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"""
Testing for the gradient boosting loss functions and initial estimators.
"""
import numpy as np
from numpy.testing import assert_almost_equal
from numpy.testing import assert_allclose
import pytest
from sklearn.utils import check_random_state
from sklearn.utils.stats import _weighted_percentile
from sklearn.ensemble._gb_losses import RegressionLossFunction
from sklearn.ensemble._gb_losses import LeastSquaresError
from sklearn.ensemble._gb_losses import LeastAbsoluteError
from sklearn.ensemble._gb_losses import HuberLossFunction
from sklearn.ensemble._gb_losses import QuantileLossFunction
from sklearn.ensemble._gb_losses import BinomialDeviance
from sklearn.ensemble._gb_losses import MultinomialDeviance
from sklearn.ensemble._gb_losses import ExponentialLoss
from sklearn.ensemble._gb_losses import LOSS_FUNCTIONS
def test_binomial_deviance():
# Check binomial deviance loss.
# Check against alternative definitions in ESLII.
bd = BinomialDeviance(2)
# pred has the same BD for y in {0, 1}
assert (bd(np.array([0.0]), np.array([0.0])) ==
bd(np.array([1.0]), np.array([0.0])))
assert_almost_equal(bd(np.array([1.0, 1.0, 1.0]),
np.array([100.0, 100.0, 100.0])),
0.0)
assert_almost_equal(bd(np.array([1.0, 0.0, 0.0]),
np.array([100.0, -100.0, -100.0])), 0)
# check if same results as alternative definition of deviance (from ESLII)
def alt_dev(y, pred):
return np.mean(np.logaddexp(0.0, -2.0 * (2.0 * y - 1) * pred))
test_data = [(np.array([1.0, 1.0, 1.0]), np.array([100.0, 100.0, 100.0])),
(np.array([0.0, 0.0, 0.0]), np.array([100.0, 100.0, 100.0])),
(np.array([0.0, 0.0, 0.0]),
np.array([-100.0, -100.0, -100.0])),
(np.array([1.0, 1.0, 1.0]),
np.array([-100.0, -100.0, -100.0]))]
for datum in test_data:
assert_almost_equal(bd(*datum), alt_dev(*datum))
# check the gradient against the
def alt_ng(y, pred):
return (2 * y - 1) / (1 + np.exp(2 * (2 * y - 1) * pred))
for datum in test_data:
assert_almost_equal(bd.negative_gradient(*datum), alt_ng(*datum))
def test_sample_weight_smoke():
rng = check_random_state(13)
y = rng.rand(100)
pred = rng.rand(100)
# least squares
loss = LeastSquaresError(1)
loss_wo_sw = loss(y, pred)
loss_w_sw = loss(y, pred, np.ones(pred.shape[0], dtype=np.float32))
assert_almost_equal(loss_wo_sw, loss_w_sw)
def test_sample_weight_init_estimators():
# Smoke test for init estimators with sample weights.
rng = check_random_state(13)
X = rng.rand(100, 2)
sample_weight = np.ones(100)
reg_y = rng.rand(100)
clf_y = rng.randint(0, 2, size=100)
for Loss in LOSS_FUNCTIONS.values():
if Loss is None:
continue
if issubclass(Loss, RegressionLossFunction):
k = 1
y = reg_y
else:
k = 2
y = clf_y
if Loss.is_multi_class:
# skip multiclass
continue
loss = Loss(k)
init_est = loss.init_estimator()
init_est.fit(X, y)
out = loss.get_init_raw_predictions(X, init_est)
assert out.shape == (y.shape[0], 1)
sw_init_est = loss.init_estimator()
sw_init_est.fit(X, y, sample_weight=sample_weight)
sw_out = loss.get_init_raw_predictions(X, sw_init_est)
assert sw_out.shape == (y.shape[0], 1)
# check if predictions match
assert_allclose(out, sw_out, rtol=1e-2)
def test_weighted_percentile():
y = np.empty(102, dtype=np.float64)
y[:50] = 0
y[-51:] = 2
y[-1] = 100000
y[50] = 1
sw = np.ones(102, dtype=np.float64)
sw[-1] = 0.0
score = _weighted_percentile(y, sw, 50)
assert score == 1
def test_weighted_percentile_equal():
y = np.empty(102, dtype=np.float64)
y.fill(0.0)
sw = np.ones(102, dtype=np.float64)
sw[-1] = 0.0
score = _weighted_percentile(y, sw, 50)
assert score == 0
def test_weighted_percentile_zero_weight():
y = np.empty(102, dtype=np.float64)
y.fill(1.0)
sw = np.ones(102, dtype=np.float64)
sw.fill(0.0)
score = _weighted_percentile(y, sw, 50)
assert score == 1.0
def test_quantile_loss_function():
# Non regression test for the QuantileLossFunction object
# There was a sign problem when evaluating the function
# for negative values of 'ytrue - ypred'
x = np.asarray([-1.0, 0.0, 1.0])
y_found = QuantileLossFunction(1, 0.9)(x, np.zeros_like(x))
y_expected = np.asarray([0.1, 0.0, 0.9]).mean()
np.testing.assert_allclose(y_found, y_expected)
def test_sample_weight_deviance():
