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utils.py
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from torch_geometric.datasets import Planetoid, Coauthor, Amazon, WikiCS, CoraFull
from torch_geometric.utils import dropout_adj
import torch.nn.functional as F
import os.path as osp
import os
import numpy as np
# np.random.seed(0)
import torch
import torch.nn as nn
torch.manual_seed(0)
torch.cuda.manual_seed_all(0)
# torch.backends.cudnn.deterministic = True
# torch.backends.cudnn.benchmark = False
from datetime import datetime
def currentTime():
return datetime.now().strftime('%Y-%m-%d %H:%M:%S')
class Augmentation:
def __init__(self, p_f1=0.2, p_f2=0.1, p_e1=0.2, p_e2=0.3):
"""
two simple graph augmentation functions --> "Node feature masking" and "Edge masking"
Random binary node feature mask following Bernoulli distribution with parameter p_f
Random binary edge mask following Bernoulli distribution with parameter p_e
"""
self.p_f1 = p_f1
self.p_f2 = p_f2
self.p_e1 = p_e1
self.p_e2 = p_e2
self.method = "BGRL"
def _feature_masking(self, data, device):
feat_mask1 = torch.FloatTensor(data.x.shape[1]).uniform_() > self.p_f1
feat_mask2 = torch.FloatTensor(data.x.shape[1]).uniform_() > self.p_f2
feat_mask1, feat_mask2 = feat_mask1.to(device), feat_mask2.to(device)
x1, x2 = data.x.clone(), data.x.clone()
x1, x2 = x1 * feat_mask1, x2 * feat_mask2
edge_index1, edge_attr1 = dropout_adj(data.edge_index, data.edge_attr, p=self.p_e1)
edge_index2, edge_attr2 = dropout_adj(data.edge_index, data.edge_attr, p=self.p_e2)
new_data1, new_data2 = data.clone(), data.clone()
new_data1.x, new_data2.x = x1, x2
new_data1.edge_index, new_data2.edge_index = edge_index1, edge_index2
new_data1.edge_attr, new_data2.edge_attr = edge_attr1, edge_attr2
return new_data1, new_data2
def __call__(self, data):
return self._feature_masking(data)
def decide_config(root, dataset):
"""
Create a configuration to download datasets
:param root: A path to a root directory where data will be stored
:param dataset: The name of the dataset to be downloaded
:return: A modified root dir, the name of the dataset class, and parameters associated to the class
"""
dataset = dataset.lower()
if dataset == 'cora' or dataset == 'citeseer' or dataset == "pubmed":
root = osp.join(root, "pyg", "planetoid")
params = {"kwargs": {"root": root, "name": dataset},
"name": dataset, "class": Planetoid, "src": "pyg"}
elif dataset == "computers":
dataset = "Computers"
root = osp.join(root, "pyg")
params = {"kwargs": {"root": root, "name": dataset},
"name": dataset, "class": Amazon, "src": "pyg"}
elif dataset == "photo":
dataset = "Photo"
root = osp.join(root, "pyg")
params = {"kwargs": {"root": root, "name": dataset},
"name": dataset, "class": Amazon, "src": "pyg"}
elif dataset == "cs" :
dataset = "CS"
root = osp.join(root, "pyg")
params = {"kwargs": {"root": root, "name": dataset},
"name": dataset, "class": Coauthor, "src": "pyg"}
elif dataset == "physics":
dataset = "Physics"
root = osp.join(root, "pyg")
params = {"kwargs": {"root": root, "name": dataset},
"name": dataset, "class": Coauthor, "src": "pyg"}
elif dataset == "wikics":
dataset = "WikiCS"
root = osp.join(root, "pyg")
params = {"kwargs": {"root": root},
"name": dataset, "class": WikiCS, "src": "pyg"}
elif dataset == "corafull":
dataset = "CoraFull"
root = osp.join(root, "pyg")
params = {"kwargs": {"root": root},
"name": dataset, "class": CoraFull, "src": "pyg"}
else:
raise Exception(
f"Unknown dataset name {dataset}, name has to be one of the following 'cora', 'citeseer', 'pubmed', 'photo', 'computers', 'cs', 'physics'")
