def initialize_params(self):
"""
Initialize the params.Sigma_s/Sigma_i,
params.J_i/J_s, params.logdet_Sigma_i/logdet_Sigma_s,
based on i_std and s_std
"""
params = self.params
dim_s = self.dim_s
dim_i = self.dim_i
s_std = self.s_std
i_std = self.i_std
nSuperpixels = self.nSuperpixels
# Covariance for each superpixel is a diagonal matrix
for i in range(dim_s):
params.Sigma_s.cpu[:,i,i].fill(s_std**2)
params.prior_sigma_s_sum.cpu[:,i,i].fill(s_std**4)
for i in range(dim_i):
params.Sigma_i.cpu[:,i,i].fill((i_std)**2)
params.Sigma_i.cpu[:,1,1].fill((i_std/2)**2) # To account for scale differences between the L,A,B
#calculate the inverse of covariance
params.J_i.cpu[:]=map(inv,params.Sigma_i.cpu)
params.J_s.cpu[:]=map(inv,params.Sigma_s.cpu)
# calculate the log of the determinant of covriance
for i in range(nSuperpixels):
junk,params.logdet_Sigma_i.cpu[i] = slogdet(params.Sigma_i.cpu[i])
junk,params.logdet_Sigma_s.cpu[i] = slogdet(params.Sigma_s.cpu[i])
del junk
self.update_params_cpu2gpu()
def drawBeta(k,s,w,size=1):
"""Draw beta from its distribution (Eq.9 Rasmussen 2000) using ARS
Make it robust with an expanding range in case of failure"""
nd = w.shape[0]
# precompute some things for speed
logdetw = slogdet(w)[1]
temp = 0
for sj in s:
sj = np.reshape(sj,(nd,nd))
temp += slogdet(sj)[1]
temp -= np.trace(np.dot(w,sj))
lb = nd - 1.0
flag = True
cnt = 0
while flag:
xi = lb + np.logspace(-3-cnt,1+cnt,200) # update range if needed
flag = False
try:
ars = ARS(logpbeta,logpbetaprime,xi=xi,lb=lb,ub=np.inf, \
k=k, s=s, w=w, nd=nd, logdetw=logdetw, temp=temp)
except:
cnt += 1
flag = True
# draw beta but also pass random seed to ARS code
return ars.draw(size,np.random.randint(MAXINT))
def logdet_low_rank(Ainv, U, C, V, diag=False):
"""
logdet(A+UCV) = logdet(C^{-1} + V A^{-1} U) + logdet(C) + logdet(A).
:param Ainv: NxN
:param U: NxK
:param C: KxK
:param V: KxN
:return:
"""
Cinv = inv(C)
sC, ldC = slogdet(C)
assert sC > 0
if diag:
ldA = -log(Ainv).sum()
tmp1 = einsum('ij,j,jk->ik', V, Ainv, U)
s1, ld1 = slogdet(Cinv + tmp1)
assert s1 > 0
else:
sAinv, ldAinv = slogdet(Ainv)
ldA = -ldAinv
assert sAinv > 0
s1, ld1 = slogdet(Cinv + V.dot(Ainv).dot(U))
assert s1 > 0
return ld1 + ldC + ldA
def loglike(self, params):
"""
Returns float
Loglikelihood used in latent factor models
Parameters
----------
params : list
Values of parameters to pass into masked elements of array
Returns
-------
loglikelihood : float
"""
latent = self.latent
per = self.periods
var_data_vert = self.var_data_vert
var_data_vertm1 = self.var_data_vertm1
lam_0, lam_1, delta_0, delta_1, mu, phi, \
sigma, dtype = self.params_to_array(params)
if self.fast_gen_pred:
a_solve, b_solve = self.opt_gen_pred_coef(lam_0, lam_1, delta_0,
delta_1, mu, phi, sigma,
dtype)
else:
a_solve, b_solve = self.gen_pred_coef(lam_0, lam_1, delta_0,
delta_1, mu, phi, sigma,
dtype)
# first solve for unknown part of information vector
lat_ser, jacob, yield_errs = self._solve_unobs(a_in=a_solve,
b_in=b_solve,
dtype=dtype)
# here is the likelihood that needs to be used
# use two matrices to take the difference
var_data_use = var_data_vert.join(lat_ser)[1:]
var_data_usem1 = var_data_vertm1.join(lat_ser.shift())[1:]
errors = var_data_use.values.T - mu - np.dot(phi,
var_data_usem1.values.T)
sign, j_logdt = nla.slogdet(jacob)
j_slogdt = sign * j_logdt
sign, sigma_logdt = nla.slogdet(np.dot(sigma, sigma.T))
sigma_slogdt = sign * sigma_logdt
var_yields_errs = np.var(yield_errs, axis=1)
like = -(per - 1) * j_slogdt - (per - 1) * 1.0 / 2 * sigma_slogdt - \
1.0 / 2 * np.sum(np.dot(np.dot(errors.T, \
la.inv(np.dot(sigma, sigma.T))), errors)) - (per - 1) / 2.0 * \
np.log(np.sum(var_yields_errs)) - 1.0 / 2 * \
np.sum(yield_errs**2/var_yields_errs[None].T)
return like
def logdet_low_rank2(Ainv, U, C, V, diag=False):
'''
computes logdet(A+UCV) using https://en.wikipedia.org/wiki/Matrix_determinant_lemma
'''
if diag:
ldA = -log(Ainv).sum()
temp = C.dot(V).dot(U * Ainv[:,None])
else:
ldA = -slogdet(Ainv)[1]
temp = C.dot(V).dot(Ainv).dot(U)
temp.flat[::temp.shape[0]+1] += 1
return slogdet(temp)[1] + ldA
def train_sgd(self, X, **kwargs):
# hyperparameters
max_iter = kwargs.get('max_iter', 1)
batch_size = kwargs.get('batch_size', min([100, X.shape[1]]))
step_width = kwargs.get('step_width', 0.001)
momentum = kwargs.get('momentum', 0.9)
shuffle = kwargs.get('shuffle', True)
pocket = kwargs.get('pocket', shuffle)
# completed basis and filters
A = self.A
W = inv(A)
# initial direction of momentum
P = 0.
if pocket:
energy = mean(self.prior_energy(dot(W, X))) - slogdet(W)[1]
for j in range(max_iter):
if shuffle:
# randomize order of data
X = X[:, permutation(X.shape[1])]
for i in range(0, X.shape[1], batch_size):
batch = X[:, i:i + batch_size]
if not batch.shape[1] < batch_size:
# calculate gradient
P = momentum * P + A.T - \
dot(self.prior_energy_gradient(dot(W, batch)), batch.T) / batch_size
# update parameters
W += step_width * P
A = inv(W)
if pocket:
# test for improvement of lower bound
if mean(self.prior_energy(dot(W, X))) - slogdet(W)[1] > energy:
if Distribution.VERBOSITY > 0:
print 'No improvement.'
