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Merge branch 'devel' of github.com:/sheffieldml/GPy into devel

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This commit is contained in:
James Hensman 2015-04-01 09:15:52 +01:00
commit 64ccd3bea9
17 changed files with 867 additions and 401 deletions
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44
GPy/kern/_src/psi_comp/sslinear_psi_comp.py
View file

@ -37,11 +37,11 @@ def psiDerivativecomputations(dL_dpsi0, dL_dpsi1, dL_dpsi2, variance, Z, variati
# Compute for psi0 and psi1
mu2S = np.square(mu)+S
dL_dvar += np.einsum('n,nq,nq->q',dL_dpsi0,gamma,mu2S) + np.einsum('nm,nq,mq,nq->q',dL_dpsi1,gamma,Z,mu)
dL_dgamma += np.einsum('n,q,nq->nq',dL_dpsi0,variance,mu2S) + np.einsum('nm,q,mq,nq->nq',dL_dpsi1,variance,Z,mu)
dL_dmu += np.einsum('n,nq,q,nq->nq',dL_dpsi0,gamma,2.*variance,mu) + np.einsum('nm,nq,q,mq->nq',dL_dpsi1,gamma,variance,Z)
dL_dS += np.einsum('n,nq,q->nq',dL_dpsi0,gamma,variance)
dL_dZ += np.einsum('nm,nq,q,nq->mq',dL_dpsi1,gamma, variance,mu)
dL_dvar += (dL_dpsi0[:,None]*gamma*mu2S).sum(axis=0) + (dL_dpsi1.T.dot(gamma*mu)*Z).sum(axis=0)
dL_dgamma += dL_dpsi0[:,None]*variance*mu2S+ dL_dpsi1.dot(Z)*mu*variance
dL_dmu += dL_dpsi0[:,None]*2.*variance*gamma*mu + dL_dpsi1.dot(Z)*gamma*variance
dL_dS += dL_dpsi0[:,None]*variance*gamma
dL_dZ += dL_dpsi1.T.dot(gamma*mu)*variance
return dL_dvar, dL_dZ, dL_dmu, dL_dS, dL_dgamma
@ -64,29 +64,23 @@ def _psi2computations(dL_dpsi2, variance, Z, mu, S, gamma):
gamma2 = np.square(gamma)
variance2 = np.square(variance)
mu2S = mu2+S # NxQ
gvm = np.einsum('nq,nq,q->nq',gamma,mu,variance)
common_sum = np.einsum('nq,mq->nm',gvm,Z)
# common_sum = np.einsum('nq,q,mq,nq->nm',gamma,variance,Z,mu) # NxM
Z_expect = np.einsum('mo,mq,oq->q',dL_dpsi2,Z,Z)
gvm = gamma*mu*variance
common_sum = gvm.dot(Z.T)
Z_expect = (np.dot(dL_dpsi2,Z)*Z).sum(axis=0)
Z_expect_var2 = Z_expect*variance2
dL_dpsi2T = dL_dpsi2+dL_dpsi2.T
tmp = np.einsum('mo,oq->mq',dL_dpsi2T,Z)
common_expect = np.einsum('mq,nm->nq',tmp,common_sum)
# common_expect = np.einsum('mo,mq,no->nq',dL_dpsi2+dL_dpsi2.T,Z,common_sum)
Z2_expect = np.einsum('om,nm->no',dL_dpsi2T,common_sum)
Z1_expect = np.einsum('om,mq->oq',dL_dpsi2T,Z)
common_expect = common_sum.dot(dL_dpsi2T).dot(Z)
Z2_expect = common_sum.dot(dL_dpsi2T)
Z1_expect = dL_dpsi2T.dot(Z)
dL_dvar = np.einsum('nq,q,q->q',2.*(gamma*mu2S-gamma2*mu2),variance,Z_expect)+\
np.einsum('nq,nq,nq->q',common_expect,gamma,mu)
dL_dvar = variance*Z_expect*2.*(gamma*mu2S-gamma2*mu2).sum(axis=0)+(common_expect*gamma*mu).sum(axis=0)
dL_dgamma = np.einsum('q,q,nq->nq',Z_expect,variance2,(mu2S-2.*gamma*mu2))+\
np.einsum('nq,q,nq->nq',common_expect,variance,mu)
dL_dgamma = Z_expect_var2*(mu2S-2.*gamma*mu2)+common_expect*mu*variance
dL_dmu = Z_expect_var2*mu*2.*(gamma-gamma2) + common_expect*gamma*variance
dL_dS = gamma*Z_expect_var2
dL_dmu = np.einsum('q,q,nq,nq->nq',Z_expect,variance2,mu,2.*(gamma-gamma2))+\
np.einsum('nq,nq,q->nq',common_expect,gamma,variance)
dL_dS = np.einsum('q,nq,q->nq',Z_expect,gamma,variance2)
# dL_dZ = 2.*(np.einsum('om,nq,q,mq,nq->oq',dL_dpsi2,gamma,variance2,Z,(mu2S-gamma*mu2))+np.einsum('om,nq,q,nq,nm->oq',dL_dpsi2,gamma,variance,mu,common_sum))
dL_dZ = Z1_expect*np.einsum('nq,q,nq->q',gamma,variance2,(mu2S-gamma*mu2))+np.einsum('nq,q,nq,nm->mq',gamma,variance,mu,Z2_expect)
dL_dZ = (gamma*(mu2S-gamma*mu2)).sum(axis=0)*variance2*Z1_expect+ Z2_expect.T.dot(gamma*mu)*variance
return dL_dvar, dL_dgamma, dL_dmu, dL_dS, dL_dZ

