Upload edit\Qwen3-TTS-test\.venv\Lib\site-packages\sklearn\decomposition\tests\test_kernel_pca.py with huggingface_hub
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edit//Qwen3-TTS-test//.venv//Lib//site-packages//sklearn//decomposition//tests//test_kernel_pca.py
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|
| 1 |
+
import warnings
|
| 2 |
+
|
| 3 |
+
import numpy as np
|
| 4 |
+
import pytest
|
| 5 |
+
|
| 6 |
+
import sklearn
|
| 7 |
+
from sklearn.datasets import load_iris, make_blobs, make_circles
|
| 8 |
+
from sklearn.decomposition import PCA, KernelPCA
|
| 9 |
+
from sklearn.exceptions import NotFittedError
|
| 10 |
+
from sklearn.linear_model import Perceptron
|
| 11 |
+
from sklearn.metrics.pairwise import rbf_kernel
|
| 12 |
+
from sklearn.model_selection import GridSearchCV
|
| 13 |
+
from sklearn.pipeline import Pipeline
|
| 14 |
+
from sklearn.preprocessing import StandardScaler
|
| 15 |
+
from sklearn.utils._testing import (
|
| 16 |
+
assert_allclose,
|
| 17 |
+
assert_array_almost_equal,
|
| 18 |
+
assert_array_equal,
|
| 19 |
+
)
|
| 20 |
+
from sklearn.utils.fixes import CSR_CONTAINERS
|
| 21 |
+
from sklearn.utils.validation import _check_psd_eigenvalues
|
| 22 |
+
|
| 23 |
+
|
| 24 |
+
def test_kernel_pca(global_random_seed):
|
| 25 |
+
"""Nominal test for all solvers and all known kernels + a custom one
|
| 26 |
+
|
| 27 |
+
It tests
|
| 28 |
+
- that fit_transform is equivalent to fit+transform
|
| 29 |
+
- that the shapes of transforms and inverse transforms are correct
|
| 30 |
+
"""
|
| 31 |
+
rng = np.random.RandomState(global_random_seed)
|
| 32 |
+
X_fit = rng.random_sample((5, 4))
|
| 33 |
+
X_pred = rng.random_sample((2, 4))
|
| 34 |
+
|
| 35 |
+
def histogram(x, y, **kwargs):
|
| 36 |
+
# Histogram kernel implemented as a callable.
|
| 37 |
+
assert kwargs == {} # no kernel_params that we didn't ask for
|
| 38 |
+
return np.minimum(x, y).sum()
|
| 39 |
+
|
| 40 |
+
for eigen_solver in ("auto", "dense", "arpack", "randomized"):
|
| 41 |
+
for kernel in ("linear", "rbf", "poly", histogram):
|
| 42 |
+
# histogram kernel produces singular matrix inside linalg.solve
|
| 43 |
+
# XXX use a least-squares approximation?
|
| 44 |
+
inv = not callable(kernel)
|
| 45 |
+
|
| 46 |
+
# transform fit data
|
| 47 |
+
kpca = KernelPCA(
|
| 48 |
+
4, kernel=kernel, eigen_solver=eigen_solver, fit_inverse_transform=inv
|
| 49 |
+
)
|
| 50 |
+
X_fit_transformed = kpca.fit_transform(X_fit)
|
| 51 |
+
X_fit_transformed2 = kpca.fit(X_fit).transform(X_fit)
|
| 52 |
+
assert_array_almost_equal(
|
| 53 |
+
np.abs(X_fit_transformed), np.abs(X_fit_transformed2)
|
| 54 |
+
)
|
| 55 |
+
|
| 56 |
+
# non-regression test: previously, gamma would be 0 by default,
|
| 57 |
+
# forcing all eigenvalues to 0 under the poly kernel
|
| 58 |
+
assert X_fit_transformed.size != 0
|
| 59 |
+
|
| 60 |
+
# transform new data
|
| 61 |
+
X_pred_transformed = kpca.transform(X_pred)
|
| 62 |
+
assert X_pred_transformed.shape[1] == X_fit_transformed.shape[1]
|
| 63 |
+
|
| 64 |
+
# inverse transform
|
| 65 |
+
if inv:
|
| 66 |
+
X_pred2 = kpca.inverse_transform(X_pred_transformed)
|
| 67 |
+
assert X_pred2.shape == X_pred.shape
|
| 68 |
+
|
| 69 |
+
|
| 70 |
+
def test_kernel_pca_invalid_parameters():
|
| 71 |
+
"""Check that kPCA raises an error if the parameters are invalid
|
| 72 |
+
|
| 73 |
+
Tests fitting inverse transform with a precomputed kernel raises a
|
| 74 |
+
ValueError.
