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gplvm.py
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gplvm.py
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import torch
import torch.nn as nn
import torch.distributions as dist
import numpy as np
from utils import *
# (1) not sure why dtype is explicitly required in some places to force float32
dtype = torch.float32
class GP(nn.Module):
def __init__(self, dim, X, y, kernel, variance=1.0, N_max=None):
super(GP, self).__init__()
self.dim = torch.tensor([dim], requires_grad=False)
self.kernel = kernel
self.variance = torch.nn.Parameter(
transform_backward(torch.tensor([variance])))
if torch.is_tensor(X):
self.X = X
else:
self.X = torch.tensor(X, requires_grad=False, dtype=dtype)
self.N_max = N_max
self.N = self.X.size()[0]
if isinstance(y, Sparse1DTensor):
self.y = y
ix = torch.tensor([k for k in y.ix.keys()], dtype=torch.int64)
self.get_batch = BatchIndices(None, ix, self.N_max)
else:
# NOTE: see (1)
self.y = torch.tensor(y.squeeze(), dtype=dtype,
requires_grad=False)
self.get_batch = BatchIndices(self.N, None, self.N_max)
def get_cov(self, ix=None):
if ix is None:
ix = torch.arange(0, self.N)
return torch.potrf(self.kernel(self.X[ix])
+ torch.eye(ix.numel())
*transform_forward(self.variance),
upper=False)
def forward(self, ix=None):
if ix is None:
ix = self.get_batch()
mn = torch.zeros(ix.numel())
cov = self.get_cov(ix=ix)
pdf = dist.multivariate_normal.MultivariateNormal(mn, scale_tril=cov)
return -pdf.log_prob(self.y[ix])
def posterior(self, Xtest):
# assumes stationary kernel
with torch.no_grad():
if isinstance(self.y, Sparse1DTensor):
ix = self.get_batch.ix
Ks = self.kernel(self.X[ix], Xtest)
L = self.get_cov(ix)
alpha = torch.trtrs(Ks, L, upper=False)[0]
fmean = torch.matmul(torch.t(alpha),
torch.trtrs(self.y.v.squeeze(), L,
upper=False)[0])
else:
Ks = self.kernel(self.X, Xtest)
L = self.get_cov()
alpha = torch.trtrs(Ks, L, upper=False)[0]
fmean = torch.matmul(torch.t(alpha),
torch.trtrs(self.y, L, upper=False)[0])
fvar = transform_forward(self.kernel.variance) - (alpha**2).sum(0)
return fmean, fvar.reshape((-1,1))
class GPLVM(nn.Module):
def __init__(self, dim, X, Y, kernel, D_max=None, **kwargs):
super(GPLVM, self).__init__()
if torch.is_tensor(X):
self.X = torch.nn.Parameter(X)
else:
# NOTE: see (1)
self.X = torch.nn.Parameter(torch.tensor(X, dtype=dtype))
self.GPs = nn.ModuleList([])
if isinstance(Y, np.ndarray):
self.D = Y.shape[1]
for d in range(self.D):
ix = np.where(np.invert(np.isnan(Y[:,d])))[0]
y = Sparse1DTensor(Y[ix,d], torch.tensor(ix))
self.GPs.append(GP(dim, self.X, y, kernel, **kwargs))
elif isinstance(Y, list):
# assumes col indexing starts at 0 and is (integer-)continuous
self.D = int(np.max(Y[2])) + 1
for d in range(self.D):
ix = np.where(Y[2]==d)[0]
y = Sparse1DTensor(Y[0][ix], torch.tensor(Y[1][ix]))
self.GPs.append(GP(dim, self.X, y, kernel, **kwargs))
else:
assert False, 'Bad Y input'
if D_max is None:
self.D_max = self.D
else:
self.D_max = D_max
self.dim = dim
self.kernel = kernel
for j in range(1, self.D):
self.GPs[j].variance = self.GPs[0].variance
self.variance = self.GPs[0].variance
self.get_batch = BatchIndices(self.D, None, self.D_max)
def forward(self, ix=None):
if ix is None:
ix = self.get_batch()
lp = torch.tensor([0.])
for j in ix:
lp += self.GPs[j]()
return lp*self.D/self.D_max