def check_filters(A, B, C, D, mu_init, sigma_init, data):
def info_normalizer(J,h):
out = 0.
out += 1/2. * h.dot(np.linalg.solve(J,h))
out -= 1/2. * np.linalg.slogdet(J)[1]
out += h.shape[0]/2. * np.log(2*np.pi)
return out
ll, filtered_mus, filtered_sigmas = kalman_filter(
mu_init, sigma_init, A, B.dot(B.T), C, D.dot(D.T), data)
py_partial_ll = info_normalizer(*dense_infoparams(
A, B, C, D, mu_init, sigma_init, data))
partial_ll, filtered_Js, filtered_hs = kalman_info_filter(
*info_params(A, B, C, D, mu_init, sigma_init, data))
ll2 = partial_ll + extra_loglike_terms(
A, B, C, D, mu_init, sigma_init, data)
filtered_mus2 = [np.linalg.solve(J,h) for J, h in zip(filtered_Js, filtered_hs)]
filtered_sigmas2 = [np.linalg.inv(J) for J in filtered_Js]
assert all(np.allclose(mu1, mu2)
for mu1, mu2 in zip(filtered_mus, filtered_mus2))
assert all(np.allclose(s1, s2)
for s1, s2 in zip(filtered_sigmas, filtered_sigmas2))
assert np.isclose(partial_ll, py_partial_ll)
assert np.isclose(ll, ll2)
def log_likelihood(self, conditional_mean, conditional_cov):
assert isinstance(self.model.emission_distn, PGMultinomialRegression)
assert conditional_mean.shape == (self.T, self.p)
assert conditional_cov.shape == (self.T, self.p, self.p)
normalizer, _, _ = kalman_filter(
self.mu_init, self.sigma_init,
self.A, self.sigma_states,
self.C, conditional_cov, conditional_mean)
return normalizer
def test_lds_log_probability_perf(T=1000, D=10, N_iter=10):
"""
Compare performance of banded method vs message passing in pylds.
"""
print("Comparing methods for T={} D={}".format(T, D))
from pylds.lds_messages_interface import kalman_info_filter, kalman_filter
# Convert LDS parameters into info form for pylds
As, bs, Qi_sqrts, ms, Ri_sqrts = make_lds_parameters(T, D)
Qis = np.matmul(Qi_sqrts, np.swapaxes(Qi_sqrts, -1, -2))
Ris = np.matmul(Ri_sqrts, np.swapaxes(Ri_sqrts, -1, -2))
x = npr.randn(T, D)
print("Timing banded method")
start = time.time()
for itr in range(N_iter):
lds_log_probability(x, As, bs, Qi_sqrts, ms, Ri_sqrts)
stop = time.time()
print("Time per iter: {:.4f}".format((stop - start) / N_iter))
# Compare to Kalman Filter
mu_init = np.zeros(D)
sigma_init = np.eye(D)
Bs = np.ones((D, 1))
sigma_states = np.linalg.inv(Qis)
Cs = np.eye(D)
Ds = np.zeros((D, 1))
sigma_obs = np.linalg.inv(Ris)
inputs = bs
data = ms
print("Timing PyLDS message passing (kalman_filter)")
start = time.time()
for itr in range(N_iter):
kalman_filter(mu_init, sigma_init,
np.concatenate([As, np.eye(D)[None, :, :]]), Bs,
np.concatenate([sigma_states,
np.eye(D)[None, :, :]]), Cs, Ds,
sigma_obs, inputs, data)
stop = time.time()
print("Time per iter: {:.4f}".format((stop - start) / N_iter))
# Info form comparison
J_init = np.zeros((D, D))
h_init = np.zeros(D)
log_Z_init = 0
J_diag, J_lower_diag, h = convert_lds_to_block_tridiag(
As, bs, Qi_sqrts, ms, Ri_sqrts)
J_pair_21 = J_lower_diag
J_pair_22 = J_diag[1:]
J_pair_11 = J_diag[:-1]
J_pair_11[1:] = 0
h_pair_2 = h[1:]
h_pair_1 = h[:-1]
h_pair_1[1:] = 0
log_Z_pair = 0
J_node = np.zeros((T, D, D))
h_node = np.zeros((T, D))
log_Z_node = 0
print("Timing PyLDS message passing (kalman_info_filter)")
start = time.time()
for itr in range(N_iter):
kalman_info_filter(J_init, h_init, log_Z_init, J_pair_11, J_pair_21,
J_pair_22, h_pair_1, h_pair_2, log_Z_pair, J_node,
h_node, log_Z_node)
stop = time.time()
print("Time per iter: {:.4f}".format((stop - start) / N_iter))
