diff --git a/GPy/models/sparse_GP.py b/GPy/models/sparse_GP.py index a348c9f4..3d44ad6b 100644 --- a/GPy/models/sparse_GP.py +++ b/GPy/models/sparse_GP.py @@ -153,14 +153,26 @@ class sparse_GP(GP): #self.partial_for_likelihood += -np.diag(np.dot((self.C - 0.5 * mdot(self.C,self.psi2_beta_scaled,self.C) ) , self.psi1VVpsi1 ))*self.likelihood.precision #dD else: #likelihood is not heterscedatic - beta = self.likelihood.precision - dbeta = 0.5 * self.N*self.D/beta - 0.5 * np.sum(np.square(self.likelihood.Y)) - dbeta += - 0.5 * self.D * (self.psi0.sum() - np.trace(self.A)/beta*sf2) - dbeta += - 0.5 * self.D * trace_dot(self.Bi,self.A)/beta - dbeta += np.trace(self.Cpsi1VVpsi1)/beta - 0.5 * trace_dot(np.dot(self.C,self.psi2_beta_scaled) , self.Cpsi1VVpsi1 )/beta - self.partial_for_likelihood = -dbeta*self.likelihood.precision**2 + self.partial_for_likelihood = - 0.5 * self.N*self.D*self.likelihood.precision + 0.5 * np.sum(np.square(self.likelihood.Y))*self.likelihood.precision**2 + self.partial_for_likelihood += 0.5 * self.D * (self.psi0.sum()*self.likelihood.precision**2 - np.trace(self.A)*self.likelihood.precision*sf2) + self.partial_for_likelihood += 0.5 * self.D * trace_dot(self.Bi,self.A)*self.likelihood.precision + self.partial_for_likelihood += self.likelihood.precision*(0.5*trace_dot(self.psi2_beta_scaled,self.E*sf2) - np.trace(self.Cpsi1VVpsi1)) + + def log_likelihood(self): + """ Compute the (lower bound on the) log marginal likelihood """ + sf2 = self.scale_factor**2 + if self.likelihood.is_heteroscedastic: + A = -0.5*self.N*self.D*np.log(2.*np.pi) +0.5*np.sum(np.log(self.likelihood.precision)) -0.5*np.sum(self.V*self.likelihood.Y) + B = -0.5*self.D*(np.sum(self.likelihood.precision.flatten()*self.psi0) - np.trace(self.A)*sf2) + else: + A = -0.5*self.N*self.D*(np.log(2.*np.pi) + np.log(self.likelihood._variance)) -0.5*self.likelihood.precision*self.likelihood.trYYT + B = -0.5*self.D*(np.sum(self.likelihood.precision*self.psi0) - np.trace(self.A)*sf2) + C = -0.5*self.D * (self.B_logdet + self.M*np.log(sf2)) + D = 0.5*np.trace(self.Cpsi1VVpsi1) + return A+B+C+D + def _set_params(self, p): self.Z = p[:self.M*self.Q].reshape(self.M, self.Q) self.kern._set_params(p[self.Z.size:self.Z.size+self.kern.Nparam]) @@ -188,18 +200,6 @@ class sparse_GP(GP): #self.likelihood.fit_FITC(self.Kmm,self.psi1,self.psi0) self._set_params(self._get_params()) # update the GP - def log_likelihood(self): - """ Compute the (lower bound on the) log marginal likelihood """ - sf2 = self.scale_factor**2 - if self.likelihood.is_heteroscedastic: - A = -0.5*self.N*self.D*np.log(2.*np.pi) +0.5*np.sum(np.log(self.likelihood.precision)) -0.5*np.sum(self.V*self.likelihood.Y) - B = -0.5*self.D*(np.sum(self.likelihood.precision.flatten()*self.psi0) - np.trace(self.A)*sf2) - else: - A = -0.5*self.N*self.D*(np.log(2.*np.pi) - np.log(self.likelihood.precision)) -0.5*self.likelihood.precision*self.likelihood.trYYT - B = -0.5*self.D*(np.sum(self.likelihood.precision*self.psi0) - np.trace(self.A)*sf2) - C = -0.5*self.D * (self.B_logdet + self.M*np.log(sf2)) - D = 0.5*np.trace(self.Cpsi1VVpsi1) - return A+B+C+D def _log_likelihood_gradients(self): return np.hstack((self.dL_dZ().flatten(), self.dL_dtheta(), self.likelihood._gradients(partial=self.partial_for_likelihood)))