def _compute_bound(self, R, logdet=None, inv=None, gradient=False):
"""
Rotate q(X) as X->RX: q(X)=N(R*mu, R*Cov*R')
Assume:
:math:`p(\mathbf{X}) = \prod^M_{m=1}
N(\mathbf{x}_m|0, \mathbf{\Lambda})`
"""
# TODO/FIXME: X and alpha should NOT contain observed values!! Check
# that.
# TODO/FIXME: Allow non-zero prior mean!
# Assume constant mean and precision matrix over plates..
# Compute rotated moments
XX_R = dot(R, self.XX, R.T)
inv_R = inv
logdet_R = logdet
# Compute entropy H(X)
logH_X = random.gaussian_entropy(-2 * self.N * logdet_R, 0)
# Compute <log p(X)>
logp_X = random.gaussian_logpdf(np.vdot(XX_R, self.Lambda), 0, 0, 0, 0)
# Compute the bound
if terms:
bound = {self.X: bound}
else:
bound = logp_X + logH_X
if not gradient:
return bound
# Compute dH(X)
dlogH_X = random.gaussian_entropy(-2 * self.N * inv_R.T, 0)
# Compute d<log p(X)>
dXX = 2 * dot(self.Lambda, R, self.XX)
dlogp_X = random.gaussian_logpdf(dXX, 0, 0, 0, 0)
if terms:
d_bound = {self.X: dlogp_X + dlogH_X}
else:
d_bound = dlogp_X + dlogH_X
return (bound, d_bound)
def test_message_to_child(self):
"""
Test the updating of GaussianMarkovChain.
Check that the moments and the lower bound contribution are computed
correctly.
"""
# TODO: Add plates and missing values!
# Dimensionalities
D = 3
N = 5
(Y, X, Mu, Lambda, A, V) = self.create_model(N, D)
# Inference with arbitrary observations
y = np.random.randn(N, D)
Y.observe(y)
X.update()
(x_vb, xnxn_vb, xpxn_vb) = X.get_moments()
# Get parameter moments
(mu0, mumu0) = Mu.get_moments()
(icov0, logdet0) = Lambda.get_moments()
(a, aa) = A.get_moments()
(icov_x, logdetx) = V.get_moments()
icov_x = np.diag(icov_x)
# Prior precision
Z = np.einsum("...kij,...kk->...ij", aa, icov_x)
U_diag = [icov0 + Z] + (N - 2) * [icov_x + Z] + [icov_x]
U_super = (N - 1) * [-np.dot(a.T, icov_x)]
U = misc.block_banded(U_diag, U_super)
# Prior mean
mu_prior = np.zeros(D * N)
mu_prior[:D] = np.dot(icov0, mu0)
# Data
Cov = np.linalg.inv(U + np.identity(D * N))
mu = np.dot(Cov, mu_prior + y.flatten())
# Moments
xx = mu[:, np.newaxis] * mu[np.newaxis, :] + Cov
mu = np.reshape(mu, (N, D))
xx = np.reshape(xx, (N, D, N, D))
# Check results
self.assertAllClose(x_vb, mu, msg="Incorrect mean")
for n in range(N):
self.assertAllClose(xnxn_vb[n, :, :], xx[n, :, n, :], msg="Incorrect second moment")
for n in range(N - 1):
self.assertAllClose(xpxn_vb[n, :, :], xx[n, :, n + 1, :], msg="Incorrect lagged second moment")
# Compute the entropy H(X)
ldet = linalg.logdet_cov(Cov)
H = random.gaussian_entropy(-ldet, N * D)
# Compute <log p(X|...)>
xx = np.reshape(xx, (N * D, N * D))
mu = np.reshape(mu, (N * D,))
ldet = -logdet0 - np.sum(np.ones((N - 1, D)) * logdetx)
P = random.gaussian_logpdf(
np.einsum("...ij,...ij", xx, U),
np.einsum("...i,...i", mu, mu_prior),
np.einsum("...ij,...ij", mumu0, icov0),
-ldet,
N * D,
)
# The VB bound from the net
l = X.lower_bound_contribution()
self.assertAllClose(l, H + P)
# Compute the true bound <log p(X|...)> + H(X)
#
# Simple tests
#
def check(N, D, plates=None, mu=None, Lambda=None, A=None, V=None):
if mu is None:
mu = np.random.randn(D)
if Lambda is None:
Lambda = random.covariance(D)
if A is None:
A = np.random.randn(D, D)
if V is None:
V = np.random.rand(D)
X = GaussianMarkovChain(mu, Lambda, A, V, plates=plates, n=N)
(u0, u1, u2) = X._message_to_child()
(mu, mumu) = Gaussian._ensure_moments(mu, GaussianMoments, ndim=1).get_moments()
(Lambda, _) = Wishart._ensure_moments(Lambda, WishartMoments, ndim=1).get_moments()
(a, aa) = Gaussian._ensure_moments(A, GaussianMoments, ndim=1).get_moments()
a = a * np.ones((N - 1, D, D)) # explicit broadcasting for simplicity
aa = aa * np.ones((N - 1, D, D, D)) # explicit broadcasting for simplicity
(v, _) = Gamma._ensure_moments(V, GammaMoments).get_moments()
v = v * np.ones((N - 1, D))
plates_C = X.plates
plates_mu = X.plates
C = np.zeros(plates_C + (N, D, N, D))
plates_mu = np.shape(mu)[:-1]
m = np.zeros(plates_mu + (N, D))
m[..., 0, :] = np.einsum("...ij,...j->...i", Lambda, mu)
C[..., 0, :, 0, :] = Lambda + np.einsum("...dij,...d->...ij", aa[..., 0, :, :, :], v[..., 0, :])
for n in range(1, N - 1):
C[..., n, :, n, :] = np.einsum("...dij,...d->...ij", aa[..., n, :, :, :], v[..., n, :]) + v[
..., n, :, None
] * np.identity(D)
for n in range(N - 1):
C[..., n, :, n + 1, :] = -np.einsum("...di,...d->...id", a[..., n, :, :], v[..., n, :])
C[..., n + 1, :, n, :] = -np.einsum("...di,...d->...di", a[..., n, :, :], v[..., n, :])
C[..., -1, :, -1, :] = v[..., -1, :, None] * np.identity(D)
C = np.reshape(C, plates_C + (N * D, N * D))
Cov = np.linalg.inv(C)
Cov = np.reshape(Cov, plates_C + (N, D, N, D))
m0 = np.einsum("...minj,...nj->...mi", Cov, m)
m1 = np.zeros(plates_C + (N, D, D))
m2 = np.zeros(plates_C + (N - 1, D, D))
for n in range(N):
m1[..., n, :, :] = Cov[..., n, :, n, :] + np.einsum("...i,...j->...ij", m0[..., n, :], m0[..., n, :])
for n in range(N - 1):
m2[..., n, :, :] = Cov[..., n, :, n + 1, :] + np.einsum(
"...i,...j->...ij", m0[..., n, :], m0[..., n + 1, :]
)
