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import numpy as np
import pytest
from sklearn.neural_network._base import binary_log_loss, log_loss
def test_binary_log_loss_1_prob_finite():
# y_proba is equal to one should result in a finite logloss
y_true = np.array([[0, 0, 1]]).T
y_prob = np.array([[0.9, 1.0, 1.0]]).T
loss = binary_log_loss(y_true, y_prob)
assert np.isfinite(loss)
@pytest.mark.parametrize(
"y_true, y_prob",
[
(
np.array([[1, 0, 0], [0, 1, 0]]),
np.array([[0.0, 1.0, 0.0], [0.9, 0.05, 0.05]]),
),
(np.array([[0, 0, 1]]).T, np.array([[0.9, 1.0, 1.0]]).T),
],
)
def test_log_loss_1_prob_finite(y_true, y_prob):
# y_proba is equal to 1 should result in a finite logloss
loss = log_loss(y_true, y_prob)
assert np.isfinite(loss)

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"""
Testing for Multi-layer Perceptron module (sklearn.neural_network)
"""
# Author: Issam H. Laradji
# License: BSD 3 clause
import re
import sys
import warnings
from io import StringIO
import joblib
import numpy as np
import pytest
from numpy.testing import (
assert_allclose,
assert_almost_equal,
assert_array_equal,
)
from sklearn.datasets import (
load_digits,
load_iris,
make_multilabel_classification,
make_regression,
)
from sklearn.exceptions import ConvergenceWarning
from sklearn.metrics import roc_auc_score
from sklearn.neural_network import MLPClassifier, MLPRegressor
from sklearn.preprocessing import LabelBinarizer, MinMaxScaler, scale
from sklearn.utils._testing import ignore_warnings
from sklearn.utils.fixes import CSR_CONTAINERS
ACTIVATION_TYPES = ["identity", "logistic", "tanh", "relu"]
X_digits, y_digits = load_digits(n_class=3, return_X_y=True)
X_digits_multi = MinMaxScaler().fit_transform(X_digits[:200])
y_digits_multi = y_digits[:200]
X_digits, y_digits = load_digits(n_class=2, return_X_y=True)
X_digits_binary = MinMaxScaler().fit_transform(X_digits[:200])
y_digits_binary = y_digits[:200]
classification_datasets = [
(X_digits_multi, y_digits_multi),
(X_digits_binary, y_digits_binary),
]
X_reg, y_reg = make_regression(
n_samples=200, n_features=10, bias=20.0, noise=100.0, random_state=7
)
y_reg = scale(y_reg)
regression_datasets = [(X_reg, y_reg)]
iris = load_iris()
X_iris = iris.data
y_iris = iris.target
def test_alpha():
# Test that larger alpha yields weights closer to zero
X = X_digits_binary[:100]
y = y_digits_binary[:100]
alpha_vectors = []
alpha_values = np.arange(2)
absolute_sum = lambda x: np.sum(np.abs(x))
for alpha in alpha_values:
mlp = MLPClassifier(hidden_layer_sizes=10, alpha=alpha, random_state=1)
with ignore_warnings(category=ConvergenceWarning):
mlp.fit(X, y)
alpha_vectors.append(
np.array([absolute_sum(mlp.coefs_[0]), absolute_sum(mlp.coefs_[1])])
)
for i in range(len(alpha_values) - 1):
assert (alpha_vectors[i] > alpha_vectors[i + 1]).all()
def test_fit():
# Test that the algorithm solution is equal to a worked out example.
X = np.array([[0.6, 0.8, 0.7]])
y = np.array([0])
mlp = MLPClassifier(
solver="sgd",
learning_rate_init=0.1,
alpha=0.1,
activation="logistic",
random_state=1,
max_iter=1,
hidden_layer_sizes=2,
momentum=0,
)
# set weights
mlp.coefs_ = [0] * 2
mlp.intercepts_ = [0] * 2
mlp.n_outputs_ = 1
mlp.coefs_[0] = np.array([[0.1, 0.2], [0.3, 0.1], [0.5, 0]])
mlp.coefs_[1] = np.array([[0.1], [0.2]])
mlp.intercepts_[0] = np.array([0.1, 0.1])
mlp.intercepts_[1] = np.array([1.0])
mlp._coef_grads = [] * 2
mlp._intercept_grads = [] * 2
mlp.n_features_in_ = 3
# Initialize parameters
mlp.n_iter_ = 0
mlp.learning_rate_ = 0.1
# Compute the number of layers
mlp.n_layers_ = 3
# Pre-allocate gradient matrices
mlp._coef_grads = [0] * (mlp.n_layers_ - 1)
mlp._intercept_grads = [0] * (mlp.n_layers_ - 1)
mlp.out_activation_ = "logistic"
mlp.t_ = 0
mlp.best_loss_ = np.inf
mlp.loss_curve_ = []
mlp._no_improvement_count = 0
mlp._intercept_velocity = [
np.zeros_like(intercepts) for intercepts in mlp.intercepts_
]
mlp._coef_velocity = [np.zeros_like(coefs) for coefs in mlp.coefs_]
mlp.partial_fit(X, y, classes=[0, 1])
