def sVector_derivs(self, r, v, mu):
"""
checked
typed
"""
e = self.eVector(r, v, mu)
emag = np.linalg.norm(e)
eUnit = e / emag
n = self.nVector(r, v, mu)
nmag = np.linalg.norm(n)
nUnit = n / nmag
rootTerm = np.sqrt(1.0 - (1.0 / emag**2))
deVectordx = self.eVector_derivs(r, v, mu)
deUnitdx = np.dot(self.mathUtil.unit_vector_deriv(e), deVectordx)
dOneByemagdx = (-1.0 / emag**2) * np.dot(eUnit, deVectordx)
dnVectordx = self.nVector_derivs(r, v, mu)
dnUnitdx = np.dot(self.mathUtil.unit_vector_deriv(n), dnVectordx)
drootTermdx = 0.5 * (1.0 - emag**(-2))**(-0.5) * 2.0 * emag**(
-3) * np.dot(eUnit, deVectordx)
term1 = np.outer(eUnit, dOneByemagdx)
term2 = (1.0 / emag) * deUnitdx
term3 = np.outer(nUnit, drootTermdx)
term4 = rootTerm * dnUnitdx
dsVectordx = -term1 - term2 + term3 + term4
return dsVectordx
def pylds_E_step(lds, data):
T = data.shape[0]
mu_init, sigma_init, A, sigma_states, C, sigma_obs = lds
normalizer, smoothed_mus, smoothed_sigmas, E_xtp1_xtT = \
_E_step(mu_init, sigma_init, A, sigma_states, C, sigma_obs, data)
EyyT = data.T.dot(data)
EyxT = data.T.dot(smoothed_mus)
ExxT = smoothed_sigmas.sum(0) + smoothed_mus.T.dot(smoothed_mus)
E_xt_xtT = \
ExxT - (smoothed_sigmas[-1]
+ np.outer(smoothed_mus[-1],smoothed_mus[-1]))
E_xtp1_xtp1T = \
ExxT - (smoothed_sigmas[0]
+ np.outer(smoothed_mus[0], smoothed_mus[0]))
E_xtp1_xtT = E_xtp1_xtT.sum(0)
E_x1_x1T = smoothed_sigmas[0] + np.outer(smoothed_mus[0], smoothed_mus[0])
E_x1 = smoothed_mus[0]
E_init_stats = E_x1_x1T, E_x1, 1.
E_pairwise_stats = E_xt_xtT, E_xtp1_xtT.T, E_xtp1_xtp1T, T - 1
E_node_stats = ExxT, EyxT.T, EyyT, T
return E_init_stats, E_pairwise_stats, E_node_stats
def wishart_updates(x, mu, mu2, e_z, prior_mu, prior_inv_wishart_scale, prior_wishart_dof, kappa):
k_approx = np.shape(mu)[0]
prior_mu_tile = np.tile(prior_mu, (k_approx, 1))
cross_term1 = np.dot(mu.T, prior_mu_tile)
prior_normal_term = kappa * (np.sum(mu2, axis = 0)\
- cross_term1 - cross_term1.T \
+ k_approx * np.outer(prior_mu, prior_mu))
predictive = np.dot(e_z, mu)
outer_mu = np.array([np.outer(mu[i,:], mu[i,:]) for i in range(k_approx)])
z_sum = np.sum(e_z, axis = 0)
cross_term2 = np.dot(x.T, predictive)
data_lh_term = np.dot(x.T, x) - cross_term2 - cross_term2.T\
+ np.einsum('kij, k -> ij', outer_mu, z_sum)
inv_scale_update = prior_inv_wishart_scale + prior_normal_term + data_lh_term
scale_update = np.linalg.inv(inv_scale_update)
dof_update = prior_wishart_dof + np.shape(x)[0] + k_approx
# there's some numerical issue in which the update is not exactly symmetric
if np.any(np.abs(scale_update - scale_update.T) >= 1e-10):
print('wishart scale not symmetric?')
