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Unverified Commit ddb5d804 authored by VoVAllen's avatar VoVAllen Committed by GitHub
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[Refactor] Break NN modules into files (#859) 

* break nn modules into files

* break mxnet nn modules

* fix lint

* fix lint
parent 4cd5c19e
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python/dgl/nn/mxnet/conv/__init__.py 0 → 100644
View file @ ddb5d804
"""MXNet modules for graph convolutions."""
# pylint: disable= no-member, arguments-differ, invalid-name
from .graphconv import GraphConv
from .relgraphconv import RelGraphConv
from .tagconv import TAGConv
__all__ = ['GraphConv', 'TAGConv', 'RelGraphConv']
python/dgl/nn/mxnet/conv/graphconv.py 0 → 100644
View file @ ddb5d804
"""MXNet modules for graph convolutions(GCN)"""
# pylint: disable= no-member, arguments-differ, invalid-name
import math
import mxnet as mx
from mxnet import gluon
from .... import function as fn
class GraphConv(gluon.Block):
r"""Apply graph convolution over an input signal.
Graph convolution is introduced in `GCN <https://arxiv.org/abs/1609.02907>`__
and can be described as below:
.. math::
h_i^{(l+1)} = \sigma(b^{(l)} + \sum_{j\in\mathcal{N}(i)}\frac{1}{c_{ij}}h_j^{(l)}W^{(l)})
where :math:`\mathcal{N}(i)` is the neighbor set of node :math:`i`. :math:`c_{ij}` is equal
to the product of the square root of node degrees:
:math:`\sqrt{|\mathcal{N}(i)|}\sqrt{|\mathcal{N}(j)|}`. :math:`\sigma` is an activation
function.
The model parameters are initialized as in the
`original implementation <https://github.com/tkipf/gcn/blob/master/gcn/layers.py>`__ where
the weight :math:`W^{(l)}` is initialized using Glorot uniform initialization
and the bias is initialized to be zero.
Notes
-----
Zero in degree nodes could lead to invalid normalizer. A common practice
to avoid this is to add a self-loop for each node in the graph, which
can be achieved by:
>>> g = ... # some DGLGraph
>>> g.add_edges(g.nodes(), g.nodes())
Parameters
----------
in_feats : int
Number of input features.
out_feats : int
Number of output features.
norm : bool, optional
If True, the normalizer :math:`c_{ij}` is applied. Default: ``True``.
bias : bool, optional
If True, adds a learnable bias to the output. Default: ``True``.
activation: callable activation function/layer or None, optional
If not None, applies an activation function to the updated node features.
Default: ``None``.
Attributes
----------
weight : mxnet.gluon.parameter.Parameter
The learnable weight tensor.
bias : mxnet.gluon.parameter.Parameter
The learnable bias tensor.
"""
def __init__(self,
in_feats,
out_feats,
norm=True,
bias=True,
activation=None):
super(GraphConv, self).__init__()
self._in_feats = in_feats
self._out_feats = out_feats
self._norm = norm
with self.name_scope():
self.weight = self.params.get('weight', shape=(in_feats, out_feats),
init=mx.init.Xavier(magnitude=math.sqrt(2.0)))
if bias:
self.bias = self.params.get('bias', shape=(out_feats,),
init=mx.init.Zero())
else:
self.bias = None
self._activation = activation
def forward(self, graph, feat):
r"""Compute graph convolution.
Notes
-----
* Input shape: :math:`(N, *, \text{in_feats})` where * means any number of additional
dimensions, :math:`N` is the number of nodes.
* Output shape: :math:`(N, *, \text{out_feats})` where all but the last dimension are
the same shape as the input.
Parameters
----------
graph : DGLGraph
The graph.
feat : mxnet.NDArray
The input feature
Returns
-------
mxnet.NDArray
The output feature
"""
graph = graph.local_var()
if self._norm:
degs = graph.in_degrees().astype('float32')
norm = mx.nd.power(mx.nd.clip(degs, a_min=1, a_max=float("inf")), -0.5)
shp = norm.shape + (1,) * (feat.ndim - 1)
norm = norm.reshape(shp).as_in_context(feat.context)
feat = feat * norm
if self._in_feats > self._out_feats:
# mult W first to reduce the feature size for aggregation.
feat = mx.nd.dot(feat, self.weight.data(feat.context))
graph.ndata['h'] = feat
graph.update_all(fn.copy_src(src='h', out='m'),
fn.sum(msg='m', out='h'))
rst = graph.ndata.pop('h')
else:
# aggregate first then mult W
graph.ndata['h'] = feat
graph.update_all(fn.copy_src(src='h', out='m'),
fn.sum(msg='m', out='h'))
rst = graph.ndata.pop('h')
rst = mx.nd.dot(rst, self.weight.data(feat.context))
if self._norm:
rst = rst * norm
if self.bias is not None:
rst = rst + self.bias.data(rst.context)
if self._activation is not None:
rst = self._activation(rst)
return rst
def __repr__(self):
summary = 'GraphConv('
summary += 'in={:d}, out={:d}, normalization={}, activation={}'.format(
self._in_feats, self._out_feats,
self._norm, self._activation)
summary += '\n)'
return summary
python/dgl/nn/mxnet/conv.py → python/dgl/nn/mxnet/conv/relgraphconv.py
View file @ ddb5d804
"""MXNet modules for graph convolutions.""" """MXNet module for RelGraphConv"""
# pylint: disable= no-member, arguments-differ, invalid-name # pylint: disable= no-member, arguments-differ, invalid-name
import math import math
import numpy as np
import mxnet as mx import mxnet as mx
from mxnet import gluon, nd from mxnet import gluon, nd
from mxnet.gluon import nn from mxnet.gluon import nn
import numpy as np from .... import function as fn
from .. import utils
from . import utils
from ... import function as fn
__all__ = ['GraphConv', 'TAGConv', 'RelGraphConv']
class GraphConv(gluon.Block):
r"""Apply graph convolution over an input signal.
Graph convolution is introduced in `GCN <https://arxiv.org/abs/1609.02907>`__
and can be described as below:
.. math::
h_i^{(l+1)} = \sigma(b^{(l)} + \sum_{j\in\mathcal{N}(i)}\frac{1}{c_{ij}}h_j^{(l)}W^{(l)})
where :math:`\mathcal{N}(i)` is the neighbor set of node :math:`i`. :math:`c_{ij}` is equal
to the product of the square root of node degrees:
:math:`\sqrt{|\mathcal{N}(i)|}\sqrt{|\mathcal{N}(j)|}`. :math:`\sigma` is an activation
function.
The model parameters are initialized as in the
`original implementation <https://github.com/tkipf/gcn/blob/master/gcn/layers.py>`__ where
the weight :math:`W^{(l)}` is initialized using Glorot uniform initialization
and the bias is initialized to be zero.
Notes
-----
Zero in degree nodes could lead to invalid normalizer. A common practice
to avoid this is to add a self-loop for each node in the graph, which
can be achieved by:
>>> g = ... # some DGLGraph
>>> g.add_edges(g.nodes(), g.nodes())
Parameters
----------
in_feats : int
Number of input features.
out_feats : int
Number of output features.
norm : bool, optional
If True, the normalizer :math:`c_{ij}` is applied. Default: ``True``.
bias : bool, optional
If True, adds a learnable bias to the output. Default: ``True``.
activation: callable activation function/layer or None, optional
If not None, applies an activation function to the updated node features.
Default: ``None``.
Attributes
----------
weight : mxnet.gluon.parameter.Parameter
The learnable weight tensor.
bias : mxnet.gluon.parameter.Parameter
The learnable bias tensor.
"""
def __init__(self,
in_feats,
out_feats,
norm=True,
bias=True,
activation=None):
super(GraphConv, self).__init__()
self._in_feats = in_feats
self._out_feats = out_feats
self._norm = norm
with self.name_scope():
self.weight = self.params.get('weight', shape=(in_feats, out_feats),
init=mx.init.Xavier(magnitude=math.sqrt(2.0)))
if bias:
self.bias = self.params.get('bias', shape=(out_feats,),
init=mx.init.Zero())
else:
self.bias = None
self._activation = activation
def forward(self, graph, feat):
r"""Compute graph convolution.
Notes
-----
* Input shape: :math:`(N, *, \text{in_feats})` where * means any number of additional
dimensions, :math:`N` is the number of nodes.
* Output shape: :math:`(N, *, \text{out_feats})` where all but the last dimension are
the same shape as the input.