# Manually worked out example
# h1 = g(X1 * W_i1 + b11) = g(0.6 * 0.1 + 0.8 * 0.3 + 0.7 * 0.5 + 0.1)
# = 0.679178699175393
# h2 = g(X2 * W_i2 + b12) = g(0.6 * 0.2 + 0.8 * 0.1 + 0.7 * 0 + 0.1)
# = 0.574442516811659
# o1 = g(h * W2 + b21) = g(0.679 * 0.1 + 0.574 * 0.2 + 1)
# = 0.7654329236196236
# d21 = -(0 - 0.765) = 0.765
# d11 = (1 - 0.679) * 0.679 * 0.765 * 0.1 = 0.01667
# d12 = (1 - 0.574) * 0.574 * 0.765 * 0.2 = 0.0374
# W1grad11 = X1 * d11 + alpha * W11 = 0.6 * 0.01667 + 0.1 * 0.1 = 0.0200
# W1grad11 = X1 * d12 + alpha * W12 = 0.6 * 0.0374 + 0.1 * 0.2 = 0.04244
# W1grad21 = X2 * d11 + alpha * W13 = 0.8 * 0.01667 + 0.1 * 0.3 = 0.043336
# W1grad22 = X2 * d12 + alpha * W14 = 0.8 * 0.0374 + 0.1 * 0.1 = 0.03992
# W1grad31 = X3 * d11 + alpha * W15 = 0.6 * 0.01667 + 0.1 * 0.5 = 0.060002
# W1grad32 = X3 * d12 + alpha * W16 = 0.6 * 0.0374 + 0.1 * 0 = 0.02244
# W2grad1 = h1 * d21 + alpha * W21 = 0.679 * 0.765 + 0.1 * 0.1 = 0.5294
# W2grad2 = h2 * d21 + alpha * W22 = 0.574 * 0.765 + 0.1 * 0.2 = 0.45911
# b1grad1 = d11 = 0.01667
# b1grad2 = d12 = 0.0374
# b2grad = d21 = 0.765
# W1 = W1 - eta * [W1grad11, .., W1grad32] = [[0.1, 0.2], [0.3, 0.1],
# [0.5, 0]] - 0.1 * [[0.0200, 0.04244], [0.043336, 0.03992],
# [0.060002, 0.02244]] = [[0.098, 0.195756], [0.2956664,
# 0.096008], [0.4939998, -0.002244]]
# W2 = W2 - eta * [W2grad1, W2grad2] = [[0.1], [0.2]] - 0.1 *
# [[0.5294], [0.45911]] = [[0.04706], [0.154089]]
# b1 = b1 - eta * [b1grad1, b1grad2] = 0.1 - 0.1 * [0.01667, 0.0374]
# = [0.098333, 0.09626]
# b2 = b2 - eta * b2grad = 1.0 - 0.1 * 0.765 = 0.9235
assert_almost_equal(
mlp.coefs_[0],
np.array([[0.098, 0.195756], [0.2956664, 0.096008], [0.4939998, -0.002244]]),
decimal=3,
)
assert_almost_equal(mlp.coefs_[1], np.array([[0.04706], [0.154089]]), decimal=3)
assert_almost_equal(mlp.intercepts_[0], np.array([0.098333, 0.09626]), decimal=3)
assert_almost_equal(mlp.intercepts_[1], np.array(0.9235), decimal=3)
# Testing output
# h1 = g(X1 * W_i1 + b11) = g(0.6 * 0.098 + 0.8 * 0.2956664 +
# 0.7 * 0.4939998 + 0.098333) = 0.677
# h2 = g(X2 * W_i2 + b12) = g(0.6 * 0.195756 + 0.8 * 0.096008 +
# 0.7 * -0.002244 + 0.09626) = 0.572
# o1 = h * W2 + b21 = 0.677 * 0.04706 +
# 0.572 * 0.154089 + 0.9235 = 1.043
# prob = sigmoid(o1) = 0.739
assert_almost_equal(mlp.predict_proba(X)[0, 1], 0.739, decimal=3)
def test_gradient():
# Test gradient.
# This makes sure that the activation functions and their derivatives
# are correct. The numerical and analytical computation of the gradient
# should be close.
for n_labels in [2, 3]:
n_samples = 5
n_features = 10
random_state = np.random.RandomState(seed=42)
X = random_state.rand(n_samples, n_features)
y = 1 + np.mod(np.arange(n_samples) + 1, n_labels)
Y = LabelBinarizer().fit_transform(y)
for activation in ACTIVATION_TYPES:
mlp = MLPClassifier(
activation=activation,
hidden_layer_sizes=10,
solver="lbfgs",
alpha=1e-5,
learning_rate_init=0.2,
max_iter=1,
random_state=1,
)
mlp.fit(X, y)
theta = np.hstack([l.ravel() for l in mlp.coefs_ + mlp.intercepts_])
layer_units = [X.shape[1]] + [mlp.hidden_layer_sizes] + [mlp.n_outputs_]
activations = []
deltas = []
coef_grads = []
intercept_grads = []
activations.append(X)
for i in range(mlp.n_layers_ - 1):
activations.append(np.empty((X.shape[0], layer_units[i + 1])))
deltas.append(np.empty((X.shape[0], layer_units[i + 1])))
fan_in = layer_units[i]
fan_out = layer_units[i + 1]
coef_grads.append(np.empty((fan_in, fan_out)))
intercept_grads.append(np.empty(fan_out))
# analytically compute the gradients
def loss_grad_fun(t):
return mlp._loss_grad_lbfgs(
t, X, Y, activations, deltas, coef_grads, intercept_grads
)
[value, grad] = loss_grad_fun(theta)
numgrad = np.zeros(np.size(theta))
n = np.size(theta, 0)
E = np.eye(n)
epsilon = 1e-5
# numerically compute the gradients
for i in range(n):
dtheta = E[:, i] * epsilon
numgrad[i] = (
loss_grad_fun(theta + dtheta)[0] - loss_grad_fun(theta - dtheta)[0]
) / (epsilon * 2.0)
assert_almost_equal(numgrad, grad)
@pytest.mark.parametrize("X,y", classification_datasets)
def test_lbfgs_classification(X, y):
# Test lbfgs on classification.
# It should achieve a score higher than 0.95 for the binary and multi-class
# versions of the digits dataset.
X_train = X[:150]
y_train = y[:150]
X_test = X[150:]
expected_shape_dtype = (X_test.shape[0], y_train.dtype.kind)
for activation in ACTIVATION_TYPES:
mlp = MLPClassifier(
solver="lbfgs",
hidden_layer_sizes=50,
max_iter=150,
shuffle=True,
random_state=1,
activation=activation,
)
mlp.fit(X_train, y_train)
y_predict = mlp.predict(X_test)
assert mlp.score(X_train, y_train) > 0.95
assert (y_predict.shape[0], y_predict.dtype.kind) == expected_shape_dtype
@pytest.mark.parametrize("X,y", regression_datasets)
def test_lbfgs_regression(X, y):
# Test lbfgs on the regression dataset.
for activation in ACTIVATION_TYPES:
mlp = MLPRegressor(
solver="lbfgs",
hidden_layer_sizes=50,
max_iter=150,
shuffle=True,
random_state=1,
activation=activation,
)
mlp.fit(X, y)
if activation == "identity":
assert mlp.score(X, y) > 0.80
else:
# Non linear models perform much better than linear bottleneck:
assert mlp.score(X, y) > 0.98
@pytest.mark.parametrize("X,y", classification_datasets)
def test_lbfgs_classification_maxfun(X, y):
