
X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=0)
clf = Ridge()
clf.fit(X_train, y_train)
score1 = get_scorer('r2')(clf, X_test, y_test)
score2 = r2_score(y_test, clf.predict(X_test))
assert_almost_equal(score1, score2)
def test_supervised_cluster_scorers():
# Test clustering scorers against gold standard labeling.
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)
km = KMeans(n_clusters=3)
km.fit(X_train)
for name in CLUSTER_SCORERS:
score1 = get_scorer(name)(km, X_test, y_test)
score2 = getattr(cluster_module, name)(y_test, km.predict(X_test))
assert_almost_equal(score1, score2)
def test_classification_scores():
"""Test classification scorers."""
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 = LinearSVC(random_state=0)
clf.fit(X_train, y_train)
for prefix, metric in [('f1', f1_score), ('precision', precision_score),
('recall', recall_score)]:
score1 = get_scorer('%s_weighted' % prefix)(clf, X_test, y_test)
score2 = metric(y_test, clf.predict(X_test), pos_label=None,
average='weighted')
assert_almost_equal(score1, score2)
score1 = get_scorer('%s_macro' % prefix)(clf, X_test, y_test)
score2 = metric(y_test, clf.predict(X_test), pos_label=None,
average='macro')
assert_almost_equal(score1, score2)
score1 = get_scorer('%s_micro' % prefix)(clf, X_test, y_test)
score2 = metric(y_test, clf.predict(X_test), pos_label=None,
average='micro')
assert_almost_equal(score1, score2)
score1 = get_scorer('%s' % prefix)(clf, X_test, y_test)
score2 = metric(y_test, clf.predict(X_test), pos_label=1)
assert_almost_equal(score1, score2)
# test fbeta score that takes an argument
scorer = make_scorer(fbeta_score, beta=2)
score1 = scorer(clf, X_test, y_test)
score2 = fbeta_score(y_test, clf.predict(X_test), beta=2,
average='weighted')
assert_almost_equal(score1, score2)
# test that custom scorer can be pickled
unpickled_scorer = pickle.loads(pickle.dumps(scorer))
score3 = unpickled_scorer(clf, X_test, y_test)
assert_almost_equal(score1, score3)
# smoke test the repr:
repr(fbeta_score)
def evaluate(self, dataset, pipelines):
if not self.is_valid(dataset):
raise AssertionError("Dataset is not appropriate for evaluation")
for subject in dataset.subject_list:
# check if we already have result for this subject/pipeline
# we might need a better granularity, if we query the DB
run_pipes = self.results.not_yet_computed(pipelines, dataset, subject)
if len(run_pipes) == 0:
continue
# get the data
X, y, metadata = self.paradigm.get_data(
dataset, [subject], self.return_epochs
)
le = LabelEncoder()
y = y if self.mne_labels else le.fit_transform(y)
groups = metadata.session.values
scorer = get_scorer(self.paradigm.scoring)
for name, clf in run_pipes.items():
# we want to store a results per session
cv = LeaveOneGroupOut()
for train, test in cv.split(X, y, groups):
t_start = time()
if isinstance(X, BaseEpochs):
cvclf = clone(clf)
cvclf.fit(X[train], y[train])
score = scorer(cvclf, X[test], y[test])
else:
result = _fit_and_score(
clone(clf),
X,
y,
scorer,
train,
test,
verbose=False,
parameters=None,
fit_params=None,
error_score=self.error_score,
)
score = result["test_scores"]
duration = time() - t_start
nchan = X.info["nchan"] if isinstance(X, BaseEpochs) else X.shape[1]
res = {
"time": duration,
"dataset": dataset,
"subject": subject,
"session": groups[test][0],
"score": score,
"n_samples": len(train),
"n_channels": nchan,
"pipeline": name,
}
yield res
def test_classification_scorer_sample_weight():
# Test that classification scorers support sample_weight or raise sensible
# errors
# Unlike the metrics invariance test, in the scorer case it's harder
# to ensure that, on the classifier output, weighted and unweighted
# scores really should be unequal.
X, y = make_classification(random_state=0)
_, y_ml = make_multilabel_classification(n_samples=X.shape[0], random_state=0)
split = train_test_split(X, y, y_ml, random_state=0)
X_train, X_test, y_train, y_test, y_ml_train, y_ml_test = split
sample_weight = np.ones_like(y_test)
sample_weight[:10] = 0
# get sensible estimators for each metric
estimator = _make_estimators(X_train, y_train, y_ml_train)
for name in get_scorer_names():
scorer = get_scorer(name)
if name in REGRESSION_SCORERS:
# skip the regression scores
continue
if name == "top_k_accuracy":
# in the binary case k > 1 will always lead to a perfect score
scorer._kwargs = {"k": 1}
if name in MULTILABEL_ONLY_SCORERS:
target = y_ml_test
else:
target = y_test
try:
weighted = scorer(
estimator[name], X_test, target, sample_weight=sample_weight
)
ignored = scorer(estimator[name], X_test[10:], target[10:])
unweighted = scorer(estimator[name], X_test, target)
assert weighted != unweighted, (
f"scorer {name} behaves identically when called with "
f"sample weights: {weighted} vs {unweighted}"
)
assert_almost_equal(
weighted,
ignored,
err_msg=(
f"scorer {name} behaves differently "
"when ignoring samples and setting "
f"sample_weight to 0: {weighted} vs {ignored}"
),
)
except TypeError as e:
assert "sample_weight" in str(e), (
f"scorer {name} raises unhelpful exception when called "
f"with sample weights: {str(e)}"
)
def get_metric(metric, gib=True, needs_proba=False, needs_threshold=False):
"""Get the right metric depending on the input type.
Parameters
----------
metric: str or callable
Metric as a string, function or scorer.
gib: bool, optional (default=True)
whether the metric is a score function or a loss function,
i.e. if True, a higher score is better and if False, lower is
better. Will be ignored if the metric is a string or a scorer.
needs_proba: bool, optional (default=False)
Whether the metric function requires probability estimates of
a classifier. Is ignored if the metric is a string or a scorer.
needs_threshold: bool, optional (default=False)
Whether the metric function takes a continuous decision
certainty. Is ignored if the metric is a string or a scorer.
Returns
-------
scorer: callable
Scorer object.
"""
def get_scorer_name(scorer):
"""Return the name of the provided scorer."""
for key, value in SCORERS.items():
if scorer.__dict__ == value.__dict__:
return key
if isinstance(metric, str):
if metric.lower() in METRIC_ACRONYMS:
metric = METRIC_ACRONYMS[metric.lower()]
elif metric not in SCORERS:
raise ValueError("Unknown value for the metric parameter, got "
f"{metric}. Try one of: {', '.join(SCORERS)}.")