20
GPy/kern/_src/psi_comp/ssrbf_psi_comp.py
View file

@ -22,12 +22,14 @@ try:
# _psi1 NxM
mu = variational_posterior.mean
S = variational_posterior.variance
gamma = variational_posterior.binary_prob
N,M,Q = mu.shape[0],Z.shape[0],mu.shape[1]
l2 = np.square(lengthscale)
log_denom1 = np.log(S/l2+1)
log_denom2 = np.log(2*S/l2+1)
log_gamma,log_gamma1 = variational_posterior.gamma_log_prob()
log_gamma = np.log(gamma)
log_gamma1 = np.log(1.-gamma)
variance = float(variance)
psi0 = np.empty(N)
psi0[:] = variance
@ -37,6 +39,7 @@ try:
from ....util.misc import param_to_array
S = param_to_array(S)
mu = param_to_array(mu)
gamma = param_to_array(gamma)
Z = param_to_array(Z)
support_code = """
@ -79,7 +82,7 @@ try:
}
}
"""
weave.inline(code, support_code=support_code, arg_names=['psi1','psi2n','N','M','Q','variance','l2','Z','mu','S','log_denom1','log_denom2','log_gamma','log_gamma1'], type_converters=weave.converters.blitz)
weave.inline(code, support_code=support_code, arg_names=['psi1','psi2n','N','M','Q','variance','l2','Z','mu','S','gamma','log_denom1','log_denom2','log_gamma','log_gamma1'], type_converters=weave.converters.blitz)
psi2 = psi2n.sum(axis=0)
return psi0,psi1,psi2,psi2n
@ -94,12 +97,13 @@ try:
mu = variational_posterior.mean
S = variational_posterior.variance
gamma = variational_posterior.binary_prob
N,M,Q = mu.shape[0],Z.shape[0],mu.shape[1]
l2 = np.square(lengthscale)
log_denom1 = np.log(S/l2+1)
log_denom2 = np.log(2*S/l2+1)
log_gamma,log_gamma1 = variational_posterior.gamma_log_prob()
gamma, gamma1 = variational_posterior.gamma_probabilities()
log_gamma = np.log(gamma)
log_gamma1 = np.log(1.-gamma)
variance = float(variance)
dvar = np.zeros(1)
@ -113,6 +117,7 @@ try:
from ....util.misc import param_to_array
S = param_to_array(S)
mu = param_to_array(mu)
gamma = param_to_array(gamma)
Z = param_to_array(Z)
support_code = """
@ -130,7 +135,6 @@ try:
double Zm1q = Z(m1,q);
double Zm2q = Z(m2,q);
double gnq = gamma(n,q);
double g1nq = gamma1(n,q);
double mu_nq = mu(n,q);
if(m2==0) {
@ -156,7 +160,7 @@ try:
dmu(n,q) += lpsi1*Zmu*d_exp1/(denom*exp_sum);
dS(n,q) += lpsi1*(Zmu2_denom-1.)*d_exp1/(denom*exp_sum)/2.;
dgamma(n,q) += lpsi1*(d_exp1*g1nq-d_exp2*gnq)/exp_sum;
dgamma(n,q) += lpsi1*(d_exp1/gnq-d_exp2/(1.-gnq))/exp_sum;
dl(q) += lpsi1*((Zmu2_denom+Snq/lq)/denom*d_exp1+Zm1q*Zm1q/(lq*lq)*d_exp2)/(2.*exp_sum);
dZ(m1,q) += lpsi1*(-Zmu/denom*d_exp1-Zm1q/lq*d_exp2)/exp_sum;
}
@ -184,7 +188,7 @@ try:
dmu(n,q) += -2.*lpsi2*muZhat/denom*d_exp1/exp_sum;
dS(n,q) += lpsi2*(2.*muZhat2_denom-1.)/denom*d_exp1/exp_sum;
dgamma(n,q) += lpsi2*(d_exp1*g1nq-d_exp2*gnq)/exp_sum;
dgamma(n,q) += lpsi2*(d_exp1/gnq-d_exp2/(1.-gnq))/exp_sum;
dl(q) += lpsi2*(((Snq/lq+muZhat2_denom)/denom+dZm1m2*dZm1m2/(4.*lq*lq))*d_exp1+Z2/(2.*lq*lq)*d_exp2)/exp_sum;
dZ(m1,q) += 2.*lpsi2*((muZhat/denom-dZm1m2/(2*lq))*d_exp1-Zm1q/lq*d_exp2)/exp_sum;
}
@ -192,7 +196,7 @@ try:
}
}
"""
weave.inline(code, support_code=support_code, arg_names=['dL_dpsi1','dL_dpsi2','psi1','psi2n','N','M','Q','variance','l2','Z','mu','S','gamma','gamma1','log_denom1','log_denom2','log_gamma','log_gamma1','dvar','dl','dmu','dS','dgamma','dZ'], type_converters=weave.converters.blitz)
weave.inline(code, support_code=support_code, arg_names=['dL_dpsi1','dL_dpsi2','psi1','psi2n','N','M','Q','variance','l2','Z','mu','S','gamma','log_denom1','log_denom2','log_gamma','log_gamma1','dvar','dl','dmu','dS','dgamma','dZ'], type_converters=weave.converters.blitz)
dl *= 2.*lengthscale
if not ARD:

2
GPy/kern/_src/splitKern.py
View file

@ -7,7 +7,7 @@ from kern import Kern,CombinationKernel
from .independent_outputs import index_to_slices
import itertools
class DiffGenomeKern(Kern):
class DEtime(Kern):
def __init__(self, kernel, idx_p, Xp, index_dim=-1, name='DiffGenomeKern'):
self.idx_p = idx_p