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dmlc--dgl
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Xiangkun Hu 5f5a6ef4f7 [Dataset] Fix the edge numbers in the GNNBenchmarkDataset doc string (#3163) 
* PPIDataset

* Revert "PPIDataset"

This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.

* Hide implementations that may cause confusions to the user

* fix number of classes in Amazon Cobuy datasets

* add four papers

* Fix doc string

* fix readme

* fix readme

Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
2021-07-21 11:07:51 +00:00

494 行
16 KiB
Python
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"""GNN Benchmark datasets for node classification."""
import scipy.sparse as sp
import numpy as np
import os
from .dgl_dataset import DGLBuiltinDataset
from .utils import save_graphs, load_graphs, _get_dgl_url, deprecate_property, deprecate_class
from ..convert import graph as dgl_graph
from .. import backend as F
from .. import transform
__all__ = ["AmazonCoBuyComputerDataset", "AmazonCoBuyPhotoDataset", "CoauthorPhysicsDataset", "CoauthorCSDataset",
"CoraFullDataset", "AmazonCoBuy", "Coauthor", "CoraFull"]
def eliminate_self_loops(A):
"""Remove self-loops from the adjacency matrix."""
A = A.tolil()
A.setdiag(0)
A = A.tocsr()
A.eliminate_zeros()
return A
class GNNBenchmarkDataset(DGLBuiltinDataset):
r"""Base Class for GNN Benchmark dataset
Reference: https://github.com/shchur/gnn-benchmark#datasets
"""
def __init__(self, name, raw_dir=None, force_reload=False, verbose=False):
_url = _get_dgl_url('dataset/' + name + '.zip')
super(GNNBenchmarkDataset, self).__init__(name=name,
url=_url,
raw_dir=raw_dir,
force_reload=force_reload,
verbose=verbose)
def process(self):
npz_path = os.path.join(self.raw_path, self.name + '.npz')
g = self._load_npz(npz_path)
g = transform.reorder_graph(
g, node_permute_algo='rcmk', edge_permute_algo='dst', store_ids=False)
self._graph = g
self._data = [g]
self._print_info()
def has_cache(self):
graph_path = os.path.join(self.save_path, 'dgl_graph_v1.bin')
if os.path.exists(graph_path):
return True
return False
def save(self):
graph_path = os.path.join(self.save_path, 'dgl_graph_v1.bin')
save_graphs(graph_path, self._graph)
def load(self):
graph_path = os.path.join(self.save_path, 'dgl_graph_v1.bin')
graphs, _ = load_graphs(graph_path)
self._graph = graphs[0]
self._data = [graphs[0]]
self._print_info()
def _print_info(self):
if self.verbose:
print(' NumNodes: {}'.format(self._graph.number_of_nodes()))
print(' NumEdges: {}'.format(self._graph.number_of_edges()))
print(' NumFeats: {}'.format(self._graph.ndata['feat'].shape[-1]))
print(' NumbClasses: {}'.format(self.num_classes))
def _load_npz(self, file_name):
with np.load(file_name, allow_pickle=True) as loader:
loader = dict(loader)
num_nodes = loader['adj_shape'][0]
adj_matrix = sp.csr_matrix((loader['adj_data'], loader['adj_indices'], loader['adj_indptr']),
shape=loader['adj_shape']).tocoo()
if 'attr_data' in loader:
# Attributes are stored as a sparse CSR matrix
attr_matrix = sp.csr_matrix((loader['attr_data'], loader['attr_indices'], loader['attr_indptr']),
shape=loader['attr_shape']).todense()
elif 'attr_matrix' in loader:
# Attributes are stored as a (dense) np.ndarray
attr_matrix = loader['attr_matrix']
else:
attr_matrix = None
if 'labels_data' in loader:
# Labels are stored as a CSR matrix
labels = sp.csr_matrix((loader['labels_data'], loader['labels_indices'], loader['labels_indptr']),
shape=loader['labels_shape']).todense()
elif 'labels' in loader:
# Labels are stored as a numpy array
labels = loader['labels']
else:
labels = None
g = dgl_graph((adj_matrix.row, adj_matrix.col))
g = transform.to_bidirected(g)
g.ndata['feat'] = F.tensor(attr_matrix, F.data_type_dict['float32'])
g.ndata['label'] = F.tensor(labels, F.data_type_dict['int64'])
return g
@property
def num_classes(self):
"""Number of classes."""
raise NotImplementedError
@property
def data(self):
deprecate_property('dataset.data', 'dataset[0]')
return self._data
def __getitem__(self, idx):
r""" Get graph by index
Parameters
----------
idx : int
Item index
Returns
-------
:class:`dgl.DGLGraph`
The graph contains:
- ``ndata['feat']``: node features
- ``ndata['label']``: node labels
"""
assert idx == 0, "This dataset has only one graph"
return self._graph
def __len__(self):
r"""Number of graphs in the dataset"""
return 1
class CoraFullDataset(GNNBenchmarkDataset):
r"""CORA-Full dataset for node classification task.
.. deprecated:: 0.5.0
- ``data`` is deprecated, it is repalced by:
