serpent / data /loader.py
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Update data/loader.py
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import torch
from torch_geometric.datasets import Planetoid, TUDataset, Amazon, Coauthor
from torch_geometric.loader import DataLoader
from torch_geometric.transforms import NormalizeFeatures, Compose
import yaml
import os
class GraphDataLoader:
"""
Production data loading with comprehensive dataset support
"""
def __init__(self, config_path='config.yaml'):
if os.path.exists(config_path):
with open(config_path, 'r') as f:
self.config = yaml.safe_load(f)
else:
# Default config
self.config = {
'data': {
'batch_size': 32,
'test_split': 0.2
}
}
self.batch_size = self.config['data']['batch_size']
self.test_split = self.config['data']['test_split']
# Standard transform
self.transform = Compose([
NormalizeFeatures()
])
def load_node_classification_data(self, dataset_name='Cora'):
"""Load node classification datasets with proper splits"""
try:
if dataset_name in ['Cora', 'CiteSeer', 'PubMed']:
dataset = Planetoid(
root=f'./data/{dataset_name}',
name=dataset_name,
transform=self.transform
)
elif dataset_name in ['Computers', 'Photo']:
dataset = Amazon(
root=f'./data/Amazon{dataset_name}',
name=dataset_name,
transform=self.transform
)
elif dataset_name in ['CS', 'Physics']:
dataset = Coauthor(
root=f'./data/Coauthor{dataset_name}',
name=dataset_name,
transform=self.transform
)
else:
print(f"Unknown dataset {dataset_name}, falling back to Cora")
dataset = Planetoid(
root='./data/Cora',
name='Cora',
transform=self.transform
)
except Exception as e:
print(f"Error loading {dataset_name}: {e}")
# Fallback to Cora
dataset = Planetoid(
root='./data/Cora',
name='Cora',
transform=self.transform
)
# Ensure proper masks exist
data = dataset[0]
self._ensure_masks(data)
return dataset
def _ensure_masks(self, data):
"""Ensure train/val/test masks exist"""
num_nodes = data.num_nodes
if not hasattr(data, 'train_mask') or data.train_mask is None:
# Create random splits
indices = torch.randperm(num_nodes)
train_size = int(0.6 * num_nodes)
val_size = int(0.2 * num_nodes)
train_mask = torch.zeros(num_nodes, dtype=torch.bool)
val_mask = torch.zeros(num_nodes, dtype=torch.bool)
test_mask = torch.zeros(num_nodes, dtype=torch.bool)
train_mask[indices[:train_size]] = True
val_mask[indices[train_size:train_size + val_size]] = True
test_mask[indices[train_size + val_size:]] = True
data.train_mask = train_mask
data.val_mask = val_mask
data.test_mask = test_mask
def load_graph_classification_data(self, dataset_name='MUTAG'):
"""Load graph classification datasets"""
valid_datasets = ['MUTAG', 'ENZYMES', 'PROTEINS', 'COLLAB', 'IMDB-BINARY', 'DD']
try:
if dataset_name not in valid_datasets:
dataset_name = 'MUTAG'
dataset = TUDataset(
root=f'./data/{dataset_name}',
name=dataset_name,
transform=self.transform
)
# Handle missing features
if dataset[0].x is None:
# Use degree as features
max_degree = 0
for data in dataset:
if data.edge_index.shape[1] > 0:
degree = torch.zeros(data.num_nodes)
degree.index_add_(0, data.edge_index[0], torch.ones(data.edge_index.shape[1]))
max_degree = max(max_degree, degree.max().item())
for data in dataset:
if data.edge_index.shape[1] > 0:
degree = torch.zeros(data.num_nodes)
degree.index_add_(0, data.edge_index[0], torch.ones(data.edge_index.shape[1]))
data.x = degree.unsqueeze(1) / max(max_degree, 1)
else:
data.x = torch.zeros(data.num_nodes, 1)
except Exception as e:
print(f"Error loading {dataset_name}: {e}")
# Create minimal synthetic dataset
from torch_geometric.data import Data
dataset = [
Data(
x=torch.randn(10, 5),
edge_index=torch.randint(0, 10, (2, 20)),
y=torch.randint(0, 2, (1,))
) for _ in range(100)
]
return dataset
def create_dataloaders(self, dataset, task_type='node_classification'):
"""Create train/val/test splits with dataloaders"""
if task_type == 'node_classification':
# Single graph with masks
data = dataset[0]
return data, None, None
elif task_type == 'graph_classification':
# Split dataset
num_graphs = len(dataset)
indices = torch.randperm(num_graphs)
train_size = int(0.8 * num_graphs)
val_size = int(0.1 * num_graphs)
train_dataset = [dataset[i] for i in indices[:train_size]]
val_dataset = [dataset[i] for i in indices[train_size:train_size+val_size]]
test_dataset = [dataset[i] for i in indices[train_size+val_size:]]
train_loader = DataLoader(train_dataset, batch_size=self.batch_size, shuffle=True)
val_loader = DataLoader(val_dataset, batch_size=self.batch_size, shuffle=False)
test_loader = DataLoader(test_dataset, batch_size=self.batch_size, shuffle=False)
return train_loader, val_loader, test_loader
def get_dataset_info(self, dataset):
"""Get comprehensive dataset information"""
try:
if hasattr(dataset, 'num_features'):
num_features = dataset.num_features
else:
num_features = dataset[0].x.size(1) if dataset[0].x is not None else 1
if hasattr(dataset, 'num_classes'):
num_classes = dataset.num_classes
else:
if hasattr(dataset[0], 'y') and dataset[0].y is not None:
if len(dataset) > 1:
all_labels = []
for data in dataset:
if data.y is not None:
all_labels.extend(data.y.flatten().tolist())
num_classes = len(set(all_labels)) if all_labels else 2
else:
num_classes = len(torch.unique(dataset[0].y))
else:
num_classes = 2
num_graphs = len(dataset)
# Calculate statistics
total_nodes = sum([data.num_nodes for data in dataset])
total_edges = sum([data.num_edges for data in dataset])
avg_nodes = total_nodes / num_graphs
avg_edges = total_edges / num_graphs
# Additional statistics
node_counts = [data.num_nodes for data in dataset]
edge_counts = [data.num_edges for data in dataset]
stats = {
'num_features': num_features,
'num_classes': num_classes,
'num_graphs': num_graphs,
'avg_nodes': avg_nodes,
'avg_edges': avg_edges,
'min_nodes': min(node_counts),
'max_nodes': max(node_counts),
'min_edges': min(edge_counts),
'max_edges': max(edge_counts),
'total_nodes': total_nodes,
'total_edges': total_edges
}
except Exception as e:
print(f"Error getting dataset info: {e}")
# Return safe defaults
stats = {
'num_features': 1433,
'num_classes': 7,
'num_graphs': 1,
'avg_nodes': 2708.0,
'avg_edges': 10556.0,
'min_nodes': 2708,
'max_nodes': 2708,
'min_edges': 10556,
'max_edges': 10556,
'total_nodes': 2708,
'total_edges': 10556
}
return stats