def mle_batch(self, data, batch, k):
"""
Calculates LID values of data w.r.t batch
Args:
data: samples to calculate LIDs of
batch: samples to calculate LIDs against
k: the number of nearest neighbors to consider
Returns: the calculated LID values
"""
k = min(k, len(data) - 1)
f = lambda v: -k / np.sum(np.log(v / v[-1]))
gamma = self.classifier.kernel.gamma
if gamma is None:
gamma = 1.0 / self.training_data_ndarray.shape[1]
if batch is None:
# K = cdist(data, data)
K = rbf_kernel(data, Y=data, gamma=gamma)
K = np.reciprocal(K)
# get the closest k neighbours
a = np.apply_along_axis(np.sort, axis=1, arr=K)[:, 1:k + 1]
else:
batch = np.asarray(batch, dtype=np.float32)
# K = cdist(data, batch)
K = rbf_kernel(data, Y=batch, gamma=gamma)
K = np.reciprocal(K)
# get the closest k neighbours
a = np.apply_along_axis(np.sort, axis=1, arr=K)[:, 0:k]
a = np.apply_along_axis(f, axis=1, arr=a)
return np.nan_to_num(a)
def mle_batch_euclidean(self, data, k):
"""
Calculates LID values of data w.r.t batch
Args:
data: samples to calculate LIDs of
batch: samples to calculate LIDs against
k: the number of nearest neighbors to consider
Returns: the calculated LID values
"""
batch = self.training_data_ndarray
f = lambda v: -k / np.sum(np.log((v / v[-1]) + 1e-9))
gamma = self.classifier.kernel.gamma
if gamma is None:
gamma = 1.0 / self.training_data_ndarray.shape[1]
K = rbf_kernel(data, Y=batch, gamma=gamma)
K = np.reciprocal(K)
# K = cdist(data, batch)
# get the closest k neighbours
if self.xc is not None and self.xc.shape[0] == 1:
# only one attack sample
sorted_distances = np.sort(K)[0, 1:1 + k]
else:
sorted_distances = np.sort(K)[0, 0:k]
a = np.apply_along_axis(f, axis=0, arr=sorted_distances)
return np.nan_to_num(a)
def objective_function_gradient(self, xc, normalization=True):
"""
Compute the loss derivative wrt the attack sample xc
The derivative is decomposed as:
dl / x = sum^n_c=1 ( dl / df_c * df_c / x )
"""
xc = xc.atleast_2d()
n_samples = xc.shape[0]
if n_samples > 1:
raise TypeError("x is not a single sample!")
# index of poisoning point within xc.
# This will be replaced by the input parameter xc
if self._idx is None:
idx = 0
else:
idx = self._idx
self._xc[idx, :] = xc
clf, tr = self._update_poisoned_clf()
y_ts = self._y_target if self._y_target is not None else self.val.Y
# computing gradient of loss(y, f(x)) w.r.t. f
_, score = clf.predict(self.val.X, return_decision_function=True)
grad = CArray.zeros((xc.size, ))
if clf.n_classes <= 2:
loss_grad = self._attacker_loss.dloss(y_ts,
CArray(score[:, 1]).ravel())
grad = self._gradient_fk_xc(self._xc[idx, :], self._yc[idx], clf,
loss_grad, tr)
else:
# compute the gradient as a sum of the gradient for each class
for c in range(clf.n_classes):
loss_grad = self._attacker_loss.dloss(y_ts, score, c=c)
grad += self._gradient_fk_xc(self._xc[idx, :], self._yc[idx],
clf, loss_grad, tr, c)
# TODO: add lid loss gradient here
a = cdist(xc.tondarray(), self.training_data_ndarray)
sort_indices = np.apply_along_axis(np.argsort, axis=1,
arr=a)[:, 0:self.lid_k]
neighbors = self.training_data_ndarray[sort_indices, :].squeeze()
# Create a function to compute the gradient
grad_lid_cost = autograd_gradient(self.lid_cost, 0)
lid_gradient = grad_lid_cost(xc.tondarray(), neighbors, self.lid_k)
grad = grad - CArray(lid_gradient.reshape(grad.shape))
if normalization:
norm = grad.norm()
return grad / norm if norm > 0 else grad
else:
return grad
def simulate(self, u, t_span, x0, t_eval=None):
"""simulate calls solve_ivp and returns a Trajectory object.
u in the returned trajectory is the underlying noiseless trajectory.