# Test lbfgs parameter max_fun.
# It should independently limit the number of iterations for lbfgs.
max_fun = 10
# classification tests
for activation in ACTIVATION_TYPES:
mlp = MLPClassifier(
solver="lbfgs",
hidden_layer_sizes=50,
max_iter=150,
max_fun=max_fun,
shuffle=True,
random_state=1,
activation=activation,
)
with pytest.warns(ConvergenceWarning):
mlp.fit(X, y)
assert max_fun >= mlp.n_iter_
@pytest.mark.parametrize("X,y", regression_datasets)
def test_lbfgs_regression_maxfun(X, y):
# Test lbfgs parameter max_fun.
# It should independently limit the number of iterations for lbfgs.
max_fun = 10
# regression tests
for activation in ACTIVATION_TYPES:
mlp = MLPRegressor(
solver="lbfgs",
hidden_layer_sizes=50,
tol=0.0,
max_iter=150,
max_fun=max_fun,
shuffle=True,
random_state=1,
activation=activation,
)
with pytest.warns(ConvergenceWarning):
mlp.fit(X, y)
assert max_fun >= mlp.n_iter_
def test_learning_rate_warmstart():
# Tests that warm_start reuse past solutions.
X = [[3, 2], [1, 6], [5, 6], [-2, -4]]
y = [1, 1, 1, 0]
for learning_rate in ["invscaling", "constant"]:
mlp = MLPClassifier(
solver="sgd",
hidden_layer_sizes=4,
learning_rate=learning_rate,
max_iter=1,
power_t=0.25,
warm_start=True,
)
with ignore_warnings(category=ConvergenceWarning):
mlp.fit(X, y)
prev_eta = mlp._optimizer.learning_rate
mlp.fit(X, y)
post_eta = mlp._optimizer.learning_rate
if learning_rate == "constant":
assert prev_eta == post_eta
elif learning_rate == "invscaling":
assert mlp.learning_rate_init / pow(8 + 1, mlp.power_t) == post_eta
def test_multilabel_classification():
# Test that multi-label classification works as expected.
# test fit method
X, y = make_multilabel_classification(
n_samples=50, random_state=0, return_indicator=True
)
mlp = MLPClassifier(
solver="lbfgs",
hidden_layer_sizes=50,
alpha=1e-5,
max_iter=150,
random_state=0,
activation="logistic",
learning_rate_init=0.2,
)
mlp.fit(X, y)
assert mlp.score(X, y) > 0.97
# test partial fit method
mlp = MLPClassifier(
solver="sgd",
hidden_layer_sizes=50,
max_iter=150,
random_state=0,
activation="logistic",
alpha=1e-5,
learning_rate_init=0.2,
)
for i in range(100):
mlp.partial_fit(X, y, classes=[0, 1, 2, 3, 4])
assert mlp.score(X, y) > 0.9
# Make sure early stopping still work now that splitting is stratified by
# default (it is disabled for multilabel classification)
mlp = MLPClassifier(early_stopping=True)
mlp.fit(X, y).predict(X)
def test_multioutput_regression():
# Test that multi-output regression works as expected
X, y = make_regression(n_samples=200, n_targets=5)
mlp = MLPRegressor(
solver="lbfgs", hidden_layer_sizes=50, max_iter=200, random_state=1
)
mlp.fit(X, y)
assert mlp.score(X, y) > 0.9
def test_partial_fit_classes_error():
# Tests that passing different classes to partial_fit raises an error
X = [[3, 2]]
y = [0]
clf = MLPClassifier(solver="sgd")
clf.partial_fit(X, y, classes=[0, 1])
with pytest.raises(ValueError):
clf.partial_fit(X, y, classes=[1, 2])
def test_partial_fit_classification():
# Test partial_fit on classification.
# `partial_fit` should yield the same results as 'fit' for binary and
# multi-class classification.
for X, y in classification_datasets:
mlp = MLPClassifier(
solver="sgd",
max_iter=100,
random_state=1,
tol=0,
alpha=1e-5,
learning_rate_init=0.2,
)
with ignore_warnings(category=ConvergenceWarning):
mlp.fit(X, y)
pred1 = mlp.predict(X)
mlp = MLPClassifier(
solver="sgd", random_state=1, alpha=1e-5, learning_rate_init=0.2
)
for i in range(100):
mlp.partial_fit(X, y, classes=np.unique(y))
pred2 = mlp.predict(X)
assert_array_equal(pred1, pred2)
assert mlp.score(X, y) > 0.95
def test_partial_fit_unseen_classes():
# Non regression test for bug 6994
# Tests for labeling errors in partial fit
clf = MLPClassifier(random_state=0)
clf.partial_fit([[1], [2], [3]], ["a", "b", "c"], classes=["a", "b", "c", "d"])
clf.partial_fit([[4]], ["d"])
assert clf.score([[1], [2], [3], [4]], ["a", "b", "c", "d"]) > 0
def test_partial_fit_regression():
# Test partial_fit on regression.
# `partial_fit` should yield the same results as 'fit' for regression.
X = X_reg
y = y_reg
for momentum in [0, 0.9]:
mlp = MLPRegressor(
solver="sgd",
max_iter=100,
activation="relu",
random_state=1,
learning_rate_init=0.01,
batch_size=X.shape[0],
momentum=momentum,
)
with warnings.catch_warnings(record=True):
# catch convergence warning
mlp.fit(X, y)
pred1 = mlp.predict(X)
mlp = MLPRegressor(
solver="sgd",
activation="relu",
learning_rate_init=0.01,
random_state=1,
batch_size=X.shape[0],
momentum=momentum,
)
for i in range(100):
mlp.partial_fit(X, y)
pred2 = mlp.predict(X)
assert_allclose(pred1, pred2)
score = mlp.score(X, y)
assert score > 0.65
def test_partial_fit_errors():
