import torch
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
import anndata
from gpsa import VariationalGPSA
from gpsa import matern12_kernel, rbf_kernel
from gpsa.plotting import callback_twod
device = "cuda" if torch.cuda.is_available() else "cpu"
N_SPATIAL_DIMS = 2
N_VIEWS = 2
M_G = 25
M_X_PER_VIEW = 25
N_OUTPUTS = 5
FIXED_VIEW_IDX = 0
N_LATENT_GPS = {"expression": None}
N_EPOCHS = 3000
PRINT_EVERY = 100
data = anndata.read_h5ad("./synthetic_data.h5ad")
X = data.obsm["spatial"]
Y = data.X
view_idx = [np.where(data.obs.batch.values == ii)[0] for ii in range(2)]
n_samples_list = [len(x) for x in view_idx]
x = torch.from_numpy(X).float().clone().to(device)
y = torch.from_numpy(Y).float().clone().to(device)
data_dict = {
"expression": {
"spatial_coords": x,
"outputs": y,
"n_samples_list": n_samples_list,
}
}
model = VariationalGPSA(
data_dict,
n_spatial_dims=N_SPATIAL_DIMS,
m_X_per_view=M_X_PER_VIEW,
m_G=M_G,
data_init=True,
minmax_init=False,
grid_init=False,
n_latent_gps=N_LATENT_GPS,
mean_function="identity_fixed",
kernel_func_warp=rbf_kernel,
kernel_func_data=rbf_kernel,
fixed_view_idx=FIXED_VIEW_IDX,
).to(device)
view_idx, Ns, _, _ = model.create_view_idx_dict(data_dict)
optimizer = torch.optim.Adam(model.parameters(), lr=1e-2)
def train(model, loss_fn, optimizer):
model.train()
# Forward pass
G_means, G_samples, F_latent_samples, F_samples = model.forward(
{"expression": x}, view_idx=view_idx, Ns=Ns, S=5
)
# Compute loss
loss = loss_fn(data_dict, F_samples)
# Compute gradients and take optimizer step
optimizer.zero_grad()
loss.backward()
optimizer.step()
return loss.item()
# Set up figure.
fig = plt.figure(figsize=(14, 7), facecolor="white", constrained_layout=True)
data_expression_ax = fig.add_subplot(121, frameon=False)
latent_expression_ax = fig.add_subplot(122, frameon=False)
plt.show(block=False)
for t in range(N_EPOCHS):
loss = train(model, model.loss_fn, optimizer)
if t % PRINT_EVERY == 0:
print("Iter: {0:<10} LL {1:1.3e}".format(t, -loss))
G_means, _, _, _ = model.forward({"expression": x}, view_idx=view_idx, Ns=Ns)
callback_twod(
model,
X,
Y,
data_expression_ax=data_expression_ax,
latent_expression_ax=latent_expression_ax,
X_aligned=G_means,
s=600,
)
plt.draw()
plt.pause(1 / 60.0)
print("Done!")
plt.close()