Source code for dgl.transforms.module

##
#   Copyright 2019-2021 Contributors
#
#   Licensed under the Apache License, Version 2.0 (the "License");
#   you may not use this file except in compliance with the License.
#   You may obtain a copy of the License at
#
#       http://www.apache.org/licenses/LICENSE-2.0
#
#   Unless required by applicable law or agreed to in writing, software
#   distributed under the License is distributed on an "AS IS" BASIS,
#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
#   See the License for the specific language governing permissions and
#   limitations under the License.
#
"""Modules for transform"""
# pylint: disable= no-member, arguments-differ, invalid-name, missing-function-docstring

from scipy.linalg import expm

from .. import backend as F, convert, function as fn, utils
from ..base import dgl_warning, DGLError
from . import functional

try:
    import torch
    from torch.distributions import Bernoulli
except ImportError:
    pass

__all__ = [
    "BaseTransform",
    "RowFeatNormalizer",
    "FeatMask",
    "RandomWalkPE",
    "LaplacianPE",
    "LapPE",
    "AddSelfLoop",
    "RemoveSelfLoop",
    "AddReverse",
    "ToSimple",
    "LineGraph",
    "KHopGraph",
    "AddMetaPaths",
    "Compose",
    "GCNNorm",
    "PPR",
    "HeatKernel",
    "GDC",
    "NodeShuffle",
    "DropNode",
    "DropEdge",
    "AddEdge",
    "SIGNDiffusion",
    "ToLevi",
    "SVDPE",
]


def update_graph_structure(g, data_dict, copy_edata=True):
    r"""Update the structure of a graph.

    Parameters
    ----------
    g : DGLGraph
        The graph to update.
    data_dict : graph data
        The dictionary data for constructing a heterogeneous graph.
    copy_edata : bool
        If True, it will copy the edge features to the updated graph.

    Returns
    -------
    DGLGraph
        The updated graph.
    """
    device = g.device
    idtype = g.idtype
    num_nodes_dict = dict()

    for ntype in g.ntypes:
        num_nodes_dict[ntype] = g.num_nodes(ntype)

    new_g = convert.heterograph(
        data_dict, num_nodes_dict=num_nodes_dict, idtype=idtype, device=device
    )

    # Copy features
    for ntype in g.ntypes:
        for key, feat in g.nodes[ntype].data.items():
            new_g.nodes[ntype].data[key] = feat

    if copy_edata:
        for c_etype in g.canonical_etypes:
            for key, feat in g.edges[c_etype].data.items():
                new_g.edges[c_etype].data[key] = feat

    return new_g


[docs]class BaseTransform: r"""An abstract class for writing transforms.""" def __call__(self, g): raise NotImplementedError def __repr__(self): return self.__class__.__name__ + "()"
[docs]class RowFeatNormalizer(BaseTransform): r""" Row-normalizes the features given in ``node_feat_names`` and ``edge_feat_names``. The row normalization formular is: .. math:: x = \frac{x}{\sum_i x_i} where :math:`x` denotes a row of the feature tensor. Parameters ---------- subtract_min: bool If True, the minimum value of whole feature tensor will be subtracted before normalization. Default: False. Subtraction will make all values non-negative. If all values are negative, after normalisation, the sum of each row of the feature tensor will be 1. node_feat_names : list[str], optional The names of the node feature tensors to be row-normalized. Default: `None`, which will not normalize any node feature tensor. edge_feat_names : list[str], optional The names of the edge feature tensors to be row-normalized. Default: `None`, which will not normalize any edge feature tensor. Example ------- The following example uses PyTorch backend. >>> import dgl >>> import torch >>> from dgl import RowFeatNormalizer Case1: Row normalize features of a homogeneous graph. >>> transform = RowFeatNormalizer(subtract_min=True, ... node_feat_names=['h'], edge_feat_names=['w']) >>> g = dgl.rand_graph(5, 20) >>> g.ndata['h'] = torch.randn((g.num_nodes(), 5)) >>> g.edata['w'] = torch.randn((g.num_edges(), 5)) >>> g = transform(g) >>> print(g.ndata['h'].sum(1)) tensor([1., 1., 1., 1., 1.]) >>> print(g.edata['w'].sum(1)) tensor([1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.]) Case2: Row normalize features of a heterogeneous graph. >>> g = dgl.heterograph({ ... ('user', 'follows', 'user'): (torch.tensor([1, 2]), torch.tensor([3, 4])), ... ('player', 'plays', 'game'): (torch.tensor([2, 2]), torch.tensor([1, 1])) ... }) >>> g.ndata['h'] = {'game': torch.randn(2, 5), 'player': torch.randn(3, 5)} >>> g.edata['w'] = { ... ('user', 'follows', 'user'): torch.randn(2, 5), ... ('player', 'plays', 'game'): torch.randn(2, 5) ... } >>> g = transform(g) >>> print(g.ndata['h']['game'].sum(1), g.ndata['h']['player'].sum(1)) tensor([1., 1.]) tensor([1., 1., 1.]) >>> print(g.edata['w'][('user', 'follows', 'user')].sum(1), ... g.edata['w'][('player', 'plays', 'game')].sum(1)) tensor([1., 1.]) tensor([1., 1.]) """ def __init__( self, subtract_min=False, node_feat_names=None, edge_feat_names=None ): self.node_feat_names = ( [] if node_feat_names is None else node_feat_names ) self.edge_feat_names = ( [] if edge_feat_names is None else edge_feat_names ) self.subtract_min = subtract_min def row_normalize(self, feat): r""" Description ----------- Row-normalize the given feature. Parameters ---------- feat : Tensor The feature to be normalized. Returns ------- Tensor The normalized feature. """ if self.subtract_min: feat = feat - feat.min() feat.div_(feat.sum(dim=-1, keepdim=True).clamp_(min=1.0)) return feat def __call__(self, g): for node_feat_name in self.node_feat_names: if isinstance(g.ndata[node_feat_name], torch.Tensor): g.ndata[node_feat_name] = self.row_normalize( g.ndata[node_feat_name] ) else: for ntype in g.ndata[node_feat_name].keys(): g.nodes[ntype].data[node_feat_name] = self.row_normalize( g.nodes[ntype].data[node_feat_name] ) for edge_feat_name in self.edge_feat_names: if isinstance(g.edata[edge_feat_name], torch.Tensor): g.edata[edge_feat_name] = self.row_normalize( g.edata[edge_feat_name] ) else: for etype in g.edata[edge_feat_name].keys(): g.edges[etype].data[edge_feat_name] = self.row_normalize( g.edges[etype].data[edge_feat_name] ) return g
