386 lines
14 KiB
Python
386 lines
14 KiB
Python
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"""Testing for kernels for Gaussian processes."""
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# Author: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
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# License: BSD 3 clause
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import pytest
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import numpy as np
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from inspect import signature
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from sklearn.gaussian_process.kernels import _approx_fprime
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from sklearn.metrics.pairwise \
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import PAIRWISE_KERNEL_FUNCTIONS, euclidean_distances, pairwise_kernels
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from sklearn.gaussian_process.kernels \
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import (RBF, Matern, RationalQuadratic, ExpSineSquared, DotProduct,
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ConstantKernel, WhiteKernel, PairwiseKernel, KernelOperator,
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Exponentiation, Kernel, CompoundKernel)
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from sklearn.base import clone
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from sklearn.utils._testing import (assert_almost_equal, assert_array_equal,
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assert_array_almost_equal,
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assert_allclose,
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assert_raise_message)
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X = np.random.RandomState(0).normal(0, 1, (5, 2))
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Y = np.random.RandomState(0).normal(0, 1, (6, 2))
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kernel_rbf_plus_white = RBF(length_scale=2.0) + WhiteKernel(noise_level=3.0)
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kernels = [RBF(length_scale=2.0), RBF(length_scale_bounds=(0.5, 2.0)),
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ConstantKernel(constant_value=10.0),
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2.0 * RBF(length_scale=0.33, length_scale_bounds="fixed"),
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2.0 * RBF(length_scale=0.5), kernel_rbf_plus_white,
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2.0 * RBF(length_scale=[0.5, 2.0]),
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2.0 * Matern(length_scale=0.33, length_scale_bounds="fixed"),
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2.0 * Matern(length_scale=0.5, nu=0.5),
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2.0 * Matern(length_scale=1.5, nu=1.5),
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2.0 * Matern(length_scale=2.5, nu=2.5),
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2.0 * Matern(length_scale=[0.5, 2.0], nu=0.5),
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3.0 * Matern(length_scale=[2.0, 0.5], nu=1.5),
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4.0 * Matern(length_scale=[0.5, 0.5], nu=2.5),
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RationalQuadratic(length_scale=0.5, alpha=1.5),
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ExpSineSquared(length_scale=0.5, periodicity=1.5),
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DotProduct(sigma_0=2.0), DotProduct(sigma_0=2.0) ** 2,
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RBF(length_scale=[2.0]), Matern(length_scale=[2.0])]
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for metric in PAIRWISE_KERNEL_FUNCTIONS:
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if metric in ["additive_chi2", "chi2"]:
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continue
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kernels.append(PairwiseKernel(gamma=1.0, metric=metric))
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@pytest.mark.parametrize('kernel', kernels)
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def test_kernel_gradient(kernel):
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# Compare analytic and numeric gradient of kernels.
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K, K_gradient = kernel(X, eval_gradient=True)
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assert K_gradient.shape[0] == X.shape[0]
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assert K_gradient.shape[1] == X.shape[0]
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assert K_gradient.shape[2] == kernel.theta.shape[0]
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def eval_kernel_for_theta(theta):
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kernel_clone = kernel.clone_with_theta(theta)
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K = kernel_clone(X, eval_gradient=False)
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return K
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K_gradient_approx = \
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_approx_fprime(kernel.theta, eval_kernel_for_theta, 1e-10)
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assert_almost_equal(K_gradient, K_gradient_approx, 4)
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@pytest.mark.parametrize(
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'kernel',
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[kernel for kernel in kernels
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# skip non-basic kernels
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if not (isinstance(kernel, KernelOperator)
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or isinstance(kernel, Exponentiation))])
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def test_kernel_theta(kernel):
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# Check that parameter vector theta of kernel is set correctly.