Parameters
----------
graph : DGLGraph
The graph.
feat : mxnet.NDArray
The input feature
Returns
-------
mxnet.NDArray
The output feature
"""
graph = graph.local_var()
if self._norm:
degs = graph.in_degrees().astype('float32')
norm = mx.nd.power(mx.nd.clip(degs, a_min=1, a_max=float("inf")), -0.5)
shp = norm.shape + (1,) * (feat.ndim - 1)
norm = norm.reshape(shp).as_in_context(feat.context)
feat = feat * norm
if self._in_feats > self._out_feats:
# mult W first to reduce the feature size for aggregation.
feat = mx.nd.dot(feat, self.weight.data(feat.context))
graph.ndata['h'] = feat
graph.update_all(fn.copy_src(src='h', out='m'),
fn.sum(msg='m', out='h'))
rst = graph.ndata.pop('h')
else:
# aggregate first then mult W
graph.ndata['h'] = feat
graph.update_all(fn.copy_src(src='h', out='m'),
fn.sum(msg='m', out='h'))
rst = graph.ndata.pop('h')
rst = mx.nd.dot(rst, self.weight.data(feat.context))
if self._norm:
rst = rst * norm
if self.bias is not None:
rst = rst + self.bias.data(rst.context)
if self._activation is not None:
rst = self._activation(rst)
return rst
def __repr__(self):
summary = 'GraphConv('
summary += 'in={:d}, out={:d}, normalization={}, activation={}'.format(
self._in_feats, self._out_feats,
self._norm, self._activation)
summary += '\n)'
return summary
class TAGConv(gluon.Block):
r"""Apply Topology Adaptive Graph Convolutional Network
.. math::
\mathbf{X}^{\prime} = \sum_{k=0}^K \mathbf{D}^{-1/2} \mathbf{A}
\mathbf{D}^{-1/2}\mathbf{X} \mathbf{\Theta}_{k},
where :math:`\mathbf{A}` denotes the adjacency matrix and
:math:`D_{ii} = \sum_{j=0} A_{ij}` its diagonal degree matrix.
Parameters
----------
in_feats : int
Number of input features.
out_feats : int
Number of output features.
k: int, optional
Number of hops :math: `k`. (default: 2)
bias: bool, optional
If True, adds a learnable bias to the output. Default: ``True``.
activation: callable activation function/layer or None, optional
If not None, applies an activation function to the updated node features.
Default: ``None``.
Attributes
----------
lin : mxnet.gluon.parameter.Parameter
The learnable weight tensor.
bias : mxnet.gluon.parameter.Parameter
The learnable bias tensor.
"""
def __init__(self,
in_feats,
out_feats,
k=2,
bias=True,
activation=None):
super(TAGConv, self).__init__()
self.out_feats = out_feats
self.k = k
self.bias = bias
self.activation = activation
self.in_feats = in_feats
self.lin = self.params.get(
'weight', shape=(self.in_feats * (self.k + 1), self.out_feats),
init=mx.init.Xavier(magnitude=math.sqrt(2.0)))
if self.bias:
self.h_bias = self.params.get('bias', shape=(out_feats,),
init=mx.init.Zero())
def forward(self, graph, feat):
r"""Compute graph convolution
Parameters
----------
graph : DGLGraph
The graph.
feat : mxnet.NDArray
The input feature of shape :math:`(N, D_{in})` where :math:`D_{in}`
is size of input feature, :math:`N` is the number of nodes.
Returns
-------
mxnet.NDArray
The output feature of shape :math:`(N, D_{out})` where :math:`D_{out}`
is size of output feature.
"""
graph = graph.local_var()
degs = graph.in_degrees().astype('float32')
norm = mx.nd.power(mx.nd.clip(degs, a_min=1, a_max=float("inf")), -0.5)
shp = norm.shape + (1,) * (feat.ndim - 1)
norm = norm.reshape(shp).as_in_context(feat.context)
rst = feat
for _ in range(self.k):
rst = rst * norm
graph.ndata['h'] = rst
graph.update_all(fn.copy_src(src='h', out='m'),
fn.sum(msg='m', out='h'))
rst = graph.ndata['h']
rst = rst * norm
feat = mx.nd.concat(feat, rst, dim=-1)
rst = mx.nd.dot(feat, self.lin.data(feat.context))
if self.bias is not None:
rst = rst + self.h_bias.data(rst.context)
if self.activation is not None:
rst = self.activation(rst)
return rst
class RelGraphConv(gluon.Block): class RelGraphConv(gluon.Block):
r"""Relational graph convolution layer. r"""Relational graph convolution layer.
......
python/dgl/nn/mxnet/conv/tagconv.py 0 → 100644
View file @ ddb5d804
"""MXNet module for TAGConv"""
# pylint: disable= no-member, arguments-differ, invalid-name
import math
import mxnet as mx
from mxnet import gluon
from .... import function as fn
class TAGConv(gluon.Block):
r"""Apply Topology Adaptive Graph Convolutional Network
.. math::
\mathbf{X}^{\prime} = \sum_{k=0}^K \mathbf{D}^{-1/2} \mathbf{A}
\mathbf{D}^{-1/2}\mathbf{X} \mathbf{\Theta}_{k},
where :math:`\mathbf{A}` denotes the adjacency matrix and
:math:`D_{ii} = \sum_{j=0} A_{ij}` its diagonal degree matrix.
Parameters
----------
in_feats : int
Number of input features.
out_feats : int
Number of output features.
k: int, optional
Number of hops :math: `k`. (default: 2)
bias: bool, optional
If True, adds a learnable bias to the output. Default: ``True``.
activation: callable activation function/layer or None, optional
If not None, applies an activation function to the updated node features.
Default: ``None``.
Attributes
----------
lin : mxnet.gluon.parameter.Parameter
The learnable weight tensor.
bias : mxnet.gluon.parameter.Parameter
The learnable bias tensor.
"""
def __init__(self,
in_feats,
out_feats,
k=2,
bias=True,
activation=None):
super(TAGConv, self).__init__()
self.out_feats = out_feats
self.k = k
self.bias = bias
self.activation = activation
self.in_feats = in_feats
self.lin = self.params.get(
'weight', shape=(self.in_feats * (self.k + 1), self.out_feats),
init=mx.init.Xavier(magnitude=math.sqrt(2.0)))
if self.bias:
self.h_bias = self.params.get('bias', shape=(out_feats,),
init=mx.init.Zero())
def forward(self, graph, feat):
r"""Compute graph convolution
Parameters
----------
graph : DGLGraph
The graph.
feat : mxnet.NDArray
The input feature of shape :math:`(N, D_{in})` where :math:`D_{in}`
is size of input feature, :math:`N` is the number of nodes.
Returns
-------
mxnet.NDArray
The output feature of shape :math:`(N, D_{out})` where :math:`D_{out}`
is size of output feature.
"""
graph = graph.local_var()
degs = graph.in_degrees().astype('float32')
norm = mx.nd.power(mx.nd.clip(degs, a_min=1, a_max=float("inf")), -0.5)
shp = norm.shape + (1,) * (feat.ndim - 1)
norm = norm.reshape(shp).as_in_context(feat.context)
rst = feat
for _ in range(self.k):
rst = rst * norm
graph.ndata['h'] = rst
graph.update_all(fn.copy_src(src='h', out='m'),
fn.sum(msg='m', out='h'))
rst = graph.ndata['h']
rst = rst * norm
feat = mx.nd.concat(feat, rst, dim=-1)
rst = mx.nd.dot(feat, self.lin.data(feat.context))
if self.bias is not None:
rst = rst + self.h_bias.data(rst.context)
if self.activation is not None:
rst = self.activation(rst)
return rst
python/dgl/nn/pytorch/conv.py deleted 100644 → 0
View file @ 4cd5c19e
This diff is collapsed.
python/dgl/nn/pytorch/conv/__init__.py 0 → 100644
View file @ ddb5d804
"""Torch modules for graph convolutions."""