# Test partial_fit error handling.
X = [[3, 2], [1, 6]]
y = [1, 0]
# no classes passed
with pytest.raises(ValueError):
MLPClassifier(solver="sgd").partial_fit(X, y, classes=[2])
# lbfgs doesn't support partial_fit
assert not hasattr(MLPClassifier(solver="lbfgs"), "partial_fit")
def test_nonfinite_params():
# Check that MLPRegressor throws ValueError when dealing with non-finite
# parameter values
rng = np.random.RandomState(0)
n_samples = 10
fmax = np.finfo(np.float64).max
X = fmax * rng.uniform(size=(n_samples, 2))
y = rng.standard_normal(size=n_samples)
clf = MLPRegressor()
msg = (
"Solver produced non-finite parameter weights. The input data may contain large"
" values and need to be preprocessed."
)
with pytest.raises(ValueError, match=msg):
clf.fit(X, y)
def test_predict_proba_binary():
# Test that predict_proba works as expected for binary class.
X = X_digits_binary[:50]
y = y_digits_binary[:50]
clf = MLPClassifier(hidden_layer_sizes=5, activation="logistic", random_state=1)
with ignore_warnings(category=ConvergenceWarning):
clf.fit(X, y)
y_proba = clf.predict_proba(X)
y_log_proba = clf.predict_log_proba(X)
(n_samples, n_classes) = y.shape[0], 2
proba_max = y_proba.argmax(axis=1)
proba_log_max = y_log_proba.argmax(axis=1)
assert y_proba.shape == (n_samples, n_classes)
assert_array_equal(proba_max, proba_log_max)
assert_allclose(y_log_proba, np.log(y_proba))
assert roc_auc_score(y, y_proba[:, 1]) == 1.0
def test_predict_proba_multiclass():
# Test that predict_proba works as expected for multi class.
X = X_digits_multi[:10]
y = y_digits_multi[:10]
clf = MLPClassifier(hidden_layer_sizes=5)
with ignore_warnings(category=ConvergenceWarning):
clf.fit(X, y)
y_proba = clf.predict_proba(X)
y_log_proba = clf.predict_log_proba(X)
(n_samples, n_classes) = y.shape[0], np.unique(y).size
proba_max = y_proba.argmax(axis=1)
proba_log_max = y_log_proba.argmax(axis=1)
assert y_proba.shape == (n_samples, n_classes)
assert_array_equal(proba_max, proba_log_max)
assert_allclose(y_log_proba, np.log(y_proba))
def test_predict_proba_multilabel():
# Test that predict_proba works as expected for multilabel.
# Multilabel should not use softmax which makes probabilities sum to 1
X, Y = make_multilabel_classification(
n_samples=50, random_state=0, return_indicator=True
)
n_samples, n_classes = Y.shape
clf = MLPClassifier(solver="lbfgs", hidden_layer_sizes=30, random_state=0)
clf.fit(X, Y)
y_proba = clf.predict_proba(X)
assert y_proba.shape == (n_samples, n_classes)
assert_array_equal(y_proba > 0.5, Y)
y_log_proba = clf.predict_log_proba(X)
proba_max = y_proba.argmax(axis=1)
proba_log_max = y_log_proba.argmax(axis=1)
assert (y_proba.sum(1) - 1).dot(y_proba.sum(1) - 1) > 1e-10
assert_array_equal(proba_max, proba_log_max)
assert_allclose(y_log_proba, np.log(y_proba))
def test_shuffle():
# Test that the shuffle parameter affects the training process (it should)
X, y = make_regression(n_samples=50, n_features=5, n_targets=1, random_state=0)
# The coefficients will be identical if both do or do not shuffle
for shuffle in [True, False]:
mlp1 = MLPRegressor(
hidden_layer_sizes=1,
max_iter=1,
batch_size=1,
random_state=0,
shuffle=shuffle,
)
mlp2 = MLPRegressor(
hidden_layer_sizes=1,
max_iter=1,
batch_size=1,
random_state=0,
shuffle=shuffle,
)
mlp1.fit(X, y)
mlp2.fit(X, y)
assert np.array_equal(mlp1.coefs_[0], mlp2.coefs_[0])
# The coefficients will be slightly different if shuffle=True
mlp1 = MLPRegressor(
hidden_layer_sizes=1, max_iter=1, batch_size=1, random_state=0, shuffle=True
)
mlp2 = MLPRegressor(
hidden_layer_sizes=1, max_iter=1, batch_size=1, random_state=0, shuffle=False
)
mlp1.fit(X, y)
mlp2.fit(X, y)
assert not np.array_equal(mlp1.coefs_[0], mlp2.coefs_[0])
@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
def test_sparse_matrices(csr_container):
# Test that sparse and dense input matrices output the same results.
X = X_digits_binary[:50]
y = y_digits_binary[:50]
X_sparse = csr_container(X)
mlp = MLPClassifier(solver="lbfgs", hidden_layer_sizes=15, random_state=1)
mlp.fit(X, y)
pred1 = mlp.predict(X)
mlp.fit(X_sparse, y)
pred2 = mlp.predict(X_sparse)
assert_almost_equal(pred1, pred2)
pred1 = mlp.predict(X)
pred2 = mlp.predict(X_sparse)
assert_array_equal(pred1, pred2)
def test_tolerance():
# Test tolerance.
# It should force the solver to exit the loop when it converges.
X = [[3, 2], [1, 6]]
y = [1, 0]
clf = MLPClassifier(tol=0.5, max_iter=3000, solver="sgd")
clf.fit(X, y)
assert clf.max_iter > clf.n_iter_
def test_verbose_sgd():