# don't update parameters
return False
# update linear features
self.A = A
return True
def mvnkld(mu0, mu1, sigma0, sigma1):
"""
Returns the Kullback-Leibler Divergence (KLD) between two normal distributions.
"""
k = len(mu0)
assert k == len(mu1)
delta = mu1 - mu0
(sign0, logdet0) = linalg.slogdet(sigma0)
(sign1, logdet1) = linalg.slogdet(sigma1)
lndet = logdet0 - logdet1
A = trace(linalg.solve(sigma1, sigma0))
B = delta.T.dot(linalg.solve(sigma1, delta))
return 0.5 * (A + B - k - lndet)
def clik(lam,n,n2,n_eq,bigE,I,WS):
""" Concentrated (negative) log-likelihood for SUR Error model
Parameters
----------
lam : n_eq x 1 array of spatial autoregressive parameters
n : number of observations in each cross-section
n2 : n/2
n_eq : number of equations
bigE : n by n_eq matrix with vectors of residuals for
each equation
I : sparse Identity matrix
WS : sparse spatial weights matrix
Returns
-------
-clik : negative (for minimize) of the concentrated
log-likelihood function
"""
WbigE = WS * bigE
spfbigE = bigE - WbigE * lam.T
sig = np.dot(spfbigE.T,spfbigE) / n
ldet = la.slogdet(sig)[1]
logjac = jacob(lam,n_eq,I,WS)
clik = - n2 * ldet + logjac
return -clik # negative for minimize
def mvnlogpdf_p (X, mu, PrecMat):
"""
Multivariate Normal Log PDF
Args:
X : NxD matrix of input data. Each ROW is a single sample.
mu : Dx1 vector for the mean.
PrecMat: DxD precision matrix.
Returns:
Nx1 vector of log probabilities.
"""
D = PrecMat.shape[0]
X = _check_single_data(X, D)
N = len(X)
_, neglogdet = linalg.slogdet(PrecMat)
normconst = -0.5 * (D * np.log(2 * constants.pi) - neglogdet)
logpdf = np.empty((N, 1))
for n, x in enumerate(X):
d = x - mu
logpdf[n] = normconst - 0.5 * d.dot(PrecMat.dot(d))
return logpdf
def addItem(self, i, newf, oldf, newt, oldt, followset, s, ss):
if newt == -1:
newt = self.K
self.K += 1
self.cholesky[newt] = cholesky(self.con.lambda0 + self.con.kappa0_outermu0).T
n = len(followset)
self.counts[newt] += n
assert self.counts[oldt] >= 0
assert self.counts[newt] > 0
self.s[newt] += s
self.ss[newt] += ss
#self.denom[newt] = self.integrateOverParameters(self.counts[newt], self.s[newt], self.ss[newt])
n = self.counts[newt]
kappan = self.con.kappa0 + n
mun = (self.con.kappa0 * self.con.mu0 + self.s[newt]) / kappan
lambdan = self.con.lambda0 + self.ss[newt] + self.con.kappa0_outermu0 - kappan * np.outer(mun, mun)
self.logdet[newt] = slogdet(lambdan)[1]
#for ind in followset:
# cholupdate(self.cholesky[newt], self.data[ind].copy())
for j in followset:
self.assignments[j] = newt
self.follow[i] = newf
self.sit_behind[newf].add(i)
def preprocess(self):
self.VarList = tuple(self.Vars)
self.NumVars = len(self.VarList)
self.VarVector = BlockMatrix((tuple(self.Vars[var] for var in self.VarList),))
self.NumDims = self.VarVector.shape[1]
self.Mean = BlockMatrix((tuple(self.Param[('Mean', var)] for var in self.VarList),))
self.DemeanedVarVector = self.VarVector - self.Mean
cov = [self.NumVars * [None] for _ in range(self.NumVars)] # careful not to create same mutable object
for i in range(self.NumVars):
for j in range(i):
if ('Cov', self.VarList[i], self.VarList[j]) in self.Param:
cov[i][j] = self.Param[('Cov', self.VarList[i], self.VarList[j])]
cov[j][i] = cov[i][j].T
else:
cov[j][i] = self.Param[('Cov', self.VarList[j], self.VarList[i])]
cov[i][j] = cov[j][i].T
cov[i][i] = self.Param[('Cov', self.VarList[i])]
self.Cov = BlockMatrix(cov)
try:
cov = CompyledFunc(var_names_and_syms={}, dict_or_expr=self.Cov)()
sign, self.LogDetCov = slogdet(cov)
self.LogDetCov *= sign
self.InvCov = inv(cov)
except:
pass
self.PreProcessed = True
def __init__(self, d, nu, mu, Lambda):
self.nu = nu
self.d = d
self.mu = mu
self.precision = inv(Lambda)
self.logdet = slogdet(Lambda)[1]
self.Z = gammaln(nu / 2) + d / 2 * (math.log(nu) + math.log(math.pi)) - gammaln((nu + d) / 2)
def _loglike_mle(self, params):
"""
Loglikelihood of AR(p) process using exact maximum likelihood
"""
nobs = self.nobs
X = self.X
endog = self.endog
k_ar = self.k_ar
k_trend = self.k_trend
# reparameterize according to Jones (1980) like in ARMA/Kalman Filter
if self.transparams:
params = self._transparams(params)
# get mean and variance for pre-sample lags
yp = endog[:k_ar].copy()
if k_trend:
c = [params[0]] * k_ar
else:
c = [0]
mup = np.asarray(c / (1 - np.sum(params[k_trend:])))
diffp = yp - mup[:, None]
# get inv(Vp) Hamilton 5.3.7
Vpinv = self._presample_varcov(params)
diffpVpinv = np.dot(np.dot(diffp.T, Vpinv), diffp).item()
ssr = sumofsq(endog[k_ar:].squeeze() - np.dot(X, params))