|
| 75 |
+
"""
|
| 76 |
+
estimator = KernelPCA(
|
| 77 |
+
n_components=10, fit_inverse_transform=True, kernel="precomputed"
|
| 78 |
+
)
|
| 79 |
+
err_ms = "Cannot fit_inverse_transform with a precomputed kernel"
|
| 80 |
+
with pytest.raises(ValueError, match=err_ms):
|
| 81 |
+
estimator.fit(np.random.randn(10, 10))
|
| 82 |
+
|
| 83 |
+
|
| 84 |
+
def test_kernel_pca_consistent_transform(global_random_seed):
|
| 85 |
+
"""Check robustness to mutations in the original training array
|
| 86 |
+
|
| 87 |
+
Test that after fitting a kPCA model, it stays independent of any
|
| 88 |
+
mutation of the values of the original data object by relying on an
|
| 89 |
+
internal copy.
|
| 90 |
+
"""
|
| 91 |
+
# X_fit_ needs to retain the old, unmodified copy of X
|
| 92 |
+
state = np.random.RandomState(global_random_seed)
|
| 93 |
+
X = state.rand(10, 10)
|
| 94 |
+
kpca = KernelPCA(random_state=state).fit(X)
|
| 95 |
+
transformed1 = kpca.transform(X)
|
| 96 |
+
|
| 97 |
+
X_copy = X.copy()
|
| 98 |
+
X[:, 0] = 666
|
| 99 |
+
transformed2 = kpca.transform(X_copy)
|
| 100 |
+
assert_array_almost_equal(transformed1, transformed2)
|
| 101 |
+
|
| 102 |
+
|
| 103 |
+
def test_kernel_pca_deterministic_output(global_random_seed):
|
| 104 |
+
"""Test that Kernel PCA produces deterministic output
|
| 105 |
+
|
| 106 |
+
Tests that the same inputs and random state produce the same output.
|
| 107 |
+
"""
|
| 108 |
+
rng = np.random.RandomState(global_random_seed)
|
| 109 |
+
X = rng.rand(10, 10)
|
| 110 |
+
eigen_solver = ("arpack", "dense")
|
| 111 |
+
|
| 112 |
+
for solver in eigen_solver:
|
| 113 |
+
transformed_X = np.zeros((20, 2))
|
| 114 |
+
for i in range(20):
|
| 115 |
+
kpca = KernelPCA(n_components=2, eigen_solver=solver, random_state=rng)
|
| 116 |
+
transformed_X[i, :] = kpca.fit_transform(X)[0]
|
| 117 |
+
assert_allclose(transformed_X, np.tile(transformed_X[0, :], 20).reshape(20, 2))
|
| 118 |
+
|
| 119 |
+
|
| 120 |
+
@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
|
| 121 |
+
def test_kernel_pca_sparse(csr_container, global_random_seed):
|
| 122 |
+
"""Test that kPCA works on a sparse data input.
|
| 123 |
+
|
| 124 |
+
Same test as ``test_kernel_pca except inverse_transform`` since it's not
|
| 125 |
+
implemented for sparse matrices.
|
| 126 |
+
"""
|
| 127 |
+
rng = np.random.RandomState(global_random_seed)
|
| 128 |
+
X_fit = csr_container(rng.random_sample((5, 4)))
|
| 129 |
+
X_pred = csr_container(rng.random_sample((2, 4)))
|
| 130 |
+
|
| 131 |
+
for eigen_solver in ("auto", "arpack", "randomized"):
|
| 132 |
+
for kernel in ("linear", "rbf", "poly"):
|
| 133 |
+
# transform fit data
|
| 134 |
+
kpca = KernelPCA(
|
| 135 |
+
4,
|
| 136 |
+
kernel=kernel,
|
| 137 |
+
eigen_solver=eigen_solver,
|
| 138 |
+
fit_inverse_transform=False,
|
| 139 |
+
random_state=0,
|
| 140 |
+
)
|
| 141 |
+
X_fit_transformed = kpca.fit_transform(X_fit)
|
| 142 |
+
X_fit_transformed2 = kpca.fit(X_fit).transform(X_fit)
|
| 143 |
+
assert_array_almost_equal(
|
| 144 |
+
np.abs(X_fit_transformed), np.abs(X_fit_transformed2)
|
| 145 |
+
)
|
| 146 |
+
|
| 147 |
+
# transform new data
|
| 148 |
+
X_pred_transformed = kpca.transform(X_pred)
|
| 149 |
+
assert X_pred_transformed.shape[1] == X_fit_transformed.shape[1]
