def test_predict_proba(self):
self.estimator = Standardization(LogisticRegression(C=1e6,
solver='lbfgs'),
predict_proba=True)
ind_outcome = self.verify_individual_multiclass_output()
with self.subTest("Test results are probabilities - sum to 1:"):
for treatment_value, y_pred in ind_outcome.groupby(level="a",
axis="columns"):
pd.testing.assert_series_equal(
pd.Series(1.0, index=y_pred.index),
y_pred.sum(axis="columns"))
def test_predict(self):
self.estimator = Standardization(LogisticRegression(C=1e6,
solver='lbfgs'),
predict_proba=False)
self.estimator.fit(self.data_3cls["X"], self.data_3cls["a"],
self.data_3cls["y"])
ind_outcome = self.estimator.estimate_individual_outcome(
self.data_3cls["X"], self.data_3cls["a"])
with self.subTest("Output size, # predictions:"):
self.assertEqual(self.data_3cls["a"].nunique(),
ind_outcome.shape[1])
self.assertNotEqual(self.data_3cls["y"].nunique(),
ind_outcome.shape[1])
def test_treatment_encoding(self):
self.estimator = Standardization(LinearRegression(),
encode_treatment=True)
a = self.data_lin["a"].replace({0: "p", 1: "q"})
self.estimator.fit(self.data_lin["X"], a, self.data_lin["y"])
with self.subTest("Treatment encoder created:"):
self.assertTrue(hasattr(self.estimator, "treatment_encoder_"))
with self.subTest("Treatment categories properly encoded"):
self.assertSetEqual(
{"p", "q"},
set(*self.estimator.treatment_encoder_.categories_))
with self.subTest("Fitted model has the right size"):
self.assertEqual(len(self.estimator.learner.coef_),
self.data_lin["X"].shape[1] + a.nunique())
def setUpClass(cls):
TestDoublyRobustBase.setUpClass()
# Avoids regularization of the model:
ipw = IPW(LogisticRegression(C=1e6, solver='lbfgs'),
use_stabilized=False)
std = Standardization(LinearRegression(normalize=True))
cls.estimator = DoublyRobustIpFeature(std, ipw)
def fit_and_predict_all_learners(self, data, estimator):
X, a, y = data["X"], data["a"], data["y"]
self.estimator.fit(X, a, y)
doubly_res = self.estimator.estimate_population_outcome(X, a)
std_res = Standardization(LinearRegression(normalize=True)).fit(X, a, y).estimate_population_outcome(X, a)
ipw_res = self.estimator.weight_model.estimate_population_outcome(X, a, y)
return doubly_res, std_res, ipw_res
class TestStandardization(TestStandardizationCommon):
@classmethod
def setUpClass(cls):
TestStandardizationCommon.setUpClass()
# Avoids regularization of the model:
cls.estimator = Standardization(LinearRegression(normalize=True))
def setUp(self):
self.estimator.fit(self.data_lin["X"], self.data_lin["a"],
self.data_lin["y"])
def test_is_fitted(self):
self.assertTrue(hasattr(self.estimator.learner, "coef_"))
def test_effect_estimation(self):
with self.subTest("Check by model coefficient:"):
self.assertAlmostEqual(self.estimator.learner.coef_[0],
self.data_lin["beta"],
places=5)
self.ensure_effect_estimation()
def test_observed_prediction(self):
self.ensure_observed_prediction()
def test_counterfactual_outcomes(self):
self.ensure_counterfactual_outcomes()
def test_treatment_encoding(self):
self.estimator = Standardization(LinearRegression(),
encode_treatment=True)
a = self.data_lin["a"].replace({0: "p", 1: "q"})
self.estimator.fit(self.data_lin["X"], a, self.data_lin["y"])
with self.subTest("Treatment encoder created:"):
self.assertTrue(hasattr(self.estimator, "treatment_encoder_"))
with self.subTest("Treatment categories properly encoded"):
self.assertSetEqual(
{"p", "q"},
set(*self.estimator.treatment_encoder_.categories_))
with self.subTest("Fitted model has the right size"):
self.assertEqual(len(self.estimator.learner.coef_),
self.data_lin["X"].shape[1] + a.nunique())
def test_pipeline_learner(self):
self.ensure_pipeline_learner()
def test_many_models(self):
self.ensure_many_models()
def ensure_many_models(self, clip_min=None, clip_max=None):
from sklearn.ensemble import GradientBoostingRegressor, RandomForestRegressor
from sklearn.neural_network import MLPRegressor
from sklearn.linear_model import ElasticNet, RANSACRegressor, HuberRegressor, PassiveAggressiveRegressor
