# Building a simple graph nets model : (for classification)

• DGL : 一个图神经网络库

:align: center

## 用DGL创建一个graph

import dgl

def build_graph():
g = dgl.DGLGraph()
# add 34 nodes into the graph; nodes are labeled from 0~33
# all 78 edges as a list of tuples, tuple(小，大)
edge_list = [(1, 0), (2, 0), (2, 1), (3, 0), (3, 1), (3, 2),
(4, 0), (5, 0), (6, 0), (6, 4), (6, 5), (7, 0), (7, 1),
(7, 2), (7, 3), (8, 0), (8, 2), (9, 2), (10, 0), (10, 4),
(10, 5), (11, 0), (12, 0), (12, 3), (13, 0), (13, 1), (13, 2),
(13, 3), (16, 5), (16, 6), (17, 0), (17, 1), (19, 0), (19, 1),
(21, 0), (21, 1), (25, 23), (25, 24), (27, 2), (27, 23),
(27, 24), (28, 2), (29, 23), (29, 26), (30, 1), (30, 8),
(31, 0), (31, 24), (31, 25), (31, 28), (32, 2), (32, 8),
(32, 14), (32, 15), (32, 18), (32, 20), (32, 22), (32, 23),
(32, 29), (32, 30), (32, 31), (33, 8), (33, 9), (33, 13),
(33, 14), (33, 15), (33, 18), (33, 19), (33, 20), (33, 22),
(33, 23), (33, 26), (33, 27), (33, 28), (33, 29), (33, 30),
(33, 31), (33, 32)]
# zip() 利用 * 号操作符，可以将元组解压为列表。
src, dst = tuple(zip(*edge_list))
# DGL构建的是一个有向图, (src, dst), (dst, src) 双向
return g


G = build_graph()
print('We have %d nodes.' % G.number_of_nodes())
print('We have %d edges.' % G.number_of_edges())

We have 34 nodes.
We have 156 edges.


import networkx as nx
import matplotlib.pyplot as plt
import matplotlib as mpl
msyh = mpl.font_manager.FontProperties(fname='./msyh.ttf')
%matplotlib inline
# 没有方向的
nx_G = G.to_networkx().to_undirected()
plt.figure(figsize=(16, 8))
plt.title('grpah可视化', fontproperties=msyh, fontsize=20)
nx.draw(nx_G, pos, with_labels=True, node_color=[[.7, .7, .7]])


## 构造nodes/edges的特征

import torch

G.ndata['feat'] = torch.eye(34)

# node 2的特征
print(G.nodes[2].data['feat'])

# node 10 and 11's features
print(G.nodes[[10, 11]].data['feat'])

tensor([[0., 0., 1., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.,
0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.]])
tensor([[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 1., 0., 0., 0., 0., 0., 0., 0.,
0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 1., 0., 0., 0., 0., 0., 0.,
0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.]])


## 图卷积神经网络 (GCN)- Graph Convolutional Network

• $l$层, 每个节点$v_i^l$都有一个one-hot编码的特征向量　$h_i^l$.
• 在GCN中每一层中的每个节点，会聚合与其邻接且指向它的节点的特征向量 $h_i^l$,在经过放射变换生成新的特征向量，更新该节点的特征向量．
• 以上图中的 $v_1^l$为例：它利用相邻节点的特征更新自己的特征．(message-passing paradigm)(消息传递范式）
• $h_1^{new} = f(h_2 + h_3 + h_4 + h_5)$
import torch.nn as nn
import torch.nn.functional as F

# Define the message & reduce function
# gcn_message : 返回每个节点携带的message
# gcn_reduce : 通过节点的mailbox收到来自邻接节点的message,计算该节点的new h(feature vector)
# NOTE: we ignore the GCN's normalization

def gcn_message(edges):
# edges : batch of edges.
# This computes a (batch of) message called 'msg' using the source node's feature 'h'.
return {'msg' : edges.src['feat']}

def gcn_reduce(nodes):
# nodes : batch of nodes.
# This computes the new 'h' features by summing received 'msg' in each node's mailbox.
return {'feat' : torch.sum(nodes.mailbox['msg'], dim=1)}

# Define the GCNLayer module
class GCNLayer(nn.Module):
def __init__(self, in_feats, out_feats):
super(GCNLayer, self).__init__()
self.linear = nn.Linear(in_feats, out_feats)

def forward(self, g, inputs):
# g : graph , inputs :node features(message)
# first set the node features
g.ndata['feat'] = inputs
# 沿着边发送message
g.send(g.edges(), gcn_message)
## check mailbox,更新自己的meaage即（feature vector)
g.recv(g.nodes(), gcn_reduce)
# get the result node features
h = g.ndata.pop('feat')
# linear transformation
return self.linear(h)