# concentrating the likelihood means that sigma2 is given by
sigma2 = 1.0 / nobs * (diffpVpinv + ssr)
self.sigma2 = sigma2
logdet = slogdet(Vpinv)[1] # TODO: add check for singularity
loglike = -1 / 2.0 * (nobs * (np.log(2 * np.pi) + np.log(sigma2)) - logdet + diffpVpinv / sigma2 + ssr / sigma2)
return loglike
def calcNumericFit(xVal, yVal, yErr):
a11 = 0
a21 = 0
a12 = 0
a22 = 0
#Berechne die Koeffizientenmatrix
for i in range(len(xVal)):
a22 = a22 + 1/(yErr[i]**2)
a12 = a12 + xVal[i]/yErr[i]**2
a21 = a21 + xVal[i]/yErr[i]**2
a11 = a11 + xVal[i]**2/yErr[i]**2
(sign, logdet) = linalg.slogdet([[a11, a21], [a12, a22]])
detCoeffMat = sign * np.exp(logdet)
xy = 0
xyxy = 0
y0 = 0
#Berechne die Koeffizienten
for i in range(len(xVal)):
xy = xy + xVal[i]*yVal[i]/(yErr[i]**2)
xyxy = xyxy + xVal[i]*yVal[i]/yErr[i]**4
y0 = y0 + yVal[i]/(yErr[i]**2)
aBest = (1/detCoeffMat) * (xy * a22 - a21 * y0)
bBest = (1/detCoeffMat) * (a11 * y0 - a21 * xy)
#Berechne die Unsicherheiten
aErr = np.sqrt(1/detCoeffMat * a22)
bErr = np.sqrt(1/detCoeffMat * a11)
return [aBest, bBest, aErr, bErr]
def mvnlogpdf (X, mu, Sigma):
"""
Multivariate Normal Log PDF
Args:
X : NxD matrix of input data. Each ROW is a single sample.
mu : Dx1 vector for the mean.
Sigma: DxD covariance matrix.
Returns:
Nx1 vector of log probabilities.
"""
D = Sigma.shape[0]
X = _check_single_data(X, D)
N = len(X)
_, logdet = linalg.slogdet(Sigma)
normconst = -0.5 * (D * np.log(2 * constants.pi) + logdet)
iS = linalg.inv(Sigma)
logpdf = np.empty((N, 1))
for n, x in enumerate(X):
d = x - mu
logpdf[n] = normconst - 0.5 * d.dot(iS.dot(d))
return logpdf
def lnprob_cov(C):
# Get first term of loglikelihood expression (y * (1/C) * y.T)
# Do computation using Cholesky decomposition
try:
U, luflag = cho_factor(C)
except LinAlgError:
# Matrix is not positive semi-definite, so replace it with the
# positive semi-definite matrix that is nearest in the Frobenius norm
E, EV = eigh(C)
E[E<0] = 1e-12
U, luflag = cho_factor(EV.dot(np.diag(Ep)).dot(EV.T))
finally:
x2 = cho_solve((U, luflag), dxy)
L1 = dxy.dot(x2)
# Get second term of loglikelihood expression (log det C)
sign, L2 = slogdet(C)
# Why am I always confused by this?
thing_to_be_minimised = (L1 + L2)
return thing_to_be_minimised
def logjacobian(self, data):
"""
Returns the log-determinant of the Jabian matrix evaluated at the given
data points.
@type data: array_like
@param data: data points stored in columns
@rtype: ndarray
@return: the logarithm of the Jacobian determinants
"""
# completed filter matrix
W = inv(self.ica.A)
# determinant of linear transformation
logjacobian = zeros([1, data.shape[1]]) + slogdet(W)[1]
# linearly transform data
data = dot(W, data)
length = len(str(len(self.ica.marginals)))
if Transform.VERBOSITY > 0:
print ('{0:>' + str(length) + '}/{1}').format(0, len(self.ica.marginals)),
for i, mog in enumerate(self.ica.marginals):
logjacobian += UnivariateGaussianization(mog).logjacobian(data[[i]])
if Transform.VERBOSITY > 0:
print (('\b' * (length * 2 + 2)) + '{0:>' + str(length) + '}/{1}').format(i + 1, len(self.ica.marginals)),
if Transform.VERBOSITY > 0:
print
return logjacobian
def posdef_diag_dom(n, m=10, s=None):
"""Generates a positive-definite, diagonally dominant n x n matrix.
Arguments:
n - width/height of the matrix
m - additional multiplier for diagonal-dominance control
(shouldn't be less than 10, though)
s - optional seed for RNG
"""
if m < 10:
print "Multiplier should be >= 10. Using m=10 instead."
m = 10
np.random.seed(s) # re-seeding RNG is needed for multiprocessing
while True:
signs = np.random.randint(2, size=(n, n))
f = (signs == 0)
signs[f] = -1
signs = np.triu(signs, k=1)
a = np.random.random((n, n))
u = a * signs
l = u.T
a = l + u
for i, row in enumerate(a):
a[i, i] = (row * row).sum() * m
if la.slogdet(a) != (0, np.inf):
break
return a
def nll(self, log_th, x_nd, y_n, grad=False, use_self_hyper=True):
"""
Returns the negative log-likelihood : -log[p(y|x,th)],
where, abc are the LOG -- hyper-parameters.
If adbc==None, then it uses the self.{a,d,b,c}
to compute the value and the gradient.
@params:
x_nd : input vectors in R^d
y_n : output at the input vectors
log_th : vector of hyperparameters
grad : if TRUE, this function also returns
the partial derivatives of nll w.r.t
each (log) hyper-parameter.
"""
## make the data-points a 2D matrix:
if x_nd.ndim==1:
x_nd = np.atleast_2d(x_nd).T
if y_n.ndim==1:
y_n = np.atleast_2d(y_n).T
if not use_self_hyper:
self.set_log_hyperparam(log_th)
log_th = np.squeeze(log_th)
N,d = x_nd.shape
assert len(y_n)==N, "x and y shape mismatch."
