def __init__(self,
input_dim,
feature_dim=None,
mean_fn=None,
embed_fn=None):
super(DMEGP, self).__init__()
# store params
self.input_dim = input_dim
self.feature_dim = feature_dim
# define mean function and embedding function
self.mean_fn = mean_fn
self.embed_fn = embed_fn
# define kernel function
if embed_fn == None:
feature_dim = input_dim
kernel = RBF(feature_dim, lengthscale=torch.ones(feature_dim))
else:
kernel = RBF(feature_dim, lengthscale=torch.ones(feature_dim))
kernel = Warping(kernel, iwarping_fn=self.embed_fn)
if mean_fn != None:
self.mean_fn = Warping_mean(self.mean_fn, self.embed_fn)
# define gaussian process regression model
self.gp_model = GPRegression(
X=torch.ones(1, feature_dim), # dummy
y=None,
kernel=kernel,
mean_function=self.mean_fn)
def __init__(self, X_curr, u_curr, X_next, option='GP', inducing_size=100, name='GP_DYNAMICS'):
"""
:param X_curr: 2 dim tensor array, state at the current time stamp, H by n
:param u_curr: 2 dim tensor array, control signal at the current time stamp, H by m
:param X_next: 2 dim tensor array, state at the next time stamp, H by n
:param option: use full GP or sparse GP
:param inducing_size: the number of inducing points if using sparse GP
:param name:
"""
super(GP_DYNAMICS).__init__(name)
if option not in ['SSGP', 'GP']:
raise ValueError('undefined regression option for gp model!')
assert(X_curr.dim() == 2 and u_curr.dim() == 2
and X_next.dim() == 2), "all data inputs can only have 2 dimensions! X_curr: {}, u_curr: {}, X_next: {}".format(X_curr.dim(), u_curr.dim(), X_next.dim())
assert(X_curr.size()[1] == u_curr.size()[1] and u_curr.size()[1] == X_next.size()[1]), "all data inputs need to have the same length! X_curr: {}, " \
"u_curr: {}, X_next: {}".format(X_curr.size(), u_curr.size(), X_next.size())
self.X_hat = torch.cat((X_curr, u_curr))
self.dX = X_next - X_curr
self.GP_dyn = []
if option == 'SSGP':
for i in range(self.dX.size()[1]):
kernel = RBF(input_dim=self.X_hat.size()[1], lengthscale=torch.ones(self.X_hat.size()[1]) * 10., variance=torch.tensor(5.0),name="GPs_dim" + str(i) + "_RBF")
range_lis = range(0, self.X_hat.size()[0])
random.shuffle(range_lis)
Xu = self.X_hat[range_lis[0:inducing_size], :]
# need to set the name for different model, otherwise pyro will clear the parameter storage
ssgpmodel = SparseGPRegression(self.X_hat, self.dX[:, i], kernel, Xu, name="SSGPs_model_dim" + str(i), jitter=1e-5)
self.GP_dyn.append(ssgpmodel)
else:
for i in range(self.dX.size()[1]):
kernel = RBF(input_dim=self.X_hat.size()[1], lengthscale=torch.ones(self.X_hat.size()[1]) * 10., variance=torch.tensor(5.0), name="GPs_dim" + str(i) + "_RBF")
gpmodel = GPRegression(self.X_hat, self.dX[:, i], kernel, name="GPs_model_dim" + str(i), jitter=1e-5)
self.GP_dyn.append(gpmodel)
self.option = option
print("for the dynamics model, input dim {} and output dim {}".format(self.X_hat.size()[1], self.dX.size()[1]))
self.Kff_inv = torch.zeros((self.dX.size()[1], self.X_hat.size()[0], self.X_hat.size()[0]))
self.K_var = torch.zeros(self.dX.size()[1], 1)
self.Beta = torch.zeros((self.dX.size()[1], self.X_hat.size()[0]))
self.lengthscale = torch.zeros((self.dX.size()[1], self.X_hat.size()[1]))
self.noise = torch.zeros((self.dX.size()[1], 1))
if self.option == 'SSGP':
self.Xu = torch.zeros((self.dX.size()[1], inducing_size))
def test_inference_deepGP():
gp1 = GPRegression(
X, None,
RBF(input_dim=3,
variance=torch.tensor(3.),
lengthscale=torch.tensor(2.)))