[docs]class FeatMask(BaseTransform): r"""Randomly mask columns of the node and edge feature tensors, as described in `Graph Contrastive Learning with Augmentations <https://arxiv.org/abs/2010.13902>`__. Parameters ---------- p : float, optional Probability of masking a column of a feature tensor. Default: `0.5`. node_feat_names : list[str], optional The names of the node feature tensors to be masked. Default: `None`, which will not mask any node feature tensor. edge_feat_names : list[str], optional The names of the edge features to be masked. Default: `None`, which will not mask any edge feature tensor. Example ------- The following example uses PyTorch backend. >>> import dgl >>> import torch >>> from dgl import FeatMask Case1 : Mask node and edge feature tensors of a homogeneous graph. >>> transform = FeatMask(node_feat_names=['h'], edge_feat_names=['w']) >>> g = dgl.rand_graph(5, 10) >>> g.ndata['h'] = torch.ones((g.num_nodes(), 10)) >>> g.edata['w'] = torch.ones((g.num_edges(), 10)) >>> g = transform(g) >>> print(g.ndata['h']) tensor([[0., 0., 1., 1., 0., 0., 1., 1., 1., 0.], [0., 0., 1., 1., 0., 0., 1., 1., 1., 0.], [0., 0., 1., 1., 0., 0., 1., 1., 1., 0.], [0., 0., 1., 1., 0., 0., 1., 1., 1., 0.], [0., 0., 1., 1., 0., 0., 1., 1., 1., 0.]]) >>> print(g.edata['w']) tensor([[1., 1., 0., 1., 0., 1., 0., 0., 0., 1.], [1., 1., 0., 1., 0., 1., 0., 0., 0., 1.], [1., 1., 0., 1., 0., 1., 0., 0., 0., 1.], [1., 1., 0., 1., 0., 1., 0., 0., 0., 1.], [1., 1., 0., 1., 0., 1., 0., 0., 0., 1.], [1., 1., 0., 1., 0., 1., 0., 0., 0., 1.], [1., 1., 0., 1., 0., 1., 0., 0., 0., 1.], [1., 1., 0., 1., 0., 1., 0., 0., 0., 1.], [1., 1., 0., 1., 0., 1., 0., 0., 0., 1.], [1., 1., 0., 1., 0., 1., 0., 0., 0., 1.]]) Case2 : Mask node and edge feature tensors of a heterogeneous graph. >>> g = dgl.heterograph({ ... ('user', 'follows', 'user'): (torch.tensor([1, 2]), torch.tensor([3, 4])), ... ('player', 'plays', 'game'): (torch.tensor([2, 2]), torch.tensor([1, 1])) ... }) >>> g.ndata['h'] = {'game': torch.ones(2, 5), 'player': torch.ones(3, 5)} >>> g.edata['w'] = {('user', 'follows', 'user'): torch.ones(2, 5)} >>> print(g.ndata['h']['game']) tensor([[1., 1., 1., 1., 1.], [1., 1., 1., 1., 1.]]) >>> print(g.edata['w'][('user', 'follows', 'user')]) tensor([[1., 1., 1., 1., 1.], [1., 1., 1., 1., 1.]]) >>> g = transform(g) >>> print(g.ndata['h']['game']) tensor([[1., 1., 0., 1., 0.], [1., 1., 0., 1., 0.]]) >>> print(g.edata['w'][('user', 'follows', 'user')]) tensor([[0., 1., 0., 1., 0.], [0., 1., 0., 1., 0.]]) """ def __init__(self, p=0.5, node_feat_names=None, edge_feat_names=None): self.p = p self.node_feat_names = ( [] if node_feat_names is None else node_feat_names ) self.edge_feat_names = ( [] if edge_feat_names is None else edge_feat_names ) self.dist = Bernoulli(p) def __call__(self, g): # Fast path if self.p == 0: return g for node_feat_name in self.node_feat_names: if isinstance(g.ndata[node_feat_name], torch.Tensor): feat_mask = self.dist.sample( torch.Size( [ g.ndata[node_feat_name].shape[-1], ] ) ) g.ndata[node_feat_name][:, feat_mask.bool().to(g.device)] = 0 else: for ntype in g.ndata[node_feat_name].keys(): mask_shape = g.ndata[node_feat_name][ntype].shape[-1] feat_mask = self.dist.sample( torch.Size( [ mask_shape, ] ) ) g.ndata[node_feat_name][ntype][ :, feat_mask.bool().to(g.device) ] = 0 for edge_feat_name in self.edge_feat_names: if isinstance(g.edata[edge_feat_name], torch.Tensor): feat_mask = self.dist.sample( torch.Size( [ g.edata[edge_feat_name].shape[-1], ] ) ) g.edata[edge_feat_name][:, feat_mask.bool().to(g.device)] = 0 else: for etype in g.edata[edge_feat_name].keys(): mask_shape = g.edata[edge_feat_name][etype].shape[-1] feat_mask = self.dist.sample( torch.Size( [ mask_shape, ] ) ) g.edata[edge_feat_name][etype][ :, feat_mask.bool().to(g.device) ] = 0 return g
[docs]class RandomWalkPE(BaseTransform): r"""Random Walk Positional Encoding, as introduced in `Graph Neural Networks with Learnable Structural and Positional Representations <https://arxiv.org/abs/2110.07875>`__ This module only works for homogeneous graphs. Parameters ---------- k : int Number of random walk steps. The paper found the best value to be 16 and 20 for two experiments. feat_name : str, optional Name to store the computed positional encodings in ndata. eweight_name : str, optional Name to retrieve the edge weights. Default: None, not using the edge weights. Example ------- >>> import dgl >>> from dgl import RandomWalkPE >>> transform = RandomWalkPE(k=2) >>> g = dgl.graph(([0, 1, 1], [1, 1, 0])) >>> g = transform(g) >>> print(g.ndata['PE']) tensor([[0.0000, 0.5000], [0.5000, 0.7500]]) """ def __init__(self, k, feat_name="PE", eweight_name=None): self.k = k self.feat_name = feat_name self.eweight_name = eweight_name def __call__(self, g): PE = functional.random_walk_pe( g, k=self.k, eweight_name=self.eweight_name ) g.ndata[self.feat_name] = F.copy_to(PE, g.device) return g
[docs]class LapPE(BaseTransform): r"""Laplacian Positional Encoding, as introduced in `Benchmarking Graph Neural Networks <https://arxiv.org/abs/2003.00982>`__ This module only works for homogeneous bidirected graphs. Parameters ---------- k : int Number of smallest non-trivial eigenvectors to use for positional encoding. feat_name : str, optional Name to store the computed positional encodings in ndata. eigval_name : str, optional If None, store laplacian eigenvectors only. Otherwise, it's the name to store corresponding laplacian eigenvalues in ndata. Default: None. padding : bool, optional If False, raise an exception when k>=n. Otherwise, add zero paddings in the end of eigenvectors and 'nan' paddings in the end of eigenvalues when k>=n. Default: False. n is the number of nodes in the given graph. Example ------- >>> import dgl >>> from dgl import LapPE >>> transform1 = LapPE(k=3) >>> transform2 = LapPE(k=5, padding=True) >>> transform3 = LapPE(k=5, feat_name='eigvec', eigval_name='eigval', padding=True) >>> g = dgl.graph(([0,1,2,3,4,2,3,1,4,0], [2,3,1,4,0,0,1,2,3,4])) >>> g1 = transform1(g) >>> print(g1.ndata['PE']) tensor([[ 0.6325, 0.1039, 0.3489], [-0.5117, 0.2826, 0.6095], [ 0.1954, 0.6254, -0.5923], [-0.5117, -0.4508, -0.3938], [ 0.1954, -0.5612, 0.0278]]) >>> g2 = transform2(g) >>> print(g2.ndata['PE']) tensor([[-0.6325, -0.1039, 0.3489, -0.2530, 0.0000], [ 0.5117, -0.2826, 0.6095, 0.4731, 0.0000], [-0.1954, -0.6254, -0.5923, -0.1361, 0.0000], [ 0.5117, 0.4508, -0.3938, -0.6295, 0.0000], [-0.1954, 0.5612, 0.0278, 0.5454, 0.0000]]) >>> g3 = transform3(g) >>> print(g3.ndata['eigval']) tensor([[0.6910, 0.6910, 1.8090, 1.8090, nan], [0.6910, 0.6910, 1.8090, 1.8090, nan], [0.6910, 0.6910, 1.8090, 1.8090, nan], [0.6910, 0.6910, 1.8090, 1.8090, nan], [0.6910, 0.6910, 1.8090, 1.8090, nan]]) >>> print(g3.ndata['eigvec']) tensor([[ 0.6325, -0.1039, 0.3489, 0.2530, 0.0000], [-0.5117, -0.2826, 0.6095, -0.4731, 0.0000], [ 0.1954, -0.6254, -0.5923, 0.1361, 0.0000], [-0.5117, 0.4508, -0.3938, 0.6295, 0.0000], [ 0.1954, 0.5612, 0.0278, -0.5454, 0.0000]]) """ def __init__(self, k, feat_name="PE", eigval_name=None, padding=False): self.k = k self.feat_name = feat_name self.eigval_name = eigval_name self.padding = padding def __call__(self, g): if self.eigval_name: PE, eigval = functional.lap_pe( g, k=self.k, padding=self.padding, return_eigval=True ) eigval = F.repeat(F.reshape(eigval, [1, -1]), g.num_nodes(), dim=0) g.ndata[self.eigval_name] = F.copy_to(eigval, g.device) else: PE = functional.lap_pe(g, k=self.k, padding=self.padding) g.ndata[self.feat_name] = F.copy_to(PE, g.device) return g
class LaplacianPE(LapPE): r"""Alias of `LapPE`.""" def __init__(self, k, feat_name="PE", eigval_name=None, padding=False): super().__init__(k, feat_name, eigval_name, padding) dgl_warning("LaplacianPE will be deprecated. Use LapPE please.")