self.assertAllClose(m0, u0 * np.ones(np.shape(m0)))
self.assertAllClose(m1, u1 * np.ones(np.shape(m1)))
self.assertAllClose(m2, u2 * np.ones(np.shape(m2)))
pass
check(4, 1)
check(4, 3)
#
# Test mu
#
# Simple
check(4, 3, mu=Gaussian(np.random.randn(3), random.covariance(3)))
# Plates
check(4, 3, mu=Gaussian(np.random.randn(5, 6, 3), random.covariance(3), plates=(5, 6)))
# Plates with moments broadcasted over plates
check(4, 3, mu=Gaussian(np.random.randn(3), random.covariance(3), plates=(5,)))
check(4, 3, mu=Gaussian(np.random.randn(1, 3), random.covariance(3), plates=(5,)))
# Plates broadcasting
check(4, 3, plates=(5,), mu=Gaussian(np.random.randn(3), random.covariance(3), plates=()))
check(4, 3, plates=(5,), mu=Gaussian(np.random.randn(1, 3), random.covariance(3), plates=(1,)))
#
# Test Lambda
#
# Simple
check(4, 3, Lambda=Wishart(10 + np.random.rand(), random.covariance(3)))
# Plates
check(4, 3, Lambda=Wishart(10 + np.random.rand(), random.covariance(3), plates=(5, 6)))
# Plates with moments broadcasted over plates
check(4, 3, Lambda=Wishart(10 + np.random.rand(), random.covariance(3), plates=(5,)))
check(4, 3, Lambda=Wishart(10 + np.random.rand(1), random.covariance(3), plates=(5,)))
# Plates broadcasting
check(4, 3, plates=(5,), Lambda=Wishart(10 + np.random.rand(), random.covariance(3), plates=()))
check(4, 3, plates=(5,), Lambda=Wishart(10 + np.random.rand(), random.covariance(3), plates=(1,)))
#
# Test A
#
# Simple
check(4, 3, A=GaussianARD(np.random.randn(3, 3), np.random.rand(3, 3), shape=(3,), plates=(3,)))
# Plates on time axis
check(5, 3, A=GaussianARD(np.random.randn(4, 3, 3), np.random.rand(4, 3, 3), shape=(3,), plates=(4, 3)))
# Plates on time axis with broadcasted moments
check(5, 3, A=GaussianARD(np.random.randn(1, 3, 3), np.random.rand(1, 3, 3), shape=(3,), plates=(4, 3)))
check(5, 3, A=GaussianARD(np.random.randn(3, 3), np.random.rand(3, 3), shape=(3,), plates=(4, 3)))
# Plates
check(
4,
3,
A=GaussianARD(
np.random.randn(5, 6, 1, 3, 3), np.random.rand(5, 6, 1, 3, 3), shape=(3,), plates=(5, 6, 1, 3)
),
)
# Plates with moments broadcasted over plates
check(4, 3, A=GaussianARD(np.random.randn(3, 3), np.random.rand(3, 3), shape=(3,), plates=(5, 1, 3)))
check(
4, 3, A=GaussianARD(np.random.randn(1, 1, 3, 3), np.random.rand(1, 1, 3, 3), shape=(3,), plates=(5, 1, 3))
)
# Plates broadcasting
check(4, 3, plates=(5,), A=GaussianARD(np.random.randn(3, 3), np.random.rand(3, 3), shape=(3,), plates=(3,)))
check(
4, 3, plates=(5,), A=GaussianARD(np.random.randn(3, 3), np.random.rand(3, 3), shape=(3,), plates=(1, 1, 3))
)
#
# Test v
#
# Simple
check(4, 3, V=Gamma(np.random.rand(1, 3), np.random.rand(1, 3), plates=(1, 3)))
check(4, 3, V=Gamma(np.random.rand(3), np.random.rand(3), plates=(3,)))
# Plates
check(4, 3, V=Gamma(np.random.rand(5, 6, 1, 3), np.random.rand(5, 6, 1, 3), plates=(5, 6, 1, 3)))
# Plates with moments broadcasted over plates
check(4, 3, V=Gamma(np.random.rand(1, 3), np.random.rand(1, 3), plates=(5, 1, 3)))
check(4, 3, V=Gamma(np.random.rand(1, 1, 3), np.random.rand(1, 1, 3), plates=(5, 1, 3)))
# Plates broadcasting
check(4, 3, plates=(5,), V=Gamma(np.random.rand(1, 3), np.random.rand(1, 3), plates=(1, 3)))
check(4, 3, plates=(5,), V=Gamma(np.random.rand(1, 1, 3), np.random.rand(1, 1, 3), plates=(1, 1, 3)))
#
# Check with input signals
#
mu = 2
Lambda = 3
A = 4
B = 5
v = 6
inputs = [[-2], [3]]
X = GaussianMarkovChain([mu], [[Lambda]], [[A, B]], [v], inputs=inputs)
V = np.array([[v * A ** 2, -v * A, 0], [-v * A, v * A ** 2, -v * A], [0, -v * A, 0]]) + np.array(
[[Lambda, 0, 0], [0, v, 0], [0, 0, v]]
)
m = (
np.array([Lambda * mu, 0, 0])
+ np.array([0, v * B * inputs[0][0], v * B * inputs[1][0]])
- np.array([v * A * B * inputs[0][0], v * A * B * inputs[1][0], 0])
)
Cov = np.linalg.inv(V)
mean = np.dot(Cov, m)
X.update()
u = X.get_moments()
self.assertAllClose(u[0], mean[:, None])
self.assertAllClose(u[1] - u[0][..., None, :] * u[0][..., :, None], Cov[(0, 1, 2), (0, 1, 2), None, None])
self.assertAllClose(u[2] - u[0][..., :-1, :, None] * u[0][..., 1:, None, :], Cov[(0, 1), (1, 2), None, None])
pass
def test_message_to_parent(self):
"""
Test the message to parents of Mixture node.
"""
K = 3
# Broadcasting the moments on the cluster axis
Mu = GaussianARD(2, 1, ndim=0, plates=(K, ))
(mu, mumu) = Mu._message_to_child()
Alpha = Gamma(3, 1, plates=(K, ))
(alpha, logalpha) = Alpha._message_to_child()
z = Categorical(np.ones(K) / K)
X = Mixture(z, GaussianARD, Mu, Alpha)
tau = 4
Y = GaussianARD(X, tau)
y = 5
Y.observe(y)
(x, xx) = X._message_to_child()
m = z._message_from_children()
self.assertAllClose(
m[0] * np.ones(K),
random.gaussian_logpdf(xx * alpha, x * alpha * mu, mumu * alpha,
logalpha, 0) * np.ones(K))
m = Mu._message_from_children()
self.assertAllClose(m[0], 1 / K * (alpha * x) * np.ones(3))
self.assertAllClose(m[1], -0.5 * 1 / K * alpha * np.ones(3))
# Some parameters do not have cluster plate axis
Mu = GaussianARD(2, 1, ndim=0, plates=(K, ))
(mu, mumu) = Mu._message_to_child()
Alpha = Gamma(3, 1) # Note: no cluster plate axis!
