Graph attention network (GAT) for node classification

import tensorflow as tf
from tensorflow import keras
from tensorflow.keras import layers
import numpy as np
import pandas as pd
import os
import warnings

warnings.filterwarnings("ignore")
pd.set_option("display.max_columns", 6)
pd.set_option("display.max_rows", 6)
np.random.seed(2)

zip_file = keras.utils.get_file(
    fname="cora.tgz",
    origin="https://linqs-data.soe.ucsc.edu/public/lbc/cora.tgz",
    extract=True,
)

data_dir = os.path.join(os.path.dirname(zip_file), "cora")

citations = pd.read_csv(
    os.path.join(data_dir, "cora.cites"),
    sep="\t",
    header=None,
    names=["target", "source"],
)

papers = pd.read_csv(
    os.path.join(data_dir, "cora.content"),
    sep="\t",
    header=None,
    names=["paper_id"] + [f"term_{idx}" for idx in range(1433)] + ["subject"],
)

class_values = sorted(papers["subject"].unique())
class_idx = {name: id for id, name in enumerate(class_values)}
paper_idx = {name: idx for idx, name in enumerate(sorted(papers["paper_id"].unique()))}

papers["paper_id"] = papers["paper_id"].apply(lambda name: paper_idx[name])
citations["source"] = citations["source"].apply(lambda name: paper_idx[name])
citations["target"] = citations["target"].apply(lambda name: paper_idx[name])
papers["subject"] = papers["subject"].apply(lambda value: class_idx[value])

print(citations)

print(papers)

# Obtain random indices
random_indices = np.random.permutation(range(papers.shape[0]))

# 50/50 split
train_data = papers.iloc[random_indices[: len(random_indices) // 2]]
test_data = papers.iloc[random_indices[len(random_indices) // 2 :]]

# Obtain paper indices which will be used to gather node states
# from the graph later on when training the model
train_indices = train_data["paper_id"].to_numpy()
test_indices = test_data["paper_id"].to_numpy()

# Obtain ground truth labels corresponding to each paper_id
train_labels = train_data["subject"].to_numpy()
test_labels = test_data["subject"].to_numpy()

# Define graph, namely an edge tensor and a node feature tensor
edges = tf.convert_to_tensor(citations[["target", "source"]])
node_states = tf.convert_to_tensor(papers.sort_values("paper_id").iloc[:, 1:-1])

# Print shapes of the graph
print("Edges shape:\t\t", edges.shape)
print("Node features shape:", node_states.shape)

class GraphAttention(layers.Layer):
    def __init__(
        self,
        units,
        kernel_initializer="glorot_uniform",
        kernel_regularizer=None,
        **kwargs,
    ):
        super().__init__(**kwargs)
        self.units = units
        self.kernel_initializer = keras.initializers.get(kernel_initializer)
        self.kernel_regularizer = keras.regularizers.get(kernel_regularizer)

    def build(self, input_shape):

        self.kernel = self.add_weight(
            shape=(input_shape[0][-1], self.units),
            trainable=True,
            initializer=self.kernel_initializer,
            regularizer=self.kernel_regularizer,
            name="kernel",
        )
        self.kernel_attention = self.add_weight(
            shape=(self.units * 2, 1),
            trainable=True,
            initializer=self.kernel_initializer,
            regularizer=self.kernel_regularizer,
            name="kernel_attention",
        )
        self.built = True

    def call(self, inputs):
        node_states, edges = inputs

        # Linearly transform node states
        node_states_transformed = tf.matmul(node_states, self.kernel)

        # (1) Compute pair-wise attention scores
        node_states_expanded = tf.gather(node_states_transformed, edges)
        node_states_expanded = tf.reshape(
            node_states_expanded, (tf.shape(edges)[0], -1)
        )
        attention_scores = tf.nn.leaky_relu(
            tf.matmul(node_states_expanded, self.kernel_attention)
        )
        attention_scores = tf.squeeze(attention_scores, -1)

        # (2) Normalize attention scores
        attention_scores = tf.math.exp(tf.clip_by_value(attention_scores, -2, 2))
        attention_scores_sum = tf.math.unsorted_segment_sum(
            data=attention_scores,
            segment_ids=edges[:, 0],
            num_segments=tf.reduce_max(edges[:, 0]) + 1,
        )
        attention_scores_sum = tf.repeat(
            attention_scores_sum, tf.math.bincount(tf.cast(edges[:, 0], "int32"))
        )
        attention_scores_norm = attention_scores / attention_scores_sum

