def __init__(self, **kwargs):
super().__init__(**kwargs)
self.conv1 = GCNConv(32,
activation='elu',
kernel_regularizer=l2(l2_reg))
self.conv2 = GCNConv(32,
activation='elu',
kernel_regularizer=l2(l2_reg))
self.flatten = Flatten()
self.fc1 = Dense(512, activation='relu')
self.fc2 = Dense(10, activation='softmax') # MNIST has 10 classes
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.conv1 = GCNConv(32,
activation="elu",
kernel_regularizer=l2(l2_reg))
self.conv2 = GCNConv(32,
activation="elu",
kernel_regularizer=l2(l2_reg))
self.flatten = GlobalSumPool()
self.fc1 = Dense(512, activation="relu")
self.fc2 = Dense(10, activation="softmax") # MNIST has 10 classes
def GCN_net():
I1 = Input(shape=(no_agents, no_features), name="gcn_input")
Adj = Input(shape=(no_agents, no_agents), name="adj")
gcn = GCNConv(arglist.no_neurons,
kernel_initializer=tf.keras.initializers.he_uniform(),
activation=tf.keras.layers.LeakyReLU(alpha=0.1),
use_bias=False,
name="Gcn")([I1, Adj])
concat = tf.keras.layers.Concatenate(axis=2)([I1, gcn])
dense = Dense(arglist.no_neurons,
kernel_initializer=tf.keras.initializers.he_uniform(),
activation=tf.keras.layers.LeakyReLU(alpha=0.1),
name="dense_layer")
last_dense = Dense(no_actions,
kernel_initializer=tf.keras.initializers.he_uniform(),
name="last_dense_layer")
split = Lambda(lambda x: tf.squeeze(
tf.split(x, num_or_size_splits=no_agents, axis=1), axis=2))(concat)
outputs = []
for j in list(range(no_agents)):
output = last_dense(dense(split[j]))
output = tf.keras.activations.tanh(output)
outputs.append(output)
V = tf.stack(outputs, axis=1)
model = Model([I1, Adj], V)
model._name = "final_network"
return model
def __init__(self, no_neighbors, num_hidden_layers, units_per_layer, lr,
obs_n_shape, act_shape_n, act_type, wd, agent_index):
"""
Implementation of a critic to represent the Q-Values. Basically just a fully-connected
regression ANN.
"""
self.num_layers = num_hidden_layers
self.lr = lr
self.obs_shape_n = obs_n_shape
self.act_shape_n = act_shape_n
self.act_type = act_type
self.clip_norm = 0.5
# self.optimizer = tf.keras.optimizers.Adam(lr=self.lr)
self.optimizer = AdamW(learning_rate=lr, weight_decay=wd)
self.no_neighbors = no_neighbors
self.no_agents = len(self.obs_shape_n)
self.no_features = self.obs_shape_n[0][0]
self.no_actions = self.act_shape_n[0][0]
# GAT
self.k_lst = list(range(self.no_neighbors + 2))[2:]
self.graph_input = tf.keras.layers.Input(
(self.no_agents, self.no_features + self.no_actions),
name="graph_input")
self.adj = tf.keras.layers.Input(shape=(self.no_agents,
self.no_agents),
name="adj")
self.gcn = GCNConv(
units_per_layer,
kernel_initializer=tf.keras.initializers.he_uniform(),
activation=tf.keras.layers.LeakyReLU(alpha=0.1),
use_bias=False)([self.graph_input, self.adj])
self.hidden_layers = []
for idx in range(2):
layer = tf.keras.layers.Dense(units_per_layer, activation='relu')
self.hidden_layers.append(layer)
self.output_layer = tf.keras.layers.Dense(1, activation='linear')
# Try ResNet Alternative
# self.flatten = tf.keras.layers.Flatten()(self.gat)
self.concat = tf.keras.layers.Concatenate(axis=2)(
[self.graph_input, self.gcn])
self.flatten = tf.keras.layers.Flatten()(self.concat)
x = self.flatten
for idx in range(2):
x = self.hidden_layers[idx](x)
x = self.output_layer(x)
# connect layers
self.model = tf.keras.Model(
inputs=[self.graph_input, self.adj], # list concatenation
outputs=[x])
# tf.keras.utils.plot_model(self.model, show_shapes=True)
self.model.compile(self.optimizer, loss='mse')
def model1():
x_in = Input(shape=(F, ))
a_in = Input((N, ), sparse=True, dtype=a_dtype)
output = GCNConv(n_out,
activation="softmax",
kernel_regularizer=l2(l2_reg),
use_bias=False)([x_in, a_in])
return x_in, a_in, output
def __init__(self,
input_tensor_spec,
action_spec,
graph,
num_actions=30,
name=None):
super(GATNetwork, self).__init__(input_tensor_spec=input_tensor_spec,
