Source code for dgl.nn.pytorch.conv.edgegatconv

"""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 ....base import DGLError
from ....utils import expand_as_pair
from ...functional import edge_softmax

# pylint: enable=W0235
[docs]class EdgeGATConv(nn.Module): r"""Graph attention layer with edge features from `SCENE <>`__ .. math:: \mathbf{v}_i^\prime = \mathbf{\Theta}_\mathrm{s} \cdot \mathbf{v}_i + \sum\limits_{j \in \mathcal{N}(v_i)} \alpha_{j, i} \left( \mathbf{\Theta}_\mathrm{n} \cdot \mathbf{v}_j + \mathbf{\Theta}_\mathrm{e} \cdot \mathbf{e}_{j,i} \right) where :math:`\mathbf{\Theta}` is used to denote learnable weight matrices for the transformation of features of the node to update (s=self), neighboring nodes (n=neighbor) and edge features (e=edge). Attention weights are obtained by .. math:: \alpha_{j, i} = \mathrm{softmax}_i \Big( \mathrm{LeakyReLU} \big( \mathbf{a}^T [ \mathbf{\Theta}_\mathrm{n} \cdot \mathbf{v}_i || \mathbf{\Theta}_\mathrm{n} \cdot \mathbf{v}_j || \mathbf{\Theta}_\mathrm{e} \cdot \mathbf{e}_{j,i} ] \big) \Big) with :math:`\mathbf{a}` corresponding to a learnable vector. :math:`\mathrm{softmax_i}` stands for the normalization by all incoming edges of node :math:`i`. Parameters ---------- in_feats : int, or pair of ints Input feature size; i.e, the number of dimensions of :math:`\mathbf{v}_i`. GATConv can be applied on homogeneous graph and unidirectional `bipartite graph <>`__. If the layer is to be applied to a unidirectional bipartite graph, ``in_feats`` specifies the input feature size on both the source and destination nodes. If a scalar is given, the source and destination node feature size would take the same value. edge_feats: int Edge feature size; i.e., the number of dimensions of :math:\mathbf{e}_{j,i}`. out_feats : int Output feature size; i.e, the number of dimensions of :math:`\mathbf{v}_i^\prime`. 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. Defaults: ``0.2``. residual : bool, optional If True, use residual connection. Defaults: ``False``. activation : callable activation function/layer or None, optional. If not None, applies an activation function to the updated node features. Default: ``None``. allow_zero_in_degree : bool, optional If there are 0-in-degree nodes in the graph, output for those nodes will be invalid since no message will be passed to those nodes. This is harmful for some applications causing silent performance regression. This module will raise a DGLError if it detects 0-in-degree nodes in input graph. By setting ``True``, it will suppress the check and let the users handle it by themselves. Defaults: ``False``. bias : bool, optional If True, learns a bias term. Defaults: ``True``. Note ---- Zero in-degree nodes will lead to invalid output value. This is because no message will be passed to those nodes, the aggregation function will be appied on empty input. A common practice to avoid this is to add a self-loop for each node in the graph if it is homogeneous, which can be achieved by: >>> g = ... # a DGLGraph >>> g = dgl.add_self_loop(g) Calling ``add_self_loop`` will not work for some graphs, for example, heterogeneous graph since the edge type can not be decided for self_loop edges. Set ``allow_zero_in_degree`` to ``True`` for those cases to unblock the code and handle zero-in-degree nodes manually. A common practise to handle this is to filter out the nodes with zero-in-degree when use after conv. Examples ---------- >>> import dgl >>> import numpy as np >>> import torch as th >>> from dgl.nn import EdgeGATConv >>> # Case 1: Homogeneous graph. >>> num_nodes, num_edges = 8, 30 >>> # Generate a graph. >>> graph = dgl.rand_graph(num_nodes,num_edges) >>> node_feats = th.rand((num_nodes, 20)) >>> edge_feats = th.rand((num_edges, 12)) >>> edge_gat = EdgeGATConv( ... in_feats=20, ... edge_feats=12, ... out_feats=15, ... num_heads=3, ... ) >>> # Forward pass. >>> new_node_feats = edge_gat(graph, node_feats, edge_feats) >>> new_node_feats.shape torch.Size([8, 3, 15]) torch.Size([30, 3, 10]) >>> # Case 2: Unidirectional bipartite graph. >>> u = [0, 1, 0, 0, 1] >>> v = [0, 1, 2, 3, 2] >>> g = dgl.heterograph({('A', 'r', 'B'): (u, v)}) >>> u_feat = th.tensor(np.random.rand(2, 25).astype(np.float32)) >>> v_feat = th.tensor(np.random.rand(4, 30).astype(np.float32)) >>> nfeats = (u_feat,v_feat) >>> efeats = th.tensor(np.random.rand(5, 15).astype(np.float32)) >>> in_feats = (25,30) >>> edge_feats = 15 >>> out_feats = 10 >>> num_heads = 3 >>> egat_model = EdgeGATConv( ... in_feats, ... edge_feats, ... out_feats, ... num_heads, ... ) >>> # Forward pass. >>> new_node_feats, attention_weights = egat_model(g, nfeats, efeats, get_attention=True) >>> new_node_feats.shape, attention_weights.shape (torch.Size([4, 3, 10]), torch.Size([5, 3, 1])) """ def __init__( self, in_feats, edge_feats, out_feats, num_heads, feat_drop=0.0, attn_drop=0.0, negative_slope=0.2, residual=True, activation=None, allow_zero_in_degree=False, bias=True, ): super(EdgeGATConv, self).__init__() self._num_heads = num_heads self._in_src_feats, self._in_dst_feats = expand_as_pair(in_feats) self._out_feats = out_feats self._allow_zero_in_degree = allow_zero_in_degree if isinstance(in_feats, tuple): self.fc_src = nn.Linear( self._in_src_feats, out_feats * num_heads, bias=False ) self.fc_dst = nn.Linear( self._in_dst_feats, out_feats * num_heads, bias=False ) else: self.fc = nn.Linear( self._in_src_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 bias: self.bias = nn.Parameter( th.FloatTensor(size=(num_heads * out_feats,)) ) else: self.register_buffer("bias", None) if residual: self.res_fc = nn.Linear( self._in_dst_feats, num_heads * out_feats, bias=False ) else: self.register_buffer("res_fc", None) self._edge_feats = edge_feats self.fc_edge = nn.Linear(edge_feats, out_feats * num_heads, bias=False) self.attn_edge = nn.Parameter( th.FloatTensor(size=(1, num_heads, out_feats)) ) self.reset_parameters() self.activation = activation
[docs] def reset_parameters(self): r""" Description ----------- Reinitialize learnable parameters. Note ---- The fc weights :math:`\mathbf{\Theta}` are and the attention weights are using xavier initialization method. """ gain = nn.init.calculate_gain("relu") if hasattr(self, "fc"): nn.init.xavier_normal_(self.fc.weight, gain=gain) else: nn.init.xavier_normal_(self.fc_src.weight, gain=gain) nn.init.xavier_normal_(self.fc_dst.weight, gain=gain) nn.init.xavier_normal_(self.attn_l, gain=gain) nn.init.xavier_normal_(self.attn_r, gain=gain) nn.init.xavier_normal_(self.fc_edge.weight, gain=gain) nn.init.xavier_normal_(self.attn_edge, gain=gain) if self.bias is not None: nn.init.constant_(self.bias, 0) if isinstance(self.res_fc, nn.Linear): nn.init.xavier_normal_(self.res_fc.weight, gain=gain)
def set_allow_zero_in_degree(self, set_value): r""" Description ----------- Set allow_zero_in_degree flag. Parameters ---------- set_value : bool The value to be set to the flag. """ self._allow_zero_in_degree = set_value
[docs] def forward(self, graph, feat, edge_feat, get_attention=False): r""" Description ----------- Compute graph attention network layer. Parameters ---------- graph : DGLGraph The graph. feat : torch.Tensor or pair of torch.Tensor If a torch.Tensor is given, 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. If a pair of torch.Tensor is given, the pair must contain two tensors of shape :math:`(N_{in}, *, D_{in_{src}})` and :math:`(N_{out}, *, D_{in_{dst}})`. edge_feat : torch.Tensor The input edge feature of shape :math:`(E, D_{in_{edge}})`, where :math:`E` is the number of edges and :math:`D_{in_{edge}}` the size of the edge features. get_attention : bool, optional Whether to return the attention values. Default to False. 