|
| 150 |
+
|
| 151 |
+
# inverse transform: not available for sparse matrices
|
| 152 |
+
# XXX: should we raise another exception type here? For instance:
|
| 153 |
+
# NotImplementedError.
|
| 154 |
+
with pytest.raises(NotFittedError):
|
| 155 |
+
kpca.inverse_transform(X_pred_transformed)
|
| 156 |
+
|
| 157 |
+
|
| 158 |
+
@pytest.mark.parametrize("solver", ["auto", "dense", "arpack", "randomized"])
|
| 159 |
+
@pytest.mark.parametrize("n_features", [4, 10])
|
| 160 |
+
def test_kernel_pca_linear_kernel(solver, n_features, global_random_seed):
|
| 161 |
+
"""Test that kPCA with linear kernel is equivalent to PCA for all solvers.
|
| 162 |
+
|
| 163 |
+
KernelPCA with linear kernel should produce the same output as PCA.
|
| 164 |
+
"""
|
| 165 |
+
rng = np.random.RandomState(global_random_seed)
|
| 166 |
+
X_fit = rng.random_sample((5, n_features))
|
| 167 |
+
X_pred = rng.random_sample((2, n_features))
|
| 168 |
+
|
| 169 |
+
# for a linear kernel, kernel PCA should find the same projection as PCA
|
| 170 |
+
# modulo the sign (direction)
|
| 171 |
+
# fit only the first four components: fifth is near zero eigenvalue, so
|
| 172 |
+
# can be trimmed due to roundoff error
|
| 173 |
+
n_comps = 3 if solver == "arpack" else 4
|
| 174 |
+
assert_array_almost_equal(
|
| 175 |
+
np.abs(KernelPCA(n_comps, eigen_solver=solver).fit(X_fit).transform(X_pred)),
|
| 176 |
+
np.abs(
|
| 177 |
+
PCA(n_comps, svd_solver=solver if solver != "dense" else "full")
|
| 178 |
+
.fit(X_fit)
|
| 179 |
+
.transform(X_pred)
|
| 180 |
+
),
|
| 181 |
+
)
|
| 182 |
+
|
| 183 |
+
|
| 184 |
+
def test_kernel_pca_n_components():
|
| 185 |
+
"""Test that `n_components` is correctly taken into account for projections
|
| 186 |
+
|
| 187 |
+
For all solvers this tests that the output has the correct shape depending
|
| 188 |
+
on the selected number of components.
|
| 189 |
+
"""
|
| 190 |
+
rng = np.random.RandomState(0)
|
| 191 |
+
X_fit = rng.random_sample((5, 4))
|
| 192 |
+
X_pred = rng.random_sample((2, 4))
|
| 193 |
+
|
| 194 |
+
for eigen_solver in ("dense", "arpack", "randomized"):
|
| 195 |
+
for c in [1, 2, 4]:
|
| 196 |
+
kpca = KernelPCA(n_components=c, eigen_solver=eigen_solver)
|
| 197 |
+
shape = kpca.fit(X_fit).transform(X_pred).shape
|
| 198 |
+
|
| 199 |
+
assert shape == (2, c)
|
| 200 |
+
|
| 201 |
+
|
| 202 |
+
def test_remove_zero_eig():
|
| 203 |
+
"""Check that the ``remove_zero_eig`` parameter works correctly.
|
| 204 |
+
|
| 205 |
+
Tests that the null-space (Zero) eigenvalues are removed when
|
| 206 |
+
remove_zero_eig=True, whereas they are not by default.
