# 使用TuDataset 中的PROTEINS数据集。
# 里边有1113个蛋白质图，区分是否为酶，即二分类问题。
# 导包
from torch_geometric.datasets import TUDataset
from torch_geometric.data import DataLoader
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.nn import Linear,Sequential,BatchNorm1d,ReLU,Dropout
from torch_geometric.nn import GCNConv,GINConv
from torch_geometric.nn import global_mean_pool,global_add_pool
# 导入数据集
dataset = TUDataset(root='',name='PROTEINS').shuffle()
# 观测图数据
print(f'Dataset:{dataset}')
print(f'Number of graphs:{len(dataset)}')
print(f'Number of nodes:{dataset[1].x.shape[0]}') # 这是针对于第一个图来说，每个图的节点数会不同
print(f'Number of features:{dataset.num_features}')
print(f'Number of classes:{dataset.num_classes}')
# 一个大的数据集进行拆分，按照 8 :1 :1的比列分为训练集，验证集和测试集
train_dataset = dataset[:int(len(dataset)*0.8)]
val_dataset = dataset[int(len(dataset)*0.8):int(len(dataset)*0.9)]
test_dataset = dataset[int(len(dataset)*0.9):]
# 打印验证：
print('----------------------------------------------')
print(f'training set ={len(train_dataset)} graphs') # 890
print(f'validation set ={len(val_dataset)} graphs')# 111
print(f'test set ={len(test_dataset)} graphs')# 112
# 进行批处理,每个批次最多64个图
train_loader = DataLoader(train_dataset,batch_size=64,shuffle=True)
val_loader = DataLoader(val_dataset,batch_size=64,shuffle=True)
test_loader = DataLoader(test_dataset,batch_size=64,shuffle=True)
# 打印验证一下：
print('------------------------------------------------')
print('\nTrain Loader')
for i,batch in enumerate(train_loader):
print(f'-Batch{i}:{batch}')
print('\nVadidation Loader')
for i,batch in enumerate(val_loader):
print(f'-Batch{i}:{batch}')
print('\nTest Loader')
for i,batch in enumerate(test_loader):
print(f'-Batch{i}:{batch}')
# 来咯，构建GCN模型，进行分类
class GCN(nn.Module):
def __init__(self,dim_h):
super().__init__()
self.conv1 = GCNConv(dataset.num_features,dim_h)
self.conv2 = GCNConv(dim_h,dim_h)
self.conv3 = GCNConv(dim_h,dim_h)
self.lin = Linear(dim_h,dataset.num_classes)
def forward(self,x,edge_index,batch):
h = self.conv1(x,edge_index)
h = h.relu()
h = self.conv2(h,edge_index)
h = h.relu()
h = self.conv3(h,edge_index)
# global_mean_pool 适合用于一些数据分布不平衡的数据
hG = global_mean_pool(h,batch)
# 分类
h = F.dropout(hG,p=0.5,training=self.training)
h = self.lin(h)
return F.log_softmax(h,dim=1)
# 定义GIN模型
class GIN(nn.Module):
def __init__(self,dim_h):
super().__init__()
self.conv1 = GINConv(
Sequential(
Linear(dataset.num_features,dim_h),
BatchNorm1d(dim_h),
ReLU(),
Linear(dim_h,dim_h),
ReLU()
)
)
self.conv2 = GINConv(
Sequential(
Linear(dim_h, dim_h),
BatchNorm1d(dim_h),
ReLU(),
Linear(dim_h, dim_h),
ReLU()
)
)
self.conv3 = GINConv(
Sequential(
Linear(dim_h, dim_h),
BatchNorm1d(dim_h),
ReLU(),
Linear(dim_h, dim_h),
ReLU()
)
)