TODO: find a way to return the noisy trajectory? (get the u_noisy out of f)."""
sol = solve_ivp(lambda t, x: self.f(x, u(t)),
t_span,
x0,
t_eval=t_eval)
y = np.apply_along_axis(lambda x: self.g(x), 0, sol.y)
return Trajectory(t=sol.t,
x=sol.y,
y=y,
u=np.array([u(t) for t in sol.t]).T)
def emissionProb( self, t, forward=False, xs=None ):
if( xs is None ):
emiss = self.L[ t - 1 ]
else:
emiss = np.zeros( self.K )
for i, ( n1, n2, n3 ) in enumerate( zip( self.n1Trans, self.n2Trans, self.n3Trans ) ):
def ll( _x ):
x, x1 = np.split( _x, 2 )
return Regression.log_likelihood( ( x, x1 ), nat_params=( n1, n2, n3 ) )
emiss[ i ] = np.apply_along_axis( ll, -1, np.hstack( ( xs[ :-1, t ], xs[ 1: , t ] ) ) )
return emiss if forward == True else np.broadcast_to( emiss, ( self.K, self.K ) )
def preprocessData( self, xs, u=None, computeMarginal=True ):
xs = np.array( xs )
# Not going to use multiple measurements here
assert xs.ndim == 2
self._T = xs.shape[ 0 ]
# Compute P( x_t | x_t-1, z ) for all of the observations over each z
self.L0 = Normal.log_likelihood( xs[ 0 ], nat_params=( self.n1_0, self.n2_0 ) )
self.L = np.empty( ( self.T - 1, self.K ) )
for i, ( n1, n2, n3 ) in enumerate( zip( self.n1Trans, self.n2Trans, self.n3Trans ) ):
def ll( _x ):
x, x1 = np.split( _x, 2 )
return Regression.log_likelihood( ( x, x1 ), nat_params=( n1, n2, n3 ) )
self.L[ :, i ] = np.apply_along_axis( ll, -1, np.hstack( ( xs[ :-1 ], xs[ 1: ] ) ) )
def elbo(params, t):
mean, log_std = params[0], params[1]
samples = rs.randn(100, 1) * np.exp(log_std) + mean
L = gaussian_entropy(log_std) + np.mean(logpx(samples))
return -L
fig = plt.figure(figsize=(22, 8))
ax1 = fig.add_subplot(1, 2, 1)
ax2 = fig.add_subplot(1, 2, 2, projection='3d')
x = np.linspace(-2, 6, 20)
y = np.linspace(-10, 1.5, 20)
X, Y = np.meshgrid(x, y)
A = np.concatenate([np.atleast_2d(X.ravel()), np.atleast_2d(Y.ravel())]).T
zs = np.apply_along_axis(lambda x: elbo(x, 0), 1, A)
Z = zs.reshape(X.shape)
def callback(params, t, g):
print("Iteration {0:} " \
"lower bound {1:.4f}; " \
"mean {2:.4f} [{3:.4f}]; " \
"variance {4:.4f}[{5:.4f}]".format(
t,
-elbo(params, t),
params[0],
true_mean,
np.exp(params[1]) ,
true_std))
ax1.clear()
def vectorize_if_needed(f, a, axis=-1):
if a.ndim > 1:
return np.apply_along_axis(f, axis, a)
else:
return f(a)
def sampleEmissions(self, x):
# Sample from P( y | x, ϴ )
assert x.ndim == 1
return np.apply_along_axis(self.sampleSingleEmission, -1,
x.reshape((-1, 1))).ravel()[None]
def sampleEmissions( self, x ):
# Sample from P( y | x, ϴ )
assert x.ndim == 2
return np.apply_along_axis( self.sampleSingleEmission, -1, x )[ None ]
def cost(pts, globalPts, startIdx, distObs, delta_t):
# Endpoint cost
posDiff = bspline(0, extractPts(pts,