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theta = kernel.theta
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_, K_gradient = kernel(X, eval_gradient=True)
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# Determine kernel parameters that contribute to theta
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init_sign = signature(kernel.__class__.__init__).parameters.values()
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args = [p.name for p in init_sign if p.name != 'self']
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theta_vars = map(lambda s: s[0:-len("_bounds")],
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filter(lambda s: s.endswith("_bounds"), args))
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assert (
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set(hyperparameter.name
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for hyperparameter in kernel.hyperparameters) ==
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set(theta_vars))
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# Check that values returned in theta are consistent with
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# hyperparameter values (being their logarithms)
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for i, hyperparameter in enumerate(kernel.hyperparameters):
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assert (theta[i] == np.log(getattr(kernel, hyperparameter.name)))
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# Fixed kernel parameters must be excluded from theta and gradient.
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for i, hyperparameter in enumerate(kernel.hyperparameters):
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# create copy with certain hyperparameter fixed
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params = kernel.get_params()
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params[hyperparameter.name + "_bounds"] = "fixed"
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kernel_class = kernel.__class__
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new_kernel = kernel_class(**params)
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# Check that theta and K_gradient are identical with the fixed
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# dimension left out
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_, K_gradient_new = new_kernel(X, eval_gradient=True)
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assert theta.shape[0] == new_kernel.theta.shape[0] + 1
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assert K_gradient.shape[2] == K_gradient_new.shape[2] + 1
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if i > 0:
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assert theta[:i] == new_kernel.theta[:i]
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assert_array_equal(K_gradient[..., :i],
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K_gradient_new[..., :i])
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if i + 1 < len(kernel.hyperparameters):
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assert theta[i + 1:] == new_kernel.theta[i:]
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assert_array_equal(K_gradient[..., i + 1:],
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K_gradient_new[..., i:])
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# Check that values of theta are modified correctly
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for i, hyperparameter in enumerate(kernel.hyperparameters):
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theta[i] = np.log(42)
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kernel.theta = theta
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assert_almost_equal(getattr(kernel, hyperparameter.name), 42)
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setattr(kernel, hyperparameter.name, 43)
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assert_almost_equal(kernel.theta[i], np.log(43))
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@pytest.mark.parametrize('kernel',
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[kernel for kernel in kernels
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# Identity is not satisfied on diagonal
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if kernel != kernel_rbf_plus_white])
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def test_auto_vs_cross(kernel):
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# Auto-correlation and cross-correlation should be consistent.
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K_auto = kernel(X)
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K_cross = kernel(X, X)
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assert_almost_equal(K_auto, K_cross, 5)
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@pytest.mark.parametrize('kernel', kernels)
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def test_kernel_diag(kernel):
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# Test that diag method of kernel returns consistent results.
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K_call_diag = np.diag(kernel(X))
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K_diag = kernel.diag(X)
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assert_almost_equal(K_call_diag, K_diag, 5)
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def test_kernel_operator_commutative():
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# Adding kernels and multiplying kernels should be commutative.
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# Check addition
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assert_almost_equal((RBF(2.0) + 1.0)(X),
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(1.0 + RBF(2.0))(X))
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# Check multiplication
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assert_almost_equal((3.0 * RBF(2.0))(X),
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(RBF(2.0) * 3.0)(X))
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def test_kernel_anisotropic():
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# Anisotropic kernel should be consistent with isotropic kernels.
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kernel = 3.0 * RBF([0.5, 2.0])
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K = kernel(X)
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X1 = np.array(X)
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X1[:, 0] *= 4
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K1 = 3.0 * RBF(2.0)(X1)
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assert_almost_equal(K, K1)
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X2 = np.array(X)
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X2[:, 1] /= 4
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K2 = 3.0 * RBF(0.5)(X2)
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assert_almost_equal(K, K2)
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# Check getting and setting via theta
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kernel.theta = kernel.theta + np.log(2)
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assert_array_equal(kernel.theta, np.log([6.0, 1.0, 4.0]))
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assert_array_equal(kernel.k2.length_scale, [1.0, 4.0])
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@pytest.mark.parametrize('kernel',
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[kernel for kernel in kernels
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if kernel.is_stationary()])
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def test_kernel_stationary(kernel):
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# Test stationarity of kernels.