# pylint: disable= no-member, arguments-differ, invalid-name
from .agnnconv import AGNNConv
from .appnpconv import APPNPConv
from .chebconv import ChebConv
from .edgeconv import EdgeConv
from .gatconv import GATConv
from .ginconv import GINConv
from .gmmconv import GMMConv
from .graphconv import GraphConv
from .nnconv import NNConv
from .relgraphconv import RelGraphConv
from .sageconv import SAGEConv
from .sgconv import SGConv
from .tagconv import TAGConv
from .gatedgraphconv import GatedGraphConv
from .densechebconv import DenseChebConv
from .densegraphconv import DenseGraphConv
from .densesageconv import DenseSAGEConv
__all__ = ['GraphConv', 'GATConv', 'TAGConv', 'RelGraphConv', 'SAGEConv',
'SGConv', 'APPNPConv', 'GINConv', 'GatedGraphConv', 'GMMConv',
'ChebConv', 'AGNNConv', 'NNConv', 'DenseGraphConv', 'DenseSAGEConv',
'DenseChebConv', 'EdgeConv']
python/dgl/nn/pytorch/conv/agnnconv.py 0 → 100644
View file @ ddb5d804
"""Torch Module for Attention-based Graph Neural Network layer"""
# pylint: disable= no-member, arguments-differ, invalid-name
import torch as th
from torch import nn
from torch.nn import functional as F
from .... import function as fn
from ..softmax import edge_softmax
class AGNNConv(nn.Module):
r"""Attention-based Graph Neural Network layer from paper `Attention-based
Graph Neural Network for Semi-Supervised Learning
<https://arxiv.org/abs/1803.03735>`__.
.. math::
H^{l+1} = P H^{l}
where :math:`P` is computed as:
.. math::
P_{ij} = \mathrm{softmax}_i ( \beta \cdot \cos(h_i^l, h_j^l))
Parameters
----------
init_beta : float, optional
The :math:`\beta` in the formula.
learn_beta : bool, optional
If True, :math:`\beta` will be learnable parameter.
"""
def __init__(self,
init_beta=1.,
learn_beta=True):
super(AGNNConv, self).__init__()
if learn_beta:
self.beta = nn.Parameter(th.Tensor([init_beta]))
else:
self.register_buffer('beta', th.Tensor([init_beta]))
def forward(self, graph, feat):
r"""Compute AGNN layer.
Parameters
----------
graph : DGLGraph
The graph.
feat : torch.Tensor
The input feature of shape :math:`(N, *)` :math:`N` is the
number of nodes, and :math:`*` could be of any shape.
Returns
-------
torch.Tensor
The output feature of shape :math:`(N, *)` where :math:`*`
should be the same as input shape.
"""
graph = graph.local_var()
graph.ndata['h'] = feat
graph.ndata['norm_h'] = F.normalize(feat, p=2, dim=-1)
# compute cosine distance
graph.apply_edges(fn.u_mul_v('norm_h', 'norm_h', 'cos'))
cos = graph.edata.pop('cos').sum(-1)
e = self.beta * cos
graph.edata['p'] = edge_softmax(graph, e)
graph.update_all(fn.u_mul_e('h', 'p', 'm'), fn.sum('m', 'h'))
return graph.ndata.pop('h')
python/dgl/nn/pytorch/conv/appnpconv.py 0 → 100644
View file @ ddb5d804
"""Torch Module for APPNPConv"""
# pylint: disable= no-member, arguments-differ, invalid-name
import torch as th
from torch import nn
from .... import function as fn
from ..utils import Identity
class APPNPConv(nn.Module):
r"""Approximate Personalized Propagation of Neural Predictions
layer from paper `Predict then Propagate: Graph Neural Networks
meet Personalized PageRank <https://arxiv.org/pdf/1810.05997.pdf>`__.
.. math::
H^{0} & = X
H^{t+1} & = (1-\alpha)\left(\hat{D}^{-1/2}
\hat{A} \hat{D}^{-1/2} H^{t} + \alpha H^{0}\right)
Parameters
----------
k : int
Number of iterations :math:`K`.
alpha : float
The teleport probability :math:`\alpha`.
edge_drop : float, optional
Dropout rate on edges that controls the
messages received by each node. Default: ``0``.
"""
def __init__(self,
k,
alpha,
edge_drop=0.):
super(APPNPConv, self).__init__()
self._k = k
self._alpha = alpha
self.edge_drop = nn.Dropout(edge_drop) if edge_drop > 0 else Identity()
def forward(self, graph, feat):
r"""Compute APPNP layer.
Parameters
----------
graph : DGLGraph
The graph.
feat : torch.Tensor
The input feature of shape :math:`(N, *)` :math:`N` is the
number of nodes, and :math:`*` could be of any shape.
Returns
-------
torch.Tensor
The output feature of shape :math:`(N, *)` where :math:`*`
should be the same as input shape.
"""
graph = graph.local_var()
norm = th.pow(graph.in_degrees().float().clamp(min=1), -0.5)
norm = norm.unsqueeze(-1).to(feat.device)
feat_0 = feat
for _ in range(self._k):
# normalization by src
feat = feat * norm
graph.ndata['h'] = feat
graph.edata['w'] = self.edge_drop(
th.ones(graph.number_of_edges(), 1).to(feat.device))
graph.update_all(fn.u_mul_e('h', 'w', 'm'),
fn.sum('m', 'h'))
feat = graph.ndata.pop('h')
# normalization by dst
feat = feat * norm
feat = (1 - self._alpha) * feat + self._alpha * feat_0
return feat
python/dgl/nn/pytorch/conv/chebconv.py 0 → 100644
View file @ ddb5d804
"""Torch Module for Chebyshev Spectral Graph Convolution layer"""
# pylint: disable= no-member, arguments-differ, invalid-name
import torch as th
from torch import nn
from torch.nn import init
from .... import laplacian_lambda_max, broadcast_nodes, function as fn
class ChebConv(nn.Module):
r"""Chebyshev Spectral Graph Convolution layer from paper `Convolutional
Neural Networks on Graphs with Fast Localized Spectral Filtering
<https://arxiv.org/pdf/1606.09375.pdf>`__.
.. math::
h_i^{l+1} &= \sum_{k=0}^{K-1} W^{k, l}z_i^{k, l}
Z^{0, l} &= H^{l}
Z^{1, l} &= \hat{L} \cdot H^{l}
Z^{k, l} &= 2 \cdot \hat{L} \cdot Z^{k-1, l} - Z^{k-2, l}
\hat{L} &= 2\left(I - \hat{D}^{-1/2} \hat{A} \hat{D}^{-1/2}\right)/\lambda_{max} - I
Parameters
----------
in_feats: int
Number of input features.
out_feats: int
Number of output features.
k : int
Chebyshev filter size.
bias : bool, optional
If True, adds a learnable bias to the output. Default: ``True``.
"""
def __init__(self,
in_feats,
out_feats,
k,
bias=True):
super(ChebConv, self).__init__()
self._in_feats = in_feats
self._out_feats = out_feats
self.fc = nn.ModuleList([
nn.Linear(in_feats, out_feats, bias=False) for _ in range(k)
])
self._k = k
if bias:
self.bias = nn.Parameter(th.Tensor(out_feats))
else:
self.register_buffer('bias', None)
self.reset_parameters()
def reset_parameters(self):
"""Reinitialize learnable parameters."""
if self.bias is not None:
init.zeros_(self.bias)
for module in self.fc.modules():
if isinstance(module, nn.Linear):
init.xavier_normal_(module.weight, init.calculate_gain('relu'))
if module.bias is not None:
init.zeros_(module.bias)
def forward(self, graph, feat, lambda_max=None):
r"""Compute ChebNet layer.
Parameters
----------
graph : DGLGraph or BatchedDGLGraph
The graph.
feat : torch.Tensor
The input feature of shape :math:`(N, D_{in})` where :math:`D_{in}`
is size of input feature, :math:`N` is the number of nodes.
lambda_max : list or tensor or None, optional.
A list(tensor) with length :math:`B`, stores the largest eigenvalue
of the normalized laplacian of each individual graph in ``graph``,
where :math:`B` is the batch size of the input graph. Default: None.
If None, this method would compute the list by calling
``dgl.laplacian_lambda_max``.
Returns
-------
torch.Tensor
The output feature of shape :math:`(N, D_{out})` where :math:`D_{out}`
is size of output feature.
