def cv(model, param_grid, X, y, n_iter=20):
""" Cross validation """
cv_results = None
print('..performing cv search...')
searches = []
# Define jobs
random_search = dcv.RandomizedSearchCV(
model,
param_grid,
n_iter=n_iter,
cv=5,
scoring=['f1_macro'], #, 'accuracy'],
return_train_score=True,
refit=False).fit(X, y)
# Gather results
cv_results = pd.DataFrame(random_search.cv_results_) #.head(1)
cv_results.sort_values(by=['mean_test_f1_macro'],
inplace=True,
ascending=False,
ignore_index=True)
print(cv_results.head())
best_params = cv_results.loc[0, 'params']
model = model.set_params(**best_params)
print('Using configuration: {}'.format(best_params))
with joblib.parallel_backend('dask'):
model.fit(X, y)
return model, cv_results
def test_random_search_cv_results():
# Make a dataset with a lot of noise to get various kind of prediction
# errors across CV folds and parameter settings
X, y = make_classification(n_samples=200,
n_features=100,
n_informative=3,
random_state=0)
# scipy.stats dists now supports `seed` but we still support scipy 0.12
# which doesn't support the seed. Hence the assertions in the test for
# random_search alone should not depend on randomization.
n_splits = 3
n_search_iter = 30
params = dict(C=expon(scale=10), gamma=expon(scale=0.1))
random_search = dcv.RandomizedSearchCV(SVC(),
n_iter=n_search_iter,
cv=n_splits,
iid=False,
param_distributions=params,
return_train_score=True)
random_search.fit(X, y)
random_search_iid = dcv.RandomizedSearchCV(SVC(),
n_iter=n_search_iter,
cv=n_splits,
iid=True,
param_distributions=params,
return_train_score=True)
random_search_iid.fit(X, y)
param_keys = ('param_C', 'param_gamma')
score_keys = ('mean_test_score', 'mean_train_score', 'rank_test_score',
'split0_test_score', 'split1_test_score',
'split2_test_score', 'split0_train_score',
'split1_train_score', 'split2_train_score', 'std_test_score',
'std_train_score', 'mean_fit_time', 'std_fit_time',
'mean_score_time', 'std_score_time')
n_cand = n_search_iter
for search, iid in zip((random_search, random_search_iid), (False, True)):
assert iid == search.iid
cv_results = search.cv_results_
# Check results structure
check_cv_results_array_types(cv_results, param_keys, score_keys)
check_cv_results_keys(cv_results, param_keys, score_keys, n_cand)
# For random_search, all the param array vals should be unmasked
assert not (any(cv_results['param_C'].mask)
or any(cv_results['param_gamma'].mask))
def test_search_basic(xy_classification):
X, y = xy_classification
param_grid = {"class_weight": [None, "balanced"]}
a = dms.GridSearchCV(SVC(kernel="rbf", gamma=0.1), param_grid)
a.fit(X, y)
param_dist = {"C": stats.uniform}
b = dms.RandomizedSearchCV(SVC(kernel="rbf", gamma=0.1), param_dist)
b.fit(X, y)
def test_search_basic(xy_classification):
X, y = xy_classification
param_grid = {'class_weight': [None, 'balanced']}
a = dms.GridSearchCV(SVC(kernel='rbf'), param_grid)
a.fit(X, y)
param_dist = {'C': stats.uniform}
b = dms.RandomizedSearchCV(SVC(kernel='rbf'), param_dist)
b.fit(X, y)
def test_grid_search_with_multioutput_data():
# Test search with multi-output estimator
X, y = make_multilabel_classification(return_indicator=True,
random_state=0)
est_parameters = {"max_depth": [1, 2, 3, 4]}
cv = KFold(random_state=0, n_splits=3, shuffle=True)
estimators = [
DecisionTreeRegressor(random_state=0),
DecisionTreeClassifier(random_state=0),
]
scoring = sklearn.metrics.make_scorer(sklearn.metrics.roc_auc_score,
average="weighted")
# Test with grid search cv
for est in estimators:
grid_search = dcv.GridSearchCV(est,
est_parameters,
cv=cv,
scoring=scoring)
grid_search.fit(X, y)
res_params = grid_search.cv_results_["params"]
for cand_i in range(len(res_params)):
