def p_b_wins(strategy, scorea = 0): # Equal to P(b<a). Ts = strategy.Ts targets = strategy.targets distr = None for T, target, i in zip(Ts, targets, itertools.count()): distrT = scipy.array([[p_x_tries(x, T, target) for x in xs]]) if distr is not None: table = scipy.fliplr(scipy.dot(distr.T, distrT)) distr = scipy.zeros((1, 2*MAX_X)) for offseti, offset in enumerate(xrange(-(MAX_X-1), MAX_X)): distr[0, -offseti-1] = scipy.trace(table, offset) distr = distr[:,:MAX_X] else: distr = distrT assert distr[0,:i].sum() == 0 E = (xs * distr[0,:]).sum() #pylab.bar(xs, distr[0,:]); pylab.show() distra = scipy.array([[p_x_tries(x, 1, 100 - scorea) for x in xs]]) m = scipy.dot(distra.T, distr) p = 0. for offseti, offset in enumerate(xrange(-(MAX_X-1), 0)): p += scipy.trace(m, offset) return p
def p_b_wins(): # Equal to P(b<a). T=6; distrb3 = scipy.array([[p_x_tries(x, T, payoff(T)) for x in xs]]) T=7; distrb6 = scipy.array([[p_x_tries(x, T, payoff(T)) for x in xs]]) T=3; distrb7 = scipy.array([[p_x_tries(x, T, payoff(T)) for x in xs]]) table36 = scipy.fliplr(scipy.dot(distrb3.T, distrb6)) distr36 = scipy.zeros((1, 2*MAX_X)) # First element should be 0. for offseti, offset in enumerate(xrange(-(MAX_X-1), MAX_X)): distr36[0,-offseti-1] = scipy.trace(table36, offset) del table36 distr36 = distr36[:,:MAX_X] assert distr36[0,0] == 0 table367 = scipy.fliplr(scipy.dot(distr36.T, distrb7)) del distr36 distr367 = scipy.zeros((1, 2*MAX_X)) # First two elements should be 0. for offseti, offset in enumerate(xrange(-(MAX_X-1), MAX_X)): distr367[0,-offseti-1] = scipy.trace(table367, offset) del table367 distr367 = distr367[:,:MAX_X] assert distr367[0,0] == 0 and distr367[0,1] == 0 #pylab.bar(xs, distr367[0,:]); pylab.show() m = scipy.dot(distra.T, distr367) p = 0. for offseti, offset in enumerate(xrange(-(MAX_X-1), 0)): p += scipy.trace(m, offset) return p
def _getFisher(self):
"""
Return the fisher information matrix over the parameters
TO CHECK: IT DOES NOT WORK PROPERLY
"""
Ctot = self.vd.getGP().getCovar()
Ki = sp.linalg.inv(Ctot.K())
n_scales = self.vd.getNumberScales()
out = sp.zeros((n_scales,n_scales))
for m in range(n_scales):
out[m,m] = 0.5 * sp.trace(sp.dot(Ki,sp.dot(Ctot.Kgrad_param(m),sp.dot(Ki,Ctot.Kgrad_param(m)))))
for n in range(m):
out[m,n]=0.5 * sp.trace(sp.dot(Ki,sp.dot(Ctot.Kgrad_param(m),sp.dot(Ki,Ctot.Kgrad_param(n)))))
out[n,m]=out[m,n]
return out
def jitEigh(A,maxTries=10,warning=True):
"""
Do a Eigenvalue Decompsition with Jitter,
works as jitChol
"""
warning = True
jitter = 0
i = 0
while(True):
if jitter == 0:
jitter = abs(SP.trace(A))/A.shape[0]*1e-6
S,U = linalg.eigh(A)
else:
if warning:
# pdb.set_trace()
# plt.figure()
# plt.imshow(A, interpolation="nearest")
# plt.colorbar()
# plt.show()
logging.error("Adding jitter of %f in jitEigh()." % jitter)
S,U = linalg.eigh(A+jitter*SP.eye(A.shape[0]))
if S.min()>1E-10:
return S,U
if i<maxTries:
jitter = jitter*10
i += 1
raise linalg.LinAlgError, "Matrix non positive definite, jitter of " + str(jitter) + " added but failed after " + str(i) + " trials."
def jitEigh(A,maxTries=10,warning=True):
"""
Do a Eigenvalue Decompsition with Jitter,
works as jitChol
"""
warning = True
jitter = 0
i = 0
while(True):
try:
if jitter == 0:
jitter = abs(SP.trace(A))/A.shape[0]*1e-6
S,U = linalg.eigh(A)
else:
logging.error("Adding jitter of %f in jitEigh()." % jitter)
S,U = linalg.eigh(A+jitter*SP.eye(A.shape[0]))
if S.min()>1E-10:
return S,U
except:
pass
if i<maxTries:
jitter = jitter*10
i += 1
raise linalg.LinAlgError, "Matrix non positive definite, jitter of " + str(jitter) + " added but failed after " + str(i) + " trials."
def check_RCF(self):
"""Tests for right canonical form.
Uses the criteria listed in sub-section 3.1, theorem 1 of arXiv:quant-ph/0608197v2.
This is a consistency check mainly intended for debugging purposes.
FIXME: The tolerances appear to be too tight!
Returns
-------
(rnsOK, ls_trOK, ls_pos, ls_diag, normOK) : tuple of bool
rnsOK: Right orthonormalization is fullfilled (self.r[n] = eye)
ls_trOK: all self.l[n] have trace 1
ls_pos: all self.l[n] are positive-definite
ls_diag: all self.l[n] are diagonal
normOK: the state it normalized
"""
rnsOK = True
ls_trOK = True
ls_herm = True
ls_pos = True
ls_diag = True
for n in xrange(1, self.N + 1):
rnsOK = rnsOK and sp.allclose(self.r[n], sp.eye(self.r[n].shape[0]), atol=self.eps*2, rtol=0)
ls_herm = ls_herm and sp.allclose(self.l[n] - m.H(self.l[n]), 0, atol=self.eps*2)
ls_trOK = ls_trOK and sp.allclose(sp.trace(self.l[n]), 1, atol=self.eps*1000, rtol=0)
ls_pos = ls_pos and all(la.eigvalsh(self.l[n]) > 0)
ls_diag = ls_diag and sp.allclose(self.l[n], sp.diag(self.l[n].diagonal()))
normOK = sp.allclose(self.l[self.N], 1., atol=self.eps*1000, rtol=0)
return (rnsOK, ls_trOK, ls_pos, ls_diag, normOK)
def grad_f0(self, a):
"Compute the gradient of the objective function: -log(det(A(a)))."
A = self.get_A(a)
Ainv = la.inv(A)
E = sp.dot(Ainv, self.D).transpose(1,0,2)
out = -sp.trace(E, axis1=1, axis2=2)
return out
def _learnStep(self):
""" Main part of the algorithm. """
I = eye(self.numParameters)
self._produceSamples()
utilities = self.shapingFunction(self._currentEvaluations)
utilities /= sum(utilities) # make the utilities sum to 1
if self.uniformBaseline:
utilities -= 1./self.batchSize
samples = array(map(self._base2sample, self._population))
dCenter = dot(samples.T, utilities)
covGradient = dot(array([outer(s,s) - I for s in samples]).T, utilities)
covTrace = trace(covGradient)
covGradient -= covTrace/self.numParameters * I
dA = 0.5 * (self.scaleLearningRate * covTrace/self.numParameters * I
+self.covLearningRate * covGradient)
self._lastLogDetA = self._logDetA
self._lastInvA = self._invA
self._center += self.centerLearningRate * dot(self._A, dCenter)
self._A = dot(self._A, expm2(dA))
self._invA = dot(expm2(-dA), self._invA)
self._logDetA += 0.5 * self.scaleLearningRate * covTrace
if self.storeAllDistributions:
self._allDistributions.append((self._center.copy(), self._A.copy()))
def _van_rossum_multiunit_dist_for_trial_pair(a, b, weighting, tau, kernel):
if kernel is None:
spike_counts = sp.atleast_2d([st.size for st in a + b])
k_dist = spike_counts.T * (spike_counts - spike_counts.T)
else:
k_dist = kernel.summed_dist_matrix(a + b)
non_diagonal = sp.logical_not(sp.eye(len(a)))
summed_population = (
sp.trace(k_dist) - sp.trace(k_dist, len(a)) - sp.trace(k_dist, -len(a)))
labeled_line = (
sp.sum(k_dist[:len(a), :len(a)][non_diagonal]) +
sp.sum(k_dist[len(a):, len(a):][non_diagonal]) -
sp.sum(k_dist[:len(a), len(a):][non_diagonal]) -
sp.sum(k_dist[len(a):, :len(a)][non_diagonal]))
return sp.sqrt(summed_population + weighting * labeled_line)
def check_RCF(self):
"""Tests for right canonical form.
Uses the criteria listed in sub-section 3.1, theorem 1 of arXiv:quant-ph/0608197v2.
"""
rnsOK = True
ls_trOK = True
ls_herm = True
ls_pos = True
ls_diag = True
for n in xrange(1, self.N + 1):
rnsOK = rnsOK and sp.allclose(
self.r[n],
sp.eye(self.r[n].shape[0]),
atol=self.eps * 2,
rtol=0)
ls_herm = ls_herm and sp.allclose(
self.l[n] - m.H(self.l[n]), 0, atol=self.eps * 2)
ls_trOK = ls_trOK and sp.allclose(
sp.trace(self.l[n]), 1, atol=self.eps * 2, rtol=0)
ls_pos = ls_pos and all(la.eigvalsh(self.l[n]) > 0)
ls_diag = ls_diag and sp.allclose(self.l[n],
sp.diag(self.l[n].diagonal()))
normOK = sp.allclose(self.l[self.N], 1., atol=self.eps, rtol=0)
return (rnsOK, ls_trOK, ls_pos, ls_diag, normOK)
def jitChol(A, maxTries=10, warning=True):
"""Do a Cholesky decomposition with jitter.
Description:
U, jitter = jitChol(A, maxTries, warning) attempts a Cholesky
decomposition on the given matrix, if matrix isn't positive
definite the function adds 'jitter' and tries again. Thereafter
the amount of jitter is multiplied by 10 each time it is added
again. This is continued for a maximum of 10 times. The amount of
jitter added is returned.
Returns:
U - the Cholesky decomposition for the matrix.
jitter - the amount of jitter that was added to the matrix.
Arguments:
A - the matrix for which the Cholesky decomposition is required.
maxTries - the maximum number of times that jitter is added before
giving up (default 10).
warning - whether to give a warning for adding jitter (default is True)
See also
CHOL, PDINV, LOGDET
Copyright (c) 2005, 2006 Neil D. Lawrence
"""
warning = True
jitter = 0
i = 0
while(True):
try:
# Try --- need to check A is positive definite
if jitter == 0:
jitter = abs(SP.trace(A))/A.shape[0]*1e-6
LC = linalg.cholesky(A, lower=True)
return LC.T, 0.0
else:
if warning:
# pdb.set_trace()
# plt.figure()
# plt.imshow(A, interpolation="nearest")
# plt.colorbar()
# plt.show()
logging.error("Adding jitter of %f in jitChol()." % jitter)
LC = linalg.cholesky(A+jitter*SP.eye(A.shape[0]), lower=True)
return LC.T, jitter
except linalg.LinAlgError:
# Seems to have been non-positive definite.
if i<maxTries:
jitter = jitter*10
else:
raise linalg.LinAlgError, "Matrix non positive definite, jitter of " + str(jitter) + " added but failed after " + str(i) + " trials."
i += 1
return LC
def grassmann_logmap(A,p, tol=1e-13, skip_orthog_check=False):
'''
Computes the manifold log-map of (nxk) orthogonal matrix A,
centered at the point p (i.e. the "pole"), which is also an
(nxk) orthogonal matrix.
The log-map takes a point on the manifold and maps it to the
tangent space which is centered at a given pole.
The dimension of the tangent space is k(n-k),
and points A,p are on Gr(n,k).
@param A: The orthogonal matrix A, representing a point on
the grassmann manifold.
@param p: An orthogonal matrix p, representing a point on
the grassmann manifold where the tangent space will be formed.
Also called the "pole".
@param tol: Numerical tolerance used to set singular values
to exactly zero when within this tolerance of zero.
@param skip_orthog_check: Set to True if you can guarantee
that the inputs are already orthogonal matrices. Otherwise,
this function will check, and if A and/or p are not orthogonal,
the closest orthogonal matrix to A (or p) will be used.
@return: A tuple (log_p(A), ||log_p(A)|| ), representing
the tangent-space mapping of A, and the distance from the
mapping of A to the pole in the tangent space.
'''
#check that A and p are orthogonal, if
# not, then compute orthogonal representations and
# send back a warning message.
if not skip_orthog_check:
if not isOrthogonal(A):
print "WARNING: You are calling grassmann_logmap function on non-orthogonal input matrix A"
print "(This function will compute an orthogonal representation for A using an SVD.)"
A = closestOrthogonal(A)
if not isOrthogonal(p):
print "WARNING: You are calling grassmann_logmap function on non-orthogonal pole p."
print "(This function will compute an orthogonal representation for p using an SVD.)"
p = closestOrthogonal(p)
#p_perp is the orthogonal complement to p, = null(p.T)
p_perp = nullspace(p.T)
#compute p_perp * p_perp.T * A * inv(p.T * A)
T = sp.dot(p.T,A)
try:
Tinv = LA.inv(T)
except(LA.LinAlgError):
Tinv = LA.pinv(T)
X = sp.dot( sp.dot( sp.dot(p_perp,p_perp.T), A), Tinv )
u, s, vh = LA.svd(X, full_matrices=False)
s[ s < tol ]= 0 #set extremely small values to zero
theta = sp.diag( sp.arctan(s) )
logA = sp.dot(u, sp.dot( theta,vh))
normA = sp.trace( sp.dot(logA.T, logA) )
return logA, normA
def covar_rescaling_factor(C):
"""
Returns the rescaling factor for the Gower normalizion on covariance matrix C
the rescaled covariance matrix has sample variance of 1
"""
n = C.shape[0]
P = sp.eye(n) - sp.ones((n,n))/float(n)
trPCP = sp.trace(sp.dot(P,sp.dot(C,P)))
r = (n-1) / trPCP
return r
def fullrho(qu, squ):
print("#Starting full density matrix simulation!")
#Build state from pure states received from the MPS processes
rho = sp.zeros((2**N, 2**N), dtype=sp.complex128)
psis = [None] * N_samp
for n in range(N_samp):
pnum, psi = squ.get()
psis[pnum] = psi
rho += sp.outer(psi, psi.conj())
squ.task_done()
rho /= sp.trace(rho)
Hfull = get_full_op(get_ham(N, lam))
linds = get_linds(N, eps)
linds = [(n, L.reshape(tuple([sp.prod(L.shape[:sp.ndim(L)/2])]*2))) for (n, L) in linds]
linds_full = [sp.kron(sp.eye(2**(n-1)), sp.kron(L, sp.eye(2**(N - n + 1) / L.shape[0]))) for (n, L) in linds]
for L in linds_full:
assert L.shape == Hfull.shape
Qfull = -1.j * Hfull - 0.5 * sp.sum([L.conj().T.dot(L) for L in linds_full], axis=0)
szs = [None] + [sp.kron(sp.kron(sp.eye(2**(n - 1)), Sz), sp.eye(2**(N - n))) for n in range(1, N + 1)]
for i in range(N_steps + 1):
rho /= sp.trace(rho)
esz = []
for n in range(1, N + 1):
esz.append(sp.trace(szs[n].dot(rho)).real)
if i % res_every == 0:
if qu is None:
print(esz)
else:
qu.put([-1, i, esz])
qu.put([-2, i, [sp.NaN] * N]) #this slot is reserved for a second "exact" result
#Do Euler steps, approximately integrating the Lindblad master equation
rho += dt * (Qfull.dot(rho) + rho.dot(Qfull.conj().T) +
sum([L.dot(rho).dot(L.conj().T) for L in linds_full]))
def _fit(self, type, vc=False):
#2. init
if type=='null':
self.gp[type].covar.Cg.setCovariance(0.5*self.covY)
self.gp[type].covar.Cn.setCovariance(0.5*self.covY)
elif type=='full':
Cg0_K = self.gp['null'].covar.Cg.K()
Cn0_K = self.gp['null'].covar.Cn.K()
self.gp[type].covar.Cr.setCovariance((Cn0_K+Cg0_K)/3.)
self.gp[type].covar.Cg.setCovariance(2.*Cg0_K/3.)
self.gp[type].covar.Cn.setCovariance(2.*Cn0_K/3.)