Z, _ = gp1.model()
gp2 = VariationalSparseGP(Z, y2D, Matern32(input_dim=3), Z.clone(),
Gaussian(torch.tensor(1e-6)))
class DeepGP(torch.nn.Module):
def __init__(self, gp1, gp2):
super(DeepGP, self).__init__()
self.gp1 = gp1
self.gp2 = gp2
def model(self):
Z, _ = self.gp1.model()
self.gp2.set_data(Z, y2D)
self.gp2.model()
def guide(self):
self.gp1.guide()
self.gp2.guide()
deepgp = DeepGP(gp1, gp2)
train(deepgp, num_steps=1)
def define_new_GP(self):
# define kernel function
if self.embed_fn == None:
feature_dim = self.input_dim
kernel = RBF(feature_dim, lengthscale=torch.ones(feature_dim))
else:
feature_dim = self.feature_dim
embed_fn = copy.deepcopy(self.embed_fn)
kernel = RBF(feature_dim, lengthscale=torch.ones(feature_dim))
kernel = Warping(kernel, iwarping_fn=embed_fn)
if self.mean_fn != None:
mean_fn = copy.deepcopy(self.mean_fn)
# define gaussian process regression model
gp_model = GPRegression(
X=torch.ones(1, feature_dim), # dummy
y=None,
kernel=kernel,
mean_function=mean_fn)
return gp_model
def test_inference(model_class, X, y, kernel, likelihood):
# skip variational GP models because variance/lengthscale highly
# depend on variational parameters
if model_class is VariationalGP or model_class is VariationalSparseGP:
return
elif model_class is GPRegression:
gp = model_class(X, y, RBF(input_dim=3), likelihood)
else: # model_class is SparseGPRegression
gp = model_class(X, y, RBF(input_dim=3), X, likelihood)
# fix inducing points because variance/lengthscale highly depend on it
gp.Xu.requires_grad_(False)
generator = dist.MultivariateNormal(torch.zeros(X.shape[0]), kernel(X))
target_y = generator(sample_shape=torch.Size([1000])).detach()
gp.set_data(X, target_y)
train(gp)
y_cov = gp.kernel(X)
target_y_cov = kernel(X)
assert_equal(y_cov, target_y_cov, prec=0.1)
def test_inference_whiten_vsgp():
N = 1000
X = dist.Uniform(torch.zeros(N), torch.ones(N)*5).sample()
y = 0.5 * torch.sin(3*X) + dist.Normal(torch.zeros(N), torch.ones(N)*0.5).sample()
kernel = RBF(input_dim=1)
Xu = torch.arange(0., 5.5, 0.5)
vsgp = VariationalSparseGP(X, y, kernel, Xu, Gaussian(), whiten=True)
train(vsgp)
Xnew = torch.arange(0., 5.05, 0.05)
loc, var = vsgp(Xnew, full_cov=False)
target = 0.5 * torch.sin(3*Xnew)
assert_equal((loc - target).abs().mean().item(), 0, prec=0.07)
def test_inference_sgpr():
N = 1000
X = dist.Uniform(torch.zeros(N), torch.ones(N)*5).sample()
y = 0.5 * torch.sin(3*X) + dist.Normal(torch.zeros(N), torch.ones(N)*0.5).sample()
kernel = RBF(input_dim=1)
Xu = torch.arange(0., 5.5, 0.5)
sgpr = SparseGPRegression(X, y, kernel, Xu)
train(sgpr)
Xnew = torch.arange(0., 5.05, 0.05)
loc, var = sgpr(Xnew, full_cov=False)
target = 0.5 * torch.sin(3*Xnew)
assert_equal((loc - target).abs().mean().item(), 0, prec=0.07)
def test_inference_vsgp():
N = 1000
X = dist.Uniform(torch.zeros(N), torch.ones(N) * 5).sample()
y = 0.5 * torch.sin(3 * X) + dist.Normal(torch.zeros(N),
torch.ones(N) * 0.5).sample()
kernel = RBF(input_dim=1)
Xu = torch.arange(0, 5.5, 0.5)
vsgp = VariationalSparseGP(X, y, kernel, Xu, Gaussian())
vsgp.optimize(optim.Adam({"lr": 0.03}), num_steps=1000)
Xnew = torch.arange(0, 5.05, 0.05)
loc, var = vsgp(Xnew, full_cov=False)
target = 0.5 * torch.sin(3 * Xnew)
assert_equal((loc - target).abs().mean().item(), 0, prec=0.06)
def _kernel():
return RBF(input_dim=3,
variance=torch.tensor(3.),
lengthscale=torch.tensor(2.))
