def create_HinSAGE_model(graph, link_prediction=False):
if link_prediction:
generator = HinSAGELinkGenerator(graph,
batch_size=2,
num_samples=[2, 1])
edge_ids_train = np.array([[1, 2], [2, 3], [1, 3]])
train_gen = generator.flow(edge_ids_train, np.array([1, 1, 0]))
else:
generator = HinSAGENodeGenerator(graph,
batch_size=2,
num_samples=[2, 2])
train_gen = generator.flow([1, 2], np.array([[1, 0], [0, 1]]))
base_model = HinSAGE(layer_sizes=[8, 8],
generator=train_gen,
bias=True,
dropout=0.5)
if link_prediction:
# Define input and output sockets of hinsage:
x_inp, x_out = base_model.build()
# Final estimator layer
prediction = link_regression(edge_embedding_method="ip")(x_out)
else:
x_inp, x_out = base_model.build()
prediction = layers.Dense(units=2, activation="softmax")(x_out)
keras_model = Model(inputs=x_inp, outputs=prediction)
return base_model, keras_model, generator, train_gen
def train_hinsage(self, S, node_identifiers, label, batch_size, epochs):
"""
This function trains a HinSAGE model, implemented in Tensorflow.
It returns the trained HinSAGE model and a pandas datarame containing the embeddings generated for the train nodes.
Parameters
----------
S : StellarGraph Object
The graph on which HinSAGE trains its aggregator functions.
node_identifiers : list
Defines the nodes that HinSAGE uses to train its aggregation functions.
label: Pandas dataframe
Defines the label of the nodes used for training, with the index representing the nodes.
batch_size: int
batch size to train the neural network in which HinSAGE is implemented.
epochs: int
Number of epochs for the neural network.
"""
# The mapper feeds data from sampled subgraph to GraphSAGE model
train_node_identifiers = node_identifiers[:round(0.8*len(node_identifiers))]
train_labels = label.loc[train_node_identifiers]
validation_node_identifiers = node_identifiers[round(0.8*len(node_identifiers)):]
validation_labels = label.loc[validation_node_identifiers]
generator = HinSAGENodeGenerator(S, batch_size, self.num_samples, head_node_type= self.embedding_for_node_type)
train_gen = generator.flow(train_node_identifiers, train_labels, shuffle=True)
test_gen = generator.flow(validation_node_identifiers, validation_labels)
# HinSAGE model
model = HinSAGE(layer_sizes=[self.embedding_size]*len(self.num_samples), generator=generator, dropout=0)
x_inp, x_out = model.build()
# Final estimator layer
prediction = layers.Dense(units=1, activation="sigmoid", dtype='float32')(x_out)
# Create Keras model for training
model = Model(inputs=x_inp, outputs=prediction)
model.compile(
optimizer=optimizers.Adam(lr=1e-3),
loss=binary_crossentropy,
)
# Train Model
model.fit(
train_gen, epochs=epochs, verbose=1, validation_data=test_gen, shuffle=False
)
trained_model = Model(inputs=x_inp, outputs=x_out)
train_gen_not_shuffled = generator.flow( node_identifiers, label, shuffle=False)
embeddings_train = trained_model.predict(train_gen_not_shuffled)
train_emb = pd.DataFrame(embeddings_train, index=node_identifiers)
return trained_model, train_emb
def get_hinsage_model(generator,
train_gen,
test_gen,
num_samples=[8, 4],
hinsage_layer_sizes=[32, 32],
bias=True,
dropout=0.0,
lr=1e-2,
edge_embedding_method='concat',
output_act='sigmoid'):
assert len(hinsage_layer_sizes) == len(num_samples)
hinsage = HinSAGE(layer_sizes=hinsage_layer_sizes,
generator=generator,
bias=bias,
dropout=dropout)
# Expose input and output sockets of hinsage:
x_inp, x_out = hinsage.in_out_tensors()
# Final estimator layer
score_prediction = link_classification(
output_dim=1,
output_act='sigmoid',
edge_embedding_method=edge_embedding_method)(x_out)
def root_mean_square_error(s_true, s_pred):
return K.sqrt(K.mean(K.pow(s_true - s_pred, 2)))
def recall_m(y_true, y_pred):
y_pred = tf.where(y_pred > 0.5, 1.0, 0.0)
true_positives = K.sum(K.round(K.clip(y_true * y_pred, 0, 1)))
possible_positives = K.sum(K.round(K.clip(y_true, 0, 1)))
recall = true_positives / (possible_positives + K.epsilon())
return recall
def precision_m(y_true, y_pred):
y_pred = tf.where(y_pred > 0.5, 1.0, 0.0)
true_positives = K.sum(K.round(K.clip(y_true * y_pred, 0, 1)))