[docs]class AddSelfLoop(BaseTransform): r"""Add self-loops for each node in the graph and return a new graph. For heterogeneous graphs, self-loops are added only for edge types with same source and destination node types. Parameters ---------- allow_duplicate : bool, optional If False, it will first remove self-loops to prevent duplicate self-loops. new_etypes : bool, optional If True, it will add an edge type 'self' per node type, which holds self-loops. edge_feat_names : list[str], optional The names of the self-loop features to apply `fill_data`. If None, it will apply `fill_data` to all self-loop features. Default: None. fill_data : int, float or str, optional The value to fill the self-loop features. Default: 1. * If ``fill_data`` is ``int`` or ``float``, self-loop features will be directly given by ``fill_data``. * if ``fill_data`` is ``str``, self-loop features will be generated by aggregating the features of the incoming edges of the corresponding nodes. The supported aggregation are: ``'mean'``, ``'sum'``, ``'max'``, ``'min'``. Example ------- >>> import dgl >>> from dgl import AddSelfLoop Case1: Add self-loops for a homogeneous graph >>> transform = AddSelfLoop(fill_data='sum') >>> g = dgl.graph(([0, 0, 2], [2, 1, 0])) >>> g.edata['he'] = torch.arange(3).float().reshape(-1, 1) >>> new_g = transform(g) >>> print(new_g.edges()) (tensor([0, 0, 2, 0, 1, 2]), tensor([2, 1, 0, 0, 1, 2])) >>> print(new_g.edata('he')) tensor([[0.], [1.], [2.], [2.], [1.], [0.]]) Case2: Add self-loops for a heterogeneous graph >>> transform = AddSelfLoop(fill_data='sum') >>> g = dgl.heterograph({ ... ('user', 'follows', 'user'): (torch.tensor([1, 2]), ... torch.tensor([0, 1])), ... ('user', 'plays', 'game'): (torch.tensor([0, 1]), ... torch.tensor([0, 1]))}) >>> g.edata['feat'] = {('user', 'follows', 'user'): torch.randn(2, 5), ... ('user', 'plays', 'game'): torch.randn(2, 5)} >>> g.edata['feat1'] = {('user', 'follows', 'user'): torch.randn(2, 15), ... ('user', 'plays', 'game'): torch.randn(2, 15)} >>> new_g = transform(g) >>> print(new_g.edges(etype='plays')) (tensor([0, 1]), tensor([0, 1])) >>> print(new_g.edges(etype='follows')) (tensor([1, 2, 0, 1, 2]), tensor([0, 1, 0, 1, 2])) >>> print(new_g.edata['feat'][('user', 'follows', 'user')].shape) torch.Size([5, 5]) Case3: Add self-etypes for a heterogeneous graph >>> transform = AddSelfLoop(new_etypes=True) >>> new_g = transform(g) >>> print(new_g.edges(etype='follows')) (tensor([1, 2, 0, 1, 2]), tensor([0, 1, 0, 1, 2])) >>> print(new_g.edges(etype=('game', 'self', 'game'))) (tensor([0, 1]), tensor([0, 1])) """ def __init__( self, allow_duplicate=False, new_etypes=False, edge_feat_names=None, fill_data=1.0, ): self.allow_duplicate = allow_duplicate self.new_etypes = new_etypes self.edge_feat_names = edge_feat_names self.fill_data = fill_data def transform_etype(self, c_etype, g): r""" Description ----------- Transform the graph corresponding to a canonical edge type. Parameters ---------- c_etype : tuple of str A canonical edge type. g : DGLGraph The graph. Returns ------- DGLGraph The transformed graph. """ utype, _, vtype = c_etype if utype != vtype: return g if not self.allow_duplicate: g = functional.remove_self_loop(g, etype=c_etype) return functional.add_self_loop( g, edge_feat_names=self.edge_feat_names, fill_data=self.fill_data, etype=c_etype, ) def __call__(self, g): for c_etype in g.canonical_etypes: g = self.transform_etype(c_etype, g) if self.new_etypes: device = g.device idtype = g.idtype data_dict = dict() # Add self etypes for ntype in g.ntypes: nids = F.arange(0, g.num_nodes(ntype), idtype, device) data_dict[(ntype, "self", ntype)] = (nids, nids) # Copy edges for c_etype in g.canonical_etypes: data_dict[c_etype] = g.edges(etype=c_etype) g = update_graph_structure(g, data_dict) return g
[docs]class RemoveSelfLoop(BaseTransform): r"""Remove self-loops for each node in the graph and return a new graph. For heterogeneous graphs, this operation only applies to edge types with same source and destination node types. Example ------- >>> import dgl >>> from dgl import RemoveSelfLoop Case1: Remove self-loops for a homogeneous graph >>> transform = RemoveSelfLoop() >>> g = dgl.graph(([1, 1], [1, 2])) >>> new_g = transform(g) >>> print(new_g.edges()) (tensor([1]), tensor([2])) Case2: Remove self-loops for a heterogeneous graph >>> g = dgl.heterograph({ ... ('user', 'plays', 'game'): ([0, 1], [1, 1]), ... ('user', 'follows', 'user'): ([1, 2], [2, 2]) ... }) >>> new_g = transform(g) >>> print(new_g.edges(etype='plays')) (tensor([0, 1]), tensor([1, 1])) >>> print(new_g.edges(etype='follows')) (tensor([1]), tensor([2])) """ def transform_etype(self, c_etype, g): r"""Transform the graph corresponding to a canonical edge type. Parameters ---------- c_etype : tuple of str A canonical edge type. g : DGLGraph The graph. Returns ------- DGLGraph The transformed graph. """ utype, _, vtype = c_etype if utype == vtype: g = functional.remove_self_loop(g, etype=c_etype) return g def __call__(self, g): for c_etype in g.canonical_etypes: g = self.transform_etype(c_etype, g) return g
[docs]class AddReverse(BaseTransform): r"""Add a reverse edge :math:`(i,j)` for each edge :math:`(j,i)` in the input graph and return a new graph. For a heterogeneous graph, it adds a "reverse" edge type for each edge type to hold the reverse edges. For example, for a canonical edge type ('A', 'r', 'B'), it adds a canonical edge type ('B', 'rev_r', 'A'). Parameters ---------- copy_edata : bool, optional If True, the features of the reverse edges will be identical to the original ones. sym_new_etype : bool, optional If False, it will not add a reverse edge type if the source and destination node type in a canonical edge type are identical. Instead, it will directly add edges to the original edge type. Example ------- The following example uses PyTorch backend. >>> import dgl >>> import torch >>> from dgl import AddReverse Case1: Add reverse edges for a homogeneous graph >>> transform = AddReverse() >>> g = dgl.graph(([0], [1])) >>> g.edata['w'] = torch.ones(1, 2) >>> new_g = transform(g) >>> print(new_g.edges()) (tensor([0, 1]), tensor([1, 0])) >>> print(new_g.edata['w']) tensor([[1., 1.], [0., 0.]]) Case2: Add reverse edges for a homogeneous graph and copy edata >>> transform = AddReverse(copy_edata=True) >>> new_g = transform(g) >>> print(new_g.edata['w']) tensor([[1., 1.], [1., 1.]]) Case3: Add reverse edges for a heterogeneous graph >>> g = dgl.heterograph({ ... ('user', 'plays', 'game'): ([0, 1], [1, 1]), ... ('user', 'follows', 'user'): ([1, 2], [2, 2]) ... }) >>> new_g = transform(g) >>> print(new_g.canonical_etypes) [('game', 'rev_plays', 'user'), ('user', 'follows', 'user'), ('user', 'plays', 