(alpha, logalpha) = Alpha._message_to_child()
z = Categorical(np.ones(K) / K)
X = Mixture(z, GaussianARD, Mu, Alpha)
tau = 4
Y = GaussianARD(X, tau)
y = 5
Y.observe(y)
(x, xx) = X._message_to_child()
m = z._message_from_children()
self.assertAllClose(
m[0] * np.ones(K),
random.gaussian_logpdf(xx * alpha, x * alpha * mu, mumu * alpha,
logalpha, 0) * np.ones(K))
m = Mu._message_from_children()
self.assertAllClose(m[0], 1 / K * (alpha * x) * np.ones(3))
self.assertAllClose(m[1], -0.5 * 1 / K * alpha * np.ones(3))
# Cluster assignments do not have as many plate axes as parameters.
M = 2
Mu = GaussianARD(2, 1, ndim=0, plates=(K, M))
(mu, mumu) = Mu._message_to_child()
Alpha = Gamma(3, 1, plates=(K, M))
(alpha, logalpha) = Alpha._message_to_child()
z = Categorical(np.ones(K) / K)
X = Mixture(z, GaussianARD, Mu, Alpha, cluster_plate=-2)
tau = 4
Y = GaussianARD(X, tau)
y = 5 * np.ones(M)
Y.observe(y)
(x, xx) = X._message_to_child()
m = z._message_from_children()
self.assertAllClose(
m[0] * np.ones(K),
np.sum(random.gaussian_logpdf(xx * alpha, x * alpha * mu,
mumu * alpha, logalpha, 0) * np.ones(
(K, M)),
axis=-1))
m = Mu._message_from_children()
self.assertAllClose(m[0] * np.ones((K, M)),
1 / K * (alpha * x) * np.ones((K, M)))
self.assertAllClose(m[1] * np.ones((K, M)),
-0.5 * 1 / K * alpha * np.ones((K, M)))
# Mixed distribution broadcasts g
# This tests for a found bug. The bug caused an error.
Z = Categorical([0.3, 0.5, 0.2])
X = Mixture(Z, Categorical, [[0.2, 0.8], [0.1, 0.9], [0.3, 0.7]])
m = Z._message_from_children()
pass
def test_message_to_parent(self):
"""
Test the message to parents of Mixture node.
"""
K = 3
# Broadcasting the moments on the cluster axis
Mu = GaussianARD(2, 1,
ndim=0,
plates=(K,))
(mu, mumu) = Mu._message_to_child()
Alpha = Gamma(3, 1,
plates=(K,))
(alpha, logalpha) = Alpha._message_to_child()
z = Categorical(np.ones(K)/K)
X = Mixture(z, GaussianARD, Mu, Alpha)
tau = 4
Y = GaussianARD(X, tau)
y = 5
Y.observe(y)
(x, xx) = X._message_to_child()
m = z._message_from_children()
self.assertAllClose(m[0] * np.ones(K),
random.gaussian_logpdf(xx*alpha,
x*alpha*mu,
mumu*alpha,
logalpha,
0)
* np.ones(K))
m = Mu._message_from_children()
self.assertAllClose(m[0],
1/K * (alpha*x) * np.ones(3))
self.assertAllClose(m[1],
-0.5 * 1/K * alpha * np.ones(3))
# Some parameters do not have cluster plate axis
Mu = GaussianARD(2, 1,
ndim=0,
plates=(K,))
(mu, mumu) = Mu._message_to_child()
Alpha = Gamma(3, 1) # Note: no cluster plate axis!
(alpha, logalpha) = Alpha._message_to_child()
z = Categorical(np.ones(K)/K)
X = Mixture(z, GaussianARD, Mu, Alpha)
tau = 4
Y = GaussianARD(X, tau)
y = 5
Y.observe(y)
(x, xx) = X._message_to_child()
m = z._message_from_children()
self.assertAllClose(m[0] * np.ones(K),
random.gaussian_logpdf(xx*alpha,
x*alpha*mu,
mumu*alpha,
logalpha,
0)
* np.ones(K))
m = Mu._message_from_children()
self.assertAllClose(m[0],
1/K * (alpha*x) * np.ones(3))
self.assertAllClose(m[1],
-0.5 * 1/K * alpha * np.ones(3))
# Cluster assignments do not have as many plate axes as parameters.
M = 2
Mu = GaussianARD(2, 1,
ndim=0,
plates=(K,M))
(mu, mumu) = Mu._message_to_child()
Alpha = Gamma(3, 1,
plates=(K,M))
(alpha, logalpha) = Alpha._message_to_child()
z = Categorical(np.ones(K)/K)
X = Mixture(z, GaussianARD, Mu, Alpha, cluster_plate=-2)
tau = 4
Y = GaussianARD(X, tau)
y = 5 * np.ones(M)
Y.observe(y)
(x, xx) = X._message_to_child()
m = z._message_from_children()
self.assertAllClose(m[0]*np.ones(K),
np.sum(random.gaussian_logpdf(xx*alpha,
x*alpha*mu,
mumu*alpha,
logalpha,
0) *
np.ones((K,M)),
axis=-1))
m = Mu._message_from_children()
self.assertAllClose(m[0] * np.ones((K,M)),
1/K * (alpha*x) * np.ones((K,M)))
self.assertAllClose(m[1] * np.ones((K,M)),
-0.5 * 1/K * alpha * np.ones((K,M)))
# Mixed distribution broadcasts g
# This tests for a found bug. The bug caused an error.
Z = Categorical([0.3, 0.5, 0.2])
X = Mixture(Z, Categorical, [[0.2,0.8], [0.1,0.9], [0.3,0.7]])
m = Z._message_from_children()
pass
def _compute_bound(self, R, logdet=None, inv=None, Q=None, gradient=False, terms=False):
"""
Rotate q(X) and q(alpha).
Assume:
p(X|alpha) = prod_m N(x_m|0,diag(alpha))
p(alpha) = prod_d G(a_d,b_d)
"""
## R = self._full_rotation_matrix(R)
## if inv is not None:
## inv = self._full_rotation_matrix(inv)
#
# Transform the distributions and moments
#
plates_alpha = self.plates_alpha
plates_X = self.plates_X
# Compute rotated second moment
if self.plate_axis is not None:
# The plate axis has been moved to be the last plate axis
if Q is None:
raise ValueError("Plates should be rotated but no Q give")
# Transform covariance
sumQ = np.sum(Q, axis=0)
QCovQ = sumQ[:, None, None] ** 2 * self.CovX
# Rotate plates
if self.precompute:
QX_QX = np.einsum("...kalb,...ik,...il->...iab", self.X_X, Q, Q)
XX = QX_QX + QCovQ
XX = sum_to_plates(XX, plates_alpha[:-1], ndim=2)
Xmu = np.einsum("...kaib,...ik->...iab", self.X_mu, Q)
Xmu = sum_to_plates(Xmu, plates_alpha[:-1], ndim=2)