predicted_positives = K.sum(K.round(K.clip(y_pred, 0, 1)))
precision = true_positives / (predicted_positives + K.epsilon())
return precision
def f1_m(y_true, y_pred):
y_pred = tf.where(y_pred > 0.5, 1.0, 0.0)
precision = precision_m(y_true, y_pred)
recall = recall_m(y_true, y_pred)
return 2 * ((precision * recall) / (precision + recall + K.epsilon()))
model = Model(inputs=x_inp, outputs=score_prediction)
model.compile(
optimizer=optimizers.Adam(lr=lr),
# loss=losses.mean_squared_error,
loss=losses.binary_crossentropy,
metrics=[
metrics.binary_accuracy,
metrics.Precision(),
metrics.Recall()
],
# metrics=[root_mean_square_error, metrics.mae, 'acc'],
)
return model
def train(
G,
user_targets,
layer_size,
num_samples,
batch_size,
num_epochs,
learning_rate,
dropout,
):
"""
Train a HinSAGE model on the specified graph G with given parameters.
Args:
G: A StellarGraph object ready for machine learning
layer_size: A list of number of hidden nodes in each layer
num_samples: Number of neighbours to sample at each layer
batch_size: Size of batch for inference
num_epochs: Number of epochs to train the model
learning_rate: Initial Learning rate
dropout: The dropout (0->1)
"""
print(G.info())
# Split "user" nodes into train/test
# Split nodes into train/test using stratification.
train_targets, test_targets = model_selection.train_test_split(
user_targets, train_size=0.25, test_size=None
)
print("Train targets:\n", train_targets.iloc[:, 0].value_counts())
print("Test targets:\n", test_targets.iloc[:, 0].value_counts())
# The mapper feeds data from sampled subgraph to GraphSAGE model
generator = HinSAGENodeGenerator(G, batch_size, num_samples, head_node_type="user")
train_gen = generator.flow_from_dataframe(train_targets, shuffle=True)
test_gen = generator.flow_from_dataframe(test_targets)
# GraphSAGE model
model = HinSAGE(layer_sizes=layer_size, generator=generator, dropout=dropout)
x_inp, x_out = model.build()
# Final estimator layer
prediction = layers.Dense(units=train_targets.shape[1], activation="softmax")(x_out)
# The elite label is only true for a small fraction of the total users,
# so weight the training loss to ensure that model learns to predict
# the positive class.
# class_count = train_targets.values.sum(axis=0)
# weights = class_count.sum()/class_count
weights = [0.01, 1.0]
print("Weighting loss by: {}".format(weights))
# Create Keras model for training
model = keras.Model(inputs=x_inp, outputs=prediction)
model.compile(
optimizer=optimizers.Adam(lr=learning_rate),
loss=weighted_binary_crossentropy(weights),
metrics=[metrics.binary_accuracy],
)
# Train model
history = model.fit_generator(
train_gen, epochs=num_epochs, verbose=2, shuffle=False
)
# Evaluate on test set and print metrics
predictions = model.predict_generator(test_gen)
binary_predictions = predictions[:, 1] > 0.5
print("\nTest Set Metrics (on {} nodes)".format(len(predictions)))
# Calculate metrics using Scikit-Learn
cm = sk_metrics.confusion_matrix(test_targets.iloc[:, 1], binary_predictions)
print("Confusion matrix:")
print(cm)
accuracy = sk_metrics.accuracy_score(test_targets.iloc[:, 1], binary_predictions)
precision = sk_metrics.precision_score(test_targets.iloc[:, 1], binary_predictions)
recall = sk_metrics.recall_score(test_targets.iloc[:, 1], binary_predictions)
f1 = sk_metrics.f1_score(test_targets.iloc[:, 1], binary_predictions)
roc_auc = sk_metrics.roc_auc_score(test_targets.iloc[:, 1], binary_predictions)
print(
"accuracy = {:0.3}, precision = {:0.3}, recall = {:0.3}, f1 = {:0.3}".format(
accuracy, precision, recall, f1
)
)
print("ROC AUC = {:0.3}".format(roc_auc))
# Save model
save_str = "_n{}_l{}_d{}_r{}".format(
"_".join([str(x) for x in num_samples]),
"_".join([str(x) for x in layer_size]),
dropout,
learning_rate,
)
model.save("yelp_model" + save_str + ".h5")
def train(
self,
layer_size,
num_samples,
train_size=0.7,
batch_size: int = 200,
num_epochs: int = 20,
learning_rate=5e-3,
dropout=0.0,
use_bias=True,
):
"""
Build and train the HinSAGE model for link attribute prediction on the specified graph G
with given parameters.