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. torch.Tensor, optional The attention values of shape :math:`(E, *, H, 1)`. This is returned only when :attr:`get_attention` is ``True``. Raises ------ DGLError If there are 0-in-degree nodes in the input graph, it will raise DGLError since no message will be passed to those nodes. This will cause invalid output. The error can be ignored by setting ``allow_zero_in_degree`` parameter to ``True``. """ with graph.local_scope(): if not self._allow_zero_in_degree: if (graph.in_degrees() == 0).any(): raise DGLError( "There are 0-in-degree nodes in the graph, " "output for those nodes will be invalid. " "This is harmful for some applications, " "causing silent performance regression. " "Adding self-loop on the input graph by " "calling `g = dgl.add_self_loop(g)` will resolve " "the issue. Setting ``allow_zero_in_degree`` " "to be `True` when constructing this module will " "suppress the check and let the code run." ) if isinstance(feat, tuple): src_prefix_shape = feat[0].shape[:-1] dst_prefix_shape = feat[1].shape[:-1] h_src = self.feat_drop(feat[0]) h_dst = self.feat_drop(feat[1]) if not hasattr(self, "fc_src"): feat_src = self.fc(h_src).view( *src_prefix_shape, self._num_heads, self._out_feats ) feat_dst = self.fc(h_dst).view( *dst_prefix_shape, self._num_heads, self._out_feats ) else: feat_src = self.fc_src(h_src).view( *src_prefix_shape, self._num_heads, self._out_feats ) feat_dst = self.fc_dst(h_dst).view( *dst_prefix_shape, self._num_heads, self._out_feats ) else: src_prefix_shape = dst_prefix_shape = feat.shape[:-1] h_src = h_dst = self.feat_drop(feat) feat_src = feat_dst = self.fc(h_src).view( *src_prefix_shape, self._num_heads, self._out_feats ) if graph.is_block: feat_dst = feat_src[: graph.number_of_dst_nodes()] h_dst = h_dst[: graph.number_of_dst_nodes()] dst_prefix_shape = ( graph.number_of_dst_nodes(), ) + dst_prefix_shape[1:] # Linearly tranform the edge features. n_edges = edge_feat.shape[:-1] feat_edge = self.fc_edge(edge_feat).view( *n_edges, self._num_heads, self._out_feats ) # Add edge features to graph. graph.edata["ft_edge"] = feat_edge el = (feat_src * self.attn_l).sum(dim=-1).unsqueeze(-1) er = (feat_dst * self.attn_r).sum(dim=-1).unsqueeze(-1) # Calculate scalar for each edge. ee = (feat_edge * self.attn_edge).sum(dim=-1).unsqueeze(-1) graph.edata["ee"] = ee graph.srcdata.update({"ft": feat_src, "el": el}) graph.dstdata.update({"er": er}) # Compute edge attention, el and er are a_l Wh_i and a_r Wh_j respectively. graph.apply_edges(fn.u_add_v("el", "er", "e_tmp")) # e_tmp combines attention weights of source and destination node. # Add the attention weight of the edge. graph.edata["e"] = graph.edata["e_tmp"] + graph.edata["ee"] # Create new edges features that combine the # features of the source node and the edge features. graph.apply_edges(fn.u_add_e("ft", "ft_edge", "ft_combined")) e = self.leaky_relu(graph.edata.pop("e")) # Compute softmax. graph.edata["a"] = self.attn_drop(edge_softmax(graph, e)) # For each edge, element-wise multiply the combined features with # the attention coefficient. graph.edata["m_combined"] = ( graph.edata["ft_combined"] * graph.edata["a"] ) # First copy the edge features and then sum them up. graph.update_all(fn.copy_e("m_combined", "m"), fn.sum("m", "ft")) rst = graph.dstdata["ft"] # Residual. if self.res_fc is not None: # Use -1 rather than self._num_heads to handle broadcasting. resval = self.res_fc(h_dst).view( *dst_prefix_shape, -1, self._out_feats ) rst = rst + resval # Bias. if self.bias is not None: rst = rst + self.bias.view( *((1,) * len(dst_prefix_shape)), self._num_heads, self._out_feats ) # Activation. if self.activation: rst = self.activation(rst) if get_attention: return rst, graph.edata["a"] else: return rst