11/26/23, 11:33 PM 1. Graph Convolutional Networks.

ipynb - Colaboratory

Graph Convolutional Networks

Chapter 1 of the Graph Neural Network Course

❤️ Created by @maximelabonne.
Companion notebook to execute the code from the following article: https://mlabonne.github.io/blog/intrognn/

1 !pip -q install torch_geometric

2
3 import torch
4 import numpy as np
5 import networkx as nx
6 import matplotlib.pyplot as plt

1 from torch_geometric.datasets import KarateClub

2
3 # Import dataset from PyTorch Geometric
4 dataset = KarateClub()
5
6 # Print information
7 print(dataset)
8 print('------------')
9 print(f'Number of graphs: {len(dataset)}')
10 print(f'Number of features: {dataset.num_features}')
11 print(f'Number of classes: {dataset.num_classes}')

KarateClub()
------------
Number of graphs: 1
Number of features: 34
Number of classes: 4

1 # Print first element

2 print(f'Graph: {dataset[0]}')

Graph: Data(x=[34, 34], edge_index=[2, 156], y=[34], train_mask=[34])

1 data = dataset[0]
2
3 print(f'x = {data.x.shape}')
4 print(data.x)

x = torch.Size([34, 34])
tensor([[1., 0., 0., ..., 0., 0., 0.],
[0., 1., 0., ..., 0., 0., 0.],
[0., 0., 1., ..., 0., 0., 0.],
...,
[0., 0., 0., ..., 1., 0., 0.],
[0., 0., 0., ..., 0., 1., 0.],
[0., 0., 0., ..., 0., 0., 1.]])

1 print(f'edge_index = {data.edge_index.shape}')
2 print(data.edge_index)

edge_index = torch.Size([2, 156])

tensor([[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1,
1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3,
3, 3, 3, 3, 3, 4, 4, 4, 5, 5, 5, 5, 6, 6, 6, 6, 7, 7,
7, 7, 8, 8, 8, 8, 8, 9, 9, 10, 10, 10, 11, 12, 12, 13, 13, 13,
13, 13, 14, 14, 15, 15, 16, 16, 17, 17, 18, 18, 19, 19, 19, 20, 20, 21,
21, 22, 22, 23, 23, 23, 23, 23, 24, 24, 24, 25, 25, 25, 26, 26, 27, 27,
27, 27, 28, 28, 28, 29, 29, 29, 29, 30, 30, 30, 30, 31, 31, 31, 31, 31,
31, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 33, 33, 33, 33, 33,
33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33],
[ 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 17, 19, 21, 31, 0, 2,
3, 7, 13, 17, 19, 21, 30, 0, 1, 3, 7, 8, 9, 13, 27, 28, 32, 0,
1, 2, 7, 12, 13, 0, 6, 10, 0, 6, 10, 16, 0, 4, 5, 16, 0, 1,
2, 3, 0, 2, 30, 32, 33, 2, 33, 0, 4, 5, 0, 0, 3, 0, 1, 2,
3, 33, 32, 33, 32, 33, 5, 6, 0, 1, 32, 33, 0, 1, 33, 32, 33, 0,
1, 32, 33, 25, 27, 29, 32, 33, 25, 27, 31, 23, 24, 31, 29, 33, 2, 23,
24, 33, 2, 31, 33, 23, 26, 32, 33, 1, 8, 32, 33, 0, 24, 25, 28, 32,
33, 2, 8, 14, 15, 18, 20, 22, 23, 29, 30, 31, 33, 8, 9, 13, 14, 15,
18, 19, 20, 22, 23, 26, 27, 28, 29, 30, 31, 32]])

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11/26/23, 11:33 PM 1. Graph Convolutional Networks.ipynb - Colaboratory

1 from torch_geometric.utils import to_dense_adj

2
3 A = to_dense_adj(data.edge_index)[0].numpy().astype(int)
4 print(f'A = {A.shape}')
5 print(A)

A = (34, 34)
[[0 1 1 ... 1 0 0]
[1 0 1 ... 0 0 0]
[1 1 0 ... 0 1 0]
...
[1 0 0 ... 0 1 1]
[0 0 1 ... 1 0 1]
[0 0 0 ... 1 1 0]]

1 print(f'y = {data.y.shape}')
2 print(data.y)

y = torch.Size([34])
tensor([1, 1, 1, 1, 3, 3, 3, 1, 0, 1, 3, 1, 1, 1, 0, 0, 3, 1, 0, 1, 0, 1, 0, 0,
2, 2, 0, 0, 2, 0, 0, 2, 0, 0])

1 print(f'train_mask = {data.train_mask.shape}')
2 print(data.train_mask)

train_mask = torch.Size([34])
tensor([ True, False, False, False, True, False, False, False, True, False,
False, False, False, False, False, False, False, False, False, False,
False, False, False, False, True, False, False, False, False, False,
False, False, False, False])