return params
def create_dirs(dirs):
for dir_tree in dirs:
sub_dirs = dir_tree.split("/")
path = ""
for sub_dir in sub_dirs:
path = osp.join(path, sub_dir)
os.makedirs(path, exist_ok=True)
def create_masks(data, name, public = None):
"""
Splits data into training, validation, and test splits in a stratified manner if
it is not already splitted. Each split is associated with a mask vector, which
specifies the indices for that split. The data will be modified in-place
:param data: Data object
:return: The modified data
"""
if public != None :
train_idx = public["train"].numpy()
valid_idx = public["valid"].numpy()
test_idx = public["test"].numpy()
_train_mask = _val_mask = _test_mask = None
for i in range(20):
data_index = np.arange(data.y.shape[0])
train_mask = torch.tensor(np.in1d(data_index, train_idx), dtype=torch.bool)
test_mask = torch.tensor(np.in1d(data_index, test_idx), dtype=torch.bool)
valid_mask = torch.tensor(np.in1d(data_index, valid_idx), dtype=torch.bool)
test_mask = test_mask.reshape(1, -1)
valid_mask = valid_mask.reshape(1, -1)
train_mask = train_mask.reshape(1, -1)
if _train_mask is None:
_train_mask = train_mask
_val_mask = valid_mask
_test_mask = test_mask
else:
_train_mask = torch.cat((_train_mask, train_mask), dim=0)
_val_mask = torch.cat((_val_mask, valid_mask), dim=0)
_test_mask = torch.cat((_test_mask, test_mask), dim=0)
data.train_mask = _train_mask
data.val_mask = _val_mask
data.test_mask = _test_mask
elif name != "WikiCS":
_train_mask = _val_mask = _test_mask = None
for i in range(20):
labels = data.y.numpy()
dev_size = int(labels.shape[0] * 0.1)
test_size = int(labels.shape[0] * 0.8)
perm = np.random.permutation(labels.shape[0])
test_index = perm[:test_size]
dev_index = perm[test_size:test_size + dev_size]
data_index = np.arange(labels.shape[0])
test_mask = torch.tensor(np.in1d(data_index, test_index), dtype=torch.bool)
dev_mask = torch.tensor(np.in1d(data_index, dev_index), dtype=torch.bool)
train_mask = ~(dev_mask + test_mask)
test_mask = test_mask.reshape(1, -1)
dev_mask = dev_mask.reshape(1, -1)
train_mask = train_mask.reshape(1, -1)
if _train_mask is None:
_train_mask = train_mask
_val_mask = dev_mask
_test_mask = test_mask
else:
_train_mask = torch.cat((_train_mask, train_mask), dim=0)
_val_mask = torch.cat((_val_mask, dev_mask), dim=0)
_test_mask = torch.cat((_test_mask, test_mask), dim=0)
data.train_mask = _train_mask
data.val_mask = _val_mask
data.test_mask = _test_mask
else: # in the case of WikiCS
data.train_mask = data.train_mask.T
data.val_mask = data.val_mask.T
return data
class EMA:
def __init__(self, beta, epochs):
super().__init__()
self.beta = beta
self.step = 0
self.total_steps = epochs
def update_average(self, old, new):
if old is None:
return new
self.step += 1
return old * self.beta + (1 - self.beta) * new
def init_weights(m):
if type(m) == nn.Linear:
torch.nn.init.xavier_uniform_(m.weight)
m.bias.data.fill_(0.01)
def update_moving_average(ema_updater, ma_model, current_model):
for current_params, ma_params in zip(current_model.parameters(), ma_model.parameters()):
old_weight, up_weight = ma_params.data, current_params.data
ma_params.data = ema_updater.update_average(old_weight, up_weight)
def set_requires_grad(model, val):
for p in model.parameters():
p.requires_grad = val
class KLD(nn.Module):
def forward(self, inputs, targets):
inputs = F.log_softmax(inputs, dim=1)
targets = F.softmax(targets, dim=1)
return F.kl_div(inputs, targets, reduction='batchmean')