def bq_state_does_not_stop(input_dim) -> Tuple[BQState, BQIterInfo]:
"""BQ state that does not trigger stopping in all stopping criteria."""
integral_mean = 1.0
integral_mean_previous = 2 * integral_mean * (1 - _rel_tol)
nevals = _nevals - 2
bq_state = BQState(
measure=LebesgueMeasure(input_dim=input_dim, domain=(0, 1)),
kernel=ExpQuad(input_shape=(input_dim, )),
integral_belief=Normal(integral_mean, 10 * _var_tol),
previous_integral_beliefs=(Normal(integral_mean_previous, _var_tol), ),
nodes=np.ones((nevals, input_dim)),
fun_evals=np.ones(nevals),
)
info = BQIterInfo.from_bq_state(bq_state)
return bq_state, info
def car_tracking():
# Below is for consistency with pytest & unittest.
# Without a seed, unittest passes but pytest fails.
# I tried multiple seeds, they all work equally well.
np.random.seed(12345)
delta_t = 0.2
var = 0.5
dynamat = np.eye(4) + delta_t * np.diag(np.ones(2), 2)
dynadiff = (
np.diag(np.array([delta_t**3 / 3, delta_t**3 / 3, delta_t, delta_t])) +
np.diag(np.array([delta_t**2 / 2, delta_t**2 / 2]), 2) +
np.diag(np.array([delta_t**2 / 2, delta_t**2 / 2]), -2))
measmat = np.eye(2, 4)
measdiff = var * np.eye(2)
mean = np.zeros(4)
cov = 0.5 * var * np.eye(4)
dynmod = pnss.DiscreteLTIGaussian(state_trans_mat=dynamat,
shift_vec=np.zeros(4),
proc_noise_cov_mat=dynadiff)
measmod = pnss.DiscreteLTIGaussian(
state_trans_mat=measmat,
shift_vec=np.zeros(2),
proc_noise_cov_mat=measdiff,
)
initrv = Normal(mean, cov)
return dynmod, measmod, initrv, {"dt": delta_t, "tmax": 20}
def logistic_ode():
# Below is for consistency with pytest & unittest.
# Without a seed, unittest passes but pytest fails.
# I tried multiple seeds, they all work equally well.
np.random.seed(12345)
delta_t = 0.2
tmax = 2
logistic = pnd.logistic((0, tmax),
initrv=Constant(np.array([0.1])),
params=(6, 1))
dynamod = pnss.IBM(ordint=3, spatialdim=1)
measmod = pnfs.DiscreteEKFComponent.from_ode(logistic,
dynamod,
np.zeros((1, 1)),
ek0_or_ek1=1)
initmean = np.array([0.1, 0, 0.0, 0.0])
initcov = np.diag([0.0, 1.0, 1.0, 1.0])
initrv = Normal(initmean, initcov)
return dynamod, measmod, initrv, {
"dt": delta_t,
"tmax": tmax,
"ode": logistic
}
def __init__(
self,
ivp: IVP,
prior: pnss.Integrator,
measurement_model: pnss.DiscreteGaussian,
with_smoothing: bool,
init_implementation: typing.Callable[[
typing.Callable,
np.ndarray,
float,
pnss.Integrator,
Normal,
typing.Optional[typing.Callable],
], Normal, ],
initrv: typing.Optional[Normal] = None,
):
if initrv is None:
initrv = Normal(
np.zeros(prior.dimension),
np.eye(prior.dimension),
cov_cholesky=np.eye(prior.dimension),
)
self.gfilt = pnfs.Kalman(dynamics_model=prior,
measurement_model=measurement_model,
initrv=initrv)
if not isinstance(prior, pnss.Integrator):
raise ValueError(
"Please initialise a Gaussian filter with an Integrator (see `probnum.statespace`)"
)
self.sigma_squared_mle = 1.0
self.with_smoothing = with_smoothing
self.init_implementation = init_implementation
super().__init__(ivp=ivp, order=prior.ordint)
def setUp(self):
initrv = Normal(20 * np.ones(2),
0.1 * np.eye(2),
cov_cholesky=np.sqrt(0.1) * np.eye(2))
self.ivp = lotkavolterra([0.0, 0.5], initrv)
step = 0.1
f = self.ivp.rhs
t0, tmax = self.ivp.timespan
y0 = self.ivp.initrv.mean
self.solution = probsolve_ivp(f,
t0,
tmax,
y0,
step=step,
adaptive=False)
def __init__(
self,
mean: Union[float, np.floating, np.ndarray],
cov: Union[float, np.floating, np.ndarray],
dim: Optional[IntArgType] = None,
) -> None:
# Extend scalar mean and covariance to higher dimensions if dim has been
# supplied by the user
# pylint: disable=fixme
# TODO: This needs to be modified to account for cases where only either the
# mean or covariance is given in scalar form
if ((np.isscalar(mean) or mean.size == 1)
and (np.isscalar(cov) or cov.size == 1) and dim is not None):
mean = np.full((dim, ), mean)
cov = cov * np.eye(dim)
# Set dimension based on the mean vector
if np.isscalar(mean):
dim = 1
else:
dim = mean.size
# If cov has been given as a vector of variances, transform to diagonal matrix
if isinstance(cov,
np.ndarray) and np.squeeze(cov).ndim == 1 and dim > 1:
cov = np.diag(np.squeeze(cov))
# Exploit random variables to carry out mean and covariance checks
self.random_variable = Normal(mean=np.squeeze(mean),
cov=np.squeeze(cov))
self.mean = self.random_variable.mean
self.cov = self.random_variable.cov
# Set diagonal_covariance flag
if dim == 1:
self.diagonal_covariance = True
else:
self.diagonal_covariance = (
np.count_nonzero(self.cov -
np.diag(np.diagonal(self.cov))) == 0)
super().__init__(
dim=dim,
domain=(np.full((dim, ), -np.Inf), np.full((dim, ), np.Inf)),
)
def benes_daum():
"""Benes-Daum testcase, example 10.17 in Applied SDEs."""