|
| 207 |
+
"""
|
| 208 |
+
X = np.array([[1 - 1e-30, 1], [1, 1], [1, 1 - 1e-20]])
|
| 209 |
+
|
| 210 |
+
# n_components=None (default) => remove_zero_eig is True
|
| 211 |
+
kpca = KernelPCA()
|
| 212 |
+
Xt = kpca.fit_transform(X)
|
| 213 |
+
assert Xt.shape == (3, 0)
|
| 214 |
+
|
| 215 |
+
kpca = KernelPCA(n_components=2)
|
| 216 |
+
Xt = kpca.fit_transform(X)
|
| 217 |
+
assert Xt.shape == (3, 2)
|
| 218 |
+
|
| 219 |
+
kpca = KernelPCA(n_components=2, remove_zero_eig=True)
|
| 220 |
+
Xt = kpca.fit_transform(X)
|
| 221 |
+
assert Xt.shape == (3, 0)
|
| 222 |
+
|
| 223 |
+
|
| 224 |
+
def test_leave_zero_eig():
|
| 225 |
+
"""Non-regression test for issue #12141 (PR #12143)
|
| 226 |
+
|
| 227 |
+
This test checks that fit().transform() returns the same result as
|
| 228 |
+
fit_transform() in case of non-removed zero eigenvalue.
|
| 229 |
+
"""
|
| 230 |
+
X_fit = np.array([[1, 1], [0, 0]])
|
| 231 |
+
|
| 232 |
+
# Assert that even with all np warnings on, there is no div by zero warning
|
| 233 |
+
with warnings.catch_warnings():
|
| 234 |
+
# There might be warnings about the kernel being badly conditioned,
|
| 235 |
+
# but there should not be warnings about division by zero.
|
| 236 |
+
# (Numpy division by zero warning can have many message variants, but
|
| 237 |
+
# at least we know that it is a RuntimeWarning so let's check only this)
|
| 238 |
+
warnings.simplefilter("error", RuntimeWarning)
|
| 239 |
+
with np.errstate(all="warn"):
|
| 240 |
+
k = KernelPCA(n_components=2, remove_zero_eig=False, eigen_solver="dense")
|
| 241 |
+
# Fit, then transform
|
| 242 |
+
A = k.fit(X_fit).transform(X_fit)
|
| 243 |
+
# Do both at once
|
| 244 |
+
B = k.fit_transform(X_fit)
|
| 245 |
+
# Compare
|
| 246 |
+
assert_array_almost_equal(np.abs(A), np.abs(B))
|
| 247 |
+
|
| 248 |
+
|
| 249 |
+
def test_kernel_pca_precomputed(global_random_seed):
|
| 250 |
+
"""Test that kPCA works with a precomputed kernel, for all solvers"""
|
| 251 |
+
rng = np.random.RandomState(global_random_seed)
|
| 252 |
+
X_fit = rng.random_sample((5, 4))
|
| 253 |
+
X_pred = rng.random_sample((2, 4))
|
| 254 |
+
|
| 255 |
+
for eigen_solver in ("dense", "arpack", "randomized"):
|
| 256 |
+
X_kpca = (
|
| 257 |
+
KernelPCA(4, eigen_solver=eigen_solver, random_state=0)
|
| 258 |
+
.fit(X_fit)
|
| 259 |
+
.transform(X_pred)
|
| 260 |
+
)
|
| 261 |
+
|
| 262 |
+
X_kpca2 = (
|
| 263 |
+
KernelPCA(
|
| 264 |
+
4, eigen_solver=eigen_solver, kernel="precomputed", random_state=0
|
| 265 |
+
)
|
| 266 |
+
.fit(np.dot(X_fit, X_fit.T))
|
| 267 |
+
.transform(np.dot(X_pred, X_fit.T))
|
| 268 |
+
)
|
| 269 |
+
|
| 270 |
+
X_kpca_train = KernelPCA(
|
| 271 |
+
4, eigen_solver=eigen_solver, kernel="precomputed", random_state=0
|
| 272 |
+
).fit_transform(np.dot(X_fit, X_fit.T))
|
| 273 |
+
|
| 274 |
+
X_kpca_train2 = (
|
| 275 |
+
KernelPCA(
|
| 276 |
+
4, eigen_solver=eigen_solver, kernel="precomputed", random_state=0
|
| 277 |
+
)
|
| 278 |
+
.fit(np.dot(X_fit, X_fit.T))
|
| 279 |
+
.transform(np.dot(X_fit, X_fit.T))
|
| 280 |
+
)
|
| 281 |
+
|
| 282 |
+
assert_array_almost_equal(np.abs(X_kpca), np.abs(X_kpca2))
|
| 283 |
+
|
| 284 |
+
assert_array_almost_equal(np.abs(X_kpca_train), np.abs(X_kpca_train2))
|
| 285 |
+
|
| 286 |
+
|
| 287 |
+
@pytest.mark.parametrize("solver", ["auto", "dense", "arpack", "randomized"])
|
| 288 |
+
def test_kernel_pca_precomputed_non_symmetric(solver):
|
| 289 |
+
"""Check that the kernel centerer works.