# Test verbose.
X = [[3, 2], [1, 6]]
y = [1, 0]
clf = MLPClassifier(solver="sgd", max_iter=2, verbose=10, hidden_layer_sizes=2)
old_stdout = sys.stdout
sys.stdout = output = StringIO()
with ignore_warnings(category=ConvergenceWarning):
clf.fit(X, y)
clf.partial_fit(X, y)
sys.stdout = old_stdout
assert "Iteration" in output.getvalue()
@pytest.mark.parametrize("MLPEstimator", [MLPClassifier, MLPRegressor])
def test_early_stopping(MLPEstimator):
X = X_digits_binary[:100]
y = y_digits_binary[:100]
tol = 0.2
mlp_estimator = MLPEstimator(
tol=tol, max_iter=3000, solver="sgd", early_stopping=True
)
mlp_estimator.fit(X, y)
assert mlp_estimator.max_iter > mlp_estimator.n_iter_
assert mlp_estimator.best_loss_ is None
assert isinstance(mlp_estimator.validation_scores_, list)
valid_scores = mlp_estimator.validation_scores_
best_valid_score = mlp_estimator.best_validation_score_
assert max(valid_scores) == best_valid_score
assert best_valid_score + tol > valid_scores[-2]
assert best_valid_score + tol > valid_scores[-1]
# check that the attributes `validation_scores_` and `best_validation_score_`
# are set to None when `early_stopping=False`
mlp_estimator = MLPEstimator(
tol=tol, max_iter=3000, solver="sgd", early_stopping=False
)
mlp_estimator.fit(X, y)
assert mlp_estimator.validation_scores_ is None
assert mlp_estimator.best_validation_score_ is None
assert mlp_estimator.best_loss_ is not None
def test_adaptive_learning_rate():
X = [[3, 2], [1, 6]]
y = [1, 0]
clf = MLPClassifier(tol=0.5, max_iter=3000, solver="sgd", learning_rate="adaptive")
clf.fit(X, y)
assert clf.max_iter > clf.n_iter_
assert 1e-6 > clf._optimizer.learning_rate
@ignore_warnings(category=RuntimeWarning)
def test_warm_start():
X = X_iris
y = y_iris
y_2classes = np.array([0] * 75 + [1] * 75)
y_3classes = np.array([0] * 40 + [1] * 40 + [2] * 70)
y_3classes_alt = np.array([0] * 50 + [1] * 50 + [3] * 50)
y_4classes = np.array([0] * 37 + [1] * 37 + [2] * 38 + [3] * 38)
y_5classes = np.array([0] * 30 + [1] * 30 + [2] * 30 + [3] * 30 + [4] * 30)
# No error raised
clf = MLPClassifier(hidden_layer_sizes=2, solver="lbfgs", warm_start=True).fit(X, y)
clf.fit(X, y)
clf.fit(X, y_3classes)
for y_i in (y_2classes, y_3classes_alt, y_4classes, y_5classes):
clf = MLPClassifier(hidden_layer_sizes=2, solver="lbfgs", warm_start=True).fit(
X, y
)
message = (
"warm_start can only be used where `y` has the same "
"classes as in the previous call to fit."
" Previously got [0 1 2], `y` has %s" % np.unique(y_i)
)
with pytest.raises(ValueError, match=re.escape(message)):
clf.fit(X, y_i)
@pytest.mark.parametrize("MLPEstimator", [MLPClassifier, MLPRegressor])
def test_warm_start_full_iteration(MLPEstimator):
# Non-regression test for:
# https://github.com/scikit-learn/scikit-learn/issues/16812
# Check that the MLP estimator accomplish `max_iter` with a
# warm started estimator.
X, y = X_iris, y_iris
max_iter = 3
clf = MLPEstimator(
hidden_layer_sizes=2, solver="sgd", warm_start=True, max_iter=max_iter
)
clf.fit(X, y)
assert max_iter == clf.n_iter_
clf.fit(X, y)
assert max_iter == clf.n_iter_
def test_n_iter_no_change():
# test n_iter_no_change using binary data set
# the classifying fitting process is not prone to loss curve fluctuations
X = X_digits_binary[:100]
y = y_digits_binary[:100]
tol = 0.01
max_iter = 3000
# test multiple n_iter_no_change
for n_iter_no_change in [2, 5, 10, 50, 100]:
clf = MLPClassifier(
tol=tol, max_iter=max_iter, solver="sgd", n_iter_no_change=n_iter_no_change
)
clf.fit(X, y)
# validate n_iter_no_change
assert clf._no_improvement_count == n_iter_no_change + 1
assert max_iter > clf.n_iter_
@ignore_warnings(category=ConvergenceWarning)
def test_n_iter_no_change_inf():
# test n_iter_no_change using binary data set
# the fitting process should go to max_iter iterations
X = X_digits_binary[:100]
y = y_digits_binary[:100]
# set a ridiculous tolerance
# this should always trigger _update_no_improvement_count()
tol = 1e9
# fit
n_iter_no_change = np.inf
max_iter = 3000
clf = MLPClassifier(
tol=tol, max_iter=max_iter, solver="sgd", n_iter_no_change=n_iter_no_change
)
clf.fit(X, y)
# validate n_iter_no_change doesn't cause early stopping
assert clf.n_iter_ == max_iter
# validate _update_no_improvement_count() was always triggered
assert clf._no_improvement_count == clf.n_iter_ - 1
def test_early_stopping_stratified():
# Make sure data splitting for early stopping is stratified
X = [[1, 2], [2, 3], [3, 4], [4, 5]]
y = [0, 0, 0, 1]
mlp = MLPClassifier(early_stopping=True)
with pytest.raises(
ValueError, match="The least populated class in y has only 1 member"
):
mlp.fit(X, y)
def test_mlp_classifier_dtypes_casting():
# Compare predictions for different dtypes
mlp_64 = MLPClassifier(
alpha=1e-5, hidden_layer_sizes=(5, 3), random_state=1, max_iter=50
)
mlp_64.fit(X_digits[:300], y_digits[:300])
pred_64 = mlp_64.predict(X_digits[300:])
proba_64 = mlp_64.predict_proba(X_digits[300:])
mlp_32 = MLPClassifier(
alpha=1e-5, hidden_layer_sizes=(5, 3), random_state=1, max_iter=50
)
mlp_32.fit(X_digits[:300].astype(np.float32), y_digits[:300])
pred_32 = mlp_32.predict(X_digits[300:].astype(np.float32))
proba_32 = mlp_32.predict_proba(X_digits[300:].astype(np.float32))
assert_array_equal(pred_64, pred_32)
assert_allclose(proba_64, proba_32, rtol=1e-02)
def test_mlp_regressor_dtypes_casting():
mlp_64 = MLPRegressor(
alpha=1e-5, hidden_layer_sizes=(5, 3), random_state=1, max_iter=50
)
mlp_64.fit(X_digits[:300], y_digits[:300])
pred_64 = mlp_64.predict(X_digits[300:])
mlp_32 = MLPRegressor(
alpha=1e-5, hidden_layer_sizes=(5, 3), random_state=1, max_iter=50
)
mlp_32.fit(X_digits[:300].astype(np.float32), y_digits[:300])
pred_32 = mlp_32.predict(X_digits[300:].astype(np.float32))
assert_allclose(pred_64, pred_32, rtol=1e-04)
@pytest.mark.parametrize("dtype", [np.float32, np.float64])
@pytest.mark.parametrize("Estimator", [MLPClassifier, MLPRegressor])
def test_mlp_param_dtypes(dtype, Estimator):
# Checks if input dtype is used for network parameters
# and predictions
X, y = X_digits.astype(dtype), y_digits
mlp = Estimator(alpha=1e-5, hidden_layer_sizes=(5, 3), random_state=1, max_iter=50)
mlp.fit(X[:300], y[:300])
pred = mlp.predict(X[300:])
assert all([intercept.dtype == dtype for intercept in mlp.intercepts_])
assert all([coef.dtype == dtype for coef in mlp.coefs_])
if Estimator == MLPRegressor:
assert pred.dtype == dtype
def test_mlp_loading_from_joblib_partial_fit(tmp_path):
"""Loading from MLP and partial fitting updates weights. Non-regression
test for #19626."""