elif type=='block':
Crf_K = self.gp['full'].covar.Cr.K()
Cnf_K = self.gp['full'].covar.Cn.K()
self.gp[type].covar.Cr.scale = sp.mean(Crf_K)
self.gp[type].covar.Cn.setCovariance(Cnf_K)
elif type=='rank1':
Crf_K = self.gp['full'].covar.Cr.K()
Cnf_K = self.gp['full'].covar.Cn.K()
self.gp[type].covar.Cr.setCovariance(Crf_K)
self.gp[type].covar.Cn.setCovariance(Cnf_K)
else:
print('poppo')
self.gp[type].optimize(factr=self.factr, verbose=False)
RV = {'Cg': self.gp[type].covar.Cg.K(),
'Cn': self.gp[type].covar.Cn.K(),
'LML': sp.array([self.gp[type].LML()]),
'LMLgrad': sp.array([sp.mean((self.gp[type].LML_grad()['covar'])**2)])}
if type=='null': RV['Cr'] = sp.zeros(RV['Cg'].shape)
else: RV['Cr'] = self.gp[type].covar.Cr.K()
if vc:
# tr(P CoR) = tr(C)tr(R) - tr(Ones C) tr(Ones R) / float(NP)
# = tr(C)tr(R) - C.sum() * R.sum() / float(NP)
trRr = (self.Xr**2).sum()
var_r = sp.trace(RV['Cr'])*trRr / float(self.Y.size-1)
var_g = sp.trace(RV['Cg'])*self.trRg / float(self.Y.size-1)
var_n = sp.trace(RV['Cn'])*self.Y.shape[0]
var_n-= RV['Cn'].sum() / float(RV['Cn'].shape[0])
var_n/= float(self.Y.size-1)
RV['var'] = sp.array([var_r, var_g, var_n])
if 0 and self.Y.size<5000:
pdb.set_trace()
Kr = sp.kron(RV['Cr'], sp.dot(self.Xr, self.Xr.T))
Kn = sp.kron(RV['Cn'], sp.eye(self.Y.shape[0]))
_var_r = sp.trace(Kr-Kr.mean(0)) / float(self.Y.size-1)
_var_n = sp.trace(Kn-Kn.mean(0)) / float(self.Y.size-1)
_var = sp.array([_var_r, var_g, _var_n])
print(((_var-RV['var'])**2).mean())
if type=='full':
# calculate within region vcs
Cr_block = sp.mean(RV['Cr']) * sp.ones(RV['Cr'].shape)
Cr_rank1 = lowrank_approx(RV['Cr'], rank=1)
var_block = sp.trace(Cr_block)*trRr / float(self.Y.size-1)
var_rank1 = sp.trace(Cr_rank1)*trRr / float(self.Y.size-1)
RV['var_r'] = sp.array([var_block, var_rank1-var_block, var_r-var_rank1])
return RV
def _calc_single_metric(trains_by_rate, metric, tau):
logger.info("Calculating metric %s for time_scale %s." % (metric, str(tau)))
result = sp.empty((cfg['evaluation_points'], cfg['evaluation_points']))
dist_mat = metrics[metric](list(itertools.chain(*trains_by_rate)), tau)
for i in xrange(cfg['evaluation_points']):
i_start = cfg['spike_trains_per_rate'] * i
i_stop = i_start + cfg['spike_trains_per_rate']
for j in xrange(i, cfg['evaluation_points']):
j_start = cfg['spike_trains_per_rate'] * j
j_stop = j_start + cfg['spike_trains_per_rate']
section = dist_mat[i_start:i_stop, j_start:j_stop]
if i == j:
result[i, i] = (sp.sum(section) - sp.trace(section)) / (
cfg['spike_trains_per_rate'] ** 2 -
cfg['spike_trains_per_rate'])
else:
result[i, j] = result[j, i] = sp.mean(section)
return result
def _em(self, X):
# Constants
n_samples, n_features = X.shape
n_components = self.n_components
max_iter = self.max_iter
# tol = self.tol
mu = X.mean(axis=0)
X_centered = X - sp.atleast_2d(mu)
# Initialize parameters
latent_mean = 0
sigma2 = 1
weight = sprd.randn(n_features, n_components)
# Main loop of EM algorithm
for i in range(max_iter):
# E step
M = sp.dot(weight.T, weight) + sigma2 * sp.eye(n_components)
inv_M = spla.inv(M)
latent_mean = sp.dot(inv_M, sp.dot(weight.T, X_centered.T)).T
# M step
expectation_zzT = n_samples * sigma2 * inv_M + sp.dot(latent_mean.T, latent_mean)
# Re-estimate W
weight = sp.dot(sp.dot(X_centered.T, latent_mean), spla.inv(expectation_zzT))
weight2 = sp.dot(weight.T, weight)
# Re-estimate \sigma^2
sigma2 = ((spla.norm(X_centered)**2 -
2 * sp.dot(latent_mean.ravel(), sp.dot(X_centered, weight).ravel()) +
sp.trace(sp.dot(expectation_zzT, weight2))) /
(n_samples * n_features))
self.predict_mean = mu
self.predict_cov = sp.dot(weight, weight.T) + sigma2 * sp.eye(n_features)
self.latent_mean = latent_mean
self.latent_cov = sigma2 * inv_M
self.sigma2 = sigma2
self.weight = weight
self.inv_M = inv_M
return self.latent_mean
def axis_angle_from_rotation_matrix(rm):
"""
Converts 3x3 rotation matrix to axis and angle representation.
:type rm: 3x3 :obj:`float` matrix
:param rm: Rotation matrix.
:rtype: :obj:`tuple`
:return: :samp:`(axis, radian_angle)` pair (angle in radians).
"""
eps = (16 * sp.finfo(rm.dtype).eps)
aa = sp.array((0, 0, 1), dtype=rm.dtype)
theta = aa[0]
c = (sp.trace(rm) - 1) / 2
if (c > 1):
c = 1
if (c < -1):
c = -1
if (math.fabs(math.fabs(c) - 1) >= eps):
theta = math.acos(c)
s = math.sqrt(1 - c * c)
inv2s = 1 / (2 * s)
aa[0] = inv2s * (rm[2, 1] - rm[1, 2])
aa[1] = inv2s * (rm[0, 2] - rm[2, 0])
aa[2] = inv2s * (rm[1, 0] - rm[0, 1])
elif (c >= 0):
theta = 0
else:
rmI = (rm + sp.eye(3, 3, dtype=rm.dtype))
theta = np.pi
for i in range(0, 3):
n2 = np.linalg.norm(rmI[:, i])
if (n2 > 0):
aa = col(rmI, i)
break
return aa, theta
def axis_angle_from_rotation_matrix(rm):
"""
Converts 3x3 rotation matrix to axis and angle representation.
:type rm: 3x3 :obj:`float` matrix
:param rm: Rotation matrix.
:rtype: :obj:`tuple`
:return: :samp:`(axis, radian_angle)` pair (angle in radians).
"""
eps = (16*sp.finfo(rm.dtype).eps)
aa = sp.array((0,0,1), dtype=rm.dtype)
theta = aa[0];
c = (sp.trace(rm) - 1)/2;
if (c > 1):
c = 1;
if (c < -1):
c = -1;
if (math.fabs(math.fabs(c)-1) >= eps):
theta = math.acos(c);
s = math.sqrt(1-c*c);
inv2s = 1/(2*s);
aa[0] = inv2s*(rm[2,1] - rm[1,2]);
aa[1] = inv2s*(rm[0,2] - rm[2,0]);
aa[2] = inv2s*(rm[1,0] - rm[0,1]);
elif (c >= 0):
theta = 0;
else:
rmI = (rm + sp.eye(3,3,dtype=rm.dtype));
theta = np.pi;
for i in range(0,3):
n2 = np.linalg.norm(rmI[:,i]);
if (n2 > 0):
aa = col(rmI, i);
break;
return aa, theta
def step(self, niter):
""" xNES """
f = self.f
mu, sigma, B_mat = self.mu, self.sigma, self.B_mat
eta_mu, eta_sigma, eta_B_mat = self.eta_mu, self.eta_sigma, self.eta_B_mat
npop = self.npop
d = self.d
sigma_old = self.sigma_old
I_mat = eye(d)
with joblib.Parallel(n_jobs=self.n_jobs) as parallel:
for i in range(niter):
if (i % 10 == 0):
print('Itter %s of %s' % (str(i), str(niter)))
print('best Train Accuracy ', self.fitness_best)
if (not self.stop):
for k in range(len(mu)):
if (not self.stop):
# if values over ~1e140, get error as too large
if (mu[k] > 1e140 or abs(mu[k]) < (1e-140)):
print('Alert! Value too large/small, mu[k] = ',
mu[k])
self.stop = True
# input("Press Enter to continue...")
z = randn(npop, d) # random [npop X d] array
x = mu + sigma * dot(
z, B_mat) # sampling next generation # broadcast
# evaluate solutions in parallel on function f
f_try = parallel(joblib.delayed(f)(z) for z in x)
f_try = asarray(f_try)
# save if best
fitness = mean(f_try) # mean fitness of next generation
if (self.fitness_best is not None):
if ((fitness - 1e-8) > (self.fitness_best)):
self.fitness_best = fitness # update best fitness
self.mu_best = mu.copy() # update best solution
self.counter = 0
else:
self.counter += 1
else: # best fitness is mean fitness
self.fitness_best = fitness
self.mu_best = mu.copy()
self.counter = 0
if (self.fitness_best is None):
self.fitness_best = mean(f_try)
self.mu_best = mu.copy()
self.counter = 0
for j in range(len(f_try)):
# validation_fit = self.f_val(x[j])
# if(f_try[j]> self.fitness_best and validation_fit>self.fitness_val):
if (f_try[j] > self.fitness_best):
self.fitness_best = f_try[j] # update best fitness
self.mu_best = x[j].copy() # update best solution
self.counter = 0
# self.fitness_val = validation_fit
if self.counter > self.patience:
self.done = True
return
self.best_testFit = self.f_test(self.mu_best)
# print('best Train Accuracy ',self.fitness_best )
# print('best Test Accuracy ',self.best_testFit )
# sort next generation w.r.t their fitnesses
unsorted_f_try = f_try
isort = argsort(f_try)
f_try = f_try[isort]
z = z[isort]
x = x[isort]
# u = utility if shaping, otherwise just use ordered fitnesses
u = self.utilities if self.use_fshape else f_try
# adaptation sampling
if self.use_adasam and sigma_old is not None: # sigma_old must be available
eta_sigma = self.adasam(eta_sigma, mu, sigma, B_mat,
sigma_old, x)
# G_delta = G_delta = u.s (s is z in gecco paper)
G_delta = dot(u, z)
# G_M = G_M = SUM u [dot] (s s_transpose - I)
G_M = dot(z.T, z * u.reshape(npop, 1)) - sum(u) * I_mat
# G_sigma = G_sigma = trace of G_M * (1/d)
G_sigma = trace(G_M) * (1.0 / d)
# G_B = G_B = G_M - G_delta*I
G_B = G_M - G_sigma * I_mat
# update old sigma
sigma_old = sigma
# update mu (center) = mu + eta_mu*sigma DOT (B, G_delta)
mu += eta_mu * sigma * dot(B_mat, G_delta)
# update sigma = sigma * exp(eta_delta * 0.5 * G_sigma)
sigma *= exp(0.5 * eta_sigma * G_sigma)
# update B = DOT (B, exp(0.5 eta_B * G_B))
B_mat = dot(B_mat, expm(0.5 * eta_B_mat * G_B))
# logging
for j in range(len(unsorted_f_try)):
self.history['fitness'].append(unsorted_f_try[j])
# self.history['fitness'].append(fitness)
self.history['sigma'].append(sigma)
self.history['eta_sigma'].append(eta_sigma)
# keep last results
self.mu, self.sigma, self.B_mat = mu, sigma, B_mat
self.eta_sigma = eta_sigma
self.sigma_old = sigma_old
print('best Test Accuracy ', self.best_testFit)
def SparseVFC(X,
Y,
Grid,
M=100,
a=5,
beta=0.1,
ecr=1e-5,
gamma=0.9,
lambda_=3,
minP=1e-5,
MaxIter=500,
theta=0.75,
div_cur_free_kernels=False):
"""Apply sparseVFC (vector field consensus) algorithm to learn an analytical function of vector field on the entire space robustly.
Reference: Regularized vector field learning with sparse approximation for mismatch removal, Ma, Jiayi, etc. al, Pattern Recognition
Arguments
---------
X: 'np.ndarray'
Current state. This corresponds to, for example, the spliced transcriptomic state.
Y: 'np.ndarray'
Velocity estimates in delta t. This corresponds to, for example, the inferred spliced transcriptomic velocity estimated calculated by velocyto, scvelo or dynamo.
Grid: 'np.ndarray'
Current state on a grid which is often used to visualize the vector field. This corresponds to, for example, the spliced transcriptomic state.
M: 'np.ndarray'
The number of basis functions to approximate the vector field. By default, it is 100.
a: 'float'
Paramerter of the model of outliers. We assume the outliers obey uniform distribution, and the volume of outlier's variation space is a. Default Value is 10.
beta: 'float'
Paramerter of Gaussian Kernel, k(x, y) = exp(-beta*||x-y||^2), Default value is 0.1.
ecr: 'float'
The minimum limitation of energy change rate in the iteration process. Default value is 1e-5.
gamma: 'float'
Percentage of inliers in the samples. This is an inital value for EM iteration, and it is not important. Default value is 0.9.
lambda_: 'float'
Represents the trade-off between the goodness of data fit and regularization. Default value is 3.
minP: 'float'
The posterior probability Matrix P may be singular for matrix inversion. We set the minimum value of P as minP. Default value is 1e-5.
MaxIter: 'int'
Maximum iterition times. Defualt value is 500.
theta: 'float'
Define how could be an inlier. If the posterior probability of a sample is an inlier is larger than theta, then it is regarded as an inlier. Default value is 0.75.
Returns
-------
VecFld: 'dict'
A dictionary which contains X, Y, beta, V, C, P, VFCIndex. Where V = f(X), P is the posterior probability and
VFCIndex is the indexes of inliers which found by VFC. Note that V = con_K(Grid, ctrl_pts, beta).dot(C) gives the prediction of velocity on Grid (can be any point in the gene expressionstate space).
"""
N, D = Y.shape
# Construct kernel matrix K
M = 500 if M is None else M
tmp_X = np.unique(X, axis=0) # return unique rows
idx = np.random.RandomState(seed=0).permutation(
tmp_X.shape[0]) # rand select some intial points
idx = idx[range(min(M, tmp_X.shape[0]))]
ctrl_pts = tmp_X[idx, :]
# ctrl_pts = X[range(500), :]
K = con_K(ctrl_pts, ctrl_pts,
beta) if div_cur_free_kernels is False else con_K_div_cur_free(
ctrl_pts, ctrl_pts)[0]
U = con_K(X, ctrl_pts,
beta) if div_cur_free_kernels is False else con_K_div_cur_free(
X, ctrl_pts)[0]
grid_U = con_K(
Grid, ctrl_pts,
beta) if div_cur_free_kernels is False else con_K_div_cur_free(
Grid, ctrl_pts)[0]
M = ctrl_pts.shape[0]
# Initialization
V = np.zeros((N, D))
C = np.zeros((M, D))
iter, tecr, E = 1, 1, 1
sigma2 = sum(sum((Y - V)**2)) / (N * D) ## test this
while iter < MaxIter and tecr > ecr and sigma2 > 1e-8:
# E_step
E_old = E
P, E = get_P(Y, V, sigma2, gamma, a)
E = E + lambda_ / 2 * scipy.trace(C.T.dot(K).dot(C))
tecr = abs((E - E_old) / E)
# print('iterate: {}, gamma: {}, the energy change rate: {}, sigma2={}\n'.format(*[iter, gamma, tecr, sigma2]))
# M-step. Solve linear system for C.
P = scipy.maximum(P, minP)
C = scipy.linalg.lstsq(((U.T * numpy.matlib.repmat(P.T, M, 1)).dot(U) + lambda_ * sigma2 * K), \
(U.T * numpy.matlib.repmat(P.T, M, 1)).dot(Y))[0]
# Update V and sigma**2
V = U.dot(C)
Sp = sum(P)
sigma2 = sum(P.T * np.sum((Y - V)**2, 1)) / np.dot(Sp, D)
# Update gamma
numcorr = len(np.where(P > theta)[0])
gamma = numcorr / X.shape[0]
if gamma > 0.95:
gamma = 0.95
elif gamma < 0.05:
gamma = 0.05
iter += 1
grid_V = np.dot(grid_U, C)
VecFld = {
"X": ctrl_pts,
"Y": Y,
"beta": beta,
"V": V,
"C": C,
"P": P,
"VFCIndex": np.where(P > theta)[0],
"sigma2": sigma2,
"grid": Grid,
"grid_V": grid_V
}
return VecFld
def jitChol(A, maxTries=10, warning=True):
"""Do a Cholesky decomposition with jitter.
Description:
U, jitter = jitChol(A, maxTries, warning) attempts a Cholesky
decomposition on the given matrix, if matrix isn't positive
definite the function adds 'jitter' and tries again. Thereafter
the amount of jitter is multiplied by 10 each time it is added
again. This is continued for a maximum of 10 times. The amount of
jitter added is returned.
Returns:
U - the Cholesky decomposition for the matrix.
jitter - the amount of jitter that was added to the matrix.
Arguments:
A - the matrix for which the Cholesky decomposition is required.
maxTries - the maximum number of times that jitter is added before
giving up (default 10).
warning - whether to give a warning for adding jitter (default is True)
See also
CHOL, PDINV, LOGDET
Copyright (c) 2005, 2006 Neil D. Lawrence
"""
warning = True
jitter = 0
i = 0
while (True):
try:
# Try --- need to check A is positive definite
if jitter == 0:
jitter = abs(SP.trace(A)) / A.shape[0] * 1e-6
LC = linalg.cholesky(A, lower=True)
return LC.T, 0.0
else:
if warning:
# pdb.set_trace()
# plt.figure()
# plt.imshow(A, interpolation="nearest")
# plt.colorbar()
# plt.show()
logging.error("Adding jitter of %f in jitChol()." % jitter)
LC = linalg.cholesky(A + jitter * SP.eye(A.shape[0]),
lower=True)
return LC.T, jitter
except linalg.LinAlgError:
# Seems to have been non-positive definite.
if i < maxTries:
jitter = jitter * 10
else:
raise (linalg.LinAlgError,
"Matrix non positive definite, jitter of " +
str(jitter) + " added but failed after " + str(i) +
" trials.")
i += 1
return LC
def step(self, niter):
""" xNES """
f = self.f
mu, sigma, bmat = self.mu, self.sigma, self.bmat
eta_mu, eta_sigma, eta_bmat = self.eta_mu, self.eta_sigma, self.eta_bmat
npop = self.npop
dim = self.dim
sigma_old = self.sigma_old
eyemat = eye(dim)
with joblib.Parallel(n_jobs=self.n_jobs) as parallel:
for i in range(niter):
s_try = randn(npop, dim)
z_try = mu + sigma * dot(s_try, bmat) # broadcast
f_try = parallel(joblib.delayed(f)(z) for z in z_try)
f_try = asarray(f_try)
# save if best
fitness = mean(f_try)
if fitness - 1e-8 > self.fitness_best:
self.fitness_best = fitness
self.mu_best = mu.copy()
self.counter = 0
else: self.counter += 1
if self.counter > self.patience:
self.done = True
return
isort = argsort(f_try)
f_try = f_try[isort]
s_try = s_try[isort]
z_try = z_try[isort]
u_try = self.utilities if self.use_fshape else f_try
if self.use_adasam and sigma_old is not None: # sigma_old must be available
eta_sigma = self.adasam(eta_sigma, mu, sigma, bmat, sigma_old, z_try)
dj_delta = dot(u_try, s_try)
dj_mmat = dot(s_try.T, s_try*u_try.reshape(npop,1)) - sum(u_try)*eyemat
dj_sigma = trace(dj_mmat)*(1.0/dim)
dj_bmat = dj_mmat - dj_sigma*eyemat
sigma_old = sigma
# update
mu += eta_mu * sigma * dot(bmat, dj_delta)
sigma *= exp(0.5 * eta_sigma * dj_sigma)
bmat = dot(bmat, expm(0.5 * eta_bmat * dj_bmat))
# logging
self.history['fitness'].append(fitness)
self.history['sigma'].append(sigma)
self.history['eta_sigma'].append(eta_sigma)
# keep last results
self.mu, self.sigma, self.bmat = mu, sigma, bmat
self.eta_sigma = eta_sigma
self.sigma_old = sigma_old
def train(self, x, y, sig=None, dc=None, threshold=None, fast=None, E_=None, Beta_=None):
"""
The function trains the pgpda model using the training samples
Inputs:
x: the samples matrix of size n x d, for the precomputed case (self.precomputed==1), x is a KERNEL object.