# 进行分类
# 看论文中的公式可知，计算后是讲三个特征concat在一起
self.lin1 = Linear(dim_h*3,dim_h*3)
self.lin2 = Linear(dim_h*3,dataset.num_classes)
def forward(self,x,edge_index,batch):
h1 = self.conv1(x,edge_index)
h2 = self.conv2(h1,edge_index)
h3 = self.conv3(h2,edge_index)
# 求和全局池化相比与其他两种池化技术（Mean global Pooling 和Max global Pooling）更具有表达能力，
# 要考虑所有的结构信息，就必须考虑GNN每一层产生的嵌入信息
# 将GNN的k个层中每层产生的节点嵌入求和后串联起来
h1 = global_add_pool(h1,batch)
h2 = global_add_pool(h2,batch)
h3 = global_add_pool(h3,batch)
h = torch.cat((h1,h2,h3),dim=1)
# 分类
h = self.lin1(h)
h = h.relu()
h = F.dropout(h,p=0.5,training=self.training)
h = self.lin2(h)
return F.log_softmax(h,dim=1)
# 开始训练咯
def train(model,loader):
# 设置为训练模式
model.train()
# 损失函数
criterion = nn.CrossEntropyLoss()
# 优化函数
optimizer = torch.optim.Adam(model.parameters(),lr=0.01)
epochs = 100
for epoch in range(epochs+1):
total_loss = 0
acc = 0
val_loss = 0
val_acc = 0
for data in loader:
# 梯度清零
optimizer.zero_grad()
# 训练
out = model(data.x,data.edge_index,data.batch)
# 计算该批次的损失值
loss = criterion(out,data.y)
# 总损失
total_loss += loss / len(loader)
# 计算该批次的准确率
acc = accuracy(out.argmax(dim=1),data.y) / len(loader)
# 反向传播
loss.backward()
# 参数更细
optimizer.step()
# 验证
val_loss,val_acc = test(model,val_loader)
# Print metrics every 20 epochs
if (epoch % 20 == 0):
print(f'Epoch {epoch:>3} | Train Loss: {total_loss:.2f} | Train Acc: {acc * 100:>5.2f}% | Val Loss: {val_loss:.2f} | Val Acc: {val_acc * 100:.2f}%')
return model
def accuracy(pred_y,y):
return ((pred_y == y).sum() / len(y)).item()
def test(model,loader):
criterion = torch.nn.CrossEntropyLoss()
model.eval()
loss = 0
acc = 0
for data in loader:
out = model(data.x,data.edge_index,data.batch)
loss += criterion(out,data.y) / len(loader)
acc += accuracy(out.argmax(dim=1),data.y) / len(loader)
return loss,acc
# 开始训练
print('GCN Training')
gcn = GCN(dim_h=32)
gcn = train(gcn,train_loader)
print('GIN Training')
gin = GIN(dim_h=32)
gin = train(gin,train_loader)
test_loss, test_acc = test(gcn, test_loader)
print(f'GCN test Loss: {test_loss:.2f} | GCN test Acc: {test_acc*100:.2f}%')
test_loss, test_acc = test(gin, test_loader)
print(f'Gin test Loss: {test_loss:.2f} | Gin test Acc: {test_acc*100:.2f}%')
GCN 思想:：
通过卷积操作来聚合每个节点以及其邻居的特征。
计算公式如下：
H l + 1 = σ ( D ~ − 1 / 2 A ~ D ~ − 1 / 2 H l W l ) H^{l+1}=\sigma(\tilde{D}^{-1/2}\tilde{A}\tilde{D}^{-1/2}H^{l}W^{l}) Hl+1=σ(D~−1/2A~D~−1/2HlWl)
GIN 思想:
目的：增强图神经网络的区分能力，能够更好地区分不同的图，引入了更加强大的聚合函数。
计算公式如下：
h v k = M L P k ( ( 1 + ε ) ⋅ h v k − 1 + ∑ u ∈ N ( v ) h u k − 1 ) h_{v}^{k}=MLP^{k}((1+\varepsilon)\cdot h_{v}^{k-1} + \sum_{u\in\mathcal{N}_(v)}h_{u}^{k-1} ) hvk=MLPk((1+ε)⋅hvk−1+∑u∈N(v)huk−1)
ε \varepsilon ε 是一个可学习的或固定的超参数，用于调节自环的贡献。
扫一扫
3036
被折叠的 条评论
为什么被折叠?
到【灌水乐园】发言
