def test_APPNP_apply_sparse():
G, features = create_graph_features()
adj = nx.to_scipy_sparse_matrix(G)
features, adj = GCN_Aadj_feats_op(features, adj)
adj = adj.tocoo()
A_indices = np.expand_dims(np.hstack((adj.row[:, None], adj.col[:, None])),
0)
A_values = np.expand_dims(adj.data, 0)
nodes = G.nodes()
node_features = pd.DataFrame.from_dict(
{n: f
for n, f in zip(nodes, features)}, orient="index")
G = StellarGraph(G, node_features=node_features)
generator = FullBatchNodeGenerator(G, sparse=True, method="gcn")
appnpnModel = APPNP([2], ["relu"], generator=generator, dropout=0.5)
x_in, x_out = appnpnModel.node_model()
model = keras.Model(inputs=x_in, outputs=x_out)
# Check fit method
out_indices = np.array([[0, 1]], dtype="int32")
preds_1 = model.predict(
[features[None, :, :], out_indices, A_indices, A_values])
assert preds_1.shape == (1, 2, 2)
# Check fit_generator method
preds_2 = model.predict_generator(generator.flow(["a", "b"]))
assert preds_2.shape == (1, 2, 2)
assert preds_1 == pytest.approx(preds_2)
def test_gat_serialize(self):
G = example_graph_1(feature_size=self.F_in)
gen = FullBatchNodeGenerator(G, sparse=self.sparse, method=self.method)
gat = GAT(
layer_sizes=self.layer_sizes,
activations=self.activations,
attn_heads=self.attn_heads,
generator=gen,
bias=True,
normalize="l2",
)
x_in, x_out = gat.node_model()
model = keras.Model(inputs=x_in, outputs=x_out)
ng = gen.flow(G.nodes())
# Save model
model_json = model.to_json()
# Set all weights to one
model_weights = [np.ones_like(w) for w in model.get_weights()]
# Load model from json & set all weights
model2 = keras.models.model_from_json(
model_json, custom_objects={"GraphAttention": GraphAttention})
model2.set_weights(model_weights)
# Test deserialized model
actual = model2.predict_generator(ng)
expected = np.ones(
(G.number_of_nodes(),
self.layer_sizes[-1])) * (1.0 / G.number_of_nodes())
assert np.allclose(expected, actual[0])
def test_gat_node_model_no_norm(self):
G = example_graph_1(feature_size=self.F_in)
gen = FullBatchNodeGenerator(G, sparse=self.sparse, method=self.method)
gat = GAT(
layer_sizes=self.layer_sizes,
activations=self.activations,
attn_heads=self.attn_heads,
generator=gen,
bias=True,
normalize=None,
)
gat._layers[1].kernel_initializer = keras.initializers.get("ones")
gat._layers[1].attn_kernel_initializer = keras.initializers.get("ones")
gat._layers[3].kernel_initializer = keras.initializers.get("ones")
gat._layers[3].attn_kernel_initializer = keras.initializers.get("ones")
x_in, x_out = gat.node_model()
model = keras.Model(inputs=x_in, outputs=x_out)
ng = gen.flow(G.nodes())
actual = model.predict_generator(ng)
expected = np.ones((G.number_of_nodes(), self.layer_sizes[-1])) * (
self.F_in * self.layer_sizes[0] * self.attn_heads)
assert np.allclose(expected, actual[0])
def test_APPNP_apply_propagate_model_dense():
G, features = create_graph_features()
adj = nx.to_scipy_sparse_matrix(G)
features, adj = GCN_Aadj_feats_op(features, adj)
adj = adj.todense()[None, :, :]
n_nodes = features.shape[0]
nodes = G.nodes()
node_features = pd.DataFrame.from_dict(
{n: f
for n, f in zip(nodes, features)}, orient="index")
G = StellarGraph(G, node_features=node_features)
generator = FullBatchNodeGenerator(G, sparse=False, method="gcn")
appnpnModel = APPNP([2], ["relu"], generator=generator, dropout=0.5)
fully_connected_model = keras.Sequential()
fully_connected_model.add(Dense(2))
x_in, x_out = appnpnModel.propagate_model(fully_connected_model)
model = keras.Model(inputs=x_in, outputs=x_out)
# Check fit method
out_indices = np.array([[0, 1]], dtype="int32")
preds_1 = model.predict([features[None, :, :], out_indices, adj])
assert preds_1.shape == (1, 2, 2)
# Check fit_generator method
preds_2 = model.predict_generator(generator.flow(["a", "b"]))
assert preds_2.shape == (1, 2, 2)
assert preds_1 == pytest.approx(preds_2)
def test_PPNP_edge_cases():
G, features = create_graph_features()
adj = nx.to_scipy_sparse_matrix(G)
features, adj = PPNP_Aadj_feats_op(features, adj)