y: the vector with label of size n
sig: the parameter of the kernel function
dc: the number of dimension of the singanl subspace
threshold: the value of the cummulative variance that should be reached
fast = option used to perform a fast CV: only the parameter dc/threshold is learn
Outputs:
None - The model is included/updated in the object
"""
# Initialization
n = y.shape[0]
C = int(y.max())
eps = sp.finfo(sp.float64).eps
list_model_dc = "NM1 NM3 NM4"
if (sig is None) and (self.sig is None):
self.sig = 0.5
elif self.sig is None:
self.sig = sig
if (dc is None) and (self.dc is None):
self.dc = 2
elif self.dc is None:
self.dc = dc
if (threshold is None) and (self.threshold is None):
self.threshold = 0.95
elif self.threshold is None:
self.threshold = threshold
# Check of consistent dimension
if list_model_dc.find(self.model) > -1:
for i in range(C):
ni = sp.size(sp.where(y == (i + 1))[0])
if self.dc >= ni - 1:
self.dc = ni - 2
# Estimate the parameters of each class
for i in range(C):
t = sp.where(y == (i + 1))[0]
self.ni.append(sp.size(t))
self.prop.append(float(self.ni[i]) / n)
if fast is None:
# Compute Mi
Ki = KERNEL()
if self.precomputed is None:
Ki.compute_kernel(x[t, :], kernel=self.kernel, sig=self.sig)
else:
Ki.K = x.K[t, :][:, t].copy()
Ki.rank = Ki.K.shape[0]
self.ri.append(Ki.rank - 1)
Ki.center_kernel()
Ki.scale_kernel(self.ni[i])
TraceKi = sp.trace(Ki.K)
# Eigenvalue decomposition
E, Beta = linalg.eigh(Ki.K)
idx = E.argsort()[::-1]
E = E[idx]
E[E < eps] = eps
Beta = Beta[:, idx]
else:
E = E_[i]
Beta = Beta_[i]
self.ri.append(E.size - 1)
TraceKi = sp.sum(E)
# Parameter estimation
if list_model_dc.find(self.model) == -1:
di = estim_d(E[0 : self.ri[i] - 1], self.threshold)
else:
di = self.dc
self.di.append(di)
self.a.append(E[0:di])
self.b.append((TraceKi - sp.sum(self.a[i])) / (self.ri[i] - di))
if self.b[i] < eps: # Sanity check for numerical precision
self.b[i] = eps
self.ib.append(1.0 / eps)
else:
self.ib.append(1 / self.b[i])
self.Beta.append(Beta[:, 0:di])
del Beta, E
# Finish the estimation for the different models
if self.model == "NM0" or self.model == "NM1":
for i in range(C):
# Compute the value of matrix A
temp = self.Beta[i] * ((1 / self.a[i] - self.ib[i]) / self.a[i]).reshape(self.di[i])
self.A.append(sp.dot(temp, self.Beta[i].T) / self.ni[i])
elif self.model == "NM2" or self.model == "NM3":
for i in range(C):
# Update the value of a
self.a[i][:] = sp.mean(self.a[i])
# Compute the value of matrix A
temp = self.Beta[i] * ((1 / self.a[i] - self.ib[i]) / self.a[i]).reshape(self.di[i])
self.A.append(sp.dot(temp, self.Beta[i].T) / self.ni[i])
elif self.model == "NM4":
# Compute the value of a
al = sp.zeros((self.dc))
for i in range(self.dc):
for j in range(C):
al[i] += self.prop[j] * self.a[j][i]
for i in range(C):
self.a[i] = al.copy()
temp = self.Beta[i] * ((1 / self.a[i] - self.ib[i]) / self.a[i]).reshape(self.di[i])
self.A.append(sp.dot(temp, self.Beta[i].T) / self.ni[i])
self.A = sp.asarray(self.A)
def m():
"""
Note4 2.3.1 10
Create the following numpy array
A = [[1,4,6],[0,-3,2],[-2,-2,-2]]
B = [[2,-1,0], [2,-1,-0],[0,0,1]]
Compute A-B, 4A + B, trace(A), tB the transpose of B, the determinant of A, AB and Bt A the
matrix product of A and B.
Create the numpy array v = [1, -1, 0]. Compute Av the matrix-vector multiplication.
Find the eigenvalues and the eigenvectors of the matrix B. Hint. Use the linear algebra module
in numpy.
Solve the system Ax = v using the solve(A,v) function of linalg.
perfom the QR factorization of A using the linalg function qr(A) (Check that Q is an orthogonal
matrix, that is Q T Q = I).
Perform the singular value decomposition of A using the linalg function svd(A)
"""
A = np.array([[1,4,6],[0,-3,2],[-2,-2,-2]])
B = np.array([[2,2,2], [-1,-1,-3],[0,0,1]])
print "A = \n", A
raw_input('press enter to get B, A-B,4A - B')
print "B = \n", B
print ''
print ''
print "The difference is \n", A-B
print ''
print ''
print "4A - B = \n", 4*A - B
raw_input ('Press enter to get the trace of A,transpose of B,determinant of A ')
print " Trace of A : ", sp.trace(A)
print ''
print ''
print " Transpose of B : \n",sp.transpose(B)
print ''
print ''
print "Determinant of A : ", np.linalg.det(A)
raw_input('press enter to get AB, The matrix product of A and B,v')
print "AB = \n",A*B
print ''
print ''
print 'Matrix product of A and B : \n',sp.dot(A,B)
print ''
print ''
v =np.array([1,-1,0])
print 'v = ',v
raw_input('press enter to get matrix-vector multiplication Av, eigen values,The eigen vectors')
print 'Matrix-vector multiplication Av : \n', sp.dot(A,v)
print ''
print ''
e_values, e_vectors = np.linalg.eig(B)
print " Eigen values of B : ",e_values
print " Eigen vectors of B : \n",e_vectors
raw_input('press enter to get System solution, QR factorization,singular value decomposition')
print "System solution Ax = v: \t", np.linalg.solve(A,v)
print ''
print ''
print 'QR factorization: \n',np.linalg.qr(A)
print ''
print ''
print 'Singular value decomposition of A: \n', np.linalg.svd(A)
def transmission(self,rrgm_out):
from scipy import matrix,trace
last_element_index = len(self.block_sizes)-1
G_pq = matrix(rrgm_out[last_element_index,0])
T = trace(matrix(-2*self.contacts[1].SigmaRet.imag)*G_pq*matrix(-2*self.contacts[0].SigmaRet.imag)*G_pq.getH())
return T
def score_2_dof(self, X, snp_dim="col", debug=False):
"""
Parameters
----------
X : (`N`, `1`) ndarray
genotype vector (TODO: X should be small)
Returns
-------
pvalue : float
P value
"""
import scipy as sp
import scipy.linalg as la
import scipy.stats as st
# 1. calculate Qs and pvs
Q_rho = sp.zeros(len(self.rho_list))
Py = P(self.gp, self.y)
for i in range(len(self.rho_list)):
rho = self.rho_list[i]
LT = sp.vstack((rho ** 0.5 * self.vec_ones, (1 - rho) ** 0.5 * self.Env.T))
LTxoPy = sp.dot(LT, X * Py)
Q_rho[i] = 0.5 * sp.dot(LTxoPy.T, LTxoPy)
# Calculating pvs is split into 2 steps
# If we only consider one value of rho i.e. equivalent to SKAT and used for interaction test
if len(self.rho_list) == 1:
rho = self.rho_list[0]
L = sp.hstack((rho ** 0.5 * self.vec_ones.T, (1 - rho) ** 0.5 * self.Env))
xoL = X * L
PxoL = P(self.gp, xoL)
LToxPxoL = 0.5 * sp.dot(xoL.T, PxoL)
try:
pval = davies_pvalue(Q_rho[0], LToxPxoL)
except AssertionError:
eighQ, UQ = la.eigh(LToxPxoL)
pval = mod_liu_corrected(Q_rho[0], eighQ)
# Script ends here for interaction test
return pval
# or if we consider multiple values of rho i.e. equivalent to SKAT-O and used for association test
else:
pliumod = sp.zeros((len(self.rho_list), 4))
for i in range(len(self.rho_list)):
rho = self.rho_list[i]
L = sp.hstack(
(rho ** 0.5 * self.vec_ones.T, (1 - rho) ** 0.5 * self.Env)
)
xoL = X * L
PxoL = P(self.gp, xoL)
LToxPxoL = 0.5 * sp.dot(xoL.T, PxoL)
eighQ, UQ = la.eigh(LToxPxoL)
pliumod[i,] = mod_liu_corrected(Q_rho[i], eighQ)
T = pliumod[:, 0].min()
# if optimal_rho == 0.999:
# optimal_rho = 1
# 2. Calculate qmin
qmin = sp.zeros(len(self.rho_list))
percentile = 1 - T
for i in range(len(self.rho_list)):
q = st.chi2.ppf(percentile, pliumod[i, 3])
# Recalculate p-value for each Q rho of seeing values at least as extreme as q again using the modified matching moments method
qmin[i] = (q - pliumod[i, 3]) / (2 * pliumod[i, 3]) ** 0.5 * pliumod[
i, 2
] + pliumod[i, 1]
# 3. Calculate quantites that occur in null distribution
Px1 = P(self.gp, X)
m = 0.5 * sp.dot(X.T, Px1)
xoE = X * self.Env
PxoE = P(self.gp, xoE)
ETxPxE = 0.5 * sp.dot(xoE.T, PxoE)
ETxPx1 = sp.dot(xoE.T, Px1)
ETxPx11xPxE = 0.25 / m * sp.dot(ETxPx1, ETxPx1.T)
ZTIminusMZ = ETxPxE - ETxPx11xPxE
eigh, vecs = la.eigh(ZTIminusMZ)
eta = sp.dot(ETxPx11xPxE, ZTIminusMZ)
vareta = 4 * sp.trace(eta)
OneZTZE = 0.5 * sp.dot(X.T, PxoE)
tau_top = sp.dot(OneZTZE, OneZTZE.T)
tau_rho = sp.zeros(len(self.rho_list))
for i in range(len(self.rho_list)):
tau_rho[i] = self.rho_list[i] * m + (1 - self.rho_list[i]) / m * tau_top
MuQ = sp.sum(eigh)
VarQ = sp.sum(eigh ** 2) * 2 + vareta
KerQ = sp.sum(eigh ** 4) / (sp.sum(eigh ** 2) ** 2) * 12
Df = 12 / KerQ
# 4. Integration
# from time import time
# start = time()
pvalue = optimal_davies_pvalue(
qmin, MuQ, VarQ, KerQ, eigh, vareta, Df, tau_rho, self.rho_list, T
)
# print("Elapsed: {} seconds".format(time() - start))
# Final correction to make sure that the p-value returned is sensible
multi = 3
if len(self.rho_list) < 3:
multi = 2
idx = sp.where(pliumod[:, 0] > 0)[0]
pval = pliumod[:, 0].min() * multi
if pvalue <= 0 or len(idx) < len(self.rho_list):
pvalue = pval
if pvalue == 0:
if len(idx) > 0:
pvalue = pliumod[:, 0][idx].min()
if debug:
info = {
"Qs": Q_rho,
"pvs_liu": pliumod,
"qmin": qmin,
"MuQ": MuQ,
"VarQ": VarQ,
"KerQ": KerQ,
"lambd": eigh,
"VarXi": vareta,
"Df": Df,
"tau": tau_rho,
}
return pvalue, info
else:
return pvalue
T.append(sp.reshape(sp.kron(Cr_h, Xr), (N,P,rankCr*S), order='F'))
KiT.append(gp.covar.solve_t(T[i]))
Ht = sp.zeros((3,3))
for i in range(3):
Ht[i,i] = (sp.einsum('qpn,qpm->nm', T[i], KiT[i])**2).sum()
for j in range(0,i):
Ht[i,j] = (sp.einsum('qpn,qpm->nm', T[i], KiT[j])**2).sum()
Ht[j,i] = Ht[i,j]
if Y.shape[0]<=1000:
Ki = la.inv(sp.kron(mvset.gp[type].covar.Cn.K(), sp.eye(Y.shape[0])))
XrXr = sp.dot(Xr, Xr.T)
KidK = [sp.dot(Ki, sp.kron(_Cr.K_grad_i(i), XrXr)) for i in range(3)]
Ht0 = sp.zeros((3,3))
for i in range(3):
for j in range(3):
Ht0[i,j] = sp.trace(sp.dot(KidK[i], KidK[j]))
pdb.set_trace()
if 0:
# 2. quadratic_term = y_Ki_dKp_Ki_dKq_Ki_y
Z = Y-sp.dot(F, mvset.gp[type].mean.B[0])
XrXrKiZ = sp.dot(Xr, sp.dot(Xr.T, gp.covar.solve_t(Z)))
XrXrKiZC = [sp.dot(XrXrKiZ, _Cr.K_grad_i(i).T) for i in range(3)]
KiXrXrKiZC = [gp.covar.solve_t(XrXrKiZC[i]) for i in range(3)]
Hq = sp.zeros((3,3))
for i in range(3):
Hq[i,i] = (XrXrKiZC[i]*KiXrXrKiZC[i]).sum()
for j in range(i):
Hq[i,j] = (XrXrKiZC[i]*KiXrXrKiZC[j]).sum()
Hq[j,i] = Hq[i,j]
if Y.shape[0]<=1000:
def bicgstab_iso(A, x, b, MVop, VVop, max_itr=500, atol=1E-14, rtol=1E-14):
"""Implements the Bi-CGSTAB method for isomorphic operations.
The Bi-CGSTAB method is used to solve linear equations Ax = b.
Should the vectors x, b be isomorphic to some other objects, say
matrices x' and b', with corresponding opeator A'
(for example, via the Choi-Jamiolkowski isomorphism), the method
can similarly be carried out in the alternative form.
With this function, the operations corresponding to matrix-vector
and vector-vector multiplication are supplied by the caller to enable
using the method in an isomorphic way.
Parameters
----------
A : ndarray
The A matrix, or equivalent.
x : ndarray
An initial value for the unknown vector, or equivalent.
b : ndarray
The b vector, or equivalent.
MVop : function(ndarray, ndarray)
The matrix-vector multiplication operation.
VVop : function(ndarray, ndarray)
The vector-vector multiplication operation.
max_itr : int
Maximum number of iterations.
atol : float
Absolute tolerance for solution.
rtol : float
Relative tolerance for solution.
Returns
-------
x : ndarray
The final value for the unknown vector x.
convg : bool
Whether the algorithm converged within max_itr iterations.
"""
r_prv = b - MVop(A, x)
r0 = r_prv.copy()
rho_prv = 1
alpha = 1
omega_prv = 1
v_prv = sp.zeros_like(x)
p_prv = sp.zeros_like(x)
for i in xrange(max_itr):
rho = sp.trace(sp.dot(r0, r_prv))
beta = (rho / rho_prv) * (alpha / omega_prv)
p = r_prv + beta * (p_prv - omega_prv * v_prv)
v = MVop(A, p)
alpha = rho / VVop(r0, v)
s = r_prv - alpha * v
t = MVop(A, s)
omega = VVop(t, s) / VVop(t, t)
x += alpha * p + omega * s
#Test x
if sp.allclose(MVop(A, x), b, atol=atol, rtol=rtol):
break
r_prv = s - omega * t
rho_prv = rho
omega_prv = omega
v_prv[:] = v
p_prv[:] = p
convg = i < max_itr - 1
return x, convg
def update(self, population):
"""Update the current covariance matrix strategies from the
*population*.
:param population: A list of individuals from which to update the
parameters.
"""
chosen, not_chosen, isPlenty = self._select(population)
count1 = 0
count2 = 0
count3 = 0
count4 = 0
count5 = 0
count6 = 0
count7 = 0
count8 = 0
# Update the internal parameters for successful offspring
# Only the offspring update the parameter set
for ind in population:
if ind.Rank < self.parents[
ind._ps[1]].Rank and ind.Rank <= self.mu:
gm = numpy.outer(ind.theta, ind.theta) - numpy.identity(
self.dim)
gsigma = 0
if trace(gm) >= 0:
count1 += 1
gm = self.gradextention * gm
gsigma = numpy.trace(gm) / self.dim
else:
count2 += 1
gsigma = numpy.trace(gm) / self.dim
ga = gm - gsigma * numpy.identity(self.dim)
proc = 0.5 * (self.etaA * ga)
GGA = scipy.linalg.expm(proc)
if self.dominates(ind, self.parents[ind._ps[1]]):
count7 += 1
if self.parents[ind._ps[1]].oddoreven == 1:
ind.domisigma = ind.domisigma * exp(
self.etasigma * gsigma / 2.0)
ind.dominateA = numpy.dot(ind.dominateA, GGA)
else:
if self.parents[ind._ps[1]].oddoreven == 0:
ind.indsigma = ind.indsigma * exp(
self.etasigma * gsigma / 2.0)
ind.indicatorA = numpy.dot(ind.indicatorA, GGA)
if numpy.sum(ind.valConstr[1:]) < numpy.sum(
self.parents[ind._ps[1]].valConstr[1:]):
count8 += 1
elif ind.Rank > self.parents[
ind._ps[1]].Rank and ind.Rank <= self.mu:
gm = numpy.outer(ind.theta, ind.theta) - numpy.identity(
self.dim)
gsimga = numpy.trace(gm) / self.dim
if gsimga > 0:
count3 += 1
else:
count4 += 1
elif ind.Rank > self.mu and self.parents[
ind._ps[1]].Rank <= self.mu:
gm = self.infeasiblew * (numpy.outer(ind.theta, ind.theta) -
numpy.identity(self.dim))
gsigma = numpy.trace(gm) / self.dim
if numpy.trace(
numpy.outer(ind.theta, ind.theta) -
numpy.identity(self.dim)) > 0:
count5 += 1
else:
count6 += 1
gm = -gm
gsigma = -gsigma
ga = gm - gsigma * numpy.identity(self.dim)
proc = 0.5 * (self.etaA * ga)
GGA = scipy.linalg.expm(proc)
if self.parents[ind._ps[1]].isFeasible and not ind.isFeasible:
if self.parents[ind._ps[1]].oddoreven == 0:
self.parents[ind._ps[1]].indsigma = self.parents[
ind._ps[1]].indsigma * exp(
self.etasigma * gsigma / 2.0)
self.parents[ind._ps[1]].indicatorA = numpy.dot(
self.parents[ind._ps[1]].indicatorA, GGA)
elif self.parents[ind._ps[1]].oddoreven == 1:
self.parents[ind._ps[1]].domisigma = self.parents[
ind._ps[1]].domisigma * exp(
self.etasigma * gsigma / 2.0)
self.parents[ind._ps[1]].dominateA = numpy.dot(
self.parents[ind._ps[1]].dominateA, GGA)
if not self.parents[ind._ps[1]].madeinfeasible:
self.parents[ind._ps[1]].madeinfeasible = True
if self.parents[ind._ps[1]].madeinfeasible:
if self.parents[ind._ps[1]].oddoreven == 0:
self.parents[ind._ps[1]].oddoreven = 1
self.parents[ind._ps[1]].phase = 1
else:
self.parents[ind._ps[1]].oddoreven = 0
self.parents[ind._ps[1]].phase = 2
else:
print(
str(ind.Rank) + " and parent achieved " +
str(self.parents[ind._ps[1]].Rank))
self.dominating_Success = count7
self.success_outer = count1
self.success = count2
self.missed_both_alive_out = count3
self.missed_both_alive_out = count4
self.parentonly_alive_out = count5
self.parentonly_alive_in = count6
self.less_constraint = count8
self.parents = copy.deepcopy(chosen)
def take_step_split(self, dtau, ham_is_Herm=True):
"""Take a time-step dtau using the split-step integrator.