metric = get_scorer(metric)
metric.name = get_scorer_name(metric)
elif hasattr(metric, "_score_func"): # Provided metric is scoring
metric.name = get_scorer_name(metric)
else: # Metric is a function with signature metric(y, y_pred)
metric = make_scorer(
score_func=metric,
greater_is_better=gib,
needs_proba=needs_proba,
needs_threshold=needs_threshold,
)
metric.name = metric._score_func.__name__
return metric
def test_multiclass_roc_no_proba_scorer_errors(scorer_name):
# Perceptron has no predict_proba
scorer = get_scorer(scorer_name)
X, y = make_classification(n_classes=3,
n_informative=3,
n_samples=20,
random_state=0)
lr = Perceptron().fit(X, y)
msg = "'Perceptron' object has no attribute 'predict_proba'"
with pytest.raises(AttributeError, match=msg):
scorer(lr, X, y)
def create_feature_reselection_experiment(maker=None, **user_kwargs):
exp_kwargs = \
dict(scorer=get_scorer('neg_median_absolute_error'),
drift_detection=False,
feature_reselection=True,
feature_reselection_estimator_size=10,
feature_reselection_strategy='quantile',
feature_reselection_threshold=0.1,
feature_reselection_quantile=0.5,
feature_reselection_number=None)
return _create_experiment(exp_kwargs, maker=maker, need_test=True, user_kwargs=user_kwargs)
def inhome_permutation_importance(estimator,
feature_groups, X, y,
scoring='f1_macro',
n_repeats=10,
random_state=23):
result = {'score_difference': np.zeros((len(feature_groups), n_repeats)),
'feature_group_names': np.zeros(len(feature_groups), dtype='O')}
X_train_original, X_test, y_train, y_test = train_test_split(X, y,
test_size=.2,
stratify=y,
random_state=random_state)
feature_list_indices = {col: idx for idx, col in enumerate(X_train_original.columns)}
scorer = get_scorer(scoring)
for i, (feature_group_name, feature_list) in enumerate(feature_groups.items()):
# print(feature_group_name)
score_difference = []
for j in range(n_repeats):
np.random.seed(random_state+j)
X_train_permuted = X_train_original.copy()
# permute feature values in selected columns
for col in feature_list:
# print(col)
col_idx = feature_list_indices[col]
permuted_indices = np.random.permutation(X_train_original.shape[0])
# col = pd.DataFrame(np.random.uniform(low=-1.0, high=1.0, size=X_train_original.shape[0])) # fill with random values from U(-1, 1)
col = X_train_permuted.iloc[permuted_indices, col_idx] # permute present values
col.index = X_train_permuted.index
X_train_permuted.iloc[:, col_idx] = col
# X_train_permuted = X_train_permuted.drop(columns=feature_list)
# train model using OLD data matrix X_train_original and evaluate
est_original = estimator.fit(X_train_original, y_train)
score_original = scorer(est_original, X_test, y_test)
# train model using NEW data matrix X_train_permuted and evaluate
est_permuted = estimator.fit(X_train_permuted, y_train)
score_permuted = scorer(est_permuted, X_test, y_test)
result['score_difference'][i, j] = score_original - score_permuted
result['feature_group_names'][i] = feature_group_name
return result
def pack_score(y_test_true_all, y_test_predict_all, scoring):
if scoring == 'neg_root_mean_squared_error':
return np.sqrt(np.mean((y_test_true_all - y_test_predict_all)**2))
scorer = get_scorer(scoring)
scorer_func = scorer._score_func
score = scorer_func(y_test_true_all, y_test_predict_all)
return score
def test_multiclass_roc_proba_scorer(scorer_name, metric):
scorer = get_scorer(scorer_name)
X, y = make_classification(n_classes=3,
n_informative=3,
n_samples=20,
random_state=0)
lr = LogisticRegression(multi_class="multinomial").fit(X, y)
y_proba = lr.predict_proba(X)
expected_score = metric(y, y_proba)
assert scorer(lr, X, y) == pytest.approx(expected_score)
def test_classification_binary_scores(scorer_name, metric):
# check consistency between score and scorer for scores supporting
# binary classification.
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 = LinearSVC(random_state=0)
clf.fit(X_train, y_train)
score = get_scorer(scorer_name)(clf, X_test, y_test)
expected_score = metric(y_test, clf.predict(X_test))
assert_almost_equal(score, expected_score)
def run_grid_search(estimator, param_grid, metric, X, y, X_test, y_test, seed,
profile):
_train_test_iter = StratifiedKFold(y,
n_folds=5,
shuffle=True,
random_state=seed)
inner_cv_func = lambda zx, zy: StratifiedShuffleSplit(
zy, n_iter=10, test_size=0.2, random_state=seed)
if metric == 'avgprec':
scoring_func = get_scorer("average_precision")
else:
scoring_func = get_scorer("roc_auc")
_grid_search = NestedGridSearchCV(estimator,
param_grid,
scoring_func,
cv=_train_test_iter,
inner_cv=inner_cv_func,
profile=profile)
_grid_search.fit(X, y, X_test=X_test, y_test=y_test)
return _grid_search
def __init__(self, estimator, k_features=1,
forward=True, floating=False,
verbose=0, scoring=None,
cv=5, n_jobs=1,
pre_dispatch='2*n_jobs',
clone_estimator=True):
self.estimator = estimator
self.k_features = k_features
self.forward = forward
self.floating = floating
self.pre_dispatch = pre_dispatch
# Want to raise meaningful error message if a
# cross-validation generator is inputted
if isinstance(cv, types.GeneratorType):
err_msg = ('Input cv is a generator object, which is not '
'supported. Instead please input an iterable yielding '
'train, test splits. This can usually be done by '
'passing a cross-validation generator to the '
'built-in list function. I.e. cv=list(<cv-generator>)')
raise TypeError(err_msg)
self.cv = cv
self.n_jobs = n_jobs
self.verbose = verbose
self.named_est = {key: value for key, value in
_name_estimators([self.estimator])}
self.clone_estimator = clone_estimator
if self.clone_estimator:
self.est_ = clone(self.estimator)
else:
self.est_ = self.estimator
self.scoring = scoring
if scoring is None:
if self.est_._estimator_type == 'classifier':
scoring = 'accuracy'
elif self.est_._estimator_type == 'regressor':
scoring = 'r2'
else:
raise AttributeError('Estimator must '
'be a Classifier or Regressor.')
if isinstance(scoring, str):
self.scorer = get_scorer(scoring)
else:
self.scorer = scoring
self.fitted = False
self.subsets_ = {}
self.interrupted_ = False
# don't mess with this unless testing
self._TESTING_INTERRUPT_MODE = False
def __init__(self,
estimator,
k_features='best',
forward=True,
floating=False,
print_progress=False,
verbose=1,
scoring=None,
cv=5,
skip_if_stuck=True,
n_jobs=1,
pre_dispatch='2*n_jobs',
clone_estimator=True):
if print_progress:
warnings.warn(
"The print_progress parameter "
"has been deprecated in "
"0.4.3 and will be removed in 0.5.0. "
"Please use the verbose parameter instead.",
DeprecationWarning)
if verbose == 0:
verbose = 1
self.estimator = estimator
self.k_features = k_features
self.forward = forward
self.floating = floating
self.pre_dispatch = pre_dispatch
self.scoring = scoring
if isinstance(scoring, str):
self.scorer = get_scorer(scoring)
else:
self.scorer = scoring
self.skip_if_stuck = skip_if_stuck
self.cv = cv
self.n_jobs = n_jobs
self.verbose = verbose
self.named_est = {
key: value
for key, value in _name_estimators([self.estimator])
}
self.clone_estimator = clone_estimator
if self.clone_estimator:
self.est_ = clone(self.estimator)
else:
self.est_ = self.estimator
self.fitted = False
self.subsets_ = {}
self.interrupted_ = False
# don't mess with this unless testing
self._TESTING_INTERRUPT_MODE = False
def test_get_feature_shap_values_per_fold(X, y):
clf = DecisionTreeClassifier(max_depth=1)
shap_values, train_score, test_score = ShapRFECV._get_feature_shap_values_per_fold(
X,
y,
clf,
train_index=[2, 3, 4, 5, 6, 7],
val_index=[0, 1],
scorer=get_scorer('roc_auc'))
assert test_score == 1
assert train_score > 0.9
assert shap_values.shape == (2, 3)
def score_explicit(self, clf, X_train, y_train, X_test, y_test):
scorer = get_scorer(self.paradigm.scoring)
t_start = time()
try:
model = clf.fit(X_train, y_train)
score = _score(model, X_test, y_test, scorer)
except ValueError as e:
if self.error_score == "raise":
raise e
score = self.error_score
duration = time() - t_start
return score, duration
def test_get_feature_shap_values_per_fold(X, y):
"""
Test with ShapRFECV with features per fold.