"""
with graph.local_scope():
norm = th.pow(
graph.in_degrees().float().clamp(min=1), -0.5).unsqueeze(-1).to(feat.device)
if lambda_max is None:
lambda_max = laplacian_lambda_max(graph)
if isinstance(lambda_max, list):
lambda_max = th.Tensor(lambda_max).to(feat.device)
if lambda_max.dim() < 1:
lambda_max = lambda_max.unsqueeze(-1) # (B,) to (B, 1)
# broadcast from (B, 1) to (N, 1)
lambda_max = broadcast_nodes(graph, lambda_max)
# T0(X)
Tx_0 = feat
rst = self.fc[0](Tx_0)
# T1(X)
if self._k > 1:
graph.ndata['h'] = Tx_0 * norm
graph.update_all(fn.copy_u('h', 'm'), fn.sum('m', 'h'))
h = graph.ndata.pop('h') * norm
# Λ = 2 * (I - D ^ -1/2 A D ^ -1/2) / lambda_max - I
# = - 2(D ^ -1/2 A D ^ -1/2) / lambda_max + (2 / lambda_max - 1) I
Tx_1 = -2. * h / lambda_max + Tx_0 * (2. / lambda_max - 1)
rst = rst + self.fc[1](Tx_1)
# Ti(x), i = 2...k
for i in range(2, self._k):
graph.ndata['h'] = Tx_1 * norm
graph.update_all(fn.copy_u('h', 'm'), fn.sum('m', 'h'))
h = graph.ndata.pop('h') * norm
# Tx_k = 2 * Λ * Tx_(k-1) - Tx_(k-2)
# = - 4(D ^ -1/2 A D ^ -1/2) / lambda_max Tx_(k-1) +
# (4 / lambda_max - 2) Tx_(k-1) -
# Tx_(k-2)
Tx_2 = -4. * h / lambda_max + Tx_1 * (4. / lambda_max - 2) - Tx_0
rst = rst + self.fc[i](Tx_2)
Tx_1, Tx_0 = Tx_2, Tx_1
# add bias
if self.bias is not None:
rst = rst + self.bias
return rst
python/dgl/nn/pytorch/conv/densechebconv.py 0 → 100644
View file @ ddb5d804
"""Torch Module for DenseChebConv"""
# pylint: disable= no-member, arguments-differ, invalid-name
import torch as th
from torch import nn
from torch.nn import init
class DenseChebConv(nn.Module):
r"""Chebyshev Spectral Graph Convolution layer from paper `Convolutional
Neural Networks on Graphs with Fast Localized Spectral Filtering
<https://arxiv.org/pdf/1606.09375.pdf>`__.
We recommend to use this module when inducing ChebConv operations on dense
graphs / k-hop graphs.
Parameters
----------
in_feats: int
Number of input features.
out_feats: int
Number of output features.
k : int
Chebyshev filter size.
bias : bool, optional
If True, adds a learnable bias to the output. Default: ``True``.
See also
--------
ChebConv
"""
def __init__(self,
in_feats,
out_feats,
k,
bias=True):
super(DenseChebConv, self).__init__()
self._in_feats = in_feats
self._out_feats = out_feats
self._k = k
self.W = nn.Parameter(th.Tensor(k, in_feats, out_feats))
if bias:
self.bias = nn.Parameter(th.Tensor(out_feats))
else:
self.register_buffer('bias', None)
self.reset_parameters()
def reset_parameters(self):
"""Reinitialize learnable parameters."""
if self.bias is not None:
init.zeros_(self.bias)
for i in range(self._k):
init.xavier_normal_(self.W[i], init.calculate_gain('relu'))
def forward(self, adj, feat, lambda_max=None):
r"""Compute (Dense) Chebyshev Spectral Graph Convolution layer.
Parameters
----------
adj : torch.Tensor
The adjacency matrix of the graph to apply Graph Convolution on,
should be of shape :math:`(N, N)`, where a row represents the destination
and a column represents the source.
feat : torch.Tensor
The input feature of shape :math:`(N, D_{in})` where :math:`D_{in}`
is size of input feature, :math:`N` is the number of nodes.
lambda_max : float or None, optional
A float value indicates the largest eigenvalue of given graph.
Default: None.
Returns
-------
torch.Tensor
The output feature of shape :math:`(N, D_{out})` where :math:`D_{out}`
is size of output feature.
"""
A = adj.to(feat)
num_nodes = A.shape[0]
in_degree = 1 / A.sum(dim=1).clamp(min=1).sqrt()
D_invsqrt = th.diag(in_degree)
I = th.eye(num_nodes).to(A)
L = I - D_invsqrt @ A @ D_invsqrt
if lambda_max is None:
lambda_ = th.eig(L)[0][:, 0]
lambda_max = lambda_.max()
L_hat = 2 * L / lambda_max - I
Z = [th.eye(num_nodes).to(A)]
for i in range(1, self._k):
if i == 1:
Z.append(L_hat)
else:
Z.append(2 * L_hat @ Z[-1] - Z[-2])
Zs = th.stack(Z, 0) # (k, n, n)
Zh = (Zs @ feat.unsqueeze(0) @ self.W)
Zh = Zh.sum(0)
if self.bias is not None:
Zh = Zh + self.bias
return Zh
python/dgl/nn/pytorch/conv/densegraphconv.py 0 → 100644
View file @ ddb5d804
"""Torch Module for DenseGraphConv"""
# pylint: disable= no-member, arguments-differ, invalid-name
import torch as th
from torch import nn
from torch.nn import init
class DenseGraphConv(nn.Module):
"""Graph Convolutional Network layer where the graph structure
is given by an adjacency matrix.
We recommend user to use this module when inducing graph convolution
on dense graphs / k-hop graphs.
Parameters
----------
in_feats : int
Input feature size.
out_feats : int
Output feature size.
norm : bool
If True, the normalizer :math:`c_{ij}` is applied. Default: ``True``.
bias : bool
If True, adds a learnable bias to the output. Default: ``True``.
activation : callable activation function/layer or None, optional
If not None, applies an activation function to the updated node features.
Default: ``None``.
See also
--------
GraphConv
"""
def __init__(self,
in_feats,
out_feats,
norm=True,
bias=True,
activation=None):
super(DenseGraphConv, self).__init__()
self._in_feats = in_feats
self._out_feats = out_feats
self._norm = norm
self.weight = nn.Parameter(th.Tensor(in_feats, out_feats))
if bias:
self.bias = nn.Parameter(th.Tensor(out_feats))
else:
self.register_buffer('bias', None)
self.reset_parameters()
self._activation = activation
def reset_parameters(self):
"""Reinitialize learnable parameters."""
init.xavier_uniform_(self.weight)
if self.bias is not None:
init.zeros_(self.bias)
def forward(self, adj, feat):
r"""Compute (Dense) Graph Convolution layer.
Parameters
----------
adj : torch.Tensor
The adjacency matrix of the graph to apply Graph Convolution on,
should be of shape :math:`(N, N)`, where a row represents the destination
and a column represents the source.
feat : torch.Tensor
The input feature of shape :math:`(N, D_{in})` where :math:`D_{in}`
is size of input feature, :math:`N` is the number of nodes.
Returns
-------
torch.Tensor
The output feature of shape :math:`(N, D_{out})` where :math:`D_{out}`
is size of output feature.
"""
adj = adj.float().to(feat.device)
if self._norm:
in_degrees = adj.sum(dim=1)
norm = th.pow(in_degrees, -0.5)
shp = norm.shape + (1,) * (feat.dim() - 1)
norm = th.reshape(norm, shp).to(feat.device)
feat = feat * norm
if self._in_feats > self._out_feats:
# mult W first to reduce the feature size for aggregation.
feat = th.matmul(feat, self.weight)
rst = adj @ feat
else:
# aggregate first then mult W
rst = adj @ feat
rst = th.matmul(rst, self.weight)
if self._norm:
rst = rst * norm
if self.bias is not None:
rst = rst + self.bias
if self._activation is not None:
rst = self._activation(rst)
return rst
python/dgl/nn/pytorch/conv/densesageconv.py 0 → 100644
View file @ ddb5d804
"""Torch Module for DenseSAGEConv"""
# pylint: disable= no-member, arguments-differ, invalid-name
from torch import nn
class DenseSAGEConv(nn.Module):
"""GraphSAGE layer where the graph structure is given by an
adjacency matrix.
We recommend to use this module when inducing GraphSAGE operations
on dense graphs / k-hop graphs.
Note that we only support gcn aggregator in DenseSAGEConv.
Parameters
----------
in_feats : int
Input feature size.
out_feats : int
Output feature size.
feat_drop : float, optional
Dropout rate on features. Default: 0.
bias : bool
If True, adds a learnable bias to the output. Default: ``True``.
norm : callable activation function/layer or None, optional
If not None, applies normalization to the updated node features.
activation : callable activation function/layer or None, optional
If not None, applies an activation function to the updated node features.
Default: ``None``.