'game')] >>> print(new_g.edges(etype='rev_plays')) (tensor([1, 1]), tensor([0, 1])) >>> print(new_g.edges(etype='follows')) (tensor([1, 2, 2, 2]), tensor([2, 2, 1, 2])) """ def __init__(self, copy_edata=False, sym_new_etype=False): self.copy_edata = copy_edata self.sym_new_etype = sym_new_etype def transform_symmetric_etype(self, c_etype, g, data_dict): r"""Transform the graph corresponding to a symmetric canonical edge type. Parameters ---------- c_etype : tuple of str A canonical edge type. g : DGLGraph The graph. data_dict : dict The edge data to update. """ if self.sym_new_etype: self.transform_asymmetric_etype(c_etype, g, data_dict) else: src, dst = g.edges(etype=c_etype) src, dst = F.cat([src, dst], dim=0), F.cat([dst, src], dim=0) data_dict[c_etype] = (src, dst) def transform_asymmetric_etype(self, c_etype, g, data_dict): r"""Transform the graph corresponding to an asymmetric canonical edge type. Parameters ---------- c_etype : tuple of str A canonical edge type. g : DGLGraph The graph. data_dict : dict The edge data to update. """ utype, etype, vtype = c_etype src, dst = g.edges(etype=c_etype) data_dict.update( { c_etype: (src, dst), (vtype, "rev_{}".format(etype), utype): (dst, src), } ) def transform_etype(self, c_etype, g, data_dict): r"""Transform the graph corresponding to a canonical edge type. Parameters ---------- c_etype : tuple of str A canonical edge type. g : DGLGraph The graph. data_dict : dict The edge data to update. """ utype, _, vtype = c_etype if utype == vtype: self.transform_symmetric_etype(c_etype, g, data_dict) else: self.transform_asymmetric_etype(c_etype, g, data_dict) def __call__(self, g): data_dict = dict() for c_etype in g.canonical_etypes: self.transform_etype(c_etype, g, data_dict) new_g = update_graph_structure(g, data_dict, copy_edata=False) # Copy and expand edata for c_etype in g.canonical_etypes: utype, etype, vtype = c_etype if utype != vtype or self.sym_new_etype: rev_c_etype = (vtype, "rev_{}".format(etype), utype) for key, feat in g.edges[c_etype].data.items(): new_g.edges[c_etype].data[key] = feat if self.copy_edata: new_g.edges[rev_c_etype].data[key] = feat else: for key, feat in g.edges[c_etype].data.items(): new_feat = ( feat if self.copy_edata else F.zeros( F.shape(feat), F.dtype(feat), F.context(feat) ) ) new_g.edges[c_etype].data[key] = F.cat( [feat, new_feat], dim=0 ) return new_g
[docs]class ToSimple(BaseTransform): r"""Convert a graph to a simple graph without parallel edges and return a new graph. Parameters ---------- return_counts : str, optional The edge feature name to hold the edge count in the original graph. aggregator : str, optional The way to coalesce features of duplicate edges. * ``'arbitrary'``: select arbitrarily from one of the duplicate edges * ``'sum'``: take the sum over the duplicate edges * ``'mean'``: take the mean over the duplicate edges Example ------- The following example uses PyTorch backend. >>> import dgl >>> import torch >>> from dgl import ToSimple Case1: Convert a homogeneous graph to a simple graph >>> transform = ToSimple() >>> g = dgl.graph(([0, 1, 1], [1, 2, 2])) >>> g.edata['w'] = torch.tensor([[0.1], [0.2], [0.3]]) >>> sg = transform(g) >>> print(sg.edges()) (tensor([0, 1]), tensor([1, 2])) >>> print(sg.edata['count']) tensor([1, 2]) >>> print(sg.edata['w']) tensor([[0.1000], [0.2000]]) Case2: Convert a heterogeneous graph to a simple graph >>> g = dgl.heterograph({ ... ('user', 'follows', 'user'): ([0, 1, 1], [1, 2, 2]), ... ('user', 'plays', 'game'): ([0, 1, 0], [1, 1, 1]) ... }) >>> sg = transform(g) >>> print(sg.edges(etype='follows')) (tensor([0, 1]), tensor([1, 2])) >>> print(sg.edges(etype='plays')) (tensor([0, 1]), tensor([1, 1])) """ def __init__(self, return_counts="count", aggregator="arbitrary"): self.return_counts = return_counts self.aggregator = aggregator def __call__(self, g): return functional.to_simple( g, return_counts=self.return_counts, copy_edata=True, aggregator=self.aggregator, )
[docs]class LineGraph(BaseTransform): r"""Return the line graph of the input graph. The line graph :math:`L(G)` of a given graph :math:`G` is a graph where the nodes in :math:`L(G)` correspond to the edges in :math:`G`. For a pair of edges :math:`(u, v)` and :math:`(v, w)` in :math:`G`, there will be an edge from the node corresponding to :math:`(u, v)` to the node corresponding to :math:`(v, w)` in :math:`L(G)`. This module only works for homogeneous graphs. Parameters ---------- backtracking : bool, optional If False, there will be an edge from the line graph node corresponding to :math:`(u, v)` to the line graph node corresponding to :math:`(v, u)`. Example ------- The following example uses PyTorch backend. >>> import dgl >>> import torch >>> from dgl import LineGraph Case1: Backtracking is True >>> transform = LineGraph() >>> g = dgl.graph(([0, 1, 1], [1, 0, 2])) >>> g.ndata['h'] = torch.tensor([[0.], [1.], [2.]]) >>> g.edata['w'] = torch.tensor([[0.], [0.1], [0.2]]) >>> new_g = transform(g) >>> print(new_g) Graph(num_nodes=3, num_edges=3, ndata_schemes={'w': Scheme(shape=(1,), dtype=torch.float32)} edata_schemes={}) >>> print(new_g.edges()) (tensor([0, 0, 1]), tensor([1, 2, 0])) Case2: Backtracking is False >>> transform = LineGraph(backtracking=False) >>> new_g = transform(g) >>> print(new_g.edges()) (tensor([0]), tensor([2])) """ def __init__(self, backtracking=True): self.backtracking = backtracking def __call__(self, g): return functional.line_graph( g, backtracking=self.backtracking, shared=True )
[docs]class KHopGraph(BaseTransform): r"""Return the graph whose edges connect the :math:`k`-hop neighbors of the original graph. This module only works for homogeneous graphs. Parameters ---------- k : int The number of hops. Example ------- >>> import dgl >>> from dgl import KHopGraph >>> transform = KHopGraph(2) >>> g = dgl.graph(([0, 1], [1, 2])) >>> new_g = transform(g) >>> print(new_g.edges()) (tensor([0]), tensor([2])) """ def __init__(self, k): self.k = k def __call__(self, g): return functional.khop_graph(g, self.k)