        # (3) Gather node states of neighbors, apply attention scores and aggregate
        node_states_neighbors = tf.gather(node_states_transformed, edges[:, 1])
        out = tf.math.unsorted_segment_sum(
            data=node_states_neighbors * attention_scores_norm[:, tf.newaxis],
            segment_ids=edges[:, 0],
            num_segments=tf.shape(node_states)[0],
        )
        return out


class MultiHeadGraphAttention(layers.Layer):
    def __init__(self, units, num_heads=8, merge_type="concat", **kwargs):
        super().__init__(**kwargs)
        self.num_heads = num_heads
        self.merge_type = merge_type
        self.attention_layers = [GraphAttention(units) for _ in range(num_heads)]

    def call(self, inputs):
        atom_features, pair_indices = inputs

        # Obtain outputs from each attention head
        outputs = [
            attention_layer([atom_features, pair_indices])
            for attention_layer in self.attention_layers
        ]
        # Concatenate or average the node states from each head
        if self.merge_type == "concat":
            outputs = tf.concat(outputs, axis=-1)
        else:
            outputs = tf.reduce_mean(tf.stack(outputs, axis=-1), axis=-1)
        # Activate and return node states
        return tf.nn.relu(outputs)

class GraphAttentionNetwork(keras.Model):
    def __init__(
        self,
        node_states,
        edges,
        hidden_units,
        num_heads,
        num_layers,
        output_dim,
        **kwargs,
    ):
        super().__init__(**kwargs)
        self.node_states = node_states
        self.edges = edges
        self.preprocess = layers.Dense(hidden_units * num_heads, activation="relu")
        self.attention_layers = [
            MultiHeadGraphAttention(hidden_units, num_heads) for _ in range(num_layers)
        ]
        self.output_layer = layers.Dense(output_dim)

    def call(self, inputs):
        node_states, edges = inputs
        x = self.preprocess(node_states)
        for attention_layer in self.attention_layers:
            x = attention_layer([x, edges]) + x
        outputs = self.output_layer(x)
        return outputs

    def train_step(self, data):
        indices, labels = data

        with tf.GradientTape() as tape:
            # Forward pass
            outputs = self([self.node_states, self.edges])
            # Compute loss
            loss = self.compiled_loss(labels, tf.gather(outputs, indices))
        # Compute gradients
        grads = tape.gradient(loss, self.trainable_weights)
        # Apply gradients (update weights)
        optimizer.apply_gradients(zip(grads, self.trainable_weights))
        # Update metric(s)
        self.compiled_metrics.update_state(labels, tf.gather(outputs, indices))

        return {m.name: m.result() for m in self.metrics}

    def predict_step(self, data):
        indices = data
        # Forward pass
        outputs = self([self.node_states, self.edges])
        # Compute probabilities
        return tf.nn.softmax(tf.gather(outputs, indices))

    def test_step(self, data):
        indices, labels = data
        # Forward pass
        outputs = self([self.node_states, self.edges])
        # Compute loss
        loss = self.compiled_loss(labels, tf.gather(outputs, indices))
        # Update metric(s)
        self.compiled_metrics.update_state(labels, tf.gather(outputs, indices))

        return {m.name: m.result() for m in self.metrics}

# Define hyper-parameters
HIDDEN_UNITS = 100
NUM_HEADS = 8
NUM_LAYERS = 3
OUTPUT_DIM = len(class_values)

NUM_EPOCHS = 100
BATCH_SIZE = 256
VALIDATION_SPLIT = 0.1
LEARNING_RATE = 3e-1
MOMENTUM = 0.9

loss_fn = keras.losses.SparseCategoricalCrossentropy(from_logits=True)
optimizer = keras.optimizers.SGD(LEARNING_RATE, momentum=MOMENTUM)
accuracy_fn = keras.metrics.SparseCategoricalAccuracy(name="acc")
early_stopping = keras.callbacks.EarlyStopping(
    monitor="val_acc", min_delta=1e-5, patience=5, restore_best_weights=True
)

# Build model
gat_model = GraphAttentionNetwork(
    node_states, edges, HIDDEN_UNITS, NUM_HEADS, NUM_LAYERS, OUTPUT_DIM
)

# Compile model
gat_model.compile(loss=loss_fn, optimizer=optimizer, metrics=[accuracy_fn])

gat_model.fit(
    x=train_indices,
    y=train_labels,
    validation_split=VALIDATION_SPLIT,
    batch_size=BATCH_SIZE,
    epochs=NUM_EPOCHS,
    callbacks=[early_stopping],
    verbose=2,
)

_, test_accuracy = gat_model.evaluate(x=test_indices, y=test_labels, verbose=0)

print("--" * 38 + f"\nTest Accuracy {test_accuracy*100:.1f}%")

test_probs = gat_model.predict(x=test_indices)

mapping = {v: k for (k, v) in class_idx.items()}

for i, (probs, label) in enumerate(zip(test_probs[:10], test_labels[:10])):
    print(f"Example {i+1}: {mapping[label]}")
    for j, c in zip(probs, class_idx.keys()):
        print(f"\tProbability of {c: <24} = {j*100:7.3f}%")
    print("---" * 20)