wehub-resource-sync
261 lines
10 KiB
Python
261 lines
10 KiB
Python
"""Torch modules for graph attention networks with fully valuable edges (EGAT)."""
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# pylint: disable= no-member, arguments-differ, invalid-name
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import torch as th
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from torch import nn
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from torch.nn import init
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from .... import function as fn
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from ....base import DGLError
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from ....utils import expand_as_pair
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from ...functional import edge_softmax
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# pylint: enable=W0235
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class EGATConv(nn.Module):
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r"""Graph attention layer that handles edge features from `Rossmann-Toolbox
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<https://pubmed.ncbi.nlm.nih.gov/34571541/>`__ (see supplementary data)
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The difference lies in how unnormalized attention scores :math:`e_{ij}` are obtained:
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.. math::
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e_{ij} &= \vec{F} (f_{ij}^{\prime})
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f_{ij}^{\prime} &= \mathrm{LeakyReLU}\left(A [ h_{i} \| f_{ij} \| h_{j}]\right)
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where :math:`f_{ij}^{\prime}` are edge features, :math:`\mathrm{A}` is weight matrix and
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:math:`\vec{F}` is weight vector. After that, resulting node features
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:math:`h_{i}^{\prime}` are updated in the same way as in regular GAT.
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Parameters
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----------
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in_node_feats : int, or pair of ints
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Input feature size; i.e, the number of dimensions of :math:`h_{i}`.
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EGATConv can be applied on homogeneous graph and unidirectional
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`bipartite graph <https://docs.dgl.ai/generated/dgl.bipartite.html?highlight=bipartite>`__.
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If the layer is to be applied to a unidirectional bipartite graph, ``in_feats``
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specifies the input feature size on both the source and destination nodes. If
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a scalar is given, the source and destination node feature size would take the
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same value.
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in_edge_feats : int
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Input edge feature size :math:`f_{ij}`.
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out_node_feats : int
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Output node feature size.
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out_edge_feats : int
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Output edge feature size :math:`f_{ij}^{\prime}`.
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num_heads : int
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Number of attention heads.
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bias : bool, optional
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If True, add bias term to :math:`f_{ij}^{\prime}`. Defaults: ``True``.
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Examples
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----------
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>>> import dgl
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>>> import torch as th
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>>> from dgl.nn import EGATConv
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>>> # Case 1: Homogeneous graph
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>>> num_nodes, num_edges = 8, 30
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>>> # generate a graph
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>>> graph = dgl.rand_graph(num_nodes,num_edges)
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>>> node_feats = th.rand((num_nodes, 20))
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>>> edge_feats = th.rand((num_edges, 12))
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>>> egat = EGATConv(in_node_feats=20,
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... in_edge_feats=12,
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... out_node_feats=15,
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... out_edge_feats=10,
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... num_heads=3)
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>>> #forward pass
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>>> new_node_feats, new_edge_feats = egat(graph, node_feats, edge_feats)
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>>> new_node_feats.shape, new_edge_feats.shape
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torch.Size([8, 3, 15]) torch.Size([30, 3, 10])
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>>> # Case 2: Unidirectional bipartite graph
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>>> u = [0, 1, 0, 0, 1]
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>>> v = [0, 1, 2, 3, 2]
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>>> g = dgl.heterograph({('A', 'r', 'B'): (u, v)})
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>>> u_feat = th.tensor(np.random.rand(2, 25).astype(np.float32))
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>>> v_feat = th.tensor(np.random.rand(4, 30).astype(np.float32))
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>>> nfeats = (u_feat,v_feat)
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>>> efeats = th.tensor(np.random.rand(5, 15).astype(np.float32))
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>>> in_node_feats = (25,30)
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>>> in_edge_feats = 15
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>>> out_node_feats = 10
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>>> out_edge_feats = 5
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>>> num_heads = 3
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>>> egat_model = EGATConv(in_node_feats,
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... in_edge_feats,
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... out_node_feats,
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... out_edge_feats,
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... num_heads,
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... bias=True)
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>>> #forward pass
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>>> new_node_feats,
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>>> new_edge_feats,
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>>> attentions = egat_model(g, nfeats, efeats, get_attention=True)
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>>> new_node_feats.shape, new_edge_feats.shape, attentions.shape
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(torch.Size([4, 3, 10]), torch.Size([5, 3, 5]), torch.Size([5, 3, 1]))
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"""
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def __init__(
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self,
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in_node_feats,
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in_edge_feats,
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out_node_feats,
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out_edge_feats,
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num_heads,
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bias=True,
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):
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super().__init__()
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self._num_heads = num_heads
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self._in_src_node_feats, self._in_dst_node_feats = expand_as_pair(
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in_node_feats
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)
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self._out_node_feats = out_node_feats
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self._out_edge_feats = out_edge_feats
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if isinstance(in_node_feats, tuple):
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self.fc_node_src = nn.Linear(
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self._in_src_node_feats, out_node_feats * num_heads, bias=False
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)
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self.fc_ni = nn.Linear(
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self._in_src_node_feats, out_edge_feats * num_heads, bias=False
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)
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self.fc_nj = nn.Linear(
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self._in_dst_node_feats, out_edge_feats * num_heads, bias=False
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)
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else:
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self.fc_node_src = nn.Linear(
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self._in_src_node_feats, out_node_feats * num_heads, bias=False
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)
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self.fc_ni = nn.Linear(
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self._in_src_node_feats, out_edge_feats * num_heads, bias=False
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)
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self.fc_nj = nn.Linear(
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self._in_src_node_feats, out_edge_feats * num_heads, bias=False
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)
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self.fc_fij = nn.Linear(
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in_edge_feats, out_edge_feats * num_heads, bias=False
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)
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self.attn = nn.Parameter(
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th.FloatTensor(size=(1, num_heads, out_edge_feats))
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)
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if bias:
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self.bias = nn.Parameter(
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th.FloatTensor(size=(num_heads * out_edge_feats,))
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)
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else:
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self.register_buffer("bias", None)
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self.reset_parameters()
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def reset_parameters(self):
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"""
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Reinitialize learnable parameters.