else:
X = self.X
mu = self.mu
QX = np.einsum("...ik,...kj->...ij", Q, X)
XX = sum_to_plates(QCovQ, plates_alpha[:-1], ndim=2) + sum_to_plates(
linalg.outer(QX, QX), plates_alpha[:-1], ndim=2, plates_from=plates_X
)
Xmu = sum_to_plates(linalg.outer(QX, self.mu), plates_alpha[:-1], ndim=2, plates_from=plates_X)
mu2 = self.mu2
D = np.shape(XX)[-1]
logdet_Q = D * np.log(np.abs(sumQ))
else:
XX = self.XX
mu2 = self.mu2
Xmu = self.Xmu
logdet_Q = 0
# Compute transformed moments
# mu2 = np.einsum('...ii->...i', mu2)
RXmu = np.einsum("...ik,...ki->...i", R, Xmu)
RXX = np.einsum("...ik,...kj->...ij", R, XX)
RXXR = np.einsum("...ik,...ik->...i", RXX, R)
# <(X-mu) * (X-mu)'>_R
XmuXmu = RXXR - 2 * RXmu + mu2
D = np.shape(R)[0]
# Compute q(alpha)
if self.update_alpha:
# Parameters
a0 = self.a0
b0 = self.b0
a = self.a
b = b0 + 0.5 * sum_to_plates(XmuXmu, plates_alpha, plates_from=None, ndim=0)
# Some expectations
alpha = a / b
logb = np.log(b)
logalpha = -logb # + const
b0_alpha = b0 * alpha
a0_logalpha = a0 * logalpha
else:
alpha = self.alpha
logalpha = 0
#
# Compute the cost
#
def sum_plates(V, *plates):
full_plates = misc.broadcasted_shape(*plates)
r = self.node_X.broadcasting_multiplier(full_plates, np.shape(V))
return r * np.sum(V)
XmuXmu_alpha = XmuXmu * alpha
if logdet is None:
logdet_R = np.linalg.slogdet(R)[1]
inv_R = np.linalg.inv(R)
else:
logdet_R = logdet
inv_R = inv
# Compute entropy H(X)
logH_X = random.gaussian_entropy(-2 * sum_plates(logdet_R + logdet_Q, plates_X), 0)
# Compute <log p(X|alpha)>
logp_X = random.gaussian_logpdf(
sum_plates(XmuXmu_alpha, plates_alpha[:-1] + [D]), 0, 0, sum_plates(logalpha, plates_X + [D]), 0
)
if self.update_alpha:
# Compute entropy H(alpha)
# This cancels out with the log(alpha) term in log(p(alpha))
logH_alpha = 0
# Compute <log p(alpha)>
logp_alpha = random.gamma_logpdf(
sum_plates(b0_alpha, plates_alpha), 0, sum_plates(a0_logalpha, plates_alpha), 0, 0
)
else:
logH_alpha = 0
logp_alpha = 0
# Compute the bound
if terms:
bound = {self.node_X: logp_X + logH_X}
if self.update_alpha:
bound.update({self.node_alpha: logp_alpha + logH_alpha})
else:
bound = 0 + logp_X + logp_alpha + logH_X + logH_alpha
if not gradient:
return bound
#
# Compute the gradient with respect R
#
broadcasting_multiplier = self.node_X.broadcasting_multiplier
def sum_plates(V, plates):
ones = np.ones(np.shape(R))
r = broadcasting_multiplier(plates, np.shape(V)[:-2])
return r * misc.sum_multiply(V, ones, axis=(-1, -2), sumaxis=False, keepdims=False)
D_XmuXmu = 2 * RXX - 2 * gaussian.transpose_covariance(Xmu)
DXmuXmu_alpha = np.einsum("...i,...ij->...ij", alpha, D_XmuXmu)
if self.update_alpha:
D_b = 0.5 * D_XmuXmu
XmuXmu_Dalpha = np.einsum(
"...i,...i,...i,...ij->...ij",
sum_to_plates(XmuXmu, plates_alpha, plates_from=None, ndim=0),
alpha,
-1 / b,
D_b,
)
D_b0_alpha = np.einsum("...i,...i,...i,...ij->...ij", b0, alpha, -1 / b, D_b)
D_logb = np.einsum("...i,...ij->...ij", 1 / b, D_b)
D_logalpha = -D_logb
D_a0_logalpha = a0 * D_logalpha
else:
XmuXmu_Dalpha = 0
D_logalpha = 0
D_XmuXmu_alpha = DXmuXmu_alpha + XmuXmu_Dalpha
D_logR = inv_R.T
# Compute dH(X)
dlogH_X = random.gaussian_entropy(-2 * sum_plates(D_logR, plates_X), 0)
# Compute d<log p(X|alpha)>
dlogp_X = random.gaussian_logpdf(
sum_plates(D_XmuXmu_alpha, plates_alpha[:-1]),
0,
0,
(sum_plates(D_logalpha, plates_X) * broadcasting_multiplier((D,), plates_alpha[-1:])),
0,
)
if self.update_alpha:
# Compute dH(alpha)
# This cancels out with the log(alpha) term in log(p(alpha))
dlogH_alpha = 0
# Compute d<log p(alpha)>
dlogp_alpha = random.gamma_logpdf(
sum_plates(D_b0_alpha, plates_alpha[:-1]), 0, sum_plates(D_a0_logalpha, plates_alpha[:-1]), 0, 0
)
else:
dlogH_alpha = 0
dlogp_alpha = 0
if terms:
raise NotImplementedError()
dR_bound = {self.node_X: dlogp_X + dlogH_X}
if self.update_alpha:
dR_bound.update({self.node_alpha: dlogp_alpha + dlogH_alpha})
else:
dR_bound = 0 * dlogp_X + dlogp_X + dlogp_alpha + dlogH_X + dlogH_alpha
if self.subset:
indices = np.ix_(self.subset, self.subset)
dR_bound = dR_bound[indices]
if self.plate_axis is None:
return (bound, dR_bound)
#
# Compute the gradient with respect to Q (if Q given)
#
# Some pre-computations
Q_RCovR = np.einsum("...ik,...kl,...il,...->...i", R, self.CovX, R, sumQ)
if self.precompute:
Xr_rX = np.einsum("...abcd,...jb,...jd->...jac", self.X_X, R, R)
QXr_rX = np.einsum("...akj,...ik->...aij", Xr_rX, Q)
RX_mu = np.einsum("...jk,...akbj->...jab", R, self.X_mu)
else:
RX = np.einsum("...ik,...k->...i", R, X)
QXR = np.einsum("...ik,...kj->...ij", Q, RX)
QXr_rX = np.einsum("...ik,...jk->...kij", QXR, RX)
RX_mu = np.einsum("...ik,...jk->...kij", RX, mu)
QXr_rX = sum_to_plates(QXr_rX, plates_alpha[:-2], ndim=3, plates_from=plates_X[:-1])
RX_mu = sum_to_plates(RX_mu, plates_alpha[:-2], ndim=3, plates_from=plates_X[:-1])
def psi(v):
"""
Compute: d/dQ 1/2*trace(diag(v)*<(X-mu)*(X-mu)>)
= Q*<X>'*R'*diag(v)*R*<X> + ones * Q diag( tr(R'*diag(v)*R*Cov) )
+ mu*diag(v)*R*<X>
"""