K,K1,K2 = self.get_covmat(x_nd, get_both=True)
## compute the determinant using LU factorization:
sign, log_det = nla.slogdet(K)
#assert sign > 0, "Periodic Cov : covariance matrix is not PSD."
## compute the inverse of the covariance matrix through gaussian
## elimination:
K_inv = nla.solve(K, np.eye(N))
Ki_y = K_inv.dot(y_n)
## negative log-likelihood:
nloglik = 0.5*( N*self.log_2pi + log_det + y_n.T.dot(Ki_y))
if grad:
num_hyper = self.n1 + self.n2
K_diff = K_inv - Ki_y.dot(Ki_y.T)
dfX = np.zeros(num_hyper)
dK1 = self.k1.get_dK_dth(log_th[:self.n1], x_nd, y_n, use_self_hyper)
dK2 = self.k2.get_dk_dth(log_th[self.n1:], x_nd, y_n, use_self_hyper)
for i in xrange(self.n1):
dfX[i] = np.sum(np.sum( K_diff * dK1[i].dot(K2)))
for i in xrange(self.n2):
dfX[i+self.n1] = np.sum(np.sum( K_diff * K1.dot(dK2[i])))
return nloglik, dfX
return nloglik
def forward_jacobian_log_det(self, x):
_, jld = np_la.slogdet(self.W)
if x.ndim == 1:
return jld
elif x.ndim == 2:
return x.shape[0] * jld
else:
raise ValueError('x must be one or two dimensional.')
def f(W, X): W = W.reshape(self.num_hiddens, self.num_hiddens) v = mean(self.prior_energy(dot(W, X))) - slogdet(W)[1] if weight_decay > 0.: v += weight_decay / 2. * sum(square(inv(W))) return v
def log_prior(self, i):
"""Return the probability of `X[i]` under the prior alone."""
mu = self.prior.m_0
covar = (self.prior.k_0 + 1) / (self.prior.k_0*(self.prior.v_0 - self.D + 1)) * self.prior.S_0
logdet_covar = slogdet(covar)[1]
inv_covar = inv(covar)
v = self.prior.v_0 - self.D + 1
return self._multivariate_students_t(i, mu, logdet_covar, inv_covar, v)
def logmvstprob(x, mu, nu, d, Lambda):
diff = x - mu[:,None]
prob = gammaln((nu + d) / 2)
prob -= gammaln(nu / 2)
prob -= d / 2 * (math.log(nu) + math.log(math.pi))
prob -= 0.5 * slogdet(Lambda)[1]
prob -= (nu + d) / 2. * math.log(1 + 1. / nu * np.dot(np.dot(diff.T, inv(Lambda)), diff)[0][0])
return prob
def logZexp(r, Q):
sd, logd = slogdet(Q)
if sd != 1:
raise LinAlgError('Q is not positive definite!')
D = r.shape[0]
return D / 2 * math.log(2 * math.pi) - logd / 2 + np.dot(r, solve(Q, r)) / 2
def calc_log_z(_mu, _lambda, _kappa, _nu):
d = len(_mu)
sign, detr = slogdet(_lambda)
log_z = (LOG2*(_nu*d/2.0)
+ (d/2.0)*math.log(2*math.pi/_kappa)
+ multigammaln(_nu/2, d) - (_nu/2.0)*detr)
return log_z
def calc_log_z(_mu, _sigma, S):
d = len(_mu)
sign, detr = slogdet(_sigma)
_sigma_inv = np.linalg.inv(_sigma)
log_z = detr/2 + np.sum(_mu*np.dot(_sigma_inv, _mu))
return log_z
def KL_gaussian(mu0, sig0, mu1, sig1):
""" KL(N_0 || N_1).
"""
D = len(mu0)
if D != len(mu1) or D != sig0.shape[0] or D != sig1.shape[0]:
raise RuntimeError("Means and covariances my be the same dimension.")
if sig0.shape[0] != sig0.shape[1] or sig1.shape[0] != sig1.shape[1]:
raise RuntimeError("Covariance matrices must be square.")
s1inv = npl.inv(sig1)
s0_ld = npl.slogdet(sig0)[1]
s1_ld = npl.slogdet(sig1)[1]
x = mu1 - mu0
tmp = np.trace(np.dot(s1inv, sig0)) + np.dot(x.T, np.dot(s1inv, x))
tmp += -D - s0_ld + s1_ld
return 0.5 * tmp
def _calculate_log_likelihood(self):
"""
Calculates the log-likelihood (up to a constant) for a given
self.theta.
"""
R = zeros((self.n, self.n))
X, Y = self.X, self.Y
thetas = power(10., self.thetas)
# exponentially weighted distance formula
for i in range(self.n):
R[i, i+1:self.n] = exp(-thetas.dot(square(X[i, ...] - X[i+1:self.n, ...]).T))
R *= (1.0 - self.nugget)
R += R.T + eye(self.n)
self.R = R
one = ones(self.n)
rhs = column_stack([Y, one])
try:
# Cholesky Decomposition
self.R_fact = cho_factor(R)
sol = cho_solve(self.R_fact, rhs)
solve = lambda x: cho_solve(self.R_fact, x)
det_factor = log(abs(prod(diagonal(self.R_fact[0])) ** 2) + 1.e-16)
except (linalg.LinAlgError, ValueError):
# Since Cholesky failed, try linear least squares
self.R_fact = None # reset this to none, so we know not to use Cholesky
sol = lstsq(self.R, rhs)[0]
solve = lambda x: lstsq(self.R, x)[0]
det_factor = slogdet(self.R)[1]
self.mu = dot(one, sol[:, :-1]) / dot(one, sol[:, -1])
y_minus_mu = Y - self.mu
self.R_solve_ymu = solve(y_minus_mu)
self.R_solve_one = sol[:, -1]
self.sig2 = dot(y_minus_mu.T, self.R_solve_ymu) / self.n
if isinstance(self.sig2, ndarray):
self.log_likelihood = -self.n/2. * slogdet(self.sig2)[1] \
- 1./2.*det_factor
else:
self.log_likelihood = -self.n/2. * log(self.sig2) \
- 1./2.*det_factor
def __init__(self,bigy,bigX,iter=False,maxiter=5,epsilon=0.00001,verbose=False):
# setting up the cross-products
self.bigy = bigy
self.bigX = bigX
self.n_eq = len(bigy.keys())
self.n = bigy[0].shape[0]
self.bigK = np.zeros((self.n_eq,1),dtype=np.int_)
for r in range(self.n_eq):
self.bigK[r] = self.bigX[r].shape[1]
self.bigXX,self.bigXy = sur_crossprod(self.bigX,self.bigy)
# OLS regression by equation, sets up initial residuals
_sur_ols(self) # creates self.bOLS and self.olsE
# SUR estimation using OLS residuals - two step estimation
self.bSUR,self.varb,self.sig = sur_est(self.bigXX,self.bigXy,self.olsE,self.bigK)
resids = sur_resids(self.bigy,self.bigX,self.bSUR) # matrix of residuals
# Sigma and log det(Sigma) for null model
self.sig_ols = self.sig