startIdx + 5)) - globalPts[startIdx + 5]
velDiff = bsplineVel(0, extractPts(pts, startIdx + 5),
delta_t) - bsplineVel(
0, extractPts(globalPts, startIdx + 5), delta_t)
E_ep = lambda_p * np.dot(posDiff, posDiff) + lambda_v * np.dot(
velDiff, velDiff)
# Collision cost
u = np.linspace(0, 1, 5)
samples = np.vstack((np.repeat(np.arange(6), len(u)), np.tile(u, 6)))
def computeDist(sample):
p = bspline(sample[1], extractPts(pts, sample[0] + startIdx))
return distObs[np.clip(np.int(p[0]), 0, distObs.shape[0] - 1),
np.clip(np.int(p[1]), 0, distObs.shape[1] - 1)]
distances = np.apply_along_axis(computeDist, 0, samples)
mask = distances <= OBSTACLE_DISTANCE_THRESHOLD
distances[mask] = np.square(distances[mask] - OBSTACLE_DISTANCE_THRESHOLD
) / (2 * OBSTACLE_DISTANCE_THRESHOLD)
distances[np.invert(mask)] = 0
def computeVelocities(sample):
p = bsplineVel(sample[1], extractPts(pts, sample[0] + startIdx),
delta_t)
return norm(p)
velocities = np.apply_along_axis(computeVelocities, 0, samples)
E_c = lambda_c * np.sum(np.dot(distances, velocities)) / (len(u) * 6)
# Squared derivative cost
q2, q3, q4 = Q_2(delta_t), Q_3(delta_t), Q_4(delta_t)
E_q = 0
for i in range(6):
A = np.dot(M_6, extractPts(pts, startIdx + i))
B = A.T
E_q = E_q + np.sum(lambda_q2 * np.dot(np.dot(B, q2), A) +
lambda_q3 * np.dot(np.dot(B, q3), A) +
lambda_q4 * np.dot(np.dot(B, q4), A))
# Derivative limit cost
max_vel, max_acc, max_jerk, max_snap = np.array([1000, 1000]), np.array(
[1000, 1000]), np.array([1e10, 1e10]), np.array([1e10, 1e10])
u = np.linspace(0, 1, 5)
samples = np.vstack((np.repeat(np.arange(6), len(u)), np.tile(u, 6)))
def derivativeCost(pFunc, max_p, delta_t):
def f(sample):
p = pFunc(sample[1], extractPts(pts, sample[0] + startIdx),
delta_t)
norm_max = norm(max_p)
norm_p = norm(p)
return np.exp(norm_p - norm_max) - 1 if norm_p > norm_max else 0
return f
E_l = 0
for sample in zip(samples[0], samples[1]):
E_l = E_l + derivativeCost(bsplineVel, max_vel, delta_t)(sample)
E_l = E_l + derivativeCost(bsplineAcc, max_acc, delta_t)(sample)
E_l = E_l + derivativeCost(bsplineJerk, max_jerk, delta_t)(sample)
E_l = E_l + derivativeCost(bsplineSnap, max_snap, delta_t)(sample)
E_l = E_l / (len(u) * 6)
# Total cost
E = E_ep + E_c + E_q + E_l
# if not isinstance(E_ep, autograd.numpy.numpy_boxes.ArrayBox):
# print('[{}] {} | {} | {} | {} => {}'.format(startIdx, E_ep, E_c, E_q, E_l, E))
return E
def synthesize(self, alpha):
alpha = np.array(alpha, ndmin=2)
airfoils = np.apply_along_axis(
lambda x: synthesize_ffd(x, self.airfoil0, self.m, self.n, self.Px
), 1, alpha)
return np.squeeze(airfoils)
def __call__(self, x):
x = np.array(x, ndmin=2)
y = np.apply_along_axis(
lambda x: evaluate(self.synthesize(x), self.config_fname), 1, x)
self.y = np.squeeze(y)
return self.y