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"""
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gain = init.calculate_gain("relu")
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init.xavier_normal_(self.fc_node_src.weight, gain=gain)
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init.xavier_normal_(self.fc_ni.weight, gain=gain)
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init.xavier_normal_(self.fc_fij.weight, gain=gain)
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init.xavier_normal_(self.fc_nj.weight, gain=gain)
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init.xavier_normal_(self.attn, gain=gain)
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init.constant_(self.bias, 0)
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def forward(
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self, graph, nfeats, efeats, edge_weight=None, get_attention=False
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):
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r"""
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Compute new node and edge features.
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Parameters
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----------
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graph : DGLGraph
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The graph.
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nfeat : torch.Tensor or pair of torch.Tensor
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If a torch.Tensor is given, the input feature of shape :math:`(N, D_{in})`
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where:
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:math:`D_{in}` is size of input node feature,
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:math:`N` is the number of nodes.
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If a pair of torch.Tensor is given, the pair must contain two tensors of shape
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:math:`(N_{in}, D_{in_{src}})` and
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:math:`(N_{out}, D_{in_{dst}})`.
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efeats: torch.Tensor
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The input edge feature of shape :math:`(E, F_{in})`
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where:
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:math:`F_{in}` is size of input node feature,
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:math:`E` is the number of edges.
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edge_weight : torch.Tensor, optional
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A 1D tensor of edge weight values. Shape: :math:`(|E|,)`.
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get_attention : bool, optional
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Whether to return the attention values. Default to False.
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Returns
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-------
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pair of torch.Tensor
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node output features followed by edge output features.
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The node output feature is of shape :math:`(N, H, D_{out})`
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The edge output feature is of shape :math:`(F, H, F_{out})`
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where:
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:math:`H` is the number of heads,
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:math:`D_{out}` is size of output node feature,
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:math:`F_{out}` is size of output edge feature.
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torch.Tensor, optional
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The attention values of shape :math:`(E, H, 1)`.
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This is returned only when :attr:`get_attention` is ``True``.
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"""
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with graph.local_scope():
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if (graph.in_degrees() == 0).any():
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raise DGLError(
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"There are 0-in-degree nodes in the graph, "
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"output for those nodes will be invalid. "
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"This is harmful for some applications, "
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"causing silent performance regression. "
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"Adding self-loop on the input graph by "
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"calling `g = dgl.add_self_loop(g)` will resolve "
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"the issue."
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)
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# calc edge attention
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# same trick way as in dgl.nn.pytorch.GATConv, but also includes edge feats
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# https://github.com/dmlc/dgl/blob/master/python/dgl/nn/pytorch/conv/gatconv.py
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if isinstance(nfeats, tuple):
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nfeats_src, nfeats_dst = nfeats
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else:
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nfeats_src = nfeats_dst = nfeats
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f_ni = self.fc_ni(nfeats_src)
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f_nj = self.fc_nj(nfeats_dst)
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f_fij = self.fc_fij(efeats)
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graph.srcdata.update({"f_ni": f_ni})
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graph.dstdata.update({"f_nj": f_nj})
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# add ni, nj factors
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graph.apply_edges(fn.u_add_v("f_ni", "f_nj", "f_tmp"))
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# add fij to node factor
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f_out = graph.edata.pop("f_tmp") + f_fij
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if self.bias is not None:
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f_out = f_out + self.bias
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f_out = nn.functional.leaky_relu(f_out)
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f_out = f_out.view(-1, self._num_heads, self._out_edge_feats)
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# compute attention factor
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e = (f_out * self.attn).sum(dim=-1).unsqueeze(-1)
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graph.edata["a"] = edge_softmax(graph, e)
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if edge_weight is not None:
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graph.edata["a"] = graph.edata["a"] * edge_weight.tile(
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1, self._num_heads, 1
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).transpose(0, 2)
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graph.srcdata["h_out"] = self.fc_node_src(nfeats_src).view(
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-1, self._num_heads, self._out_node_feats
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)
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# calc weighted sum
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graph.update_all(
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fn.u_mul_e("h_out", "a", "m"), fn.sum("m", "h_out")
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)
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h_out = graph.dstdata["h_out"].view(
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-1, self._num_heads, self._out_node_feats
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)
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if get_attention:
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return h_out, f_out, graph.edata.pop("a")
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else:
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return h_out, f_out
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