print(scale_update - scale_update.T)
scale_update = 0.5 * (scale_update + scale_update.T)
return scale_update, np.array([dof_update])
def eVector_derivs(self, r, v, mu):
"""
checked
"""
drdx = self.drdx(r)
dvdx = self.dvdx(v)
drvdx = np.dot(r, dvdx) + np.dot(v, drdx)
drvvdx = np.outer(v, drvdx) + np.dot(np.dot(r, v), dvdx)
rmag = np.linalg.norm(r)
drmagdr = self.mathUtil.column_vector_norm2_deriv(r)
dOneByRmagdx = (-1.0 / rmag**2) * np.dot(drmagdr, drdx)
vmag = np.linalg.norm(v)
dvmagdv = self.mathUtil.column_vector_norm2_deriv(v)
dvmag2dx = 2.0 * vmag * np.dot(dvmagdv, dvdx)
term1 = np.outer(
r, (dvmag2dx - mu * dOneByRmagdx)) + (vmag**2 - mu / rmag) * drdx
term2 = drvvdx
deVectordxUnscaled = term1 - term2
# final scaling
deVectordx = (1.0 / mu) * deVectordxUnscaled
return deVectordx
def lunch_estimator(model):
'''
Huber sandwich estimator
'''
X = model.training_data.X.copy()
Y = model.training_data.Y.copy()
N = X.shape[0]
D = model.params.get_free().shape[0]
gradTgrad = np.zeros((D,D))
grad_sum = np.zeros(D)
hess_sum = np.zeros((D,D))
w0 = model.params.get_free().copy()
for n in range(N):
model.training_data.X = X[n].reshape(1,-1)
model.training_data.Y = Y[n].reshape(1,-1)
grad_n = autograd.jacobian(model.eval_objective)(model.params.get_free())
model.params.set_free(w0)
gradTgrad += np.outer(grad_n, grad_n)
grad_sum += grad_n
hess_sum += autograd.hessian(model.eval_objective)(model.params.get_free())
model.params.set_free(w0)
est_fisher = np.linalg.inv(hess_sum / N)
est_score_score = (gradTgrad - np.outer(grad_sum, grad_sum)) / N
model.training_data.X = X
model.training_data.Y = Y
return est_fisher.dot(est_score_score).dot(est_fisher)
def plot_points(self, params, iter, gradient):
phisim = np.linspace((-math.pi) / 2., (math.pi / 2.))
thetasim = np.linspace(0, 2 * np.pi)
print params
pointscoord = np.full((3, 6), 0.0)
for i in range(6):
pointscoord[0, i] = params[i]
pointscoord[1, i] = params[i + 1]
pointscoord[2, i] = params[i + 2]
x = np.outer(np.sin(thetasim), np.cos(phisim))
y = np.outer(np.sin(thetasim), np.sin(phisim))
z = np.outer(np.cos(thetasim), np.ones_like(phisim))
fig, ax = plt.subplots(subplot_kw={'projection': '3d'})
ax.plot_wireframe(sph.radius * x,
sph.radius * y,
sph.radius * z,
color='g')
ax.scatter(pointscoord[:3, 0],
pointscoord[:3, 1],
pointscoord[:3, 2],
c='r')
ax.scatter(pointscoord[:3, 3],
pointscoord[:3, 4],
pointscoord[:3, 5],
c='r')
plt.show()
def update_hessian_inverse(self, x, obj, p, state_aux):
method = self.setting.step_method
a, Hinv = state_aux
n = x.size
s = a * p
y = obj.gradient(x + a * p) - obj.gradient(x)
if method == 'bfgs':
ssT = np.outer(s, s)
ysT = np.outer(y, s)
yTs = np.dot(y, s)
C = np.eye(n) - ysT / yTs
Hinv_new = np.dot(C.T, np.dot(Hinv, C)) + ssT / yTs
elif method == 'dfp':
Hinv_y = np.dot(Hinv, y)
y_Hinv_y = np.dot(y, Hinv_y)
ssT = np.outer(s, s)
yTs = np.dot(y, s)
Hinv_new = Hinv - np.outer(Hinv_y, Hinv_y) / y_Hinv_y + ssT / yTs
elif method == 'sr1':
Hinv_y = np.dot(Hinv, y)
s_minus_Hinv_y = s - Hinv_y
denominator = np.dot(s_minus_Hinv_y, y)
if np.abs(denominator) > self.setting.sr1_skip_tol * la.norm(
y) * la.norm(s_minus_Hinv_y):
Hinv_new = Hinv + np.outer(s_minus_Hinv_y,
s_minus_Hinv_y) / denominator
else: # skipping rule to avoid huge search directions under denominator collapse
Hinv_new = np.copy(Hinv)
else:
raise ValueError('Invalid step method!')