def f(t, x):
return np.tanh(x)
def df(t, x):
return 1.0 - np.tanh(x)**2
def l(t):
return np.ones(1)
initmean = np.zeros(1)
initcov = 3.0 * np.eye(1)
initrv = Normal(initmean, initcov)
dynamod = pnss.SDE(dimension=1, driftfun=f, dispmatfun=l, jacobfun=df)
measmod = pnss.DiscreteLTIGaussian(np.eye(1), np.zeros(1), np.eye(1))
return dynamod, measmod, initrv, {}
def integrate(self, fun: Callable, measure: IntegrationMeasure,
nevals: int) -> Tuple[Normal, Dict]:
r"""Integrate the function ``fun``.
Parameters
----------
fun:
The integrand function :math:`f`.
measure :
An integration measure :math:`\mu`.
nevals :
Number of function evaluations.
Returns
-------
F :
The integral of ``fun`` against ``measure``.
info :
Information on the performance of the method.
"""
# Acquisition policy
nodes = self.policy(nevals, measure)
fun_evals = fun(nodes)
# compute integral mean and variance
# Define kernel embedding
kernel_embedding = KernelEmbedding(self.kernel, measure)
gram = self.kernel(nodes, nodes)
kernel_mean = kernel_embedding.kernel_mean(nodes)
initial_error = kernel_embedding.kernel_variance()
weights = self._solve_gram(gram, kernel_mean)
integral_mean = np.squeeze(weights.T @ fun_evals)
integral_variance = initial_error - weights.T @ kernel_mean
integral = Normal(integral_mean, integral_variance)
# Information on result
info = {"model_fit_diagnostic": None}
return integral, info
def __init__(
self,
mean: Union[float, np.floating, np.ndarray],
cov: Union[float, np.floating, np.ndarray],
input_dim: Optional[IntArgType] = None,
) -> None:
# Extend scalar mean and covariance to higher dimensions if input_dim has been
# supplied by the user
if ((np.isscalar(mean) or mean.size == 1)
and (np.isscalar(cov) or cov.size == 1)
and input_dim is not None):
mean = np.full((input_dim, ), mean)
cov = cov * np.eye(input_dim)
# Set dimension based on the mean vector
if np.isscalar(mean):
input_dim = 1
else:
input_dim = mean.size
super().__init__(
input_dim=input_dim,
domain=(np.full((input_dim, ),
-np.Inf), np.full((input_dim, ), np.Inf)),
)
# Exploit random variables to carry out mean and covariance checks
# squeezes are needed due to the way random variables are currently implemented
# pylint: disable=no-member
self.random_variable = Normal(mean=np.squeeze(mean),
cov=np.squeeze(cov))
self.mean = np.reshape(self.random_variable.mean, (self.input_dim, ))
self.cov = np.reshape(self.random_variable.cov,
(self.input_dim, self.input_dim))
# Set diagonal_covariance flag
if input_dim == 1:
self.diagonal_covariance = True
else:
self.diagonal_covariance = (
np.count_nonzero(self.cov -
np.diag(np.diagonal(self.cov))) == 0)
def test_state_from_new_data(state, request):
old_state = request.getfixturevalue(state)
new_nevals = 5
# some new data
x = np.zeros([new_nevals, old_state.input_dim])
y = np.ones(new_nevals)
integral = Normal(0, 1)
gram = np.eye(new_nevals)
kernel_means = np.ones(new_nevals)
# previously no data given
s = BQState.from_new_data(
nodes=x,
fun_evals=y,
integral_belief=integral,
prev_state=old_state,
gram=gram,
kernel_means=kernel_means,
)
# types
assert isinstance(s.kernel, Kernel)
assert isinstance(s.measure, IntegrationMeasure)
assert isinstance(s.kernel_embedding, KernelEmbedding)
assert isinstance(s.nodes, np.ndarray)
assert isinstance(s.fun_evals, np.ndarray)
assert isinstance(s.gram, np.ndarray)
assert isinstance(s.kernel_means, np.ndarray)
assert isinstance(s.integral_belief, Normal)
assert isinstance(s.previous_integral_beliefs, tuple)
# shapes
assert s.nodes.shape == (new_nevals, s.input_dim)
assert s.fun_evals.shape == (new_nevals, )
assert len(s.previous_integral_beliefs) == 1
assert s.gram.shape == (new_nevals, new_nevals)
assert s.kernel_means.shape == (new_nevals, )
# values
assert s.input_dim == s.measure.input_dim
def pendulum():