|
| 290 |
+
|
| 291 |
+
Tests that a non symmetric precomputed kernel is actually accepted
|
| 292 |
+
because the kernel centerer does its job correctly.
|
| 293 |
+
"""
|
| 294 |
+
|
| 295 |
+
# a non symmetric gram matrix
|
| 296 |
+
K = [[1, 2], [3, 40]]
|
| 297 |
+
kpca = KernelPCA(
|
| 298 |
+
kernel="precomputed", eigen_solver=solver, n_components=1, random_state=0
|
| 299 |
+
)
|
| 300 |
+
kpca.fit(K) # no error
|
| 301 |
+
|
| 302 |
+
# same test with centered kernel
|
| 303 |
+
Kc = [[9, -9], [-9, 9]]
|
| 304 |
+
kpca_c = KernelPCA(
|
| 305 |
+
kernel="precomputed", eigen_solver=solver, n_components=1, random_state=0
|
| 306 |
+
)
|
| 307 |
+
kpca_c.fit(Kc)
|
| 308 |
+
|
| 309 |
+
# comparison between the non-centered and centered versions
|
| 310 |
+
assert_array_equal(kpca.eigenvectors_, kpca_c.eigenvectors_)
|
| 311 |
+
assert_array_equal(kpca.eigenvalues_, kpca_c.eigenvalues_)
|
| 312 |
+
|
| 313 |
+
|
| 314 |
+
def test_gridsearch_pipeline():
|
| 315 |
+
"""Check that kPCA works as expected in a grid search pipeline
|
| 316 |
+
|
| 317 |
+
Test if we can do a grid-search to find parameters to separate
|
| 318 |
+
circles with a perceptron model.
|
| 319 |
+
"""
|
| 320 |
+
X, y = make_circles(n_samples=400, factor=0.3, noise=0.05, random_state=0)
|
| 321 |
+
kpca = KernelPCA(kernel="rbf", n_components=2)
|
| 322 |
+
pipeline = Pipeline([("kernel_pca", kpca), ("Perceptron", Perceptron(max_iter=5))])
|
| 323 |
+
param_grid = dict(kernel_pca__gamma=2.0 ** np.arange(-2, 2))
|
| 324 |
+
grid_search = GridSearchCV(pipeline, cv=3, param_grid=param_grid)
|
| 325 |
+
grid_search.fit(X, y)
|
| 326 |
+
assert grid_search.best_score_ == 1
|
| 327 |
+
|
| 328 |
+
|
| 329 |
+
def test_gridsearch_pipeline_precomputed():
|
| 330 |
+
"""Check that kPCA works as expected in a grid search pipeline (2)
|
| 331 |
+
|
| 332 |
+
Test if we can do a grid-search to find parameters to separate
|
| 333 |
+
circles with a perceptron model. This test uses a precomputed kernel.
|
| 334 |
+
"""
|
| 335 |
+
X, y = make_circles(n_samples=400, factor=0.3, noise=0.05, random_state=0)
|
| 336 |
+
kpca = KernelPCA(kernel="precomputed", n_components=2)
|
| 337 |
+
pipeline = Pipeline([("kernel_pca", kpca), ("Perceptron", Perceptron(max_iter=5))])
|
| 338 |
+
param_grid = dict(Perceptron__max_iter=np.arange(1, 5))
|
| 339 |
+
grid_search = GridSearchCV(pipeline, cv=3, param_grid=param_grid)
|
| 340 |
+
X_kernel = rbf_kernel(X, gamma=2.0)
|
| 341 |
+
grid_search.fit(X_kernel, y)
|
| 342 |
+
assert grid_search.best_score_ == 1
|
| 343 |
+
|
| 344 |
+
|
| 345 |
+
def test_nested_circles():
|
| 346 |
+
"""Check that kPCA projects in a space where nested circles are separable
|
| 347 |
+
|
| 348 |
+
Tests that 2D nested circles become separable with a perceptron when
|
| 349 |
+
projected in the first 2 kPCA using an RBF kernel, while raw samples
|
| 350 |
+
are not directly separable in the original space.