state_spec=(),
name=name)
#features = pd.DataFrame(
# {'cluster': [i // 30 for i in graph.nodes], 'controller': [0 for i in graph.nodes]}, index=graph.nodes)
#sg_graph = sg.StellarGraph.from_networkx(graph, node_features=features)
#print(sg_graph.info())
#generator = FullBatchNodeGenerator(sg_graph, 'gat')
#print(generator.Aadj)
#self.tf_clusters = tf.constant(generator.features[:, 0][np.newaxis, ...], dtype=tf.int32)
#self.net = GAT(
# layer_sizes=[64, 30],
# activations=['relu', 'softmax'],
# attn_heads=8,
# generator=generator,
# in_dropout=0.5,
# attn_dropout=0.5,
# normalize=None
#)
#self.inp, self.out = self.net.in_out_tensors()
self.graph_conv_1 = GCNConv(64)
#self.graph_conv_2 = GCNConv(64)
self.graph_conv_3 = GCNConv(1)
#self.graph_conv_1.build(((1, 180, 1), (1, 180, 180)))
#self.dropout_1 = tf.keras.layers.Dropout(0.5)
self.dense_1 = dense(180)
#self.graph_gat_1 = GATConv(16, 6)
#self.graph_gat_2 = GATConv(1)
adj_matrix = nx.to_numpy_array(graph)
idn_matrix = np.identity(adj_matrix.shape[0])
adj_loop_matrix = adj_matrix + idn_matrix
self.adjacency_matrix = adj_loop_matrix[np.newaxis, ...]
self.gcn_adj = gcn_filter(self.adjacency_matrix)
self.tf_adj = tf.constant(self.adjacency_matrix)
self.tf_gcn_adj = tf.constant(self.gcn_adj)
self.flatten = tf.keras.layers.Flatten()
def get_neighborhood_encoder(self):
app_input = self.appearance_encoder.input
morph_input = self.morphology_encoder.input
centroid_input = self.centroid_encoder.input
adj_input = Input(shape=(None, None), name='encoder_adj_input')
app_features = self.appearance_encoder.output
morph_features = self.morphology_encoder.output
centroid_features = self.centroid_encoder.output
adj = adj_input
# Concatenate features
node_features = Concatenate(axis=-1)(
[app_features, morph_features, centroid_features])
node_features = Dense(self.n_filters, name='dense_ne0')(node_features)
node_features = BatchNormalization(axis=-1,
name='bn_ne0')(node_features)
node_features = Activation('relu', name='relu_ne0')(node_features)
# Apply graph convolution
for i in range(self.n_layers):
name = '{}{}'.format(self.graph_layer, i)
if self.graph_layer == 'gcn':
graph_layer = GCNConv(self.n_filters,
activation=None,
name=name)
elif self.graph_layer == 'gcs':
graph_layer = GCSConv(self.n_filters,
activation=None,
name=name)
else:
raise ValueError('Unexpected graph_layer: {}'.format(
self.graph_layer))
node_features = graph_layer([node_features, adj])
node_features = BatchNormalization(
axis=-1, name='bn_ne{}'.format(i + 1))(node_features)
node_features = Activation(
'relu', name='relu_ne{}'.format(i + 1))(node_features)
concat = Concatenate(axis=-1)(
[app_features, morph_features, node_features])
node_features = Dense(self.embedding_dim, name='dense_nef')(concat)
node_features = BatchNormalization(axis=-1,
name='bn_nef')(node_features)
node_features = Activation('relu', name='relu_nef')(node_features)
inputs = [app_input, morph_input, centroid_input, adj_input]
outputs = [node_features, centroid_input]
return Model(inputs=inputs,
outputs=outputs,
name='neighborhood_encoder')
def get_adj(arr, k_lst, no_agents):
"""
Take as input the new obs. In position 4 to k, there are the x and y coordinates of each agent
Make an adjacency matrix, where each agent communicates with the k closest ones
"""
points = [i[2:4] for i in arr]
adj = np.zeros((no_agents, no_agents), dtype=float)
# construct a kd-tree
tree = cKDTree(points)
for cnt, row in enumerate(points):
# find k nearest neighbors for each element of data, squeezing out the zero result (the first nearest
# neighbor is always itself)
dd, ii = tree.query(row, k=k_lst)
# apply an index filter on data to get the nearest neighbor elements
adj[cnt][ii] = 1
# adjacency[cnt, ii] = 1.0
# add self-loops and symmetric normalization
adj = GCNConv.preprocess(adj).astype('f4')
return adj
def getdata(self):