from sklearn.neighbors import KNeighborsRegressor
from sklearn.svm import SVR, LinearSVR
from sklearn.ensemble import GradientBoostingClassifier, RandomForestClassifier
from sklearn.neural_network import MLPClassifier
from sklearn.neighbors import KNeighborsClassifier
from sklearn.exceptions import ConvergenceWarning
warnings.filterwarnings('ignore', category=ConvergenceWarning)
data = self.create_uninformative_ox_dataset()
for propensity_learner in [
GradientBoostingClassifier(n_estimators=10),
RandomForestClassifier(n_estimators=100),
MLPClassifier(hidden_layer_sizes=(5, )),
KNeighborsClassifier(n_neighbors=20)
]:
weight_model = IPW(propensity_learner,
clip_min=clip_min,
clip_max=clip_max)
propensity_learner_name = str(propensity_learner).split(
"(", maxsplit=1)[0]
for outcome_learner in [
GradientBoostingRegressor(n_estimators=10),
RandomForestRegressor(n_estimators=10),
MLPRegressor(hidden_layer_sizes=(5, )),
ElasticNet(),
RANSACRegressor(),
HuberRegressor(),
PassiveAggressiveRegressor(),
KNeighborsRegressor(),
SVR(),
LinearSVR()
]:
outcome_learner_name = str(outcome_learner).split(
"(", maxsplit=1)[0]
outcome_model = Standardization(outcome_learner)
with self.subTest("Test fit & predict using {} & {}".format(
propensity_learner_name, outcome_learner_name)):
model = self.estimator.__class__(outcome_model,
weight_model)
model.fit(data["X"],
data["a"],
data["y"],
refit_weight_model=False)
model.estimate_individual_outcome(data["X"], data["a"])
self.assertTrue(True) # Fit did not crash
def test_standardization_matches_causallib(linear_data_pandas):
w, t, y = linear_data_pandas
causallib_standardization = Standardization(LinearRegression())
causallib_standardization.fit(w, t, y)
individual_potential_outcomes = causallib_standardization.estimate_individual_outcome(
w, t)
causallib_ite_estimates = individual_potential_outcomes[
1] - individual_potential_outcomes[0]
mean_potential_outcomes = causallib_standardization.estimate_population_outcome(
w, t)
causallib_ate_estimate = mean_potential_outcomes[
1] - mean_potential_outcomes[0]
standardization = StandardizationEstimator()
standardization.fit(w, t, y)
assert causallib_ate_estimate == standardization.estimate_ate()
pd.testing.assert_series_equal(causallib_ite_estimates,
standardization.estimate_ite())
def __init__(self, outcome_model=LinearRegression()):
super().__init__(causallib_estimator=Standardization(learner=outcome_model))
def test_many_models(self):
from sklearn.ensemble import GradientBoostingRegressor, RandomForestRegressor
from sklearn.neural_network import MLPRegressor
from sklearn.linear_model import ElasticNet, RANSACRegressor, HuberRegressor, PassiveAggressiveRegressor
from sklearn.neighbors import KNeighborsRegressor
from sklearn.svm import SVR, LinearSVR
from sklearn.ensemble import GradientBoostingClassifier, RandomForestClassifier
from sklearn.neural_network import MLPClassifier
from sklearn.neighbors import KNeighborsClassifier
from sklearn.exceptions import ConvergenceWarning
warnings.filterwarnings('ignore', category=ConvergenceWarning)
data = self.create_uninformative_ox_dataset()
for propensity_learner in [
GradientBoostingClassifier(n_estimators=10),
RandomForestClassifier(n_estimators=100),
MLPClassifier(hidden_layer_sizes=(5, )),
KNeighborsClassifier(n_neighbors=20)
]:
weight_model = IPW(propensity_learner)
propensity_learner_name = str(propensity_learner).split(
"(", maxsplit=1)[0]
for outcome_learner in [
GradientBoostingRegressor(n_estimators=10),
RandomForestRegressor(n_estimators=10),
RANSACRegressor(),
HuberRegressor(),
SVR(),
LinearSVR()
]:
outcome_learner_name = str(outcome_learner).split(
"(", maxsplit=1)[0]
outcome_model = Standardization(outcome_learner)
with self.subTest("Test fit using {} & {}".format(
propensity_learner_name, outcome_learner_name)):
model = self.estimator.__class__(outcome_model,
weight_model)
model.fit(data["X"],
data["a"],
data["y"],
refit_weight_model=False)
self.assertTrue(True) # Fit did not crash
for outcome_learner in [
MLPRegressor(hidden_layer_sizes=(5, )),
