diff --git a/GPy/inference/latent_function_inference/var_dtc.py b/GPy/inference/latent_function_inference/var_dtc.py index cfc2bb47..6599ac66 100644 --- a/GPy/inference/latent_function_inference/var_dtc.py +++ b/GPy/inference/latent_function_inference/var_dtc.py @@ -34,7 +34,9 @@ class VarDTC(LatentFunctionInference): self.get_YYTfactor.limit = limit def _get_trYYT(self, Y): - return np.sum(np.square(Y)) + return np.einsum("ij,ij->", Y, Y) + # faster than, but same as: + # return np.sum(np.square(Y)) def __getstate__(self): # has to be overridden, as Cacher objects cannot be pickled. @@ -103,7 +105,7 @@ class VarDTC(LatentFunctionInference): psi0 = kern.Kdiag(X) psi1 = kern.K(X, Z) if het_noise: - tmp = psi1 * (np.sqrt(beta.reshape(num_data, 1))) + tmp = psi1 * (np.sqrt(beta)) else: tmp = psi1 * (np.sqrt(beta)) tmp, _ = dtrtrs(Lm, tmp.T, lower=1) @@ -137,14 +139,14 @@ class VarDTC(LatentFunctionInference): # log marginal likelihood log_marginal = _compute_log_marginal_likelihood(likelihood, num_data, output_dim, beta, het_noise, - psi0, A, LB, trYYT, data_fit, VVT_factor) + psi0, A, LB, trYYT, data_fit, Y) #noise derivatives dL_dR = _compute_dL_dR(likelihood, het_noise, uncertain_inputs, LB, _LBi_Lmi_psi1Vf, DBi_plus_BiPBi, Lm, A, psi0, psi1, beta, - data_fit, num_data, output_dim, trYYT, Y) + data_fit, num_data, output_dim, trYYT, Y, VVT_factor) dL_dthetaL = likelihood.exact_inference_gradients(dL_dR,Y_metadata) @@ -184,14 +186,14 @@ class VarDTC(LatentFunctionInference): return post, log_marginal, grad_dict def _compute_dL_dpsi(num_inducing, num_data, output_dim, beta, Lm, VVT_factor, Cpsi1Vf, DBi_plus_BiPBi, psi1, het_noise, uncertain_inputs): - dL_dpsi0 = -0.5 * output_dim * (beta[:,None] * np.ones([num_data, 1])).flatten() + dL_dpsi0 = -0.5 * output_dim * (beta* np.ones([num_data, 1])).flatten() dL_dpsi1 = np.dot(VVT_factor, Cpsi1Vf.T) dL_dpsi2_beta = 0.5 * backsub_both_sides(Lm, output_dim * np.eye(num_inducing) - DBi_plus_BiPBi) if het_noise: if uncertain_inputs: - dL_dpsi2 = beta[:, None, None] * dL_dpsi2_beta[None, :, :] + dL_dpsi2 = beta[:, None] * dL_dpsi2_beta[None, :, :] else: - dL_dpsi1 += 2.*np.dot(dL_dpsi2_beta, (psi1 * beta.reshape(num_data, 1)).T).T + dL_dpsi1 += 2.*np.dot(dL_dpsi2_beta, (psi1 * beta).T).T dL_dpsi2 = None else: dL_dpsi2 = beta * dL_dpsi2_beta @@ -202,7 +204,7 @@ def _compute_dL_dpsi(num_inducing, num_data, output_dim, beta, Lm, VVT_factor, C return dL_dpsi0, dL_dpsi1, dL_dpsi2 -def _compute_dL_dR(likelihood, het_noise, uncertain_inputs, LB, _LBi_Lmi_psi1Vf, DBi_plus_BiPBi, Lm, A, psi0, psi1, beta, data_fit, num_data, output_dim, trYYT, Y): +def _compute_dL_dR(likelihood, het_noise, uncertain_inputs, LB, _LBi_Lmi_psi1Vf, DBi_plus_BiPBi, Lm, A, psi0, psi1, beta, data_fit, num_data, output_dim, trYYT, Y, VVT_factr=None): # the partial derivative vector for the likelihood if likelihood.size == 0: # save computation here. @@ -217,8 +219,7 @@ def _compute_dL_dR(likelihood, het_noise, uncertain_inputs, LB, _LBi_Lmi_psi1Vf, Lmi_psi1, nil = dtrtrs(Lm, psi1.T, lower=1, trans=0) _LBi_Lmi_psi1, _ = dtrtrs(LB, Lmi_psi1, lower=1, trans=0) - - dL_dR = -0.5 * beta + 0.5 * (beta*Y)**2 + dL_dR = -0.5 * beta + 0.5 * VVT_factr**2 dL_dR += 0.5 * output_dim * (psi0 - np.sum(Lmi_psi1**2,0))[:,None] * beta**2 dL_dR += 0.5*np.sum(mdot(LBi.T,LBi,Lmi_psi1)*Lmi_psi1,0)[:,None]*beta**2 @@ -232,10 +233,10 @@ def _compute_dL_dR(likelihood, het_noise, uncertain_inputs, LB, _LBi_Lmi_psi1Vf, dL_dR += beta * (0.5 * np.sum(A * DBi_plus_BiPBi) - data_fit) return dL_dR -def _compute_log_marginal_likelihood(likelihood, num_data, output_dim, beta, het_noise, psi0, A, LB, trYYT, data_fit,Y): +def _compute_log_marginal_likelihood(likelihood, num_data, output_dim, beta, het_noise, psi0, A, LB, trYYT, data_fit, Y): #compute log marginal likelihood if het_noise: - lik_1 = -0.5 * num_data * output_dim * np.log(2. * np.pi) + 0.5 * np.sum(np.log(beta)) - 0.5 * np.sum(beta * np.square(Y).sum(axis=-1)) + lik_1 = -0.5 * num_data * output_dim * np.log(2. * np.pi) + 0.5 * output_dim * np.sum(np.log(beta)) - 0.5 * np.sum(beta.ravel() * np.square(Y).sum(axis=-1)) lik_2 = -0.5 * output_dim * (np.sum(beta.flatten() * psi0) - np.trace(A)) else: lik_1 = -0.5 * num_data * output_dim * (np.log(2. * np.pi) - np.log(beta)) - 0.5 * beta * trYYT diff --git a/GPy/likelihoods/mixed_noise.py b/GPy/likelihoods/mixed_noise.py index 9692bb07..2eaab818 100644 --- a/GPy/likelihoods/mixed_noise.py +++ b/GPy/likelihoods/mixed_noise.py @@ -23,7 +23,7 @@ class MixedNoise(Likelihood): variance = np.zeros(ind.size) for lik, j in zip(self.likelihoods_list, range(len(self.likelihoods_list))): variance[ind==j] = lik.variance - return variance + return variance[:,None] def betaY(self,Y,Y_metadata): #TODO not here.