return Hinv_new
def rank_2_H_update(H, s, y, d):
Hy = np.matmul(H, y)
temp = np.outer(s - Hy, d)
ddT = np.outer(d, d)
dTy = np.inner(d, y)
return H + (temp + np.transpose(temp)) / dTy - np.inner(
y, s - Hy) * ddT / (dTy**2)
def dPositionVectordh(self, x, mu):
"""
derivatives of position vector wrt angular momentum vector
typed
"""
TA = x[5]
cTA = np.cos(TA)
sTA = np.sin(TA)
h = self.hVector(x)
e = self.eVector(x, mu)
hMag = self.hMag(x)
eMag = self.eMag(x, mu)
eUnit = e / eMag
crossProduct = np.cross(h, e)
crossProductMag = np.linalg.norm(crossProduct)
factor = 1.0 / (mu * (1.0 + eMag * cTA))
term1 = cTA * np.outer(eUnit, 2.0 * h)
#term2 = sTA * np.dot((1.0 / crossProductMag) * (np.identity(3) - (1.0 / crossProductMag**2) * np.outer(crossProduct, crossProduct)), -self.mathUtil.crossmat(e))
term2 = (sTA / crossProductMag) * (
2. * np.outer(crossProduct, h) + hMag**2 * np.dot(
(-np.identity(3) + (1. / crossProductMag**2) * np.outer(
crossProduct, crossProduct)), self.mathUtil.crossmat(e)))
drdh = factor * (term1 + term2)
return drdh
def dVelocityVectordh(self, x, mu):
"""
derivatives of Velocity vector wrt angular momentum vector
typed
"""
TA = x[5]
sTA = np.sin(TA)
cTA = np.cos(TA)
h = self.hVector(x)
e = self.eVector(x, mu)
eCross = self.mathUtil.crossmat(e)
hMag = np.linalg.norm(h)
eMag = np.linalg.norm(e)
eUnit = e / eMag
crossProduct = np.cross(h, e)
crossProductMag = np.linalg.norm(crossProduct)
factor1 = 1.0 / hMag**3
term1 = factor1 * (-np.outer(
sTA * eUnit - ((eMag + cTA) / crossProductMag) * crossProduct, h))
factor2 = (-(eMag + cTA)) / (hMag * crossProductMag)
term2 = factor2 * (-eCross + (1.0 / crossProductMag**2) * np.dot(
np.outer(crossProduct, crossProduct), eCross))
dvdh = -mu * (term1 + term2)
return dvdh
def dVelocityVectorde(self, x, mu):
"""
derivatives of Velocity vector wrt eccentricity vector
typed
"""
TA = x[5]
sTA = np.sin(TA)
cTA = np.cos(TA)
h = self.hVector(x)
e = self.eVector(x, mu)
hCross = self.mathUtil.crossmat(h)
hMag = np.linalg.norm(h)
eMag = np.linalg.norm(e)
crossProduct = np.cross(h, e)
crossProductMag = np.linalg.norm(crossProduct)
term1 = sTA * (1.0 / eMag) * (np.identity(3) -
(1.0 / eMag**2) * np.outer(e, e))
term21 = np.outer((1.0 / crossProductMag) * crossProduct,
(1.0 / eMag) * e)
term22 = (eMag + cTA) * (1.0 / crossProductMag) * (
hCross - (1.0 / crossProductMag**2) *
np.dot(np.outer(crossProduct, crossProduct), hCross))
term2 = -(term21 + term22)
factor = -mu / hMag
dvde = factor * (term1 + term2)
return dvde
def pylds_E_step(lds, data):
T = data.shape[0]
mu_init, sigma_init, A, sigma_states, C, sigma_obs = lds
normalizer, smoothed_mus, smoothed_sigmas, E_xtp1_xtT = \
_E_step(mu_init, sigma_init, A, sigma_states, C, sigma_obs, data)
EyyT = data.T.dot(data)
EyxT = data.T.dot(smoothed_mus)
ExxT = smoothed_sigmas.sum(0) + smoothed_mus.T.dot(smoothed_mus)
E_xt_xtT = \
ExxT - (smoothed_sigmas[-1]
+ np.outer(smoothed_mus[-1],smoothed_mus[-1]))
E_xtp1_xtp1T = \
ExxT - (smoothed_sigmas[0]
+ np.outer(smoothed_mus[0], smoothed_mus[0]))
E_xtp1_xtT = E_xtp1_xtT.sum(0)
E_x1_x1T = smoothed_sigmas[0] + np.outer(smoothed_mus[0], smoothed_mus[0])
E_x1 = smoothed_mus[0]
E_init_stats = E_x1_x1T, E_x1, 1.
E_pairwise_stats = E_xt_xtT, E_xtp1_xtT.T, E_xtp1_xtp1T, T-1
E_node_stats = ExxT, EyxT.T, EyyT, T
return E_init_stats, E_pairwise_stats, E_node_stats
def hypergeom_mat(N, n):
K = np.outer(np.ones(n + 1), np.arange(N + 1))
k = np.outer(np.arange(n + 1), np.ones(N + 1))
ret = log_binom(K, k)
ret = ret + ret[::-1, ::-1]
ret = ret - log_binom(N, n)
return np.exp(ret)
def step3(L, Sigma, mu, mun):
temp2 = np.dot(-J12.T, Sigma)
Sigma_21 = solve_posdef_from_cholesky(L, temp2)
ExnxT = Sigma_21 + np.outer(mun, mu)
ExxT = Sigma + np.outer(mu, mu)
return mu, ExxT, ExnxT
def rank_2_H_update(H,s,y,d):
Hy = np.matmul(H,y)
temp = np.outer(s-Hy,d)
ddT = np.outer(d,d)
dTy = np.inner(d,y)
if dTy**2 == 0:
raise ZeroDivisionError
return H + (temp + np.transpose(temp))/dTy - np.inner(y,s-Hy)*ddT/(dTy**2)
def costL1(K):
loss = 0.