# Load data
self.data
adj = self.data.a
# The adjacency matrix is stored as an attribute of the dataset.
# Create filter for GCN and convert to sparse tensor.
self.data.a = GCNConv.preprocess(self.data.a)
self.data.a = sp_matrix_to_sp_tensor(self.data.a)
# Train/valid/test split
data_tr, data_te = self.data[:-10000], self.data[-10000:]
np.random.shuffle(data_tr)
data_tr, data_va = data_tr[:-10000], data_tr[-10000:]
# We use a MixedLoader since the dataset is in mixed mode
loader_tr = MixedLoader(data_tr, batch_size=batch_size, epochs=epochs)
loader_va = MixedLoader(data_va, batch_size=batch_size)
loader_te = MixedLoader(data_te, batch_size=batch_size)
return adj, loader_tr, loader_va, loader_te
# Data splits idx = ogb_dataset.get_idx_split() idx_tr, idx_va, idx_te = idx["train"], idx["valid"], idx["test"] mask_tr = np.zeros(N, dtype=bool) mask_va = np.zeros(N, dtype=bool) mask_te = np.zeros(N, dtype=bool) mask_tr[idx_tr] = True mask_va[idx_va] = True mask_te[idx_te] = True masks = [mask_tr, mask_va, mask_te] # Model definition x_in = Input(shape=(F, )) a_in = Input((N, ), sparse=True) x_1 = GCNConv(channels, activation="relu")([x_in, a_in]) x_1 = BatchNormalization()(x_1) x_1 = Dropout(dropout)(x_1) x_2 = GCNConv(channels, activation="relu")([x_1, a_in]) x_2 = BatchNormalization()(x_2) x_2 = Dropout(dropout)(x_2) x_3 = GCNConv(n_out, activation="softmax")([x_2, a_in]) # Build model model = Model(inputs=[x_in, a_in], outputs=x_3) optimizer = Adam(lr=learning_rate) loss_fn = SparseCategoricalCrossentropy() model.summary() # Training function
# Data splits idx = ogb_dataset.get_idx_split() idx_tr, idx_va, idx_te = idx["train"], idx["valid"], idx["test"] mask_tr = np.zeros(N, dtype=bool) mask_va = np.zeros(N, dtype=bool) mask_te = np.zeros(N, dtype=bool) mask_tr[idx_tr] = True mask_va[idx_va] = True mask_te[idx_te] = True masks = [mask_tr, mask_va, mask_te] # Model definition x_in = Input(shape=(F, )) a_in = Input((N, ), sparse=True) x_1 = GCNConv(channels, activation='relu')([x_in, a_in]) x_1 = BatchNormalization()(x_1) x_1 = Dropout(dropout)(x_1) x_2 = GCNConv(channels, activation='relu')([x_1, a_in]) x_2 = BatchNormalization()(x_2) x_2 = Dropout(dropout)(x_2) x_3 = GCNConv(n_out, activation='softmax')([x_2, a_in]) # Build model model = Model(inputs=[x_in, a_in], outputs=x_3) optimizer = Adam(lr=learning_rate) loss_fn = SparseCategoricalCrossentropy() model.summary() # Training function
#we then build a graph using NetworkX(Adjacency Matrix) usingt he obtained nodes and edges list
G = nx.Graph()
G.add_nodes_from(nodes)
G.add_edges_from(edge_list)
A = nx.adjacency_matrix(G)
print('Graph info: ', nx.info(G))
#We now build and train the Graph Convolution Networks
#initializing the parameters
channels = 16 #number of channels in the first layer
dropout = 0.5
l2_reg = 5e-4
learning_rate = 1e-2
epochs = 200