This is the one-site version of a DMRG-like time integrator described
at:
http://arxiv.org/abs/1408.5056
It has a fourth-order local error and is symmetric. It requires
iteratively computing two matrix exponentials per site, and thus
has less predictable CPU time requirements than the Euler or RK4
methods.
NOTE:
This requires the expokit extension, which is included in evoMPS but
must be compiled during, e.g. using setup.py to build all extensions.
Parameters
----------
dtau : complex
The (imaginary or real) amount of imaginary time (tau) to step.
ham_is_Herm : bool
Whether the Hamiltonian is really Hermitian. If so, the lanczos
method will be used for imaginary time evolution.
"""
#TODO: Compute eta.
self.eta_sq.fill(0)
self.eta = 0
assert self.canonical_form == 'right', 'take_step_split only implemented for right canonical form'
assert self.ham_sites == 2, 'take_step_split only implemented for nearest neighbour Hamiltonians'
dtau *= -1
from expokit_expmv import zexpmv, zexpmvh
if sp.iscomplex(dtau) or not ham_is_Herm:
expmv = zexpmv
fac = 1.j
dtau = sp.imag(dtau)
else:
expmv = zexpmvh
fac = 1
norm_est = abs(self.H_expect.real)
KL = [None] * (self.N + 1)
KL[1] = sp.zeros((self.D[1], self.D[1]), dtype=self.typ)
for n in xrange(1, self.N + 1):
lop = Vari_Opt_Single_Site_Op(self, n, KL[n - 1], tau=fac)
#print "Befor A", n, sp.inner(self.A[n].ravel().conj(), lop.matvec(self.A[n].ravel())).real
An = expmv(lop, self.A[n].ravel(), dtau/2., norm_est=norm_est)
self.A[n] = An.reshape((self.q[n], self.D[n - 1], self.D[n]))
self.l[n] = tm.eps_l_noop(self.l[n - 1], self.A[n], self.A[n])
norm = m.adot(self.l[n], self.r[n])
self.A[n] /= sp.sqrt(norm)
#print "After A", n, sp.inner(self.A[n].ravel().conj(), lop.matvec(self.A[n].ravel())).real, norm.real
#shift centre matrix right (RCF is like having a centre "matrix" at "1")
G = tm.restore_LCF_l_seq(self.A[n - 1:n + 1], self.l[n - 1:n + 1],
sanity_checks=self.sanity_checks)
if n > 1:
self.AA[n - 1] = tm.calc_AA(self.A[n - 1], self.A[n])
self.C[n - 1] = tm.calc_C_mat_op_AA(self.ham[n - 1], self.AA[n - 1])
KL[n], ex = tm.calc_K_l(KL[n - 1], self.C[n - 1], self.l[n - 2],
self.r[n], self.A[n], self.AA[n - 1])
if n < self.N:
lop2 = Vari_Opt_SC_op(self, n, KL[n], tau=fac)
#print "Befor G", n, sp.inner(G.ravel().conj(), lop2.matvec(G.ravel())).real
G = expmv(lop2, G.ravel(), -dtau/2., norm_est=norm_est)
G = G.reshape((self.D[n], self.D[n]))
norm = sp.trace(self.l[n].dot(G).dot(self.r[n].dot(G.conj().T)))
G /= sp.sqrt(norm)
#print "After G", n, sp.inner(G.ravel().conj(), lop2.matvec(G.ravel())).real, norm.real
for s in xrange(self.q[n + 1]):
self.A[n + 1][s] = G.dot(self.A[n + 1][s])
self.AA[n] = tm.calc_AA(self.A[n], self.A[n + 1])
self.C[n] = tm.calc_C_mat_op_AA(self.ham[n], self.AA[n])
for n in xrange(self.N, 0, -1):
lop = Vari_Opt_Single_Site_Op(self, n, KL[n - 1], tau=fac, sanity_checks=self.sanity_checks)
#print "Before A", n, sp.inner(self.A[n].ravel().conj(), lop.matvec(self.A[n].ravel())).real
An = expmv(lop, self.A[n].ravel(), dtau/2., norm_est=norm_est)
self.A[n] = An.reshape((self.q[n], self.D[n - 1], self.D[n]))
self.l[n] = tm.eps_l_noop(self.l[n - 1], self.A[n], self.A[n])
norm = m.adot(self.l[n], self.r[n])
self.A[n] /= sp.sqrt(norm)
#print "After A", n, sp.inner(self.A[n].ravel().conj(), lop.matvec(self.A[n].ravel())).real, norm.real
#shift centre matrix left (LCF is like having a centre "matrix" at "N")
Gi = tm.restore_RCF_r_seq(self.A[n - 1:n + 1], self.r[n - 1:n + 1],
sanity_checks=self.sanity_checks)
if n < self.N:
self.AA[n] = tm.calc_AA(self.A[n], self.A[n + 1])
self.C[n] = tm.calc_C_mat_op_AA(self.ham[n], self.AA[n])
self.calc_K(n_low=n, n_high=n)
if n > 1:
lop2 = Vari_Opt_SC_op(self, n - 1, KL[n - 1], tau=fac, sanity_checks=self.sanity_checks)
Gi = expmv(lop2, Gi.ravel(), -dtau/2., norm_est=norm_est)
Gi = Gi.reshape((self.D[n - 1], self.D[n - 1]))
norm = sp.trace(self.l[n - 1].dot(Gi).dot(self.r[n - 1].dot(Gi.conj().T)))
G /= sp.sqrt(norm)
#print "After G", n, sp.inner(Gi.ravel().conj(), lop2.matvec(Gi.ravel())).real, norm.real
for s in xrange(self.q[n - 1]):
self.A[n - 1][s] = self.A[n - 1][s].dot(Gi)
self.AA[n - 1] = tm.calc_AA(self.A[n - 1], self.A[n])
self.C[n - 1] = tm.calc_C_mat_op_AA(self.ham[n - 1], self.AA[n - 1])
def run_test_norm(T, ALPHAS, Ns, B, labeled, u, W_0, little_oh=False):
TRC = np.zeros((len(ALPHAS), len(T)))
TRCBC = np.zeros((len(ALPHAS), len(T)))
normC = np.zeros((len(ALPHAS), len(T)))
normC_tau_inv_u = np.zeros((len(ALPHAS), len(T)))
normC_tau_inv_u_p1 = np.zeros((len(ALPHAS), len(T)))
normC_tau_inv_u_p2 = np.zeros((len(ALPHAS), len(T)))
BIAS = np.zeros((len(ALPHAS), len(T)))
K = len(Ns)
N = sum(Ns)
u_n = u[:, 0] / sp.linalg.norm(u[:, 0])
print(np.linalg.norm(u_n))
for j, tau in enumerate(T):
if little_oh:
eps = tau**3.
else:
eps = tau**2.
w, v = get_eig_Lnorm_withW0(eps, Ns, W_0)
for i, alpha in enumerate(ALPHAS):
gamma = tau**alpha
d = (tau**(2 * alpha)) * np.power(
w + tau**2.,
-alpha) # diagonalization of C_t,e - will be used later
d_inv = 1. / d # the eigenvalues of C_\tau,\eps^{-1}
C_tau_inv_u = (v * d_inv.reshape(1, N)).dot(v.T.dot(u_n))
normC_tau_inv_u[i, j] = sp.linalg.norm(C_tau_inv_u)
# first term of the triangle inequality
vK = v[:, :
K] # using only the first K eigenvectors of C_\tau, \eps^{-1}
dK = d_inv[:K]
C_tau_inv_u_p1 = (vK * dK.reshape(1, K)).dot(vK.T.dot(u_n))
normC_tau_inv_u_p1[i, j] = sp.linalg.norm(C_tau_inv_u_p1)
# second term of the triangle inequality, using the K+1,...,Nth eigenpairs of C_\tau,\eps^{-1}
v_K = v[:, K:]
d_K = d_inv[K:]
C_tau_inv_u_p2 = (v_K * d_K.reshape(1, N - K)).dot(v_K.T.dot(u_n))
normC_tau_inv_u_p2[i, j] = sp.linalg.norm(C_tau_inv_u_p2)
# prior_inv : C_{tau,eps}^{-1}, where
# C_{tau, eps}^{-1} = tau^{-2alpha}(L + tau^2 I)^alpha
prior_inv = v.dot(
sp.sparse.diags([1. / thing for thing in d],
format='csr').dot(v.T))
# B/gamma^2
B_over_gamma2 = B / (gamma * gamma)
# post_inv : (B/gamma^2 + C_{tau,\eps}^{-1})^{-1}
post_inv = prior_inv + B_over_gamma2
# C^{-1}
post = post_inv.I
bias = sp.linalg.norm(post.dot(prior_inv.dot(u_n)))
BIAS[i, j] = bias
normC[i, j] = sp.linalg.norm(post)
trC = sp.trace(post)
TRC[i, j] = trC
post2 = post.dot(post)
trCBC = sp.trace(post2[np.ix_(labeled[0], labeled[0])])
TRCBC[i, j] = trCBC / (gamma**2.)
return TRC, TRCBC, normC, normC_tau_inv_u, normC_tau_inv_u_p1, normC_tau_inv_u_p2, BIAS
def contract_uni(A, B):
M = sp.dot(matmul.H(A[0][0]), B[0][0]) + sp.dot(matmul.H(A[0][1]), B[0][1])
tr = sp.trace(matmul.H(A[0][0])) * sp.trace(B[0][0]) + sp.trace(
matmul.H(A[0][1])) * sp.trace(B[0][1])
return tr.real
def bicgstab_iso(A, x, b, MVop, VVop, max_itr=500, atol=1E-14, rtol=1E-14):
"""Implements the Bi-CGSTAB method for isomorphic operations.
The Bi-CGSTAB method is used to solve linear equations Ax = b.
Should the vectors x, b be isomorphic to some other objects, say
matrices x' and b', with corresponding opeator A'
(for example, via the Choi-Jamiolkowski isomorphism), the method
can similarly be carried out in the alternative form.
With this function, the operations corresponding to matrix-vector
and vector-vector multiplication are supplied by the caller to enable
using the method in an isomorphic way.
Parameters
----------
A : ndarray
The A matrix, or equivalent.
x : ndarray
An initial value for the unknown vector, or equivalent.
b : ndarray
The b vector, or equivalent.
MVop : function(ndarray, ndarray)
The matrix-vector multiplication operation.
VVop : function(ndarray, ndarray)
The vector-vector multiplication operation.
max_itr : int
Maximum number of iterations.
atol : float
Absolute tolerance for solution.
rtol : float
Relative tolerance for solution.
Returns
-------
x : ndarray
The final value for the unknown vector x.
convg : bool
Whether the algorithm converged within max_itr iterations.
"""
r_prv = b - MVop(A, x)
r0 = r_prv.copy()
rho_prv = 1
alpha = 1
omega_prv = 1
v_prv = sp.zeros_like(x)
p_prv = sp.zeros_like(x)
for i in xrange(max_itr):
rho = sp.trace(sp.dot(r0, r_prv))
beta = (rho / rho_prv) * (alpha / omega_prv)
p = r_prv + beta * (p_prv - omega_prv * v_prv)
v = MVop(A, p)
alpha = rho / VVop(r0, v)
s = r_prv - alpha * v
t = MVop(A, s)
omega = VVop(t, s) / VVop(t, t)
x += alpha * p + omega * s
#Test x
if sp.allclose(MVop(A, x), b, atol=atol, rtol=rtol):
break
r_prv = s - omega * t
rho_prv = rho
omega_prv = omega
v_prv[:] = v
p_prv[:] = p
convg = i < max_itr - 1
return x, convg
def mkl_train(fname_l, reg, ltrain, no_mkl, flip):
global cache
d0 = io.loadmat(fname_l[0])
if flip:
keytrain = "kernel_traintest"
keytest = "kernel_traintrain"
else:
keytrain = "kernel_traintrain"
keytest = "kernel_traintest"
ltr = ltrain.astype(double)
#l = ((l==thecat)-1*(l!=thecat)).astype(double)
labels = Features.Labels(ltr)
if True:
tr1_l = []
tr2_l = []
ker_l = []
feat_l = []
combker = Kernel.CombinedKernel()
combfeat = Features.CombinedFeatures()
m,n = d0[keytrain].shape
yy,xx = mgrid[:m,:n]
#print "loading nfiles=", len(fname_l)
for i,fname in enumerate(fname_l):
if fname in cache_train:
kermat, tr1, tr2 = cache_train[fname]
else:
#print "loading", fname
d = io.loadmat(fname)
kermat = (d[keytrain]).astype(double)
#kermat += kermat.min()
del d
#kdiag =
#kermat /= kdiag
tr1 = trace(kermat)*len(fname_l)#*diag(kermat)
if tr1 == 0:
print "trace is 0, skipping"
continue
print i+1, "trace", tr1, "min", kermat.min(), "max", kermat.max(), fname
kermat /= tr1
#print kermat
#kermat = exp(kermat*len(kermat))
#tr2 = trace(kermat)
#kermat /= tr2
#print kermat
tr2 = 0
cache_train[fname] = kermat, tr1, tr2
#print diag(kermat)
ker = Kernel.CustomKernel()
ker.set_full_kernel_matrix_from_full(kermat)
feat = Features.DummyFeatures(n)
combker.append_kernel(ker)
combfeat.append_feature_obj(feat)
ker_l += [ker]
feat_l += [feat]
tr1_l += [tr1]
tr2_l += [tr2]
#combker.init(combfeat, combfeat)
cache = {'ker_l': ker_l, 'feat_l': feat_l, 'tr1_l':tr1_l, 'tr2_l':tr2_l,
'combker': combker, 'combfeat': combfeat}
del xx, yy
if no_mkl:
#w_l = array([.2, .8])
#w_l /= w_l.sum()
for i,ker in enumerate(ker_l):
ker.set_combined_kernel_weight(1./(len(ker_l)))
#ker.set_combined_kernel_weight(w_l[i])
tstart = time.time()
#svm1 = Classifier.SVMLight(reg, combker, labels)
#svm1 = Classifier.LibSVM(reg, combker, labels)
#svm1 = Classifier.GMNPSVM(reg, combker, labels)
#svm1 = Classifier.SVMSGD(reg, combker, labels)
#svm1 = Classifier.CPLEXSVM(reg, combker, labels)
if len(fname_l) == 1:
no_mkl = True
#svm1 = Classifier.LibSVM(reg, combker, labels)
svm1 = Classifier.SVMLight(reg, combker, labels)
else:
svm1 = Classifier.SVMLight(reg, combker, labels)
svm1.set_mkl_enabled(not no_mkl)
#svm1.set_C(reg/10., reg)
#print svm1.get_C1(), svm1.get_C2()
svm1.parallel.set_num_threads(4)
#print ker_l[0]
kkk = combker.get_kernel_matrix()
assert(not isnan(kkk).any())
assert(not isinf(kkk).any())# trace(kkk)
#svm1.set_linadd_enabled(True)
#svm1.set_shrinking_enabled(True)
#svm1.set_bias_enabled(False)
#svm1.set_epsilon(1e-1)
#svm1.set_tube_epsilon(1e-4)
#svm1.set_weight_epsilon(0)
#svm1.set_C_mkl(1e3)
#ipshell()
svm1.set_mkl_norm(1)
svm1.train()
alphas = svm1.get_alphas()
bias = svm1.get_bias()
svs = svm1.get_support_vectors()
#print ker_l[0]
#svm1 = Classifier.SVMLight(reg, ker, labels)
#svm1.train()
#print svm1.get_alphas()
weight_l = []
for i,ker in enumerate(ker_l):
weight = ker.get_combined_kernel_weight()
weight_l += [weight]
print weight_l
print "-w " + " -w ".join([str(e) for e in weight_l])
kweights = array(weight_l)
kweights /= kweights.sum()
traces1 = array(tr1_l)
#traces2 = array(tr2_l)
#raise
#tend = time.time()
#print "time:", tend-tstart
#kernel_train = combker.get_kernel_matrix()
# weight_l = []
# for i,ker in enumerate(ker_l):
# weight = ker.get_combined_kernel_weight()
# weight_l += [weight]
#combker.init(combfeat,combfeat)
#print svm1.classify().get_labels()[:10]
#kk = combker.get_kernel_matrix()
#print "trace=", trace(kk)
#trainperf = (sign(svm1.classify().get_labels())==ltr).mean()
#print "trainperf=", trainperf, weight_l
#print svm1.get_alphas()
#raise
# mkl = {"svm": svm1,
# "ker_l": ker_l,
# "feat_l": feat_l,
# "tr_l": tr_l,
# "combker": combker,
# "combfeat": combfeat,
# }
#print bias
mkl = {"alphas": alphas.astype('float32'),
"bias": array(bias).astype('float32'),
"svs": svs.astype('int32'),
"kweights": kweights.astype('float32'),
"traces1": traces1.astype('float32'),
#"traces2": traces2.astype('float32'),
}
#print svm1.get_alphas()
return mkl
def _fit(self, type, vc=False):
# 2. init
if type == 'null':
self.gp[type].covar.Cn.setCovariance(sp.eye(2))
elif type == 'full':
Cr0_K = 1e-4 * sp.ones((2, 2)) + 1e-4 * sp.eye(2)
Cn0_K = 0.99 * self.gp['null'].covar.Cn.K()
self.gp[type].covar.Cr.setCovariance(Cr0_K)
self.gp[type].covar.Cn.setCovariance(Cn0_K)
elif type == 'block':
Crf_K = self.gp['full'].covar.Cr.K()
Cnf_K = self.gp['full'].covar.Cn.K()
self.gp[type].covar.Cr.scale = sp.mean(Crf_K)
self.gp[type].covar.Cn.setCovariance(Cnf_K)
elif type == 'rank1':
Crf_K = self.gp['full'].covar.Cr.K()
Cnf_K = self.gp['full'].covar.Cn.K()
self.gp[type].covar.Cr.setCovariance(Crf_K)
self.gp[type].covar.Cn.setCovariance(Cnf_K)
else:
print('poppo')
conv = self.gp[type].optimize(factr=self.factr, verbose=False)[0]
B = self.gp[type].mean.b.reshape((int(self.mean.W.shape[1] / 2), 2),
order='F')
RV = {
'Cr': self.gp[type].covar.Cr.K(),
'Cn': self.gp[type].covar.Cn.K(),
'B': B,
'conv': sp.array([conv]),
'LML': sp.array([self.gp[type].LML()]),
'LMLgrad':
sp.array([sp.mean((self.gp[type].LML_grad()['covar'])**2)])
}
if vc:
# tr(P WW) = tr(PWWP) = ((PW)**2).sum()
# tr(P D) = (PD).sum() = D.sum() - 1/n * (Ones*D).sum()
# = D.sum() - D.sum()
def var_WW(W):
PW = W - W.mean(0)
rv = (PW**2).sum()
rv /= float(W.shape[0] - 1)
return rv
var_r = var_WW(self.gp[type].covar.W())
var_c = sp.var(sp.dot(self.mean.W, self.gp[type].mean.b))
D = self.gp[type].covar.d_inv()**(-1)
var_n = (1 - 1 / float(D.shape[0])) * \
D.sum() / float(self.Y.size - 1)
# var_n = sp.diagonal(sp.diag(D)-sp.diag(D).mean(0)).sum()/float(self.Y.size-1)
RV['var'] = sp.array([var_r, var_c, var_n])