Ker = np.dot(K, K.T)
for q in S:
i, j, k = q
Mt = (2. * np.outer(X[i], X[j]) - 2. * np.outer(X[i], X[k]) -
np.outer(X[j], X[j]) + np.outer(X[k], X[k]))
loss = loss + np.log(1. + np.exp(-np.trace(np.dot(Mt, Ker))))
# add L1 penalty
loss = loss / len(S) + lam1 * norm1(Ker.flatten())
return loss
def test_expected_multivariate_normal_logpdf_simple(D=10):
# Test single datapoint log pdf
x = npr.randn(D)
mu = npr.randn(D)
L = npr.randn(D, D)
Sigma = np.dot(L, L.T)
# Check that when the covariance is zero we get the regular mvn pdf
xxT = np.outer(x, x)
mumuT = np.outer(mu, mu)
ll1 = expected_multivariate_normal_logpdf(x, xxT, mu, mumuT, Sigma)
ll2 = multivariate_normal_logpdf(x, mu, Sigma)
assert np.allclose(ll1, ll2)
def compute_operator_from_data(self, datain, cdata, dataout):
# for i in range(len(cdata)-1):
self.counter += 1
fk = np.hstack((psix(datain), np.dot(psiu(datain), cdata)))
fkpo = np.hstack((psix(dataout), np.dot(psiu(dataout), cdata)))
self.G = self.G + (np.outer(fk, fk) - self.G) / self.counter
self.A = self.A + (np.outer(fk, fkpo) - self.A) / self.counter
# self.G = self.G + np.outer(fk, fk)
# self.A = self.A + np.outer(fk, fkpo)
self.K = np.linalg.pinv(self.G).dot(self.A)
Kcont = np.real(logm(self.K, disp=False)[0] / self.sampling_time)
self.Kx = Kcont.T[0:NUM_STATE_OBS_, 0:NUM_STATE_OBS_]
self.Ku = Kcont.T[0:NUM_STATE_OBS_, NUM_STATE_OBS_:NUM_OBS_]
def _kernel(self, sigma, X, basis):
if basis is None:
basis = X
n_x, d = X.shape
n_y, d = basis.shape
#dist = -2*np.matmul(np.multiply(X, 1./sigma),basis.T) + np.outer(np.matmul(np.square(X), (1./sigma).T), np.ones([1, n_y])) + np.outer( np.ones([n_x,1]),np.matmul(np.square(basis),(1./sigma).T))
dist = -2 * np.matmul(np.multiply(X, sigma), basis.T) + np.outer(
np.reshape(np.matmul(np.square(X), sigma.T), [-1, 1]),
np.ones([1, n_y])) + np.outer(
np.ones([n_x, 1]),
np.reshape(np.matmul(np.square(basis), sigma.T), [1, -1]))
return np.exp(-dist)
def _square_dist(self, X, basis=None):
if basis is None:
n, d = X.shape
dist = np.matmul(X, X.T)
diag_dist = np.outer(np.diagonal(dist), np.ones([1, n]))
dist = diag_dist + diag_dist.T - 2 * dist
else:
n_x, d = X.shape
n_y, d = basis.shape
dist = -2 * np.matmul(X, basis.T) + np.outer(
np.sum(np.square(X), axis=1), np.ones([1, n_y])) + np.outer(
np.ones([n_x, 1]), np.sum(np.square(basis), axis=1))
return dist
def alleged_BFGS(n, f, dfdx,x_start, TEMP_B0, BFGS_alpha):
# Initialize delta_xq and gamma
delta_xq = np.zeros((2, 1))
gamma = np.zeros((2, 1))
part1 = np.zeros((2, 2))
part2 = np.zeros((2, 2))
part3 = np.zeros((2, 2))
part4 = np.zeros((2, 2))
part5 = np.zeros((2, 2))
part6 = np.zeros((2, 1))
part7 = np.zeros((1, 1))
part8 = np.zeros((2, 2))
part9 = np.zeros((2, 2))
# Initialize xq
xq = np.empty((n + 1, 2))
xq[0] = x_start
# Initialize gradient storage
g = np.zeros((n + 1, 2))
g[0] = dfdx(xq[0])
# Initialize hessian storage
h = np.zeros((n + 1, 2, 2))
h[0] = TEMP_B0
for i in range(n):
search_dirn = np.linalg.solve(h[i], g[i])
# Compute search direction and magnitude (dx)
# with dx = -alpha * inv(h) * grad
delta_xq = -np.dot(BFGS_alpha[i], np.linalg.solve(h[i], g[i]))