"""
clf = DecisionTreeClassifier(max_depth=1)
shap_elimination = ShapRFECV(clf)
shap_values, train_score, test_score = shap_elimination._get_feature_shap_values_per_fold(
X, y, clf, train_index=[2, 3, 4, 5, 6, 7], val_index=[0, 1], scorer=get_scorer("roc_auc")
)
assert test_score == 1
assert train_score > 0.9
assert shap_values.shape == (2, 3)
def _get_scorer_from_string(self, scoring):
if scoring == 'my_scorer':
if not self.kernel:
myfunc = importlib.import_module(
'modules.myfuncs.%s' % self.configs['fit'].get('myfunc'))
method_name = 'get_my_scorer'
if not self.kernel:
method_name = 'myfunc.%s' % method_name
scorer = eval(method_name)()
else:
scorer = get_scorer(scoring)
return scorer
def _test_ridge_loo(filter_):
# test that can work with both dense or sparse matrices
n_samples = X_diabetes.shape[0]
ret = []
fit_intercept = filter_ == DENSE_FILTER
ridge_gcv = _RidgeGCV(fit_intercept=fit_intercept)
# check best alpha
ridge_gcv.fit(filter_(X_diabetes), y_diabetes)
alpha_ = ridge_gcv.alpha_
ret.append(alpha_)
# check that we get same best alpha with custom loss_func
f = ignore_warnings
scoring = make_scorer(mean_squared_error, greater_is_better=False)
ridge_gcv2 = RidgeCV(fit_intercept=False, scoring=scoring)
f(ridge_gcv2.fit)(filter_(X_diabetes), y_diabetes)
assert ridge_gcv2.alpha_ == pytest.approx(alpha_)
# check that we get same best alpha with custom score_func
func = lambda x, y: -mean_squared_error(x, y)
scoring = make_scorer(func)
ridge_gcv3 = RidgeCV(fit_intercept=False, scoring=scoring)
f(ridge_gcv3.fit)(filter_(X_diabetes), y_diabetes)
assert ridge_gcv3.alpha_ == pytest.approx(alpha_)
# check that we get same best alpha with a scorer
scorer = get_scorer('neg_mean_squared_error')
ridge_gcv4 = RidgeCV(fit_intercept=False, scoring=scorer)
ridge_gcv4.fit(filter_(X_diabetes), y_diabetes)
assert ridge_gcv4.alpha_ == pytest.approx(alpha_)
# check that we get same best alpha with sample weights
if filter_ == DENSE_FILTER:
ridge_gcv.fit(filter_(X_diabetes), y_diabetes,
sample_weight=np.ones(n_samples))
assert ridge_gcv.alpha_ == pytest.approx(alpha_)
# simulate several responses
Y = np.vstack((y_diabetes, y_diabetes)).T
ridge_gcv.fit(filter_(X_diabetes), Y)
Y_pred = ridge_gcv.predict(filter_(X_diabetes))
ridge_gcv.fit(filter_(X_diabetes), y_diabetes)
y_pred = ridge_gcv.predict(filter_(X_diabetes))
assert_allclose(np.vstack((y_pred, y_pred)).T,
Y_pred, rtol=1e-5)
return ret
def y_randomization_test(yx, model_dicts, crys_prop, scoring='f1_macro', n_repeats=25, savefig=False):
fig, ax = plt.subplots(nrows=len(model_dicts[crys_prop]), ncols=1,
figsize=(6.5, len(model_dicts[crys_prop])*3),
sharex=True)
scorer = get_scorer(scoring)
for i, (model_name, model) in enumerate(model_dicts[crys_prop].items()):
X = yx.iloc[:, 1:].copy()
y = yx.iloc[:, 0].astype(int).copy()
X_train, X_test, y_train, y_test = train_test_split(X, y, stratify=y, test_size=0.2, random_state=23)
m = copy(model)
y_initial_score = scorer(m.fit(X_train, y_train), X_test, y_test)
y_randomized_scores = []
for jj in range(n_repeats):
X_train, X_test, y_train, y_test = train_test_split(X, y, stratify=y, test_size=0.2, random_state=23+jj)
m = copy(model)
np.random.seed(92)
np.random.shuffle(y_train)
score_y_randomized = scorer(m.fit(X_train, y_train), X_test, y_test)
y_randomized_scores.append(score_y_randomized)
#y_initial_score = train_test_estimate(X, y, copy(model), scorer)
#y_randomized_scores = []
#for _ in range(n_repeats):
# np.random.seed(92)
# np.random.shuffle(y)
# score_y_randomized = train_test_estimate(X, y, copy(model), scorer)
# y_randomized_scores.append(score_y_randomized)
ax[i].hist(y_randomized_scores, bins=15, color='blue', label='y-randomized')
ax[i].axvline(y_initial_score, color='red', lw=4, label='y-initial')
ax[i].set_title('%s model' % (model_name))
ax[i].legend(loc='upper left')
ax[i].set_xlim(0.0, 1.0)
ax[len(model_dicts[crys_prop])-1].set_xlabel(scoring)
fig.suptitle(f'$\Delta${crys_prop} prediction', y=.995, fontsize=20)
fig.tight_layout(rect=[0, 0, 1, 0.975])
if savefig:
fig.savefig(f'y_randomization_test_{crys_prop}.png', dpi=dpi)
plt.show()
def test_rfecv():
generator = check_random_state(0)
iris = load_iris()
X = np.c_[iris.data, generator.normal(size=(len(iris.data), 6))]
y = list(iris.target) # regression test: list should be supported
# Test using the score function
rfecv = RFECV(estimator=SVC(kernel="linear"), step=1, cv=5)
rfecv.fit(X, y)
# non-regression test for missing worst feature:
assert_equal(len(rfecv.grid_scores_), X.shape[1])
assert_equal(len(rfecv.ranking_), X.shape[1])
X_r = rfecv.transform(X)
# All the noisy variable were filtered out
assert_array_equal(X_r, iris.data)
# same in sparse
rfecv_sparse = RFECV(estimator=SVC(kernel="linear"), step=1, cv=5)
X_sparse = sparse.csr_matrix(X)
rfecv_sparse.fit(X_sparse, y)
X_r_sparse = rfecv_sparse.transform(X_sparse)
assert_array_equal(X_r_sparse.toarray(), iris.data)
# Test using a customized loss function
scoring = make_scorer(zero_one_loss, greater_is_better=False)
rfecv = RFECV(estimator=SVC(kernel="linear"),
step=1,
cv=5,
scoring=scoring)
ignore_warnings(rfecv.fit)(X, y)
X_r = rfecv.transform(X)
assert_array_equal(X_r, iris.data)
# Test using a scorer
scorer = get_scorer('accuracy')
rfecv = RFECV(estimator=SVC(kernel="linear"), step=1, cv=5, scoring=scorer)
rfecv.fit(X, y)
X_r = rfecv.transform(X)
assert_array_equal(X_r, iris.data)
# Test fix on grid_scores
def test_scorer(estimator, X, y):
return 1.0
rfecv = RFECV(estimator=SVC(kernel="linear"),
step=1,
cv=5,
scoring=test_scorer)
rfecv.fit(X, y)
assert_array_equal(rfecv.grid_scores_, np.ones(len(rfecv.grid_scores_)))
def _test_ridge_loo(filter_):
# test that can work with both dense or sparse matrices
n_samples = X_diabetes.shape[0]
ret = []
fit_intercept = filter_ == DENSE_FILTER
ridge_gcv = _RidgeGCV(fit_intercept=fit_intercept)
# check best alpha
ridge_gcv.fit(filter_(X_diabetes), y_diabetes)
alpha_ = ridge_gcv.alpha_
ret.append(alpha_)
# check that we get same best alpha with custom loss_func
f = ignore_warnings
scoring = make_scorer(mean_squared_error, greater_is_better=False)
ridge_gcv2 = RidgeCV(fit_intercept=False, scoring=scoring)
f(ridge_gcv2.fit)(filter_(X_diabetes), y_diabetes)
assert ridge_gcv2.alpha_ == pytest.approx(alpha_)
# check that we get same best alpha with custom score_func
func = lambda x, y: -mean_squared_error(x, y)
scoring = make_scorer(func)
ridge_gcv3 = RidgeCV(fit_intercept=False, scoring=scoring)
f(ridge_gcv3.fit)(filter_(X_diabetes), y_diabetes)
assert ridge_gcv3.alpha_ == pytest.approx(alpha_)
# check that we get same best alpha with a scorer
scorer = get_scorer('neg_mean_squared_error')
ridge_gcv4 = RidgeCV(fit_intercept=False, scoring=scorer)
ridge_gcv4.fit(filter_(X_diabetes), y_diabetes)
assert ridge_gcv4.alpha_ == pytest.approx(alpha_)
# check that we get same best alpha with sample weights
if filter_ == DENSE_FILTER:
ridge_gcv.fit(filter_(X_diabetes),
y_diabetes,
sample_weight=np.ones(n_samples))
assert ridge_gcv.alpha_ == pytest.approx(alpha_)
# simulate several responses
Y = np.vstack((y_diabetes, y_diabetes)).T
ridge_gcv.fit(filter_(X_diabetes), Y)
Y_pred = ridge_gcv.predict(filter_(X_diabetes))
ridge_gcv.fit(filter_(X_diabetes), y_diabetes)
y_pred = ridge_gcv.predict(filter_(X_diabetes))
assert_allclose(np.vstack((y_pred, y_pred)).T, Y_pred, rtol=1e-5)
return ret
def custom_paired_ttest_cv(estimator1, estimator2, X, y,
cv=10,
scoring=None,
shuffle=False,
random_seed=None):
kf = StratifiedKFold(random_state=random_seed, n_splits=cv, shuffle=True)
if scoring is None:
if estimator1._estimator_type == 'classifier':
scoring = 'accuracy'
elif estimator1._estimator_type == 'regressor':
scoring = 'r2'
else:
raise AttributeError('Estimator must '
'be a Classifier or Regressor.')