sols = np.diag(np.diag(self.sig))
self.ldetS0 = np.log(np.diag(sols)).sum()
det0 = self.ldetS0
# setup for iteration
det1 = la.slogdet(self.sig)[1]
self.ldetS1 = det1
#self.niter = 0
if iter: # iterated FGLS aka ML
n_iter = 0
while np.abs(det1-det0) > epsilon and n_iter <= maxiter:
n_iter += 1
det0 = det1
self.bSUR,self.varb,self.sig = sur_est(self.bigXX,self.bigXy,\
resids,self.bigK)
resids = sur_resids(self.bigy,self.bigX,self.bSUR)
det1 = la.slogdet(self.sig)[1]
if verbose:
print(n_iter,det0,det1)
self.bigE = sur_resids(self.bigy,self.bigX,self.bSUR)
self.ldetS1 = det1
self.niter = n_iter
else:
self.niter = 1
self.bigE = resids
self.bigYP = sur_predict(self.bigy,self.bigX,self.bSUR) # LA added 10/30/16
self.corr = sur_corr(self.sig)
lik = self.n_eq * (1.0 + np.log(2.0*np.pi)) + self.ldetS1
self.llik = - (self.n / 2.0) * lik
def log_pdf(X, mu, C):
n, d = X.shape
inv = la.solve(C, (X - mu).T).T
maha = np.einsum('ij,ij->i', (X - mu), inv)
# Directly calculates log(det(C)), bypassing the numerical issues
# of calculating the determinant of C, which can be very close to zero
_, logdet = la.slogdet(C)
log2pi = np.log(2 * np.pi)
return -0.5 * (d * log2pi + logdet + maha)
def _logdet_MM(self):
if not self._restricted:
return 0.0
M = self._mean.AX
ldet = slogdet(M.T @ M)
if ldet[0] != 1.0:
raise ValueError("The determinant of MрхђM should be positive.")
return ldet[1]
def callback_one(ip,d):
pp = objective.inflate(ip)
print
print 'CALLBACK:'
for term,ppp,dd in zip(terms,pp,d):
M = ppp['M']
M = (M+np.transpose(M))/2
N = M.shape[0]
s , lldet = slogdet(np.identity(N)-M)
df = term.df(ppp,dd)
dM = term.inflate(df)['M']
ds , dldet = slogdet(np.identity(N)-M+0.001*dM)
w,v = eig( np.identity(N) - M )
print 'eig M' , w.real
print [term.f(ppp,dd)]
print 'Iteration s, ldet I-M: %d , %f %d , %f norm theta %f norm M %f barr %d' % \
(s , lldet , ds, dldet, norm(ppp['theta']), norm(M), term.barrier(ppp,dd))
print
def llk(x):
A = 10 ** x[0]
l = 10 ** x[1]
k = sqk(A, l)
Ac, R, Q, V = buildmats(k)
lk = -0.5 * Y.T.dot(Ksolve(Ac, R, Q, V ,Y)) - 0.5 * (slogdet(spl.toeplitz(Ac))[1]+slogdet(Q)[1])
pr = -0.5 * x[0] ** 2 - 0.5 * x[1] ** 2
return -lk - pr
def value(self, mean, cov):
ym = self._y - mean
Kiym = solve(cov, ym)
(s, logdet) = slogdet(cov)
assert s == 1.
n = len(self._y)
return -(logdet + ym.dot(Kiym) + n * log(2 * pi)) / 2
def energy(self):
F = self.N * np.log(2 * np.pi * self.sigma2)
log_det = np.prod(
la.slogdet(self.C @ self.XtX + self.sigma2 * np.eye(self.D)))
F += log_det
F += (la.norm(self.y)**2 -
self.Xty.T @ self.Sigma_W @ self.Xty) / self.sigma2
self.F = F / 2
return self.F
def __init__(self,bigy,bigX,iter=False,maxiter=5,epsilon=0.00001,verbose=False):
# setting up the cross-products
self.bigy = bigy
self.bigX = bigX
self.n_eq = len(bigy.keys())
self.n = bigy[0].shape[0]
self.bigK = np.zeros((self.n_eq,1),dtype=np.int_)
for r in range(self.n_eq):
self.bigK[r] = self.bigX[r].shape[1]
self.bigXX,self.bigXy = sur_crossprod(self.bigX,self.bigy)
# OLS regression by equation, sets up initial residuals
self.sur_ols() # creates self.bOLS and self.olsE
# SUR estimation using OLS residuals - two step estimation
self.bSUR,self.varb,self.sig = sur_est(self.bigXX,self.bigXy,self.olsE,self.bigK)
resids = sur_resids(self.bigy,self.bigX,self.bSUR) # matrix of residuals
# Sigma and log det(Sigma) for null model
self.sig_ols = self.sig
sols = np.diag(np.diag(self.sig))
self.ldetS0 = np.log(np.diag(sols)).sum()
det0 = self.ldetS0
# setup for iteration
det1 = la.slogdet(self.sig)[1]
self.ldetS1 = det1
#self.niter = 0
if iter: # iterated FGLS aka ML
n_iter = 0
while np.abs(det1-det0) > epsilon and n_iter <= maxiter:
n_iter += 1
det0 = det1
self.bSUR,self.varb,self.sig = sur_est(self.bigXX,self.bigXy,\
resids,self.bigK)
resids = sur_resids(self.bigy,self.bigX,self.bSUR)
det1 = la.slogdet(self.sig)[1]
if verbose:
print (n_iter,det0,det1)
self.bigE = sur_resids(self.bigy,self.bigX,self.bSUR)
self.ldetS1 = det1
self.niter = n_iter
else:
self.niter = 1
self.bigE = resids
self.corr = sur_corr(self.sig)
lik = self.n_eq * (1.0 + np.log(2.0*np.pi)) + self.ldetS1
self.llik = - (self.n / 2.0) * lik
def test_loglikelihood(self):
gsm = GSM(3, 1)
samples = gsm.sample(100000)
# compute entropy analytically
entropy = 0.5 * slogdet(2. * pi * e * gsm.covariance / gsm.scales)[1]
# compare with estimated entropy
self.assertAlmostEqual(entropy, -mean(gsm.loglikelihood(samples)), 1)
def expected_log_likelihood(self, data):
W = inv(self.psi)
N = data.shape[1]
x = data - self.m
return -sum(x * dot(W, x), 0)[None, :] * self.nu / 2 \
- self.dim / 2. / self.s \
+ sum(psi((self.nu + 1. - arange(1, self.dim + 1)) / 2.)) / 2. \
+ slogdet(W)[1] / 2. \
- self.dim / 2. * log(pi)
def model_evidence(self):
self.ensure_gram_matrix()
t = self._train_t
datafit = t.T.dot(self._Cinvt)
s, logdet = slogdet(self._C)
complexity = s * logdet
nomalization = len(t) * np.log(np.pi * 2)
return -0.5 * (datafit + complexity + nomalization)
def log_prior(self, i):
"""Return the probability of `X[i]` under the prior alone."""