See also
--------
SAGEConv
"""
def __init__(self,
in_feats,
out_feats,
feat_drop=0.,
bias=True,
norm=None,
activation=None):
super(DenseSAGEConv, self).__init__()
self._in_feats = in_feats
self._out_feats = out_feats
self._norm = norm
self.feat_drop = nn.Dropout(feat_drop)
self.activation = activation
self.fc = nn.Linear(in_feats, out_feats, bias=bias)
self.reset_parameters()
def reset_parameters(self):
"""Reinitialize learnable parameters."""
gain = nn.init.calculate_gain('relu')
nn.init.xavier_uniform_(self.fc.weight, gain=gain)
def forward(self, adj, feat):
r"""Compute (Dense) Graph SAGE layer.
Parameters
----------
adj : torch.Tensor
The adjacency matrix of the graph to apply Graph Convolution on,
should be of shape :math:`(N, N)`, where a row represents the destination
and a column represents the source.
feat : torch.Tensor
The input feature of shape :math:`(N, D_{in})` where :math:`D_{in}`
is size of input feature, :math:`N` is the number of nodes.
Returns
-------
torch.Tensor
The output feature of shape :math:`(N, D_{out})` where :math:`D_{out}`
is size of output feature.
"""
adj = adj.float().to(feat.device)
feat = self.feat_drop(feat)
in_degrees = adj.sum(dim=1).unsqueeze(-1)
h_neigh = (adj @ feat + feat) / (in_degrees + 1)
rst = self.fc(h_neigh)
# activation
if self.activation is not None:
rst = self.activation(rst)
# normalization
if self._norm is not None:
rst = self._norm(rst)
return rst
python/dgl/nn/pytorch/conv/edgeconv.py 0 → 100644
View file @ ddb5d804
"""Torch Module for EdgeConv Layer"""
# pylint: disable= no-member, arguments-differ, invalid-name
from torch import nn
from .... import function as fn
class EdgeConv(nn.Module):
r"""EdgeConv layer.
Introduced in "`Dynamic Graph CNN for Learning on Point Clouds
<https://arxiv.org/pdf/1801.07829>`__". Can be described as follows:
.. math::
x_i^{(l+1)} = \max_{j \in \mathcal{N}(i)} \mathrm{ReLU}(
\Theta \cdot (x_j^{(l)} - x_i^{(l)}) + \Phi \cdot x_i^{(l)})
where :math:`\mathcal{N}(i)` is the neighbor of :math:`i`.
Parameters
----------
in_feat : int
Input feature size.
out_feat : int
Output feature size.
batch_norm : bool
Whether to include batch normalization on messages.
"""
def __init__(self, in_feat, out_feat, batch_norm=False):
super(EdgeConv, self).__init__()
self.batch_norm = batch_norm
self.theta = nn.Linear(in_feat, out_feat)
self.phi = nn.Linear(in_feat, out_feat)
if batch_norm:
self.bn = nn.BatchNorm1d(out_feat)
def message(self, edges):
"""The message computation function.
"""
theta_x = self.theta(edges.dst['x'] - edges.src['x'])
phi_x = self.phi(edges.src['x'])
return {'e': theta_x + phi_x}
def forward(self, g, h):
"""Forward computation
Parameters
----------
g : DGLGraph
The graph.
h : Tensor
:math:`(N, D)` where :math:`N` is the number of nodes and
:math:`D` is the number of feature dimensions.
Returns
-------
torch.Tensor
New node features.
"""
with g.local_scope():
g.ndata['x'] = h
if not self.batch_norm:
g.update_all(self.message, fn.max('e', 'x'))
else:
g.apply_edges(self.message)
# Although the official implementation includes a per-edge
# batch norm within EdgeConv, I choose to replace it with a
# global batch norm for a number of reasons:
#
# (1) When the point clouds within each batch do not have the
# same number of points, batch norm would not work.
#
# (2) Even if the point clouds always have the same number of
# points, the points may as well be shuffled even with the
# same (type of) object (and the official implementation
# *does* shuffle the points of the same example for each
# epoch).
#
# For example, the first point of a point cloud of an
# airplane does not always necessarily reside at its nose.
#
# In this case, the learned statistics of each position
# by batch norm is not as meaningful as those learned from
# images.
g.edata['e'] = self.bn(g.edata['e'])
g.update_all(fn.copy_e('e', 'e'), fn.max('e', 'x'))
return g.ndata['x']
python/dgl/nn/pytorch/conv/gatconv.py 0 → 100644
View file @ ddb5d804
"""Torch modules for graph attention networks(GAT)."""
# pylint: disable= no-member, arguments-differ, invalid-name
import torch as th
from torch import nn
from .... import function as fn
from ..softmax import edge_softmax
from ..utils import Identity
# pylint: enable=W0235
class GATConv(nn.Module):
r"""Apply `Graph Attention Network <https://arxiv.org/pdf/1710.10903.pdf>`__
over an input signal.
.. math::
h_i^{(l+1)} = \sum_{j\in \mathcal{N}(i)} \alpha_{i,j} W^{(l)} h_j^{(l)}
where :math:`\alpha_{ij}` is the attention score bewteen node :math:`i` and
node :math:`j`:
.. math::
\alpha_{ij}^{l} & = \mathrm{softmax_i} (e_{ij}^{l})
e_{ij}^{l} & = \mathrm{LeakyReLU}\left(\vec{a}^T [W h_{i} \| W h_{j}]\right)
Parameters
----------
in_feats : int
Input feature size.
out_feats : int
Output feature size.
num_heads : int
Number of heads in Multi-Head Attention.
feat_drop : float, optional
Dropout rate on feature, defaults: ``0``.
attn_drop : float, optional
Dropout rate on attention weight, defaults: ``0``.
negative_slope : float, optional
LeakyReLU angle of negative slope.
residual : bool, optional
If True, use residual connection.
activation : callable activation function/layer or None, optional.
If not None, applies an activation function to the updated node features.
Default: ``None``.
"""
def __init__(self,
in_feats,
out_feats,
num_heads,
feat_drop=0.,
attn_drop=0.,
negative_slope=0.2,
residual=False,
activation=None):
super(GATConv, self).__init__()
self._num_heads = num_heads
self._in_feats = in_feats
self._out_feats = out_feats
self.fc = nn.Linear(in_feats, out_feats * num_heads, bias=False)
self.attn_l = nn.Parameter(th.FloatTensor(size=(1, num_heads, out_feats)))
self.attn_r = nn.Parameter(th.FloatTensor(size=(1, num_heads, out_feats)))
self.feat_drop = nn.Dropout(feat_drop)
self.attn_drop = nn.Dropout(attn_drop)
self.leaky_relu = nn.LeakyReLU(negative_slope)
if residual:
if in_feats != out_feats:
self.res_fc = nn.Linear(in_feats, num_heads * out_feats, bias=False)
else:
self.res_fc = Identity()
else:
self.register_buffer('res_fc', None)
self.reset_parameters()
self.activation = activation
def reset_parameters(self):
"""Reinitialize learnable parameters."""
gain = nn.init.calculate_gain('relu')
nn.init.xavier_normal_(self.fc.weight, gain=gain)
nn.init.xavier_normal_(self.attn_l, gain=gain)
nn.init.xavier_normal_(self.attn_r, gain=gain)
if isinstance(self.res_fc, nn.Linear):
nn.init.xavier_normal_(self.res_fc.weight, gain=gain)
def forward(self, graph, feat):
r"""Compute graph attention network layer.
Parameters
----------
graph : DGLGraph
The graph.
feat : torch.Tensor
The input feature of shape :math:`(N, D_{in})` where :math:`D_{in}`
is size of input feature, :math:`N` is the number of nodes.
Returns
-------
torch.Tensor
The output feature of shape :math:`(N, H, D_{out})` where :math:`H`
is the number of heads, and :math:`D_{out}` is size of output feature.