pre_trained_estimator = MLPRegressor(
hidden_layer_sizes=(42,), random_state=42, learning_rate_init=0.01, max_iter=200
)
features, target = [[2]], [4]
# Fit on x=2, y=4
pre_trained_estimator.fit(features, target)
# dump and load model
pickled_file = tmp_path / "mlp.pkl"
joblib.dump(pre_trained_estimator, pickled_file)
load_estimator = joblib.load(pickled_file)
# Train for a more epochs on point x=2, y=1
fine_tune_features, fine_tune_target = [[2]], [1]
for _ in range(200):
load_estimator.partial_fit(fine_tune_features, fine_tune_target)
# finetuned model learned the new target
predicted_value = load_estimator.predict(fine_tune_features)
assert_allclose(predicted_value, fine_tune_target, rtol=1e-4)
@pytest.mark.parametrize("Estimator", [MLPClassifier, MLPRegressor])
def test_preserve_feature_names(Estimator):
"""Check that feature names are preserved when early stopping is enabled.
Feature names are required for consistency checks during scoring.
Non-regression test for gh-24846
"""
pd = pytest.importorskip("pandas")
rng = np.random.RandomState(0)
X = pd.DataFrame(data=rng.randn(10, 2), columns=["colname_a", "colname_b"])
y = pd.Series(data=np.full(10, 1), name="colname_y")
model = Estimator(early_stopping=True, validation_fraction=0.2)
with warnings.catch_warnings():
warnings.simplefilter("error", UserWarning)
model.fit(X, y)
@pytest.mark.parametrize("MLPEstimator", [MLPClassifier, MLPRegressor])
def test_mlp_warm_start_with_early_stopping(MLPEstimator):
"""Check that early stopping works with warm start."""
mlp = MLPEstimator(
max_iter=10, random_state=0, warm_start=True, early_stopping=True
)
mlp.fit(X_iris, y_iris)
n_validation_scores = len(mlp.validation_scores_)
mlp.set_params(max_iter=20)
mlp.fit(X_iris, y_iris)
assert len(mlp.validation_scores_) > n_validation_scores
@pytest.mark.parametrize("MLPEstimator", [MLPClassifier, MLPRegressor])
@pytest.mark.parametrize("solver", ["sgd", "adam", "lbfgs"])
def test_mlp_warm_start_no_convergence(MLPEstimator, solver):
"""Check that we stop the number of iteration at `max_iter` when warm starting.
Non-regression test for:
https://github.com/scikit-learn/scikit-learn/issues/24764
"""
model = MLPEstimator(
solver=solver,
warm_start=True,
early_stopping=False,
max_iter=10,
n_iter_no_change=np.inf,
random_state=0,
)
with pytest.warns(ConvergenceWarning):
model.fit(X_iris, y_iris)
assert model.n_iter_ == 10
model.set_params(max_iter=20)
with pytest.warns(ConvergenceWarning):
model.fit(X_iris, y_iris)
assert model.n_iter_ == 20
@pytest.mark.parametrize("MLPEstimator", [MLPClassifier, MLPRegressor])
def test_mlp_partial_fit_after_fit(MLPEstimator):
"""Check partial fit does not fail after fit when early_stopping=True.
Non-regression test for gh-25693.
"""
mlp = MLPEstimator(early_stopping=True, random_state=0).fit(X_iris, y_iris)
msg = "partial_fit does not support early_stopping=True"
with pytest.raises(ValueError, match=msg):
mlp.partial_fit(X_iris, y_iris)

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import re
import sys
from io import StringIO
import numpy as np
import pytest
from sklearn.datasets import load_digits
from sklearn.neural_network import BernoulliRBM
from sklearn.utils._testing import (
assert_allclose,
assert_almost_equal,
assert_array_equal,
)
from sklearn.utils.fixes import CSC_CONTAINERS, CSR_CONTAINERS, LIL_CONTAINERS
from sklearn.utils.validation import assert_all_finite
Xdigits, _ = load_digits(return_X_y=True)
Xdigits -= Xdigits.min()
Xdigits /= Xdigits.max()
def test_fit():
X = Xdigits.copy()
rbm = BernoulliRBM(
n_components=64, learning_rate=0.1, batch_size=10, n_iter=7, random_state=9
)
rbm.fit(X)
assert_almost_equal(rbm.score_samples(X).mean(), -21.0, decimal=0)
# in-place tricks shouldn't have modified X
assert_array_equal(X, Xdigits)
def test_partial_fit():
X = Xdigits.copy()
rbm = BernoulliRBM(
n_components=64, learning_rate=0.1, batch_size=20, random_state=9
)
n_samples = X.shape[0]
n_batches = int(np.ceil(float(n_samples) / rbm.batch_size))
batch_slices = np.array_split(X, n_batches)
for i in range(7):
for batch in batch_slices:
rbm.partial_fit(batch)
assert_almost_equal(rbm.score_samples(X).mean(), -21.0, decimal=0)
assert_array_equal(X, Xdigits)
def test_transform():
X = Xdigits[:100]
rbm1 = BernoulliRBM(n_components=16, batch_size=5, n_iter=5, random_state=42)
rbm1.fit(X)
Xt1 = rbm1.transform(X)
Xt2 = rbm1._mean_hiddens(X)
assert_array_equal(Xt1, Xt2)
@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
def test_small_sparse(csr_container):