if 0 and self.Y.size < 5000:
pdb.set_trace()
Kr = sp.kron(RV['Cr'], sp.dot(self.Xr, self.Xr.T))
Kn = sp.kron(RV['Cn'], sp.eye(self.Y.shape[0]))
_var_r = sp.trace(Kr - Kr.mean(0)) / float(self.Y.size - 1)
_var_n = sp.trace(Kn - Kn.mean(0)) / float(self.Y.size - 1)
_var = sp.array([_var_r, var_c, _var_n])
print(((_var - RV['var'])**2).mean())
if type == 'full':
def build_W(C):
S, U = la.eigh(C)
I = S > 1e-9
Ch = U[:, I] * S[I]**0.5
RV = sp.zeros(
(self.Y.shape[0], Ch.shape[1] * self.Xr.shape[1]))
RV[self.Ie] = sp.kron(Ch[0], self.Xr[self.Ie])
RV[~self.Ie] = sp.kron(Ch[1], self.Xr[~self.Ie])
return RV
# calculate within region vcs
Cr_block = sp.mean(RV['Cr']) * sp.ones(RV['Cr'].shape)
Cr_rank1 = lowrank_approx(RV['Cr'], rank=1)
var_block = var_WW(build_W(Cr_block))
var_rank1 = var_WW(build_W(Cr_rank1))
# trRr = (self.Xr**2).sum()
# var_block = sp.trace(Cr_block)*trRr / float(self.Y.size-1)
# var_rank1 = sp.trace(Cr_rank1)*trRr / float(self.Y.size-1)
RV['var_r'] = sp.array(
[var_block, var_rank1 - var_block, var_r - var_rank1])
return RV
def compute_divKL(direction, variables, model, idx):
"""
Function that computes the Kullback–Leibler divergence of the model_cv using the variables : idx +/- one of variables
Inputs:
variables: the variable to add to idx
model_cv: the model build with all the variables
idx: the pool of retained variables
Output:
divKL: the estimated Kullback–Leibler divergence
Used in GMM.forward_selection() and GMM.backward_selection()
"""
# Get machine precision
eps = sp.finfo(sp.float64).eps
# Initialization
divKL = sp.zeros(variables.size)
invCov = sp.empty((model.C,len(idx),len(idx)))
if len(idx)==0:
for k,var in enumerate(variables):
for i in xrange(model.C):
alphaI = 1/float(model.cov[i,var,var])
if alphaI < eps:
alphaI = eps
for j in xrange(i+1,model.C):
alphaJ = 1/float(model.cov[j,var,var])
if alphaJ < eps:
alphaJ = eps
md = (model.mean[i,var]-model.mean[j,var])
divKL[k] += 0.5*( alphaI*model.cov[j,var,var] + alphaJ*model.cov[i,var,var] + md*(alphaI + alphaJ)*md ) * model.prop[i]*model.prop[j]
else:
# Compute invcov de idx
for c in xrange(model.C):
vp,Q,_ = model.decomposition(model.cov[c,idx,:][:,idx])
invCov[c,:,:] = sp.dot(Q,((1/vp)*Q).T)
del vp,Q
if direction=='forward':
invCov_update = sp.empty((model.C,len(idx)+1,len(idx)+1))
elif direction=='backward':
invCov_update = sp.empty((model.C,len(idx)-1,len(idx)-1))
for k,var in enumerate(variables):
if direction=='forward':
id_t = list(idx)
id_t.append(var)
elif direction=='backward':
id_t = list(idx)
id_t.remove(var)
mask = sp.ones(len(idx), dtype=bool)
mask[k] = False
if direction=='forward':
for c in xrange(model.C):
alpha = model.cov[c,var,var] - sp.dot(model.cov[c,var,:][idx], sp.dot(invCov[c,:,:],model.cov[c,var,:][idx].T) )
if alpha < eps:
alpha = eps
invCov_update[c,:-1,:][:,:-1] = invCov[c,:,:] + 1/alpha * sp.outer( sp.dot(invCov[c,:,:],model.cov[c,var,:][idx].T) , sp.dot(model.cov[c,var,:][idx],invCov[c,:,:]) )
invCov_update[c,:-1,-1] = - 1/alpha * sp.dot(invCov[c,:,:],model.cov[c,var,:][idx].T)
invCov_update[c,-1,:-1] = - 1/alpha * sp.dot(model.cov[c,var,:][idx],invCov[c,:,:])
invCov_update[c,-1,-1] = 1/alpha
elif direction=='backward':
for c in xrange(model.C):
invCov_update[c,:,:] = invCov[c,mask,:][:,mask] - 1/invCov[c,k,k] * sp.outer(model.cov[c,var,:][id_t] , model.cov[c,var,:][id_t])
for i in xrange(model.C):
for j in xrange(i+1,model.C):
md = (model.mean[i,id_t]-model.mean[j,id_t])
divKL[k] += 0.5*( sp.trace( sp.dot( invCov_update[j,:,:],model.cov[i,id_t,:][:,id_t] ) + sp.dot( invCov_update[i,:,:],model.cov[j,id_t,:][:,id_t] ) ) + sp.dot(md,sp.dot(invCov_update[j,:,:]+invCov_update[i,:,:],md.T)) ) * model.prop[i]*model.prop[j]
return divKL
def sample_path(tdvp_class,num):
"""
Performs a complete dissipative evolution for the defined number
of steps and probes global operators after each step.
Parameters
----------
tdvp_class : tdvp_gen_instance
class object to work on. Must be derived from
tdvp_gen_dissipative
num : int
(Unique) Job number in the distributed computation framework.
Also used to seed RNG in case the results shall be deterministically
reproducible.
"""
# Re-seed the random generator with a number based on the iteration number
rand.seed((num))
print ">> Starting job #"+str(num)
#print ">> [" + str(num) + "] seeded with " + str(2222+num)
return_dict = {}
t = 0.
q = sp.empty(N + 1, dtype=sp.int32)
q.fill(qn)
"""
Now we are ready to create an instance of the generic evoMPS class extended
by take_step_dissipative(). In fact, the class to be used comes from the grid,
so it could in general be a non-generic instance.
"""
s = tdvp_class(N, D, q, ham)
#s.randomize()
#start = sp.array([[1, 1, 1, 1], [1, 1, 1, 1], [1, 1, 1, 1], [1, 1, 1, 1]]) / 4.0; #Totally mixed start
#start = sp.array([[.9997 + 0.j,0,0,1e-5],[.0,0,.01,0],[0, 0, 1e-5,0],[.0,1e-8,0,0.1]]) #zEROstart
#start = sp.array([[.01,0,0,1e-5],[.0,0,.01,0],[0, .97 + 0.j, 1e-5,0],[.0,1e-8,0,0.1]]) #UPstart
start = sp.array([[.01,0,0,1e-5],[0, .97 + 0.j, 1e-5,0],[.0,0,.01,0],[.0,1e-8,0,0.1]]) #DOWNstart
#start = sp.array([[.01,0,0,1e-5],[0, .0001 + 0.j, 1e-5,0],[.0,0,.01,0],[.0,1e-8,0,0.999]]) #AFstart
#start = sp.array([[0.0001, 0.00948, 0.0005, 0.0001],[0.0005, 0.0474, 0.0025, 0.0005], [0.0001, 0.00948,
#0.0005, 0.0001],[0.00948, 0.898704, 0.0474,
#0.00948]]) # Half Doubly occupied starting state
start = start / sp.trace(start)
for i in xrange(1,N):
s.apply_op_1s(start,i)
#s.apply_op_1s(start_1,i)
#s.apply_op_1s(start_2,i+1)
#s.A[N] = sp.array([[1 + 0.j, 0, 0, 0], [1, 0, 0, 0], [1, 0, 0, 0], [1, 0, 0, 0]]);
#print s.A[N-1]
#quit()
for i in xrange(total_steps):
# Define necessary operators...
#print "Starting step", i
p1 = sp.array([[1, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0]]);
p2 = sp.array([[0, 0, 0, 0], [0, 1, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0]]);
p3 = sp.array([[0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 1, 0], [0, 0, 0, 0]]);
p4 = sp.array([[0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 1]]);
EINS1 = sp.eye(2);
EINS2 = sp.eye(4);
EINS3 = sp.eye(8);
EINS4 = sp.eye(16);
PLUS = [[0, 0],[1, 0]];
MINUS = [[0, 1],[0, 0]];
PLUSMINUS = [[0, 0],[0, 1]];
MINUSPLUS = [[1, 0],[0, 0]];
Z = [[1, 0],[0, -1]];
X = [[0, 1],[1, 0]];
Y = [[0, -1.j],[1.j, 0]];
C1UP = sp.kron(MINUS, EINS3);
C1DAGUP = sp.kron(PLUS, EINS3);
C1DOWN = sp.kron(Z, sp.kron(MINUS, EINS2));
C1DAGDOWN = sp.kron(Z, sp.kron(PLUS, EINS2));
C2UP = sp.kron(Z, sp.kron(Z, sp.kron(MINUS, EINS1)));
C2DAGUP = sp.kron(Z, sp.kron(Z, sp.kron(PLUS, EINS1)));
C2DOWN = sp.kron(Z, sp.kron(Z, sp.kron(Z, MINUS)));
C2DAGDOWN = sp.kron(Z, sp.kron(Z, sp.kron(Z, PLUS)));
N1UP = sp.dot(C1DAGUP,C1UP);
N1DOWN = sp.dot(C1DAGDOWN,C1DOWN);
N2UP = sp.dot(C2DAGUP,C2UP);
N2DOWN = sp.dot(C2DAGDOWN,C2DOWN);
P1UP = sp.dot(C1DAGUP,C1UP) - sp.dot(C1DAGUP,sp.dot(C1UP,sp.dot(C1DAGDOWN,C1DOWN)));
P1DOWN = sp.dot(C1DAGDOWN,C1DOWN) - sp.dot(C1DAGDOWN,sp.dot(C1DOWN,sp.dot(C1DAGUP,C1UP)));
P2UP = sp.dot(C2DAGUP,C2UP) - sp.dot(C2DAGUP,sp.dot(C2UP,sp.dot(C2DAGDOWN,C2DOWN)));
P2DOWN = sp.dot(C2DAGDOWN,C2DOWN) - sp.dot(C2DAGDOWN,sp.dot(C2DOWN,sp.dot(C2DAGUP,C2UP)));
JEINS12UP = sqrtgamma1 * sp.dot(C1DAGDOWN,sp.dot(C2UP,sp.dot(P1UP,P2UP)));
JEINS12DOWN = sqrtgamma1 * sp.dot(C1DAGUP,sp.dot(C2DOWN,sp.dot(P1DOWN,P2DOWN)));
JEINS21UP = sqrtgamma1 * sp.dot(C2DAGDOWN,sp.dot(C1UP,sp.dot(P2UP,P1UP)));
JEINS21DOWN = sqrtgamma1 * sp.dot(C2DAGUP,sp.dot(C1DOWN,sp.dot(P2DOWN,P1DOWN)));
JZWEI12UP = sqrtgamma1 * sp.conj(JEINS12UP).T;
JZWEI12DOWN = sqrtgamma1 * sp.conj(JEINS12DOWN).T;
JZWEI21UP = sqrtgamma1 * sp.conj(JEINS21UP).T;
JZWEI21DOWN = sqrtgamma1 * sp.conj(JEINS21DOWN).T;
JDREI12 = sqrtgamma2 * sp.dot(C1DAGDOWN,sp.dot(C2DOWN,N2UP));
JDREI21 = sqrtgamma2 * sp.dot(C2DAGDOWN,sp.dot(C1DOWN,N1UP));
H = C1DAGUP.dot(C2UP) + C2DAGUP.dot(C1UP) + (C1DAGDOWN.dot(C2DOWN)) + (C2DAGDOWN.dot(C1DOWN)) + U * ((C1DAGUP.dot(C1UP.dot(C1DAGDOWN.dot(C1DOWN))))+(C2DAGUP.dot(C2UP.dot(C2DAGDOWN.dot(C2DOWN)))))
LHL = (JEINS12UP.conj().T.dot(JEINS12UP) +
JEINS12DOWN.conj().T.dot(JEINS12DOWN) +
JEINS21UP.conj().T.dot(JEINS21UP) +
JEINS21DOWN.conj().T.dot(JEINS21DOWN) +
JZWEI12UP.conj().T.dot(JZWEI12UP) +
JZWEI12DOWN.conj().T.dot(JZWEI12DOWN) +
JZWEI21UP.conj().T.dot(JZWEI21UP) +
JZWEI21DOWN.conj().T.dot(JZWEI21DOWN) +
JDREI12.conj().T.dot(JDREI12) +
JDREI21.conj().T.dot(JDREI21)
)
Q = H - 0.5 * LHL
L1_up = JEINS12UP + JEINS21UP
L1_down = JEINS12DOWN + JEINS21DOWN
L2_up = JZWEI12UP + JZWEI21UP
L2_down = JZWEI12DOWN + JZWEI21DOWN
L3 = JDREI12 + JDREI21
# Integrate exactly.
#s.update(auto_truncate=True, restore_CF=True)
#s.take_step_RK4(step)
# Or.... take a dissipative approach.
s.take_step_dissipative(step, l_nns)
# Real time evolution
timestep_meas = sp.zeros((4), dtype=sp.complex128);
NsSum = sp.zeros((3), dtype=sp.complex128);
DoubleSum = 0
mafSum = 0
mafAbsSum = 0
AFBSum = 0
entSum = 0
afbop = sp.kron(p2+p3,p2+p3).reshape(4,4,4,4)
afbop = afbop/sp.trace(afbop)
for site in xrange(1,N+1):
timestep_meas[0]+= np.real(s.expect_1s(p1,site)) / N;
timestep_meas[1]+= np.real(s.expect_1s(p2,site)) / N;
timestep_meas[2]+= np.real(s.expect_1s(p3,site)) / N;
timestep_meas[3]+= np.real(s.expect_1s(p4,site)) / N;
DoubleSum+= 2 * np.real(s.expect_1s(sp.array([[0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 1]]),site)) / (N);
rho1 = s.density_1s(site)
entSum += - sp.trace(rho1.dot(np.log(rho1))) / N
if site < N:
AFBSum+= np.real(s.expect_2s(afbop,site)) / (2*(N-1))
mafSum+=(np.real(s.expect_2s((N1UP + N2UP).reshape(4,4,4,4),site)) - np.real(s.expect_2s((N1DOWN + N2DOWN).reshape(4,4,4,4),site))) / (2*(N-1)); # Fraction of sites with antiferromagnetic neighbors
mafAbsSum= np.abs((np.real(s.expect_2s((N1UP+N2UP).reshape(4,4,4,4),site)) + np.real(s.expect_2s((N1DOWN + N2DOWN).reshape(4,4,4,4),site)))) / (2*(N-1));
nupval = np.real(s.expect_2s((N1UP + N2UP).reshape(4,4,4,4),site)) / (2*(N-1));
ndownval = np.real(s.expect_2s((N1DOWN + N2DOWN).reshape(4,4,4,4),site)) / (2*(N-1));
nsumval = np.real(s.expect_2s((N1UP + N2UP + N1DOWN + N2DOWN).reshape(4,4,4,4),site)) / (2*(N-1));
NsSum[0]+= nsumval
NsSum[1]+= nupval
NsSum[2]+= ndownval
MP[i] = timestep_meas
DO[i] = DoubleSum
Ns[i] = NsSum
maf[i] = mafSum
mafabs[i] = mafAbsSum
AFB[i] = AFBSum
ENT[i] = entSum
#print "Step", i, "completed."
t += step
if(i == 5* total_steps / 10):
print "job ",num,": 50% Complete."
return_dict["MP"] = MP
return_dict["Ns"] = Ns
return_dict["DO"] = DO
return_dict["maf"] = maf
return_dict["mafabs"] = mafabs
return_dict["AFB"] = AFB
return_dict["ENT"] = ENT
print "<< Job #"+str(num)+" done."
return return_dict
def score_2_dof(self, X, snp_dim='col', debug=False):
"""
Parameters
----------
X : (`N`, `1`) ndarray
genotype vector (TODO: X should be small)
Returns
-------
pvalue : float
P value
"""
#1. calculate Qs and pvs
Q_rho = sp.zeros(len(self.rho_list))
Py = P(self.gp, self.y)
xoPy = X * Py
for i in xrange(len(self.rho_list)):
rho = self.rho_list[i]
LT = sp.vstack((rho**0.5 * self.vec_ones,
(1 - rho)**0.5 * self.Env.T))
LTxoPy = sp.dot(LT, X * Py)
Q_rho[i] = 0.5 * sp.dot(LTxoPy.T, LTxoPy)
# Calculating pvs is split into 2 steps
# If we only consider one value of rho i.e. equivalent to SKAT and used for interaction test
if len(self.rho_list) == 1:
rho = self.rho_list[0]
L = sp.hstack((rho**0.5 * self.vec_ones.T,
(1 - rho)**0.5 * self.Env))
xoL = X * L
PxoL = P(self.gp, xoL)
LToxPxoL = 0.5 * sp.dot(xoL.T, PxoL)
pval = self.qwedaviesskat.getPv(Q_rho[0], LToxPxoL)
# Script ends here for interaction test
return pval
#or if we consider multiple values of rho i.e. equivalent to SKAT-O and used for association test
else:
pliumod = sp.zeros((len(self.rho_list), 4))
for i in xrange(len(self.rho_list)):
rho = self.rho_list[i]
L = sp.hstack((rho**0.5 * self.vec_ones.T,
(1 - rho)**0.5 * self.Env))
xoL = X * L
PxoL = P(self.gp, xoL)
LToxPxoL = 0.5 * sp.dot(xoL.T, PxoL)
eighQ, UQ = la.eigh(LToxPxoL)
pliumod[i, ] = self.qweliumod.getPv(Q_rho[i], eighQ)
T = pliumod[:, 0].min()
rho_opt = pliumod[:, 0].argmin()
optimal_rho = self.rho_list[rho_opt]
# if optimal_rho == 0.999:
# optimal_rho = 1
# 2. Calculate qmin
qmin = sp.zeros(len(self.rho_list))
percentile = 1 - T
for i in xrange(len(self.rho_list)):
q = st.chi2.ppf(percentile, pliumod[i, 3])
# Recalculate p-value for each Q rho of seeing values at least as extreme as q again using the modified matching moments method
qmin[i] = (q - pliumod[i, 3]) / (
2 * pliumod[i, 3])**0.5 * pliumod[i, 2] + pliumod[i, 1]
# 3. Calculate quantites that occur in null distribution
Px1 = P(self.gp, X)
m = 0.5 * sp.dot(X.T, Px1)
xoE = X * self.Env
PxoE = P(self.gp, xoE)
ETxPxE = 0.5 * sp.dot(xoE.T, PxoE)
ETxPx1 = sp.dot(xoE.T, Px1)
ETxPx11xPxE = 0.25 / m * sp.dot(ETxPx1, ETxPx1.T)
ZTIminusMZ = ETxPxE - ETxPx11xPxE
eigh, vecs = la.eigh(ZTIminusMZ)
eta = sp.dot(ETxPx11xPxE, ZTIminusMZ)
vareta = 4 * sp.trace(eta)
OneZTZE = 0.5 * sp.dot(X.T, PxoE)
tau_top = sp.dot(OneZTZE, OneZTZE.T)
tau_rho = sp.zeros(len(self.rho_list))
for i in xrange(len(self.rho_list)):
tau_rho[i] = self.rho_list[i] * m + (
1 - self.rho_list[i]) / m * tau_top
MuQ = sp.sum(eigh)
VarQ = sp.sum(eigh**2) * 2 + vareta
KerQ = sp.sum(eigh**4) / (sp.sum(eigh**2)**2) * 12
Df = 12 / KerQ
#4. Integration
pvalue = self.qwedavies.getPv(qmin, MuQ, VarQ, KerQ, eigh, vareta,
Df, tau_rho, self.rho_list, T)
# Final correction to make sure that the p-value returned is sensible
multi = 3
if len(self.rho_list) < 3:
multi = 2
idx = sp.where(pliumod[:, 0] > 0)[0]
pval = pliumod[:, 0].min() * multi
if pvalue <= 0 or len(idx) < len(self.rho_list):
pvalue = pval
if pvalue == 0:
if len(idx) > 0:
pvalue = pliumod[:, 0][idx].min()
if debug:
info = {
'Qs': Q_rho,
'pvs_liu': pliumod,
'qmin': qmin,
'MuQ': MuQ,
'VarQ': VarQ,
'KerQ': KerQ,
'lambd': eigh,
'VarXi': vareta,
'Df': Df,
'tau': tau_rho
}
return pvalue, info
else:
return pvalue
def sample_path(tdvp_class, num):
"""
Performs a complete dissipative evolution for the defined number
of steps and probes global operators after each step.
