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more skeletal work on the uncollapsed GP

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None of the gradients work, but lots more things are in place
This commit is contained in:
James Hensman 2012-12-07 16:35:15 -08:00
parent 1c0a223329
commit fe13d2c09a
2 changed files with 32 additions and 27 deletions
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1
GPy/models/__init__.py
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@ -9,3 +9,4 @@ from warped_GP import warpedGP
from GP_EP import GP_EP
from generalized_FITC import generalized_FITC
from sparse_GPLVM import sparse_GPLVM
from uncollapsed_sparse_GP import uncollapsed_sparse_GP

58
GPy/models/uncollapsed_sparse_GP.py
View file

@ -32,35 +32,37 @@ class uncollapsed_sparse_GP(sparse_GP_regression):
:type normalize_(X|Y): bool
"""
def __init__(self, X, Y, q_u=None, *args, **kwargs)
D = Y.shape[1]
def __init__(self, X, Y, q_u=None, M=10, *args, **kwargs):
self.D = Y.shape[1]
if q_u is None:
if Z is None:
M = Z.shape[0]
if 'Z' in kwargs.keys():
self.M = Z.shape[0]
else:
M=M
q_u = np.hstack((np.ones(M*D)),np.eye(M).flatten())
self.M = M
q_u = np.hstack((np.ones(self.M*self.D),-0.5*np.eye(self.M).flatten()))
self.set_vb_param(q_u)
sparse_GP_regression.__init__(self, X, Y, *args, **kwargs)
sparse_GP_regression.__init__(self, X, Y, M=M,*args, **kwargs)
def _computations(self):
self.V = self.beta*self.Y
self.VmT = np.dot(self.V,self.q_u_expectation[0].T)
self.psi1V = np.dot(self.psi1, self.V)
self.psi1VVpsi1 = np.dot(self.psi1V, self.psi1V.T)
self.Kmmi, self.Lm, self.Lmi, self.Kmm_logdet = pdinv(self.Kmm)
self.A = mdot(self.Lmi, self.psi2, self.Lmi.T)
self.B = np.eye(self.M) + self.beta * self.A
self.Lambda = mdot(self.Lmi.T,self.B,sel.Lmi)
self.A = self.beta * mdot(self.Lmi, self.psi2, self.Lmi.T)
self.B = np.eye(self.M) * self.A
self.Lambda = mdot(self.Lmi.T,self.B,self.Lmi)
self.trace_K = self.psi0 - np.trace(self.A)/self.beta
self.projected_mean = mdot(self.psi1.T,self.Kmmi,self.q_u_expectation[0])
# Compute dL_dpsi
self.dL_dpsi0 = - 0.5 * self.D * self.beta * np.ones(self.N)
self.dL_dpsi1 =
self.dL_dpsi2 =
self.dL_dpsi1 = np.dot(self.VmT,self.Kmmi).T
self.dL_dpsi2 = - 0.5 * self.beta * (-self.D*self.Kmmi + mdot(self.Kmmi,self.q_u_expectation[1],self.Kmmi))
# Compute dL_dKmm
self.dL_dKmm =
self.dL_dKmm +=
self.dL_dKmm +=
tmp = np.dot(0.5*np.eye(self.M) + np.dot(self.A,self.Kmmi),self.q_u_expectation[1]) -0.5*self.Kmm - np.dot(self.psi1,self.VmT)
self.dL_dKmm = mdot(self.Kmmi,tmp,self.Kmmi)
def log_likelihood(self):
"""
@ -68,10 +70,10 @@ class uncollapsed_sparse_GP(sparse_GP_regression):
"""
A = -0.5*self.N*self.D*(np.log(2.*np.pi) - np.log(self.beta))
B = -0.5*self.beta*self.D*self.trace_K
C = -self.D *(self.Kmm_hld +0.5*np.sum(self.Lambda * self.mmT_S) + self.M/2.)
E = -0.5*self.beta*self.trYYT
F = np.sum(np.dot(self.V.T,self.projected_mean))
return A+B+C+D+E+F
C = -0.5*self.D *(self.Kmm_logdet + np.sum(self.Lambda * self.q_u_expectation[1]) + self.M/2.)
D = -0.5*self.beta*self.trYYT
E = np.sum(np.dot(self.V.T,self.projected_mean))
return A+B+C+D+E
def dL_dbeta(self):
"""
@ -80,18 +82,18 @@ class uncollapsed_sparse_GP(sparse_GP_regression):
"""
dA_dbeta = 0.5 * self.N*self.D/self.beta
dB_dbeta = - 0.5 * self.D * self.trace_K
dC_dbeta = - 0.5 * self.D * #TODO
dC_dbeta = - 0.5 * self.D * 1.#TODO
dD_dbeta = - 0.5 * self.trYYT
return np.squeeze(dA_dbeta + dB_dbeta + dC_dbeta + dD_dbeta + dE_dbeta)
return np.squeeze(dA_dbeta + dB_dbeta + dC_dbeta + dD_dbeta)
def _raw_predict(self, Xnew, slices):
"""Internal helper function for making predictions, does not account for normalisation"""
Kx = self.kern.cross_compute(Xnew)
Kxx = self.kern.compute_new(Xnew)
mu = mdot(Kx.T,self.Kmmi,self.mu)
Kx = self.kern.K(Xnew,self.Z)
Kxx = self.kern.K(Xnew)
mu = mdot(Kx,self.Kmmi,self.q_u_expectation[0])
tmp = self.Kmmi- mdot(self.Kmmi,self.q_u_cov,self.Kmmi)
var = Kxx - mdot(Kx.T,tmp,Kx) + np.eye(Xnew.shape[0])/self.beta
var = Kxx - mdot(Kx,tmp,Kx.T) + np.eye(Xnew.shape[0])/self.beta
return mu,var
@ -100,7 +102,7 @@ class uncollapsed_sparse_GP(sparse_GP_regression):
self.q_u_prec = -2.*vb_param[self.M*self.D:].reshape(self.M,self.M)
self.q_u_cov, q_u_Li, q_u_L, tmp = pdinv(self.q_u_prec)
self.q_u_logdet = -tmp
self.q_u_mean = -2.*np.dot(self.q_u_cov,vb_param[:self.M*self.D].reshape(self.M,self.D))
self.q_u_mean = np.dot(self.q_u_cov,vb_param[:self.M*self.D].reshape(self.M,self.D))
self.q_u_expectation = (self.q_u_mean, np.dot(self.q_u_mean,self.q_u_mean.T)+self.q_u_cov)
@ -127,4 +129,6 @@ class uncollapsed_sparse_GP(sparse_GP_regression):
add the distribution q(u) to the plot from sparse_GP_regression
"""
sparse_GP_regression.plot(self,*args,**kwargs)
#TODO: plot the q(u) dist.
if self.Q==1:
pb.errorbar(self.Z[:,0],self.q_u_expectation[0][:,0],yerr=2*np.sqrt(np.diag(self.q_u_cov)),fmt=None,ecolor='b')