"""
graph = graph.local_var()
h = self.feat_drop(feat)
feat = self.fc(h).view(-1, self._num_heads, self._out_feats)
el = (feat * self.attn_l).sum(dim=-1).unsqueeze(-1)
er = (feat * self.attn_r).sum(dim=-1).unsqueeze(-1)
graph.ndata.update({'ft': feat, 'el': el, 'er': er})
# compute edge attention
graph.apply_edges(fn.u_add_v('el', 'er', 'e'))
e = self.leaky_relu(graph.edata.pop('e'))
# compute softmax
graph.edata['a'] = self.attn_drop(edge_softmax(graph, e))
# message passing
graph.update_all(fn.u_mul_e('ft', 'a', 'm'),
fn.sum('m', 'ft'))
rst = graph.ndata['ft']
# residual
if self.res_fc is not None:
resval = self.res_fc(h).view(h.shape[0], -1, self._out_feats)
rst = rst + resval
# activation
if self.activation:
rst = self.activation(rst)
return rst
python/dgl/nn/pytorch/conv/gatedgraphconv.py 0 → 100644
View file @ ddb5d804
"""Torch Module for Gated Graph Convolution layer"""
# pylint: disable= no-member, arguments-differ, invalid-name
import torch as th
from torch import nn
from torch.nn import init
from .... import function as fn
class GatedGraphConv(nn.Module):
r"""Gated Graph Convolution layer from paper `Gated Graph Sequence
Neural Networks <https://arxiv.org/pdf/1511.05493.pdf>`__.
.. math::
h_{i}^{0} & = [ x_i \| \mathbf{0} ]
a_{i}^{t} & = \sum_{j\in\mathcal{N}(i)} W_{e_{ij}} h_{j}^{t}
h_{i}^{t+1} & = \mathrm{GRU}(a_{i}^{t}, h_{i}^{t})
Parameters
----------
in_feats : int
Input feature size.
out_feats : int
Output feature size.
n_steps : int
Number of recurrent steps.
n_etypes : int
Number of edge types.
bias : bool
If True, adds a learnable bias to the output. Default: ``True``.
"""
def __init__(self,
in_feats,
out_feats,
n_steps,
n_etypes,
bias=True):
super(GatedGraphConv, self).__init__()
self._in_feats = in_feats
self._out_feats = out_feats
self._n_steps = n_steps
self.edge_embed = nn.Embedding(n_etypes, out_feats * out_feats)
self.gru = nn.GRUCell(out_feats, out_feats, bias=bias)
self.reset_parameters()
def reset_parameters(self):
"""Reinitialize learnable parameters."""
gain = init.calculate_gain('relu')
self.gru.reset_parameters()
init.xavier_normal_(self.edge_embed.weight, gain=gain)
def forward(self, graph, feat, etypes):
"""Compute Gated Graph Convolution layer.
Parameters
----------
graph : DGLGraph
The graph.
feat : torch.Tensor
The input feature of shape :math:`(N, D_{in})` where :math:`N`
is the number of nodes of the graph and :math:`D_{in}` is the
input feature size.
etypes : torch.LongTensor
The edge type tensor of shape :math:`(E,)` where :math:`E` is
the number of edges of the graph.
Returns
-------
torch.Tensor
The output feature of shape :math:`(N, D_{out})` where :math:`D_{out}`
is the output feature size.
"""
graph = graph.local_var()
zero_pad = feat.new_zeros((feat.shape[0], self._out_feats - feat.shape[1]))
feat = th.cat([feat, zero_pad], -1)
# NOTE(zihao): there is still room to optimize, we may do kernel fusion
# for such operations in the future.
graph.edata['w'] = self.edge_embed(etypes).view(-1, self._out_feats, self._out_feats)
for _ in range(self._n_steps):
graph.ndata['h'] = feat.unsqueeze(-1) # (N, D, 1)
graph.update_all(fn.u_mul_e('h', 'w', 'm'),
fn.sum('m', 'a'))
a = graph.ndata.pop('a').sum(dim=1) # (N, D)
feat = self.gru(a, feat)
return feat
python/dgl/nn/pytorch/conv/ginconv.py 0 → 100644
View file @ ddb5d804
"""Torch Module for Graph Isomorphism Network layer"""
# pylint: disable= no-member, arguments-differ, invalid-name
import torch as th
from torch import nn
from .... import function as fn
class GINConv(nn.Module):
r"""Graph Isomorphism Network layer from paper `How Powerful are Graph
Neural Networks? <https://arxiv.org/pdf/1810.00826.pdf>`__.
.. math::
h_i^{(l+1)} = f_\Theta \left((1 + \epsilon) h_i^{l} +
\mathrm{aggregate}\left(\left\{h_j^{l}, j\in\mathcal{N}(i)
\right\}\right)\right)
Parameters
----------
apply_func : callable activation function/layer or None
If not None, apply this function to the updated node feature,
the :math:`f_\Theta` in the formula.
aggregator_type : str
Aggregator type to use (``sum``, ``max`` or ``mean``).
init_eps : float, optional
Initial :math:`\epsilon` value, default: ``0``.
learn_eps : bool, optional
If True, :math:`\epsilon` will be a learnable parameter.
"""
def __init__(self,
apply_func,
aggregator_type,
init_eps=0,
learn_eps=False):
super(GINConv, self).__init__()
self.apply_func = apply_func
if aggregator_type == 'sum':
self._reducer = fn.sum
elif aggregator_type == 'max':
self._reducer = fn.max
elif aggregator_type == 'mean':
self._reducer = fn.mean
else:
raise KeyError('Aggregator type {} not recognized.'.format(aggregator_type))
# to specify whether eps is trainable or not.
if learn_eps:
self.eps = th.nn.Parameter(th.FloatTensor([init_eps]))
else:
self.register_buffer('eps', th.FloatTensor([init_eps]))
def forward(self, graph, feat):
r"""Compute Graph Isomorphism Network layer.
Parameters
----------
graph : DGLGraph
The graph.
feat : torch.Tensor
The input feature of shape :math:`(N, D)` where :math:`D`
could be any positive integer, :math:`N` is the number
of nodes. If ``apply_func`` is not None, :math:`D` should
fit the input dimensionality requirement of ``apply_func``.
Returns
-------
torch.Tensor
The output feature of shape :math:`(N, D_{out})` where
:math:`D_{out}` is the output dimensionality of ``apply_func``.
If ``apply_func`` is None, :math:`D_{out}` should be the same
as input dimensionality.
"""
graph = graph.local_var()
graph.ndata['h'] = feat
graph.update_all(fn.copy_u('h', 'm'), self._reducer('m', 'neigh'))
rst = (1 + self.eps) * feat + graph.ndata['neigh']
if self.apply_func is not None:
rst = self.apply_func(rst)
return rst
python/dgl/nn/pytorch/conv/gmmconv.py 0 → 100644
View file @ ddb5d804
"""Torch Module for GMM Conv"""
# pylint: disable= no-member, arguments-differ, invalid-name
import torch as th
from torch import nn
from torch.nn import init
from .... import function as fn
from ..utils import Identity
class GMMConv(nn.Module):
r"""The Gaussian Mixture Model Convolution layer from `Geometric Deep
Learning on Graphs and Manifolds using Mixture Model CNNs
<http://openaccess.thecvf.com/content_cvpr_2017/papers/Monti_Geometric_Deep_Learning_CVPR_2017_paper.pdf>`__.
.. math::
h_i^{l+1} & = \mathrm{aggregate}\left(\left\{\frac{1}{K}
\sum_{k}^{K} w_k(u_{ij}), \forall j\in \mathcal{N}(i)\right\}\right)
w_k(u) & = \exp\left(-\frac{1}{2}(u-\mu_k)^T \Sigma_k^{-1} (u - \mu_k)\right)
Parameters
----------
in_feats : int
Number of input features.
out_feats : int
Number of output features.
dim : int
Dimensionality of pseudo-coordinte.
n_kernels : int
Number of kernels :math:`K`.
aggregator_type : str
Aggregator type (``sum``, ``mean``, ``max``).
residual : bool
If True, use residual connection inside this layer.
bias : bool
If True, adds a learnable bias to the output. Default: ``True``.
"""
def __init__(self,
in_feats,
out_feats,
dim,
n_kernels,
aggregator_type,
residual=True,
bias=True):
super(GMMConv, self).__init__()
self._in_feats = in_feats
self._out_feats = out_feats
self._dim = dim
self._n_kernels = n_kernels
if aggregator_type == 'sum':
self._reducer = fn.sum
elif aggregator_type == 'mean':
self._reducer = fn.mean
elif aggregator_type == 'max':
self._reducer = fn.max
else:
raise KeyError("Aggregator type {} not recognized.".format(aggregator_type))
self.mu = nn.Parameter(th.Tensor(n_kernels, dim))
self.inv_sigma = nn.Parameter(th.Tensor(n_kernels, dim))
self.fc = nn.Linear(in_feats, n_kernels * out_feats, bias=False)
if residual:
if in_feats != out_feats:
self.res_fc = nn.Linear(in_feats, out_feats, bias=False)
else:
self.res_fc = Identity()
else:
self.register_buffer('res_fc', None)
if bias:
self.bias = nn.Parameter(th.Tensor(out_feats))
else:
self.register_buffer('bias', None)
self.reset_parameters()
def reset_parameters(self):
"""Reinitialize learnable parameters."""
gain = init.calculate_gain('relu')
init.xavier_normal_(self.fc.weight, gain=gain)
if isinstance(self.res_fc, nn.Linear):
init.xavier_normal_(self.res_fc.weight, gain=gain)
init.normal_(self.mu.data, 0, 0.1)
init.normal_(self.inv_sigma.data, 1, 0.1)
if self.bias is not None:
init.zeros_(self.bias.data)
def forward(self, graph, feat, pseudo):
"""Compute Gaussian Mixture Model Convolution layer.