mu = self.prior.m_0
covar = (self.prior.k_0 +
1) / (self.prior.k_0 *
(self.prior.v_0 - self.D + 1)) * self.prior.S_0
logdet_covar = slogdet(covar)[1]
inv_covar = inv(covar)
v = self.prior.v_0 - self.D + 1
return self._multivariate_students_t(i, mu, logdet_covar, inv_covar, v)
def KL(self, othr):
j, k = self._ci(othr)
k = min(k, self.Ncov / 2, othr.Ncov / 2)
delta = self.MomAct[j:k] - othr.MomAct[j:k]
ChSelf = cho_factor(self.Cov[j:k, j:k])
h = cho_solve(ChSelf, delta)
r = cho_solve(ChSelf, othr.Cov[j:k, j:k])
return (np.trace(r) + delta.dot(h) - slogdet(r)[1] - k + j) / 2
def _logdetH(self):
"""
log(｜H｜) for H = s⁻¹XᵀQD⁻¹QᵀX.
"""
if not self._restricted:
return 0.0
ldet = slogdet(self._tXTBtX / self.scale)
if ldet[0] != 1.0:
raise ValueError("The determinant of H should be positive.")
return ldet[1]
def mwdp_fusion(prior, cov_prior, meas, cov_meas):
"""
Fuse ellipses A and B in original state space using representation with highest likelihood; assumes independent
measurement dimensions for the switch of covariance elements
:param prior: Prior ellipse in original state space
:param cov_prior: Covariance of prior ellipse
:param meas: Measured ellipse in original state space
:param cov_meas: Covariance of measured ellipse
:return: Mean and covariance of fusion with highest likelihood representation and number of 90 degree
shifts of ellipse B to get highest likelihood representation
"""
res_orig_alt_rots = np.zeros((4, 5))
res_orig_alt_rots_cov = np.zeros((4, 5, 5))
res_orig_log_lik = np.zeros(4)
innov = np.zeros((4, 5))
meas_alt = np.zeros(5)
meas_alt[M] = meas[M]
# test all 4 representations
for k in range(4):
# shift orientation and if necessary switch semi-axis in mean and orientation
meas_alt[AL] = (meas[AL] + k * np.pi * 0.5) % (2 * np.pi)
if k % 2 != 0:
meas_alt[L] = meas[W]
meas_alt[W] = meas[L]
cov_meas_alt = np.copy(cov_meas)
cov_meas_alt[3, 3] = cov_meas[4, 4]
cov_meas_alt[4, 4] = cov_meas[3, 3]
else:
meas_alt[L] = meas[L]
meas_alt[W] = meas[W]
cov_meas_alt = np.copy(cov_meas)
# Kalman update
S_orig_alt = cov_prior + cov_meas_alt
if np.linalg.det(S_orig_alt) == 0:
print('Singular S_orig')
# print(S_orig)
continue
K_orig_alt = np.dot(cov_prior, np.linalg.inv(S_orig_alt))
innov[k] = meas_alt - prior
# use shorter angle difference
innov[k, 2] = ((innov[k, 2] + np.pi) % (2 * np.pi)) - np.pi
res_orig_alt_rots[k] = prior + np.dot(K_orig_alt, innov[k])
res_orig_alt_rots_cov[k] = cov_prior - np.dot(
np.dot(K_orig_alt, S_orig_alt), K_orig_alt.T)
# calculate log-likelihood
res_orig_log_lik[k] = -0.5 * np.dot(np.dot(innov[k], inv(S_orig_alt)),
innov[k])
sign, logdet_inv = slogdet(inv(S_orig_alt))
res_orig_log_lik[k] += 0.5 * logdet_inv - 2.5 * np.log(2 * np.pi)
return res_orig_alt_rots[np.argmax(res_orig_log_lik)], res_orig_alt_rots_cov[np.argmax(res_orig_log_lik)],\
np.argmax(res_orig_log_lik)
def maxdiv_gaussian_globalcov(X,
intervals,
mode='I_OMEGA',
gaussian_mode='GLOBAL_COV',
**kwargs):
""" Scores given intervals by assuming gaussian distributions with equal covariance.
`X` is a d-by-n matrix with `n` data points, each with `d` attributes.
`intervals` has to be an iterable of `(a, b, score)` tuples, which define an
interval `[a,b)` which is suspected to be an anomaly.
Returns: a list of `(a, b, score)` tuples. `a` and `b` are the same as in the given
`intervals` iterable, but the scores will indicate whether a given interval
is an anomaly or not.