|
| 351 |
+
"""
|
| 352 |
+
X, y = make_circles(n_samples=400, factor=0.3, noise=0.05, random_state=0)
|
| 353 |
+
|
| 354 |
+
# 2D nested circles are not linearly separable
|
| 355 |
+
train_score = Perceptron(max_iter=5).fit(X, y).score(X, y)
|
| 356 |
+
assert train_score < 0.8
|
| 357 |
+
|
| 358 |
+
# Project the circles data into the first 2 components of a RBF Kernel
|
| 359 |
+
# PCA model.
|
| 360 |
+
# Note that the gamma value is data dependent. If this test breaks
|
| 361 |
+
# and the gamma value has to be updated, the Kernel PCA example will
|
| 362 |
+
# have to be updated too.
|
| 363 |
+
kpca = KernelPCA(
|
| 364 |
+
kernel="rbf", n_components=2, fit_inverse_transform=True, gamma=2.0
|
| 365 |
+
)
|
| 366 |
+
X_kpca = kpca.fit_transform(X)
|
| 367 |
+
|
| 368 |
+
# The data is perfectly linearly separable in that space
|
| 369 |
+
train_score = Perceptron(max_iter=5).fit(X_kpca, y).score(X_kpca, y)
|
| 370 |
+
assert train_score == 1.0
|
| 371 |
+
|
| 372 |
+
|
| 373 |
+
def test_kernel_conditioning():
|
| 374 |
+
"""Check that ``_check_psd_eigenvalues`` is correctly called in kPCA
|
| 375 |
+
|
| 376 |
+
Non-regression test for issue #12140 (PR #12145).
|
| 377 |
+
"""
|
| 378 |
+
|
| 379 |
+
# create a pathological X leading to small non-zero eigenvalue
|
| 380 |
+
X = [[5, 1], [5 + 1e-8, 1e-8], [5 + 1e-8, 0]]
|
| 381 |
+
kpca = KernelPCA(kernel="linear", n_components=2, fit_inverse_transform=True)
|
| 382 |
+
kpca.fit(X)
|
| 383 |
+
|
| 384 |
+
# check that the small non-zero eigenvalue was correctly set to zero
|
| 385 |
+
assert kpca.eigenvalues_.min() == 0
|
| 386 |
+
assert np.all(kpca.eigenvalues_ == _check_psd_eigenvalues(kpca.eigenvalues_))
|
| 387 |
+
|
| 388 |
+
|
| 389 |
+
@pytest.mark.parametrize("solver", ["auto", "dense", "arpack", "randomized"])
|
| 390 |
+
def test_precomputed_kernel_not_psd(solver):
|
| 391 |
+
"""Check how KernelPCA works with non-PSD kernels depending on n_components
|
| 392 |
+
|
| 393 |
+
Tests for all methods what happens with a non PSD gram matrix (this
|
| 394 |
+
can happen in an isomap scenario, or with custom kernel functions, or
|
| 395 |
+
maybe with ill-posed datasets).
|
| 396 |
+
|
| 397 |
+
When ``n_component`` is large enough to capture a negative eigenvalue, an
|
| 398 |
+
error should be raised. Otherwise, KernelPCA should run without error
|
| 399 |
+
since the negative eigenvalues are not selected.
|
| 400 |
+
"""
|
| 401 |
+
|
| 402 |
+
# a non PSD kernel with large eigenvalues, already centered
|
| 403 |
+
# it was captured from an isomap call and multiplied by 100 for compacity
|
| 404 |
+
K = [
|
| 405 |
+
[4.48, -1.0, 8.07, 2.33, 2.33, 2.33, -5.76, -12.78],
|
| 406 |
+
[-1.0, -6.48, 4.5, -1.24, -1.24, -1.24, -0.81, 7.49],
|
| 407 |
+
[8.07, 4.5, 15.48, 2.09, 2.09, 2.09, -11.1, -23.23],
|
| 408 |
+
[2.33, -1.24, 2.09, 4.0, -3.65, -3.65, 1.02, -0.9],
|
| 409 |
+
[2.33, -1.24, 2.09, -3.65, 4.0, -3.65, 1.02, -0.9],
|
| 410 |
+
[2.33, -1.24, 2.09, -3.65, -3.65, 4.0, 1.02, -0.9],
|
| 411 |
+
[-5.76, -0.81, -11.1, 1.02, 1.02, 1.02, 4.86, 9.75],
|
| 412 |
+
[-12.78, 7.49, -23.23, -0.9, -0.9, -0.9, 9.75, 21.46],
|
| 413 |
+
]
|
| 414 |
+
# this gram matrix has 5 positive eigenvalues and 3 negative ones
|
| 415 |
+
# [ 52.72, 7.65, 7.65, 5.02, 0. , -0. , -6.13, -15.11]
|
| 416 |
+
|
| 417 |
+
# 1. ask for enough components to get a significant negative one
|
| 418 |
+
kpca = KernelPCA(kernel="precomputed", eigen_solver=solver, n_components=7)
|
| 419 |
+
# make sure that the appropriate error is raised
|
| 420 |
+
with pytest.raises(ValueError, match="There are significant negative eigenvalues"):
|
| 421 |
+
kpca.fit(K)
|
| 422 |
+
|
| 423 |
+
# 2. ask for a small enough n_components to get only positive ones
|
| 424 |
+
kpca = KernelPCA(kernel="precomputed", eigen_solver=solver, n_components=2)
|
| 425 |
+
if solver == "randomized":