Parameters
----------
graph : DGLGraph
The graph.
feat : torch.Tensor
The input feature of shape :math:`(N, D_{in})` where :math:`N`
is the number of nodes of the graph and :math:`D_{in}` is the
input feature size.
pseudo : torch.Tensor
The pseudo coordinate tensor of shape :math:`(E, D_{u})` where
:math:`E` is the number of edges of the graph and :math:`D_{u}`
is the dimensionality of pseudo coordinate.
Returns
-------
torch.Tensor
The output feature of shape :math:`(N, D_{out})` where :math:`D_{out}`
is the output feature size.
"""
graph = graph.local_var()
graph.ndata['h'] = self.fc(feat).view(-1, self._n_kernels, self._out_feats)
E = graph.number_of_edges()
# compute gaussian weight
gaussian = -0.5 * ((pseudo.view(E, 1, self._dim) -
self.mu.view(1, self._n_kernels, self._dim)) ** 2)
gaussian = gaussian * (self.inv_sigma.view(1, self._n_kernels, self._dim) ** 2)
gaussian = th.exp(gaussian.sum(dim=-1, keepdim=True)) # (E, K, 1)
graph.edata['w'] = gaussian
graph.update_all(fn.u_mul_e('h', 'w', 'm'), self._reducer('m', 'h'))
rst = graph.ndata['h'].sum(1)
# residual connection
if self.res_fc is not None:
rst = rst + self.res_fc(feat)
# bias
if self.bias is not None:
rst = rst + self.bias
return rst
python/dgl/nn/pytorch/conv/graphconv.py 0 → 100644
View file @ ddb5d804
"""Torch modules for graph convolutions(GCN)."""
# pylint: disable= no-member, arguments-differ, invalid-name
import torch as th
from torch import nn
from torch.nn import init
from .... import function as fn
# pylint: disable=W0235
class GraphConv(nn.Module):
r"""Apply graph convolution over an input signal.
Graph convolution is introduced in `GCN <https://arxiv.org/abs/1609.02907>`__
and can be described as below:
.. math::
h_i^{(l+1)} = \sigma(b^{(l)} + \sum_{j\in\mathcal{N}(i)}\frac{1}{c_{ij}}h_j^{(l)}W^{(l)})
where :math:`\mathcal{N}(i)` is the neighbor set of node :math:`i`. :math:`c_{ij}` is equal
to the product of the square root of node degrees:
:math:`\sqrt{|\mathcal{N}(i)|}\sqrt{|\mathcal{N}(j)|}`. :math:`\sigma` is an activation
function.
The model parameters are initialized as in the
`original implementation <https://github.com/tkipf/gcn/blob/master/gcn/layers.py>`__ where
the weight :math:`W^{(l)}` is initialized using Glorot uniform initialization
and the bias is initialized to be zero.
Notes
-----
Zero in degree nodes could lead to invalid normalizer. A common practice
to avoid this is to add a self-loop for each node in the graph, which
can be achieved by:
>>> g = ... # some DGLGraph
>>> g.add_edges(g.nodes(), g.nodes())
Parameters
----------
in_feats : int
Input feature size.
out_feats : int
Output feature size.
norm : bool, optional
If True, the normalizer :math:`c_{ij}` is applied. Default: ``True``.
bias : bool, optional
If True, adds a learnable bias to the output. Default: ``True``.
activation: callable activation function/layer or None, optional
If not None, applies an activation function to the updated node features.
Default: ``None``.
Attributes
----------
weight : torch.Tensor
The learnable weight tensor.
bias : torch.Tensor
The learnable bias tensor.
"""
def __init__(self,
in_feats,
out_feats,
norm=True,
bias=True,
activation=None):
super(GraphConv, self).__init__()
self._in_feats = in_feats
self._out_feats = out_feats
self._norm = norm
self.weight = nn.Parameter(th.Tensor(in_feats, out_feats))
if bias:
self.bias = nn.Parameter(th.Tensor(out_feats))
else:
self.register_parameter('bias', None)
self.reset_parameters()
self._activation = activation
def reset_parameters(self):
"""Reinitialize learnable parameters."""
init.xavier_uniform_(self.weight)
if self.bias is not None:
init.zeros_(self.bias)
def forward(self, graph, feat):
r"""Compute graph convolution.
Notes
-----
* Input shape: :math:`(N, *, \text{in_feats})` where * means any number of additional
dimensions, :math:`N` is the number of nodes.
* Output shape: :math:`(N, *, \text{out_feats})` where all but the last dimension are
the same shape as the input.
Parameters
----------
graph : DGLGraph
The graph.
feat : torch.Tensor
The input feature
Returns
-------
torch.Tensor
The output feature
"""
graph = graph.local_var()
if self._norm:
norm = th.pow(graph.in_degrees().float().clamp(min=1), -0.5)
shp = norm.shape + (1,) * (feat.dim() - 1)
norm = th.reshape(norm, shp).to(feat.device)
feat = feat * norm
if self._in_feats > self._out_feats:
# mult W first to reduce the feature size for aggregation.
feat = th.matmul(feat, self.weight)
graph.ndata['h'] = feat
graph.update_all(fn.copy_src(src='h', out='m'),
fn.sum(msg='m', out='h'))
rst = graph.ndata['h']
else:
# aggregate first then mult W
graph.ndata['h'] = feat
graph.update_all(fn.copy_src(src='h', out='m'),
fn.sum(msg='m', out='h'))
rst = graph.ndata['h']
rst = th.matmul(rst, self.weight)
if self._norm:
rst = rst * norm
if self.bias is not None:
rst = rst + self.bias
if self._activation is not None:
rst = self._activation(rst)
return rst
def extra_repr(self):
"""Set the extra representation of the module,
which will come into effect when printing the model.
"""
summary = 'in={_in_feats}, out={_out_feats}'
summary += ', normalization={_norm}'
if '_activation' in self.__dict__:
summary += ', activation={_activation}'
return summary.format(**self.__dict__)
python/dgl/nn/pytorch/conv/nnconv.py 0 → 100644
View file @ ddb5d804
"""Torch Module for NNConv layer"""
# pylint: disable= no-member, arguments-differ, invalid-name
import torch as th
from torch import nn
from torch.nn import init
from .... import function as fn
from ..utils import Identity
class NNConv(nn.Module):
r"""Graph Convolution layer introduced in `Neural Message Passing
for Quantum Chemistry <https://arxiv.org/pdf/1704.01212.pdf>`__.
.. math::
h_{i}^{l+1} = h_{i}^{l} + \mathrm{aggregate}\left(\left\{
f_\Theta (e_{ij}) \cdot h_j^{l}, j\in \mathcal{N}(i) \right\}\right)
Parameters
----------
in_feats : int
Input feature size.
out_feats : int
Output feature size.
edge_func : callable activation function/layer
Maps each edge feature to a vector of shape
``(in_feats * out_feats)`` as weight to compute
messages.
Also is the :math:`f_\Theta` in the formula.
aggregator_type : str
Aggregator type to use (``sum``, ``mean`` or ``max``).
residual : bool, optional
If True, use residual connection. Default: ``False``.
bias : bool, optional
If True, adds a learnable bias to the output. Default: ``True``.