K_sum=27),
T(Cosine(3, variance, lengthscale), X=X, Z=Z, K_sum=-0.193233),
T(Linear(3, variance), X=X, Z=Z, K_sum=291),
T(Exponential(3, variance, lengthscale), X=X, Z=Z, K_sum=2.685679),
T(Matern32(3, variance, lengthscale), X=X, Z=Z, K_sum=3.229314),
T(Matern52(3, variance, lengthscale), X=X, Z=Z, K_sum=3.391847),
T(Periodic(3, variance, lengthscale, period=torch.ones(1)),
X=X,
Z=Z,
K_sum=18),
T(Polynomial(3, variance, degree=2), X=X, Z=Z, K_sum=7017),
T(RationalQuadratic(3, variance, lengthscale, scale_mixture=torch.ones(1)),
X=X,
Z=Z,
K_sum=5.684670),
T(RBF(3, variance, lengthscale), X=X, Z=Z, K_sum=3.681117),
T(WhiteNoise(3, variance, lengthscale), X=X, Z=Z, K_sum=0),
T(WhiteNoise(3, variance, lengthscale), X=X, Z=None, K_sum=6),
T(
Coregionalize(3, components=torch.eye(3, 3)),
X=torch.tensor([[1., 0., 0.], [0.5, 0., 0.5]]),
Z=torch.tensor([[1., 0., 0.], [0., 1., 0.]]),
K_sum=2.25,
),
T(
Coregionalize(3, rank=2),
X=torch.tensor([[1., 0., 0.], [0.5, 0., 0.5]]),
Z=torch.tensor([[1., 0., 0.], [0., 1., 0.]]),
K_sum=None, # kernel is randomly initialized
),
T(
from collections import namedtuple
import pytest
import torch
from pyro.contrib.gp.kernels import RBF
from pyro.contrib.gp.likelihoods import Binary, MultiClass, Poisson
from pyro.contrib.gp.models import VariationalGP, VariationalSparseGP
T = namedtuple("TestGPLikelihood",
["model_class", "X", "y", "kernel", "likelihood"])
X = torch.tensor([[1.0, 5.0, 3.0], [4.0, 3.0, 7.0], [3.0, 4.0, 6.0]])
kernel = RBF(input_dim=3,
variance=torch.tensor(1.),
lengthscale=torch.tensor(3.))
noise = torch.tensor(1e-6)
y_binary1D = torch.tensor([0.0, 1.0, 0.0])
y_binary2D = torch.tensor([[0.0, 1.0, 1.0], [1.0, 0.0, 1.0]])
binary_likelihood = Binary()
y_count1D = torch.tensor([0.0, 1.0, 4.0])
y_count2D = torch.tensor([[5.0, 9.0, 3.0], [4.0, 0.0, 1.0]])
poisson_likelihood = Poisson()
y_multiclass1D = torch.tensor([2.0, 0.0, 1.0])
y_multiclass2D = torch.tensor([[2.0, 1.0, 1.0], [0.0, 2.0, 1.0]])
multiclass_likelihood = MultiClass(num_classes=3)
TEST_CASES = [
T(VariationalGP, X, y_binary1D, kernel, binary_likelihood),
T(VariationalGP, X, y_binary2D, kernel, binary_likelihood),
def __init__(self, X_s, y_s, X_o, y_o, option='GP', inducing_size=100, name='GP_ADF_RTSS'):
"""
:param X_s: training inputs for the state transition model N by D tensor
:param y_s: training outputs for the state transition model N by E tensor
:param X_o: training inputs for the observation model N by E tensor
:param y_o: training outputs for the observation model N by F tensor
:param state_dim: dimension for the state, D
:param observation_dim: dimension for the output, E
:param transition_kernel: kernel function for the
:param observation_kernel:
:param options:
"""
super(GP_ADF_RTSS, self).__init__(name)
if option not in ['SSGP', 'GP']:
raise ValueError('undefined regression option for gp model!')
assert(X_s.dim() == 2 and y_s.dim() == 2
and X_o.dim() == 2 and y_o.dim() == 2), "all data inputs can only have 2 dimensions"
# # use RBF kernel for state transition model and observation model
# self.state_transition_kernel = RBF(input_dim=state_dim, lengthscale=torch.ones(state_dim) * 0.1)
# self.observation_kernel = RBF(input_dim=observation_dim, lengthscale=torch.ones(observation_dim) * 0.1)
self.X_s = X_s
self.y_s = y_s
self.X_o = X_o
self.y_o = y_o
# print(X_s.dtype)
# print(y_s.dtype)
# print(X_o.dtype)
# print(y_o.dtype)
# choose the model type and initialize based on the option
self.state_transition_model_list = []
self.observation_model_list = []
if option == 'SSGP':
for i in range(self.y_s.size()[1]):
kernel = RBF(input_dim=self.X_s.size()[1], lengthscale=torch.ones(self.X_s.size()[1]) * 10., variance=torch.tensor(5.0),name="GPs_dim" + str(i) + "_RBF")
range_lis = range(0, X_s.size()[0])
random.shuffle(range_lis)
Xu = X_s[range_lis[0:inducing_size], :]
# need to set the name for different model, otherwise pyro will clear the parameter storage
ssgpmodel = SparseGPRegression(X_s, y_s[:, i], kernel, Xu, name="SSGPs_model_dim" + str(i), jitter=1e-5)
self.state_transition_model_list.append(ssgpmodel)
for i in range(self.y_o.size()[1]):
kernel = RBF(input_dim=self.X_o.size()[1], lengthscale=torch.ones(self.X_o.size()[1]) * 10, variance=torch.tensor(5.0), name="GPo_dim" + str(i) + "_RBF")
range_lis = range(0, y_o.size()[0])
random.shuffle(range_lis)
Xu = X_o[range_lis[0:inducing_size], :]
ssgpmodel = SparseGPRegression(X_o, y_o[:, i], kernel, Xu, name="SSGPo_model_dim" + str(i), noise=torch.tensor(2.))