if isinstance(scoring, str):
scorer = get_scorer(scoring)
else:
scorer = scoring
score_diff = []
# this is probably wrong :(
for train_index, test_index in kf.split(X, y):
##### THIS IS WHERE IT BECOMES "CUSTOM"
if isinstance(X, pd.DataFrame):
X_train = X.iloc[train_index]
X_test = X.iloc[test_index]
else:
X_train = [X[i] for i in train_index]
X_test = [X[i] for i in test_index]
#####
y_train, y_test = y[train_index], y[test_index]
estimator1.fit(X_train, y_train)
estimator2.fit(X_train, y_train)
est1_score = scorer(estimator1, X_test, y_test)
est2_score = scorer(estimator2, X_test, y_test)
score_diff.append(est1_score - est2_score)
avg_diff = np.mean(score_diff)
numerator = avg_diff * np.sqrt(cv)
denominator = np.sqrt(sum([(diff - avg_diff)**2 for diff in score_diff])
/ (cv - 1))
t_stat = numerator / denominator
pvalue = stats.t.sf(np.abs(t_stat), cv - 1)*2.
return float(t_stat), float(pvalue)
def fit_and_dump(_x, _y, args):
data = _x.copy()
_x = categorical_to_numeric(_x)
_y = _y[args.event].cat.codes.values
model = create_estimator(data, _y, args.seed)
if args.metric == 'avgprec':
scoring_func = get_scorer("average_precision")
else:
scoring_func = get_scorer("roc_auc")
model.set_params(scorer=scoring_func)
print("Number of base estimators: %d" % len(model.base_estimators))
print("Purging MongoDB cv_scores database")
client = MongoClient(mongodb_host)
db = client.ensemble_selection_classification
db.cv_scores.remove({})
print("Fitting %r" % model)
_create_directories(args.models_dir, model.base_estimators)
return model.fit(_x.values, _y)
def train(self, X, y, X_test):
# searcher = MCTSSearcher(self.search_space_fn, use_meta_learner=self.use_meta_learner, max_node_space=10,
# candidates_size=10,
# optimize_direction=OptimizeDirection.Maximize)
searcher = EvolutionSearcher(
self.search_space_fn,
optimize_direction=self.optimize_direction,
population_size=30,
sample_size=10,
regularized=True,
candidates_size=10,
use_meta_learner=self.use_meta_learner)
# searcher = RandomSearcher(lambda: search_space_general(early_stopping_rounds=20, verbose=0),
# optimize_direction=OptimizeDirection.Maximize)
es = EarlyStoppingCallback(self.earlystop_rounds,
self.optimize_direction,
time_limit=self.time_limit,
expected_reward=self.expected_reward)
hk = HyperGBM(searcher,
reward_metric=self.reward_metric,
cache_dir=f'hypergbm_cache',
clear_cache=True,
callbacks=[es, SummaryCallback()])
log_callback = ConsoleCallback()
self.experiment = CompeteExperiment(
hk,
X,
y,
X_test=X_test,
eval_size=self.eval_size,
train_test_split_strategy=self.train_test_split_strategy,
cv=self.cv,
num_folds=self.num_folds,
callbacks=[],
scorer=get_scorer(self.scorer),
drop_feature_with_collinearity=self.drop_feature_with_collinearity,
drift_detection=True,
n_est_feature_importance=5,
importance_threshold=1e-5,
two_stage_importance_selection=self.two_stage_importance_selection,
ensemble_size=self.ensemble_size,
pseudo_labeling=self.pseudo_labeling,
pseudo_labeling_proba_threshold=self.
pseudo_labeling_proba_threshold,
pseudo_labeling_resplit=self.pseudo_labeling_resplit,
retrain_on_wholedata=self.retrain_on_wholedata,
)
self.estimator = self.experiment.run(use_cache=self.use_cache,
max_trials=self.max_trials)
def score(self, X, y):
"""Score each estimator/data slice couple.
Parameters
----------
X : array, shape (n_samples, nd_features, n_estimators)
The input samples. For each data slice, the corresponding estimator
scores the prediction: e.g. [estimators[ii].score(X[..., ii], y)
for ii in range(n_estimators)]
The feature dimension can be multidimensional e.g.
X.shape = (n_samples, n_features_1, n_features_2, n_estimators)
y : array, shape (n_samples,) | (n_samples, n_targets)
The target values.
Returns
-------
score : array, shape (n_samples, n_estimators)
Score for each estimator / data slice couple.
"""
from sklearn.metrics import make_scorer, get_scorer
self._check_Xy(X)
if X.shape[-1] != len(self.estimators_):
raise ValueError('The number of estimators does not match '
'X.shape[-1]')
# If scoring is None (default), the predictions are internally
# generated by estimator.score(). Else, we must first get the
# predictions based on the scorer.
if not isinstance(self.scoring, str):
scoring_ = (make_scorer(self.scoring)
if self.scoring is not None else self.scoring)
elif self.scoring is not None:
scoring_ = get_scorer(self.scoring)
# For predictions/transforms the parallelization is across the data and
# not across the estimators to avoid memory load.
parallel, p_func, n_jobs = parallel_func(_sl_score, self.n_jobs)
n_jobs = min(n_jobs, X.shape[-1])
X_splits = np.array_split(X, n_jobs, axis=-1)
est_splits = np.array_split(self.estimators_, n_jobs)
score = parallel(
p_func(est, scoring_, X, y)
for (est, x) in zip(est_splits, X_splits))
if n_jobs > 1:
score = np.concatenate(score, axis=0)
else:
score = score[0]
return score
def __init__(self, estimator, k_features=1,
forward=True, floating=False,
verbose=0, scoring=None,
cv=5, n_jobs=1,
pre_dispatch='2*n_jobs',
clone_estimator=True):
self.estimator = estimator
self.k_features = k_features
self.forward = forward
self.floating = floating
self.pre_dispatch = pre_dispatch
# Want to raise meaningful error message if a
# cross-validation generator is inputted
if isinstance(cv, types.GeneratorType):
err_msg = ('Input cv is a generator object, which is not '
'supported. Instead please input an iterable yielding '
'train, test splits. This can usually be done by '
'passing a cross-validation generator to the '
'built-in list function. I.e. cv=list(<cv-generator>)')
raise TypeError(err_msg)
self.cv = cv
self.n_jobs = n_jobs
self.verbose = verbose
self.clone_estimator = clone_estimator
if self.clone_estimator:
self.est_ = clone(self.estimator)
else:
self.est_ = self.estimator
self.scoring = scoring
if scoring is None:
if self.est_._estimator_type == 'classifier':
scoring = 'accuracy'
elif self.est_._estimator_type == 'regressor':
scoring = 'r2'
else:
raise AttributeError('Estimator must '
'be a Classifier or Regressor.')
if isinstance(scoring, str):
self.scorer = get_scorer(scoring)
else:
self.scorer = scoring
self.fitted = False
self.subsets_ = {}
self.interrupted_ = False
# don't mess with this unless testing
self._TESTING_INTERRUPT_MODE = False
def score(self, X, y):
"""Score each estimator/data slice couple.