# BernoulliRBM should work on small sparse matrices.
X = csr_container(Xdigits[:4])
BernoulliRBM().fit(X) # no exception
@pytest.mark.parametrize("sparse_container", CSC_CONTAINERS + CSR_CONTAINERS)
def test_small_sparse_partial_fit(sparse_container):
X_sparse = sparse_container(Xdigits[:100])
X = Xdigits[:100].copy()
rbm1 = BernoulliRBM(
n_components=64, learning_rate=0.1, batch_size=10, random_state=9
)
rbm2 = BernoulliRBM(
n_components=64, learning_rate=0.1, batch_size=10, random_state=9
)
rbm1.partial_fit(X_sparse)
rbm2.partial_fit(X)
assert_almost_equal(
rbm1.score_samples(X).mean(), rbm2.score_samples(X).mean(), decimal=0
)
def test_sample_hiddens():
rng = np.random.RandomState(0)
X = Xdigits[:100]
rbm1 = BernoulliRBM(n_components=2, batch_size=5, n_iter=5, random_state=42)
rbm1.fit(X)
h = rbm1._mean_hiddens(X[0])
hs = np.mean([rbm1._sample_hiddens(X[0], rng) for i in range(100)], 0)
assert_almost_equal(h, hs, decimal=1)
@pytest.mark.parametrize("csc_container", CSC_CONTAINERS)
def test_fit_gibbs(csc_container):
# XXX: this test is very seed-dependent! It probably needs to be rewritten.
# Gibbs on the RBM hidden layer should be able to recreate [[0], [1]]
# from the same input
rng = np.random.RandomState(42)
X = np.array([[0.0], [1.0]])
rbm1 = BernoulliRBM(n_components=2, batch_size=2, n_iter=42, random_state=rng)
# you need that much iters
rbm1.fit(X)
assert_almost_equal(
rbm1.components_, np.array([[0.02649814], [0.02009084]]), decimal=4
)
assert_almost_equal(rbm1.gibbs(X), X)
# Gibbs on the RBM hidden layer should be able to recreate [[0], [1]] from
# the same input even when the input is sparse, and test against non-sparse
rng = np.random.RandomState(42)
X = csc_container([[0.0], [1.0]])
rbm2 = BernoulliRBM(n_components=2, batch_size=2, n_iter=42, random_state=rng)
rbm2.fit(X)
assert_almost_equal(
rbm2.components_, np.array([[0.02649814], [0.02009084]]), decimal=4
)
assert_almost_equal(rbm2.gibbs(X), X.toarray())
assert_almost_equal(rbm1.components_, rbm2.components_)
def test_gibbs_smoke():
# Check if we don't get NaNs sampling the full digits dataset.
# Also check that sampling again will yield different results.
X = Xdigits
rbm1 = BernoulliRBM(n_components=42, batch_size=40, n_iter=20, random_state=42)
rbm1.fit(X)
X_sampled = rbm1.gibbs(X)
assert_all_finite(X_sampled)
X_sampled2 = rbm1.gibbs(X)
assert np.all((X_sampled != X_sampled2).max(axis=1))
@pytest.mark.parametrize("lil_containers", LIL_CONTAINERS)
def test_score_samples(lil_containers):
# Test score_samples (pseudo-likelihood) method.
# Assert that pseudo-likelihood is computed without clipping.
# See Fabian's blog, http://bit.ly/1iYefRk
rng = np.random.RandomState(42)
X = np.vstack([np.zeros(1000), np.ones(1000)])
rbm1 = BernoulliRBM(n_components=10, batch_size=2, n_iter=10, random_state=rng)
rbm1.fit(X)
assert (rbm1.score_samples(X) < -300).all()
# Sparse vs. dense should not affect the output. Also test sparse input
# validation.
rbm1.random_state = 42
d_score = rbm1.score_samples(X)
rbm1.random_state = 42
s_score = rbm1.score_samples(lil_containers(X))
assert_almost_equal(d_score, s_score)
