diff --git a/GPy/mappings/__init__.py b/GPy/mappings/__init__.py index b0d90ba2..97573aba 100644 --- a/GPy/mappings/__init__.py +++ b/GPy/mappings/__init__.py @@ -1,7 +1,7 @@ # Copyright (c) 2013, GPy authors (see AUTHORS.txt). # Licensed under the BSD 3-clause license (see LICENSE.txt) -#from kernel import Kernel +from kernel import Kernel from linear import Linear from mlp import MLP #from rbf import RBF diff --git a/GPy/mappings/kernel.py b/GPy/mappings/kernel.py index a794e561..07ac3cf6 100644 --- a/GPy/mappings/kernel.py +++ b/GPy/mappings/kernel.py @@ -3,7 +3,7 @@ import numpy as np from ..core.mapping import Mapping -from ..kern.kern import kern +import GPy class Kernel(Mapping): """ @@ -25,7 +25,7 @@ class Kernel(Mapping): def __init__(self, X, output_dim=1, kernel=None): Mapping.__init__(self, input_dim=X.shape[1], output_dim=output_dim) if kernel is None: - kernel = kern.rbf(self.input_dim) + kernel = GPy.kern.rbf(self.input_dim) self.kern = kernel self.X = X self.num_data = X.shape[0] diff --git a/GPy/mappings/mlp.py b/GPy/mappings/mlp.py index ce0e04b0..61b2f80e 100644 --- a/GPy/mappings/mlp.py +++ b/GPy/mappings/mlp.py @@ -89,6 +89,7 @@ class MLP(Mapping): def df_dtheta(self, dL_df, X): self._df_computations(dL_df, X) + g = np.array([]) for gW, gbias in zip(self._dL_dW, self._dL_dbias): g = np.hstack((g, gW.flatten(), gbias)) return g @@ -117,7 +118,6 @@ class MLP(Mapping): self._dL_dW[0] = (dL_da[:, :, None]*X[:, None, :]).sum(0).T self._dL_dbias[0] = (dL_da.sum(0)) self._dL_dX = (dL_da[:, None, :]*W[None, :, :]).sum(2) - g = np.array([]) def df_dX(self, dL_df, X): diff --git a/GPy/testing/gplvm_tests.py b/GPy/testing/gplvm_tests.py index ebb5c4e5..6223d833 100644 --- a/GPy/testing/gplvm_tests.py +++ b/GPy/testing/gplvm_tests.py @@ -7,33 +7,33 @@ import GPy class GPLVMTests(unittest.TestCase): def test_bias_kern(self): - N, num_inducing, input_dim, D = 10, 3, 2, 4 - X = np.random.rand(N, input_dim) + num_data, num_inducing, input_dim, output_dim = 10, 3, 2, 4 + X = np.random.rand(num_data, input_dim) k = GPy.kern.rbf(input_dim) + GPy.kern.white(input_dim, 0.00001) K = k.K(X) - Y = np.random.multivariate_normal(np.zeros(N),K,input_dim).T + Y = np.random.multivariate_normal(np.zeros(num_data),K,output_dim).T k = GPy.kern.bias(input_dim) + GPy.kern.white(input_dim, 0.00001) m = GPy.models.GPLVM(Y, input_dim, kernel = k) m.randomize() self.assertTrue(m.checkgrad()) def test_linear_kern(self): - N, num_inducing, input_dim, D = 10, 3, 2, 4 - X = np.random.rand(N, input_dim) + num_data, num_inducing, input_dim, output_dim = 10, 3, 2, 4 + X = np.random.rand(num_data, input_dim) k = GPy.kern.rbf(input_dim) + GPy.kern.white(input_dim, 0.00001) K = k.K(X) - Y = np.random.multivariate_normal(np.zeros(N),K,input_dim).T + Y = np.random.multivariate_normal(np.zeros(num_data),K,output_dim).T k = GPy.kern.linear(input_dim) + GPy.kern.white(input_dim, 0.00001) m = GPy.models.GPLVM(Y, input_dim, kernel = k) m.randomize() self.assertTrue(m.checkgrad()) def test_rbf_kern(self): - N, num_inducing, input_dim, D = 10, 3, 2, 4 - X = np.random.rand(N, input_dim) + num_data, num_inducing, input_dim, output_dim = 10, 3, 2, 4 + X = np.random.rand(num_data, input_dim) k = GPy.kern.rbf(input_dim) + GPy.kern.white(input_dim, 0.00001) K = k.K(X) - Y = np.random.multivariate_normal(np.zeros(N),K,input_dim).T + Y = np.random.multivariate_normal(np.zeros(num_data),K,output_dim).T k = GPy.kern.rbf(input_dim) + GPy.kern.white(input_dim, 0.00001) m = GPy.models.GPLVM(Y, input_dim, kernel = k) m.randomize()