可能没有说清楚,我用networkx构蛋白质图,每个残基作为一个节点,并给每个节点添加了一个19维的特征,将图保存为了pkl文件,每个蛋白质为一张图,现在我想用pyg将图导入,用于下一步图神经网络的训练,请给出导入数据的代码以及模型搭建、训练的示例代码
时间: 2024-09-24 16:09:27 浏览: 38
手写了卷积神经网络内核,来处理图上的节点分类与链路预测任务,在三个数据集cora,citeseer,ppi上进行试验.zip
在PyTorch Geometric (PyG)中处理这种类型的蛋白质图数据通常需要先加载pkl文件,然后创建`DataList`或`Data`对象。这里是一个基本的步骤:
```python
import torch
from torch_geometric.data import Data, DataLoader
from torch.nn import Linear
from torch_geometric.nn import GCNConv
from networkx.readwrite import pickle
# 加载pkl文件
def load_protein_graphs(pkl_file_path):
graphs = []
with open(pkl_file_path, 'rb') as f:
for protein_data in pickle.load(f):
nodes = protein_data['nodes'] # 节点列表
edges = protein_data['edges'] # 边列表
features = torch.tensor(protein_data['features'], dtype=torch.float) # 19维特征
graph = Data(x=features, edge_index=edges) # 创建Data对象
graphs.append(graph)
return graphs
# 读取并加载数据
protein_graphs = load_protein_graphs('protein_graphs.pkl')
train_data, val_data, test_data = train_val_test_split(protein_graphs, split_ratio=[0.8, 0.1, 0.1]) # 分割数据集
# 数据加载器
train_loader = DataLoader(train_data, batch_size=32, shuffle=True)
val_loader = DataLoader(val_data, batch_size=32, shuffle=False)
test_loader = DataLoader(test_data, batch_size=32, shuffle=False)
# 模型搭建
class ProteinGraphModel(torch.nn.Module):
def __init__(self):
super(ProteinGraphModel, self).__init__()
self.conv1 = GCNConv(protein_features_dim, 64) # 假设蛋白特征维度为protein_features_dim
self.conv2 = GCNConv(64, num_classes) # num_classes为目标类别数
def forward(self, data):
x, edge_index = data.x, data.edge_index
x = F.relu(self.conv1(x, edge_index))
x = F.dropout(x, training=self.training)
x = self.conv2(x, edge_index)
return F.log_softmax(x, dim=1)
model = ProteinGraphModel()
# 训练示例
optimizer = torch.optim.Adam(model.parameters(), lr=0.01)
criterion = torch.nn.NLLLoss()
for epoch in range(num_epochs): # 设定总迭代次数num_epochs
for data in train_loader:
optimizer.zero_grad()
out = model(data)
loss = criterion(out[data.train_mask], data.y[data.train_mask])
loss.backward()
optimizer.step()
# 记录学习过程
print(f"Epoch {epoch+1}/{num_epochs}, Loss: {loss.item()}")
# 验证和测试阶段
with torch.no_grad():
model.eval()
train_acc = accuracy(model, train_loader)
val_acc = accuracy(model, val_loader)
test_acc = accuracy(model, test_loader)
print(f"Train Acc: {train_acc}, Val Acc: {val_acc}, Test Acc: {test_acc}")
```
在这个例子中,你需要替换`protein_features_dim`为实际的19维特征维度。此外,记得根据你的需求调整模型结构、损失函数和优化器参数。别忘了运行完训练后评估模型性能。
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