ubuntu安装pytorch_geometric

我首先是在base环境中安装的
base环境如下

首先不要直接安装torch-scatter,会出错，正确做法是，首先安装torch

pip3 install torch torchvision torchaudio --extra-index-url https://download.pytorch.org/whl/cpu

成功安装torch后如图

然后输入

 pip install torch-scatter

但是出现以下错误

解决办法是

sudo apt install g++

然后再安装就可以成功安装torch-scatter

然后安装torch_sparse
但是直接安装还是出错误

解决办法是

pip install torch-sparse==0.6.13

然后安装torch_cluster

pip install torch-cluster

然后安装torch-spline-conv

 pip install torch-spline-conv

然后安装torch-geometric

pip install torch-geometric

这里为止就安装成功了

测试代码参考如下
https://colab.research.google.com/drive/14OvFnAXggxB8vM4e8vSURUp1TaKnovzX?usp=sharing#scrollTo=pcr9joFQ6Mri

import torch
from torch_geometric.data import Data

edge_index = torch.tensor([[0, 1, 1, 2],
                           [1, 0, 2, 1]], dtype=torch.long)
x = torch.tensor([[-1], [0], [1]], dtype=torch.float)

data = Data(x=x, edge_index=edge_index)
data

结果如下

import torch
from torch_geometric.data import Data

edge_index = torch.tensor([[0, 1],
                           [1, 0],
                           [1, 2],
                           [2, 1]], dtype=torch.long)
x = torch.tensor([[-1], [0], [1]], dtype=torch.float)

data = Data(x=x, edge_index=edge_index.t().contiguous())
data

结果如下

# Install required packages.
import os
import torch
os.environ['TORCH'] = torch.__version__
print(torch.__version__)



# Helper function for visualization.
%matplotlib inline
import matplotlib.pyplot as plt
from sklearn.manifold import TSNE

def visualize(h, color):
    z = TSNE(n_components=2).fit_transform(h.detach().cpu().numpy())

    plt.figure(figsize=(10,10))
    plt.xticks([])
    plt.yticks([])

    plt.scatter(z[:, 0], z[:, 1], s=70, c=color, cmap="Set2")
    plt.show()

结果如下

在这里插入代码片

from torch_geometric.datasets import Planetoid
from torch_geometric.transforms import NormalizeFeatures

dataset = Planetoid(root='data/Planetoid', name='Cora', transform=NormalizeFeatures())

print()
print(f'Dataset: {dataset}:')
print('======================')
print(f'Number of graphs: {len(dataset)}')
print(f'Number of features: {dataset.num_features}')
print(f'Number of classes: {dataset.num_classes}')

data = dataset[0]  # Get the first graph object.

print()
print(data)
print('===========================================================================================================')

# Gather some statistics about the graph.
print(f'Number of nodes: {data.num_nodes}')
print(f'Number of edges: {data.num_edges}')
print(f'Average node degree: {data.num_edges / data.num_nodes:.2f}')
print(f'Number of training nodes: {data.train_mask.sum()}')
print(f'Training node label rate: {int(data.train_mask.sum()) / data.num_nodes:.2f}')
print(f'Has isolated nodes: {data.has_isolated_nodes()}')
print(f'Has self-loops: {data.has_self_loops()}')
print(f'Is undirected: {data.is_undirected()}')

import torch
from torch.nn import Linear
import torch.nn.functional as F


class MLP(torch.nn.Module):
    def __init__(self, hidden_channels):
        super().__init__()
        torch.manual_seed(12345)
        self.lin1 = Linear(dataset.num_features, hidden_channels)
        self.lin2 = Linear(hidden_channels, dataset.num_classes)

    def forward(self, x):
        x = self.lin1(x)
        x = x.relu()
        x = F.dropout(x, p=0.5, training=self.training)
        x = self.lin2(x)
        return x

model = MLP(hidden_channels=16)
print(model)

结果如下

from IPython.display import Javascript  # Restrict height of output cell.
display(Javascript('''google.colab.output.setIframeHeight(0, true, {maxHeight: 300})'''))

model = MLP(hidden_channels=16)
criterion = torch.nn.CrossEntropyLoss()  # Define loss criterion.
optimizer = torch.optim.Adam(model.parameters(), lr=0.01, weight_decay=5e-4)  # Define optimizer.

def train():
    model.train()
    optimizer.zero_grad()  # Clear gradients.
    out = model(data.x)  # Perform a single forward pass.
    loss = criterion(out[data.train_mask], data.y[data.train_mask])  # Compute the loss solely based on the training nodes.
    loss.backward()  # Derive gradients.
    optimizer.step()  # Update parameters based on gradients.
    return loss

def test():
    model.eval()
    out = model(data.x)
    pred = out.argmax(dim=1)  # Use the class with highest probability.
    test_correct = pred[data.test_mask] == data.y[data.test_mask]  # Check against ground-truth labels.
    test_acc = int(test_correct.sum()) / int(data.test_mask.sum())  # Derive ratio of correct predictions.
    return test_acc

for epoch in range(1, 201):
    loss = train()
    print(f'Epoch: {epoch:03d}, Loss: {loss:.4f}')

test_acc = test()
print(f'Test Accuracy: {test_acc:.4f}')

from torch_geometric.nn import GCNConv


class GCN(torch.nn.Module):
    def __init__(self, hidden_channels):
        super().__init__()
        torch.manual_seed(1234567)
        self.conv1 = GCNConv(dataset.num_features, hidden_channels)
        self.conv2 = GCNConv(hidden_channels, dataset.num_classes)

    def forward(self, x, edge_index):
        x = self.conv1(x, edge_index)
        x = x.relu()
        x = F.dropout(x, p=0.5, training=self.training)
        x = self.conv2(x, edge_index)
        return x

model = GCN(hidden_channels=16)
print(model)

model = GCN(hidden_channels=16)
model.eval()

out = model(data.x, data.edge_index)
visualize(out, color=data.y)

在这里插入代码片

from IPython.display import Javascript  # Restrict height of output cell.
display(Javascript('''google.colab.output.setIframeHeight(0, true, {maxHeight: 300})'''))

model = GCN(hidden_channels=16)
optimizer = torch.optim.Adam(model.parameters(), lr=0.01, weight_decay=5e-4)
criterion = torch.nn.CrossEntropyLoss()

def train():
    model.train()
    optimizer.zero_grad()  # Clear gradients.
    out = model(data.x, data.edge_index)  # Perform a single forward pass.
    loss = criterion(out[data.train_mask], data.y[data.train_mask])  # Compute the loss solely based on the training nodes.
    loss.backward()  # Derive gradients.
    optimizer.step()  # Update parameters based on gradients.
    return loss

def test():
    model.eval()
    out = model(data.x, data.edge_index)
    pred = out.argmax(dim=1)  # Use the class with highest probability.
    test_correct = pred[data.test_mask] == data.y[data.test_mask]  # Check against ground-truth labels.
    test_acc = int(test_correct.sum()) / int(data.test_mask.sum())  # Derive ratio of correct predictions.
    return test_acc


for epoch in range(1, 101):
    loss = train()
    print(f'Epoch: {epoch:03d}, Loss: {loss:.4f}')

test_acc = test()
print(f'Test Accuracy: {test_acc:.4f}')

model.eval()

out = model(data.x, data.edge_index)
visualize(out, color=data.y)

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