est.set_params(**res_params[cand_i])
for i, (train, test) in enumerate(cv.split(X, y)):
est.fit(X[train], y[train])
correct_score = scoring(est, X[test], y[test])
assert_almost_equal(
correct_score,
grid_search.cv_results_["split%d_test_score" % i][cand_i],
)
# Test with a randomized search
for est in estimators:
random_search = dcv.RandomizedSearchCV(est,
est_parameters,
cv=cv,
n_iter=3,
scoring=scoring)
random_search.fit(X, y)
res_params = random_search.cv_results_["params"]
for cand_i in range(len(res_params)):
est.set_params(**res_params[cand_i])
for i, (train, test) in enumerate(cv.split(X, y)):
est.fit(X[train], y[train])
correct_score = scoring(est, X[test], y[test])
assert_almost_equal(
correct_score,
random_search.cv_results_["split%d_test_score" %
i][cand_i],
)
def test_trivial_cv_results_attr():
# Test search over a "grid" with only one point.
# Non-regression test: grid_scores_ wouldn't be set by dcv.GridSearchCV.
clf = MockClassifier()
grid_search = dcv.GridSearchCV(clf, {"foo_param": [1]})
grid_search.fit(X, y)
assert hasattr(grid_search, "cv_results_")
random_search = dcv.RandomizedSearchCV(clf, {"foo_param": [0]}, n_iter=1)
random_search.fit(X, y)
assert hasattr(grid_search, "cv_results_")
def test_pickle():
# Test that a fit search can be pickled
clf = MockClassifier()
grid_search = dcv.GridSearchCV(clf, {"foo_param": [1, 2, 3]}, refit=True)
grid_search.fit(X, y)
grid_search_pickled = pickle.loads(pickle.dumps(grid_search))
assert_array_almost_equal(grid_search.predict(X),
grid_search_pickled.predict(X))
random_search = dcv.RandomizedSearchCV(clf, {"foo_param": [1, 2, 3]},
refit=True,
n_iter=3)
random_search.fit(X, y)
random_search_pickled = pickle.loads(pickle.dumps(random_search))
assert_array_almost_equal(random_search.predict(X),
random_search_pickled.predict(X))
def test_grid_search_with_multioutput_data():
# Test search with multi-output estimator
X, y = make_multilabel_classification(return_indicator=True,
random_state=0)
est_parameters = {"max_depth": [1, 2, 3, 4]}
cv = KFold(random_state=0)
estimators = [
DecisionTreeRegressor(random_state=0),
DecisionTreeClassifier(random_state=0)
]
# Test with grid search cv
for est in estimators:
grid_search = dcv.GridSearchCV(est, est_parameters, cv=cv)
grid_search.fit(X, y)
res_params = grid_search.cv_results_['params']
for cand_i in range(len(res_params)):
est.set_params(**res_params[cand_i])
for i, (train, test) in enumerate(cv.split(X, y)):
est.fit(X[train], y[train])
correct_score = est.score(X[test], y[test])
assert_almost_equal(
correct_score,
grid_search.cv_results_['split%d_test_score' % i][cand_i])
# Test with a randomized search
for est in estimators:
random_search = dcv.RandomizedSearchCV(est,
est_parameters,
cv=cv,
n_iter=3)
random_search.fit(X, y)
res_params = random_search.cv_results_['params']
for cand_i in range(len(res_params)):
est.set_params(**res_params[cand_i])
for i, (train, test) in enumerate(cv.split(X, y)):
est.fit(X[train], y[train])
correct_score = est.score(X[test], y[test])
assert_almost_equal(
correct_score,
random_search.cv_results_['split%d_test_score' %
i][cand_i])
def fit_knn(X, y, n_iter):
"""Fit a KNN model on geographical coordinates only"""
columns_tf = make_column_transformer(("passthrough", ["X", "Y"]))
model = make_pipeline(columns_tf, KNeighborsClassifier())
param_space = {
"kneighborsclassifier__n_neighbors": loguniform_int(1, 500),
"kneighborsclassifier__weights": ["uniform", "distance"],
}
model = dcv.RandomizedSearchCV(model,
param_space,
scoring="neg_log_loss",
n_iter=n_iter,
random_state=42,
cv=5)
model.fit(X, y)
return model
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 = dcv.GridSearchCV(