es_patience = 10
A = GCNConv.preprocess(A).astype('f4')
#defining the model
X_in = Input(shape = (F, ))
fltr_in = Input((N, ), sparse=True)
dropout_1= Dropout(dropout)(X_in)
graph_conv_1 = GCNConv(channels, activation='relu',
kernel_regularizer = l2(l2_reg),
use_bias=False)([dropout_1, fltr_in])
dropout_2 = Dropout(dropout)(graph_conv_1)
graph_conv_2 = GCNConv(num_classes, activation='softmax',
use_bias=False)([dropout_2, fltr_in])
#we then build the mode as follows:
model = Model(inputs=[X_in, fltr_in], outputs = graph_conv_2)
optimizer = Adam(lr=learning_rate)
model.compile(optimizer=optimizer, loss = 'categorical_crossentropy', weighted_metrics=['acc'])
from spektral.layers.ops import sp_matrix_to_sp_tensor tf.config.experimental_run_functions_eagerly(True) # Parameters batch_size = 32 # Batch size epochs = 1000 # Number of training epochs patience = 10 # Patience for early stopping l2_reg = 5e-4 # Regularization rate for l2 # Load data data = MNIST() # The adjacency matrix is stored as an attribute of the dataset. # Create filter for GCN and convert to sparse tensor. data.a = GCNConv.preprocess(data.a) data.a = sp_matrix_to_sp_tensor(data.a) # Train/valid/test split data_tr, data_te = data[:-10000], data[-10000:] np.random.shuffle(data_tr) data_tr, data_va = data_tr[:-10000], data_tr[-10000:] # We use a MixedLoader since the dataset is in mixed mode loader_tr = MixedLoader(data_tr, batch_size=batch_size, epochs=epochs) loader_va = MixedLoader(data_va, batch_size=batch_size) loader_te = MixedLoader(data_te, batch_size=batch_size) # Build model class Net(Model):
learning_rate = 1e-2 # Learning rate
epochs = 200 # Number of training epochs
patience = 10 # Patience for early stopping
a_dtype = dataset[0].a.dtype # Only needed for TF 2.1
N = dataset.n_nodes # Number of nodes in the graph
F = dataset.n_node_features # Original size of node features
n_out = dataset.n_labels # Number of classes
# Model definition
x_in = Input(shape=(F, ))
a_in = Input((N, ), sparse=True, dtype=a_dtype)
do_1 = Dropout(dropout)(x_in)
gc_1 = GCNConv(channels,
activation='relu',
kernel_regularizer=l2(l2_reg),
use_bias=False)([do_1, a_in])
do_2 = Dropout(dropout)(gc_1)
gc_2 = GCNConv(n_out, activation='softmax', use_bias=False)([do_2, a_in])
# Build model
model = Model(inputs=[x_in, a_in], outputs=gc_2)
optimizer = Adam(lr=learning_rate)
model.compile(
optimizer=optimizer,
loss=CategoricalCrossentropy(reduction='sum'), # To compute mean
weighted_metrics=['acc'])
model.summary()
# Train model
loader_tr = SingleLoader(dataset, sample_weights=weights_tr)
from spektral.layers import GCNConv
from spektral.layers.ops import sp_matrix_to_sp_tensor
# Parameters
batch_size = 32 # Batch size
epochs = 1000 # Number of training epochs
patience = 10 # Patience for early stopping
l2_reg = 5e-4 # Regularization rate for l2
# Load data
data = MNIST()