# Precompute all terms to plates_alpha because v has shape
# plates_alpha.
# Gradient of 0.5*v*<x>*<x>
v_QXrrX = np.einsum("...kij,...ik->...ij", QXr_rX, v)
# Gradient of 0.5*v*Cov
Q_tr_R_v_R_Cov = np.einsum("...k,...k->...", Q_RCovR, v)[..., None, :]
# Gradient of mu*v*x
mu_v_R_X = np.einsum("...ik,...kji->...ij", v, RX_mu)
return v_QXrrX + Q_tr_R_v_R_Cov - mu_v_R_X
def sum_plates(V, plates):
ones = np.ones(np.shape(Q))
r = self.node_X.broadcasting_multiplier(plates, np.shape(V)[:-2])
return r * misc.sum_multiply(V, ones, axis=(-1, -2), sumaxis=False, keepdims=False)
if self.update_alpha:
D_logb = psi(1 / b)
XX_Dalpha = -psi(alpha / b * sum_to_plates(XmuXmu, plates_alpha))
D_logalpha = -D_logb
else:
XX_Dalpha = 0
D_logalpha = 0
DXX_alpha = 2 * psi(alpha)
D_XX_alpha = DXX_alpha + XX_Dalpha
D_logdetQ = D / sumQ
N = np.shape(Q)[-1]
# Compute dH(X)
dQ_logHX = random.gaussian_entropy(-2 * sum_plates(D_logdetQ, plates_X[:-1]), 0)
# Compute d<log p(X|alpha)>
dQ_logpX = random.gaussian_logpdf(
sum_plates(D_XX_alpha, plates_alpha[:-2]),
0,
0,
(sum_plates(D_logalpha, plates_X[:-1]) * broadcasting_multiplier((N, D), plates_alpha[-2:])),
0,
)
if self.update_alpha:
D_alpha = -psi(alpha / b)
D_b0_alpha = b0 * D_alpha
D_a0_logalpha = a0 * D_logalpha
# Compute dH(alpha)
# This cancels out with the log(alpha) term in log(p(alpha))
dQ_logHalpha = 0
# Compute d<log p(alpha)>
dQ_logpalpha = random.gamma_logpdf(
sum_plates(D_b0_alpha, plates_alpha[:-2]), 0, sum_plates(D_a0_logalpha, plates_alpha[:-2]), 0, 0
)
else:
dQ_logHalpha = 0
dQ_logpalpha = 0
if terms:
raise NotImplementedError()
dQ_bound = {self.node_X: dQ_logpX + dQ_logHX}
if self.update_alpha:
dQ_bound.update({self.node_alpha: dQ_logpalpha + dQ_logHalpha})
else:
dQ_bound = 0 * dQ_logpX + dQ_logpX + dQ_logpalpha + dQ_logHX + dQ_logHalpha
return (bound, dR_bound, dQ_bound)
def _compute_bound(self, R, logdet=None, inv=None, gradient=False, terms=False):
"""
Rotate q(X) as X->RX: q(X)=N(R*mu, R*Cov*R')
Assume:
:math:`p(\mathbf{X}) = \prod^M_{m=1}
N(\mathbf{x}_m|0, \mathbf{\Lambda})`
Assume unit innovation noise covariance.
"""
# TODO/FIXME: X and alpha should NOT contain observed values!! Check
# that.
# Assume constant mean and precision matrix over plates..
if inv is None:
invR = np.linalg.inv(R)
else:
invR = inv
if logdet is None:
logdetR = np.linalg.slogdet(R)[1]
else:
logdetR = logdet
# Transform moments of X and A:
Lambda_R_X0X0 = sum_to_plates(dot(self.Lambda, R, self.X0X0), (), plates_from=self.X_node.plates, ndim=2)
R_XnXn = dot(R, self.XnXn)
RA_XpXp_A = dot(R, self.A_XpXp_A)
sumr = np.sum(R, axis=0)
R_CovA_XpXp = sumr * self.CovA_XpXp
# Compute entropy H(X)
M = self.N * np.prod(self.X_node.plates) # total number of rotated vectors
logH_X = random.gaussian_entropy(-2 * M * logdetR, 0)
# Compute <log p(X)>
yy = tracedot(R_XnXn, R.T) + tracedot(Lambda_R_X0X0, R.T)
yz = tracedot(dot(R, self.A_XpXn), R.T) + tracedot(self.Lambda_mu_X0, R.T)
zz = tracedot(RA_XpXp_A, R.T) + np.einsum("...k,...k->...", R_CovA_XpXp, sumr)
logp_X = random.gaussian_logpdf(yy, yz, zz, 0, 0)
# Compute the bound
if terms:
bound = {self.X_node: logp_X + logH_X}
else:
bound = logp_X + logH_X
if not gradient:
return bound
# Compute dH(X)
dlogH_X = random.gaussian_entropy(-2 * M * invR.T, 0)
# Compute d<log p(X)>
dyy = 2 * (R_XnXn + Lambda_R_X0X0)
dyz = dot(R, self.A_XpXn + self.A_XpXn.T) + self.Lambda_mu_X0
dzz = 2 * (RA_XpXp_A + R_CovA_XpXp[None, :])
dlogp_X = random.gaussian_logpdf(dyy, dyz, dzz, 0, 0)
if terms:
d_bound = {self.X_node: dlogp_X + dlogH_X}
else:
d_bound = +dlogp_X + dlogH_X
return (bound, d_bound)
def test_message_to_parent(self):
"""
Test the message to parents of Mixture node.
"""
K = 3
# Broadcasting the moments on the cluster axis
Mu = GaussianARD(2, 1,
ndim=0,
plates=(K,))
(mu, mumu) = Mu._message_to_child()
Alpha = Gamma(3, 1,
plates=(K,))
(alpha, logalpha) = Alpha._message_to_child()
z = Categorical(np.ones(K)/K)
X = Mixture(z, GaussianARD, Mu, Alpha)
tau = 4
Y = GaussianARD(X, tau)
y = 5
Y.observe(y)
(x, xx) = X._message_to_child()
m = z._message_from_children()
self.assertAllClose(m[0] * np.ones(K),
random.gaussian_logpdf(xx*alpha,
x*alpha*mu,
mumu*alpha,
logalpha,
0)
* np.ones(K))
m = Mu._message_from_children()
self.assertAllClose(m[0],
1/K * (alpha*x) * np.ones(3))
self.assertAllClose(m[1],
-0.5 * 1/K * alpha * np.ones(3))
# Some parameters do not have cluster plate axis
Mu = GaussianARD(2, 1,
ndim=0,
plates=(K,))
(mu, mumu) = Mu._message_to_child()
Alpha = Gamma(3, 1) # Note: no cluster plate axis!
(alpha, logalpha) = Alpha._message_to_child()
z = Categorical(np.ones(K)/K)
X = Mixture(z, GaussianARD, Mu, Alpha)
tau = 4
Y = GaussianARD(X, tau)
y = 5
Y.observe(y)
(x, xx) = X._message_to_child()
m = z._message_from_children()
self.assertAllClose(m[0] * np.ones(K),
random.gaussian_logpdf(xx*alpha,
x*alpha*mu,
mumu*alpha,
logalpha,
0)
* np.ones(K))
m = Mu._message_from_children()
self.assertAllClose(m[0],
1/K * (alpha*x) * np.ones(3))
self.assertAllClose(m[1],
-0.5 * 1/K * alpha * np.ones(3))
# Cluster assignments do not have as many plate axes as parameters.
M = 2
Mu = GaussianARD(2, 1,
ndim=0,
plates=(K,M))
(mu, mumu) = Mu._message_to_child()
Alpha = Gamma(3, 1,
plates=(K,M))
(alpha, logalpha) = Alpha._message_to_child()
z = Categorical(np.ones(K)/K)
X = Mixture(z, GaussianARD, Mu, Alpha, cluster_plate=-2)
tau = 4
Y = GaussianARD(X, tau)
y = 5 * np.ones(M)
Y.observe(y)
(x, xx) = X._message_to_child()
m = z._message_from_children()
self.assertAllClose(m[0]*np.ones(K),
np.sum(random.gaussian_logpdf(xx*alpha,
x*alpha*mu,
mumu*alpha,
logalpha,
0) *
np.ones((K,M)),
axis=-1))
m = Mu._message_from_children()
self.assertAllClose(m[0] * np.ones((K,M)),
1/K * (alpha*x) * np.ones((K,M)))
self.assertAllClose(m[1] * np.ones((K,M)),
-0.5 * 1/K * alpha * np.ones((K,M)))