Parameters
----------
X : array, shape (n_samples, nd_features, n_estimators)
The input samples. For each data slice, the corresponding estimator
scores the prediction: e.g. [estimators[ii].score(X[..., ii], y)
for ii in range(n_estimators)]
The feature dimension can be multidimensional e.g.
X.shape = (n_samples, n_features_1, n_features_2, n_estimators)
y : array, shape (n_samples,) | (n_samples, n_targets)
The target values.
Returns
-------
score : array, shape (n_samples, n_estimators)
Score for each estimator / data slice couple.
"""
from sklearn.metrics import make_scorer, get_scorer
self._check_Xy(X)
if X.shape[-1] != len(self.estimators_):
raise ValueError('The number of estimators does not match '
'X.shape[-1]')
# If scoring is None (default), the predictions are internally
# generated by estimator.score(). Else, we must first get the
# predictions based on the scorer.
if not isinstance(self.scoring, str):
scoring_ = (make_scorer(self.scoring) if self.scoring is
not None else self.scoring)
elif self.scoring is not None:
scoring_ = get_scorer(self.scoring)
# For predictions/transforms the parallelization is across the data and
# not across the estimators to avoid memory load.
parallel, p_func, n_jobs = parallel_func(_sl_score, self.n_jobs)
n_jobs = min(n_jobs, X.shape[-1])
X_splits = np.array_split(X, n_jobs, axis=-1)
est_splits = np.array_split(self.estimators_, n_jobs)
score = parallel(p_func(est, scoring_, X, y)
for (est, x) in zip(est_splits, X_splits))
if n_jobs > 1:
score = np.concatenate(score, axis=0)
else:
score = score[0]
return score
def evaluate(self, X, y, X_vald=None, y_vald=None):
clf = RandomForestClassifier(n_estimators=32, max_depth=3,
n_jobs=-1) # used as base classifier
if X_vald is None:
return cross_val_score(clf,
X,
y,
scoring=self._metric,
cv=self._cv_folds,
n_jobs=-1).mean()
else:
clf.fit(X, y)
sk = get_scorer(self._metric)
return sk(clf, X_vald, y_vald)
def __init__(self, n_jobs=-1, offset_scale=1.0, n_buckets=2, initial_offsets=None, scoring='accuracy'):
self.n_jobs = int(n_jobs)
self.offset_scale = float(offset_scale)
self.n_buckets = int(n_buckets)
if initial_offsets is None:
self.initial_offsets_ = [-0.5] * self.n_buckets
pass
else:
self.initial_offsets_ = list(initial_offsets)
assert(len(self.initial_offsets_) == self.n_buckets)
pass
from sklearn.metrics import get_scorer
self.scoring = get_scorer(scoring)
pass
def __init__(self, estimator, k_features=1,
forward=True, floating=False,
verbose=0, scoring=None,
cv=5, skip_if_stuck=True, n_jobs=1,
pre_dispatch='2*n_jobs',
clone_estimator=True):
self.estimator = estimator
self.k_features = k_features
self.forward = forward
self.floating = floating
self.pre_dispatch = pre_dispatch
self.cv = cv
self.n_jobs = n_jobs
self.named_est = {key: value for key, value in
_name_estimators([self.estimator])}
self.skip_if_stuck = skip_if_stuck
self.cv = cv
self.n_jobs = n_jobs
self.verbose = verbose
self.named_est = {key: value for key, value in
_name_estimators([self.estimator])}
self.clone_estimator = clone_estimator
if self.clone_estimator:
self.est_ = clone(self.estimator)
else:
self.est_ = self.estimator
self.scoring = scoring
if scoring is None:
if self.est_._estimator_type == 'classifier':
scoring = 'accuracy'
elif self.est_._estimator_type == 'regressor':
scoring = 'r2'
else:
raise AttributeError('Estimator must '
'be a Classifier or Regressor.')
if isinstance(scoring, str):
self.scorer = get_scorer(scoring)
else:
self.scorer = scoring
self.fitted = False
self.subsets_ = {}
self.interrupted_ = False
# don't mess with this unless testing
self._TESTING_INTERRUPT_MODE = False
def __init__(self, estimator, k_features=1,
forward=True, floating=False,
verbose=0, scoring=None,
cv=5, n_jobs=1,
pre_dispatch='2*n_jobs',
clone_estimator=True):
self.estimator = estimator
self.k_features = k_features
self.forward = forward
self.floating = floating
self.pre_dispatch = pre_dispatch
self.cv = cv
self.n_jobs = n_jobs
self.named_est = {key: value for key, value in
_name_estimators([self.estimator])}
self.cv = cv
self.n_jobs = n_jobs
self.verbose = verbose
self.named_est = {key: value for key, value in
_name_estimators([self.estimator])}
self.clone_estimator = clone_estimator
if self.clone_estimator:
self.est_ = clone(self.estimator)
else:
self.est_ = self.estimator
self.scoring = scoring
if scoring is None:
if self.est_._estimator_type == 'classifier':
scoring = 'accuracy'
elif self.est_._estimator_type == 'regressor':
scoring = 'r2'
else:
raise AttributeError('Estimator must '
'be a Classifier or Regressor.')
