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Revert "[predict] added noiseless convenience function to gp, bc of whining about it..."

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This reverts commit 2001cd6dfd.
This commit is contained in:
Max Zwiessele 2016-04-01 15:47:03 +01:00
parent b63af98f1f
commit 7c95076b9f
2 changed files with 19 additions and 54 deletions
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49
GPy/core/gp.py
View file

@ -217,13 +217,9 @@ class GP(Model):
mu += self.mean_function.f(Xnew)
return mu, var
def predict(self, Xnew, full_cov=False, Y_metadata=None, kern=None, likelihood=None, include_likelihood=True):
def predict(self, Xnew, full_cov=False, Y_metadata=None, kern=None, likelihood=None):
"""
Predict the function(s) at the new point(s) Xnew. This includes the likelihood
variance added to the predicted underlying function (usually referred to as f).
In order to predict without adding in the likelihood give
`include_likelihood=False`, or refer to self.predict_noiseless().
Predict the function(s) at the new point(s) Xnew.
:param Xnew: The points at which to make a prediction
:type Xnew: np.ndarray (Nnew x self.input_dim)
@ -233,8 +229,6 @@ class GP(Model):
:param Y_metadata: metadata about the predicting point to pass to the likelihood
:param kern: The kernel to use for prediction (defaults to the model
kern). this is useful for examining e.g. subprocesses.
:param bool include_likelihood: Whether or not to add likelihood noise to the predicted underlying latent function f.
:returns: (mean, var):
mean: posterior mean, a Numpy array, Nnew x self.input_dim
var: posterior variance, a Numpy array, Nnew x 1 if full_cov=False, Nnew x Nnew otherwise
@ -249,40 +243,11 @@ class GP(Model):
if self.normalizer is not None:
mu, var = self.normalizer.inverse_mean(mu), self.normalizer.inverse_variance(var)
if include_likelihood:
# now push through likelihood
if likelihood is None:
likelihood = self.likelihood
mu, var = likelihood.predictive_values(mu, var, full_cov, Y_metadata=Y_metadata)
return mu, var
def predict_noiseless(self, Xnew, full_cov=False, Y_metadata=None, kern=None):
"""
Convenience function to predict the underlying function of the GP (often
referred to as f) without adding the likelihood variance on the
prediction function.
This is most likely what you want to use for your predictions.
:param Xnew: The points at which to make a prediction
:type Xnew: np.ndarray (Nnew x self.input_dim)
:param full_cov: whether to return the full covariance matrix, or just
the diagonal
:type full_cov: bool
:param Y_metadata: metadata about the predicting point to pass to the likelihood
:param kern: The kernel to use for prediction (defaults to the model
kern). this is useful for examining e.g. subprocesses.
:returns: (mean, var):
mean: posterior mean, a Numpy array, Nnew x self.input_dim
var: posterior variance, a Numpy array, Nnew x 1 if full_cov=False, Nnew x Nnew otherwise
If full_cov and self.input_dim > 1, the return shape of var is Nnew x Nnew x self.input_dim. If self.input_dim == 1, the return shape is Nnew x Nnew.
This is to allow for different normalizations of the output dimensions.
Note: If you want the predictive quantiles (e.g. 95% confidence interval) use :py:func:"~GPy.core.gp.GP.predict_quantiles".
"""
return self.predict(Xnew, full_cov, Y_metadata, kern, None, False)
# now push through likelihood
if likelihood is None:
likelihood = self.likelihood
mean, var = likelihood.predictive_values(mu, var, full_cov, Y_metadata=Y_metadata)
return mean, var
def predict_quantiles(self, X, quantiles=(2.5, 97.5), Y_metadata=None, kern=None, likelihood=None):
"""