nodes = G.nodes()
node_features = pd.DataFrame.from_dict(
{n: f
for n, f in zip(nodes, features)}, orient="index")
G = StellarGraph(G, node_features=node_features)
ppnp_sparse_failed = False
try:
generator = FullBatchNodeGenerator(G, sparse=True, method="ppnp")
except ValueError as e:
ppnp_sparse_failed = True
assert ppnp_sparse_failed
generator = FullBatchNodeGenerator(G, sparse=False, method="ppnp")
try:
ppnpModel = PPNP([2, 2], ["relu"], generator=generator, dropout=0.5)
except ValueError as e:
error = e
assert str(
error) == "The number of layers should equal the number of activations"
try:
ppnpModel = PPNP([2], ["relu"], generator=[0, 1], dropout=0.5)
except TypeError as e:
error = e
assert str(
error) == "Generator should be a instance of FullBatchNodeGenerator"
def test_GCN_apply_sparse():
G, features = create_graph_features()
adj = nx.to_numpy_array(G)[None, :, :]
n_nodes = features.shape[0]
nodes = G.nodes()
node_features = pd.DataFrame.from_dict(
{n: f
for n, f in zip(nodes, features)}, orient="index")
G = StellarGraph(G, node_features=node_features)
generator = FullBatchNodeGenerator(G, sparse=False, method="none")
gcnModel = GCN([2], ["relu"], generator=generator, dropout=0.5)
x_in, x_out = gcnModel.node_model()
model = keras.Model(inputs=x_in, outputs=x_out)
# Check fit method
out_indices = np.array([[0, 1]], dtype="int32")
preds_1 = model.predict([features[None, :, :], out_indices, adj])
assert preds_1.shape == (1, 2, 2)
# Check fit_generator method
preds_2 = model.predict_generator(generator.flow(["a", "b"]))
assert preds_2.shape == (1, 2, 2)
assert preds_1 == pytest.approx(preds_2)
def test_gat_node_model_no_norm(self):
G = example_graph_1(feature_size=self.F_in)
gen = FullBatchNodeGenerator(G)
gat = GAT(
layer_sizes=self.layer_sizes,
activations=self.activations,
attn_heads=self.attn_heads,
generator=gen,
bias=True,
normalize=None,
)
gat._layers[1].kernel_initializer = keras.initializers.get("ones")
gat._layers[1].attn_kernel_initializer = keras.initializers.get("ones")
gat._layers[3].kernel_initializer = keras.initializers.get("ones")
gat._layers[3].attn_kernel_initializer = keras.initializers.get("ones")
assert len(gat.node_model()) == 2
x_in, x_out = gat.node_model()
assert len(x_in) == 2
assert int(x_in[0].shape[-1]) == self.F_in
assert x_in[1]._keras_shape == (None, G.number_of_nodes())
assert int(x_out.shape[-1]) == self.layer_sizes[-1]
model = keras.Model(inputs=x_in, outputs=x_out)
X = gen.features
A = gen.Aadj
actual = model.predict([X, A])
expected = np.ones((G.number_of_nodes(), self.layer_sizes[-1])) * (
self.F_in * self.layer_sizes[0] * self.attn_heads)
assert expected == pytest.approx(actual)
def test_GCN_regularisers():
G, features = create_graph_features()
adj = nx.to_numpy_array(G)[None, :, :]
n_nodes = features.shape[0]
nodes = G.nodes()
node_features = pd.DataFrame.from_dict(
{n: f
for n, f in zip(nodes, features)}, orient="index")
G = StellarGraph(G, node_features=node_features)
generator = FullBatchNodeGenerator(G, sparse=False, method="none")
gcn = GCN([2], generator)
gcn = GCN([2], generator, kernel_initializer="ones")
gcn = GCN([2], generator, kernel_initializer=initializers.ones())
with pytest.raises(ValueError):
gcn = GCN([2], generator, kernel_initializer="fred")
gcn = GCN([2], generator, bias_initializer="zeros")
gcn = GCN([2], generator, bias_initializer=initializers.zeros())
with pytest.raises(ValueError):
gcn = GCN([2], generator, bias_initializer="barney")
def test_GCN_activations():
G, features = create_graph_features()
adj = nx.to_numpy_array(G)[None, :, :]
n_nodes = features.shape[0]
nodes = G.nodes()
node_features = pd.DataFrame.from_dict(
{n: f
for n, f in zip(nodes, features)}, orient="index")
G = StellarGraph(G, node_features=node_features)
generator = FullBatchNodeGenerator(G, sparse=False, method="none")
gcn = GCN([2], generator)
assert gcn.activations == ["relu"]
gcn = GCN([2, 2], generator)
assert gcn.activations == ["relu", "relu"]
gcn = GCN([2], generator, activations=["linear"])