1 print(f'Edges are directed: {data.is_directed()}')

2 print(f'Graph has isolated nodes: {data.has_isolated_nodes()}')
3 print(f'Graph has loops: {data.has_self_loops()}')

Edges are directed: False

Graph has isolated nodes: False
Graph has loops: False

1 from torch_geometric.utils import to_networkx

2
3 G = to_networkx(data, to_undirected=True)
4 plt.figure(figsize=(12,12))
5 plt.axis('off')
6 nx.draw_networkx(G,
7 pos=nx.spring_layout(G, seed=0),
8 with_labels=True,
9 node_size=800,
10 node_color=data.y,
11 cmap="hsv",
12 vmin=-2,
13 vmax=3,
14 width=0.8,
15 edge_color="grey",
16 font_size=14
17 )
18 plt.show()

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11/26/23, 11:33 PM 1. Graph Convolutional Networks.ipynb - Colaboratory

1 from torch.nn import Linear

2 from torch_geometric.nn import GCNConv
3
4
5 class GCN(torch.nn.Module):
6 def __init__(self):
7 super().__init__()
8 self.gcn = GCNConv(dataset.num_features, 3)
9 self.out = Linear(3, dataset.num_classes)
10
11 def forward(self, x, edge_index):
12 h = self.gcn(x, edge_index).relu()
13 z = self.out(h)
14 return h, z
15
16 model = GCN()
17 print(model)

GCN(
(gcn): GCNConv(34, 3)
(out): Linear(in_features=3, out_features=4, bias=True)
)

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11/26/23, 11:33 PM 1. Graph Convolutional Networks.ipynb - Colaboratory
1 criterion = torch.nn.CrossEntropyLoss()
2 optimizer = torch.optim.Adam(model.parameters(), lr=0.02)
3
4 # Calculate accuracy
5 def accuracy(pred_y, y):
6 return (pred_y == y).sum() / len(y)
7
8 # Data for animations
9 embeddings = []
10 losses = []
11 accuracies = []
12 outputs = []
13
14 # Training loop
15 for epoch in range(201):
16 # Clear gradients
17 optimizer.zero_grad()
18
19 # Forward pass
20 h, z = model(data.x, data.edge_index)
21
22 # Calculate loss function
23 loss = criterion(z, data.y)
24
25 # Calculate accuracy
26 acc = accuracy(z.argmax(dim=1), data.y)
27
28 # Compute gradients
29 loss.backward()
30
31 # Tune parameters
32 optimizer.step()
33
34 # Store data for animations
35 embeddings.append(h)
36 losses.append(loss)
37 accuracies.append(acc)
38 outputs.append(z.argmax(dim=1))
39
40 # Print metrics every 10 epochs
41 if epoch % 10 == 0:
42 print(f'Epoch {epoch:>3} | Loss: {loss:.2f} | Acc: {acc*100:.2f}%')

Epoch 0 | Loss: 1.40 | Acc: 41.18%

Epoch 10 | Loss: 1.21 | Acc: 47.06%
Epoch 20 | Loss: 1.02 | Acc: 67.65%
Epoch 30 | Loss: 0.80 | Acc: 73.53%
Epoch 40 | Loss: 0.59 | Acc: 73.53%
Epoch 50 | Loss: 0.39 | Acc: 94.12%
Epoch 60 | Loss: 0.23 | Acc: 97.06%
Epoch 70 | Loss: 0.13 | Acc: 100.00%
Epoch 80 | Loss: 0.07 | Acc: 100.00%
Epoch 90 | Loss: 0.05 | Acc: 100.00%
Epoch 100 | Loss: 0.03 | Acc: 100.00%
Epoch 110 | Loss: 0.02 | Acc: 100.00%
Epoch 120 | Loss: 0.02 | Acc: 100.00%
Epoch 130 | Loss: 0.02 | Acc: 100.00%
Epoch 140 | Loss: 0.01 | Acc: 100.00%
Epoch 150 | Loss: 0.01 | Acc: 100.00%
Epoch 160 | Loss: 0.01 | Acc: 100.00%
Epoch 170 | Loss: 0.01 | Acc: 100.00%
Epoch 180 | Loss: 0.01 | Acc: 100.00%
Epoch 190 | Loss: 0.01 | Acc: 100.00%
Epoch 200 | Loss: 0.01 | Acc: 100.00%

