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Martin Bubel 2023-10-06 08:13:42 +02:00
parent 779f31da9c
commit 0b92d3a57c
1 changed files with 169 additions and 68 deletions
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231
GPy/testing/inference_tests.py
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@ -8,18 +8,21 @@ The test cases for various inference algorithms
import unittest import unittest
import numpy as np import numpy as np
import GPy import GPy
#np.seterr(invalid='raise')
# np.seterr(invalid='raise')
class InferenceXTestCase(unittest.TestCase): class InferenceXTestCase(unittest.TestCase):
def genData(self): def genData(self):
np.random.seed(1111) np.random.seed(1111)
Ylist = GPy.examples.dimensionality_reduction._simulate_matern(5, 1, 1, 10, 3, False)[0] Ylist = GPy.examples.dimensionality_reduction._simulate_matern(
5, 1, 1, 10, 3, False
)[0]
return Ylist[0] return Ylist[0]
def test_inferenceX_BGPLVM_Linear(self): def test_inferenceX_BGPLVM_Linear(self):
Ys = self.genData() Ys = self.genData()
m = GPy.models.BayesianGPLVM(Ys,3,kernel=GPy.kern.Linear(3,ARD=True)) m = GPy.models.BayesianGPLVM(Ys, 3, kernel=GPy.kern.Linear(3, ARD=True))
m.optimize() m.optimize()
x, mi = m.infer_newX(m.Y, optimize=True) x, mi = m.infer_newX(m.Y, optimize=True)
np.testing.assert_array_almost_equal(m.X.mean, mi.X.mean, decimal=2) np.testing.assert_array_almost_equal(m.X.mean, mi.X.mean, decimal=2)
@ -27,8 +30,9 @@ class InferenceXTestCase(unittest.TestCase):
def test_inferenceX_BGPLVM_RBF(self): def test_inferenceX_BGPLVM_RBF(self):
Ys = self.genData() Ys = self.genData()
m = GPy.models.BayesianGPLVM(Ys,3,kernel=GPy.kern.RBF(3,ARD=True)) m = GPy.models.BayesianGPLVM(Ys, 3, kernel=GPy.kern.RBF(3, ARD=True))
import warnings import warnings
with warnings.catch_warnings(): with warnings.catch_warnings():
warnings.simplefilter("ignore") warnings.simplefilter("ignore")
m.optimize() m.optimize()
@ -38,67 +42,110 @@ class InferenceXTestCase(unittest.TestCase):
def test_inferenceX_GPLVM_Linear(self): def test_inferenceX_GPLVM_Linear(self):
Ys = self.genData() Ys = self.genData()
m = GPy.models.GPLVM(Ys,3,kernel=GPy.kern.Linear(3,ARD=True)) m = GPy.models.GPLVM(Ys, 3, kernel=GPy.kern.Linear(3, ARD=True))
m.optimize() m.optimize()
x, mi = m.infer_newX(m.Y, optimize=True) x, mi = m.infer_newX(m.Y, optimize=True)
np.testing.assert_array_almost_equal(m.X, mi.X, decimal=2) np.testing.assert_array_almost_equal(m.X, mi.X, decimal=2)
def test_inferenceX_GPLVM_RBF(self): def test_inferenceX_GPLVM_RBF(self):
Ys = self.genData() Ys = self.genData()
m = GPy.models.GPLVM(Ys,3,kernel=GPy.kern.RBF(3,ARD=True)) m = GPy.models.GPLVM(Ys, 3, kernel=GPy.kern.RBF(3, ARD=True))
m.optimize() m.optimize()
x, mi = m.infer_newX(m.Y, optimize=True) x, mi = m.infer_newX(m.Y, optimize=True)
np.testing.assert_array_almost_equal(m.X, mi.X, decimal=2) np.testing.assert_array_almost_equal(m.X, mi.X, decimal=2)
class InferenceGPEP(unittest.TestCase):
class InferenceGPEP(unittest.TestCase):
def genData(self): def genData(self):
np.random.seed(1) np.random.seed(1)
k = GPy.kern.RBF(1, variance=7., lengthscale=0.2) k = GPy.kern.RBF(1, variance=7.0, lengthscale=0.2)
X = np.random.rand(200,1) X = np.random.rand(200, 1)
f = np.random.multivariate_normal(np.zeros(200), k.K(X) + 1e-5 * np.eye(X.shape[0])) f = np.random.multivariate_normal(
np.zeros(200), k.K(X) + 1e-5 * np.eye(X.shape[0])
)
lik = GPy.likelihoods.Bernoulli() lik = GPy.likelihoods.Bernoulli()
p = lik.gp_link.transf(f) # squash the latent function p = lik.gp_link.transf(f) # squash the latent function
Y = lik.samples(f).reshape(-1,1) Y = lik.samples(f).reshape(-1, 1)
return X, Y return X, Y
def genNoisyData(self): def genNoisyData(self):
np.random.seed(1) np.random.seed(1)
X = np.random.rand(100,1) X = np.random.rand(100, 1)
self.real_std = 0.1 self.real_std = 0.1
noise = np.random.randn(*X[:, 0].shape)*self.real_std noise = np.random.randn(*X[:, 0].shape) * self.real_std
Y = (np.sin(X[:, 0]*2*np.pi) + noise)[:, None] Y = (np.sin(X[:, 0] * 2 * np.pi) + noise)[:, None]
self.f = np.random.rand(X.shape[0],1) self.f = np.random.rand(X.shape[0], 1)
Y_extra_noisy = Y.copy() Y_extra_noisy = Y.copy()