>>> dataset = CoraFullDataset()
>>> graph = dataset[0]
Extended Cora dataset. Nodes represent paper and edges represent citations.
Reference: `<https://github.com/shchur/gnn-benchmark#datasets>`_
Statistics:
- Nodes: 19,793
- Edges: 126,842 (note that the original dataset has 65,311 edges but DGL adds
the reverse edges and remove the duplicates, hence with a different number)
- Number of Classes: 70
- Node feature size: 8,710
Parameters
----------
raw_dir : str
Raw file directory to download/contains the input data directory.
Default: ~/.dgl/
force_reload : bool
Whether to reload the dataset. Default: False
verbose: bool
Whether to print out progress information. Default: True.
Attributes
----------
num_classes : int
Number of classes for each node.
data : list
A list of DGLGraph objects
Examples
--------
>>> data = CoraFullDataset()
>>> g = data[0]
>>> num_class = data.num_classes
>>> feat = g.ndata['feat'] # get node feature
>>> label = g.ndata['label'] # get node labels
"""
def __init__(self, raw_dir=None, force_reload=False, verbose=False):
super(CoraFullDataset, self).__init__(name="cora_full",
raw_dir=raw_dir,
force_reload=force_reload,
verbose=verbose)
@property
def num_classes(self):
"""Number of classes.
Return
-------
int
"""
return 70
class CoauthorCSDataset(GNNBenchmarkDataset):
r""" 'Computer Science (CS)' part of the Coauthor dataset for node classification task.
.. deprecated:: 0.5.0
- ``data`` is deprecated, it is repalced by:
>>> dataset = CoauthorCSDataset()
>>> graph = dataset[0]
Coauthor CS and Coauthor Physics are co-authorship graphs based on the Microsoft Academic Graph
from the KDD Cup 2016 challenge. Here, nodes are authors, that are connected by an edge if they
co-authored a paper; node features represent paper keywords for each author’s papers, and class
labels indicate most active fields of study for each author.
Reference: `<https://github.com/shchur/gnn-benchmark#datasets>`_
Statistics:
- Nodes: 18,333
- Edges: 163,788 (note that the original dataset has 81,894 edges but DGL adds
the reverse edges and remove the duplicates, hence with a different number)
- Number of classes: 15
- Node feature size: 6,805
Parameters
----------
raw_dir : str
Raw file directory to download/contains the input data directory.
Default: ~/.dgl/
force_reload : bool
Whether to reload the dataset. Default: False
verbose: bool
Whether to print out progress information. Default: True.
Attributes
----------
num_classes : int
Number of classes for each node.
data : list
A list of DGLGraph objects
Examples
--------
>>> data = CoauthorCSDataset()
>>> g = data[0]
>>> num_class = data.num_classes
>>> feat = g.ndata['feat'] # get node feature
>>> label = g.ndata['label'] # get node labels
"""
def __init__(self, raw_dir=None, force_reload=False, verbose=False):
super(CoauthorCSDataset, self).__init__(name='coauthor_cs',
raw_dir=raw_dir,
force_reload=force_reload,
verbose=verbose)
@property
def num_classes(self):
"""Number of classes.
Return
-------
int
"""
return 15
class CoauthorPhysicsDataset(GNNBenchmarkDataset):
r""" 'Physics' part of the Coauthor dataset for node classification task.
.. deprecated:: 0.5.0
- ``data`` is deprecated, it is repalced by:
>>> dataset = CoauthorPhysicsDataset()
>>> graph = dataset[0]
Coauthor CS and Coauthor Physics are co-authorship graphs based on the Microsoft Academic Graph
from the KDD Cup 2016 challenge. Here, nodes are authors, that are connected by an edge if they
co-authored a paper; node features represent paper keywords for each author’s papers, and class
labels indicate most active fields of study for each author.
Reference: `<https://github.com/shchur/gnn-benchmark#datasets>`_
Statistics
- Nodes: 34,493
- Edges: 495,924 (note that the original dataset has 247,962 edges but DGL adds
the reverse edges and remove the duplicates, hence with a different number)
- Number of classes: 5
- Node feature size: 8,415
Parameters
----------
raw_dir : str
Raw file directory to download/contains the input data directory.
Default: ~/.dgl/
force_reload : bool
Whether to reload the dataset. Default: False
verbose: bool
Whether to print out progress information. Default: True.
Attributes
----------
num_classes : int
Number of classes for each node.
data : list
A list of DGLGraph objects
Examples
--------
>>> data = CoauthorPhysicsDataset()
>>> g = data[0]
>>> num_class = data.num_classes
>>> feat = g.ndata['feat'] # get node feature
>>> label = g.ndata['label'] # get node labels
"""