# delta_xq = - np.linalg.solve(h[i], g[i])
xq[i + 1] = xq[i] + delta_xq
# Get gradient update for next step
g[i + 1] = dfdx(xq[i + 1])
# Get hessian update for next step
gamma = g[i + 1] - g[i]
part1 = np.outer(gamma, gamma)
part2 = np.outer(gamma, delta_xq)
part3 = np.dot(np.linalg.pinv(part2), part1)
part4 = np.outer(delta_xq, delta_xq)
part5 = np.dot(h[i], part4)
part6 = np.dot(part5, h[i])
part7 = np.dot(delta_xq, h[i])
part8 = np.dot(part7, delta_xq)
part9 = np.dot(part6, 1 / part8)
h[i + 1] = h[i] + part3 - part9
return xq
def dPositionVectorde(self, x, mu):
"""
derivatives of position vector wrt eccentricity vector
typed
"""
TA = x[5]
cTA = np.cos(TA)
sTA = np.sin(TA)
h = self.hVector(x)
e = self.eVector(x, mu)
hMag = self.hMag(x)
eMag = self.eMag(x, mu)
eUnit = e / eMag
crossProduct = np.cross(h, e)
crossProductMag = np.linalg.norm(crossProduct)
crossProductUnit = crossProduct / crossProductMag
factor = hMag**2 / mu
#term1_old = np.outer((-cTA / ((1.0 + eMag * cTA)**2)) * eUnit, eUnit * cTA + crossProduct / crossProductMag * sTA)
term1 = (-cTA / (1. + eMag * cTA)**2) * np.outer(
cTA * eUnit + sTA * crossProductUnit, eUnit)
factor2 = 1.0 / (1.0 + eMag * cTA)
#term2_old = factor2 * ((cTA / eMag) * (np.identity(3) - (1.0 / eMag**2) * np.outer(e, e)) + (sTA / crossProductMag) * np.dot((np.identity(3) - (1.0 / crossProductMag**2) * np.outer(crossProduct, crossProduct)), self.mathUtil.crossmat(h)))
term2 = factor2 * (
(cTA / eMag) * (np.identity(3) - (1. / eMag**2) * np.outer(e, e)) +
(sTA / crossProductMag) * np.dot(
(np.identity(3) - (1. / crossProductMag**2) * np.outer(
crossProduct, crossProduct)), self.mathUtil.crossmat(h)))
#term2 = term2_old
# print(term1_old)
# print("\n")
# print(term1)
# print("\n")
# print("\n")
# print("\n")
# print("\n")
# print(term2_old)
# print("\n")
# print(term2)
# print("\n")
# print(term3)
# print("\n")
drde = factor * (term1 + term2)
return drde
def _sample_mu_k_Sigma_k(self, k):
"""Draw posterior updates for `mu_k` and `Sigma_k`.
"""
W_k = self.W[self.Z == k]
N_k = W_k.shape[0]
if N_k > 0:
W_k_bar = W_k.mean(axis=0)
diff = W_k - W_k_bar
mu_post = (self.prior_obs * self.mu0) + (N_k * W_k_bar)
mu_post /= (N_k + self.prior_obs)
SSE = np.dot(diff.T, diff)
prior_diff = W_k_bar - self.mu0
SSE_prior = np.outer(prior_diff.T, prior_diff)
nu_post = self.nu0 + N_k
lambda_post = self.prior_obs + N_k
Psi_post = self.Psi0 + SSE
Psi_post += ((self.prior_obs * N_k) / lambda_post) * SSE_prior
self.Sigma[k] = invwishart.rvs(nu_post, Psi_post)
cov = self.Sigma[k] / lambda_post
self.mu[k] = self.rng.multivariate_normal(mu_post, cov)
else:
self.Sigma[k] = invwishart.rvs(self.nu0, self.Psi0)
cov = self.Sigma[k] / self.prior_obs
self.mu[k] = self.rng.multivariate_normal(self.mu0, cov)
def _posterior_mvn_t(self, W_k, W_star_m):
"""Calculates the multivariate-t likelihood for joining new cluster.
"""
if W_k.shape[0] > 0:
W_bar = W_k.mean(axis=0)
diff = W_k - W_bar
SSE = np.dot(diff.T, diff)
N_k = W_k.shape[0]
prior_diff = W_bar - self.mu0
SSE_prior = np.outer(prior_diff.T, prior_diff)
else:
W_bar = 0.