|
| 426 |
+
# the randomized method is still inconsistent with the others on this
|
| 427 |
+
# since it selects the eigenvalues based on the largest 2 modules, not
|
| 428 |
+
# on the largest 2 values.
|
| 429 |
+
#
|
| 430 |
+
# At least we can ensure that we return an error instead of returning
|
| 431 |
+
# the wrong eigenvalues
|
| 432 |
+
with pytest.raises(
|
| 433 |
+
ValueError, match="There are significant negative eigenvalues"
|
| 434 |
+
):
|
| 435 |
+
kpca.fit(K)
|
| 436 |
+
else:
|
| 437 |
+
# general case: make sure that it works
|
| 438 |
+
kpca.fit(K)
|
| 439 |
+
|
| 440 |
+
|
| 441 |
+
@pytest.mark.parametrize("n_components", [4, 10, 20])
|
| 442 |
+
def test_kernel_pca_solvers_equivalence(n_components):
|
| 443 |
+
"""Check that 'dense' 'arpack' & 'randomized' solvers give similar results"""
|
| 444 |
+
|
| 445 |
+
# Generate random data
|
| 446 |
+
n_train, n_test = 1_000, 100
|
| 447 |
+
X, _ = make_circles(
|
| 448 |
+
n_samples=(n_train + n_test), factor=0.3, noise=0.05, random_state=0
|
| 449 |
+
)
|
| 450 |
+
X_fit, X_pred = X[:n_train, :], X[n_train:, :]
|
| 451 |
+
|
| 452 |
+
# reference (full)
|
| 453 |
+
ref_pred = (
|
| 454 |
+
KernelPCA(n_components, eigen_solver="dense", random_state=0)
|
| 455 |
+
.fit(X_fit)
|
| 456 |
+
.transform(X_pred)
|
| 457 |
+
)
|
| 458 |
+
|
| 459 |
+
# arpack
|
| 460 |
+
a_pred = (
|
| 461 |
+
KernelPCA(n_components, eigen_solver="arpack", random_state=0)
|
| 462 |
+
.fit(X_fit)
|
| 463 |
+
.transform(X_pred)
|
| 464 |
+
)
|
| 465 |
+
# check that the result is still correct despite the approx
|
| 466 |
+
assert_array_almost_equal(np.abs(a_pred), np.abs(ref_pred))
|
| 467 |
+
|
| 468 |
+
# randomized
|
| 469 |
+
r_pred = (
|
| 470 |
+
KernelPCA(n_components, eigen_solver="randomized", random_state=0)
|
| 471 |
+
.fit(X_fit)
|
| 472 |
+
.transform(X_pred)
|
| 473 |
+
)
|
| 474 |
+
# check that the result is still correct despite the approximation
|
| 475 |
+
assert_array_almost_equal(np.abs(r_pred), np.abs(ref_pred))
|
| 476 |
+
|
| 477 |
+
|
| 478 |
+
def test_kernel_pca_inverse_transform_reconstruction():
|
| 479 |
+
"""Test if the reconstruction is a good approximation.
|
| 480 |
+
|
| 481 |
+
Note that in general it is not possible to get an arbitrarily good
|
| 482 |
+
reconstruction because of kernel centering that does not
|
| 483 |
+
preserve all the information of the original data.