# Test if deviance supports sample weights.
rng = check_random_state(13)
sample_weight = np.ones(100)
reg_y = rng.rand(100)
clf_y = rng.randint(0, 2, size=100)
mclf_y = rng.randint(0, 3, size=100)
for Loss in LOSS_FUNCTIONS.values():
if Loss is None:
continue
if issubclass(Loss, RegressionLossFunction):
k = 1
y = reg_y
p = reg_y
else:
k = 2
y = clf_y
p = clf_y
if Loss.is_multi_class:
k = 3
y = mclf_y
# one-hot encoding
p = np.zeros((y.shape[0], k), dtype=np.float64)
for i in range(k):
p[:, i] = y == i
loss = Loss(k)
deviance_w_w = loss(y, p, sample_weight)
deviance_wo_w = loss(y, p)
assert deviance_wo_w == deviance_w_w
@pytest.mark.parametrize(
'n_classes, n_samples', [(3, 100), (5, 57), (7, 13)]
)
def test_multinomial_deviance(n_classes, n_samples):
# Check multinomial deviance with and without sample weights.
rng = np.random.RandomState(13)
sample_weight = np.ones(n_samples)
y_true = rng.randint(0, n_classes, size=n_samples)
y_pred = np.zeros((n_samples, n_classes), dtype=np.float64)
for klass in range(y_pred.shape[1]):
y_pred[:, klass] = y_true == klass
loss = MultinomialDeviance(n_classes)
loss_wo_sw = loss(y_true, y_pred)
assert loss_wo_sw > 0
loss_w_sw = loss(y_true, y_pred, sample_weight=sample_weight)
assert loss_wo_sw == pytest.approx(loss_w_sw)
# Multinomial deviance uses weighted average loss rather than
# weighted sum loss, so we make sure that the value remains the same
# when we device the weight by 2.
loss_w_sw = loss(y_true, y_pred, sample_weight=0.5 * sample_weight)
assert loss_wo_sw == pytest.approx(loss_w_sw)
def test_mdl_computation_weighted():
raw_predictions = np.array([[1., -1., -.1], [-2., 1., 2.]])
y_true = np.array([0, 1])
weights = np.array([1, 3])
expected_loss = 1.0909323
# MultinomialDeviance loss computation with weights.
loss = MultinomialDeviance(3)
assert (loss(y_true, raw_predictions, weights)
== pytest.approx(expected_loss))
@pytest.mark.parametrize('n', [0, 1, 2])
def test_mdl_exception(n):
# Check that MultinomialDeviance throws an exception when n_classes <= 2
err_msg = 'MultinomialDeviance requires more than 2 classes.'
with pytest.raises(ValueError, match=err_msg):
MultinomialDeviance(n)
def test_init_raw_predictions_shapes():
# Make sure get_init_raw_predictions returns float64 arrays with shape
# (n_samples, K) where K is 1 for binary classification and regression, and
# K = n_classes for multiclass classification
rng = np.random.RandomState(0)
n_samples = 100
X = rng.normal(size=(n_samples, 5))
y = rng.normal(size=n_samples)
for loss in (LeastSquaresError(n_classes=1),
LeastAbsoluteError(n_classes=1),
QuantileLossFunction(n_classes=1),
HuberLossFunction(n_classes=1)):
init_estimator = loss.init_estimator().fit(X, y)
raw_predictions = loss.get_init_raw_predictions(y, init_estimator)
assert raw_predictions.shape == (n_samples, 1)
assert raw_predictions.dtype == np.float64
y = rng.randint(0, 2, size=n_samples)
for loss in (BinomialDeviance(n_classes=2),
ExponentialLoss(n_classes=2)):
init_estimator = loss.init_estimator().fit(X, y)
raw_predictions = loss.get_init_raw_predictions(y, init_estimator)
assert raw_predictions.shape == (n_samples, 1)
assert raw_predictions.dtype == np.float64
for n_classes in range(3, 5):
y = rng.randint(0, n_classes, size=n_samples)
loss = MultinomialDeviance(n_classes=n_classes)
init_estimator = loss.init_estimator().fit(X, y)
raw_predictions = loss.get_init_raw_predictions(y, init_estimator)
assert raw_predictions.shape == (n_samples, n_classes)
assert raw_predictions.dtype == np.float64
def test_init_raw_predictions_values():