[docs]class AddMetaPaths(BaseTransform): r"""Add new edges to an input graph based on given metapaths, as described in `Heterogeneous Graph Attention Network <https://arxiv.org/abs/1903.07293>`__. Formally, a metapath is a path of the form .. math:: \mathcal{V}_1 \xrightarrow{R_1} \mathcal{V}_2 \xrightarrow{R_2} \ldots \xrightarrow{R_{\ell-1}} \mathcal{V}_{\ell} in which :math:`\mathcal{V}_i` represents a node type and :math:`\xrightarrow{R_j}` represents a relation type connecting its two adjacent node types. The adjacency matrix corresponding to the metapath is obtained by sequential multiplication of adjacency matrices along the metapath. Parameters ---------- metapaths : dict[str, list] The metapaths to add, mapping a metapath name to a metapath. For example, :attr:`{'co-author': [('person', 'author', 'paper'), ('paper', 'authored by', 'person')]}` keep_orig_edges : bool, optional If True, it will keep the edges of the original graph. Otherwise, it will drop them. Example ------- >>> import dgl >>> from dgl import AddMetaPaths >>> transform = AddMetaPaths({ ... 'accepted': [('person', 'author', 'paper'), ('paper', 'accepted', 'venue')], ... 'rejected': [('person', 'author', 'paper'), ('paper', 'rejected', 'venue')] ... }) >>> g = dgl.heterograph({ ... ('person', 'author', 'paper'): ([0, 0, 1], [1, 2, 2]), ... ('paper', 'accepted', 'venue'): ([1], [0]), ... ('paper', 'rejected', 'venue'): ([2], [1]) ... }) >>> new_g = transform(g) >>> print(new_g.edges(etype=('person', 'accepted', 'venue'))) (tensor([0]), tensor([0])) >>> print(new_g.edges(etype=('person', 'rejected', 'venue'))) (tensor([0, 1]), tensor([1, 1])) """ def __init__(self, metapaths, keep_orig_edges=True): self.metapaths = metapaths self.keep_orig_edges = keep_orig_edges def __call__(self, g): data_dict = dict() for meta_etype, metapath in self.metapaths.items(): meta_g = functional.metapath_reachable_graph(g, metapath) u_type = metapath[0][0] v_type = metapath[-1][-1] data_dict[(u_type, meta_etype, v_type)] = meta_g.edges() if self.keep_orig_edges: for c_etype in g.canonical_etypes: data_dict[c_etype] = g.edges(etype=c_etype) new_g = update_graph_structure(g, data_dict, copy_edata=True) else: new_g = update_graph_structure(g, data_dict, copy_edata=False) return new_g
[docs]class Compose(BaseTransform): r"""Create a transform composed of multiple transforms in sequence. Parameters ---------- transforms : list of Callable A list of transform objects to apply in order. A transform object should inherit :class:`~dgl.BaseTransform` and implement :func:`~dgl.BaseTransform.__call__`. Example ------- >>> import dgl >>> from dgl import transforms as T >>> g = dgl.graph(([0, 0], [1, 1])) >>> transform = T.Compose([T.ToSimple(), T.AddReverse()]) >>> new_g = transform(g) >>> print(new_g.edges()) (tensor([0, 1]), tensor([1, 0])) """ def __init__(self, transforms): self.transforms = transforms def __call__(self, g): for transform in self.transforms: g = transform(g) return g def __repr__(self): args = [" " + str(transform) for transform in self.transforms] return self.__class__.__name__ + "([\n" + ",\n".join(args) + "\n])"
[docs]class GCNNorm(BaseTransform): r"""Apply symmetric adjacency normalization to an input graph and save the result edge weights, as described in `Semi-Supervised Classification with Graph Convolutional Networks <https://arxiv.org/abs/1609.02907>`__. For a heterogeneous graph, this only applies to symmetric canonical edge types, whose source and destination node types are identical. Parameters ---------- eweight_name : str, optional :attr:`edata` name to retrieve and store edge weights. The edge weights are optional. Example ------- >>> import dgl >>> import torch >>> from dgl import GCNNorm >>> transform = GCNNorm() >>> g = dgl.graph(([0, 1, 2], [0, 0, 1])) Case1: Transform an unweighted graph >>> g = transform(g) >>> print(g.edata['w']) tensor([0.5000, 0.7071, 0.0000]) Case2: Transform a weighted graph >>> g.edata['w'] = torch.tensor([0.1, 0.2, 0.3]) >>> g = transform(g) >>> print(g.edata['w']) tensor([0.3333, 0.6667, 0.0000]) """ def __init__(self, eweight_name="w"): self.eweight_name = eweight_name def calc_etype(self, c_etype, g): r""" Description ----------- Get edge weights for an edge type. """ ntype = c_etype[0] with g.local_scope(): if self.eweight_name in g.edges[c_etype].data: g.update_all( fn.copy_e(self.eweight_name, "m"), fn.sum("m", "deg"), etype=c_etype, ) deg_inv_sqrt = 1.0 / F.sqrt(g.nodes[ntype].data["deg"]) g.nodes[ntype].data["w"] = F.replace_inf_with_zero(deg_inv_sqrt) g.apply_edges( lambda edge: { "w": edge.src["w"] * edge.data[self.eweight_name] * edge.dst["w"] }, etype=c_etype, ) else: deg = g.in_degrees(etype=c_etype) deg_inv_sqrt = 1.0 / F.sqrt(F.astype(deg, F.float32)) g.nodes[ntype].data["w"] = F.replace_inf_with_zero(deg_inv_sqrt) g.apply_edges( lambda edges: {"w": edges.src["w"] * edges.dst["w"]}, etype=c_etype, ) return g.edges[c_etype].data["w"] def __call__(self, g): result = dict() for c_etype in g.canonical_etypes: utype, _, vtype = c_etype if utype == vtype: result[c_etype] = self.calc_etype(c_etype, g) for c_etype, eweight in result.items(): g.edges[c_etype].data[self.eweight_name] = eweight return g
[docs]class PPR(BaseTransform): r"""Apply personalized PageRank (PPR) to an input graph for diffusion, as introduced in `The pagerank citation ranking: Bringing order to the web <http://ilpubs.stanford.edu:8090/422/>`__. A sparsification will be applied to the weighted adjacency matrix after diffusion. Specifically, edges whose weight is below a threshold will be dropped. This module only works for homogeneous graphs. Parameters ---------- alpha : float, optional Restart probability, which commonly lies in :math:`[0.05, 0.2]`. eweight_name : str, optional :attr:`edata` name to retrieve and store edge weights. If it does not exist in an input graph, this module initializes a weight of 1 for all edges. The edge weights should be a tensor of shape :math:`(E)`, where E is the number of edges. eps : float, optional The threshold to preserve edges in sparsification after diffusion. Edges of a weight smaller than eps will be dropped. avg_degree : int, optional The desired average node degree of the result graph. This is the other way to control the sparsity of the result graph and will only be effective if :attr:`eps` is not given. Example ------- >>> import dgl >>> import torch >>> from dgl import PPR >>> transform = PPR(avg_degree=2) >>> g = dgl.graph(([0, 1, 2, 3, 4], [2, 3, 4, 5, 3])) >>> g.edata['w'] = torch.tensor([0.1, 0.2, 0.3, 0.4, 0.5]) >>> new_g = transform(g) >>> print(new_g.edata['w']) tensor([0.1500, 0.1500, 0.1500, 0.0255, 0.0163, 0.1500, 0.0638, 0.0383, 0.1500, 0.0510, 0.0217, 0.1500]) """ def __init__(self, alpha=0.15, eweight_name="w", eps=None, avg_degree=5): self.alpha = alpha self.eweight_name = eweight_name self.eps = eps self.avg_degree = avg_degree def get_eps(self, num_nodes, mat): r"""Get the threshold for graph sparsification.""" if self.eps is None: # Infer from self.avg_degree if self.avg_degree > num_nodes: return float("-inf") sorted_weights = torch.sort(mat.flatten(), descending=True).values return sorted_weights[self.avg_degree * num_nodes - 1] else: return self.eps def __call__(self, g): # Step1: PPR diffusion # (Ξ± - 1) A device = g.device eweight = (self.alpha - 1) * g.edata.get( self.eweight_name, F.ones((g.num_edges(),), F.float32, device) ) num_nodes = g.num_nodes() mat = F.zeros((num_nodes, num_nodes), F.float32, device) src, dst = g.edges() src, dst = F.astype(src, F.int64), F.astype(dst, F.int64) mat[dst, src] = eweight # I_n + (Ξ± - 1) A nids = F.astype(g.nodes(), F.int64) mat[nids, nids] = mat[nids, nids] + 1 # Ξ± (I_n + (Ξ± - 1) A)^-1 diff_mat = self.alpha * F.inverse(mat) # Step2: sparsification num_nodes = g.num_nodes() eps = self.get_eps(num_nodes, diff_mat) dst, src = (diff_mat >= eps).nonzero(as_tuple=False).t() data_dict = {g.canonical_etypes[0]: (src, dst)} new_g = update_graph_structure(g, data_dict, copy_edata=False) new_g.edata[self.eweight_name] = diff_mat[dst, src] return new_g