# Mixed distribution broadcasts g
# This tests for a found bug. The bug caused an error.
Z = Categorical([0.3, 0.5, 0.2])
X = Mixture(Z, Categorical, [[0.2,0.8], [0.1,0.9], [0.3,0.7]])
m = Z._message_from_children()
#
# Test nested mixtures
#
t1 = [1, 1, 0, 3, 3]
t2 = [2]
p = Dirichlet([1, 1], plates=(4, 3))
X = Mixture(t1, Mixture, t2, Categorical, p)
X.observe([1, 1, 0, 0, 0])
p.update()
self.assertAllClose(
p.phi[0],
[
[[1, 1], [1, 1], [2, 1]],
[[1, 1], [1, 1], [1, 3]],
[[1, 1], [1, 1], [1, 1]],
[[1, 1], [1, 1], [3, 1]],
]
)
# Test sample plates in nested mixtures
t1 = Categorical([0.3, 0.7], plates=(5,))
t2 = [[1], [1], [0], [3], [3]]
t3 = 2
p = Dirichlet([1, 1], plates=(2, 4, 3))
X = Mixture(t1, Mixture, t2, Mixture, t3, Categorical, p)
X.observe([1, 1, 0, 0, 0])
p.update()
self.assertAllClose(
p.phi[0],
[
[
[[1, 1], [1, 1], [1.3, 1]],
[[1, 1], [1, 1], [1, 1.6]],
[[1, 1], [1, 1], [1, 1]],
[[1, 1], [1, 1], [1.6, 1]],
],
[
[[1, 1], [1, 1], [1.7, 1]],
[[1, 1], [1, 1], [1, 2.4]],
[[1, 1], [1, 1], [1, 1]],
[[1, 1], [1, 1], [2.4, 1]],
]
]
)
# Check that Gate and nested Mixture are equal
t1 = Categorical([0.3, 0.7], plates=(5,))
t2 = Categorical([0.1, 0.3, 0.6], plates=(5, 1))
p = Dirichlet([1, 2, 3, 4], plates=(2, 3))
X = Mixture(t1, Mixture, t2, Categorical, p)
X.observe([3, 3, 1, 2, 2])
t1_msg = t1._message_from_children()
t2_msg = t2._message_from_children()
p_msg = p._message_from_children()
t1 = Categorical([0.3, 0.7], plates=(5,))
t2 = Categorical([0.1, 0.3, 0.6], plates=(5, 1))
p = Dirichlet([1, 2, 3, 4], plates=(2, 3))
X = Categorical(Gate(t1, Gate(t2, p)))
X.observe([3, 3, 1, 2, 2])
t1_msg2 = t1._message_from_children()
t2_msg2 = t2._message_from_children()
p_msg2 = p._message_from_children()
self.assertAllClose(t1_msg[0], t1_msg2[0])
self.assertAllClose(t2_msg[0], t2_msg2[0])
self.assertAllClose(p_msg[0], p_msg2[0])
pass
def test_message_to_child(self):
"""
Test the updating of GaussianMarkovChain.
Check that the moments and the lower bound contribution are computed
correctly.
"""
# TODO: Add plates and missing values!
# Dimensionalities
D = 3
N = 5
(Y, X, Mu, Lambda, A, V) = self.create_model(N, D)
# Inference with arbitrary observations
y = np.random.randn(N,D)
Y.observe(y)
X.update()
(x_vb, xnxn_vb, xpxn_vb) = X.get_moments()
# Get parameter moments
(mu0, mumu0) = Mu.get_moments()
(icov0, logdet0) = Lambda.get_moments()
(a, aa) = A.get_moments()
(icov_x, logdetx) = V.get_moments()
icov_x = np.diag(icov_x)
# Prior precision
Z = np.einsum('...kij,...kk->...ij', aa, icov_x)
U_diag = [icov0+Z] + (N-2)*[icov_x+Z] + [icov_x]
U_super = (N-1) * [-np.dot(a.T, icov_x)]
U = misc.block_banded(U_diag, U_super)
# Prior mean
mu_prior = np.zeros(D*N)
mu_prior[:D] = np.dot(icov0,mu0)
# Data
Cov = np.linalg.inv(U + np.identity(D*N))
mu = np.dot(Cov, mu_prior + y.flatten())
# Moments
xx = mu[:,np.newaxis]*mu[np.newaxis,:] + Cov
mu = np.reshape(mu, (N,D))
xx = np.reshape(xx, (N,D,N,D))
# Check results
self.assertAllClose(x_vb, mu,
msg="Incorrect mean")
for n in range(N):
self.assertAllClose(xnxn_vb[n,:,:], xx[n,:,n,:],
msg="Incorrect second moment")
for n in range(N-1):
self.assertAllClose(xpxn_vb[n,:,:], xx[n,:,n+1,:],
msg="Incorrect lagged second moment")
# Compute the entropy H(X)
ldet = linalg.logdet_cov(Cov)
H = random.gaussian_entropy(-ldet, N*D)
# Compute <log p(X|...)>
xx = np.reshape(xx, (N*D, N*D))
mu = np.reshape(mu, (N*D,))
ldet = -logdet0 - np.sum(np.ones((N-1,D))*logdetx)
P = random.gaussian_logpdf(np.einsum('...ij,...ij',
xx,
U),
np.einsum('...i,...i',
mu,
mu_prior),
np.einsum('...ij,...ij',
mumu0,
icov0),
-ldet,
N*D)
# The VB bound from the net
l = X.lower_bound_contribution()
self.assertAllClose(l, H+P)
# Compute the true bound <log p(X|...)> + H(X)
#
# Simple tests
#
def check(N, D, plates=None, mu=None, Lambda=None, A=None, V=None):
if mu is None:
mu = np.random.randn(D)
if Lambda is None:
Lambda = random.covariance(D)
if A is None:
A = np.random.randn(D,D)
if V is None:
V = np.random.rand(D)
X = GaussianMarkovChain(mu,
Lambda,
A,
V,
plates=plates,
n=N)
(u0, u1, u2) = X._message_to_child()
(mu, mumu) = Gaussian._ensure_moments(mu, GaussianMoments, ndim=1).get_moments()
(Lambda, _) = Wishart._ensure_moments(Lambda, WishartMoments, ndim=1).get_moments()
(a, aa) = Gaussian._ensure_moments(A, GaussianMoments, ndim=1).get_moments()
a = a * np.ones((N-1,D,D)) # explicit broadcasting for simplicity
aa = aa * np.ones((N-1,D,D,D)) # explicit broadcasting for simplicity
(v, _) = Gamma._ensure_moments(V, GammaMoments).get_moments()
v = v * np.ones((N-1,D))
plates_C = X.plates
plates_mu = X.plates
C = np.zeros(plates_C + (N,D,N,D))
plates_mu = np.shape(mu)[:-1]
m = np.zeros(plates_mu + (N,D))
m[...,0,:] = np.einsum('...ij,...j->...i', Lambda, mu)
C[...,0,:,0,:] = Lambda + np.einsum('...dij,...d->...ij',
aa[...,0,:,:,:],
v[...,0,:])
for n in range(1,N-1):
C[...,n,:,n,:] = (np.einsum('...dij,...d->...ij',
aa[...,n,:,:,:],
v[...,n,:])
+ v[...,n,:,None] * np.identity(D))
for n in range(N-1):
C[...,n,:,n+1,:] = -np.einsum('...di,...d->...id',
a[...,n,:,:],
v[...,n,:])
C[...,n+1,:,n,:] = -np.einsum('...di,...d->...di',
a[...,n,:,:],
v[...,n,:])
C[...,-1,:,-1,:] = v[...,-1,:,None]*np.identity(D)
C = np.reshape(C, plates_C+(N*D,N*D))
