def breast_cancer(x_train, y_train, x_val, y_val, params):
print("Iteration parameters: ", params)
def weights_init_uniform_rule(m):
classname = m.__class__.__name__
if classname.find('Linear') != -1:
n = m.in_features
y = 1.0 / np.sqrt(n)
m.weight.data.uniform_(-y, y)
m.bias.data.fill_(0)
manager = DataManager.from_numpy(train_inputs=x_train,
train_labels=y_train,
batch_size=params["batch_size"],
validation_inputs=x_val,
validation_labels=y_val)
net = BreastCancerNet(n_feature=x_train.shape[1],
first_neuron=params["first_neuron"],
second_neuron=params["second_neuron"],
dropout=params["dropout"])
net.apply(weights_init_uniform_rule)
net.init_history()
model = DeepLearningInterface(model=net,
optimizer_name=params["optimizer_name"],
learning_rate=params["learning_rate"],
loss_name=params["loss_name"],
metrics=["accuracy"])
model.add_observer("after_epoch", update_talos_history)
model.training(manager=manager,
nb_epochs=params["epochs"],
checkpointdir=None,
fold_index=0,
with_validation=True)
return net, net.parameters()
masker = MultiNiftiMasker(mask_img=mask_img, standardize=True)
masker.fit()
if not os.path.isfile(DATAFILE):
y = np.concatenate(masker.transform(func_filenames), axis=0)
print(y.shape)
np.save(DATAFILE, y)
else:
y = np.load(DATAFILE)
iterator = masker.inverse_transform(y).get_fdata()
iterator = iterator.transpose((3, 0, 1, 2))
iterator = np.expand_dims(iterator, axis=1)
print(iterator.shape)
# Data iterator
manager = DataManager.from_numpy(train_inputs=iterator,
batch_size=BATCH_SIZE,
add_input=True)
# Create model
name = "ResAENet"
model_weights = os.path.join(WORKDIR, "checkpoint_" + name,
"model_0_epoch_{0}.pth".format(EPOCH))
if os.path.isfile(model_weights):
pretrained = model_weights
else:
pretrained = None
params = NetParameters(input_shape=(61, 73, 61),
cardinality=1,
layers=[3, 4, 6, 3],
n_channels_in=1,
decode=True)
# Show example noisy training data that have the signatures applied.
# It's not obvious to the human eye the subtle differences, but the cross
# row and column above perturbed the below matrices with the y weights.
# Show in the title how much each signature is weighted by.
plt.figure(figsize=(16, 4))
for idx in range(3):
plt.subplot(1, 3, idx + 1)
plt.imshow(np.squeeze(x_train[idx]), interpolation="None")
plt.colorbar()
plt.title(y_train[idx])
manager = DataManager.from_numpy(train_inputs=x_train,
train_labels=y_train,
validation_inputs=x_valid,
validation_labels=y_valid,
test_inputs=x_test,
test_labels=y_test,
batch_size=128,
continuous_labels=True)
interfaces = pynet.get_interfaces()["graph"]
net_params = pynet.NetParameters(input_shape=(90, 90),
in_channels=1,
num_classes=2,
nb_e2e=32,
nb_e2n=64,
nb_n2g=30,
dropout=0.5,
leaky_alpha=0.1,
twice_e2e=False,
dense_sml=True)
my_loss = pynet.get_tools()["losses"]["MSELoss"]()
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
losses = pynet.get_tools(tool_name="losses")
setup_logging(level="info")
#############################################################################
# Kang dataset
# ------------
#
# Fetch & load the Kang dataset:
data, trainset, testset, membership_mask = fetch_kang(datasetdir=datasetdir,
random_state=0)
gtpath = os.path.join(datasetdir, "kang_recons.h5ad")
manager = DataManager.from_numpy(train_inputs=trainset,
validation_inputs=testset,
test_inputs=data.X,
batch_size=batch_size,
sampler="random",
add_input=True)
#############################################################################
# Training
# --------
#
# Create/train the model:
if checkpointdir is not None:
weights_filename = os.path.join(
checkpointdir, "model_0_epoch_{0}.pth".format(nb_epochs - 1))
params = NetParameters(membership_mask=membership_mask,
latent_dim=latent_dim,
hidden_layers=[12],
nb_features = 50
for name, nb_samples in (("train", 1000), ("test", 2)):
x1 = torch.randn(nb_samples, 50)
x2 = torch.randn(nb_samples, 50) + 1.5
x = torch.cat([x1, x2], dim=0)
y1 = torch.zeros(nb_samples, 1)
y2 = torch.ones(nb_samples, 1)
y = torch.cat([y1, y2], dim=0)
toy_data[name] = (x, y)
if name == "train":
plt.figure()
plt.scatter(x1[:, 0], x1[:, 1], color="b")
plt.scatter(x2[:, 0], x2[:, 1], color="r")
manager = DataManager.from_numpy(train_inputs=toy_data["train"][0],
train_labels=toy_data["train"][1],
batch_size=50,
test_inputs=toy_data["test"][0],
test_labels=toy_data["test"][1])
class DenseFeedForwardNet(nn.Module):
def __init__(self, nb_features):
""" Initialize the instance.