assert gcn.activations == ["linear"]
with pytest.raises(ValueError):
# More regularisers than layers
gcn = GCN([2], generator, activations=["relu", "linear"])
with pytest.raises(ValueError):
# Fewer regularisers than layers
gcn = GCN([2, 2], generator, activations=["relu"])
with pytest.raises(ValueError):
# Unknown regularisers
gcn = GCN([2], generator, activations=["bleach"])
def test_gat_serialize(self):
G = example_graph_1(feature_size=self.F_in)
gen = FullBatchNodeGenerator(G)
gat = GAT(
layer_sizes=self.layer_sizes,
activations=self.activations,
attn_heads=self.attn_heads,
generator=gen,
bias=True,
normalize="l2",
)
x_in, x_out = gat.node_model()
model = keras.Model(inputs=x_in, outputs=x_out)
# Save model
model_json = model.to_json()
# Set all weights to one
model_weights = [np.ones_like(w) for w in model.get_weights()]
# Load model from json & set all weights
model2 = keras.models.model_from_json(
model_json, custom_objects={"GraphAttention": GraphAttention})
model2.set_weights(model_weights)
# Test loaded model
X = gen.features
A = gen.Aadj
actual = model2.predict([X, A])
expected = np.ones(
(G.number_of_nodes(),
self.layer_sizes[-1])) * (1.0 / G.number_of_nodes())
assert expected == pytest.approx(actual)
def test_gat_node_model_wrong_norm(self):
G = example_graph_1(feature_size=self.F_in)
gen = FullBatchNodeGenerator(G)
with pytest.raises(ValueError):
gat = GAT(
layer_sizes=self.layer_sizes,
activations=self.activations,
attn_heads=self.attn_heads,
generator=gen,
bias=True,
normalize="whatever",
)
def test_GCN_init():
G, features = create_graph_features()
nodes = G.nodes()
node_features = pd.DataFrame.from_dict(
{n: f
for n, f in zip(nodes, features)}, orient="index")
G = StellarGraph(G, node_type_name="node", node_features=node_features)
generator = FullBatchNodeGenerator(G)
gcnModel = GCN([2], ["relu"], generator=generator, dropout=0.5)
assert gcnModel.layer_sizes == [2]
assert gcnModel.activations == ["relu"]
assert gcnModel.dropout == 0.5
def test_gat_sparse_node_model_constructor(self):
G = example_graph_1(feature_size=self.F_in)
gen = FullBatchNodeGenerator(G, sparse=self.sparse, method=self.method)
gat = GAT(
layer_sizes=self.layer_sizes,
activations=self.activations,
attn_heads=self.attn_heads,
generator=gen,
bias=True,
)
assert len(gat.node_model()) == 2
x_in, x_out = gat.node_model()
assert len(x_in) == 4 if self.sparse else 3
assert int(x_in[0].shape[-1]) == self.F_in
assert int(x_out.shape[-1]) == self.layer_sizes[-1]
def test_gat_node_model_constructor(self):
G = example_graph_1(feature_size=self.F_in)
gen = FullBatchNodeGenerator(G)
gat = GAT(
layer_sizes=self.layer_sizes,
activations=self.activations,
attn_heads=self.attn_heads,
generator=gen,
bias=True,
)
assert len(gat.node_model()) == 2
x_in, x_out = gat.node_model()
assert len(x_in) == 2
assert int(x_in[0].shape[-1]) == self.F_in
assert x_in[1]._keras_shape == (None, G.number_of_nodes())
assert int(x_out.shape[-1]) == self.layer_sizes[-1]
def test_GCN_apply():
G, features = create_graph_features()
adj = nx.adjacency_matrix(G)
nodes = G.nodes()
node_features = pd.DataFrame.from_dict(
{n: f for n, f in zip(nodes, features)}, orient="index"
)
G = StellarGraph(G, node_type_name="node", node_features=node_features)
generator = FullBatchNodeGenerator(G)
gcnModel = GCN([2], ["relu"], generator=generator, dropout=0.5)
x_in, x_out = gcnModel.node_model()
model = keras.Model(inputs=x_in, outputs=x_out)
preds = model.predict([features, adj], batch_size=adj.shape[0])
assert preds.shape == (3, 2)
def test_constructor(self):
G = example_graph_1(feature_size=self.F_in)
gen = FullBatchNodeGenerator(G, sparse=self.sparse, method=self.method)
# test error if no activations are passed:
with pytest.raises(TypeError):
gat = GAT(layer_sizes=self.layer_sizes, generator=gen, bias=True)
# test error where layer_sizes is not a list:
with pytest.raises(TypeError):
gat = GAT(
layer_sizes=10,
activations=self.activations,
attn_heads=self.attn_heads,