# Below is for consistency with pytest & unittest.
# Without a seed, unittest passes but pytest fails.
# I tried multiple seeds, they all work equally well.
np.random.seed(12345)
delta_t = 0.0075
var = 0.32**2
g = 9.81
def f(t, x):
x1, x2 = x
y1 = x1 + x2 * delta_t
y2 = x2 - g * np.sin(x1) * delta_t
return np.array([y1, y2])
def df(t, x):
x1, x2 = x
y1 = [1, delta_t]
y2 = [-g * np.cos(x1) * delta_t, 1]
return np.array([y1, y2])
def h(t, x):
x1, x2 = x
return np.array([np.sin(x1)])
def dh(t, x):
x1, x2 = x
return np.array([[np.cos(x1), 0.0]])
q = 1.0 * (np.diag(np.array([delta_t**3 / 3, delta_t])) +
np.diag(np.array([delta_t**2 / 2]), 1) +
np.diag(np.array([delta_t**2 / 2]), -1))
r = var * np.eye(1)
initmean = np.ones(2)
initcov = var * np.eye(2)
dynamod = pnss.DiscreteGaussian(2, 2, f, lambda t: q, df)
measmod = pnss.DiscreteGaussian(2, 1, h, lambda t: r, dh)
initrv = Normal(initmean, initcov)
return dynamod, measmod, initrv, {"dt": delta_t, "tmax": 4}
def _estimate_local_error(self, pred_rv, t_new, calibrated_proc_noise_cov,
calibrated_proc_noise_cov_cholesky, **kwargs):
"""Estimate the local errors.
This corresponds to the approach in [1], implemented such that it is compatible
with the EKF1 and UKF.
References
----------
.. [1] Schober, M., Särkkä, S. and Hennig, P..
A probabilistic model for the numerical solution of initial
value problems.
Statistics and Computing, 2019.
"""
local_pred_rv = Normal(
pred_rv.mean,
calibrated_proc_noise_cov,
cov_cholesky=calibrated_proc_noise_cov_cholesky,
)
local_meas_rv, _ = self.gfilt.measure(local_pred_rv, t_new)
error = local_meas_rv.cov.diagonal()
return np.sqrt(np.abs(error))
def ornstein_uhlenbeck():
# Below is for consistency with pytest & unittest.
# Without a seed, unittest passes but pytest fails.
# I tried multiple seeds, they all work equally well.
np.random.seed(12345)
delta_t = 0.2
lam, q, r = 0.21, 0.5, 0.1
drift = -lam * np.eye(1)
force = np.zeros(1)
disp = np.sqrt(q) * np.eye(1)
dynmod = pnss.LTISDE(
driftmat=drift,
forcevec=force,
dispmat=disp,
)
measmod = pnss.DiscreteLTIGaussian(
state_trans_mat=np.eye(1),
shift_vec=np.zeros(1),
proc_noise_cov_mat=r * np.eye(1),
)
initrv = Normal(10 * np.ones(1), np.eye(1))
return dynmod, measmod, initrv, {"dt": delta_t, "tmax": 20}
def __call__(
self,
bq_state: BQState,
new_nodes: np.ndarray,
new_fun_evals: np.ndarray,
*args,
**kwargs,
) -> Tuple[Normal, BQState]:
"""Updates integral belief and BQ state according to the new data given.
Parameters
----------
bq_state :
Current state of the Bayesian quadrature loop.
new_nodes :
*shape=(n_eval_new, input_dim)* -- New nodes that have been added.
new_fun_evals :
*shape=(n_eval_new,)* -- Function evaluations at the given node.
Returns
-------
updated_belief :
Gaussian integral belief after conditioning on the new nodes and evaluations.
updated_state :
Updated version of ``bq_state`` that contains all updated quantities.