SSE = 0.
N_k = 0.
SSE_prior = 0.
mu_posterior = (self.prior_obs * self.mu0) + (N_k * W_bar)
mu_posterior /= (N_k + self.prior_obs)
nu_posterior = self.nu0 + N_k
lambda_posterior = self.prior_obs + N_k
psi_posterior = self.Psi0 + SSE
psi_posterior += ((self.prior_obs * N_k) /
(self.prior_obs + N_k)) * SSE_prior
psi_posterior *= (lambda_posterior +
1.) / (lambda_posterior *
(nu_posterior - self.D + 1.))
df_posterior = (nu_posterior - self.D + 1.)
return multivariate_t.logpdf(W_star_m, mu_posterior, psi_posterior,
df_posterior)
def angle_axis_rotation_matrix(angle, axis, axis_already_normalized=False):
# Gives the rotation matrix from an angle and an axis.
# An implmentation of https://en.wikipedia.org/wiki/Rotation_matrix#Rotation_matrix_from_axis_and_angle
# Inputs:
# * angle: can be one angle or a vector (1d ndarray) of angles. Given in radians.
# * axis: a 1d numpy array of length 3 (x,y,z). Represents the angle.
# * axis_already_normalized: boolean, skips normalization for speed if you flag this true.
# Outputs:
# * If angle is a scalar, returns a 3x3 rotation matrix.
# * If angle is a vector, returns a 3x3xN rotation matrix.
if not axis_already_normalized:
axis = axis / np.linalg.norm(axis)
sintheta = np.sin(angle)
costheta = np.cos(angle)
cpm = np.array(
[[0, -axis[2], axis[1]],
[axis[2], 0, -axis[0]],
[-axis[1], axis[0], 0]]
) # The cross product matrix of the rotation axis vector
outer_axis = np.outer(axis, axis)
angle = np.array(angle) # make sure angle is a ndarray
if len(angle.shape) == 0: # is a scalar
rot_matrix = costheta * np.eye(3) + sintheta * cpm + (1 - costheta) * outer_axis
return rot_matrix
else: # angle is assumed to be a 1d ndarray
rot_matrix = costheta * np.expand_dims(np.eye(3), 2) + sintheta * np.expand_dims(cpm, 2) + (
1 - costheta) * np.expand_dims(outer_axis, 2)
return rot_matrix
def prediction_grad(x, y, W, V, b, c):
"""
Function to compute gradients for 1 hidden layer neural network
"""
l1_out = np.dot(W, x) + b
l1_act = np.tanh(l1_out)
final_out = np.dot(V, l1_act) + c
ex_fv = np.exp(final_out)
ex_sum = np.sum(np.exp(final_out))
gt_calc = ex_fv / ex_sum
init_unit = np.zeros(len(c))
init_unit[y] = 1
der_l1_act = 1 - np.square(l1_act) #Check this part
dldf = -init_unit.reshape(len(c), 1) + gt_calc
dldc = dldf
dldv = np.dot(dldf, l1_act.T)
dldb = der_l1_act * (np.dot(V.T, dldf))
dldw = np.outer(dldb, x.T)
return dldw, dldv, dldb, dldc
def predict_cumulative_hazard(self, X, times=None, ancillary_X=None):
"""
Return the cumulative hazard rate of subjects in X at time points.
Parameters
----------
X: numpy array or DataFrame
a (n,d) covariate numpy array or DataFrame. If a DataFrame, columns
can be in any order. If a numpy array, columns must be in the
same order as the training data.
times: iterable, optional
an iterable of increasing times to predict the cumulative hazard at. Default
is the set of all durations (observed and unobserved). Uses a linear interpolation if
points in time are not in the index.
ancillary_X: numpy array or DataFrame, optional
a (n,d) covariate numpy array or DataFrame. If a DataFrame, columns
can be in any order. If a numpy array, columns must be in the
same order as the training data.
Returns
-------
cumulative_hazard_ : DataFrame
the cumulative hazard of individuals over the timeline
"""
times = coalesce(times, self.timeline, np.unique(self.durations))
alpha_, beta_ = self._prep_inputs_for_prediction_and_return_scores(X, ancillary_X)
return pd.DataFrame(np.log1p(np.outer(times, 1 / alpha_) ** beta_), columns=_get_index(X), index=times)
def generalized_outer_product(mat):
if len(mat.shape) == 1:
return np.outer(mat, mat)
elif len(mat.shape) == 2:
return np.einsum('ij,ik->ijk', mat, mat)
else:
raise ArithmeticError
def rfnorm2mat(normal):
""" Matrix to reflect in plane through origin, orthogonal to `normal`
Parameters
----------
normal : array-like, shape (3,)
vector normal to plane of reflection
Returns
-------
mat : array shape (3,3)
Notes
-----
http://en.wikipedia.org/wiki/Reflection_(mathematics)
The reflection of a vector `v` in a plane normal to vector `a` is:
.. math::
\\mathrm{Ref}_a(v) = v - 2\\frac{v\\cdot a}{a\\cdot a}a
The entries of the corresponding orthogonal transformation matrix
`R` are given by:
.. math::
R_{ij} = I_{ij} - 2\\frac{a_i a_j}{\|a\|^2}
where $I$ is the identity matrix.