SVC(gamma="auto"), param_grid=param_grid, return_train_score=True
)
random_search = dcv.RandomizedSearchCV(
SVC(gamma="auto"),
n_iter=3,
param_distributions=param_grid,
return_train_score=True,
)
for search in (grid_search, random_search):
search.fit(X, y)
cv_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(
cv_results["mean_test_score"][0], cv_results["mean_test_score"][1]
)
assert_almost_equal(
cv_results["mean_train_score"][0], cv_results["mean_train_score"][1]
)
try:
assert_almost_equal(
cv_results["mean_test_score"][1], cv_results["mean_test_score"][2]
)
except AssertionError:
pass
try:
assert_almost_equal(
cv_results["mean_train_score"][1], cv_results["mean_train_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])
def fit_linear(X, y, n_iter):
"""Fit a logistic regression model"""
model = LogisticRegression(max_iter=500,
penalty="elasticnet",
solver="saga")
model = make_pipeline(columns_transform(), model)
param_space = {
"logisticregression__l1_ratio": st.uniform(0, 1),
"logisticregression__C": st.loguniform(1e-4, 1e4),
}
model = dcv.RandomizedSearchCV(model,
param_space,
scoring="neg_log_loss",
n_iter=n_iter,
random_state=42,
cv=5)
model.fit(X, y)
return model
def fit_gbdt(X, y, n_iter):
"""Fit a gradient boosted decision trees model"""
model = LGBMClassifier(n_estimators=2000, random_state=42)
model = make_pipeline(columns_transform(), model)
param_space = {
"lgbmclassifier__min_data_in_leaf": loguniform_int(5, 500),
"lgbmclassifier__num_leaves": loguniform_int(31, 500),
"lgbmclassifier__reg_alpha": st.loguniform(1e-10, 1.0),
"lgbmclassifier__reg_lambda": st.loguniform(1e-10, 1.0),
"lgbmclassifier__learning_rate": st.loguniform(1e-4, 1e-1),
}
model = dcv.RandomizedSearchCV(model,
param_space,
scoring="neg_log_loss",
n_iter=n_iter,
random_state=42,
cv=5)
model.fit(X, y)
return model
def fit_mlp(X, y, n_iter):
"""Fit a simple multi-layer perceptron model"""
model = MLPClassifier(random_state=42, early_stopping=True)
model = make_pipeline(columns_transform(), model)
layers_options = [
[n_units] * n_layers
for n_units, n_layers in it.product([32, 64, 128, 256, 512], [1, 2])
]
param_space = {
"mlpclassifier__hidden_layer_sizes": layers_options,
"mlpclassifier__alpha": st.loguniform(1e-5, 1e-2),
"mlpclassifier__learning_rate_init": st.loguniform(1e-4, 1e-1),
}
model = dcv.RandomizedSearchCV(model,
param_space,
scoring="neg_log_loss",
n_iter=n_iter,
random_state=42,
cv=5)
model.fit(X, y)
return model
def test_search_iid_param():
# 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
# create "cv" for splits
cv = [[mask, ~mask], [~mask, mask]]
# once with iid=True (default)
grid_search = dcv.GridSearchCV(SVC(gamma="auto"),
param_grid={"C": [1, 10]},
cv=cv,
return_train_score=True)
random_search = dcv.RandomizedSearchCV(
SVC(gamma="auto"),
n_iter=2,
param_distributions={"C": [1, 10]},
return_train_score=True,
cv=cv,
)
for search in (grid_search, random_search):
search.fit(X, y)
assert search.iid
test_cv_scores = np.array(
list(search.cv_results_["split%d_test_score" % s_i][0]
for s_i in range(search.n_splits_)))
train_cv_scores = np.array(
list(search.cv_results_["split%d_train_"
"score" % s_i][0]
for s_i in range(search.n_splits_)))
test_mean = search.cv_results_["mean_test_score"][0]
test_std = search.cv_results_["std_test_score"][0]
train_cv_scores = np.array(
list(search.cv_results_["split%d_train_"
"score" % s_i][0]
for s_i in range(search.n_splits_)))
train_mean = search.cv_results_["mean_train_score"][0]
train_std = search.cv_results_["std_train_score"][0]
# Test the first candidate
assert search.cv_results_["param_C"][0] == 1
assert_array_almost_equal(test_cv_scores, [1, 1.0 / 3.0])
assert_array_almost_equal(train_cv_scores, [1, 1])