"""
# Update nodes and function evaluations
old_nodes = bq_state.nodes
nodes = np.concatenate((bq_state.nodes, new_nodes), axis=0)
fun_evals = np.append(bq_state.fun_evals, new_fun_evals)
# kernel quantities
if old_nodes.size == 0:
gram = bq_state.kernel.matrix(new_nodes)
kernel_means = bq_state.kernel_embedding.kernel_mean(new_nodes)
else:
gram_new_new = bq_state.kernel.matrix(new_nodes)
gram_old_new = bq_state.kernel.matrix(new_nodes, old_nodes)
gram = np.hstack((
np.vstack((bq_state.gram, gram_old_new)),
np.vstack((gram_old_new.T, gram_new_new)),
))
kernel_means = np.concatenate((
bq_state.kernel_means,
bq_state.kernel_embedding.kernel_mean(new_nodes),
))
initial_integral_variance = bq_state.kernel_embedding.kernel_variance()
weights = self._solve_gram(gram, kernel_means)
# integral mean and variance
integral_mean = weights @ fun_evals
integral_variance = initial_integral_variance - weights @ kernel_means
updated_belief = Normal(integral_mean, integral_variance)
updated_state = BQState.from_new_data(
nodes=nodes,
fun_evals=fun_evals,
integral_belief=updated_belief,
prev_state=bq_state,
gram=gram,
kernel_means=kernel_means,
)
return updated_belief, updated_state
def bq_iterator(
self,
fun: Optional[Callable] = None,
nodes: Optional[np.ndarray] = None,
fun_evals: Optional[np.ndarray] = None,
integral_belief: Optional[Normal] = None,
bq_state: Optional[BQState] = None,
info: Optional[BQIterInfo] = None,
) -> Tuple[Normal, np.ndarray, np.ndarray, BQState, BQIterInfo]:
"""Generator that implements the iteration of the BQ method.
This function exposes the state of the BQ method one step at a time while
running the loop.
Parameters
----------
fun
Function to be integrated. It needs to accept a shape=(n_eval, input_dim)
``np.ndarray`` and return a shape=(n_eval,) ``np.ndarray``.
nodes
*shape=(n_eval, input_dim)* -- Optional nodes at which function evaluations
are available as ``fun_evals`` from start.
fun_evals
*shape=(n_eval,)* -- Optional function evaluations at ``nodes`` available
from the start.
integral_belief
Current belief about the integral.
bq_state
State of the Bayesian quadrature methods. Contains all necessary information
about the problem and the computation.
info
The state of the iteration.
Yields
------
new_integral_belief :
Updated belief about the integral.
new_nodes :
*shape=(n_new_eval, input_dim)* -- The new location(s) at which
``new_fun_evals`` are available found during the iteration.
new_fun_evals :
*shape=(n_new_eval,)* -- The function evaluations at the new locations
``new_nodes``.
new_bq_state :
Updated state of the Bayesian quadrature methods.
new_info :
Updated state of the iteration.
"""
# Setup BQ state
if bq_state is None:
if integral_belief is None:
# The following is valid only when the prior is zero-mean.
integral_belief = Normal(
0.0,
KernelEmbedding(self.kernel,
self.measure).kernel_variance())
bq_state = BQState(
measure=self.measure,
kernel=self.kernel,
integral_belief=integral_belief,
)
integral_belief = bq_state.integral_belief
# Setup iteration info
if info is None:
info = BQIterInfo.from_bq_state(bq_state)
if nodes is not None:
if fun_evals is None:
fun_evals = fun(nodes)
integral_belief, bq_state = self.belief_update(
bq_state=bq_state,
new_nodes=nodes,
new_fun_evals=fun_evals,
)
# make sure info get the number of initial nodes
info.nevals = fun_evals.size
# Evaluate stopping criteria for the initial belief
_has_converged = self.has_converged(bq_state=bq_state, info=info)
yield integral_belief, None, None, bq_state, info
while True:
# Have we already converged?
if _has_converged:
break
# Select new nodes via policy
new_nodes = self.policy(bq_state=bq_state)
# Evaluate the integrand at new nodes
new_fun_evals = fun(new_nodes)
integral_belief, bq_state = self.belief_update(
bq_state=bq_state,
new_nodes=new_nodes,
new_fun_evals=new_fun_evals,
)
# Update the state of the iteration
info = BQIterInfo.from_iteration(info=info,
dnevals=self.policy.batch_size)
# Evaluate stopping criteria
_has_converged = self.has_converged(bq_state=bq_state, info=info)
yield integral_belief, new_nodes, new_fun_evals, bq_state, info
def _rescale(self, rvs):
"""Rescales covariances according to estimate sigma squared value."""
rvs = [Normal(rv.mean, self.sigma_squared_mle * rv.cov) for rv in rvs]
return rvs