Parameters
----------
nb_features: int
the size of the feature vector.
"""
super(DenseFeedForwardNet, self).__init__()
self.layers = nn.Sequential(
# Show in the title how much each signature is weighted by.
plt.figure(figsize=(16, 4))
for idx in range(3):
plt.subplot(1, 3, idx + 1)
plt.imshow(np.squeeze(x_train[idx]), interpolation="None")
plt.colorbar()
plt.title(y_train[idx])
data = np.concatenate(data, axis=0)
labels = np.asarray(labels)
print("dataset: x {0} - y {1}".format(data.shape, labels.shape))
# Create data manager
manager = DataManager.from_numpy(
train_inputs=data, train_labels=np.zeros(labels.shape),
batch_size=BATCH_SIZE)
class FKmeans(object):
def __init__(self, n_clusters):
self.n_clusters = n_clusters
def fit(self, data):
n_data, d = data.shape
self.clus = faiss.Kmeans(d, self.n_clusters)
self.clus.seed = np.random.randint(1234)
self.clus.niter = 20
self.clus.max_points_per_centroid = 10000000
self.clus.train(data)
[np.round(np.mean(labels[tri])) for tri in ico_triangles])
plot_trisurf(fig, ax, ico_vertices, ico_triangles, tri_texture)
data = np.zeros((N_SAMPLES, N_CLASSES, len(labels)), dtype=float)
for klass in (0, 1):
k_indices = np.argwhere(labels == 0).squeeze()
for loc, scale in SAMPLES[klass]:
data[:, klass, k_indices] = np.random.normal(loc=loc,
scale=scale,
size=len(k_indices))
labels = np.ones((N_SAMPLES, 1)) * labels
print("dataset: x {0} - y {1}".format(data.shape, labels.shape))
# Create data manager
manager = DataManager.from_numpy(train_inputs=data,
train_labels=labels,
test_inputs=data,
test_labels=labels,
batch_size=BATCH_SIZE)
# Create model
net_params = pynet.NetParameters(in_order=ICO_ORDER,
in_channels=2,
out_channels=N_CLASSES,
depth=3,
start_filts=32,
conv_mode="1ring",
up_mode="transpose",
cachedir=os.path.join(OUTDIR, "cache"))
model = SphericalUNetEncoder(net_params,
optimizer_name="SGD",
learning_rate=0.1,
n_feats=n_feats,
n_classes=n_classes,
train=True,
snr=snr)
ds_val = SyntheticDataset(n_samples=n_samples,
lat_dim=true_lat_dims,
n_feats=n_feats,
n_classes=n_classes,
train=False,
snr=snr)
image_datasets = {"train": ds_train, "val": ds_val}
manager = DataManager.from_numpy(train_inputs=ds_train.data,
train_outputs=None,
train_labels=ds_train.labels,
validation_inputs=ds_val.data,
validation_outputs=None,
validation_labels=ds_val.labels,
batch_size=batch_size,
sampler="random",
add_input=True)
print("- datasets:", image_datasets)
print("- shapes:", ds_train.data.shape, ds_val.data.shape)
# Display generated data
method = manifold.TSNE(n_components=2, init="pca", random_state=0)
y_train = method.fit_transform(ds_train.data)
y_val = method.fit_transform(ds_val.data)
fig, axs = plt.subplots(nrows=3, ncols=2)
for cnt, (name, y, labels) in enumerate(
(("train", y_train, ds_train.labels), ("val", y_val, ds_val.labels))):
colors = labels.astype(float)