Parameters
----------
tdvp_class : tdvp_gen_instance
class object to work on. Must be derived from
tdvp_gen_dissipative
num : int
(Unique) Job number in the distributed computation framework.
Also used to seed RNG in case the results shall be deterministically
reproducible.
"""
# Re-seed the random generator with a number based on the iteration number
rand.seed((num))
print ">> Starting job #" + str(num)
#print ">> [" + str(num) + "] seeded with " + str(2222+num)
return_dict = {}
t = 0.
q = sp.empty(N + 1, dtype=sp.int32)
q.fill(qn)
"""
Now we are ready to create an instance of the generic evoMPS class extended
by take_step_dissipative(). In fact, the class to be used comes from the grid,
so it could in general be a non-generic instance.
"""
s = tdvp_class(N, D, q, ham, ham_sites=2)
#s.randomize()
#start = sp.array([[1, 1, 1, 1], [1, 1, 1, 1], [1, 1, 1, 1], [1, 1, 1, 1]]) / 4.0; #Totally mixed start
#start = sp.array([[.9997 + 0.j,0,0,1e-5],[.0,0,.01,0],[0, 0, 1e-5,0],[.0,1e-8,0,0.1]]) #zEROstart
start = sp.array([[.01, 0, 0, 1e-5], [.0, 0, .01, 0],
[0, .97 + 0.j, 1e-5, 0], [.0, 1e-8, 0, 0.1]]) #UPstart
#start = sp.array([[.01,0,0,1e-5],[0, .97 + 0.j, 1e-5,0],[.0,0,.01,0],[.0,1e-8,0,0.1]]) #DOWNstart
#start = sp.array([[.01,0,0,1e-5],[0, .0001 + 0.j, 1e-5,0],[.0,0,.01,0],[.0,1e-8,0,0.999]]) #AFstart
#start = sp.array([[0.0001, 0.00948, 0.0005, 0.0001],[0.0005, 0.0474, 0.0025, 0.0005], [0.0001, 0.00948,
#0.0005, 0.0001],[0.00948, 0.898704, 0.0474,
#0.00948]]) # Half Doubly occupied starting state
start = start / sp.trace(start)
for i in xrange(1, N):
s.apply_op_1s(start, i)
#s.apply_op_1s(start_1,i)
#s.apply_op_1s(start_2,i+1)
#s.A[N] = sp.array([[1 + 0.j, 0, 0, 0], [1, 0, 0, 0], [1, 0, 0, 0], [1, 0, 0, 0]]);
#print s.A[N-1]
#quit()
s.update()
for i in xrange(total_steps):
# Define necessary operators...
#print "Starting step", i
p1 = sp.array([[1, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0]])
p2 = sp.array([[0, 0, 0, 0], [0, 1, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0]])
p3 = sp.array([[0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 1, 0], [0, 0, 0, 0]])
p4 = sp.array([[0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 1]])
EINS1 = sp.eye(2)
EINS2 = sp.eye(4)
EINS3 = sp.eye(8)
EINS4 = sp.eye(16)
PLUS = [[0, 0], [1, 0]]
MINUS = [[0, 1], [0, 0]]
PLUSMINUS = [[0, 0], [0, 1]]
MINUSPLUS = [[1, 0], [0, 0]]
Z = [[1, 0], [0, -1]]
X = [[0, 1], [1, 0]]
Y = [[0, -1.j], [1.j, 0]]
C1UP = sp.kron(MINUS, EINS3)
C1DAGUP = sp.kron(PLUS, EINS3)
C1DOWN = sp.kron(Z, sp.kron(MINUS, EINS2))
C1DAGDOWN = sp.kron(Z, sp.kron(PLUS, EINS2))
C2UP = sp.kron(Z, sp.kron(Z, sp.kron(MINUS, EINS1)))
C2DAGUP = sp.kron(Z, sp.kron(Z, sp.kron(PLUS, EINS1)))
C2DOWN = sp.kron(Z, sp.kron(Z, sp.kron(Z, MINUS)))
C2DAGDOWN = sp.kron(Z, sp.kron(Z, sp.kron(Z, PLUS)))
N1UP = sp.dot(C1DAGUP, C1UP)
N1DOWN = sp.dot(C1DAGDOWN, C1DOWN)
N2UP = sp.dot(C2DAGUP, C2UP)
N2DOWN = sp.dot(C2DAGDOWN, C2DOWN)
P1UP = sp.dot(C1DAGUP, C1UP) - sp.dot(
C1DAGUP, sp.dot(C1UP, sp.dot(C1DAGDOWN, C1DOWN)))
P1DOWN = sp.dot(C1DAGDOWN, C1DOWN) - sp.dot(
C1DAGDOWN, sp.dot(C1DOWN, sp.dot(C1DAGUP, C1UP)))
P2UP = sp.dot(C2DAGUP, C2UP) - sp.dot(
C2DAGUP, sp.dot(C2UP, sp.dot(C2DAGDOWN, C2DOWN)))
P2DOWN = sp.dot(C2DAGDOWN, C2DOWN) - sp.dot(
C2DAGDOWN, sp.dot(C2DOWN, sp.dot(C2DAGUP, C2UP)))
JEINS12UP = sqrtgamma1 * sp.dot(C1DAGDOWN,
sp.dot(C2UP, sp.dot(P1UP, P2UP)))
JEINS12DOWN = sqrtgamma1 * sp.dot(
C1DAGUP, sp.dot(C2DOWN, sp.dot(P1DOWN, P2DOWN)))
JEINS21UP = sqrtgamma1 * sp.dot(C2DAGDOWN,
sp.dot(C1UP, sp.dot(P2UP, P1UP)))
JEINS21DOWN = sqrtgamma1 * sp.dot(
C2DAGUP, sp.dot(C1DOWN, sp.dot(P2DOWN, P1DOWN)))
JZWEI12UP = sqrtgamma1 * sp.conj(JEINS12UP).T
JZWEI12DOWN = sqrtgamma1 * sp.conj(JEINS12DOWN).T
JZWEI21UP = sqrtgamma1 * sp.conj(JEINS21UP).T
JZWEI21DOWN = sqrtgamma1 * sp.conj(JEINS21DOWN).T
JDREI12 = sqrtgamma2 * sp.dot(C1DAGDOWN, sp.dot(C2DOWN, N2UP))
JDREI21 = sqrtgamma2 * sp.dot(C2DAGDOWN, sp.dot(C1DOWN, N1UP))
H = C1DAGUP.dot(C2UP) + C2DAGUP.dot(C1UP) + (C1DAGDOWN.dot(C2DOWN)) + (
C2DAGDOWN.dot(C1DOWN)) + U * (
(C1DAGUP.dot(C1UP.dot(C1DAGDOWN.dot(C1DOWN)))) +
(C2DAGUP.dot(C2UP.dot(C2DAGDOWN.dot(C2DOWN)))))
LHL = (JEINS12UP.conj().T.dot(JEINS12UP) +
JEINS12DOWN.conj().T.dot(JEINS12DOWN) +
JEINS21UP.conj().T.dot(JEINS21UP) +
JEINS21DOWN.conj().T.dot(JEINS21DOWN) +
JZWEI12UP.conj().T.dot(JZWEI12UP) +
JZWEI12DOWN.conj().T.dot(JZWEI12DOWN) +
JZWEI21UP.conj().T.dot(JZWEI21UP) +
JZWEI21DOWN.conj().T.dot(JZWEI21DOWN) +
JDREI12.conj().T.dot(JDREI12) + JDREI21.conj().T.dot(JDREI21))
Q = H - 0.5 * LHL
L1_up = JEINS12UP + JEINS21UP
L1_down = JEINS12DOWN + JEINS21DOWN
L2_up = JZWEI12UP + JZWEI21UP
L2_down = JZWEI12DOWN + JZWEI21DOWN
L3 = JDREI12 + JDREI21
# Integrate exactly.
#s.update(auto_truncate=True, restore_CF=True)
#s.take_step_RK4(step)
# Or.... take a dissipative approach.
s.take_step_dissipative(step, l_nns)
# Real time evolution
timestep_meas = sp.zeros((4), dtype=sp.complex128)
NsSum = sp.zeros((3), dtype=sp.complex128)
DoubleSum = 0
mafSum = 0
mafAbsSum = 0
AFBSum = 0
entSum = 0
afbop = sp.kron(p2 + p3, p2 + p3).reshape(4, 4, 4, 4)
afbop = afbop / sp.trace(afbop)
for site in xrange(1, N + 1):
timestep_meas[0] += np.real(s.expect_1s(p1, site)) / N
timestep_meas[1] += np.real(s.expect_1s(p2, site)) / N
timestep_meas[2] += np.real(s.expect_1s(p3, site)) / N
timestep_meas[3] += np.real(s.expect_1s(p4, site)) / N
DoubleSum += 2 * np.real(
s.expect_1s(
sp.array([[0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0],
[0, 0, 0, 1]]), site)) / (N)
rho1 = s.density_1s(site)
entSum += -sp.trace(rho1.dot(np.log(rho1))) / N
if site < N:
AFBSum += np.real(s.expect_2s(afbop, site)) / (2 * (N - 1))
mafSum += (np.real(
s.expect_2s(
(N1UP + N2UP).reshape(4, 4, 4, 4), site)) - np.real(
s.expect_2s((N1DOWN + N2DOWN).reshape(4, 4, 4, 4),
site))) / (2 * (N - 1))
# Fraction of sites with antiferromagnetic neighbors
mafAbsSum = np.abs((np.real(
s.expect_2s(
(N1UP + N2UP).reshape(4, 4, 4, 4), site)) + np.real(
s.expect_2s((N1DOWN + N2DOWN).reshape(4, 4, 4, 4),
site)))) / (2 * (N - 1))
#nupval = np.real(s.expect_2s((N1UP + N2UP).reshape(4,4,4,4),site)) / (2*(N-1));
nupval = np.real(
s.expect_2s(
(N1UP + N2UP).reshape(4, 4, 4, 4), site)) / (2 *
(N - 1))
#ndownval = np.real(s.expect_2s((N1DOWN + N2DOWN).reshape(4,4,4,4),site)) / (2*(N-1));
ndownval = np.real(
s.expect_2s((N1DOWN + N2DOWN).reshape(4, 4, 4, 4),
site)) / (2 * (N - 1))
nsumval = np.real(
s.expect_2s((N1UP + N2UP + N1DOWN + N2DOWN).reshape(
4, 4, 4, 4), site)) / (2 * (N - 1))
NsSum[0] += nsumval
NsSum[1] += nupval
NsSum[2] += ndownval
rho2 = s.density_2s(site, site + 1)
spin_structure_op_up = sp.kron(
Z, sp.kron(EINS1, sp.kron(Z, EINS1)))
spin_structure_op_down = sp.kron(EINS1,
sp.kron(Z, sp.kron(EINS1, Z)))
norm_factor = 4.0 / (N**2)
spin_structure_up_value = np.real(
norm_factor *
(sp.exp(1.j * sp.pi) *
sp.trace(sp.dot(rho2, spin_structure_op_up))))
spin_structure_down_value = np.real(
norm_factor *
(sp.exp(-1.j * sp.pi) *
sp.trace(sp.dot(rho2, spin_structure_op_down))))
SSTRUCT[i, 0] += spin_structure_up_value / N
SSTRUCT[i, 1] += spin_structure_down_value / N
MP[i] = timestep_meas
DO[i] = DoubleSum
Ns[i] = NsSum
maf[i] = mafSum
mafabs[i] = mafAbsSum
AFB[i] = AFBSum
ENT[i] = entSum
#print "Step", i, "completed."
t += step
if (i == 1 * total_steps / 10):
print "job ", num, ": 10% Complete."
if (i == 2 * total_steps / 10):
print "job ", num, ": 20% Complete."
if (i == 3 * total_steps / 10):
print "job ", num, ": 30% Complete."
if (i == 4 * total_steps / 10):
print "job ", num, ": 40% Complete."
if (i == 5 * total_steps / 10):
print "job ", num, ": 50% Complete."
if (i == 6 * total_steps / 10):
print "job ", num, ": 60% Complete."
if (i == 7 * total_steps / 10):
print "job ", num, ": 70% Complete."
if (i == 8 * total_steps / 10):
print "job ", num, ": 80% Complete."
if (i == 9 * total_steps / 10):
print "job ", num, ": 90% Complete."
return_dict["MP"] = MP
return_dict["Ns"] = Ns
return_dict["DO"] = DO
return_dict["maf"] = maf
return_dict["mafabs"] = mafabs
return_dict["AFB"] = AFB
return_dict["ENT"] = ENT
return_dict["SSTRUCT"] = SSTRUCT
print "<< Job #" + str(num) + " done."
return return_dict
def _fit(self, type, vc=False):
# 2. init
if type == 'null':
self.gp[type].covar.Cg.setCovariance(0.5 * self.covY)
self.gp[type].covar.Cn.setCovariance(0.5 * self.covY)
elif type == 'full':
Cg0_K = self.gp['null'].covar.Cg.K()
Cn0_K = self.gp['null'].covar.Cn.K()
self.gp[type].covar.Cr.setCovariance((Cn0_K + Cg0_K) / 3.)
self.gp[type].covar.Cg.setCovariance(2. * Cg0_K / 3.)
self.gp[type].covar.Cn.setCovariance(2. * Cn0_K / 3.)
elif type == 'block':
Crf_K = self.gp['full'].covar.Cr.K()
Cnf_K = self.gp['full'].covar.Cn.K()
self.gp[type].covar.Cr.scale = sp.mean(Crf_K)
self.gp[type].covar.Cn.setCovariance(Cnf_K)
elif type == 'rank1':
Crf_K = self.gp['full'].covar.Cr.K()
Cnf_K = self.gp['full'].covar.Cn.K()
self.gp[type].covar.Cr.setCovariance(Crf_K)
self.gp[type].covar.Cn.setCovariance(Cnf_K)
else:
print('poppo')
self.gp[type].optimize(factr=self.factr, verbose=False)
RV = {
'Cg': self.gp[type].covar.Cg.K(),
'Cn': self.gp[type].covar.Cn.K(),
'LML': sp.array([self.gp[type].LML()]),
'LMLgrad':
sp.array([sp.mean((self.gp[type].LML_grad()['covar'])**2)])
}
if type == 'null':
RV['Cr'] = sp.zeros(RV['Cg'].shape)
else:
RV['Cr'] = self.gp[type].covar.Cr.K()
if vc:
# tr(P CoR) = tr(C)tr(R) - tr(Ones C) tr(Ones R) / float(NP)
# = tr(C)tr(R) - C.sum() * R.sum() / float(NP)
trRr = (self.Xr**2).sum()
var_r = sp.trace(RV['Cr']) * trRr / float(self.Y.size - 1)
var_g = sp.trace(RV['Cg']) * self.trRg / float(self.Y.size - 1)
var_n = sp.trace(RV['Cn']) * self.Y.shape[0]
var_n -= RV['Cn'].sum() / float(RV['Cn'].shape[0])
var_n /= float(self.Y.size - 1)
RV['var'] = sp.array([var_r, var_g, var_n])
if 0 and self.Y.size < 5000:
pdb.set_trace()
Kr = sp.kron(RV['Cr'], sp.dot(self.Xr, self.Xr.T))
Kn = sp.kron(RV['Cn'], sp.eye(self.Y.shape[0]))
_var_r = sp.trace(Kr - Kr.mean(0)) / float(self.Y.size - 1)
_var_n = sp.trace(Kn - Kn.mean(0)) / float(self.Y.size - 1)
_var = sp.array([_var_r, var_g, _var_n])
print(((_var - RV['var'])**2).mean())
if type == 'full':
# calculate within region vcs
Cr_block = sp.mean(RV['Cr']) * sp.ones(RV['Cr'].shape)
Cr_rank1 = lowrank_approx(RV['Cr'], rank=1)
var_block = sp.trace(Cr_block) * trRr / float(self.Y.size - 1)
var_rank1 = sp.trace(Cr_rank1) * trRr / float(self.Y.size - 1)
RV['var_r'] = sp.array(
[var_block, var_rank1 - var_block, var_r - var_rank1])
return RV
def train(self,
x,
y,
sig=None,
dc=None,
threshold=None,
fast=None,
E_=None,
Beta_=None):
'''
The function trains the pgpda model using the training samples
Inputs:
x: the samples matrix of size n x d, for the precomputed case (self.precomputed==1), x is a KERNEL object.