# Define a 2-layer GCN model
class GCN(nn.Module):
def __init__(self, in_feats, hidden_size, num_classes):
super(GCN, self).__init__()
self.gcn1 = GCNLayer(in_feats, hidden_size)
self.gcn2 = GCNLayer(hidden_size, num_classes)

def forward(self, g, inputs):
h = self.gcn1(g, inputs)   #　没有显式的调用类GCNLayer的forward()方法
h = torch.relu(h)
h = self.gcn2(g, h)
return h

# in_feats : node初始化特征维度
# hidden_size : 隐藏层，图中节点的数量
# num_classes : 图中，community的数量
net = GCN(34, 5, 2)


## 数据的准备和初始化

• 特征向量的初始化（one-hot编码）
• 其实这是一个半监督学习，只有地0, 33个成员有明确的label.
inputs = torch.eye(34)    # nodes特征向量初始化，即one-hot编码
labeled_nodes = torch.tensor([0, 33])  # labeled_nodes, 两个community中中心节点０，３３
labels = torch.tensor([0, 1])  # ０，１ 表示两个不同的群体


## training

optimizer = torch.optim.Adam(net.parameters(), lr=0.01)
all_logits = []
train_loss = []
for epoch in range(50):
logits = net(G, inputs)
# 保存中间结果用于可视化
all_logits.append(logits.detach())
logp = F.log_softmax(logits, 1)
# we only compute loss for labeled nodes
loss = F.nll_loss(logp[labeled_nodes], labels)
train_loss.append(loss.item())
loss.backward()
optimizer.step()
if epoch%10 == 0:
print('Epoch %d | Loss: %.4f' % (epoch+10, loss.item()))

Epoch 10 | Loss: 1.0756
Epoch 20 | Loss: 0.2680
Epoch 30 | Loss: 0.0105
Epoch 40 | Loss: 0.0007
Epoch 50 | Loss: 0.0002

plt.figure(figsize=(14, 7))
plt.plot(train_loss)
plt.title('Train loss',fontsize=20)
plt.grid()


# init_features and new_features

original_features = inputs.detach().numpy()
now_features = logits.detach().numpy()
print('original input shape :',original_features.shape)
print('now_features shape :',now_features.shape)

original input shape : (34, 34)
now_features shape : (34, 2)

original_features

array([[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.]], dtype=float32)

now_features

array([[ 5.637299  , -3.288989  ],
[ 4.512527  , -1.8517829 ],
[ 4.158336  ,  2.1036315 ],
[ 4.244565  , -3.1265435 ],
[ 2.0464027 , -2.2225604 ],
[ 2.312477  , -2.3433352 ],
[ 2.2144208 , -2.490665  ],
[ 3.8895829 , -3.0338702 ],
[ 3.1264923 ,  2.0993629 ],
[ 1.4217453 ,  0.24895817],
[ 1.9483465 , -2.3698897 ],
[ 1.3896602 , -1.5943918 ],
[ 2.007552  , -1.8470225 ],
[ 4.3145075 , -1.6916609 ],
[ 0.5206586 ,  2.8570418 ],
[ 0.5206586 ,  2.8570418 ],
[ 0.7254505 , -1.423414  ],
[ 2.2787623 , -2.311398  ],
[ 0.5206586 ,  2.8570418 ],
[ 2.7036874 , -0.9691887 ],
[ 0.5206586 ,  2.8570418 ],
[ 2.2787623 , -2.311398  ],
[ 0.5206586 ,  2.8570418 ],
[ 0.759069  ,  5.7162037 ],
[ 0.24731699,  1.3865811 ],
[ 0.3594055 ,  0.51410866],
[ 0.5375926 ,  1.8520871 ],
[ 1.6634679 ,  1.1023602 ],
[ 1.5355374 ,  0.53307414],
[ 0.6524333 ,  4.1704736 ],
[ 1.5976448 ,  2.5490031 ],
[ 2.212409  ,  3.619369  ],
[ 2.5465662 ,  6.8266993 ],
[ 2.0438857 , 11.185618  ]], dtype=float32)


# 训练过程的可视化

import matplotlib.animation as animation
import matplotlib.pyplot as plt
import pandas as pd
from IPython.display import HTML
import warnings
warnings.filterwarnings('ignore')
%matplotlib notebook
# 2维空间中的位置变化
def plot_scatter(i):
pos = all_logits[i]
plt.scatter(pos[:,0], pos[:,1],s=10)

# 图网络可视化
def draw(i):
cls1color = '#00FFFF'
cls2color = '#FF00FF'
pos = {}
colors = []
for v in range(34):
pos[v] = all_logits[i][v].numpy()
cls = pos[v].argmax()
colors.append(cls1color if cls else cls2color)
ax.cla()
ax.axis('off')
ax.set_title('Epoch: %d' % i)
nx.draw_networkx(nx_G.to_undirected(), pos, node_color=colors,
with_labels=True, node_size=300, ax=ax)

fig = plt.figure(dpi=100)
ani_1 = animation.FuncAnimation(fig, draw, frames=len(all_logits), interval=200)
HTML(ani.to_jshtml())
`