"""
dimension, n = X.shape
numValidSamples = n if not np.ma.isMaskedArray(X) else X[0, :].count()
X_integral = np.cumsum(X if not np.ma.isMaskedArray(X) else X.filled(0),
axis=1)
sums_all = X_integral[:, -1]
if (gaussian_mode == 'GLOBAL_COV') and (dimension > 1):
cov = np.ma.cov(X).filled(0)
cov_chol = cho_factor(cov)
logdet = slogdet(cov)[1]
scores = []
eps = 1e-7
for a, b, base_score in intervals:
extreme_interval_length = b - a if not np.ma.isMaskedArray(X) else X[
0, a:b].count()
non_extreme_points = numValidSamples - extreme_interval_length
sums_extreme = X_integral[:, b - 1] - (X_integral[:, a -
1] if a > 0 else 0)
sums_non_extreme = sums_all - sums_extreme
sums_extreme /= extreme_interval_length
sums_non_extreme /= non_extreme_points
diff = sums_extreme - sums_non_extreme
if (gaussian_mode == 'GLOBAL_COV') and (dimension > 1):
score = diff.T.dot(cho_solve(cov_chol, diff))
if (mode == 'CROSSENT') or (mode == 'CROSSENT_TS'):
score += slogdet
else:
score = np.sum(diff * diff)
if (mode == 'CROSSENT') or (mode == 'CROSSENT_TS'):
score += dimension * (1 + np.log(2 * np.pi))
scores.append((a, b, score))
return scores
def initialize(self):
"""
Initialize the gibbs sampler state.
I start with log N tables and randomly initialize customers to those tables.
"""
# First check the prior degrees of freedom.
# It has to be >= num_dimension
if self.prior.nu < self.embedding_size:
self.log.warn(
"The initial degrees of freedom of the prior is less than the dimension!. "
"Setting it to the number of dimensions: {}".format(
self.embedding_size))
self.prior.nu = self.embedding_size
deg_of_freedom = self.prior.nu - self.embedding_size + 1
# Now calculate the covariance matrix of the multivariate T-distribution
coeff = (self.prior.kappa + 1.) / (self.prior.kappa * deg_of_freedom)
sigma_T = self.prior.sigma * coeff
# This features in the original code, but doesn't get used
# Or is it just to check that the invert doesn't fail?
#sigma_Tinv = inv(sigma_T)
sigma_TDet_sign, sigma_TDet = slogdet(sigma_T)
if sigma_TDet_sign != 1:
raise ValueError(
"sign of log determinant of initial sigma is {}".format(
sigma_TDet_sign))
# Storing zeros in sumTableCustomers and later will keep on adding each customer.
self.sum_squared_table_customers[:] = 0
# Means are set to the prior and then updated as we add each assignment
self.table_means.np[:] = self.prior.mu
# Initialize the cholesky decomp of each table, with no counts yet
for table in range(self.num_tables):
self.table_cholesky_ltriangular_mat.np[
table] = self.prior.chol_sigma.copy()
# Randomly assign customers to tables
self.table_assignments = []
pbar = get_progress_bar(len(self.corpus),
title="Initializing",
show_progress=self.show_progress)
for doc_num, doc in enumerate(pbar(self.corpus)):
tables = list(np.random.randint(self.num_tables, size=len(doc)))
self.table_assignments.append(tables)
for (word, table) in zip(doc, tables):
self.table_counts.np[table] += 1
self.table_counts_per_doc[table, doc_num] += 1
# update the sumTableCustomers
self.sum_squared_table_customers[table] += np.outer(
self.vocab_embeddings[word], self.vocab_embeddings[word])
self.update_table_params(table, word)
def findCost(self, y, t):
# Cost function is tc'y - log det(-sum... + I)
res = t * np.dot(self.C, y)
A = np.zeros((self.COUNT, self.COUNT),dtype=np.complex128)
for i in range(len(y)):
A -= y[i] * self.F_MATRICES[i]
A += np.identity(self.COUNT)
# Find log determinant, there is an alternative calculation
(sign, logdet) = slogdet(A)
res -= sign*logdet
return res
def log_gaussian_pdf(x_i, mu_c, sigma_c):
"""
Computes log N(x_i | mu_c, sigma_c)
"""
n = len(mu_c)
a = n * np.log(2 * np.pi)
_, b = slogdet(sigma_c)
y = np.linalg.solve(sigma_c, x_i - mu_c)
c = np.dot(x_i - mu_c, y)
return -0.5 * (a + b + c)
def draw_beta_full_cov(k, s, w, size=1):
"""
draw beta from posterior (depends on k, s, w), eq 9 (Rasmussen 2000), using ARS
the covariance matrix of the model is full cov
Make it robust with an expanding range in case of failure
"""
D = w.shape[0]
# compute Determinant of w, det(w)
logdet_w = slogdet(w)[1]
# compute cumculative sum j from i to k, [ log(det(sj))- trace(w * sj)]
cumculative_sum_equation = 0
for sj in s:
sj = np.reshape(sj, (D, D))
cumculative_sum_equation += slogdet(sj)[1]
cumculative_sum_equation -= np.trace(np.dot(w, sj))
lb = D
ars = ARS(log_p_beta_full_cov, log_p_beta_prime_full_cov, xi=[lb + 1, lb + 1000], lb=lb, ub=float("inf"), \
k=k, s=s, w=w, D=D, logdet_w=logdet_w, cumculative_sum_equation=cumculative_sum_equation)
return ars.draw(size)
def numeric(self, values):
"""Returns the logdet of PSD matrix A.
For PSD matrix A, this is the sum of logs of eigenvalues of A
and is equivalent to the nuclear norm of the matrix logarithm of A.
"""
sign, logdet = LA.slogdet(values[0])
if sign == 1:
return logdet
else:
return -np.inf
def test_sparse_inv_covariance(self, q, alpha_ratio, figname):
# minimize -log(det(S)) + trace(S*Q) + \alpha*||S||_1 subject to S is symmetric PSD.
# Problem data.
# q: Dimension of matrix.
p = 1000 # Number of samples.
ratio = 0.9 # Fraction of zeros in S.
S_true = sparse.csc_matrix(make_sparse_spd_matrix(q, ratio))
Sigma = sparse.linalg.inv(S_true).todense()
z_sample = np.real(sp.linalg.sqrtm(Sigma)).dot(np.random.randn(
q, p)) # make sure it's real matrices.
Q = np.cov(z_sample)
print('Q is positive definite? {}'.format(bool(LA.slogdet(Q)[0])))
mask = np.ones(Q.shape, dtype=bool)
np.fill_diagonal(mask, 0)
alpha_max = np.max(np.abs(Q)[mask])
alpha = alpha_ratio * alpha_max # 0.001 for q = 100, 0.01 for q = 50.