generator=gen,
bias=True,
)
# test error where layer_sizes values are not valid
with pytest.raises(ValueError):
gat = GAT(
layer_sizes=[4, 0],
activations=self.activations,
attn_heads=self.attn_heads,
generator=gen,
bias=True,
)
# test for incorrect length of att_heads list:
with pytest.raises(ValueError):
gat = GAT(
layer_sizes=self.layer_sizes,
activations=self.activations,
attn_heads=[8, 8, 1],
generator=gen,
bias=True,
)
# test for invalid values in att_heads list:
with pytest.raises(ValueError):
gat = GAT(
layer_sizes=self.layer_sizes,
activations=self.activations,
attn_heads=[8, 0],
generator=gen,
bias=True,
)
# test for invalid type of att_heads argument:
with pytest.raises(TypeError):
gat = GAT(
layer_sizes=self.layer_sizes,
activations=self.activations,
attn_heads=8.0,
generator=gen,
bias=True,
)
# test error where activations is not a list:
with pytest.raises(TypeError):
gat = GAT(
layer_sizes=self.layer_sizes,
activations="relu",
generator=gen,
bias=True,
)
# test attn_heads_reduction errors:
with pytest.raises(TypeError):
gat = GAT(
layer_sizes=self.layer_sizes,
activations=self.activations,
attn_heads=self.attn_heads,
attn_heads_reduction="concat",
generator=gen,
bias=True,
)
with pytest.raises(ValueError):
gat = GAT(
layer_sizes=self.layer_sizes,
activations=self.activations,
attn_heads=self.attn_heads,
attn_heads_reduction=["concat", "concat", "average"],
generator=gen,
bias=True,
)
with pytest.raises(ValueError):
gat = GAT(
layer_sizes=self.layer_sizes,
activations=self.activations,
attn_heads=self.attn_heads,
attn_heads_reduction=["concat", "sum"],
generator=gen,
bias=True,
)
# test error where len(activations) is not equal to len(layer_sizes):
with pytest.raises(ValueError):
gat = GAT(
layer_sizes=self.layer_sizes,
activations=["relu"],
generator=gen,
bias=True,
)
# Default attention heads reductions:
gat = GAT(
layer_sizes=self.layer_sizes,
activations=self.activations,
attn_heads=self.attn_heads,
generator=gen,
bias=True,
)
assert gat.activations == self.activations
assert gat.attn_heads_reduction == ["concat", "average"]
assert gat.generator == gen
# User-specified attention heads reductions:
gat = GAT(
layer_sizes=self.layer_sizes,
activations=self.activations,
attn_heads=self.attn_heads,
attn_heads_reduction=["concat", "concat"],
generator=gen,
bias=True,
)
assert gat.attn_heads_reduction == ["concat", "concat"]
def test_APPNP_edge_cases():
G, features = create_graph_features()
adj = nx.to_scipy_sparse_matrix(G)
features, adj = GCN_Aadj_feats_op(features, adj)
adj = adj.todense()[None, :, :]
n_nodes = features.shape[0]
nodes = G.nodes()
node_features = pd.DataFrame.from_dict(
{n: f
for n, f in zip(nodes, features)}, orient="index")
G = StellarGraph(G, node_features=node_features)
generator = FullBatchNodeGenerator(G, sparse=False, method="gcn")
try:
appnpModel = APPNP([2, 2], ["relu"], generator=generator, dropout=0.5)
except ValueError as e:
error = e
assert str(
error) == "The number of layers should equal the number of activations"
try:
appnpModel = APPNP([2], ["relu"], generator=[0, 1], dropout=0.5)
except TypeError as e:
error = e
assert str(
error) == "Generator should be a instance of FullBatchNodeGenerator"
try:
appnpModel = APPNP([2], ["relu"],
generator=generator,
dropout=0.0,
approx_iter=-1)
except ValueError as e:
error = e
assert str(error) == "approx_iter should be a positive integer"
try:
appnpModel = APPNP([2], ["relu"],
generator=generator,
dropout=0.0,
approx_iter=1.2)
except ValueError as e:
error = e
assert str(error) == "approx_iter should be a positive integer"
try:
appnpModel = APPNP([2], ["relu"],
generator=generator,
dropout=0.0,
teleport_probability=1.2)
except ValueError as e:
error = e
assert str(
error) == "teleport_probability should be between 0 and 1 (inclusive)"
try:
appnpModel = APPNP([2], ["relu"],
generator=generator,
dropout=0.0,
teleport_probability=1.2)
except ValueError as e:
error = e
assert str(
error) == "teleport_probability should be between 0 and 1 (inclusive)"
