diff --git a/GPy/examples/sparse_GPLVM_demo.py b/GPy/examples/sparse_GPLVM_demo.py index 6ca6c941..5df72b8d 100644 --- a/GPy/examples/sparse_GPLVM_demo.py +++ b/GPy/examples/sparse_GPLVM_demo.py @@ -9,7 +9,7 @@ np.random.seed(1) print "sparse GPLVM with RBF kernel" N = 100 -M = 4 +M = 8 Q = 1 D = 2 #generate GPLVM-like data @@ -19,9 +19,7 @@ K = k.K(X) Y = np.random.multivariate_normal(np.zeros(N),K,D).T m = GPy.models.sparse_GPLVM(Y, Q, M=M) -m.constrain_positive('(rbf|bias|noise)') -m.constrain_bounded('white', 1e-3, 0.1) -# m.plot() +m.constrain_positive('(rbf|bias|noise|white)') pb.figure() m.plot() diff --git a/GPy/examples/sparse_GP_regression_demo.py b/GPy/examples/sparse_GP_regression_demo.py index d67a3831..2a73e149 100644 --- a/GPy/examples/sparse_GP_regression_demo.py +++ b/GPy/examples/sparse_GP_regression_demo.py @@ -12,7 +12,7 @@ import GPy np.random.seed(2) pb.ion() N = 1200 -M = 20 +M = 5 ###################################### ## 1 dimensional example diff --git a/GPy/models/GPLVM.py b/GPy/models/GPLVM.py index 44147b73..89df21c0 100644 --- a/GPy/models/GPLVM.py +++ b/GPy/models/GPLVM.py @@ -54,7 +54,7 @@ class GPLVM(GP_regression): def plot(self): assert self.Y.shape[1]==2 - pb.scatter(self.Y[:,0],self.Y[:,1],40,self.X[:,0].copy(),linewidth=0) + pb.scatter(self.Y[:,0],self.Y[:,1],40,self.X[:,0].copy(),linewidth=0,cmap=pb.cm.jet) Xnew = np.linspace(self.X.min(),self.X.max(),200)[:,None] mu, var = self.predict(Xnew) pb.plot(mu[:,0], mu[:,1],'k',linewidth=1.5) diff --git a/GPy/models/sparse_GP_regression.py b/GPy/models/sparse_GP_regression.py index 6d1b1f44..2dbd7c72 100644 --- a/GPy/models/sparse_GP_regression.py +++ b/GPy/models/sparse_GP_regression.py @@ -60,10 +60,11 @@ class sparse_GP_regression(GP_regression): if self.has_uncertain_inputs: self.X_uncertainty /= np.square(self._Xstd) - def _compute_kernel_matrices(self): - # kernel computations, using BGPLVM notation + def _computations(self): + # TODO find routine to multiply triangular matrices #TODO: slices for psi statistics (easy enough) + # kernel computations, using BGPLVM notation self.Kmm = self.kern.K(self.Z) if self.has_uncertain_inputs: self.psi0 = self.kern.psi0(self.Z,self.X, self.X_uncertainty).sum() @@ -75,19 +76,16 @@ class sparse_GP_regression(GP_regression): self.psi1 = self.kern.K(self.Z,self.X) #self.psi2 = np.dot(self.psi1,self.psi1.T) #self.psi2 = self.psi1.T[:,:,None]*self.psi1.T[:,None,:] - self.psi1_scaled = self.psi1/self.scale_factor - #self.psi2_scaled = psi1_scaled.T[:,:,None]*psi1_scaled.T[:,None,:] - self.psi2_scaled = np.dot(self.psi1_scaled,self.psi1_scaled.T) + tmp = self.psi1/(self.scale_factor/np.sqrt(self.beta)) + self.psi2_beta_scaled = np.dot(tmp,tmp.T) - def _computations(self): - # TODO find routine to multiply triangular matrices sf = self.scale_factor sf2 = sf**2 - self.Kmmi, self.Lm, self.Lmi, self.Kmm_logdet = pdinv(self.Kmm) + self.Kmmi, self.Lm, self.Lmi, self.Kmm_logdet = pdinv(self.Kmm)#+np.eye(self.M)*1e-3) self.V = (self.beta/self.scale_factor)*self.Y - self.A = mdot(self.Lmi, self.beta*self.psi2_scaled, self.Lmi.T) + self.A = mdot(self.Lmi, self.psi2_beta_scaled, self.Lmi.T) self.B = np.eye(self.M)/sf2 + self.A self.Bi, self.LB, self.LBi, self.B_logdet = pdinv(self.B) @@ -106,8 +104,8 @@ class sparse_GP_regression(GP_regression): # Compute dL_dKmm self.dL_dKmm = -0.5 * self.D * mdot(self.Lmi.T, self.A, self.Lmi)*sf2 # dB - self.dL_dKmm += -0.5 * self.D * (- self.C/sf2 - 2.*self.beta*mdot(self.C, self.psi2_scaled, self.Kmmi) + self.Kmmi) # dC - self.dL_dKmm += np.dot(np.dot(self.E*sf2, self.beta*self.psi2_scaled) - np.dot(self.C, self.psi1VVpsi1), self.Kmmi) + 0.5*self.E # dD + self.dL_dKmm += -0.5 * self.D * (- self.C/sf2 - 2.