Args:
layer_size: a list of number of hidden nodes in each layer
num_samples: number of neighbours to sample at each layer
batch_size: size of mini batch
num_epochs: number of epochs to train the model (epoch = all training batches are streamed through the model once)
learning_rate: initial learning rate
dropout: dropout probability in the range [0, 1)
use_bias: tells whether to use a bias terms in HinSAGE model
Returns:
"""
# Training and test edges
edges = list(self.g.edges(data=True))
edges_train, edges_test = model_selection.train_test_split(
edges, train_size=train_size)
# Edgelists:
edgelist_train = [(e[0], e[1]) for e in edges_train]
edgelist_test = [(e[0], e[1]) for e in edges_test]
labels_train = [e[2]["score"] for e in edges_train]
labels_test = [e[2]["score"] for e in edges_test]
# Our machine learning task of learning user-movie ratings can be framed as a supervised Link Attribute Inference:
# given a graph of user-movie ratings, we train a model for rating prediction using the ratings edges_train,
# and evaluate it using the test ratings edges_test. The model also requires the user-movie graph structure.
# To proceed, we need to create a StellarGraph object from the ingested graph, for training the model:
# When sampling the GraphSAGE subgraphs, we want to treat user-movie links as undirected
self.g = sg.StellarGraph(self.g, node_features="feature")
# Next, we create the link generators for preparing and streaming training and testing data to the model.
# The mappers essentially sample k-hop subgraphs of G with randomly selected head nodes, as required by
# the HinSAGE algorithm, and generate minibatches of those samples to be fed to the input layer of the HinSAGE model.
generator = HinSAGELinkGenerator(self.g,
batch_size,
num_samples,
head_node_types=["user", "movie"])
train_gen = generator.flow(edgelist_train, labels_train)
test_gen = generator.flow(edgelist_test, labels_test)
# Build the model by stacking a two-layer HinSAGE model and a link regression layer on top.
assert len(layer_size) == len(
num_samples
), "layer_size and num_samples must be of the same length! Stopping."
hinsage = HinSAGE(layer_sizes=layer_size,
generator=generator,
bias=use_bias,
dropout=dropout)
# Define input and output sockets of hinsage:
x_inp, x_out = hinsage.build()
# Final estimator layer
score_prediction = link_regression(
edge_embedding_method=args.edge_embedding_method)(x_out)
# Create Keras model for training
model = Model(inputs=x_inp, outputs=score_prediction)
model.compile(
optimizer=optimizers.Adam(lr=learning_rate),
loss=losses.mean_squared_error,
metrics=[root_mean_square_error, metrics.mae],
)
# Train model
print("Training the model for {} epochs with initial learning rate {}".