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K = kernel(X, X + 1)
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assert_almost_equal(K[0, 0], np.diag(K))
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@pytest.mark.parametrize('kernel', kernels)
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def test_kernel_input_type(kernel):
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# Test whether kernels is for vectors or structured data
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if isinstance(kernel, Exponentiation):
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assert(kernel.requires_vector_input ==
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kernel.kernel.requires_vector_input)
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if isinstance(kernel, KernelOperator):
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assert(kernel.requires_vector_input ==
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(kernel.k1.requires_vector_input or
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kernel.k2.requires_vector_input))
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def test_compound_kernel_input_type():
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kernel = CompoundKernel([WhiteKernel(noise_level=3.0)])
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assert not kernel.requires_vector_input
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kernel = CompoundKernel([WhiteKernel(noise_level=3.0),
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RBF(length_scale=2.0)])
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assert kernel.requires_vector_input
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def check_hyperparameters_equal(kernel1, kernel2):
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# Check that hyperparameters of two kernels are equal
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for attr in set(dir(kernel1) + dir(kernel2)):
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if attr.startswith("hyperparameter_"):
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attr_value1 = getattr(kernel1, attr)
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attr_value2 = getattr(kernel2, attr)
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assert attr_value1 == attr_value2
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@pytest.mark.parametrize("kernel", kernels)
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def test_kernel_clone(kernel):
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# Test that sklearn's clone works correctly on kernels.
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kernel_cloned = clone(kernel)
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# XXX: Should this be fixed?
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# This differs from the sklearn's estimators equality check.
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assert kernel == kernel_cloned
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assert id(kernel) != id(kernel_cloned)
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# Check that all constructor parameters are equal.
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assert kernel.get_params() == kernel_cloned.get_params()
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# Check that all hyperparameters are equal.
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check_hyperparameters_equal(kernel, kernel_cloned)
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@pytest.mark.parametrize('kernel', kernels)
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def test_kernel_clone_after_set_params(kernel):
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# This test is to verify that using set_params does not
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# break clone on kernels.
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# This used to break because in kernels such as the RBF, non-trivial
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# logic that modified the length scale used to be in the constructor
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# See https://github.com/scikit-learn/scikit-learn/issues/6961
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# for more details.
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bounds = (1e-5, 1e5)
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kernel_cloned = clone(kernel)
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params = kernel.get_params()
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# RationalQuadratic kernel is isotropic.
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isotropic_kernels = (ExpSineSquared, RationalQuadratic)
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if 'length_scale' in params and not isinstance(kernel,
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isotropic_kernels):
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length_scale = params['length_scale']
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if np.iterable(length_scale):
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# XXX unreached code as of v0.22
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params['length_scale'] = length_scale[0]
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params['length_scale_bounds'] = bounds
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else:
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params['length_scale'] = [length_scale] * 2
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params['length_scale_bounds'] = bounds * 2
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kernel_cloned.set_params(**params)
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kernel_cloned_clone = clone(kernel_cloned)
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assert (kernel_cloned_clone.get_params() == kernel_cloned.get_params())
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assert id(kernel_cloned_clone) != id(kernel_cloned)
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check_hyperparameters_equal(kernel_cloned, kernel_cloned_clone)
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def test_matern_kernel():
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# Test consistency of Matern kernel for special values of nu.
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K = Matern(nu=1.5, length_scale=1.0)(X)
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# the diagonal elements of a matern kernel are 1
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assert_array_almost_equal(np.diag(K), np.ones(X.shape[0]))
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# matern kernel for coef0==0.5 is equal to absolute exponential kernel
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K_absexp = np.exp(-euclidean_distances(X, X, squared=False))
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K = Matern(nu=0.5, length_scale=1.0)(X)
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assert_array_almost_equal(K, K_absexp)
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# matern kernel with coef0==inf is equal to RBF kernel
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K_rbf = RBF(length_scale=1.0)(X)
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K = Matern(nu=np.inf, length_scale=1.0)(X)
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assert_array_almost_equal(K, K_rbf)
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assert_allclose(K, K_rbf)
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# test that special cases of matern kernel (coef0 in [0.5, 1.5, 2.5])
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# result in nearly identical results as the general case for coef0 in
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# [0.5 + tiny, 1.5 + tiny, 2.5 + tiny]
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tiny = 1e-10
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for nu in [0.5, 1.5, 2.5]:
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K1 = Matern(nu=nu, length_scale=1.0)(X)
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K2 = Matern(nu=nu + tiny, length_scale=1.0)(X)
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assert_array_almost_equal(K1, K2)
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# test that coef0==large is close to RBF
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large = 100
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K1 = Matern(nu=large, length_scale=1.0)(X)
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K2 = RBF(length_scale=1.0)(X)
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assert_array_almost_equal(K1, K2, decimal=2)
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@pytest.mark.parametrize("kernel", kernels)
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def test_kernel_versus_pairwise(kernel):
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# Check that GP kernels can also be used as pairwise kernels.