# ElasticNet(), # supports sample_weights since v0.23, remove to support v<0.23
PassiveAggressiveRegressor(),
KNeighborsRegressor()
]:
outcome_learner_name = str(outcome_learner).split(
"(", maxsplit=1)[0]
outcome_model = Standardization(outcome_learner)
with self.subTest("Test fit using {} & {}".format(
propensity_learner_name, outcome_learner_name)):
model = self.estimator.__class__(outcome_model,
weight_model)
with self.assertRaises(TypeError):
# Joffe forces learning with sample_weights,
# not all ML models support that and so calling should fail
model.fit(data["X"],
data["a"],
data["y"],
refit_weight_model=False)
def test_decision_function(self):
self.estimator = Standardization(SVC(decision_function_shape='ovr'),
predict_proba=True)
self.verify_individual_multiclass_output()
class TestStandardizationClassification(TestStandardizationCommon):
@classmethod
def setUpClass(cls):
# Three-class outcome, since decision_function might return a vector when n_classes=2, and we wish to check the
# matrix form of the output behaves as expected:
X, y = make_classification(n_features=3,
n_informative=2,
n_redundant=0,
n_repeated=0,
n_classes=3,
n_clusters_per_class=1,
flip_y=0.0,
class_sep=10.0)
X, a = X[:, :-1], X[:, -1]
a = (a > np.median(a)).astype(int)
cls.data_3cls = {
"X": pd.DataFrame(X),
"a": pd.Series(a),
"y": pd.Series(y)
}
# X, y = make_classification(n_features=2, n_informative=1, n_redundant=0, n_repeated=0, n_classes=2,
# n_clusters_per_class=1, flip_y=0.0, class_sep=10.0)
# X, a = X[:, :-1], X[:, -1]
# a = (a > np.median(a)).astype(int)
# cls.data_2cls = {"X": pd.DataFrame(X), "a": pd.Series(a), "y": pd.Series(y)}
def verify_individual_multiclass_output(self):
self.estimator.fit(self.data_3cls["X"], self.data_3cls["a"],
self.data_3cls["y"])
ind_outcome = self.estimator.estimate_individual_outcome(
self.data_3cls["X"], self.data_3cls["a"])
with self.subTest("Output size, # samples:"):
self.assertEqual(self.data_3cls["X"].shape[0],
ind_outcome.shape[0])
with self.subTest("Output size, # predictions:"):
with self.subTest(
"Output's multiindex level names are describing treatment and outcome"
):
self.assertEqual(["a", "y"], ind_outcome.columns.names)
with self.subTest(
"Output's number of predictions is the same as number of outcome and treatment values"
):
self.assertEqual(
self.data_3cls["a"].nunique() *
self.data_3cls["y"].nunique(), ind_outcome.shape[1])
self.assertEqual(
self.data_3cls["a"].nunique(),
ind_outcome.columns.get_level_values("a").unique().size)
self.assertEqual(
self.data_3cls["y"].nunique(),
ind_outcome.columns.get_level_values("y").unique().size)
return ind_outcome
def test_predict_proba(self):
self.estimator = Standardization(LogisticRegression(C=1e6,
solver='lbfgs'),
predict_proba=True)
ind_outcome = self.verify_individual_multiclass_output()
with self.subTest("Test results are probabilities - sum to 1:"):
for treatment_value, y_pred in ind_outcome.groupby(level="a",
axis="columns"):
pd.testing.assert_series_equal(
pd.Series(1.0, index=y_pred.index),
y_pred.sum(axis="columns"))
def test_decision_function(self):
self.estimator = Standardization(SVC(decision_function_shape='ovr'),
predict_proba=True)
self.verify_individual_multiclass_output()
def test_predict(self):
self.estimator = Standardization(LogisticRegression(C=1e6,
solver='lbfgs'),
predict_proba=False)
self.estimator.fit(self.data_3cls["X"], self.data_3cls["a"],
self.data_3cls["y"])
ind_outcome = self.estimator.estimate_individual_outcome(
self.data_3cls["X"], self.data_3cls["a"])
with self.subTest("Output size, # predictions:"):
self.assertEqual(self.data_3cls["a"].nunique(),
ind_outcome.shape[1])
self.assertNotEqual(self.data_3cls["y"].nunique(),
ind_outcome.shape[1])
def setUpClass(cls):
TestStandardizationCommon.setUpClass()
# Avoids regularization of the model:
cls.estimator = Standardization(LinearRegression(normalize=True))
def init(self, reduced, importance_sampling):
self._estimator = TMLE(
Standardization(self.outcome_model_cont),
IPW(self.treatment_model),
reduced=reduced, importance_sampling=importance_sampling,
)