Cov = np.linalg.inv(C)
Cov = np.reshape(Cov, plates_C+(N,D,N,D))
m0 = np.einsum('...minj,...nj->...mi', Cov, m)
m1 = np.zeros(plates_C+(N,D,D))
m2 = np.zeros(plates_C+(N-1,D,D))
for n in range(N):
m1[...,n,:,:] = Cov[...,n,:,n,:] + np.einsum('...i,...j->...ij',
m0[...,n,:],
m0[...,n,:])
for n in range(N-1):
m2[...,n,:,:] = Cov[...,n,:,n+1,:] + np.einsum('...i,...j->...ij',
m0[...,n,:],
m0[...,n+1,:])
self.assertAllClose(m0, u0*np.ones(np.shape(m0)))
self.assertAllClose(m1, u1*np.ones(np.shape(m1)))
self.assertAllClose(m2, u2*np.ones(np.shape(m2)))
pass
check(4,1)
check(4,3)
#
# Test mu
#
# Simple
check(4,3,
mu=Gaussian(np.random.randn(3),
random.covariance(3)))
# Plates
check(4,3,
mu=Gaussian(np.random.randn(5,6,3),
random.covariance(3),
plates=(5,6)))
# Plates with moments broadcasted over plates
check(4,3,
mu=Gaussian(np.random.randn(3),
random.covariance(3),
plates=(5,)))
check(4,3,
mu=Gaussian(np.random.randn(1,3),
random.covariance(3),
plates=(5,)))
# Plates broadcasting
check(4,3,
plates=(5,),
mu=Gaussian(np.random.randn(3),
random.covariance(3),
plates=()))
check(4,3,
plates=(5,),
mu=Gaussian(np.random.randn(1,3),
random.covariance(3),
plates=(1,)))
#
# Test Lambda
#
# Simple
check(4,3,
Lambda=Wishart(10+np.random.rand(),
random.covariance(3)))
# Plates
check(4,3,
Lambda=Wishart(10+np.random.rand(),
random.covariance(3),
plates=(5,6)))
# Plates with moments broadcasted over plates
check(4,3,
Lambda=Wishart(10+np.random.rand(),
random.covariance(3),
plates=(5,)))
check(4,3,
Lambda=Wishart(10+np.random.rand(1),
random.covariance(3),
plates=(5,)))
# Plates broadcasting
check(4,3,
plates=(5,),
Lambda=Wishart(10+np.random.rand(),
random.covariance(3),
plates=()))
check(4,3,
plates=(5,),
Lambda=Wishart(10+np.random.rand(),
random.covariance(3),
plates=(1,)))
#
# Test A
#
# Simple
check(4,3,
A=GaussianARD(np.random.randn(3,3),
np.random.rand(3,3),
shape=(3,),
plates=(3,)))
# Plates on time axis
check(5,3,
A=GaussianARD(np.random.randn(4,3,3),
np.random.rand(4,3,3),
shape=(3,),
plates=(4,3)))
# Plates on time axis with broadcasted moments
check(5,3,
A=GaussianARD(np.random.randn(1,3,3),
np.random.rand(1,3,3),
shape=(3,),
plates=(4,3)))
check(5,3,
A=GaussianARD(np.random.randn(3,3),
np.random.rand(3,3),
shape=(3,),
plates=(4,3)))
# Plates
check(4,3,
A=GaussianARD(np.random.randn(5,6,1,3,3),
np.random.rand(5,6,1,3,3),
shape=(3,),
plates=(5,6,1,3)))
# Plates with moments broadcasted over plates
check(4,3,
A=GaussianARD(np.random.randn(3,3),
np.random.rand(3,3),
shape=(3,),
plates=(5,1,3)))
check(4,3,
A=GaussianARD(np.random.randn(1,1,3,3),
np.random.rand(1,1,3,3),
shape=(3,),
plates=(5,1,3)))
# Plates broadcasting
check(4,3,
plates=(5,),
A=GaussianARD(np.random.randn(3,3),
np.random.rand(3,3),
shape=(3,),
plates=(3,)))
check(4,3,
plates=(5,),
A=GaussianARD(np.random.randn(3,3),
np.random.rand(3,3),
shape=(3,),
plates=(1,1,3)))
#
# Test v
#
# Simple
check(4,3,
V=Gamma(np.random.rand(1,3),
np.random.rand(1,3),
plates=(1,3)))
check(4,3,
V=Gamma(np.random.rand(3),
np.random.rand(3),
plates=(3,)))
# Plates
check(4,3,
V=Gamma(np.random.rand(5,6,1,3),
np.random.rand(5,6,1,3),
plates=(5,6,1,3)))
# Plates with moments broadcasted over plates
check(4,3,
V=Gamma(np.random.rand(1,3),
np.random.rand(1,3),
plates=(5,1,3)))
check(4,3,
V=Gamma(np.random.rand(1,1,3),
np.random.rand(1,1,3),
plates=(5,1,3)))
# Plates broadcasting
check(4,3,
plates=(5,),
V=Gamma(np.random.rand(1,3),
np.random.rand(1,3),
plates=(1,3)))
check(4,3,
plates=(5,),
V=Gamma(np.random.rand(1,1,3),
np.random.rand(1,1,3),
plates=(1,1,3)))
#
# Check with input signals
#
mu = 2
Lambda = 3
A = 4
B = 5
v = 6
inputs = [[-2], [3]]
X = GaussianMarkovChain([mu], [[Lambda]], [[A,B]], [v], inputs=inputs)
V = (np.array([[v*A**2, -v*A, 0],
[-v*A, v*A**2, -v*A],
[0, -v*A, 0]]) +
np.array([[Lambda, 0, 0],
[0, v, 0],
[0, 0, v]]))
m = (np.array([Lambda*mu, 0, 0]) +
np.array([0, v*B*inputs[0][0], v*B*inputs[1][0]]) -
np.array([v*A*B*inputs[0][0], v*A*B*inputs[1][0], 0]))
Cov = np.linalg.inv(V)
mean = np.dot(Cov, m)
X.update()
u = X.get_moments()
self.assertAllClose(u[0], mean[:,None])
self.assertAllClose(u[1] - u[0][...,None,:]*u[0][...,:,None],
Cov[(0,1,2),(0,1,2),None,None])
self.assertAllClose(u[2] - u[0][...,:-1,:,None]*u[0][...,1:,None,:],
Cov[(0,1),(1,2),None,None])
pass
def test_message_to_parent(self):
"""
Test the message to parents of Mixture node.
"""
K = 3
# Broadcasting the moments on the cluster axis
Mu = GaussianARD(2, 1,
ndim=0,
plates=(K,))
(mu, mumu) = Mu._message_to_child()
Alpha = Gamma(3, 1,
plates=(K,))
(alpha, logalpha) = Alpha._message_to_child()
z = Categorical(np.ones(K)/K)
X = Mixture(z, GaussianARD, Mu, Alpha)
tau = 4
Y = GaussianARD(X, tau)
y = 5
Y.observe(y)
(x, xx) = X._message_to_child()
m = X._message_to_parent(0)
self.assertAllClose(m[0],
random.gaussian_logpdf(xx*alpha,
x*alpha*mu,
mumu*alpha,
logalpha,
0))
m = X._message_to_parent(1)
self.assertAllClose(m[0],
1/K * (alpha*x) * np.ones(3))
self.assertAllClose(m[1],
-0.5 * 1/K * alpha * np.ones(3))
# Some parameters do not have cluster plate axis
Mu = GaussianARD(2, 1,
ndim=0,
plates=(K,))
(mu, mumu) = Mu._message_to_child()
Alpha = Gamma(3, 1) # Note: no cluster plate axis!