# Make sure the get_init_raw_predictions() returns the expected values for
# each loss.
rng = np.random.RandomState(0)
n_samples = 100
X = rng.normal(size=(n_samples, 5))
y = rng.normal(size=n_samples)
# Least squares loss
loss = LeastSquaresError(n_classes=1)
init_estimator = loss.init_estimator().fit(X, y)
raw_predictions = loss.get_init_raw_predictions(y, init_estimator)
# Make sure baseline prediction is the mean of all targets
assert_almost_equal(raw_predictions, y.mean())
# Least absolute and huber loss
for Loss in (LeastAbsoluteError, HuberLossFunction):
loss = Loss(n_classes=1)
init_estimator = loss.init_estimator().fit(X, y)
raw_predictions = loss.get_init_raw_predictions(y, init_estimator)
# Make sure baseline prediction is the median of all targets
assert_almost_equal(raw_predictions, np.median(y))
# Quantile loss
for alpha in (.1, .5, .9):
loss = QuantileLossFunction(n_classes=1, alpha=alpha)
init_estimator = loss.init_estimator().fit(X, y)
raw_predictions = loss.get_init_raw_predictions(y, init_estimator)
# Make sure baseline prediction is the alpha-quantile of all targets
assert_almost_equal(raw_predictions, np.percentile(y, alpha * 100))
y = rng.randint(0, 2, size=n_samples)
# Binomial deviance
loss = BinomialDeviance(n_classes=2)
init_estimator = loss.init_estimator().fit(X, y)
# Make sure baseline prediction is equal to link_function(p), where p
# is the proba of the positive class. We want predict_proba() to return p,
# and by definition
# p = inverse_link_function(raw_prediction) = sigmoid(raw_prediction)
# So we want raw_prediction = link_function(p) = log(p / (1 - p))
raw_predictions = loss.get_init_raw_predictions(y, init_estimator)
p = y.mean()
assert_almost_equal(raw_predictions, np.log(p / (1 - p)))
# Exponential loss
loss = ExponentialLoss(n_classes=2)
init_estimator = loss.init_estimator().fit(X, y)
raw_predictions = loss.get_init_raw_predictions(y, init_estimator)
p = y.mean()
assert_almost_equal(raw_predictions, .5 * np.log(p / (1 - p)))
# Multinomial deviance loss
for n_classes in range(3, 5):
y = rng.randint(0, n_classes, size=n_samples)
loss = MultinomialDeviance(n_classes=n_classes)
init_estimator = loss.init_estimator().fit(X, y)
raw_predictions = loss.get_init_raw_predictions(y, init_estimator)
for k in range(n_classes):
p = (y == k).mean()
assert_almost_equal(raw_predictions[:, k], np.log(p))
@pytest.mark.parametrize('seed', range(5))
def test_lad_equals_quantile_50(seed):
# Make sure quantile loss with alpha = .5 is equivalent to LAD
lad = LeastAbsoluteError(n_classes=1)
ql = QuantileLossFunction(n_classes=1, alpha=0.5)
n_samples = 50
rng = np.random.RandomState(seed)
raw_predictions = rng.normal(size=(n_samples))
y_true = rng.normal(size=(n_samples))
lad_loss = lad(y_true, raw_predictions)
ql_loss = ql(y_true, raw_predictions)
assert_almost_equal(lad_loss, 2 * ql_loss)
weights = np.linspace(0, 1, n_samples) ** 2
lad_weighted_loss = lad(y_true, raw_predictions, sample_weight=weights)
ql_weighted_loss = ql(y_true, raw_predictions, sample_weight=weights)
assert_almost_equal(lad_weighted_loss, 2 * ql_weighted_loss)
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