"""
normal = np.asarray(normal, dtype=np.float)
norm2 = (normal**2).sum()
M = np.eye(3)
return M - 2.0 * np.outer(normal, normal) / norm2
def generalized_outer_product(mat):
if len(mat.shape) == 1:
return np.outer(mat, mat)
elif len(mat.shape) == 2:
return np.einsum('ij,ik->ijk', mat, mat)
else:
raise ArithmeticError
def predict_cumulative_hazard(self, X, times=None, ancillary_X=None):
"""
Return the cumulative hazard rate of subjects in X at time points.
Parameters
----------
X: numpy array or DataFrame
a (n,d) covariate numpy array or DataFrame. If a DataFrame, columns
can be in any order. If a numpy array, columns must be in the
same order as the training data.
times: iterable, optional
an iterable of increasing times to predict the cumulative hazard at. Default
is the set of all durations (observed and unobserved). Uses a linear interpolation if
points in time are not in the index.
ancillary_X: numpy array or DataFrame, optional
a (n,d) covariate numpy array or DataFrame. If a DataFrame, columns
can be in any order. If a numpy array, columns must be in the
same order as the training data.
Returns
-------
cumulative_hazard_ : DataFrame
the cumulative hazard of individuals over the timeline
"""
times = coalesce(times, self.timeline, np.unique(self.durations))
alpha_, beta_ = self._prep_inputs_for_prediction_and_return_scores(X, ancillary_X)
return pd.DataFrame(np.log1p(np.outer(times, 1 / alpha_) ** beta_), columns=_get_index(X), index=times)
def rVector_derivs(self, x):
"""
bplane R unit vector derivatives
typed
"""
s = self.sVector(x)
t = self.tVector(x)
crossProduct = np.cross(s, t)
crossProductMag = np.linalg.norm(crossProduct)
dcrossProductds, dcrossProductdt = self.mathUtil.d_crossproduct(s, t)
dsdx = self.sVector_derivs(x)
dtdx = self.tVector_derivs(x)
dRdxNotUnit = np.dot(dcrossProductds, dsdx) + np.dot(
dcrossProductdt, dtdx)
dOneByCrossProductMagdx = (-1.0 / crossProductMag**3) * np.dot(
crossProduct, dRdxNotUnit)
dRdx = (1.0 / crossProductMag) * dRdxNotUnit + np.outer(
crossProduct, dOneByCrossProductMagdx)
#term1 = (1.0 / crossProductMag) * dRdxNotUnit
#term2 = np.outer(crossProduct, dOneByCrossProductMagdx)
#print('***')
#print('dRdx')
#print('crossProduct: ', crossProduct)
#print('dRdxNotUnit column1: ', dRdxNotUnit[0:3,1])
#print(crossProduct[0]*dRdxNotUnit[0,1], crossProduct[1]*dRdxNotUnit[1,1])
#print(crossProduct[2], dOneByCrossProductMagdx[1])
#print(dRdxNotUnit[2,1], term2[2,1])
#print('***')
return dRdx
def tVector_derivs(self, x):
"""
derivatives of the T unit vector
typed
"""
# choose the reference vector here
k = self.mathUtil.k_unit()
referenceVector = k
dreferenceVectordx = np.zeros(
(3,
6)) # for k reference vector (or any constant reference vector)
s = self.sVector(x)
crossProduct = np.cross(s, referenceVector)
crossProductMag = np.linalg.norm(crossProduct)
dcrossProductds, dcrossProductdreferenceVector = self.mathUtil.d_crossproduct(
s, referenceVector)
dsdx = self.sVector_derivs(x)
dtdxNotUnit = np.dot(dcrossProductds, dsdx) + np.dot(
dcrossProductdreferenceVector, dreferenceVectordx)
dOneByCrossProductMagdx = (-1.0 / crossProductMag**3) * np.dot(
crossProduct, dtdxNotUnit)
dtdx = (1.0 / crossProductMag) * dtdxNotUnit + np.outer(
crossProduct, dOneByCrossProductMagdx)
return dtdx