"""
def __init__(self,
in_feats,
out_feats,
edge_func,
aggregator_type,
residual=False,
bias=True):
super(NNConv, self).__init__()
self._in_feats = in_feats
self._out_feats = out_feats
self.edge_nn = edge_func
if aggregator_type == 'sum':
self.reducer = fn.sum
elif aggregator_type == 'mean':
self.reducer = fn.mean
elif aggregator_type == 'max':
self.reducer = fn.max
else:
raise KeyError('Aggregator type {} not recognized: '.format(aggregator_type))
self._aggre_type = aggregator_type
if residual:
if in_feats != out_feats:
self.res_fc = nn.Linear(in_feats, out_feats, bias=False)
else:
self.res_fc = Identity()
else:
self.register_buffer('res_fc', None)
if bias:
self.bias = nn.Parameter(th.Tensor(out_feats))
else:
self.register_buffer('bias', None)
self.reset_parameters()
def reset_parameters(self):
"""Reinitialize learnable parameters."""
gain = init.calculate_gain('relu')
if self.bias is not None:
nn.init.zeros_(self.bias)
if isinstance(self.res_fc, nn.Linear):
nn.init.xavier_normal_(self.res_fc.weight, gain=gain)
def forward(self, graph, feat, efeat):
r"""Compute MPNN Graph Convolution layer.
Parameters
----------
graph : DGLGraph
The graph.
feat : torch.Tensor
The input feature of shape :math:`(N, D_{in})` where :math:`N`
is the number of nodes of the graph and :math:`D_{in}` is the
input feature size.
efeat : torch.Tensor
The edge feature of shape :math:`(N, *)`, should fit the input
shape requirement of ``edge_nn``.
Returns
-------
torch.Tensor
The output feature of shape :math:`(N, D_{out})` where :math:`D_{out}`
is the output feature size.
"""
graph = graph.local_var()
# (n, d_in, 1)
graph.ndata['h'] = feat.unsqueeze(-1)
# (n, d_in, d_out)
graph.edata['w'] = self.edge_nn(efeat).view(-1, self._in_feats, self._out_feats)
# (n, d_in, d_out)
graph.update_all(fn.u_mul_e('h', 'w', 'm'), self.reducer('m', 'neigh'))
rst = graph.ndata.pop('neigh').sum(dim=1) # (n, d_out)
# residual connection
if self.res_fc is not None:
rst = rst + self.res_fc(feat)
# bias
if self.bias is not None:
rst = rst + self.bias
return rst
python/dgl/nn/pytorch/conv/relgraphconv.py 0 → 100644
View file @ ddb5d804
"""Torch Module for Relational graph convolution layer"""
# pylint: disable= no-member, arguments-differ, invalid-name
import torch as th
from torch import nn
from .... import function as fn
from .. import utils
class RelGraphConv(nn.Module):
r"""Relational graph convolution layer.
Relational graph convolution is introduced in "`Modeling Relational Data with Graph
Convolutional Networks <https://arxiv.org/abs/1703.06103>`__"
and can be described as below:
.. math::
h_i^{(l+1)} = \sigma(\sum_{r\in\mathcal{R}}
\sum_{j\in\mathcal{N}^r(i)}\frac{1}{c_{i,r}}W_r^{(l)}h_j^{(l)}+W_0^{(l)}h_i^{(l)})
where :math:`\mathcal{N}^r(i)` is the neighbor set of node :math:`i` w.r.t. relation
:math:`r`. :math:`c_{i,r}` is the normalizer equal
to :math:`|\mathcal{N}^r(i)|`. :math:`\sigma` is an activation function. :math:`W_0`
is the self-loop weight.
The basis regularization decomposes :math:`W_r` by:
.. math::
W_r^{(l)} = \sum_{b=1}^B a_{rb}^{(l)}V_b^{(l)}
where :math:`B` is the number of bases.
The block-diagonal-decomposition regularization decomposes :math:`W_r` into :math:`B`
number of block diagonal matrices. We refer :math:`B` as the number of bases.
Parameters
----------
in_feat : int
Input feature size.
out_feat : int
Output feature size.
num_rels : int
Number of relations.
regularizer : str
Which weight regularizer to use "basis" or "bdd"
num_bases : int, optional
Number of bases. If is none, use number of relations. Default: None.
bias : bool, optional
True if bias is added. Default: True
activation : callable, optional
Activation function. Default: None
self_loop : bool, optional
True to include self loop message. Default: False
dropout : float, optional
Dropout rate. Default: 0.0
"""
def __init__(self,
in_feat,
out_feat,
num_rels,
regularizer="basis",
num_bases=None,
bias=True,
activation=None,
self_loop=False,
dropout=0.0):
super(RelGraphConv, self).__init__()
self.in_feat = in_feat
self.out_feat = out_feat
self.num_rels = num_rels
self.regularizer = regularizer
self.num_bases = num_bases
if self.num_bases is None or self.num_bases > self.num_rels or self.num_bases < 0:
self.num_bases = self.num_rels
self.bias = bias
self.activation = activation
self.self_loop = self_loop
if regularizer == "basis":
# add basis weights
self.weight = nn.Parameter(th.Tensor(self.num_bases, self.in_feat, self.out_feat))
if self.num_bases < self.num_rels:
# linear combination coefficients
self.w_comp = nn.Parameter(th.Tensor(self.num_rels, self.num_bases))
nn.init.xavier_uniform_(self.weight, gain=nn.init.calculate_gain('relu'))
if self.num_bases < self.num_rels:
nn.init.xavier_uniform_(self.w_comp,
gain=nn.init.calculate_gain('relu'))
# message func
self.message_func = self.basis_message_func
elif regularizer == "bdd":
if in_feat % num_bases != 0 or out_feat % num_bases != 0:
raise ValueError('Feature size must be a multiplier of num_bases.')
# add block diagonal weights
self.submat_in = in_feat // self.num_bases
self.submat_out = out_feat // self.num_bases
# assuming in_feat and out_feat are both divisible by num_bases
self.weight = nn.Parameter(th.Tensor(
self.num_rels, self.num_bases * self.submat_in * self.submat_out))
nn.init.xavier_uniform_(self.weight, gain=nn.init.calculate_gain('relu'))
# message func
self.message_func = self.bdd_message_func
else:
raise ValueError("Regularizer must be either 'basis' or 'bdd'")
# bias
if self.bias:
self.h_bias = nn.Parameter(th.Tensor(out_feat))
nn.init.zeros_(self.h_bias)
# weight for self loop
if self.self_loop:
self.loop_weight = nn.Parameter(th.Tensor(in_feat, out_feat))
nn.init.xavier_uniform_(self.loop_weight,
gain=nn.init.calculate_gain('relu'))
self.dropout = nn.Dropout(dropout)
def basis_message_func(self, edges):
"""Message function for basis regularizer"""
if self.num_bases < self.num_rels:
# generate all weights from bases
weight = self.weight.view(self.num_bases,
self.in_feat * self.out_feat)
weight = th.matmul(self.w_comp, weight).view(
self.num_rels, self.in_feat, self.out_feat)
else:
weight = self.weight
msg = utils.bmm_maybe_select(edges.src['h'], weight, edges.data['type'])
if 'norm' in edges.data:
msg = msg * edges.data['norm']
return {'msg': msg}
def bdd_message_func(self, edges):
"""Message function for block-diagonal-decomposition regularizer"""
if edges.src['h'].dtype == th.int64 and len(edges.src['h'].shape) == 1:
raise TypeError('Block decomposition does not allow integer ID feature.')
weight = self.weight.index_select(0, edges.data['type']).view(
-1, self.submat_in, self.submat_out)
node = edges.src['h'].view(-1, 1, self.submat_in)
msg = th.bmm(node, weight).view(-1, self.out_feat)
if 'norm' in edges.data:
msg = msg * edges.data['norm']
return {'msg': msg}
def forward(self, g, x, etypes, norm=None):
""" Forward computation
Parameters
----------
g : DGLGraph
The graph.
x : torch.Tensor
Input node features. Could be either
* :math:`(|V|, D)` dense tensor
* :math:`(|V|,)` int64 vector, representing the categorical values of each
node. We then treat the input feature as an one-hot encoding feature.
etypes : torch.Tensor
Edge type tensor. Shape: :math:`(|E|,)`
norm : torch.Tensor
Optional edge normalizer tensor. Shape: :math:`(|E|, 1)`
Returns
-------
torch.Tensor
New node features.
"""
g = g.local_var()
g.ndata['h'] = x
g.edata['type'] = etypes
if norm is not None:
g.edata['norm'] = norm
if self.self_loop:
loop_message = utils.matmul_maybe_select(x, self.loop_weight)
# message passing
g.update_all(self.message_func, fn.sum(msg='msg', out='h'))
# apply bias and activation
node_repr = g.ndata['h']
if self.bias:
node_repr = node_repr + self.h_bias
if self.self_loop:
node_repr = node_repr + loop_message
if self.activation:
node_repr = self.activation(node_repr)
node_repr = self.dropout(node_repr)
return node_repr
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