format(num_epochs, learning_rate))
history = model.fit_generator(
train_gen,
validation_data=test_gen,
epochs=num_epochs,
verbose=2,
shuffle=True,
use_multiprocessing=True,
workers=multiprocessing.cpu_count() // 2,
)
# Evaluate and print metrics
test_metrics = model.evaluate_generator(test_gen)
print("Test Evaluation:")
for name, val in zip(model.metrics_names, test_metrics):
print("\t{}: {:0.4f}".format(name, val))
def create_embeddings(node_type, num_samples, hinsage_layer_sizes, epochs,
patience, batch_size, dropout, activations):
# Check if num_samples and layer_size are compatible
assert len(hinsage_layer_sizes) == len(num_samples)
generator = HinSAGENodeGenerator(G,
batch_size,
num_samples=num_samples,
head_node_type=node_type)
# HinSAGE layers
hinsage = HinSAGE(layer_sizes=hinsage_layer_sizes,
activations=activations,
generator=generator,
bias=True,
normalize="l2",
dropout=dropout)
def run_deep_graph_infomax(base_model, generator, epochs, node_type):
corrupted_generator = CorruptedGenerator(generator)
gen = corrupted_generator.flow(G.nodes(node_type=node_type))
infomax = DeepGraphInfomax(base_model, corrupted_generator)
x_in, x_out = infomax.in_out_tensors()
print("Starting Training")
ttrain = time.time()
# Train
model = Model(inputs=x_in, outputs=x_out)
model.compile(loss=tf.nn.sigmoid_cross_entropy_with_logits,
optimizer=Adam(lr=1e-3))
es = EarlyStopping(monitor="loss", min_delta=0, patience=patience)
history = model.fit(gen,
epochs=epochs,
verbose=verbose,
callbacks=[es])
# sg.utils.plot_history(history)
ttrain1 = time.time()
print(
f"Training complete in {(ttrain1-ttrain):.2f} s ({(ttrain1-ttrain)/60:.2f} min)"
)
x_emb_in, x_emb_out = base_model.in_out_tensors()
# for full batch models, squeeze out the batch dim (which is 1)
if generator.num_batch_dims() == 2:
x_emb_out = tf.squeeze(x_emb_out, axis=0)
return x_emb_in, x_emb_out
# Run Deep Graph Infomax
x_emb_in, x_emb_out = run_deep_graph_infomax(hinsage,
generator,
epochs=epochs,
node_type=node_type)
emb_model = Model(inputs=x_emb_in, outputs=x_emb_out)
all_embeddings = emb_model.predict(
generator.flow(G.nodes(node_type=node_type)))
# TSNE visualization of embeddings
ttsne = time.time()
print("Creating TSNE")
embeddings_2d = pd.DataFrame(
TSNE(n_components=2).fit_transform(all_embeddings),
index=G.nodes(node_type=node_type))
# draw the points (colors based on ExtendedCaseGraphID)
node_ids = G.nodes(node_type=node_type).tolist()
ext_targets = v_sample.loc[[int(node_id) for node_id in node_ids
]].ExtendedCaseGraphID
label_map = {
l: i * 10
for i, l in enumerate(np.unique(ext_targets), start=10)
if pd.notna(l)
}
node_colours = [
label_map[target] if pd.notna(target) else 0
for target in ext_targets
]
ttsne1 = time.time()
print(
f"TSNE completed in {(ttsne1-ttsne):.2f} s ({(ttsne1-ttsne)/60:.2f} min)"
)
alpha = 0.7
fig, ax = plt.subplots(figsize=(15, 15))
ax.scatter(
embeddings_2d[0],
embeddings_2d[1],
c=node_colours,
cmap="jet",
alpha=alpha,
)
ax.set(aspect="equal")
plt.title(
f'TSNE visualization of HinSAGE "{node_type}" embeddings with Deep Graph Infomax'
)
plt.savefig(f"./embeddings/HinSAGE_DGI_embeddings_{node_type}.pdf")
return all_embeddings, embeddings_2d
def run_for_node_type(v_type, hinsage_layer_sizes, num_samples,
activations, epochs):
nan_tflag = data_splits[v_type].iloc[0].values[0]
train_tflag = data_splits[v_type].iloc[1].values[0]
test_tflag = data_splits[v_type].iloc[2].values[0]
train_cv_set = v_sets[v_type][nan_tflag:nan_tflag + train_tflag]