Y_extra_noisy[50] += 4. Y_extra_noisy[50] += 4.0
# Y_extra_noisy[80:83] -= 2. # Y_extra_noisy[80:83] -= 2.
return X, Y, Y_extra_noisy return X, Y, Y_extra_noisy
def test_inference_EP(self): def test_inference_EP(self):
from paramz import ObsAr from paramz import ObsAr
X, Y = self.genData() X, Y = self.genData()
lik = GPy.likelihoods.Bernoulli() lik = GPy.likelihoods.Bernoulli()
k = GPy.kern.RBF(1, variance=7., lengthscale=0.2) k = GPy.kern.RBF(1, variance=7.0, lengthscale=0.2)
inf = GPy.inference.latent_function_inference.expectation_propagation.EP(max_iters=30, delta=0.5) inf = GPy.inference.latent_function_inference.expectation_propagation.EP(
self.model = GPy.core.GP(X=X, max_iters=30, delta=0.5
Y=Y, )
kernel=k, self.model = GPy.core.GP(
inference_method=inf, X=X, Y=Y, kernel=k, inference_method=inf, likelihood=lik
likelihood=lik) )
K = self.model.kern.K(X) K = self.model.kern.K(X)
mean_prior = np.zeros(K.shape[0]) mean_prior = np.zeros(K.shape[0])
post_params, ga_approx, cav_params, log_Z_tilde = self.model.inference_method.expectation_propagation(mean_prior, K, ObsAr(Y), lik, None) (
post_params,
ga_approx,
cav_params,
log_Z_tilde,
) = self.model.inference_method.expectation_propagation(
mean_prior, K, ObsAr(Y), lik, None
)
mu_tilde = ga_approx.v / ga_approx.tau.astype(float) mu_tilde = ga_approx.v / ga_approx.tau.astype(float)
p, m, d = self.model.inference_method._inference(Y, mean_prior, K, ga_approx, cav_params, lik, Y_metadata=None, Z_tilde=log_Z_tilde) p, m, d = self.model.inference_method._inference(
p0, m0, d0 = super(GPy.inference.latent_function_inference.expectation_propagation.EP, inf).inference(k, X,lik ,mu_tilde[:,None], mean_function=None, variance=1./ga_approx.tau, K=K, Z_tilde=log_Z_tilde + np.sum(- 0.5*np.log(ga_approx.tau) + 0.5*(ga_approx.v*ga_approx.v*1./ga_approx.tau))) Y,
mean_prior,
K,
ga_approx,
cav_params,
lik,
Y_metadata=None,
Z_tilde=log_Z_tilde,
)
p0, m0, d0 = super(
GPy.inference.latent_function_inference.expectation_propagation.EP, inf
).inference(
k,
X,
lik,
mu_tilde[:, None],
mean_function=None,
variance=1.0 / ga_approx.tau,
K=K,
Z_tilde=log_Z_tilde
+ np.sum(
-0.5 * np.log(ga_approx.tau)
+ 0.5 * (ga_approx.v * ga_approx.v * 1.0 / ga_approx.tau)
),
)
assert (np.sum(np.array([m - m0, assert (
np.sum(d['dL_dK'] - d0['dL_dK']), np.sum(
np.sum(d['dL_dthetaL'] - d0['dL_dthetaL']), np.array(
np.sum(d['dL_dm'] - d0['dL_dm']), [
m - m0,
np.sum(d["dL_dK"] - d0["dL_dK"]),
np.sum(d["dL_dthetaL"] - d0["dL_dthetaL"]),
np.sum(d["dL_dm"] - d0["dL_dm"]),
np.sum(p._woodbury_vector - p0._woodbury_vector), np.sum(p._woodbury_vector - p0._woodbury_vector),
np.sum(p.woodbury_inv - p0.woodbury_inv)])) < 1e6) np.sum(p.woodbury_inv - p0.woodbury_inv),
]
)
)
< 1e6
)
# NOTE: adding a test like above for parameterized likelihood- the above test is # NOTE: adding a test like above for parameterized likelihood- the above test is
# only for probit likelihood which does not have any tunable hyperparameter which is why # only for probit likelihood which does not have any tunable hyperparameter which is why
@ -110,70 +157,124 @@ class InferenceGPEP(unittest.TestCase):
# and it is possible that any error might creep up because of quadrature implementation. # and it is possible that any error might creep up because of quadrature implementation.