# for first split, 1/4 of dataset is in test, for second 3/4.
# take weighted average and weighted std
expected_test_mean = 1 * 1.0 / 4.0 + 1.0 / 3.0 * 3.0 / 4.0
expected_test_std = np.sqrt(1.0 / 4 * (expected_test_mean - 1)**2 +
3.0 / 4 *
(expected_test_mean - 1.0 / 3.0)**2)
assert_almost_equal(test_mean, expected_test_mean)
assert_almost_equal(test_std, expected_test_std)
# For the train scores, we do not take a weighted mean irrespective of
# i.i.d. or not
assert_almost_equal(train_mean, 1)
assert_almost_equal(train_std, 0)
# once with iid=False
grid_search = dcv.GridSearchCV(
SVC(gamma="auto"),
param_grid={"C": [1, 10]},
cv=cv,
iid=False,
return_train_score=True,
)
random_search = dcv.RandomizedSearchCV(
SVC(gamma="auto"),
n_iter=2,
param_distributions={"C": [1, 10]},
cv=cv,
iid=False,
return_train_score=True,
)
for search in (grid_search, random_search):
search.fit(X, y)
assert not search.iid
test_cv_scores = np.array(
list(search.cv_results_["split%d_test_score" % s][0]
for s in range(search.n_splits_)))
test_mean = search.cv_results_["mean_test_score"][0]
test_std = search.cv_results_["std_test_score"][0]
train_cv_scores = np.array(
list(search.cv_results_["split%d_train_"
"score" % s][0]
for s in range(search.n_splits_)))
train_mean = search.cv_results_["mean_train_score"][0]
train_std = search.cv_results_["std_train_score"][0]
assert search.cv_results_["param_C"][0] == 1
# scores are the same as above
assert_array_almost_equal(test_cv_scores, [1, 1.0 / 3.0])
# Unweighted mean/std is used
assert_almost_equal(test_mean, np.mean(test_cv_scores))
assert_almost_equal(test_std, np.std(test_cv_scores))
# For the train scores, we do not take a weighted mean irrespective of
# i.i.d. or not
assert_almost_equal(train_mean, 1)
assert_almost_equal(train_std, 0)
'gbc__min_samples_leaf': min_samples_leafs,
}
# create model
gbc = Pipeline([('vect', CountVectorizer(analyzer=lambda x: x)),
('scale', MaxAbsScaler()),
('gbc', GradientBoostingClassifier(verbose=1,
random_state=7))])
print("Tuning Model")
# Cross validation
clf = dcv.RandomizedSearchCV(gbc,
tuned_parameters,
cv=5,
n_iter=n_iter,
refit=True,
scoring='accuracy',
cache_cv=True,
scheduler=client)
clf.fit(x_train, y_train)
# Print results
for param, score in zip(clf.cv_results_['params'],
clf.cv_results_['mean_test_score']):
print(param, score)
print("the best model is" + str(clf.best_params_))
score = clf.best_estimator_.score(x_test, y_test)