# Convert problem to standard form.
# f_1(S_1) = -log(det(S_1)) + trace(S_1*Q) on symmetric PSD matrices, f_2(S_2) = \alpha*||S_2||_1.
# A_1 = I, A_2 = -I, b = 0.
prox_list = [
lambda v, t: prox_neg_log_det(
v.reshape(
(q, q), order='C'), t, lin_term=t * Q).ravel(order='C'),
lambda v, t: prox_norm1(v, t * alpha)
]
A_list = [sparse.eye(q * q), -sparse.eye(q * q)]
b = np.zeros(q * q)
# Solve with DRS.
drs_result = a2dr(prox_list,
A_list,
b,
anderson=False,
precond=True,
max_iter=self.MAX_ITER)
print('Finished DRS.')
# Solve with A2DR.
a2dr_result = a2dr(prox_list,
A_list,
b,
anderson=True,
precond=True,
max_iter=self.MAX_ITER)
# lam_accel = 0 seems to work well sometimes, although it oscillates a lot.
a2dr_S = a2dr_result["x_vals"][-1].reshape((q, q), order='C')
self.compare_total(drs_result, a2dr_result, figname)
print('Finished A2DR.')
print('recovered sparsity = {}'.format(
np.sum(a2dr_S != 0) * 1.0 / a2dr_S.shape[0]**2))
def _logdetXX(self):
"""
log(｜XᵀX｜).
"""
if not self._restricted:
return 0.0
ldet = slogdet(self._Xsvd.US.T @ self._Xsvd.US)
if ldet[0] != 1.0:
raise ValueError("The determinant of XᵀX should be positive.")
return ldet[1]
def __init__(self, means, covs, weights=None):
if weights is None:
weights = np.ones(len(means), dtype=float)
assert len(means) == len(weights) and len(means) == len(covs)
self.K = len(means)
self.means = [np.array(m) for m in means]
self.icovs = [linalg.inv(c) for c in covs]
self.logws = [np.log(0.5 * w / np.pi) - 0.5 * linalg.slogdet(c)[1]
for w, c in zip(weights / np.sum(weights), covs)]
def log_pdf(x, mu, T, n):
[k, N] = x.shape
xm = x - mu
(sign, logdet) = slogdet(T)
logc = math.lgamma((n + k) / 2.0)
logc += 0.5 * logdet
logc -= math.lgamma(n / 2.0)
logc -= np.log(n * math.pi) * (k / 2.0)
logp = -0.5 * (n + k) * np.log(1 + xm.T * T * xm / n)
logp = logp + logc
return float(logp)
def log_marg_k(self, k):
"""
Return the log marginal probability of the data vectors assigned to
component `k`.
The log marginal probability p(X) = p(x_1, x_2, ..., x_N) is returned
for the data vectors assigned to component `k`. See (266) in Murphy's
bayesGauss notes, p. 21.
"""
k_N = self.prior.k_0 + self.counts[k]
v_N = self.prior.v_0 + self.counts[k]
m_N = self.m_N_numerators[k] / k_N
S_N = self.S_N_partials[k] - k_N * np.outer(m_N, m_N)
i = np.arange(1, self.D + 1, dtype=np.int)
return (-self.counts[k] * self.D / 2. * self._cached_log_pi +
self.D / 2. * math.log(self.prior.k_0) -
self.D / 2. * math.log(k_N) +
self.prior.v_0 / 2. * slogdet(self.prior.S_0)[1] -
v_N / 2. * slogdet(S_N)[1] +
np.sum(self._cached_gammaln_by_2[v_N + 1 - i] -
self._cached_gammaln_by_2[self.prior.v_0 + 1 - i]))
def scan_energies(self, k, Earray, m=range(-6, 7)):
self.bsize = len(m)
self.m = m
sign = []
logdet = []
for E in Earray:
H, S = self.fill_arrays(k, E)
# val = det(H - E * S)
val = slogdet(H - E * S)
sign.append(val[0])
logdet.append(val[1])
return array(sign), array(logdet)
def value(self):
mean = self._mean.value()
cov = self._cov.value()
ym = self._y - mean
Kiym = solve(cov, ym)
(s, logdet) = slogdet(cov)
if not s == 1.0:
raise RuntimeError("This determinant should not be negative.")
n = len(self._y)
return -(logdet + ym.dot(Kiym) + n * log(2 * pi)) / 2
def get_logdet(m):
from numpy.linalg import slogdet
logdet = slogdet(m)
if logdet[0] == -1: # pragma: no cover
raise ValueError("Matrix is not positive definite")
elif logdet[0] == 0: # pragma: no cover
raise ValueError("Matrix is singular")
else:
logdet = logdet[1]
return logdet
def test_affine_preconditioner_logjacobian(self):
meanIn = randn(5, 1)
meanOut = randn(2, 1)
preIn = randn(5, 5)
preOut = randn(2, 2)
predictor = randn(2, 5)
pre = AffinePreconditioner(meanIn, meanOut, preIn, preOut, predictor)
self.assertAlmostEqual(
mean(pre.logjacobian(randn(5, 10), randn(2, 10))),
slogdet(preOut)[1])
def stnll(x, m, a, c, B, D):
'''
Compute Student-t negative log likelihood (Appendix A, eqn. (20))
'''
mu = m
nu = a-D+1
Lambda = c*float(nu)/(c+1)*B
S = np.dot(np.dot((x-mu).T, Lambda), (x-mu))
_, logdetL = slogdet(Lambda)
return float(nu+D)/2.*np.log(1.+S/float(nu))\
- 0.5*logdetL+gammaln(nu/2.)\
- gammaln((float(nu)+D)/2.)+D/2.*np.log(float(nu)*np.pi)
def __init__(self, data, label, alpha=1e-6):
GaussianClassifier.__init__(self, data, label, alpha)
self.log_determinants = np.ndarray(shape=self.num_classes,
dtype=np.float)
for i in range(self.num_classes):
s, logdet = la.slogdet(self.variances[i])
if s == 0:
raise Exception("singular matrix")
self.log_determinants[i] = logdet
self.precisions = np.array(
[la.inv(self.variances[i]) for i in range(self.num_classes)])
del self.variances