if isinstance(scoring, str):
self.scorer = get_scorer(scoring)
else:
self.scorer = scoring
self.fitted = False
self.subsets_ = {}
self.interrupted_ = False
# don't mess with this unless testing
self._TESTING_INTERRUPT_MODE = False
def __init__(self, estimator, k_features,
forward=True, floating=False,
print_progress=True, scoring='accuracy',
cv=5, skip_if_stuck=True, n_jobs=1,
pre_dispatch='2*n_jobs'):
self.estimator = clone(estimator)
self.k_features = k_features
self.forward = forward
self.floating = floating
self.pre_dispatch = pre_dispatch
self.scoring = scoring
self.scorer = get_scorer(scoring)
self.skip_if_stuck = skip_if_stuck
self.cv = cv
self.print_progress = print_progress
self.n_jobs = n_jobs
def test_deprecated_names():
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)
for name in ('mean_absolute_error', 'mean_squared_error',
'median_absolute_error', 'log_loss'):
warning_msg = "Scoring method %s was renamed to" % name
for scorer in (get_scorer(name), SCORERS[name]):
assert_warns_message(DeprecationWarning,
warning_msg,
scorer, clf, X, y)
assert_warns_message(DeprecationWarning,
warning_msg,
cross_val_score, clf, X, y, scoring=name)
def __init__(self, estimator, min_features=1, max_features=1,
print_progress=True, scoring='accuracy',
cv=5, n_jobs=1,
pre_dispatch='2*n_jobs',
clone_estimator=True):
self.estimator = estimator
self.min_features = min_features
self.max_features = max_features
self.pre_dispatch = pre_dispatch
self.scoring = scoring
self.scorer = get_scorer(scoring)
self.cv = cv
self.print_progress = print_progress
self.n_jobs = n_jobs
self.named_est = {key: value for key, value in
_name_estimators([self.estimator])}
self.clone_estimator = clone_estimator
if self.clone_estimator:
self.est_ = clone(self.estimator)
else:
self.est_ = self.estimator
self.fitted = False
def test_rfecv():
generator = check_random_state(0)
iris = load_iris()
X = np.c_[iris.data, generator.normal(size=(len(iris.data), 6))]
y = list(iris.target) # regression test: list should be supported
# Test using the score function
rfecv = RFECV(estimator=SVC(kernel="linear"), step=1, cv=5)
rfecv.fit(X, y)
# non-regression test for missing worst feature:
assert_equal(len(rfecv.grid_scores_), X.shape[1])
assert_equal(len(rfecv.ranking_), X.shape[1])
X_r = rfecv.transform(X)
# All the noisy variable were filtered out
assert_array_equal(X_r, iris.data)
# same in sparse
rfecv_sparse = RFECV(estimator=SVC(kernel="linear"), step=1, cv=5)
X_sparse = sparse.csr_matrix(X)
rfecv_sparse.fit(X_sparse, y)
X_r_sparse = rfecv_sparse.transform(X_sparse)
assert_array_equal(X_r_sparse.toarray(), iris.data)
# Test using a customized loss function
scoring = make_scorer(zero_one_loss, greater_is_better=False)
rfecv = RFECV(estimator=SVC(kernel="linear"), step=1, cv=5,
scoring=scoring)
ignore_warnings(rfecv.fit)(X, y)
X_r = rfecv.transform(X)
assert_array_equal(X_r, iris.data)
# Test using a scorer
scorer = get_scorer('accuracy')
rfecv = RFECV(estimator=SVC(kernel="linear"), step=1, cv=5,
scoring=scorer)
rfecv.fit(X, y)
X_r = rfecv.transform(X)
assert_array_equal(X_r, iris.data)
# Test fix on grid_scores
def test_scorer(estimator, X, y):
return 1.0
rfecv = RFECV(estimator=SVC(kernel="linear"), step=1, cv=5,
scoring=test_scorer)
rfecv.fit(X, y)
assert_array_equal(rfecv.grid_scores_, np.ones(len(rfecv.grid_scores_)))
# In the event of cross validation score ties, the expected behavior of
# RFECV is to return the FEWEST features that maximize the CV score.
# Because test_scorer always returns 1.0 in this example, RFECV should
# reduce the dimensionality to a single feature (i.e. n_features_ = 1)
assert_equal(rfecv.n_features_, 1)
# Same as the first two tests, but with step=2
rfecv = RFECV(estimator=SVC(kernel="linear"), step=2, cv=5)
rfecv.fit(X, y)
assert_equal(len(rfecv.grid_scores_), 6)
assert_equal(len(rfecv.ranking_), X.shape[1])
X_r = rfecv.transform(X)
assert_array_equal(X_r, iris.data)
rfecv_sparse = RFECV(estimator=SVC(kernel="linear"), step=2, cv=5)
X_sparse = sparse.csr_matrix(X)
rfecv_sparse.fit(X_sparse, y)
X_r_sparse = rfecv_sparse.transform(X_sparse)
assert_array_equal(X_r_sparse.toarray(), iris.data)
# Verifying that steps < 1 don't blow up.
rfecv_sparse = RFECV(estimator=SVC(kernel="linear"), step=.2, cv=5)
X_sparse = sparse.csr_matrix(X)
rfecv_sparse.fit(X_sparse, y)
X_r_sparse = rfecv_sparse.transform(X_sparse)
assert_array_equal(X_r_sparse.toarray(), iris.data)
def paired_ttest_5x2cv(estimator1, estimator2, X, y,
scoring=None,
random_seed=None):
"""
Implements the 5x2cv paired t test proposed
by Dieterrich (1998)
to compare the performance of two models.
Parameters
----------
estimator1 : scikit-learn classifier or regressor
estimator2 : scikit-learn classifier or regressor
X : {array-like, sparse matrix}, shape = [n_samples, n_features]
Training vectors, where n_samples is the number of samples and
n_features is the number of features.
y : array-like, shape = [n_samples]
Target values.
scoring : str, callable, or None (default: None)
If None (default), uses 'accuracy' for sklearn classifiers
and 'r2' for sklearn regressors.
If str, uses a sklearn scoring metric string identifier, for example
{accuracy, f1, precision, recall, roc_auc} for classifiers,
{'mean_absolute_error', 'mean_squared_error'/'neg_mean_squared_error',
'median_absolute_error', 'r2'} for regressors.
If a callable object or function is provided, it has to be conform with
sklearn's signature ``scorer(estimator, X, y)``; see
http://scikit-learn.org/stable/modules/generated/sklearn.metrics.make_scorer.html
for more information.
random_seed : int or None (default: None)
Random seed for creating the test/train splits.
Returns
----------
t : float
The t-statistic
pvalue : float
Two-tailed p-value.
If the chosen significance level is larger
than the p-value, we reject the null hypothesis
and accept that there are significant differences
in the two compared models.
"""
rng = np.random.RandomState(random_seed)
if scoring is None:
if estimator1._estimator_type == 'classifier':
scoring = 'accuracy'
elif estimator1._estimator_type == 'regressor':
scoring = 'r2'
else:
raise AttributeError('Estimator must '
'be a Classifier or Regressor.')
if isinstance(scoring, str):
scorer = get_scorer(scoring)
else:
scorer = scoring
variance_sum = 0.
first_diff = None
def score_diff(X_1, X_2, y_1, y_2):
estimator1.fit(X_1, y_1)
estimator2.fit(X_1, y_1)
est1_score = scorer(estimator1, X_2, y_2)
est2_score = scorer(estimator2, X_2, y_2)
score_diff = est1_score - est2_score
return score_diff
for i in range(5):
randint = rng.randint(low=0, high=32767)
X_1, X_2, y_1, y_2 = \
train_test_split(X, y, test_size=0.5,
random_state=randint)
score_diff_1 = score_diff(X_1, X_2, y_1, y_2)
score_diff_2 = score_diff(X_2, X_1, y_2, y_1)
score_mean = (score_diff_1 + score_diff_2) / 2.
score_var = ((score_diff_1 - score_mean)**2 +
(score_diff_2 - score_mean)**2)
variance_sum += score_var
if first_diff is None:
first_diff = score_diff_1
numerator = first_diff
denominator = np.sqrt(1/5. * variance_sum)
t_stat = numerator / denominator
pvalue = stats.t.sf(np.abs(t_stat), 5)*2.
return float(t_stat), float(pvalue)
def tune(X, y, estimator, param_grid):
gcv = GridSearchCV(estimator, param_grid, refit=True, scoring=get_scorer('roc_auc'),
n_jobs=-1, verbose=5)
gcv.fit(X, y)
return gcv.best_estimator_
def paired_ttest_resampled(estimator1, estimator2, X, y,
num_rounds=30, test_size=0.3,
scoring=None,
random_seed=None):
"""
Implements the resampled paired t test procedure
to compare the performance of two models
(also called k-hold-out paired t test).
Parameters
----------
estimator1 : scikit-learn classifier or regressor
estimator2 : scikit-learn classifier or regressor
X : {array-like, sparse matrix}, shape = [n_samples, n_features]
Training vectors, where n_samples is the number of samples and
n_features is the number of features.
y : array-like, shape = [n_samples]
Target values.
num_rounds : int (default: 30)
Number of resampling iterations
(i.e., train/test splits)
test_size : float or int (default: 0.3)
If float, should be between 0.0 and 1.0 and
represent the proportion of the dataset to use
as a test set.
If int, represents the absolute number of test exsamples.
scoring : str, callable, or None (default: None)
If None (default), uses 'accuracy' for sklearn classifiers
and 'r2' for sklearn regressors.
If str, uses a sklearn scoring metric string identifier, for example
{accuracy, f1, precision, recall, roc_auc} for classifiers,
{'mean_absolute_error', 'mean_squared_error'/'neg_mean_squared_error',
'median_absolute_error', 'r2'} for regressors.