def __init__(self, raw_dir=None, force_reload=False, verbose=False):
super(CoauthorPhysicsDataset, self).__init__(name='coauthor_physics',
raw_dir=raw_dir,
force_reload=force_reload,
verbose=verbose)
@property
def num_classes(self):
"""Number of classes.
Return
-------
int
"""
return 5
class AmazonCoBuyComputerDataset(GNNBenchmarkDataset):
r""" 'Computer' part of the AmazonCoBuy dataset for node classification task.
.. deprecated:: 0.5.0
- ``data`` is deprecated, it is repalced by:
>>> dataset = AmazonCoBuyComputerDataset()
>>> graph = dataset[0]
Amazon Computers and Amazon Photo are segments of the Amazon co-purchase graph [McAuley et al., 2015],
where nodes represent goods, edges indicate that two goods are frequently bought together, node
features are bag-of-words encoded product reviews, and class labels are given by the product category.
Reference: `<https://github.com/shchur/gnn-benchmark#datasets>`_
Statistics:
- Nodes: 13,752
- Edges: 491,722 (note that the original dataset has 245,778 edges but DGL adds
the reverse edges and remove the duplicates, hence with a different number)
- Number of classes: 10
- Node feature size: 767
Parameters
----------
raw_dir : str
Raw file directory to download/contains the input data directory.
Default: ~/.dgl/
force_reload : bool
Whether to reload the dataset. Default: False
verbose: bool
Whether to print out progress information. Default: True.
Attributes
----------
num_classes : int
Number of classes for each node.
data : list
A list of DGLGraph objects
Examples
--------
>>> data = AmazonCoBuyComputerDataset()
>>> g = data[0]
>>> num_class = data.num_classes
>>> feat = g.ndata['feat'] # get node feature
>>> label = g.ndata['label'] # get node labels
"""
def __init__(self, raw_dir=None, force_reload=False, verbose=False):
super(AmazonCoBuyComputerDataset, self).__init__(name='amazon_co_buy_computer',
raw_dir=raw_dir,
force_reload=force_reload,
verbose=verbose)
@property
def num_classes(self):
"""Number of classes.
Return
-------
int
"""
return 10
class AmazonCoBuyPhotoDataset(GNNBenchmarkDataset):
r"""AmazonCoBuy dataset for node classification task.
.. deprecated:: 0.5.0
- ``data`` is deprecated, it is repalced by:
>>> dataset = AmazonCoBuyPhotoDataset()
>>> graph = dataset[0]
Amazon Computers and Amazon Photo are segments of the Amazon co-purchase graph [McAuley et al., 2015],
where nodes represent goods, edges indicate that two goods are frequently bought together, node
features are bag-of-words encoded product reviews, and class labels are given by the product category.
Reference: `<https://github.com/shchur/gnn-benchmark#datasets>`_
Statistics
- Nodes: 7,650
- Edges: 238,163 (note that the original dataset has 119,043 edges but DGL adds
the reverse edges and remove the duplicates, hence with a different number)
- Number of classes: 8
- Node feature size: 745
Parameters
----------
raw_dir : str
Raw file directory to download/contains the input data directory.
Default: ~/.dgl/
force_reload : bool
Whether to reload the dataset. Default: False
verbose: bool
Whether to print out progress information. Default: True.
Attributes
----------
num_classes : int
Number of classes for each node.
data : list
A list of DGLGraph objects
Examples
--------
>>> data = AmazonCoBuyPhotoDataset()
>>> g = data[0]
>>> num_class = data.num_classes
>>> feat = g.ndata['feat'] # get node feature
>>> label = g.ndata['label'] # get node labels
"""
def __init__(self, raw_dir=None, force_reload=False, verbose=False):
super(AmazonCoBuyPhotoDataset, self).__init__(name='amazon_co_buy_photo',
raw_dir=raw_dir,
force_reload=force_reload,
verbose=verbose)
@property
def num_classes(self):
"""Number of classes.
Return
-------
int
"""
return 8
class CoraFull(CoraFullDataset):
def __init__(self, **kwargs):
deprecate_class('CoraFull', 'CoraFullDataset')
super(CoraFull, self).__init__(**kwargs)
def AmazonCoBuy(name):
if name == 'computers':
deprecate_class('AmazonCoBuy', 'AmazonCoBuyComputerDataset')
return AmazonCoBuyComputerDataset()
elif name == 'photo':
deprecate_class('AmazonCoBuy', 'AmazonCoBuyPhotoDataset')
return AmazonCoBuyPhotoDataset()
else:
raise ValueError('Dataset name should be "computers" or "photo".')
def Coauthor(name):
if name == 'cs':
deprecate_class('Coauthor', 'CoauthorCSDataset')
return CoauthorCSDataset()
elif name == 'physics':
deprecate_class('Coauthor', 'CoauthorPhysicsDataset')
return CoauthorPhysicsDataset()
else:
raise ValueError('Dataset name should be "cs" or "physics".')
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