y: the vector with label of size n
sig: the parameter of the kernel function
dc: the number of dimension of the singanl subspace
threshold: the value of the cummulative variance that should be reached
fast = option used to perform a fast CV: only the parameter dc/threshold is learn
Outputs:
None - The model is included/updated in the object
'''
# Initialization
n = y.shape[0]
C = int(y.max())
eps = sp.finfo(sp.float64).eps
list_model_dc = 'NM1 NM3 NM4'
if (sig is None) and (self.sig is None):
self.sig = 0.5
elif self.sig is None:
self.sig = sig
if (dc is None) and (self.dc is None):
self.dc = 2
elif self.dc is None:
self.dc = dc
if (threshold is None) and (self.threshold is None):
self.threshold = 0.95
elif self.threshold is None:
self.threshold = threshold
# Check of consistent dimension
if (list_model_dc.find(self.model) > -1):
for i in range(C):
ni = sp.size(sp.where(y == (i + 1))[0])
if self.dc >= ni - 1:
self.dc = ni - 2
# Estimate the parameters of each class
for i in range(C):
t = sp.where(y == (i + 1))[0]
self.ni.append(sp.size(t))
self.prop.append(float(self.ni[i]) / n)
if fast is None:
# Compute Mi
Ki = KERNEL()
if self.precomputed is None:
Ki.compute_kernel(x[t, :],
kernel=self.kernel,
sig=self.sig)
else:
Ki.K = x.K[t, :][:, t].copy()
Ki.rank = Ki.K.shape[0]
self.ri.append(Ki.rank - 1)
Ki.center_kernel()
Ki.scale_kernel(self.ni[i])
TraceKi = sp.trace(Ki.K)
# Eigenvalue decomposition
E, Beta = linalg.eigh(Ki.K)
idx = E.argsort()[::-1]
E = E[idx]
E[E < eps] = eps
Beta = Beta[:, idx]
else:
E = E_[i]
Beta = Beta_[i]
self.ri.append(E.size - 1)
TraceKi = sp.sum(E)
# Parameter estimation
if list_model_dc.find(self.model) == -1:
di = estim_d(E[0:self.ri[i] - 1], self.threshold)
else:
di = self.dc
self.di.append(di)
self.a.append(E[0:di])
self.b.append((TraceKi - sp.sum(self.a[i])) / (self.ri[i] - di))
if self.b[i] < eps: # Sanity check for numerical precision
self.b[i] = eps
self.ib.append(1.0 / eps)
else:
self.ib.append(1 / self.b[i])
self.Beta.append(Beta[:, 0:di])
del Beta, E
# Finish the estimation for the different models
if self.model == 'NM0' or self.model == 'NM1':
for i in range(C):
# Compute the value of matrix A
temp = self.Beta[i] * ((1 / self.a[i] - self.ib[i]) /
self.a[i]).reshape(self.di[i])
self.A.append(sp.dot(temp, self.Beta[i].T) / self.ni[i])
elif self.model == 'NM2' or self.model == 'NM3':
for i in range(C):
# Update the value of a
self.a[i][:] = sp.mean(self.a[i])
# Compute the value of matrix A
temp = self.Beta[i] * ((1 / self.a[i] - self.ib[i]) /
self.a[i]).reshape(self.di[i])
self.A.append(sp.dot(temp, self.Beta[i].T) / self.ni[i])
elif self.model == 'NM4':
# Compute the value of a
al = sp.zeros((self.dc))
for i in range(self.dc):
for j in range(C):
al[i] += self.prop[j] * self.a[j][i]
for i in range(C):
self.a[i] = al.copy()
temp = self.Beta[i] * ((1 / self.a[i] - self.ib[i]) /
self.a[i]).reshape(self.di[i])
self.A.append(sp.dot(temp, self.Beta[i].T) / self.ni[i])
self.A = sp.asarray(self.A)
def test_gpbase(self):
covar = linear.LinearCF(n_dimensions=self.n_dimensions)
n_train = self.X['train'].shape[0]
theta = 1E-1
prior_cov = priors.GaussianPrior(key='covar',theta=SP.array([1.]))
prior_lik = priors.GaussianPrior(key='lik',theta=SP.array([1.]))
prior = priors.PriorList([prior_cov,prior_lik])
lik = likelihood_base.GaussIsoLik()
gp = gp_base.GP(covar_r=covar,likelihood=lik,prior=prior)
gp.setData(Y=self.Yuni['train'],X=self.X['train'])
# log likelihood and gradient derivation
hyperparams = {'covar':SP.array([0.5]), 'lik':SP.array([0.5])}
LML = gp.LML(hyperparams)
LMLgrad = gp.LMLgrad(hyperparams)
K = covar.K(hyperparams['covar']) + lik.K(hyperparams['lik'],n_train)
Kgrad_covar = covar.Kgrad_theta(hyperparams['covar'],0)
Kgrad_lik = lik.Kgrad_theta(hyperparams['lik'],n_train,0)
KinvY = LA.solve(K,self.Yuni['train'])
_LML = self.n_train/2*SP.log(2*SP.pi) + 0.5*SP.log(LA.det(K)) + 0.5*(self.Yuni['train']*KinvY).sum() + prior.LML(hyperparams)
LMLgrad_covar = 0.5 * SP.trace(LA.solve(K, Kgrad_covar)) - 0.5*SP.dot(KinvY.T,SP.dot(Kgrad_covar,KinvY))
LMLgrad_covar+= prior_cov.LMLgrad(hyperparams)['covar']
LMLgrad_lik = 0.5 * SP.trace(LA.solve(K, Kgrad_lik)) - 0.5*SP.dot(KinvY.T,SP.dot(Kgrad_lik,KinvY))
LMLgrad_lik+= prior_lik.LMLgrad(hyperparams)['lik']
assert SP.allclose(LML,_LML), 'ouch, marginal log likelihood does not match'
assert SP.allclose(LMLgrad['covar'], LMLgrad_covar), 'ouch, gradient with respect to theta does not match'
assert SP.allclose(LMLgrad['lik'], LMLgrad_lik), 'ouch, gradient with respect to theta does not match'
# predict
Ystar = gp.predict(hyperparams,self.X['test'])
Kstar = covar.Kcross(hyperparams['covar'])
_Ystar = SP.dot(Kstar.T,LA.solve(K,self.Yuni['train'])).flatten()
assert SP.allclose(Ystar,_Ystar), 'ouch, predictions, do not match'
# optimize
opts = {'gradcheck':True,'messages':False}
hyperparams_opt,lml_opt = optimize_base.opt_hyper(gp,hyperparams,opts=opts)
# log likelihood and gradient derivation
LML = gp.LML(hyperparams_opt)
LMLgrad = gp.LMLgrad(hyperparams_opt)
K = covar.K(hyperparams_opt['covar']) + lik.K(hyperparams_opt['lik'],n_train)
Kgrad_covar = covar.Kgrad_theta(hyperparams_opt['covar'],0)
Kgrad_lik = lik.Kgrad_theta(hyperparams_opt['lik'],n_train,0)
KinvY = LA.solve(K,self.Yuni['train'])
_LML = self.n_train/2*SP.log(2*SP.pi) + 0.5*SP.log(LA.det(K)) + 0.5*(self.Yuni['train']*KinvY).sum() + prior.LML(hyperparams_opt)
LMLgrad_covar = 0.5 * SP.trace(LA.solve(K, Kgrad_covar)) - 0.5*SP.dot(KinvY.T,SP.dot(Kgrad_covar,KinvY))
LMLgrad_covar+= prior_cov.LMLgrad(hyperparams_opt)['covar']
LMLgrad_lik = 0.5 * SP.trace(LA.solve(K, Kgrad_lik)) - 0.5*SP.dot(KinvY.T,SP.dot(Kgrad_lik,KinvY))
LMLgrad_lik+= prior_lik.LMLgrad(hyperparams_opt)['lik']
assert SP.allclose(LML,_LML), 'ouch, marginal log likelihood does not match'
assert SP.allclose(LMLgrad['covar'], LMLgrad_covar), 'ouch, gradient with respect to theta does not match'
assert SP.allclose(LMLgrad['lik'], LMLgrad_lik), 'ouch, gradient with respect to theta does not match'
# predict
Ystar = gp.predict(hyperparams_opt,self.X['test'])
Kstar = covar.Kcross(hyperparams_opt['covar'])
_Ystar = SP.dot(Kstar.T,LA.solve(K,self.Yuni['train'])).flatten()
assert SP.allclose(Ystar,_Ystar), 'ouch, predictions, do not match'
def test_gpbase(self):
covar = linear.LinearCF(n_dimensions=self.n_dimensions)
n_train = self.X['train'].shape[0]
theta = 1E-1
prior_cov = priors.GaussianPrior(key='covar', theta=SP.array([1.]))
prior_lik = priors.GaussianPrior(key='lik', theta=SP.array([1.]))
prior = priors.PriorList([prior_cov, prior_lik])
lik = likelihood_base.GaussIsoLik()
gp = gp_base.GP(covar_r=covar, likelihood=lik, prior=prior)
gp.setData(Y=self.Yuni['train'], X=self.X['train'])
# log likelihood and gradient derivation
hyperparams = {'covar': SP.array([0.5]), 'lik': SP.array([0.5])}
LML = gp.LML(hyperparams)
LMLgrad = gp.LMLgrad(hyperparams)
K = covar.K(hyperparams['covar']) + lik.K(hyperparams['lik'], n_train)
Kgrad_covar = covar.Kgrad_theta(hyperparams['covar'], 0)
Kgrad_lik = lik.Kgrad_theta(hyperparams['lik'], n_train, 0)
KinvY = LA.solve(K, self.Yuni['train'])
_LML = self.n_train / 2 * SP.log(2 * SP.pi) + 0.5 * SP.log(
LA.det(K)) + 0.5 * (self.Yuni['train'] *
KinvY).sum() + prior.LML(hyperparams)
LMLgrad_covar = 0.5 * SP.trace(LA.solve(
K, Kgrad_covar)) - 0.5 * SP.dot(KinvY.T, SP.dot(
Kgrad_covar, KinvY))
LMLgrad_covar += prior_cov.LMLgrad(hyperparams)['covar']
LMLgrad_lik = 0.5 * SP.trace(LA.solve(K, Kgrad_lik)) - 0.5 * SP.dot(
KinvY.T, SP.dot(Kgrad_lik, KinvY))
LMLgrad_lik += prior_lik.LMLgrad(hyperparams)['lik']
assert SP.allclose(
LML, _LML), 'ouch, marginal log likelihood does not match'
assert SP.allclose(
LMLgrad['covar'], LMLgrad_covar
), 'ouch, gradient with respect to theta does not match'
assert SP.allclose(
LMLgrad['lik'],
LMLgrad_lik), 'ouch, gradient with respect to theta does not match'
# predict
Ystar = gp.predict(hyperparams, self.X['test'])
Kstar = covar.Kcross(hyperparams['covar'])
_Ystar = SP.dot(Kstar.T, LA.solve(K, self.Yuni['train'])).flatten()
assert SP.allclose(Ystar, _Ystar), 'ouch, predictions, do not match'
# optimize
opts = {'gradcheck': True, 'messages': False}
hyperparams_opt, lml_opt = optimize_base.opt_hyper(gp,
hyperparams,
opts=opts)
# log likelihood and gradient derivation
LML = gp.LML(hyperparams_opt)
LMLgrad = gp.LMLgrad(hyperparams_opt)
K = covar.K(hyperparams_opt['covar']) + lik.K(hyperparams_opt['lik'],
n_train)
Kgrad_covar = covar.Kgrad_theta(hyperparams_opt['covar'], 0)
Kgrad_lik = lik.Kgrad_theta(hyperparams_opt['lik'], n_train, 0)
KinvY = LA.solve(K, self.Yuni['train'])
_LML = self.n_train / 2 * SP.log(2 * SP.pi) + 0.5 * SP.log(
LA.det(K)) + 0.5 * (self.Yuni['train'] *
KinvY).sum() + prior.LML(hyperparams_opt)
LMLgrad_covar = 0.5 * SP.trace(LA.solve(
K, Kgrad_covar)) - 0.5 * SP.dot(KinvY.T, SP.dot(
Kgrad_covar, KinvY))
LMLgrad_covar += prior_cov.LMLgrad(hyperparams_opt)['covar']
LMLgrad_lik = 0.5 * SP.trace(LA.solve(K, Kgrad_lik)) - 0.5 * SP.dot(
KinvY.T, SP.dot(Kgrad_lik, KinvY))
LMLgrad_lik += prior_lik.LMLgrad(hyperparams_opt)['lik']
assert SP.allclose(
LML, _LML), 'ouch, marginal log likelihood does not match'
assert SP.allclose(
LMLgrad['covar'], LMLgrad_covar
), 'ouch, gradient with respect to theta does not match'
assert SP.allclose(
LMLgrad['lik'],
LMLgrad_lik), 'ouch, gradient with respect to theta does not match'
# predict
Ystar = gp.predict(hyperparams_opt, self.X['test'])
Kstar = covar.Kcross(hyperparams_opt['covar'])
_Ystar = SP.dot(Kstar.T, LA.solve(K, self.Yuni['train'])).flatten()
assert SP.allclose(Ystar, _Ystar), 'ouch, predictions, do not match'
def take_step_implicit(self, dtau, midpoint=True):
"""A backward (implicit) integration step.
Based on p. 8-10 of arXiv:1103.0936v2 [cond-mat.str-el].
NOTE: Not currently working as well as expected. Iterative solution of
implicit equation stops converging at some point...
This is made trickier by the gauge freedom. We solve the implicit equation iteratively, aligning the tangent
vectors along the gauge orbits for each step to obtain the physically relevant difference dA. The gauge-alignment is done
by solving a matrix equation.
The iteration seems to be difficult. At the moment, iteration over the whole chain is combined with iteration over a single
site (a single A[n]). Iteration over the chain is needed because the evolution of a single site depends on the state of the
whole chain. The algorithm runs through the chain from N to 1, iterating a few times over each site (depending on how many
chain iterations we have done, since iterating over a single site becomes more fruitful as the rest of the chain stabilizes).
In running_update mode, which is likely the most sensible choice, the current midpoint guess is updated after visiting each
site. I.e. The trial backwards step at site n is based on the updates that were made to site n + 1, n + 2 during the current chain
iteration.
Parameters
----------
dtau : complex
The (imaginary or real) amount of imaginary time (tau) to step.
midpoint : bool
Whether to use approximately time-symmetric midpoint integration,
or just a backward-Euler step.
"""
#---------------------------
#Hard-coded params:
debug = True
dbg_bstep = False
safe_mode = True
tol = sp.finfo(sp.complex128).eps * 3
max_iter = 10
itr_switch_mode = 10
#---------------------------
if midpoint:
dtau = dtau / 2
self.restore_RCF()
#Take a copy of the current state
A0 = sp.empty_like(self.A)
for n in xrange(1, self.N + 1):
A0[n] = self.A[n].copy()
#Take initial forward-Euler step
self.take_step(dtau)
itr = 0
delta = 1
delta_prev = 0
final_check = False
while delta > tol * (self.N - 1) and itr < max_iter or final_check:
print "OUTER"
running_update = itr < itr_switch_mode
A_np1 = A0[self.N]
#Prepare for next calculation of B from the new A
self.restore_RCF() #updates l and r
if running_update:
self.calc_C() #we really do need all of these, since B directly uses C[n-1]
self.calc_K()
g0_n = sp.eye(self.D[self.N - 1], dtype=self.typ) #g0_n is the gauge transform matrix needed to solve the implicit equation
#Loop through the chain, optimizing the individual A's
delta = 0
for n in reversed(xrange(1, self.N)): #We start at N - 1, since the right vector can't be altered here.
print "SWEEP"
if not running_update: #save new A[n + 1] and replace with old version for building B
A_np1_new = self.A[n + 1].copy()
self.A[n + 1] = A_np1
A_np1 = self.A[n].copy()
max_itr_n = 1 #wait until the next run-through of the chain to change A[n] again
else:
max_itr_n = itr + 1 #do more iterations here as the outer loop progresses
delta_n = 1
itr_n = 0
while True:
print "INNER"
#Find transformation to gauge-align A0 with the backwards-obtained A.. is this enough?
M = m.mmul(A0[n][0], g0_n, self.r[n], m.H(self.A[n][0]))
for s in xrange(1, self.q[n]):
M += m.mmul(A0[n][s], g0_n, self.r[n], m.H(self.A[n][s]))
g0_nm1 = la.solve(self.r[n - 1], M, sym_pos=True, overwrite_b=True)
if not (delta_n > tol and itr_n < max_itr_n):
break
B = self.calc_B(n)
if B is None:
delta_n = 0
fnorm = 0
break
g0_nm1_inv = la.inv(g0_nm1) #sadly, we need the inverse too...
r_dA = sp.zeros_like(self.r[n - 1])
dA = sp.empty_like(self.A[n])
sqsum = 0
for s in xrange(self.q[n]):
dA[s] = m.mmul(g0_nm1_inv, A0[n][s], g0_n)
dA[s] -= self.A[n][s]
dA[s] -= dtau * B[s]
if not final_check:
self.A[n][s] += dA[s]
for s in xrange(self.q[n]):
r_dA += m.mmul(dA[s], self.r[n], m.H(dA[s]))
sqsum += sum(dA[s]**2)
fnorm = sp.sqrt(sqsum)
delta_n = sp.sqrt(sp.trace(m.mmul(self.l[n - 1], r_dA)))
if running_update: #Since we want to use the current A[n] and A[n + 1], we need this:
if safe_mode:
self.restore_RCF()
self.calc_C()
self.calc_K()
else:
self.restore_RCF(start=n) #will also renormalize
self.calc_C(n_low=n-1, n_high=n)
self.calc_K(n_low=n, n_high=n+1)
itr_n += 1
if final_check:
break
if not running_update: #save new A[n + 1] and replace with old version for building B
self.A[n + 1] = A_np1_new
if debug:
print "delta_%d: %g, (%d iterations)" % (n, delta_n.real, itr_n) + ", fnorm = " + str(fnorm)
delta += delta_n
if safe_mode:
self.calc_r()
else:
self.calc_r(n - 2, n - 1) #We only need these for the next step.
g0_n = g0_nm1
itr += 1
if debug:
print "delta: %g delta delta: %g (%d iterations)" % (delta.real, (delta - delta_prev).real, itr)
delta_prev = delta
if debug:
if final_check:
break
elif delta <= tol * (self.N - 1) or itr >= max_iter:
print "Final check to get final delta:"
final_check = True
#Test backward step!
if dbg_bstep:
Anew = sp.empty_like(self.A)
for n in xrange(1, self.N + 1):
Anew[n] = self.A[n].copy()
# self.calc_l()
# self.simple_renorm()
# self.restore_RCF()
self.calc_C()
self.calc_K()
self.take_step(-dtau)
self.restore_RCF()
delta2 = 0
for n in reversed(xrange(1, self.N + 1)):
#print n
dA = A0[n] - self.A[n]
#Surely this dA should also preserve the gauge choice, since both A's are in ON_R...