*mdot(self.C, self.psi2_beta_scaled, self.Kmmi) + self.Kmmi) # dC + self.dL_dKmm += np.dot(np.dot(self.E*sf2, self.psi2_beta_scaled) - np.dot(self.C, self.psi1VVpsi1), self.Kmmi) + 0.5*self.E # dD def log_likelihood(self): """ Compute the (lower bound on the) log marginal likelihood """ @@ -122,8 +120,6 @@ class sparse_GP_regression(GP_regression): self.Z = p[:self.M*self.Q].reshape(self.M, self.Q) self.beta = p[self.M*self.Q] self.kern.set_param(p[self.Z.size + 1:]) - self.beta2 = self.beta**2 - self._compute_kernel_matrices() self._computations() def get_param(self): @@ -139,10 +135,9 @@ class sparse_GP_regression(GP_regression): #TODO: suport heteroscedatic noise sf2 = self.scale_factor**2 dA_dbeta = 0.5 * self.N*self.D/self.beta - 0.5 * self.trYYT - dB_dbeta = - 0.5 * self.D * self.psi0 - np.trace(self.A)/self.beta*sf2 + dB_dbeta = - 0.5 * self.D * (self.psi0 - np.trace(self.A)/self.beta*sf2) dC_dbeta = - 0.5 * self.D * np.sum(self.Bi*self.A)/self.beta - tmp = mdot(self.Bi, self.Lmi, self.psi1V) - dD_dbeta = (np.sum(np.square(self.C)) - 0.5 * np.sum(self.A * np.dot(tmp, tmp.T)))/self.beta + dD_dbeta = np.sum((self.C - 0.5 * mdot(self.C,self.psi2_beta_scaled,self.C) ) * self.psi1VVpsi1 )/self.beta return np.squeeze(dA_dbeta + dB_dbeta + dC_dbeta + dD_dbeta) @@ -184,14 +179,14 @@ class sparse_GP_regression(GP_regression): """Internal helper function for making predictions, does not account for normalisation""" Kx = self.kern.K(self.Z, Xnew) - mu = mdot(Kx.T, self.LBL_inv, self.psi1V) + mu = mdot(Kx.T, self.C/self.scale_factor, self.psi1V) if full_cov: Kxx = self.kern.K(Xnew) - var = Kxx - mdot(Kx.T, (self.Kmmi - self.LBL_inv), Kx) + np.eye(Xnew.shape[0])/self.beta # TODO: This beta doesn't belong here in the EP case. + var = Kxx - mdot(Kx.T, (self.Kmmi - self.C/self.scale_factor**2), Kx) + np.eye(Xnew.shape[0])/self.beta # TODO: This beta doesn't belong here in the EP case. else: Kxx = self.kern.Kdiag(Xnew) - var = Kxx - np.sum(Kx*np.dot(self.Kmmi - self.LBL_inv, Kx),0) + 1./self.beta # TODO: This beta doesn't belong here in the EP case. + var = Kxx - np.sum(Kx*np.dot(self.Kmmi - self.C/self.scale_factor**2, Kx),0) + 1./self.beta # TODO: This beta doesn't belong here in the EP case. return mu,var diff --git a/grid_parameters.py b/grid_parameters.py index 011204ee..64d82755 100644 --- a/grid_parameters.py +++ b/grid_parameters.py @@ -6,8 +6,8 @@ import GPy pb.close('all') -N = 1000 -M = 10 +N = 200 +M = 15 resolution=5 X = np.linspace(0,12,N)[:,None] @@ -16,15 +16,22 @@ Y = np.sin(X) + np.random.randn(*X.shape)/np.sqrt(50.) #k = GPy.kern.rbf(1) k = GPy.kern.Matern32(1) + GPy.kern.white(1) -models = [GPy.models.sparse_GP_regression(X,Y,Z=Z,kernel=k), - GPy.models.sgp_debugB(X,Y,Z=Z,kernel=k), - GPy.models.sgp_debugC(X,Y,Z=Z,kernel=k)]#, +models = [GPy.models.sparse_GP_regression(X,Y,Z=Z,kernel=k) + ,GPy.models.sparse_GP_regression(X,Y,Z=Z,kernel=k) + ,GPy.models.sparse_GP_regression(X,Y,Z=Z,kernel=k) + ,GPy.models.sparse_GP_regression(X,Y,Z=Z,kernel=k)] +models[0].scale_factor = 1. +models[1].scale_factor = 10. +models[2].scale_factor = 100. +models[3].scale_factor = 1000. + #GPy.models.sgp_debugB(X,Y,Z=Z,kernel=k), + #GPy.models.sgp_debugC(X,Y,Z=Z,kernel=k)]#, #GPy.models.sgp_debugE(X,Y,Z=Z,kernel=k)] -[m.constrain_fixed('white',0.001) for m in models] +[m.constrain_fixed('white',0.1) for m in models] #xx,yy = np.mgrid[1.5:4:0+resolution*1j,-2:2:0+resolution*1j] -xx,yy = np.mgrid[3:16:0+resolution*1j,-2:2:0+resolution*1j] +xx,yy = np.mgrid[3:16:0+resolution*1j,-2:1:0+resolution*1j] lls = [] cgs = []