|
| 484 |
+
"""
|
| 485 |
+
X, *_ = make_blobs(n_samples=100, n_features=4, random_state=0)
|
| 486 |
+
|
| 487 |
+
kpca = KernelPCA(
|
| 488 |
+
n_components=20, kernel="rbf", fit_inverse_transform=True, alpha=1e-3
|
| 489 |
+
)
|
| 490 |
+
X_trans = kpca.fit_transform(X)
|
| 491 |
+
X_reconst = kpca.inverse_transform(X_trans)
|
| 492 |
+
assert np.linalg.norm(X - X_reconst) / np.linalg.norm(X) < 1e-1
|
| 493 |
+
|
| 494 |
+
|
| 495 |
+
def test_kernel_pca_raise_not_fitted_error():
|
| 496 |
+
X = np.random.randn(15).reshape(5, 3)
|
| 497 |
+
kpca = KernelPCA()
|
| 498 |
+
kpca.fit(X)
|
| 499 |
+
with pytest.raises(NotFittedError):
|
| 500 |
+
kpca.inverse_transform(X)
|
| 501 |
+
|
| 502 |
+
|
| 503 |
+
def test_32_64_decomposition_shape():
|
| 504 |
+
"""Test that the decomposition is similar for 32 and 64 bits data
|
| 505 |
+
|
| 506 |
+
Non regression test for
|
| 507 |
+
https://github.com/scikit-learn/scikit-learn/issues/18146
|
| 508 |
+
"""
|
| 509 |
+
X, y = make_blobs(
|
| 510 |
+
n_samples=30, centers=[[0, 0, 0], [1, 1, 1]], random_state=0, cluster_std=0.1
|
| 511 |
+
)
|
| 512 |
+
X = StandardScaler().fit_transform(X)
|
| 513 |
+
X -= X.min()
|
| 514 |
+
|
| 515 |
+
# Compare the shapes (corresponds to the number of non-zero eigenvalues)
|
| 516 |
+
kpca = KernelPCA()
|
| 517 |
+
assert kpca.fit_transform(X).shape == kpca.fit_transform(X.astype(np.float32)).shape
|
| 518 |
+
|
| 519 |
+
|
| 520 |
+
def test_kernel_pca_feature_names_out():
|
| 521 |
+
"""Check feature names out for KernelPCA."""
|
| 522 |
+
X, *_ = make_blobs(n_samples=100, n_features=4, random_state=0)
|
| 523 |
+
kpca = KernelPCA(n_components=2).fit(X)
|
| 524 |
+
|
| 525 |
+
names = kpca.get_feature_names_out()
|
| 526 |
+
assert_array_equal([f"kernelpca{i}" for i in range(2)], names)
|
| 527 |
+
|
| 528 |
+
|
| 529 |
+
def test_kernel_pca_inverse_correct_gamma(global_random_seed):
|
| 530 |
+
"""Check that gamma is set correctly when not provided.
|
| 531 |
+
|
| 532 |
+
Non-regression test for #26280
|
| 533 |
+
"""
|
| 534 |
+
rng = np.random.RandomState(global_random_seed)
|
| 535 |
+
X = rng.random_sample((5, 4))
|
| 536 |
+
|
| 537 |
+
kwargs = {
|
| 538 |
+
"n_components": 2,
|
| 539 |
+
"random_state": rng,
|
| 540 |
+
"fit_inverse_transform": True,
|
| 541 |
+
"kernel": "rbf",
|
| 542 |
+
}
|
| 543 |
+
|
| 544 |
+
expected_gamma = 1 / X.shape[1]
|
| 545 |
+
kpca1 = KernelPCA(gamma=None, **kwargs).fit(X)
|
| 546 |
+
kpca2 = KernelPCA(gamma=expected_gamma, **kwargs).fit(X)
|
| 547 |
+
|
| 548 |
+
assert kpca1.gamma_ == expected_gamma
|
| 549 |
+
assert kpca2.gamma_ == expected_gamma
|
| 550 |
+
|
| 551 |
+
X1_recon = kpca1.inverse_transform(kpca1.transform(X))
|
| 552 |
+
X2_recon = kpca2.inverse_transform(kpca1.transform(X))
|
| 553 |
+
|
| 554 |
+
assert_allclose(X1_recon, X2_recon)
|
| 555 |
+
|
| 556 |
+
|
| 557 |
+
def test_kernel_pca_pandas_output():
|
| 558 |
+
"""Check that KernelPCA works with pandas output when the solver is arpack.
|
| 559 |
+
|
| 560 |
+
Non-regression test for:
|
| 561 |
+
https://github.com/scikit-learn/scikit-learn/issues/27579
|
| 562 |
+
"""
|
| 563 |
+
pytest.importorskip("pandas")
|
| 564 |
+
X, _ = load_iris(as_frame=True, return_X_y=True)
|
| 565 |
+
with sklearn.config_context(transform_output="pandas"):
|
| 566 |
+
KernelPCA(n_components=2, eigen_solver="arpack").fit_transform(X)
|