def test_inference_EP_non_classification(self): def test_inference_EP_non_classification(self):
from paramz import ObsAr from paramz import ObsAr
X, Y, Y_extra_noisy = self.genNoisyData() X, Y, Y_extra_noisy = self.genNoisyData()
deg_freedom = 5. deg_freedom = 5.0
init_noise_var = 0.08 init_noise_var = 0.08
lik_studentT = GPy.likelihoods.StudentT(deg_free=deg_freedom, sigma2=init_noise_var) lik_studentT = GPy.likelihoods.StudentT(
deg_free=deg_freedom, sigma2=init_noise_var
)
# like_gaussian_noise = GPy.likelihoods.MixedNoise() # like_gaussian_noise = GPy.likelihoods.MixedNoise()
k = GPy.kern.RBF(1, variance=2., lengthscale=1.1) k = GPy.kern.RBF(1, variance=2.0, lengthscale=1.1)
ep_inf_alt = GPy.inference.latent_function_inference.expectation_propagation.EP(max_iters=4, delta=0.5) ep_inf_alt = GPy.inference.latent_function_inference.expectation_propagation.EP(
max_iters=4, delta=0.5
)
# ep_inf_nested = GPy.inference.latent_function_inference.expectation_propagation.EP(ep_mode='nested', max_iters=100, delta=0.5) # ep_inf_nested = GPy.inference.latent_function_inference.expectation_propagation.EP(ep_mode='nested', max_iters=100, delta=0.5)
m = GPy.core.GP(X=X,Y=Y_extra_noisy,kernel=k,likelihood=lik_studentT,inference_method=ep_inf_alt) m = GPy.core.GP(
X=X,
Y=Y_extra_noisy,
kernel=k,
likelihood=lik_studentT,
inference_method=ep_inf_alt,
)
K = m.kern.K(X) K = m.kern.K(X)
mean_prior = np.zeros(K.shape[0]) mean_prior = np.zeros(K.shape[0])
post_params, ga_approx, cav_params, log_Z_tilde = m.inference_method.expectation_propagation(mean_prior, K, ObsAr(Y_extra_noisy), lik_studentT, None) (
post_params,
ga_approx,
cav_params,
log_Z_tilde,
) = m.inference_method.expectation_propagation(
mean_prior, K, ObsAr(Y_extra_noisy), lik_studentT, None
)
mu_tilde = ga_approx.v / ga_approx.tau.astype(float) mu_tilde = ga_approx.v / ga_approx.tau.astype(float)
p, m, d = m.inference_method._inference(Y_extra_noisy, mean_prior, K, ga_approx, cav_params, lik_studentT, Y_metadata=None, Z_tilde=log_Z_tilde) p, m, d = m.inference_method._inference(
p0, m0, d0 = super(GPy.inference.latent_function_inference.expectation_propagation.EP, ep_inf_alt).inference(k, X,lik_studentT ,mu_tilde[:,None], mean_function=None, variance=1./ga_approx.tau, K=K, Z_tilde=log_Z_tilde + np.sum(- 0.5*np.log(ga_approx.tau) + 0.5*(ga_approx.v*ga_approx.v*1./ga_approx.tau))) Y_extra_noisy,
mean_prior,
K,
ga_approx,
cav_params,
lik_studentT,
Y_metadata=None,
Z_tilde=log_Z_tilde,
)
p0, m0, d0 = super(
GPy.inference.latent_function_inference.expectation_propagation.EP,
ep_inf_alt,
).inference(
k,
X,
lik_studentT,
mu_tilde[:, None],
mean_function=None,
variance=1.0 / ga_approx.tau,
K=K,
Z_tilde=log_Z_tilde
+ np.sum(
-0.5 * np.log(ga_approx.tau)
+ 0.5 * (ga_approx.v * ga_approx.v * 1.0 / ga_approx.tau)
),
)
assert (np.sum(np.array([m - m0, assert (
np.sum(d['dL_dK'] - d0['dL_dK']), np.sum(
np.sum(d['dL_dthetaL'] - d0['dL_dthetaL']), np.array(
np.sum(d['dL_dm'] - d0['dL_dm']), [
m - m0,
np.sum(d["dL_dK"] - d0["dL_dK"]),
np.sum(d["dL_dthetaL"] - d0["dL_dthetaL"]),
