import os
import os.path as osp
import shutil
import torch
from torch_geometric.data import InMemoryDataset, download_url, extract_zip
from torch_geometric.io import read_tu_data
[docs]class TUDataset(InMemoryDataset):
r"""A variety of graph kernel benchmark datasets, *.e.g.* "IMDB-BINARY",
"REDDIT-BINARY" or "PROTEINS", collected from the `TU Dortmund University
<http://graphkernels.cs.tu-dortmund.de>`_.
In addition, this dataset wrapper provides `cleaned dataset versions
<https://github.com/nd7141/graph_datasets>`_ as motivated by the
`"Understanding Isomorphism Bias in Graph Data Sets"
<https://arxiv.org/abs/1910.12091>`_ paper, containing only non-isomorphic
graphs.
.. note::
Some datasets may not come with any node labels.
You can then either make use of the argument :obj:`use_node_attr`
to load additional continuous node attributes (if present) or provide
synthetic node features using transforms such as
like :class:`torch_geometric.transforms.Constant` or
:class:`torch_geometric.transforms.OneHotDegree`.
Args:
root (string): Root directory where the dataset should be saved.
name (string): The `name <http://graphkernels.cs.tu-dortmund.de>`_ of
the dataset.
transform (callable, optional): A function/transform that takes in an
:obj:`torch_geometric.data.Data` object and returns a transformed
version. The data object will be transformed before every access.
(default: :obj:`None`)
pre_transform (callable, optional): A function/transform that takes in
an :obj:`torch_geometric.data.Data` object and returns a
transformed version. The data object will be transformed before
being saved to disk. (default: :obj:`None`)
pre_filter (callable, optional): A function that takes in an
:obj:`torch_geometric.data.Data` object and returns a boolean
value, indicating whether the data object should be included in the
final dataset. (default: :obj:`None`)
use_node_attr (bool, optional): If :obj:`True`, the dataset will
contain additional continuous node attributes (if present).
(default: :obj:`False`)
use_edge_attr (bool, optional): If :obj:`True`, the dataset will
contain additional continuous edge attributes (if present).
(default: :obj:`False`)
cleaned: (bool, optional): If :obj:`True`, the dataset will
contain only non-isomorphic graphs. (default: :obj:`False`)
"""
url = ('http://ls11-www.cs.tu-dortmund.de/people/morris/'
'graphkerneldatasets')
cleaned_url = ('https://raw.githubusercontent.com/nd7141/'
'graph_datasets/master/datasets')
def __init__(self, root, name, transform=None, pre_transform=None,
pre_filter=None, use_node_attr=False, use_edge_attr=False,
cleaned=False):
self.name = name
self.cleaned = cleaned
super(TUDataset, self).__init__(root, transform, pre_transform,
pre_filter)
self.data, self.slices = torch.load(self.processed_paths[0])
if self.data.x is not None and not use_node_attr:
num_node_attributes = self.num_node_attributes
self.data.x = self.data.x[:, num_node_attributes:]
if self.data.edge_attr is not None and not use_edge_attr:
num_edge_attributes = self.num_edge_attributes
self.data.edge_attr = self.data.edge_attr[:, num_edge_attributes:]
@property
def raw_dir(self):
name = 'raw{}'.format('_cleaned' if self.cleaned else '')
return osp.join(self.root, self.name, name)
@property
def processed_dir(self):
name = 'processed{}'.format('_cleaned' if self.cleaned else '')
return osp.join(self.root, self.name, name)
@property
def num_node_labels(self):
if self.data.x is None:
return 0
for i in range(self.data.x.size(1)):
x = self.data.x[:, i:]
if ((x == 0) | (x == 1)).all() and (x.sum(dim=1) == 1).all():
return self.data.x.size(1) - i
return 0
@property
def num_node_attributes(self):
if self.data.x is None:
return 0
return self.data.x.size(1) - self.num_node_labels
@property
def num_edge_labels(self):
if self.data.edge_attr is None:
return 0
for i in range(self.data.edge_attr.size(1)):
if self.data.edge_attr[:, i:].sum() == self.data.edge_attr.size(0):
return self.data.edge_attr.size(1) - i
return 0
@property
def num_edge_attributes(self):
if self.data.edge_attr is None:
return 0
return self.data.edge_attr.size(1) - self.num_edge_labels
@property
def raw_file_names(self):
names = ['A', 'graph_indicator']
return ['{}_{}.txt'.format(self.name, name) for name in names]
@property
def processed_file_names(self):
return 'data.pt'
def download(self):
url = self.cleaned_url if self.cleaned else self.url
folder = osp.join(self.root, self.name)
path = download_url('{}/{}.zip'.format(url, self.name), folder)
extract_zip(path, folder)
os.unlink(path)
shutil.rmtree(self.raw_dir)
os.rename(osp.join(folder, self.name), self.raw_dir)
def process(self):
self.data, self.slices = read_tu_data(self.raw_dir, self.name)
if self.pre_filter is not None:
data_list = [self.get(idx) for idx in range(len(self))]
data_list = [data for data in data_list if self.pre_filter(data)]
self.data, self.slices = self.collate(data_list)
if self.pre_transform is not None:
data_list = [self.get(idx) for idx in range(len(self))]
data_list = [self.pre_transform(data) for data in data_list]
self.data, self.slices = self.collate(data_list)
torch.save((self.data, self.slices), self.processed_paths[0])
def __repr__(self):
return '{}({})'.format(self.name, len(self))