def is_bidirected(g): """Return whether the graph is a bidirected graph. A graph is bidirected if for any edge :math:`(u, v)` in :math:`G` with weight :math:`w`, there exists an edge :math:`(v, u)` in :math:`G` with the same weight. """ src, dst = g.edges() num_nodes = g.num_nodes() # Sort first by src then dst idx_src_dst = src * num_nodes + dst perm_src_dst = F.argsort(idx_src_dst, dim=0, descending=False) src1, dst1 = src[perm_src_dst], dst[perm_src_dst] # Sort first by dst then src idx_dst_src = dst * num_nodes + src perm_dst_src = F.argsort(idx_dst_src, dim=0, descending=False) src2, dst2 = src[perm_dst_src], dst[perm_dst_src] return F.allclose(src1, dst2) and F.allclose(src2, dst1) # pylint: disable=C0103
[docs]class HeatKernel(BaseTransform): r"""Apply heat kernel to an input graph for diffusion, as introduced in `Diffusion kernels on graphs and other discrete structures <https://www.ml.cmu.edu/research/dap-papers/kondor-diffusion-kernels.pdf>`__. A sparsification will be applied to the weighted adjacency matrix after diffusion. Specifically, edges whose weight is below a threshold will be dropped. This module only works for homogeneous graphs. Parameters ---------- t : float, optional Diffusion time, which commonly lies in :math:`[2, 10]`. eweight_name : str, optional :attr:`edata` name to retrieve and store edge weights. If it does not exist in an input graph, this module initializes a weight of 1 for all edges. The edge weights should be a tensor of shape :math:`(E)`, where E is the number of edges. eps : float, optional The threshold to preserve edges in sparsification after diffusion. Edges of a weight smaller than eps will be dropped. avg_degree : int, optional The desired average node degree of the result graph. This is the other way to control the sparsity of the result graph and will only be effective if :attr:`eps` is not given. Example ------- >>> import dgl >>> import torch >>> from dgl import HeatKernel >>> transform = HeatKernel(avg_degree=2) >>> g = dgl.graph(([0, 1, 2, 3, 4], [2, 3, 4, 5, 3])) >>> g.edata['w'] = torch.tensor([0.1, 0.2, 0.3, 0.4, 0.5]) >>> new_g = transform(g) >>> print(new_g.edata['w']) tensor([0.1353, 0.1353, 0.1353, 0.0541, 0.0406, 0.1353, 0.1353, 0.0812, 0.1353, 0.1083, 0.0541, 0.1353]) """ def __init__(self, t=2.0, eweight_name="w", eps=None, avg_degree=5): self.t = t self.eweight_name = eweight_name self.eps = eps self.avg_degree = avg_degree def get_eps(self, num_nodes, mat): r"""Get the threshold for graph sparsification.""" if self.eps is None: # Infer from self.avg_degree if self.avg_degree > num_nodes: return float("-inf") sorted_weights = torch.sort(mat.flatten(), descending=True).values return sorted_weights[self.avg_degree * num_nodes - 1] else: return self.eps def __call__(self, g): # Step1: heat kernel diffusion # t A device = g.device eweight = self.t * g.edata.get( self.eweight_name, F.ones((g.num_edges(),), F.float32, device) ) num_nodes = g.num_nodes() mat = F.zeros((num_nodes, num_nodes), F.float32, device) src, dst = g.edges() src, dst = F.astype(src, F.int64), F.astype(dst, F.int64) mat[dst, src] = eweight # t (A - I_n) nids = F.astype(g.nodes(), F.int64) mat[nids, nids] = mat[nids, nids] - self.t if is_bidirected(g): e, V = torch.linalg.eigh(mat, UPLO="U") diff_mat = V @ torch.diag(e.exp()) @ V.t() else: diff_mat_np = expm(mat.cpu().numpy()) diff_mat = torch.Tensor(diff_mat_np).to(device) # Step2: sparsification num_nodes = g.num_nodes() eps = self.get_eps(num_nodes, diff_mat) dst, src = (diff_mat >= eps).nonzero(as_tuple=False).t() data_dict = {g.canonical_etypes[0]: (src, dst)} new_g = update_graph_structure(g, data_dict, copy_edata=False) new_g.edata[self.eweight_name] = diff_mat[dst, src] return new_g
[docs]class GDC(BaseTransform): r"""Apply graph diffusion convolution (GDC) to an input graph, as introduced in `Diffusion Improves Graph Learning <https://www.in.tum.de/daml/gdc/>`__. A sparsification will be applied to the weighted adjacency matrix after diffusion. Specifically, edges whose weight is below a threshold will be dropped. This module only works for homogeneous graphs. Parameters ---------- coefs : list[float], optional List of coefficients. :math:`\theta_k` for each power of the adjacency matrix. eweight_name : str, optional :attr:`edata` name to retrieve and store edge weights. If it does not exist in an input graph, this module initializes a weight of 1 for all edges. The edge weights should be a tensor of shape :math:`(E)`, where E is the number of edges. eps : float, optional The threshold to preserve edges in sparsification after diffusion. Edges of a weight smaller than eps will be dropped. avg_degree : int, optional The desired average node degree of the result graph. This is the other way to control the sparsity of the result graph and will only be effective if :attr:`eps` is not given. Example ------- >>> import dgl >>> import torch >>> from dgl import GDC >>> transform = GDC([0.3, 0.2, 0.1], avg_degree=2) >>> g = dgl.graph(([0, 1, 2, 3, 4], [2, 3, 4, 5, 3])) >>> g.edata['w'] = torch.tensor([0.1, 0.2, 0.3, 0.4, 0.5]) >>> new_g = transform(g) >>> print(new_g.edata['w']) tensor([0.3000, 0.3000, 0.0200, 0.3000, 0.0400, 0.3000, 0.1000, 0.0600, 0.3000, 0.0800, 0.0200, 0.3000]) """ def __init__(self, coefs, eweight_name="w", eps=None, avg_degree=5): self.coefs = coefs self.eweight_name = eweight_name self.eps = eps self.avg_degree = avg_degree def get_eps(self, num_nodes, mat): r"""Get the threshold for graph sparsification.""" if self.eps is None: # Infer from self.avg_degree if self.avg_degree > num_nodes: return float("-inf") sorted_weights = torch.sort(mat.flatten(), descending=True).values return sorted_weights[self.avg_degree * num_nodes - 1] else: return self.eps def __call__(self, g): # Step1: diffusion # A device = g.device eweight = g.edata.get( self.eweight_name, F.ones((g.num_edges(),), F.float32, device) ) num_nodes = g.num_nodes() adj = F.zeros((num_nodes, num_nodes), F.float32, device) src, dst = g.edges() src, dst = F.astype(src, F.int64), F.astype(dst, F.int64) adj[dst, src] = eweight # theta_0 I_n mat = torch.eye(num_nodes, device=device) diff_mat = self.coefs[0] * mat # add theta_k A^k for coef in self.coefs[1:]: mat = mat @ adj diff_mat += coef * mat # Step2: sparsification num_nodes = g.num_nodes() eps = self.get_eps(num_nodes, diff_mat) dst, src = (diff_mat >= eps).nonzero(as_tuple=False).t() data_dict = {g.canonical_etypes[0]: (src, dst)} new_g = update_graph_structure(g, data_dict, copy_edata=False) new_g.edata[self.eweight_name] = diff_mat[dst, src] return new_g