# Test numerical stability (#2785): would previously generate infinities
# and crash with an exception.
with np.errstate(under="ignore"):
rbm1.score_samples([np.arange(1000) * 100])
def test_rbm_verbose():
rbm = BernoulliRBM(n_iter=2, verbose=10)
old_stdout = sys.stdout
sys.stdout = StringIO()
try:
rbm.fit(Xdigits)
finally:
sys.stdout = old_stdout
@pytest.mark.parametrize("csc_container", CSC_CONTAINERS)
def test_sparse_and_verbose(csc_container):
# Make sure RBM works with sparse input when verbose=True
old_stdout = sys.stdout
sys.stdout = StringIO()
X = csc_container([[0.0], [1.0]])
rbm = BernoulliRBM(
n_components=2, batch_size=2, n_iter=1, random_state=42, verbose=True
)
try:
rbm.fit(X)
s = sys.stdout.getvalue()
# make sure output is sound
assert re.match(
r"\[BernoulliRBM\] Iteration 1,"
r" pseudo-likelihood = -?(\d)+(\.\d+)?,"
r" time = (\d|\.)+s",
s,
)
finally:
sys.stdout = old_stdout
@pytest.mark.parametrize(
"dtype_in, dtype_out",
[(np.float32, np.float32), (np.float64, np.float64), (int, np.float64)],
)
def test_transformer_dtypes_casting(dtype_in, dtype_out):
X = Xdigits[:100].astype(dtype_in)
rbm = BernoulliRBM(n_components=16, batch_size=5, n_iter=5, random_state=42)
Xt = rbm.fit_transform(X)
# dtype_in and dtype_out should be consistent
assert Xt.dtype == dtype_out, "transform dtype: {} - original dtype: {}".format(
Xt.dtype, X.dtype
)
def test_convergence_dtype_consistency():
# float 64 transformer
X_64 = Xdigits[:100].astype(np.float64)
rbm_64 = BernoulliRBM(n_components=16, batch_size=5, n_iter=5, random_state=42)
Xt_64 = rbm_64.fit_transform(X_64)
# float 32 transformer
X_32 = Xdigits[:100].astype(np.float32)
rbm_32 = BernoulliRBM(n_components=16, batch_size=5, n_iter=5, random_state=42)
Xt_32 = rbm_32.fit_transform(X_32)
# results and attributes should be close enough in 32 bit and 64 bit
assert_allclose(Xt_64, Xt_32, rtol=1e-06, atol=0)
assert_allclose(
rbm_64.intercept_hidden_, rbm_32.intercept_hidden_, rtol=1e-06, atol=0
)
assert_allclose(
rbm_64.intercept_visible_, rbm_32.intercept_visible_, rtol=1e-05, atol=0
)
assert_allclose(rbm_64.components_, rbm_32.components_, rtol=1e-03, atol=0)
assert_allclose(rbm_64.h_samples_, rbm_32.h_samples_)
@pytest.mark.parametrize("method", ["fit", "partial_fit"])
def test_feature_names_out(method):
"""Check `get_feature_names_out` for `BernoulliRBM`."""
n_components = 10
rbm = BernoulliRBM(n_components=n_components)
getattr(rbm, method)(Xdigits)
names = rbm.get_feature_names_out()
expected_names = [f"bernoullirbm{i}" for i in range(n_components)]
assert_array_equal(expected_names, names)

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import numpy as np
from sklearn.neural_network._stochastic_optimizers import (
AdamOptimizer,
BaseOptimizer,
SGDOptimizer,
)
from sklearn.utils._testing import assert_array_equal
shapes = [(4, 6), (6, 8), (7, 8, 9)]
def test_base_optimizer():
for lr in [10**i for i in range(-3, 4)]:
optimizer = BaseOptimizer(lr)
assert optimizer.trigger_stopping("", False)
def test_sgd_optimizer_no_momentum():
params = [np.zeros(shape) for shape in shapes]
rng = np.random.RandomState(0)
for lr in [10**i for i in range(-3, 4)]:
optimizer = SGDOptimizer(params, lr, momentum=0, nesterov=False)
grads = [rng.random_sample(shape) for shape in shapes]
expected = [param - lr * grad for param, grad in zip(params, grads)]
optimizer.update_params(params, grads)
for exp, param in zip(expected, params):
assert_array_equal(exp, param)
def test_sgd_optimizer_momentum():
params = [np.zeros(shape) for shape in shapes]
lr = 0.1
rng = np.random.RandomState(0)
for momentum in np.arange(0.5, 0.9, 0.1):
optimizer = SGDOptimizer(params, lr, momentum=momentum, nesterov=False)
velocities = [rng.random_sample(shape) for shape in shapes]
optimizer.velocities = velocities
grads = [rng.random_sample(shape) for shape in shapes]
updates = [
momentum * velocity - lr * grad for velocity, grad in zip(velocities, grads)
]
expected = [param + update for param, update in zip(params, updates)]
optimizer.update_params(params, grads)
for exp, param in zip(expected, params):
assert_array_equal(exp, param)
def test_sgd_optimizer_trigger_stopping():
params = [np.zeros(shape) for shape in shapes]
lr = 2e-6
optimizer = SGDOptimizer(params, lr, lr_schedule="adaptive")
assert not optimizer.trigger_stopping("", False)
assert lr / 5 == optimizer.learning_rate
assert optimizer.trigger_stopping("", False)
def test_sgd_optimizer_nesterovs_momentum():
params = [np.zeros(shape) for shape in shapes]
lr = 0.1
rng = np.random.RandomState(0)
for momentum in np.arange(0.5, 0.9, 0.1):
optimizer = SGDOptimizer(params, lr, momentum=momentum, nesterov=True)
velocities = [rng.random_sample(shape) for shape in shapes]
optimizer.velocities = velocities
grads = [rng.random_sample(shape) for shape in shapes]
updates = [
momentum * velocity - lr * grad for velocity, grad in zip(velocities, grads)
]
updates = [
momentum * update - lr * grad for update, grad in zip(updates, grads)
]
expected = [param + update for param, update in zip(params, updates)]
optimizer.update_params(params, grads)
for exp, param in zip(expected, params):
assert_array_equal(exp, param)
def test_adam_optimizer():
params = [np.zeros(shape) for shape in shapes]
lr = 0.001
epsilon = 1e-8
rng = np.random.RandomState(0)
for beta_1 in np.arange(0.9, 1.0, 0.05):
for beta_2 in np.arange(0.995, 1.0, 0.001):
optimizer = AdamOptimizer(params, lr, beta_1, beta_2, epsilon)
ms = [rng.random_sample(shape) for shape in shapes]
vs = [rng.random_sample(shape) for shape in shapes]
t = 10
optimizer.ms = ms
optimizer.vs = vs
optimizer.t = t - 1
grads = [rng.random_sample(shape) for shape in shapes]
ms = [beta_1 * m + (1 - beta_1) * grad for m, grad in zip(ms, grads)]
vs = [beta_2 * v + (1 - beta_2) * (grad**2) for v, grad in zip(vs, grads)]
learning_rate = lr * np.sqrt(1 - beta_2**t) / (1 - beta_1**t)
updates = [
-learning_rate * m / (np.sqrt(v) + epsilon) for m, v in zip(ms, vs)
]
expected = [param + update for param, update in zip(params, updates)]
optimizer.update_params(params, grads)
for exp, param in zip(expected, params):
assert_array_equal(exp, param)