# The adjacency matrix is stored as an attribute of the dataset.
# Create filter for GCN and convert to sparse tensor.
adj = data.a
adj = GCNConv.preprocess(adj)
adj = sp_matrix_to_sp_tensor(adj)
# Train/valid/test split
data_tr, data_te = data[:-10000], data[-10000:]
np.random.shuffle(data_tr)
data_tr, data_va = data_tr[:-10000], data_tr[-10000:]
# Build model
class Net(Model):
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.conv1 = GCNConv(32,
activation='elu',
kernel_regularizer=l2(l2_reg))
l2_reg = 5e-6 # L2 regularization rate
learning_rate = 0.2 # Learning rate
epochs = 20000 # Number of training epochs
patience = 200 # Patience for early stopping
a_dtype = dataset[0].a.dtype # Only needed for TF 2.1
N = dataset.n_nodes # Number of nodes in the graph
F = dataset.n_node_features # Original size of node features
n_out = dataset.n_labels # Number of classes
# Model definition
x_in = Input(shape=(F, ))
a_in = Input((N, ), sparse=True, dtype=a_dtype)
output = GCNConv(n_out,
activation="softmax",
kernel_regularizer=l2(l2_reg),
use_bias=False)([x_in, a_in])
# Build model
model = Model(inputs=[x_in, a_in], outputs=output)
optimizer = Adam(lr=learning_rate)
model.compile(optimizer=optimizer,
loss="categorical_crossentropy",
weighted_metrics=["acc"])
model.summary()
# Train model
loader_tr = SingleLoader(dataset, sample_weights=mask_tr)
loader_va = SingleLoader(dataset, sample_weights=mask_va)
model.fit(
loader_tr.load(),
from spektral.datasets.citation import Cora
from spektral.layers import GCNConv
from spektral.transforms import LayerPreprocess, AdjToSpTensor
from spektral.utils import tic, toc
# Load data
dataset = Cora(transforms=[LayerPreprocess(GCNConv), AdjToSpTensor()])
graph = dataset[0]
x, a, y = graph.x, graph.a, graph.y
mask_tr, mask_va, mask_te = dataset.mask_tr, dataset.mask_va, dataset.mask_te
# Define model
x_in = Input(shape=(dataset.n_node_features, ))
a_in = Input((dataset.n_nodes, ), sparse=True)
x_1 = GCNConv(16, 'relu', True, kernel_regularizer=l2(5e-4))([x_in, a_in])
x_1 = Dropout(0.5)(x_1)
x_2 = GCNConv(y.shape[1], 'softmax', True)([x_1, a_in])
# Build model
model = Model(inputs=[x_in, a_in], outputs=x_2)
optimizer = Adam(lr=1e-2)
loss_fn = CategoricalCrossentropy()
# Training step
@tf.function
def train():
with tf.GradientTape() as tape:
predictions = model([x, a], training=True)
loss = loss_fn(y[mask_tr], predictions[mask_tr])
idx_tr, idx_va, idx_te = np.split(idxs, [split_va, split_te]) dataset_tr = dataset[idx_tr] dataset_va = dataset[idx_va] dataset_te = dataset[idx_te] loader_tr = BatchLoader(dataset_tr, batch_size=batch_size) loader_va = BatchLoader(dataset_va, batch_size=batch_size) loader_te = BatchLoader(dataset_te, batch_size=batch_size) ################################################################################ # BUILD MODEL ################################################################################ X_in = Input(shape=(None, F)) A_in = Input(shape=(None, None)) X_1 = GCNConv(32, activation="relu")([X_in, A_in]) X_1, A_1 = MinCutPool(N // 2)([X_1, A_in]) X_2 = GCNConv(32, activation="relu")([X_1, A_1]) X_3 = GlobalSumPool()(X_2) output = Dense(n_out)(X_3) # Build model model = Model(inputs=[X_in, A_in], outputs=output) opt = Adam(lr=learning_rate) model.compile(optimizer=opt, loss="categorical_crossentropy", metrics=["acc"]) model.summary() ################################################################################ # FIT MODEL ################################################################################ model.fit(
n_out = dataset.n_labels # Dimension of the target # Train/test split idx = ogb_dataset.get_idx_split() idx_tr, idx_va, idx_te = idx["train"], idx["valid"], idx["test"] dataset_tr = dataset[idx_tr] dataset_va = dataset[idx_va] dataset_te = dataset[idx_te] ################################################################################ # BUILD MODEL ################################################################################ X_in = Input(shape=(None, F)) A_in = Input(shape=(None, None)) X_1 = GCNConv(32, activation='relu')([X_in, A_in]) X_1, A_1 = MinCutPool(N // 2)([X_1, A_in]) X_2 = GCNConv(32, activation='relu')([X_1, A_1]) X_3 = GlobalSumPool()(X_2) output = Dense(n_out)(X_3) # Build model model = Model(inputs=[X_in, A_in], outputs=output) opt = Adam(lr=learning_rate) model.compile(optimizer=opt, loss='mse') model.summary() ################################################################################ # FIT MODEL ################################################################################ loader_tr = BatchLoader(dataset_tr, batch_size=batch_size)