[docs]class NodeShuffle(BaseTransform): r"""Randomly shuffle the nodes. Example ------- >>> import dgl >>> import torch >>> from dgl import NodeShuffle >>> transform = NodeShuffle() >>> g = dgl.graph(([0, 1], [1, 2])) >>> g.ndata['h1'] = torch.tensor([[1., 2.], [3., 4.], [5., 6.]]) >>> g.ndata['h2'] = torch.tensor([[7., 8.], [9., 10.], [11., 12.]]) >>> g = transform(g) >>> print(g.ndata['h1']) tensor([[5., 6.], [3., 4.], [1., 2.]]) >>> print(g.ndata['h2']) tensor([[11., 12.], [ 9., 10.], [ 7., 8.]]) """ def __call__(self, g): g = g.clone() for ntype in g.ntypes: nids = F.astype(g.nodes(ntype), F.int64) perm = F.rand_shuffle(nids) for key, feat in g.nodes[ntype].data.items(): g.nodes[ntype].data[key] = feat[perm] return g
# pylint: disable=C0103
[docs]class DropNode(BaseTransform): r"""Randomly drop nodes, as described in `Graph Contrastive Learning with Augmentations <https://arxiv.org/abs/2010.13902>`__. Parameters ---------- p : float, optional Probability of a node to be dropped. Example ------- >>> import dgl >>> import torch >>> from dgl import DropNode >>> transform = DropNode() >>> g = dgl.rand_graph(5, 20) >>> g.ndata['h'] = torch.arange(g.num_nodes()) >>> g.edata['h'] = torch.arange(g.num_edges()) >>> new_g = transform(g) >>> print(new_g) Graph(num_nodes=3, num_edges=7, ndata_schemes={'h': Scheme(shape=(), dtype=torch.int64)} edata_schemes={'h': Scheme(shape=(), dtype=torch.int64)}) >>> print(new_g.ndata['h']) tensor([0, 1, 2]) >>> print(new_g.edata['h']) tensor([0, 6, 14, 5, 17, 3, 11]) """ def __init__(self, p=0.5): self.p = p self.dist = Bernoulli(p) def __call__(self, g): g = g.clone() # Fast path if self.p == 0: return g for ntype in g.ntypes: samples = self.dist.sample(torch.Size([g.num_nodes(ntype)])) nids_to_remove = g.nodes(ntype)[samples.bool().to(g.device)] g.remove_nodes(nids_to_remove, ntype=ntype) return g
# pylint: disable=C0103
[docs]class DropEdge(BaseTransform): r"""Randomly drop edges, as described in `DropEdge: Towards Deep Graph Convolutional Networks on Node Classification <https://arxiv.org/abs/1907.10903>`__ and `Graph Contrastive Learning with Augmentations <https://arxiv.org/abs/2010.13902>`__. Parameters ---------- p : float, optional Probability of an edge to be dropped. Example ------- >>> import dgl >>> import torch >>> from dgl import DropEdge >>> transform = DropEdge() >>> g = dgl.rand_graph(5, 20) >>> g.edata['h'] = torch.arange(g.num_edges()) >>> new_g = transform(g) >>> print(new_g) Graph(num_nodes=5, num_edges=12, ndata_schemes={} edata_schemes={'h': Scheme(shape=(), dtype=torch.int64)}) >>> print(new_g.edata['h']) tensor([0, 1, 3, 7, 8, 10, 11, 12, 13, 15, 18, 19]) """ def __init__(self, p=0.5): self.p = p self.dist = Bernoulli(p) def __call__(self, g): g = g.clone() # Fast path if self.p == 0: return g for c_etype in g.canonical_etypes: samples = self.dist.sample(torch.Size([g.num_edges(c_etype)])) eids_to_remove = g.edges(form="eid", etype=c_etype)[ samples.bool().to(g.device) ] g.remove_edges(eids_to_remove, etype=c_etype) return g
[docs]class AddEdge(BaseTransform): r"""Randomly add edges, as described in `Graph Contrastive Learning with Augmentations <https://arxiv.org/abs/2010.13902>`__. Parameters ---------- ratio : float, optional Number of edges to add divided by the number of existing edges. Example ------- >>> import dgl >>> from dgl import AddEdge >>> transform = AddEdge() >>> g = dgl.rand_graph(5, 20) >>> new_g = transform(g) >>> print(new_g.num_edges()) 24 """ def __init__(self, ratio=0.2): self.ratio = ratio def __call__(self, g): # Fast path if self.ratio == 0.0: return g device = g.device idtype = g.idtype g = g.clone() for c_etype in g.canonical_etypes: utype, _, vtype = c_etype num_edges_to_add = int(g.num_edges(c_etype) * self.ratio) src = F.randint( [num_edges_to_add], idtype, device, low=0, high=g.num_nodes(utype), ) dst = F.randint( [num_edges_to_add], idtype, device, low=0, high=g.num_nodes(vtype), ) g.add_edges(src, dst, etype=c_etype) return g
[docs]class SIGNDiffusion(BaseTransform): r"""The diffusion operator from `SIGN: Scalable Inception Graph Neural Networks <https://arxiv.org/abs/2004.11198>`__ It performs node feature diffusion with :math:`TX, \cdots, T^{k}X`, where :math:`T` is a diffusion matrix and :math:`X` is the input node features. Specifically, this module provides four options for :math:`T`. **raw**: raw adjacency matrix :math:`A` **rw**: random walk (row-normalized) adjacency matrix :math:`D^{-1}A`, where :math:`D` is the degree matrix. **gcn**: symmetrically normalized adjacency matrix used by `GCN <https://arxiv.org/abs/1609.02907>`__, :math:`D^{-1/2}AD^{-1/2}` **ppr**: approximate personalized PageRank used by `APPNP <https://arxiv.org/abs/1810.05997>`__ .. math:: H^{0} &= X H^{l+1} &= (1-\alpha)\left(D^{-1/2}AD^{-1/2} H^{l}\right) + \alpha X This module only works for homogeneous graphs. Parameters ---------- k : int The maximum number of times for node feature diffusion. in_feat_name : str, optional :attr:`g.ndata[{in_feat_name}]` should store the input node features. Default: 'feat' out_feat_name : str, optional :attr:`g.ndata[{out_feat_name}_i]` will store the result of diffusing input node features for i times. Default: 'out_feat' eweight_name : str, optional Name to retrieve edge weights from :attr:`g.edata`. Default: None, treating the graph as unweighted. diffuse_op : str, optional The diffusion operator to use, which can be 'raw', 'rw', 'gcn', or 'ppr'. Default: 'raw' alpha : float, optional Restart probability if :attr:`diffuse_op` is :attr:`'ppr'`, which commonly lies in :math:`[0.05, 0.2]`. Default: 0.2 Example ------- >>> import dgl >>> import torch >>> from dgl import SIGNDiffusion >>> transform = SIGNDiffusion(k=2, eweight_name='w') >>> num_nodes = 5 >>> num_edges = 20 >>> g = dgl.rand_graph(num_nodes, num_edges) >>> g.ndata['feat'] = torch.randn(num_nodes, 10) >>> g.edata['w'] = torch.randn(num_edges) >>> transform(g) Graph(num_nodes=5, num_edges=20, ndata_schemes={'feat': Scheme(shape=(10,), dtype=torch.float32), 'out_feat_1': Scheme(shape=(10,), dtype=torch.float32), 'out_feat_2': Scheme(shape=(10,), dtype=torch.float32)} edata_schemes={'w': Scheme(shape=(), dtype=torch.float32)}) """ def __init__( self, k, in_feat_name="feat", out_feat_name="out_feat", eweight_name=None, diffuse_op="raw", alpha=0.2, ): self.k = k self.in_feat_name = in_feat_name self.out_feat_name = out_feat_name self.eweight_name = eweight_name self.diffuse_op = diffuse_op self.alpha = alpha if diffuse_op == "raw": self.diffuse = self.raw elif diffuse_op == "rw": self.diffuse = self.rw elif diffuse_op == "gcn": self.diffuse = self.gcn elif diffuse_op == "ppr": self.diffuse = self.ppr else: raise DGLError( "Expect diffuse_op to be from ['raw', 'rw', 'gcn', 'ppr'], \ got {}".format( diffuse_op ) ) def __call__(self, g): feat_list = self.diffuse(g) for i in range(1, self.k + 1): g.ndata[self.out_feat_name + "_" + str(i)] = feat_list[i - 1] return g def raw(self, g): use_eweight = False if (self.eweight_name is not None) and self.eweight_name in g.edata: use_eweight = True feat_list = [] with g.local_scope(): if use_eweight: message_func = fn.u_mul_e( self.in_feat_name, self.eweight_name, "m" ) else: message_func = fn.copy_u(self.in_feat_name, "m") for _ in range(self.k): g.update_all(message_func, fn.sum("m", self.in_feat_name)) feat_list.append(g.ndata[self.in_feat_name]) return feat_list def rw(self, g): use_eweight = False if (self.eweight_name is not None) and self.eweight_name in g.edata: use_eweight = True feat_list = [] with g.local_scope(): g.ndata["h"] = g.ndata[self.in_feat_name] if use_eweight: message_func = fn.u_mul_e("h", self.eweight_name, "m") reduce_func = fn.sum("m", "h") # Compute the diagonal entries of D from the weighted A g.update_all( fn.copy_e(self.eweight_name, "m"), fn.sum("m", "z") ) else: message_func = fn.copy_u("h", "m") reduce_func = fn.mean("m", "h") for _ in range(self.k): g.update_all(message_func, reduce_func) if use_eweight: g.ndata["h"] = g.ndata["h"] / F.reshape( g.ndata["z"], (g.num_nodes(), 1) ) feat_list.append(g.ndata["h"]) return feat_list def gcn(self, g): feat_list = [] with g.local_scope(): if self.eweight_name is None: eweight_name = "w" if eweight_name in g.edata: g.edata.pop(eweight_name) else: eweight_name = self.eweight_name transform = GCNNorm(eweight_name=eweight_name) transform(g) for _ in range(self.k): g.update_all( fn.u_mul_e(self.in_feat_name, eweight_name, "m"), fn.sum("m", self.in_feat_name), ) feat_list.append(g.ndata[self.in_feat_name]) return feat_list def ppr(self, g): feat_list = [] with g.local_scope(): if self.eweight_name is None: eweight_name = "w" if eweight_name in g.edata: g.edata.pop(eweight_name) else: eweight_name = self.eweight_name transform = GCNNorm(eweight_name=eweight_name) transform(g) in_feat = g.ndata[self.in_feat_name] for _ in range(self.k): g.update_all( fn.u_mul_e(self.in_feat_name, eweight_name, "m"), fn.sum("m", self.in_feat_name), ) g.ndata[self.in_feat_name] = (1 - self.alpha) * g.ndata[ self.in_feat_name ] + self.alpha * in_feat feat_list.append(g.ndata[self.in_feat_name]) return feat_list
[docs]class ToLevi(BaseTransform): r"""This function transforms the original graph to its heterogeneous Levi graph, by converting edges to intermediate nodes, only support homogeneous directed graph. Example ------- >>> import dgl >>> import torch as th >>> from dgl import ToLevi >>> transform = ToLevi() >>> g = dgl.graph(([0, 1, 2, 3], [1, 2, 3, 0])) >>> g.ndata['h'] = th.randn((g.num_nodes(), 2)) >>> g.edata['w'] = th.randn((g.num_edges(), 2)) >>> lg = transform(g) >>> lg Grpah(num_nodes={'edge': 4, 'node': 4}, num_edges={('edge', 'e2n', 'node'): 4, ('node', 'n2e', 'edge'): 4}, metagraph=[('edge', 'node', 'e2n'), ('node', 'edge', 'n2e')]) >>> lg.nodes('node') tensor([0, 1, 2, 3]) >>> lg.nodes('edge') tensor([0, 1, 2, 3]) >>> lg.nodes['node'].data['h'].shape torch.Size([4, 2]) >>> lg.nodes['edge'].data['w'].shape torch.Size([4, 2]) """ def __init__(self): pass def __call__(self, g): r""" Parameters ---------- g : DGLGraph The input graph, should be a homogeneous directed graph. Returns ------- DGLGraph The Levi graph of input, will be a heterogeneous graph, where nodes of ntypes ``'node'`` and ``'edge'`` have corresponding IDs of nodes and edges in the original graph. Edge features of the input graph are copied to corresponding new nodes of ntype ``'edge'``. """ device = g.device idtype = g.idtype edge_list = g.edges() n2e = edge_list[0], F.arange(0, g.num_edges(), idtype, device) e2n = F.arange(0, g.num_edges(), idtype, device), edge_list[1] graph_data = { ("node", "n2e", "edge"): n2e, ("edge", "e2n", "node"): e2n, } levi_g = convert.heterograph(graph_data, idtype=idtype, device=device) # Copy ndata and edata # Since the node types in dgl.heterograph are in alphabetical order # ('edge' < 'node'), edge_frames should be in front of node_frames. node_frames = utils.extract_node_subframes(g, nodes_or_device=device) edge_frames = utils.extract_edge_subframes(g, edges_or_device=device) utils.set_new_frames(levi_g, node_frames=edge_frames + node_frames) return levi_g
[docs]class SVDPE(BaseTransform): r"""SVD-based Positional Encoding, as introduced in `Global Self-Attention as a Replacement for Graph Convolution <https://arxiv.org/pdf/2108.03348.pdf>`__ This function computes the largest :math:`k` singular values and corresponding left and right singular vectors to form positional encodings, which could be stored in ndata. Parameters ---------- k : int Number of largest singular values and corresponding singular vectors used for positional encoding. feat_name : str, optional Name to store the computed positional encodings in ndata. Default : ``svd_pe`` padding : bool, optional If False, raise an error when :math:`k > N`, where :math:`N` is the number of nodes in :attr:`g`. If True, add zero paddings in the end of encodings when :math:`k > N`. Default : False. random_flip : bool, optional If True, randomly flip the signs of encoding vectors. Proposed to be activated during training for better generalization. Default : True. Example ------- >>> import dgl >>> from dgl import SVDPE >>> transform = SVDPE(k=2, feat_name="svd_pe") >>> g = dgl.graph(([0,1,2,3,4,2,3,1,4,0], [2,3,1,4,0,0,1,2,3,4])) >>> g_ = transform(g) >>> print(g_.ndata['svd_pe']) tensor([[-6.3246e-01, -1.1373e-07, -6.3246e-01, 0.0000e+00], [-6.3246e-01, 7.6512e-01, -6.3246e-01, -7.6512e-01], [ 6.3246e-01, 4.7287e-01, 6.3246e-01, -4.7287e-01], [-6.3246e-01, -7.6512e-01, -6.3246e-01, 7.6512e-01], [ 6.3246e-01, -4.7287e-01, 6.3246e-01, 4.7287e-01]]) """ def __init__(self, k, feat_name="svd_pe", padding=False, random_flip=True): self.k = k self.feat_name = feat_name self.padding = padding self.random_flip = random_flip def __call__(self, g): encoding = functional.svd_pe( g, k=self.k, padding=self.padding, random_flip=self.random_flip ) g.ndata[self.feat_name] = F.copy_to(encoding, g.device) return g