(alpha, logalpha) = Alpha._message_to_child()
z = Categorical(np.ones(K)/K)
X = Mixture(z, GaussianARD, Mu, Alpha)
tau = 4
Y = GaussianARD(X, tau)
y = 5
Y.observe(y)
(x, xx) = X._message_to_child()
m = X._message_to_parent(0)
self.assertAllClose(m[0],
random.gaussian_logpdf(xx*alpha,
x*alpha*mu,
mumu*alpha,
logalpha,
0))
m = X._message_to_parent(1)
self.assertAllClose(m[0],
1/K * (alpha*x) * np.ones(3))
self.assertAllClose(m[1],
-0.5 * 1/K * alpha * np.ones(3))
# Cluster assignments do not have as many plate axes as parameters.
M = 2
Mu = GaussianARD(2, 1,
ndim=0,
plates=(K,M))
(mu, mumu) = Mu._message_to_child()
Alpha = Gamma(3, 1,
plates=(K,M))
(alpha, logalpha) = Alpha._message_to_child()
z = Categorical(np.ones(K)/K)
X = Mixture(z, GaussianARD, Mu, Alpha, cluster_plate=-2)
tau = 4
Y = GaussianARD(X, tau)
y = 5 * np.ones(M)
Y.observe(y)
(x, xx) = X._message_to_child()
m = X._message_to_parent(0)
self.assertAllClose(m[0]*np.ones(K),
np.sum(random.gaussian_logpdf(xx*alpha,
x*alpha*mu,
mumu*alpha,
logalpha,
0) *
np.ones((K,M)),
axis=-1))
m = X._message_to_parent(1)
self.assertAllClose(m[0] * np.ones((K,M)),
1/K * (alpha*x) * np.ones((K,M)))
self.assertAllClose(m[1] * np.ones((K,M)),
-0.5 * 1/K * alpha * np.ones((K,M)))
pass
def test_message_to_parent(self):
"""
Test the message to parents of Mixture node.
"""
K = 3
# Broadcasting the moments on the cluster axis
Mu = GaussianARD(2, 1,
ndim=0,
plates=(K,))
(mu, mumu) = Mu._message_to_child()
Alpha = Gamma(3, 1,
plates=(K,))
(alpha, logalpha) = Alpha._message_to_child()
z = Categorical(np.ones(K))
X = Mixture(z, GaussianARD, Mu, Alpha)
tau = 4
Y = GaussianARD(X, tau)
y = 5
Y.observe(y)
(x, xx) = X._message_to_child()
m = X._message_to_parent(0)
self.assertAllClose(m[0],
random.gaussian_logpdf(xx*alpha,
x*alpha*mu,
mumu*alpha,
logalpha,
0))
m = X._message_to_parent(1)
self.assertAllClose(m[0],
1/K * (alpha*x) * np.ones(3))
self.assertAllClose(m[1],
-0.5 * 1/K * alpha * np.ones(3))
# Some parameters do not have cluster plate axis
Mu = GaussianARD(2, 1,
ndim=0,
plates=(K,))
(mu, mumu) = Mu._message_to_child()
Alpha = Gamma(3, 1) # Note: no cluster plate axis!
(alpha, logalpha) = Alpha._message_to_child()
z = Categorical(np.ones(K))
X = Mixture(z, GaussianARD, Mu, Alpha)
tau = 4
Y = GaussianARD(X, tau)
y = 5
Y.observe(y)
(x, xx) = X._message_to_child()
m = X._message_to_parent(0)
self.assertAllClose(m[0],
random.gaussian_logpdf(xx*alpha,
x*alpha*mu,
mumu*alpha,
logalpha,
0))
m = X._message_to_parent(1)
self.assertAllClose(m[0],
1/K * (alpha*x) * np.ones(3))
self.assertAllClose(m[1],
-0.5 * 1/K * alpha * np.ones(3))
# Cluster assignments do not have as many plate axes as parameters.
M = 2
Mu = GaussianARD(2, 1,
ndim=0,
plates=(K,M))
(mu, mumu) = Mu._message_to_child()
Alpha = Gamma(3, 1,
plates=(K,M))
(alpha, logalpha) = Alpha._message_to_child()
z = Categorical(np.ones(K))
X = Mixture(z, GaussianARD, Mu, Alpha, cluster_plate=-2)
tau = 4
Y = GaussianARD(X, tau)
y = 5 * np.ones(M)
Y.observe(y)
(x, xx) = X._message_to_child()
m = X._message_to_parent(0)
self.assertAllClose(m[0]*np.ones(K),
np.sum(random.gaussian_logpdf(xx*alpha,
x*alpha*mu,
mumu*alpha,
logalpha,
0) *
np.ones((K,M)),
axis=-1))
m = X._message_to_parent(1)
self.assertAllClose(m[0] * np.ones((K,M)),
1/K * (alpha*x) * np.ones((K,M)))
self.assertAllClose(m[1] * np.ones((K,M)),
-0.5 * 1/K * alpha * np.ones((K,M)))
pass
def test_moments(self):
"""
Test the updating of GaussianMarkovChain.
Check that the moments and the lower bound contribution are computed
correctly.
"""
# TODO: Add plates and missing values!
# Dimensionalities
D = 3
N = 5
(Y, X, Mu, Lambda, A, V) = self.create_model(N, D)
# Inference with arbitrary observations
y = np.random.randn(N,D)
Y.observe(y)
X.update()
(x_vb, xnxn_vb, xpxn_vb) = X.get_moments()
# Get parameter moments
(mu0, mumu0) = Mu.get_moments()
(icov0, logdet0) = Lambda.get_moments()
(a, aa) = A.get_moments()
(icov_x, logdetx) = V.get_moments()
icov_x = np.diag(icov_x)
# Prior precision
Z = np.einsum('...kij,...kk->...ij', aa, icov_x)
U_diag = [icov0+Z] + (N-2)*[icov_x+Z] + [icov_x]
U_super = (N-1) * [-np.dot(a.T, icov_x)]
U = utils.block_banded(U_diag, U_super)
# Prior mean
mu_prior = np.zeros(D*N)
mu_prior[:D] = np.dot(icov0,mu0)
# Data
Cov = np.linalg.inv(U + np.identity(D*N))
mu = np.dot(Cov, mu_prior + y.flatten())
# Moments
xx = mu[:,np.newaxis]*mu[np.newaxis,:] + Cov
mu = np.reshape(mu, (N,D))
xx = np.reshape(xx, (N,D,N,D))
# Check results
testing.assert_allclose(x_vb, mu,
err_msg="Incorrect mean")
for n in range(N):
testing.assert_allclose(xnxn_vb[n,:,:], xx[n,:,n,:],
err_msg="Incorrect second moment")
for n in range(N-1):
testing.assert_allclose(xpxn_vb[n,:,:], xx[n,:,n+1,:],
err_msg="Incorrect lagged second moment")
# Compute the entropy H(X)
ldet = linalg.logdet_cov(Cov)
H = random.gaussian_entropy(-ldet, N*D)
# Compute <log p(X|...)>
xx = np.reshape(xx, (N*D, N*D))
mu = np.reshape(mu, (N*D,))
ldet = -logdet0 - np.sum(np.ones((N-1,D))*logdetx)
P = random.gaussian_logpdf(np.einsum('...ij,...ij',
xx,
U),
np.einsum('...i,...i',
mu,
mu_prior),
np.einsum('...ij,...ij',
mumu0,
icov0),
-ldet,
N*D)
# The VB bound from the net
l = X.lower_bound_contribution()
testing.assert_allclose(l, H+P)