24
GPy/testing/model_tests.py
View file

@ -27,7 +27,7 @@ class MiscTests(unittest.TestCase):
Test whether the predicted variance of normal GP goes negative under numerical unstable situation.
Thanks simbartonels@github for reporting the bug and providing the following example.
"""
# set seed for reproducability
np.random.seed(3)
# Definition of the Branin test function
@ -69,13 +69,13 @@ class MiscTests(unittest.TestCase):
K_hat = k.K(self.X_new) - k.K(self.X_new, self.X).dot(Kinv).dot(k.K(self.X, self.X_new))
mu_hat = k.K(self.X_new, self.X).dot(Kinv).dot(m.Y_normalized)
mu, covar = m.predict_noiseless(self.X_new, full_cov=True)
mu, covar = m._raw_predict(self.X_new, full_cov=True)
self.assertEquals(mu.shape, (self.N_new, self.D))
self.assertEquals(covar.shape, (self.N_new, self.N_new))
np.testing.assert_almost_equal(K_hat, covar)
np.testing.assert_almost_equal(mu_hat, mu)
mu, var = m.predict_noiseless(self.X_new)
mu, var = m._raw_predict(self.X_new)
self.assertEquals(mu.shape, (self.N_new, self.D))
self.assertEquals(var.shape, (self.N_new, 1))
np.testing.assert_almost_equal(np.diag(K_hat)[:, None], var)
@ -166,7 +166,7 @@ class MiscTests(unittest.TestCase):
# S = \int (f(x) - m)^2q(x|mu,S) dx = \int f(x)^2 q(x) dx - mu**2 = 4(mu^2 + S) - (2.mu)^2 = 4S
Y_mu_true = 2*X_pred_mu
Y_var_true = 4*X_pred_var
Y_mu_pred, Y_var_pred = m.predict_noiseless(X_pred)
Y_mu_pred, Y_var_pred = m._raw_predict(X_pred)
np.testing.assert_allclose(Y_mu_true, Y_mu_pred, rtol=1e-4)
np.testing.assert_allclose(Y_var_true, Y_var_pred, rtol=1e-4)
@ -181,13 +181,13 @@ class MiscTests(unittest.TestCase):
K_hat = k.K(self.X_new) - k.K(self.X_new, Z).dot(Kinv).dot(k.K(Z, self.X_new))
K_hat = np.clip(K_hat, 1e-15, np.inf)
mu, covar = m.predict_noiseless(self.X_new, full_cov=True)
mu, covar = m._raw_predict(self.X_new, full_cov=True)
self.assertEquals(mu.shape, (self.N_new, self.D))
self.assertEquals(covar.shape, (self.N_new, self.N_new))
np.testing.assert_almost_equal(K_hat, covar)
# np.testing.assert_almost_equal(mu_hat, mu)
mu, var = m.predict_noiseless(self.X_new)
mu, var = m._raw_predict(self.X_new)
self.assertEquals(mu.shape, (self.N_new, self.D))
self.assertEquals(var.shape, (self.N_new, 1))
np.testing.assert_almost_equal(np.diag(K_hat)[:, None], var)
@ -365,7 +365,7 @@ class MiscTests(unittest.TestCase):
warp_m = GPy.models.WarpedGP(self.X, self.Y, kernel=warp_k, warping_function=warp_f)
warp_m.optimize()
warp_preds = warp_m.predict(self.X)
np.testing.assert_almost_equal(preds, warp_preds)
@unittest.skip('Comment this to plot the modified sine function')
@ -378,7 +378,7 @@ class MiscTests(unittest.TestCase):
Y = np.sin(X) + np.random.normal(0,0.1,151)
Y = np.exp(Y) - 5
#Y = np.array([np.power(abs(y),float(1)/3) * (1,-1)[y<0] for y in Y]) + 0
#np.seterr(over='raise')
import matplotlib.pyplot as plt
warp_k = GPy.kern.RBF(1)
@ -390,7 +390,7 @@ class MiscTests(unittest.TestCase):
#warp_m.randomize()
#warp_m['.*warp_tanh.psi*'][:,0:2].constrain_bounded(0,100)
#warp_m['.*warp_tanh.psi*'][:,0:1].constrain_fixed(1)
#print(warp_m.checkgrad())
#warp_m.plot()
#plt.show()
@ -406,7 +406,7 @@ class MiscTests(unittest.TestCase):
warp_f.plot(X.min()-10, X.max()+10)
plt.show()
class GradientTests(np.testing.TestCase):
def setUp(self):
@ -738,12 +738,12 @@ class GradientTests(np.testing.TestCase):
lik = GPy.likelihoods.Gaussian()
m = GPy.models.GPVariationalGaussianApproximation(X, Y, kernel=kern, likelihood=lik)
self.assertTrue(m.checkgrad())
def test_ssgplvm(self):
from GPy import kern
from GPy.models import SSGPLVM
from GPy.examples.dimensionality_reduction import _simulate_matern
D1, D2, D3, N, num_inducing, Q = 13, 5, 8, 45, 3, 9
_, _, Ylist = _simulate_matern(D1, D2, D3, N, num_inducing, False)
Y = Ylist[0]