If a callable object or function is provided, it has to be conform with
sklearn's signature ``scorer(estimator, X, y)``; see
http://scikit-learn.org/stable/modules/generated/sklearn.metrics.make_scorer.html
for more information.
random_seed : int or None (default: None)
Random seed for creating the test/train splits.
Returns
----------
t : float
The t-statistic
pvalue : float
Two-tailed p-value.
If the chosen significance level is larger
than the p-value, we reject the null hypothesis
and accept that there are significant differences
in the two compared models.
"""
if (not isinstance(test_size, int) and not isinstance(test_size, float)):
raise ValueError('train_size must be of '
'type int or float. Got %s.' % type(test_size))
rng = np.random.RandomState(random_seed)
if scoring is None:
if estimator1._estimator_type == 'classifier':
scoring = 'accuracy'
elif estimator1._estimator_type == 'regressor':
scoring = 'r2'
else:
raise AttributeError('Estimator must '
'be a Classifier or Regressor.')
if isinstance(scoring, str):
scorer = get_scorer(scoring)
else:
scorer = scoring
score_diff = []
for i in range(num_rounds):
randint = rng.randint(low=0, high=32767)
X_train, X_test, y_train, y_test = \
train_test_split(X, y, test_size=test_size,
random_state=randint)
estimator1.fit(X_train, y_train)
estimator2.fit(X_train, y_train)
est1_score = scorer(estimator1, X_test, y_test)
est2_score = scorer(estimator2, X_test, y_test)
score_diff.append(est1_score - est2_score)
avg_diff = np.mean(score_diff)
numerator = avg_diff * np.sqrt(num_rounds)
denominator = np.sqrt(sum([(diff - avg_diff)**2 for diff in score_diff])
/ (num_rounds - 1))
t_stat = numerator / denominator
pvalue = stats.t.sf(np.abs(t_stat), num_rounds - 1)*2.
return float(t_stat), float(pvalue)
def combined_ftest_5x2cv(estimator1, estimator2, X, y,
scoring=None,
random_seed=None):
"""
Implements the 5x2cv combined F test proposed
by Alpaydin 1999,
to compare the performance of two models.
Parameters
----------
estimator1 : scikit-learn classifier or regressor
estimator2 : scikit-learn classifier or regressor
X : {array-like, sparse matrix}, shape = [n_samples, n_features]
Training vectors, where n_samples is the number of samples and
n_features is the number of features.
y : array-like, shape = [n_samples]
Target values.
scoring : str, callable, or None (default: None)
If None (default), uses 'accuracy' for sklearn classifiers
and 'r2' for sklearn regressors.
If str, uses a sklearn scoring metric string identifier, for example
{accuracy, f1, precision, recall, roc_auc} for classifiers,
{'mean_absolute_error', 'mean_squared_error'/'neg_mean_squared_error',
'median_absolute_error', 'r2'} for regressors.
If a callable object or function is provided, it has to be conform with
sklearn's signature ``scorer(estimator, X, y)``; see
http://scikit-learn.org/stable/modules/generated/sklearn.metrics.make_scorer.html
for more information.
random_seed : int or None (default: None)
Random seed for creating the test/train splits.
Returns
----------
f : float
The F-statistic
pvalue : float
Two-tailed p-value.
If the chosen significance level is larger
than the p-value, we reject the null hypothesis
and accept that there are significant differences
in the two compared models.
Examples
-----------
For usage examples, please see
http://rasbt.github.io/mlxtend/user_guide/evaluate/combined_ftest_5x2cv/
"""
rng = np.random.RandomState(random_seed)
if scoring is None:
if estimator1._estimator_type == 'classifier':
scoring = 'accuracy'
elif estimator1._estimator_type == 'regressor':
scoring = 'r2'
else:
raise AttributeError('Estimator must '
'be a Classifier or Regressor.')
if isinstance(scoring, str):
scorer = get_scorer(scoring)
else:
scorer = scoring
variances = []
differences = []
def score_diff(X_1, X_2, y_1, y_2):
estimator1.fit(X_1, y_1)
estimator2.fit(X_1, y_1)
est1_score = scorer(estimator1, X_2, y_2)
est2_score = scorer(estimator2, X_2, y_2)
score_diff = est1_score - est2_score
return score_diff
for i in range(5):
randint = rng.randint(low=0, high=32767)
X_1, X_2, y_1, y_2 = \
train_test_split(X, y, test_size=0.5,
random_state=randint)
score_diff_1 = score_diff(X_1, X_2, y_1, y_2)
score_diff_2 = score_diff(X_2, X_1, y_2, y_1)
score_mean = (score_diff_1 + score_diff_2) / 2.
score_var = ((score_diff_1 - score_mean)**2 +
(score_diff_2 - score_mean)**2)
differences.extend([score_diff_1**2, score_diff_2**2])
variances.append(score_var)
numerator = sum(differences)
denominator = 2*(sum(variances))
f_stat = numerator / denominator
p_value = scipy.stats.f.sf(f_stat, 10, 5)
return float(f_stat), float(p_value)
def test_SearchLight():
"""Test _SearchLight"""
from sklearn.linear_model import Ridge, LogisticRegression
from sklearn.pipeline import make_pipeline
from sklearn.metrics import roc_auc_score, get_scorer, make_scorer
X, y = make_data()
n_epochs, _, n_time = X.shape
# init
assert_raises(ValueError, _SearchLight, 'foo')
sl = _SearchLight(Ridge())
sl = _SearchLight(LogisticRegression())
# fit
assert_equal(sl.__repr__()[:14], '<_SearchLight(')
sl.fit(X, y)
assert_equal(sl.__repr__()[-28:], ', fitted with 10 estimators>')
assert_raises(ValueError, sl.fit, X[1:], y)
assert_raises(ValueError, sl.fit, X[:, :, 0], y)
# transforms
assert_raises(ValueError, sl.predict, X[:, :, :2])
y_pred = sl.predict(X)
assert_true(y_pred.dtype == int)
assert_array_equal(y_pred.shape, [n_epochs, n_time])
y_proba = sl.predict_proba(X)
assert_true(y_proba.dtype == float)
assert_array_equal(y_proba.shape, [n_epochs, n_time, 2])
# score
score = sl.score(X, y)
assert_array_equal(score.shape, [n_time])
assert_true(np.sum(np.abs(score)) != 0)
assert_true(score.dtype == float)
sl = _SearchLight(LogisticRegression())
assert_equal(sl.scoring, None)
# Scoring method
for err, scoring in [(ValueError, 'foo'), (TypeError, 999)]:
sl = _SearchLight(LogisticRegression(), scoring=scoring)
sl.fit(X, y)
assert_raises(err, sl.score, X, y)
# Check sklearn's roc_auc fix: scikit-learn/scikit-learn#6874
# -- 3 class problem
sl = _SearchLight(LogisticRegression(random_state=0), scoring='roc_auc')
y = np.arange(len(X)) % 3
sl.fit(X, y)
assert_raises(ValueError, sl.score, X, y)
# -- 2 class problem not in [0, 1]
y = np.arange(len(X)) % 2 + 1
sl.fit(X, y)
score = sl.score(X, y)
assert_array_equal(score, [roc_auc_score(y - 1, _y_pred - 1)
for _y_pred in sl.decision_function(X).T])
y = np.arange(len(X)) % 2
for method, scoring in [
('predict_proba', 'roc_auc'), ('predict', roc_auc_score)]:
sl1 = _SearchLight(LogisticRegression(), scoring=scoring)
sl1.fit(X, y)
np.random.seed(0)
X = np.random.randn(*X.shape) # randomize X to avoid AUCs in [0, 1]
score_sl = sl1.score(X, y)
assert_array_equal(score_sl.shape, [n_time])
assert_true(score_sl.dtype == float)