train_cv_ids = train_cv_set.index.values.tolist()
train_cv_labels = v_data.loc[[
int(node_id) for node_id in train_cv_ids
]].ExtendedCaseGraphID
test_set = v_sets[v_type][-test_tflag:]
test_ids = test_set.index.values.tolist()
generator = HinSAGENodeGenerator(G,
batch_size,
num_samples,
head_node_type=v_type)
hinsage = HinSAGE(layer_sizes=hinsage_layer_sizes,
activations=activations,
generator=generator,
bias=True,
normalize="l2",
dropout=dropout)
def run_deep_graph_infomax(base_model, generator, epochs):
print(f"Starting training for {v_type} type: ")
t0 = time.time()
corrupted_generator = CorruptedGenerator(generator)
gen = corrupted_generator.flow(G.nodes(node_type=v_type))
infomax = DeepGraphInfomax(base_model, corrupted_generator)
x_in, x_out = infomax.in_out_tensors()
# Train with DGI
model = Model(inputs=x_in, outputs=x_out)
model.compile(loss=tf.nn.sigmoid_cross_entropy_with_logits,
optimizer=Adam(lr=1e-3))
es = EarlyStopping(monitor="loss", min_delta=0, patience=10)
history = model.fit(gen,
epochs=epochs,
verbose=verbose,
callbacks=[es])
#sg.utils.plot_history(history)
x_emb_in, x_emb_out = base_model.in_out_tensors()
if generator.num_batch_dims() == 2:
x_emb_out = tf.squeeze(x_emb_out, axis=0)
t1 = time.time()
print(f'Time required: {t1-t0:.2f} s ({(t1-t0)/60:.1f} min)')
return x_emb_in, x_emb_out, model
#? Train HinSAGE model:
x_emb_in, x_emb_out, _model = run_deep_graph_infomax(hinsage,
generator,
epochs=epochs)
emb_model = Model(inputs=x_emb_in, outputs=x_emb_out)
train_cv_embs = emb_model.predict(
generator.flow(train_cv_set.index.values))
#? Optional: Plot embeddings of training and CV set of current node type
if (visualize == True):
train_cv_embs_2d = pd.DataFrame(
TSNE(n_components=2).fit_transform(train_cv_embs),
index=train_cv_set.index.values)
label_map = {
l: i * 10
for i, l in enumerate(np.unique(train_cv_labels), start=10)
if pd.notna(l)
}
node_colours = [
label_map[target] if pd.notna(target) else 0
for target in train_cv_labels
]
alpha = 0.7
fig, ax = plt.subplots(figsize=(15, 15))
ax.scatter(
train_cv_embs_2d[0],
train_cv_embs_2d[1],
c=node_colours,
cmap="jet",
alpha=alpha,
)
ax.set(aspect="equal")
plt.title(
f"TSNE of HinSAGE {v_type} embeddings with DGI- coloring on ExtendedCaseGraphID"
)
plt.show()
return 1
#? Split training and cross valuation set using 80% 20% simple ordered split
n_embs = train_cv_embs.shape[0]
train_size = int(n_embs * 0.80)
cv_size = int(n_embs * 0.20)
train_set = train_cv_embs[:train_size]
train_labels = np.ravel(
pd.DataFrame(train_cv_labels.values[:train_size]).fillna(0))
cv_set = train_cv_embs[-cv_size:]
cv_labels = np.ravel(
pd.DataFrame(train_cv_labels.values[-cv_size:]).fillna(0))
#? CLASSIFY
print(f"Running Classifier for {v_type} type")
classifier = DecisionTreeClassifier()
classifier.fit(
X=train_set,
y=train_labels,
)
cv_pred = classifier.predict(cv_set)
f1_avg = f1_score(cv_labels, cv_pred, average='weighted')
acc = (cv_pred == cv_labels).mean()
print(f"{v_type} CV Metrics: f1: {f1_avg:.6f} - acc: {acc:.6f}")
#? Now Run on test set
test_embs = emb_model.predict(generator.flow(test_set.index.values))
test_pred = classifier.predict(test_embs)
#? Save predictions
outdir = './output'
outname = f"{v_type}_predictions.csv"
if not os.path.exists(outdir):
os.mkdir(outdir)
fullname = os.path.join(outdir, outname)
output = pd.DataFrame(test_ids)
output = output.rename(columns={0: 'node_id'})
output['ExtendedCaseGraphID'] = test_pred
output = output.set_index('node_id')
output.to_csv(fullname)
return output