np.sum(d["dL_dm"] - d0["dL_dm"]),
np.sum(p._woodbury_vector - p0._woodbury_vector), np.sum(p._woodbury_vector - p0._woodbury_vector),
np.sum(p.woodbury_inv - p0.woodbury_inv)])) < 1e6) np.sum(p.woodbury_inv - p0.woodbury_inv),
]
)
)
< 1e6
)
class VarDtcTest(unittest.TestCase): class VarDtcTest(unittest.TestCase):
def test_var_dtc_inference_with_mean(self): def test_var_dtc_inference_with_mean(self):
""" Check dL_dm in var_dtc is calculated correctly""" """Check dL_dm in var_dtc is calculated correctly"""
np.random.seed(1) np.random.seed(1)
x = np.linspace(0.,2*np.pi,100)[:,None] x = np.linspace(0.0, 2 * np.pi, 100)[:, None]
y = -np.cos(x)+np.random.randn(*x.shape)*0.3+1 y = -np.cos(x) + np.random.randn(*x.shape) * 0.3 + 1
m = GPy.models.SparseGPRegression(x,y, mean_function=GPy.mappings.Linear(input_dim=1, output_dim=1)) m = GPy.models.SparseGPRegression(
x, y, mean_function=GPy.mappings.Linear(input_dim=1, output_dim=1)
)
self.assertTrue(m.checkgrad()) self.assertTrue(m.checkgrad())
class HMCSamplerTest(unittest.TestCase): class HMCSamplerTest(unittest.TestCase):
def test_sampling(self): def test_sampling(self):
np.random.seed(1) np.random.seed(1)
x = np.linspace(0.,2*np.pi,100)[:,None] x = np.linspace(0.0, 2 * np.pi, 100)[:, None]
y = -np.cos(x)+np.random.randn(*x.shape)*0.3+1 y = -np.cos(x) + np.random.randn(*x.shape) * 0.3 + 1
m = GPy.models.GPRegression(x,y) m = GPy.models.GPRegression(x, y)
m.kern.lengthscale.set_prior(GPy.priors.Gamma.from_EV(1.,10.)) m.kern.lengthscale.set_prior(GPy.priors.Gamma.from_EV(1.0, 10.0))
m.kern.variance.set_prior(GPy.priors.Gamma.from_EV(1.,10.)) m.kern.variance.set_prior(GPy.priors.Gamma.from_EV(1.0, 10.0))
m.likelihood.variance.set_prior(GPy.priors.Gamma.from_EV(1.,10.)) m.likelihood.variance.set_prior(GPy.priors.Gamma.from_EV(1.0, 10.0))
hmc = GPy.inference.mcmc.HMC(m,stepsize=1e-2) hmc = GPy.inference.mcmc.HMC(m, stepsize=1e-2)
s = hmc.sample(num_samples=3) s = hmc.sample(num_samples=3)
class MCMCSamplerTest(unittest.TestCase):
class MCMCSamplerTest(unittest.TestCase):
def test_sampling(self): def test_sampling(self):
np.random.seed(1) np.random.seed(1)
x = np.linspace(0.,2*np.pi,100)[:,None] x = np.linspace(0.0, 2 * np.pi, 100)[:, None]
y = -np.cos(x)+np.random.randn(*x.shape)*0.3+1 y = -np.cos(x) + np.random.randn(*x.shape) * 0.3 + 1
m = GPy.models.GPRegression(x,y) m = GPy.models.GPRegression(x, y)
m.kern.lengthscale.set_prior(GPy.priors.Gamma.from_EV(1.,10.)) m.kern.lengthscale.set_prior(GPy.priors.Gamma.from_EV(1.0, 10.0))
m.kern.variance.set_prior(GPy.priors.Gamma.from_EV(1.,10.)) m.kern.variance.set_prior(GPy.priors.Gamma.from_EV(1.0, 10.0))
m.likelihood.variance.set_prior(GPy.priors.Gamma.from_EV(1.,10.)) m.likelihood.variance.set_prior(GPy.priors.Gamma.from_EV(1.0, 10.0))
mcmc = GPy.inference.mcmc.Metropolis_Hastings(m) mcmc = GPy.inference.mcmc.Metropolis_Hastings(m)
mcmc.sample(Ntotal=100, Nburn=10) mcmc.sample(Ntotal=100, Nburn=10)
if __name__ == "__main__": if __name__ == "__main__":
unittest.main() unittest.main()