self.state_transition_model_list.append(ssgpmodel)
else:
for i in range(self.y_s.size()[1]):
kernel = RBF(input_dim=self.X_s.size()[1], lengthscale=torch.ones(self.X_s.size()[1]) * 10., variance=torch.tensor(5.0), name="GPs_dim" + str(i) + "_RBF")
gpmodel = GPRegression(X_s, y_s[:, i], kernel, name="GPs_model_dim" + str(i), jitter=1e-5)
self.state_transition_model_list.append(gpmodel)
for i in range(self.y_o.size()[1]):
kernel = RBF(input_dim=self.X_o.size()[1], lengthscale=torch.ones(self.X_o.size()[1]) * 10., variance=torch.tensor(5.0), name="GPo_dim" + str(i) + "_RBF")
gpmodel = GPRegression(X_o, y_o[:, i], kernel, name="GPo_model_dim"+ str(i), noise=torch.tensor(2.))
self.observation_model_list.append(gpmodel)
self.option = option
#
# if model_file:
# self.load_model(model_file)
self.mu_s_curr = torch.zeros(y_s.size()[1])
self.sigma_s_curr = torch.eye(y_s.size()[1])
self.mu_o_curr = torch.zeros(y_o.size()[1])
self.sigma_o_curr = torch.eye(y_s.size()[1])
self.mu_hat_s_curr = torch.zeros(y_s.size()[1])
self.sigma_hat_s_curr = torch.eye(y_s.size()[1])
self.mu_hat_s_prev = torch.zeros(y_s.size()[1])
self.sigma_hat_s_prev = torch.eye(y_s.size()[1])
# For backwards smoothing
self.mu_hat_s_curr_lis = []
self.sigma_hat_s_curr_lis = []
self.mu_s_curr_lis = []
self.sigma_s_curr_lis = []
self.sigma_Xpf_Xcd_lis = []
self.Kff_s_inv = torch.zeros((y_s.size()[1], X_s.size()[0], X_s.size()[0]))
self.Kff_o_inv = torch.zeros((y_o.size()[1], X_o.size()[0], X_o.size()[0]))
self.K_s_var = torch.zeros(y_s.size()[1], 1)
self.K_o_var = torch.zeros(y_o.size()[1], 1)
self.Beta_s = torch.zeros((y_s.size()[1], X_s.size()[0]))
self.Beta_o = torch.zeros((y_o.size()[1], X_o.size()[0]))
self.lengthscale_s = torch.zeros((y_s.size()[1], X_s.size()[1]))
self.lengthscale_o = torch.zeros((y_o.size()[1], X_o.size()[1]))
self.noise_s = torch.zeros((y_s.size()[1], 1))
self.noise_o = torch.zeros((y_o.size()[1], 1))
if self.option == 'SSGP':
self.Xu_s = torch.zeros((y_s.size()[1], inducing_size))
self.Xu_o = torch.zeros((y_o.size()[1], inducing_size))
self.noise_s = torch.zeros((y_s.size()[1], inducing_size))
self.noise_o = torch.zeros((y_o.size()[1], inducing_size))
print("for state transition model, input dim {} and output dim {}".format(X_s.size()[1], y_s.size()[1]))
print("for observation model, input dim {} and output dim {}".format(X_o.size()[1], y_o.size()[1]))
X=X, Z=Z, K_sum=3.391847
),
T(
Periodic(3, variance, lengthscale, period=torch.ones(1)),
X=X, Z=Z, K_sum=18
),
T(
Polynomial(3, variance, degree=2),
X=X, Z=Z, K_sum=7017
),
T(
RationalQuadratic(3, variance, lengthscale, scale_mixture=torch.ones(1)),
X=X, Z=Z, K_sum=5.684670
),
T(
RBF(3, variance, lengthscale),
X=X, Z=Z, K_sum=3.681117
),
T(
WhiteNoise(3, variance, lengthscale),
X=X, Z=Z, K_sum=0
),
T(
WhiteNoise(3, variance, lengthscale),
X=X, Z=None, K_sum=6
),
T(
Coregionalize(3, components=torch.eye(3, 3)),
X=torch.tensor([[1., 0., 0.],
[0.5, 0., 0.5]]),
Z=torch.tensor([[1., 0., 0.],