def test_jacobian_higher_order():
fun = lambda x: np.sin(np.outer(x, x)) + np.cos(np.dot(x, x))
jacobian(fun)(npr.randn(3)).shape == (3, 3, 3)
jacobian(jacobian(fun))(npr.randn(3)).shape == (3, 3, 3, 3)
jacobian(jacobian(jacobian(fun)))(npr.randn(3)).shape == (3, 3, 3, 3, 3)
check_grads(lambda x: np.sum(jacobian(fun)(x)), npr.randn(3))
check_grads(lambda x: np.sum(jacobian(jacobian(fun))(x)), npr.randn(3))
def diff(r, R, u):
""" return Jacobian of exp(r_hat) * u
R = exp(r) <- caller will already have this, so pass it in """
# derivation: http://arxiv.org/abs/1312.0788
uhat = hat(u)
rnorm = np.dot(r, r)
if rnorm == 0:
return -uhat
return -np.dot(np.dot(R, uhat), (
np.outer(r, r) + np.dot(R.T - np.eye(3), hat(r)))) / rnorm
def natural_rts_backward_step(next_smooth, next_pred, filtered, pair_param):
# p = "predicted", f = "filtered", s = "smoothed", n = "next"
(Jns, hns, mun), (Jnp, hnp), (Jf, hf) = next_smooth, next_pred, filtered
J11, J12, J22, _ = pair_param
# convert from natural parameter to the usual J definitions
Jns, Jnp, Jf, J11, J12, J22 = -2*Jns, -2*Jnp, -2*Jf, -2*J11, -J12, -2*J22
J11, J12, J22 = Jf + J11, J12, Jns - Jnp + J22
L = np.linalg.cholesky(J22)
temp = solve_triangular(L, J12.T)
Js = J11 - np.dot(temp.T, temp)
hs = hf - np.dot(temp.T, solve_triangular(L, hns - hnp))
mu, sigma = info_to_mean((Js, hs))
ExnxT = -solve_posdef_from_cholesky(L, np.dot(J12.T, sigma)) + np.outer(mun, mu)
ExxT = sigma + np.outer(mu, mu)
return -1./2*Js, hs, (mu, ExxT, ExnxT)
def diff(r, R, u):
""" return Jacobian of exp(r_hat) * u
R = exp(r) <- caller will already have this, so pass it in """
# derivation: http://arxiv.org/abs/1312.0788
# THIS IS WRONG! which even a rudimentary test will prove
# for now use cv2.Rodrigues
uhat = hat(u)
rnorm = np.dot(r, r)
if rnorm == 0:
return -uhat
return -np.dot(np.dot(R, uhat), (
np.outer(r, r) + np.dot(R.T - np.eye(3), hat(r)))) / rnorm
def pylds_E_step_inhomog(lds, data):
T = data.shape[0]
mu_init, sigma_init, A, sigma_states, C, sigma_obs = lds
normalizer, smoothed_mus, smoothed_sigmas, E_xtp1_xtT = \
_E_step(mu_init, sigma_init, A, sigma_states, C, sigma_obs, data)
EyyT = np.einsum('ti,tj->tij', data, data)
EyxT = np.einsum('ti,tj->tij', data, smoothed_mus)
ExxT = smoothed_sigmas + np.einsum('ti,tj->tij', smoothed_mus, smoothed_mus)
E_xt_xtT = ExxT[:-1]
E_xtp1_xtp1T = ExxT[1:]
E_xtp1_xtT = E_xtp1_xtT
E_x1_x1T = smoothed_sigmas[0] + np.outer(smoothed_mus[0], smoothed_mus[0])
E_x1 = smoothed_mus[0]
E_init_stats = E_x1_x1T, E_x1, 1.
E_pairwise_stats = E_xt_xtT.sum(0), E_xtp1_xtT.sum(0).T, E_xtp1_xtp1T.sum(0), T-1
E_node_stats = ExxT, np.transpose(EyxT, (0, 2, 1)), EyyT, np.ones(T)
return E_init_stats, E_pairwise_stats, E_node_stats
def covgrad(x, mean, cov):
# I think once we have Cholesky we can make this nicer.
solved = np.linalg.solve(cov, x - mean)
return lower_half(np.linalg.inv(cov) - np.outer(solved, solved))
def fun( x, y): return to_scalar(np.outer(x, y)) def dfun(x, y): return to_scalar(grad(fun)(x, y))
def unit(filtered_message):
J, h = filtered_message
mu, Sigma = natural_to_mean(filtered_message)
ExxT = Sigma + np.outer(mu, mu)
return make_tuple(J, h, mu), [(mu, ExxT, 0.)]
def generalized_outer_product(x):
if np.ndim(x) == 1:
return np.outer(x, x)
return np.matmul(x, np.swapaxes(x, -1, -2))