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11/26/23, 11:33 PM 1. Graph Convolutional Networks.ipynb - Colaboratory
1 %%capture
2 from IPython.display import HTML
3 from matplotlib import animation
4 plt.rcParams["animation.bitrate"] = 3000
5
6 def animate(i):
7 G = to_networkx(data, to_undirected=True)
8 nx.draw_networkx(G,
9 pos=nx.spring_layout(G, seed=0),
10 with_labels=True,
11 node_size=800,
12 node_color=outputs[i],
13 cmap="hsv",
14 vmin=-2,
15 vmax=3,
16 width=0.8,
17 edge_color="grey",
18 font_size=14
19 )
20 plt.title(f'Epoch {i} | Loss: {losses[i]:.2f} | Acc: {accuracies[i]*100:.2f}%',
21 fontsize=18, pad=20)
22
23 fig = plt.figure(figsize=(12, 12))
24 plt.axis('off')
25
26 anim = animation.FuncAnimation(fig, animate, \
27 np.arange(0, 200, 10), interval=500, repeat=True)
28 html = HTML(anim.to_html5_video())

1 display(html)

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11/26/23, 11:33 PM 1. Graph Convolutional Networks.ipynb - Colaboratory

1 # Print embeddings
2 print(f'Final embeddings = {h.shape}')
3 print(h)

Final embeddings = torch.Size([34, 3])

tensor([[1.9099e+00, 2.3584e+00, 7.4027e-01],
[2.6203e+00, 2.7997e+00, 0.0000e+00],
[2.2567e+00, 2.2962e+00, 6.4663e-01],
[2.0802e+00, 2.8785e+00, 0.0000e+00],
[0.0000e+00, 0.0000e+00, 2.9694e+00],
[0.0000e+00, 0.0000e+00, 3.3817e+00],
[0.0000e+00, 1.5008e-04, 3.4246e+00],
[1.7593e+00, 2.4292e+00, 2.4551e-01],
[1.9757e+00, 6.1032e-01, 1.8986e+00],
[1.7770e+00, 1.9950e+00, 6.7018e-01],
[0.0000e+00, 1.1683e-04, 2.9738e+00],
[1.8988e+00, 2.0512e+00, 2.6225e-01],
[1.7081e+00, 2.3618e+00, 1.9609e-01],
[1.8303e+00, 2.1591e+00, 3.5906e-01],
[2.0755e+00, 2.7468e-01, 1.9804e+00],
[1.9676e+00, 3.7185e-01, 2.0011e+00],
[0.0000e+00, 0.0000e+00, 3.4787e+00],
[1.6945e+00, 2.0350e+00, 1.9789e-01],
[1.9808e+00, 3.2633e-01, 2.1349e+00],
[1.7846e+00, 1.9585e+00, 4.8021e-01],
[2.0420e+00, 2.7512e-01, 1.9810e+00],
[1.7665e+00, 2.1357e+00, 4.0325e-01],
[1.9870e+00, 3.3886e-01, 2.0421e+00],
[2.0614e+00, 5.1042e-01, 2.4872e+00],
[1.8381e-01, 2.1094e+00, 2.2035e+00],
[1.8858e-01, 2.0701e+00, 2.1601e+00],
[2.2553e+00, 4.1764e-01, 2.0231e+00],
[1.6532e+00, 8.6745e-01, 2.2131e+00],
[2.4265e-01, 2.1862e+00, 1.6104e+00],
[2.5709e+00, 4.6342e-02, 2.3627e+00],
[2.1778e+00, 4.4730e-01, 2.0077e+00],
[3.8906e-02, 2.3443e+00, 1.9195e+00],
[3.0748e+00, 0.0000e+00, 3.0789e+00],
[3.4316e+00, 1.9716e-01, 2.5231e+00]], grad_fn=<ReluBackward0>)

1 # Get first embedding at epoch = 0

2 embed = h.detach().cpu().numpy()
3
4 fig = plt.figure(figsize=(12, 12))
5 ax = fig.add_subplot(projection='3d')
6 ax.patch.set_alpha(0)
7 plt.tick_params(left=False,
8 bottom=False,
9 labelleft=False,
10 labelbottom=False)
11 ax.scatter(embed[:, 0], embed[:, 1], embed[:, 2],
12 s=200, c=data.y, cmap="hsv", vmin=-2, vmax=3)
13
14 plt.show()

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11/26/23, 11:33 PM 1. Graph Convolutional Networks.ipynb - Colaboratory

1 %%capture
2
3 def animate(i):
4 embed = embeddings[i].detach().cpu().numpy()
5 ax.clear()
6 ax.scatter(embed[:, 0], embed[:, 1], embed[:, 2],
7 s=200, c=data.y, cmap="hsv", vmin=-2, vmax=3)
8 plt.title(f'Epoch {i} | Loss: {losses[i]:.2f} | Acc: {accuracies[i]*100:.2f}%',
9 fontsize=18, pad=40)
10
11 fig = plt.figure(figsize=(12, 12))
12 plt.axis('off')
13 ax = fig.add_subplot(projection='3d')
14 plt.tick_params(left=False,
15 bottom=False,
16 labelleft=False,
17 labelbottom=False)
18
19 anim = animation.FuncAnimation(fig, animate, \
20 np.arange(0, 200, 10), interval=800, repeat=True)
21 html = HTML(anim.to_html5_video())

1 display(html)

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