# Check that scoring was applied adequately
if isinstance(scoring, str):
scoring = get_scorer(scoring)
else:
scoring = make_scorer(scoring)
score_manual = [scoring(est, x, y) for est, x in zip(
sl1.estimators_, X.transpose(2, 0, 1))]
assert_array_equal(score_manual, score_sl)
# n_jobs
sl = _SearchLight(LogisticRegression(random_state=0), n_jobs=1,
scoring='roc_auc')
score_1job = sl.fit(X, y).score(X, y)
sl.n_jobs = 2
score_njobs = sl.fit(X, y).score(X, y)
assert_array_equal(score_1job, score_njobs)
sl.predict(X)
# n_jobs > n_estimators
sl.fit(X[..., [0]], y)
sl.predict(X[..., [0]])
# pipeline
class _LogRegTransformer(LogisticRegression):
# XXX needs transformer in pipeline to get first proba only
def transform(self, X):
return super(_LogRegTransformer, self).predict_proba(X)[..., 1]
pipe = make_pipeline(_SearchLight(_LogRegTransformer()),
LogisticRegression())
pipe.fit(X, y)
pipe.predict(X)
# n-dimensional feature space
X = np.random.rand(10, 3, 4, 2)
y = np.arange(10) % 2
y_preds = list()
for n_jobs in [1, 2]:
pipe = _SearchLight(make_pipeline(Vectorizer(), LogisticRegression()),
n_jobs=n_jobs)
y_preds.append(pipe.fit(X, y).predict(X))
features_shape = pipe.estimators_[0].steps[0][1].features_shape_
assert_array_equal(features_shape, [3, 4])
assert_array_equal(y_preds[0], y_preds[1])
def _test_ridge_loo(filter_):
# test that can work with both dense or sparse matrices
n_samples = X_diabetes.shape[0]
ret = []
ridge_gcv = _RidgeGCV(fit_intercept=False)
ridge = Ridge(alpha=1.0, fit_intercept=False)
# generalized cross-validation (efficient leave-one-out)
decomp = ridge_gcv._pre_compute(X_diabetes, y_diabetes)
errors, c = ridge_gcv._errors(1.0, y_diabetes, *decomp)
values, c = ridge_gcv._values(1.0, y_diabetes, *decomp)
# brute-force leave-one-out: remove one example at a time
errors2 = []
values2 = []
for i in range(n_samples):
sel = np.arange(n_samples) != i
X_new = X_diabetes[sel]
y_new = y_diabetes[sel]
ridge.fit(X_new, y_new)
value = ridge.predict([X_diabetes[i]])[0]
error = (y_diabetes[i] - value) ** 2
errors2.append(error)
values2.append(value)
# check that efficient and brute-force LOO give same results
assert_almost_equal(errors, errors2)
assert_almost_equal(values, values2)
# generalized cross-validation (efficient leave-one-out,
# SVD variation)
decomp = ridge_gcv._pre_compute_svd(X_diabetes, y_diabetes)
errors3, c = ridge_gcv._errors_svd(ridge.alpha, y_diabetes, *decomp)
values3, c = ridge_gcv._values_svd(ridge.alpha, y_diabetes, *decomp)
# check that efficient and SVD efficient LOO give same results
assert_almost_equal(errors, errors3)
assert_almost_equal(values, values3)
# check best alpha
ridge_gcv.fit(filter_(X_diabetes), y_diabetes)
alpha_ = ridge_gcv.alpha_
ret.append(alpha_)
# check that we get same best alpha with custom loss_func
f = ignore_warnings
scoring = make_scorer(mean_squared_error, greater_is_better=False)
ridge_gcv2 = RidgeCV(fit_intercept=False, scoring=scoring)
f(ridge_gcv2.fit)(filter_(X_diabetes), y_diabetes)
assert_equal(ridge_gcv2.alpha_, alpha_)
# check that we get same best alpha with custom score_func
func = lambda x, y: -mean_squared_error(x, y)
scoring = make_scorer(func)
ridge_gcv3 = RidgeCV(fit_intercept=False, scoring=scoring)
f(ridge_gcv3.fit)(filter_(X_diabetes), y_diabetes)
assert_equal(ridge_gcv3.alpha_, alpha_)
# check that we get same best alpha with a scorer
scorer = get_scorer('mean_squared_error')
ridge_gcv4 = RidgeCV(fit_intercept=False, scoring=scorer)
ridge_gcv4.fit(filter_(X_diabetes), y_diabetes)
assert_equal(ridge_gcv4.alpha_, alpha_)
# check that we get same best alpha with sample weights
ridge_gcv.fit(filter_(X_diabetes), y_diabetes,
sample_weight=np.ones(n_samples))
assert_equal(ridge_gcv.alpha_, alpha_)
# simulate several responses
Y = np.vstack((y_diabetes, y_diabetes)).T
ridge_gcv.fit(filter_(X_diabetes), Y)
Y_pred = ridge_gcv.predict(filter_(X_diabetes))
ridge_gcv.fit(filter_(X_diabetes), y_diabetes)
y_pred = ridge_gcv.predict(filter_(X_diabetes))
assert_array_almost_equal(np.vstack((y_pred, y_pred)).T,
Y_pred, decimal=5)
return ret
def paired_ttest_kfold_cv(estimator1, estimator2, X, y,
cv=10,
scoring=None,
shuffle=False,
random_seed=None):
"""
Implements the k-fold paired t test procedure
to compare the performance of two models.
Parameters
----------
estimator1 : scikit-learn classifier or regressor
estimator2 : scikit-learn classifier or regressor
X : {array-like, sparse matrix}, shape = [n_samples, n_features]
Training vectors, where n_samples is the number of samples and
n_features is the number of features.
y : array-like, shape = [n_samples]
Target values.
cv : int (default: 10)
Number of splits and iteration for the
cross-validation procedure
scoring : str, callable, or None (default: None)
If None (default), uses 'accuracy' for sklearn classifiers
and 'r2' for sklearn regressors.
If str, uses a sklearn scoring metric string identifier, for example
{accuracy, f1, precision, recall, roc_auc} for classifiers,
{'mean_absolute_error', 'mean_squared_error'/'neg_mean_squared_error',
'median_absolute_error', 'r2'} for regressors.
If a callable object or function is provided, it has to be conform with
sklearn's signature ``scorer(estimator, X, y)``; see
http://scikit-learn.org/stable/modules/generated/sklearn.metrics.make_scorer.html
for more information.
shuffle : bool (default: True)
Whether to shuffle the dataset for generating
the k-fold splits.
random_seed : int or None (default: None)
Random seed for shuffling the dataset
for generating the k-fold splits.
Ignored if shuffle=False.
Returns
----------
t : float
The t-statistic
pvalue : float
Two-tailed p-value.
If the chosen significance level is larger
than the p-value, we reject the null hypothesis
and accept that there are significant differences
in the two compared models.
"""
kf = KFold(n_splits=cv, random_state=random_seed, shuffle=shuffle)
if scoring is None:
if estimator1._estimator_type == 'classifier':
scoring = 'accuracy'
elif estimator1._estimator_type == 'regressor':
scoring = 'r2'
else:
raise AttributeError('Estimator must '
'be a Classifier or Regressor.')
if isinstance(scoring, str):
scorer = get_scorer(scoring)
else:
scorer = scoring
score_diff = []
for train_index, test_index in kf.split(X):
X_train, X_test = X[train_index], X[test_index]
y_train, y_test = y[train_index], y[test_index]
estimator1.fit(X_train, y_train)
estimator2.fit(X_train, y_train)
est1_score = scorer(estimator1, X_test, y_test)
est2_score = scorer(estimator2, X_test, y_test)
score_diff.append(est1_score - est2_score)
avg_diff = np.mean(score_diff)
numerator = avg_diff * np.sqrt(cv)
denominator = np.sqrt(sum([(diff - avg_diff)**2 for diff in score_diff])
/ (cv - 1))
t_stat = numerator / denominator
pvalue = stats.t.sf(np.abs(t_stat), cv - 1)*2.
return float(t_stat), float(pvalue)