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
#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):
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))