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# Test auto-kernel
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if kernel != kernel_rbf_plus_white:
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# For WhiteKernel: k(X) != k(X,X). This is assumed by
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# pairwise_kernels
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K1 = kernel(X)
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K2 = pairwise_kernels(X, metric=kernel)
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assert_array_almost_equal(K1, K2)
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# Test cross-kernel
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K1 = kernel(X, Y)
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K2 = pairwise_kernels(X, Y, metric=kernel)
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assert_array_almost_equal(K1, K2)
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@pytest.mark.parametrize("kernel", kernels)
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def test_set_get_params(kernel):
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# Check that set_params()/get_params() is consistent with kernel.theta.
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# Test get_params()
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index = 0
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params = kernel.get_params()
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for hyperparameter in kernel.hyperparameters:
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if isinstance("string", type(hyperparameter.bounds)):
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if hyperparameter.bounds == "fixed":
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continue
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size = hyperparameter.n_elements
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if size > 1: # anisotropic kernels
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assert_almost_equal(np.exp(kernel.theta[index:index + size]),
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params[hyperparameter.name])
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index += size
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else:
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assert_almost_equal(np.exp(kernel.theta[index]),
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params[hyperparameter.name])
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index += 1
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# Test set_params()
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index = 0
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value = 10 # arbitrary value
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for hyperparameter in kernel.hyperparameters:
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if isinstance("string", type(hyperparameter.bounds)):
|
||
|
|
if hyperparameter.bounds == "fixed":
|
||
|
|
continue
|
||
|
|
size = hyperparameter.n_elements
|
||
|
|
if size > 1: # anisotropic kernels
|
||
|
|
kernel.set_params(**{hyperparameter.name: [value] * size})
|
||
|
|
assert_almost_equal(np.exp(kernel.theta[index:index + size]),
|
||
|
|
[value] * size)
|
||
|
|
index += size
|
||
|
|
else:
|
||
|
|
kernel.set_params(**{hyperparameter.name: value})
|
||
|
|
assert_almost_equal(np.exp(kernel.theta[index]), value)
|
||
|
|
index += 1
|
||
|
|
|
||
|
|
|
||
|
|
@pytest.mark.parametrize("kernel", kernels)
|
||
|
|
def test_repr_kernels(kernel):
|
||
|
|
# Smoke-test for repr in kernels.
|
||
|
|
|
||
|
|
repr(kernel)
|
||
|
|
|
||
|
|
|
||
|
|
def test_warns_on_get_params_non_attribute():
|
||
|
|
class MyKernel(Kernel):
|
||
|
|
def __init__(self, param=5):
|
||
|
|
pass
|
||
|
|
|
||
|
|
def __call__(self, X, Y=None, eval_gradient=False):
|
||
|
|
return X
|
||
|
|
|
||
|
|
def diag(self, X):
|
||
|
|
return np.ones(X.shape[0])
|
||
|
|
|
||
|
|
def is_stationary(self):
|
||
|
|
return False
|
||
|
|
|
||
|
|
est = MyKernel()
|
||
|
|
with pytest.warns(FutureWarning, match='AttributeError'):
|
||
|
|
params = est.get_params()
|
||
|
|
|
||
|
|
assert params['param'] is None
|
||
|
|
|
||
|
|
|
||
|
|
def test_rational_quadratic_kernel():
|
||
|
|
kernel = RationalQuadratic(length_scale=[1., 1.])
|
||
|
|
assert_raise_message(AttributeError,
|
||
|
|
"RationalQuadratic kernel only supports isotropic "
|
||
|
|
"version, please use a single "
|
||
|
|
"scalar for length_scale", kernel, X)
|