#print dA/A0[n]
r_dA = sp.zeros_like(self.r[n - 1])
sqsum = 0
for s in xrange(self.q[n]):
r_dA += m.mmul(dA[s], self.r[n], m.H(dA[s]))
sqsum += sum(dA[s]**2)
delta_n = sp.sqrt(sp.trace(m.mmul(self.l[n - 1], r_dA)))
delta2 += delta_n
if debug:
print "A[%d] OK?: " % n + str(sp.allclose(dA, 0)) + ", delta = " + str(delta_n) + ", fnorm = " + str(sp.sqrt(sqsum))
#print delta_n
if debug:
print "Total delta: " + str(delta2)
for n in xrange(1, self.N + 1):
self.A[n] = Anew[n]
else:
delta2 = 0
if midpoint:
#Take a final step from the midpoint
#self.restore_RCF() #updates l and r
self.calc_l()
self.simple_renorm()
self.calc_C()
self.calc_K()
self.take_step(dtau)
return itr, delta, delta2
def restore_RCF(self, dbg=False):
if dbg:
self.calc_l()
self.calc_r()
print "BEFORE..."
h_before, h_left_before, h_right_before = self.restore_RCF_dbg()
print (h_left_before, h_before, h_right_before)
self.restore_RCF_r()
if dbg:
self.calc_l()
print "MIDDLE..."
h_mid, h_left_mid, h_right_mid = self.restore_RCF_dbg()
print (h_left_mid, h_mid, h_right_mid)
fac = 1 / self.l[0].trace().real
if dbg:
print "Scale l[0]: %g" % fac
self.l[0] *= fac
self.u_gnd_l.r *= 1/fac
self.restore_RCF_l()
if dbg:
print "Uni left:"
self.u_gnd_l.A = self.A[0]
self.u_gnd_l.l = self.l[0]
self.u_gnd_l.calc_lr() #Ensures largest ev of E=1
self.l[0] = self.u_gnd_l.l #No longer diagonal!
self.A[0] = self.u_gnd_l.A
if self.sanity_checks:
if not sp.allclose(self.l[0], sp.diag(sp.diag(self.l[0])), atol=1E-12, rtol=1E-12):
print "Sanity Fail in restore_RCF!: True l[0] not diagonal!"
self.l[0] = mm.simple_diag_matrix(sp.diag(self.l[0]))
fac = 1 / sp.trace(self.l[0]).real
if dbg:
print "Scale l[0]: %g" % fac
self.l[0] *= fac
self.u_gnd_l.r *= 1/fac
self.u_gnd_l.l = self.l[0]
if dbg:
print "Uni right:"
self.u_gnd_r.A = self.A[self.N + 1]
self.u_gnd_r.r = self.r[self.N]
self.u_gnd_r.calc_lr() #Ensures largest ev of E=1
self.r[self.N] = self.u_gnd_r.r
self.A[self.N + 1] = self.u_gnd_r.A
if self.sanity_checks:
if not sp.allclose(self.r[self.N], sp.eye(self.D[self.N]), atol=1E-12, rtol=1E-12):
print "Sanity Fail in restore_RCF!: True r[N] not eye!"
self.r[self.N] = mm.eyemat(self.D[self.N], dtype=self.typ)
self.u_gnd_r.r = self.r[self.N]
self.r[self.N + 1] = self.r[self.N]
self.l[self.N + 1][:] = self.eps_l(self.N + 1, self.l[self.N])
if self.sanity_checks:
l_n = self.l[0]
for n in xrange(0, self.N + 1):
l_n = self.eps_l(n, l_n)
if not sp.allclose(l_n, self.l[n], atol=1E-12, rtol=1E-12):
print "Sanity Fail in restore_RCF!: l_%u is bad" % n
r_nm1 = self.r[self.N + 1]
for n in reversed(xrange(1, self.N + 2)):
r_nm1 = self.eps_r(n, r_nm1)
if not sp.allclose(r_nm1, self.r[n - 1], atol=1E-12, rtol=1E-12):
print "Sanity Fail in restore_RCF!: r_%u is bad" % (n - 1)
if dbg:
print "AFTER..."
h_after, h_left_after, h_right_after = self.restore_RCF_dbg()
print (h_left_after, h_after, h_right_after)
print h_after - h_before
print (h_after.sum() - h_before.sum() + h_left_after - h_left_before
+ h_right_after - h_right_before)
def evolute(self, ngen, x0=None, verbose=True):
"""
This function evolutes the XNES algorithm for number of generations.
:param ngen: (int) number of generations to evolute
:param x0: (list) initial guess for the search (must be of same size as ``len(bounds)``)
:param verbose: (bool) print statistics to screen
:return: (dict) dictionary containing major XNES search results
"""
f = self.f
self.verbose = verbose
if x0 is not None:
assert len(
x0
) == self.npop, 'the length of x0 ({}) MUST equal to npop ({})'.format(
len(x0), self.npop)
self.mu = np.array(x0)
else:
self.mu = self.init_sample(self.bounds)
mu, sigma, bmat = self.mu, self.sigma, self.bmat
eta_mu, eta_sigma, eta_bmat = self.eta_mu, self.eta_sigma, self.eta_bmat
npop = self.npop
dim = self.dim
sigma_old = self.sigma_old
eyemat = eye(dim)
with joblib.Parallel(n_jobs=self.ncores) as parallel:
for i in range(ngen):
s_try = randn(npop, dim)
z_try = mu + sigma * dot(s_try, bmat) # broadcast
for k in range(len(z_try)):
z_try[k] = self.ensure_bounds(vec=z_try[k],
bounds=self.bounds)
f_try = parallel(joblib.delayed(f)(z) for z in z_try)
f_try = asarray(f_try)
# save if best
fitness = mean(f_try)
isort = argsort(f_try)
f_try = f_try[isort]
s_try = s_try[isort]
z_try = z_try[isort]
for m in range(len(f_try)):
if f_try[m] > self.fitness_best:
self.fitness_best = f_try[m]
self.x_best = copy.deepcopy(z_try[m])
if fitness - 1e-8 > self.fitness_best:
self.mu_best = mu.copy()
self.counter = 0
else:
self.counter += 1
u_try = self.utilities if self.use_fshape else f_try
if self.use_adasam and sigma_old is not None: # sigma_old must be available
eta_sigma = self.adasam(eta_sigma, mu, sigma, bmat,
sigma_old, z_try)
dj_delta = dot(u_try, s_try)
dj_mmat = dot(s_try.T, s_try *
u_try.reshape(npop, 1)) - sum(u_try) * eyemat
dj_sigma = trace(dj_mmat) * (1.0 / dim)
dj_bmat = dj_mmat - dj_sigma * eyemat
sigma_old = sigma
# update
mu += eta_mu * sigma * dot(bmat, dj_delta)
sigma *= exp(0.5 * eta_sigma * dj_sigma)
bmat = dot(bmat, expm(0.5 * eta_bmat * dj_bmat))
# logging
self.history['fitness'].append(self.fitness_best)
self.history['sigma'].append(sigma)
self.history['eta_sigma'].append(eta_sigma)
# Print data
if self.verbose and i % self.npop:
print(
'^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^'
)
print(
'XNES step {}/{}, NPOP={}, ETA_MU={}, ETA_SIGMA={}, ETA_BMAT={}, Ncores={}'
.format((i + 1) * self.npop, ngen * self.npop,
self.npop, np.round(self.eta_mu, 2),
np.round(self.eta_sigma, 2),
np.round(self.eta_bmat, 2), self.ncores))
print(
'^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^'
)
print('Best Swarm Fitness:',
np.round(self.fitness_best, 6))
print('Best Swarm Position:', np.round(self.x_best, 6))
print('MU:', np.round(mu, 3))
print('Sigma:', np.round(sigma, 3))
print('BMAT:', np.round(bmat, 3))
print(
'^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^'
)
# keep last results
self.mu, self.sigma, self.bmat = mu, sigma, bmat
self.eta_sigma = eta_sigma
self.sigma_old = sigma_old
if self.verbose:
print(
'------------------------ NES Summary --------------------------'
)
print('Best fitness (y) found:', self.fitness_best)
print('Best individual (x) found:', self.x_best)
print(
'--------------------------------------------------------------'
)
#-------------------------------------
#return population ranked for PESA2
#-------------------------------------
pesa_pop = defaultdict(list)
for i in range(len(z_try)):
pesa_pop[i].append(list(z_try[i]))
pesa_pop[i].append(f_try[i])
return self.x_best, self.fitness_best, pesa_pop
def groupBrainSync(S):
# Group BrainSync algorithm developed by Haleh Akrami
numT = S.shape[0]
numV = S.shape[1]
SubNum = S.shape[2]
# init random matrix for Os
Os = sp.zeros((numT, numT, SubNum))
for i in range(SubNum): #initializeing O
# R = 2 * rnd.random(size=(numT, numT)) - 1; #define a random matrix with unity distributian from -1 to 1
Os[:, :, i] = special_ortho_group.rvs(
numT) #(sp.dot(R , R.T)^(-1/2) , R; #orthogonal rows of matrix
Error = 1
PreError = 1
relcost = 1
alpha = 1e-6
var = 0
Costdif = sp.zeros(10000)
print('init done')
# Initialize PreError from gloal average
X = sp.zeros((numT, numV))
for j in range(SubNum): #calculate X
X = sp.dot(Os[:, :, j], S[:, :, j]) + X
X = X / SubNum
InError = 0
for j in range(SubNum):
etemp = sp.dot(Os[:, :, j], S[:, :, j]) - X
InError = InError + sp.trace(sp.dot(etemp,
etemp.T)) #calculating error
# Find best Orthogognal map, by minimizing error (distance) from average
while relcost > alpha:
var = var + 1
print('subject iteration')
for i in tqdm(range(SubNum)):
X = sp.zeros((numT, numV))
for j in range(SubNum): #calculate X average excluded subject i
if j != i:
X = sp.dot(Os[:, :, j], S[:, :, j]) + X
# Y is i excluded average
Y = X / (SubNum - 1)
# Update Orthogonal matrix with BrainSync projection technique
U, _, V = sp.linalg.svd(sp.dot(Y, S[:, :, i].T))
Os[:, :, i] = sp.dot(U, V)
# print('calculate error')
Error = 0
# New Average with all subject updated orthogonal matrix
# update last subject outside loop
X2 = (X + sp.dot(Os[:, :, i], S[:, :, i])) / SubNum
# Calculate error of all subjects from average map
for j in range(SubNum):
etemp = sp.dot(Os[:, :, j], S[:, :, j]) - X2
Error = Error + sp.trace(sp.dot(etemp,
etemp.T)) #calculating error
relcost = np.abs(Error - PreError) / np.abs(InError)
Costdif[var] = PreError - Error
PreError = Error
print('Error = %g, var = %g, relcost = %g\n' % (Error, var, relcost))
Costdif = Costdif[:var] # = []
Costdif = Costdif[1:]
TotalError = Error
return X2, Os, Costdif, TotalError
def mkl_train(
fname_l,
reg,
ltrain,
no_mkl,
flip,
mkl_norm=DEFAULT_MKL_NORM,
bias_enabled=DEFAULT_BIAS_ENABLED,
epsilon=DEFAULT_EPSILON,
C_mkl=DEFAULT_C_MKL,
mkl_epsilon=DEFAULT_MKL_EPSILON,
tube_epsilon=DEFAULT_TUBE_EPSILON,
):
global cache
print "-" * 80
print "reg =", reg
print "mkl_norm =", mkl_norm
print "bias_enabled =", bias_enabled
print "epsilon =", epsilon
print "C_mkl =", C_mkl
print "mkl_epsilon =", mkl_epsilon
print "tube_epsilon =", tube_epsilon
print "-" * 80
d0 = io.loadmat(fname_l[0])
if flip:
keytrain = "kernel_traintest"
keytest = "kernel_traintrain"
else:
keytrain = "kernel_traintrain"
keytest = "kernel_traintest"
ltr = ltrain.astype(double)
# l = ((l==thecat)-1*(l!=thecat)).astype(double)
labels = Features.Labels(ltr)
if True:
tr1_l = []
tr2_l = []
ker_l = []
# feat_l = []
combker = Kernel.CombinedKernel()
# combfeat = Features.CombinedFeatures()
m, n = d0[keytrain].shape
yy, xx = mgrid[:m, :n]
print "loading nfiles=", len(fname_l)
for i, fname in enumerate(fname_l):
# if fname in cache_train:
# kermat, tr1, tr2 = cache_train[fname]
# else:
if True:
# print "loading", fname
d = io.loadmat(fname)
# kermat = (d[keytrain]).astype(double)
kermat = d[keytrain]
# kermat += kermat.min()
del d
# kdiag =
# kermat /= kdiag
tr1 = trace(kermat) * len(fname_l) # *diag(kermat)
if tr1 == 0:
print "trace is 0, skipping"
continue
print i + 1, "trace", tr1, "min", kermat.min(), "max", kermat.max(), fname
kermat /= tr1
# print kermat
# kermat = exp(kermat*len(kermat))
# tr2 = trace(kermat)
# kermat /= tr2
# print kermat
tr2 = 0
# cache_train[fname] = kermat, tr1, tr2
# print diag(kermat)
yy, xx = mgrid[: kermat.shape[0], : kermat.shape[1]]
kermat_triangle = kermat[yy <= xx]
ker = Kernel.CustomKernel()
ker.set_triangle_kernel_matrix_from_triangle(kermat_triangle.astype(double))
combker.append_kernel(ker)
del kermat
ker_l += [ker]
tr1_l += [tr1]
tr2_l += [tr2]
cache = {
"ker_l": ker_l,
#'feat_l': feat_l,
"tr1_l": tr1_l,
"tr2_l": tr2_l,
"combker": combker,
#'combfeat': combfeat,
}
del xx, yy
if no_mkl:
# w_l = array([.2, .8])
# w_l /= w_l.sum()
for i, ker in enumerate(ker_l):
ker.set_combined_kernel_weight(1.0 / (len(ker_l)))
# ker.set_combined_kernel_weight(w_l[i])
tstart = time.time()
# svm1 = Classifier.SVMLight(reg, combker, labels)
# svm1 = Classifier.LibSVM(reg, combker, labels)
# svm1 = Classifier.GMNPSVM(reg, combker, labels)
# svm1 = Classifier.SVMSGD(reg, combker, labels)
# svm1 = Classifier.CPLEXSVM(reg, combker, labels)
if len(fname_l) == 1:
no_mkl = True
# svm1 = Classifier.LibSVM(reg, combker, labels)
svm1 = Classifier.SVMLight(reg, combker, labels)
else:
# svm1 = Classifier.SVMLight(reg, combker, labels)
svm1 = Classifier.MKLClassification()
svm1.set_C(reg, reg)
svm1.set_kernel(combker)
svm1.set_labels(labels)
print combker.get_subkernel_weights()
# raise
# svm1.set_mkl_enabled(not no_mkl)
# svm1.set_C(reg/10., reg)
# print svm1.get_C1(), svm1.get_C2()
svm1.parallel.set_num_threads(4)
# print ker_l[0]
kkk = combker.get_kernel_matrix()
assert not isnan(kkk).any()
assert not isinf(kkk).any()
# ipshell()
# svm1.set_linadd_enabled(True)
# svm1.set_shrinking_enabled(True)
svm1.set_bias_enabled(bias_enabled)
svm1.set_epsilon(epsilon)
svm1.set_tube_epsilon(tube_epsilon)
svm1.set_mkl_epsilon(mkl_epsilon)
svm1.set_C_mkl(C_mkl)
svm1.set_mkl_norm(mkl_norm)
assert svm1.train()
www = combker.get_subkernel_weights()
# print "sum before", www.sum()
print "-w " + " -w ".join([str(e) for e in www])
print "rectify"
www[www < MKL_WEIGHTS_CUTOFF] = 0
www = sp.array(www, dtype="float64")
# print "sum after", www.sum()
www /= www.sum()
print "-w " + " -w ".join([str(e) for e in www])
alphas = svm1.get_alphas()
bias = svm1.get_bias()
svs = svm1.get_support_vectors()
# weight_l = []
# for i,ker in enumerate(ker_l):
# weight = ker.get_combined_kernel_weight()
# weight_l += [weight]
weight_l = www
# print weight_l
# print "-w " + " -w ".join([str(e) for e in weight_l])
kweights = array(weight_l)
kweights /= kweights.sum()
traces1 = array(tr1_l)
# traces2 = array(tr2_l)
# raise
# tend = time.time()
# print "time:", tend-tstart
# kernel_train = combker.get_kernel_matrix()
# weight_l = []
# for i,ker in enumerate(ker_l):
# weight = ker.get_combined_kernel_weight()
# weight_l += [weight]
# combker.init(combfeat,combfeat)
# print svm1.classify().get_labels()[:10]
# kk = combker.get_kernel_matrix()
# print "trace=", trace(kk)
# trainperf = (sign(svm1.classify().get_labels())==ltr).mean()
# print "trainperf=", trainperf, weight_l
# print svm1.get_alphas()
# raise
# mkl = {"svm": svm1,
# "ker_l": ker_l,
# "feat_l": feat_l,
# "tr_l": tr_l,
# "combker": combker,
# "combfeat": combfeat,
# }
# print bias
mkl = {
"alphas": alphas.astype("float32"),
"bias": array(bias).astype("float32"),
"svs": svs.astype("int32"),
"kweights": kweights.astype("float32"),
"traces1": traces1.astype("float32"),
# "traces2": traces2.astype('float32'),
}
# print svm1.get_alphas()
return mkl
for i in range(3):
Ht[i, i] = (sp.einsum('qpn,qpm->nm', T[i], KiT[i])**2).sum()
for j in range(0, i):
Ht[i, j] = (sp.einsum('qpn,qpm->nm', T[i], KiT[j])**2).sum()
Ht[j, i] = Ht[i, j]
if Y.shape[0] <= 1000:
Ki = la.inv(
sp.kron(mvset.gp[type].covar.Cn.K(), sp.eye(Y.shape[0])))
XrXr = sp.dot(Xr, Xr.T)
KidK = [
sp.dot(Ki, sp.kron(_Cr.K_grad_i(i), XrXr)) for i in range(3)
]
Ht0 = sp.zeros((3, 3))
for i in range(3):
for j in range(3):
Ht0[i, j] = sp.trace(sp.dot(KidK[i], KidK[j]))
pdb.set_trace()
if 0:
# 2. quadratic_term = y_Ki_dKp_Ki_dKq_Ki_y
Z = Y - sp.dot(F, mvset.gp[type].mean.B[0])
XrXrKiZ = sp.dot(Xr, sp.dot(Xr.T, gp.covar.solve_t(Z)))
XrXrKiZC = [sp.dot(XrXrKiZ, _Cr.K_grad_i(i).T) for i in range(3)]
KiXrXrKiZC = [gp.covar.solve_t(XrXrKiZC[i]) for i in range(3)]
Hq = sp.zeros((3, 3))
for i in range(3):
Hq[i, i] = (XrXrKiZC[i] * KiXrXrKiZC[i]).sum()
for j in range(i):
Hq[i, j] = (XrXrKiZC[i] * KiXrXrKiZC[j]).sum()
Hq[j, i] = Hq[i, j]
if Y.shape[0] <= 1000:
