geometric_layers.py

 
 
 
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch_scatter import scatter
 
 
def _init_weights(layer, normalize):
    """
    Initializes the weights and biases.
    """
    for m in layer.modules():
        if isinstance(m, nn.Linear):
            nn.init.xavier_normal_(m.weight.data)
            if not normalize:
                m.bias.data.fill_(0.1)
        elif isinstance(m, nn.BatchNorm1d) or isinstance(m, nn.LayerNorm):
            m.weight.data.fill_(1)
            m.bias.data.zero_()
 
 
class EdgeLayer(nn.Module):
    """
    Updates edge features in MetaLayer:
 
    .. math::
        e_{ij}^{'} = \\phi^{e}(e_{ij}, v_{i}, v_{j}, u),
 
    where :math:`\\phi^{e}` is a neural network of the form
 
    .. figure:: figs/MLP_structure.png
        :width: 42em
        :align: center
 
    Args:
        nfeat_in_dim (int): Node features input dimension (number of node features in input).
        efeat_in_dim (int): Edge features input dimension (number of edge features in input).
        gfeat_in_dim (int): Gloabl features input dimension (number of global features in input).
        efeat_hid_dim (int): Edge features dimension in hidden layers.
        efeat_out_dim (int): Edge features output dimension.
        num_hid_layers (int): Number of hidden layers.
        dropout (float): Dropout rate :math:`r \\in [0,1]`.
        normalize (str): Type of normalization (batch/layer).
 
 
    :return: Updated edge features tensor.
    :rtype: `Tensor <https://pytorch.org/docs/stable/tensors.html#torch.Tensor>`_
    """
 
    def __init__(
        self,
        nfeat_in_dim,
        efeat_in_dim,
        gfeat_in_dim,
        efeat_hid_dim,
        efeat_out_dim,
        num_hid_layers,
        dropout,
        normalize=True,
    ):
        """
        Initialization.
        """
        super(EdgeLayer, self).__init__()
 
        
        self.nonlin_function = F.elu
        
        self.num_hid_layers = num_hid_layers
        
        self.dropout_prob = dropout
        
        self.normalize = normalize
 
        
        self.lin_in = nn.Linear(
            efeat_in_dim + 2 * nfeat_in_dim + gfeat_in_dim, efeat_hid_dim
        )
        
        self.lins_hid = nn.ModuleList(
            [
                nn.Linear(efeat_hid_dim, efeat_hid_dim)
                for _ in range(self.num_hid_layers)
            ]
        )
        
        self.lin_out = nn.Linear(efeat_hid_dim, efeat_out_dim, bias=not normalize)
 
        if normalize:
            
            self.norm = nn.BatchNorm1d(efeat_out_dim)
 
        _init_weights(self, normalize)
 
    def forward(self, src, dest, edge_attr, u, batch):
        """
        Called internally by PyTorch to propagate the input through the network.
         - src, dest: [E, F_x], where E is the number of edges.
         - edge_attr: [E, F_e]
         - u: [B, F_u], where B is the number of graphs.
         - batch: [E] with max entry B - 1.
        """
        out = (
            torch.cat([edge_attr, src, dest, u[batch]], dim=1)
            if u.shape != torch.Size([0])
            else torch.cat([edge_attr, src, dest], dim=1)
        )
 
        out = self.nonlin_function(self.lin_in(out))
        out = F.dropout(out, self.dropout_prob, training=self.training)
 
        out_skip = out
 
        for lin_hid in self.lins_hid:
            out = self.nonlin_function(lin_hid(out))
            out = F.dropout(out, self.dropout_prob, training=self.training)
 
        if self.num_hid_layers > 1:
            out += out_skip
 
        if self.normalize:
            out = self.nonlin_function(self.norm(self.lin_out(out)))
        else:
            out = self.nonlin_function(self.lin_out(out))
 
        return out
 
 
class NodeLayer(nn.Module):
    """
    Updates node features in MetaLayer:
 
    .. math::
        v_{i}^{'} = \\phi^{v}(v_{i}, \\rho^{e \\to v}(v_{i}), u)
 
    with
 
    .. math::
        \\rho^{e \\to v}(v_{i}) = \\frac{\\sum_{j=1,\\ j \\neq i}^{N} (e_{ji} + e _{ij})}{2 \\cdot (N-1)},
 
    where :math:`\\phi^{v}` is a neural network of the form
 
    .. figure:: figs/MLP_structure.png
        :width: 42em
        :align: center
 
    Args:
        nfeat_in_dim (int): Node features input dimension (number of node features in input).
        efeat_in_dim (int): Edge features input dimension (number of edge features in input).
        gfeat_in_dim (int): Gloabl features input dimension (number of global features in input).
        nfeat_hid_dim (int): Node features dimension in hidden layers.
        nfeat_out_dim (int): Node features output dimension.
        num_hid_layers (int): Number of hidden layers.
        dropout (float): Dropout rate :math:`r \\in [0,1]`.
        normalize (str): Type of normalization (batch/layer).
 
    :return: Updated node features tensor.
    :rtype: `Tensor <https://pytorch.org/docs/stable/tensors.html#torch.Tensor>`_
    """
 
    def __init__(
        self,
        nfeat_in_dim,
        efeat_in_dim,
        gfeat_in_dim,
        nfeat_hid_dim,
        nfeat_out_dim,
        num_hid_layers,
        dropout,
        normalize=True,
    ):
        """
        Initialization.
        """
        super(NodeLayer, self).__init__()
 
        
        self.nonlin_function = F.elu
        
        self.num_hid_layers = num_hid_layers
        
        self.dropout_prob = dropout
        
        self.normalize = normalize
 
        
        self.lin_in = nn.Linear(
            gfeat_in_dim + nfeat_in_dim + efeat_in_dim, nfeat_hid_dim
        )
        
        self.lins_hid = nn.ModuleList(
            [
                nn.Linear(nfeat_hid_dim, nfeat_hid_dim)
                for _ in range(self.num_hid_layers)
            ]
        )
        
        self.lin_out = nn.Linear(nfeat_hid_dim, nfeat_out_dim, bias=not normalize)
 
        if normalize:
            
            self.norm = nn.BatchNorm1d(nfeat_out_dim)
 
        _init_weights(self, normalize)
 
    def forward(self, x, edge_index, edge_attr, u, batch):
        """
        Called internally by PyTorch to propagate the input through the network.
         - x: [N, F_x], where N is the number of nodes.
         - edge_index: [2, E] with max entry N - 1.
         - edge_attr: [E, F_e]
         - u: [B, F_u]
         - batch: [N] with max entry B - 1.
 
        Edge labels are averaged (dim_size = N: number of nodes in the graph)
        """
        out = scatter(
            edge_attr, edge_index[1], dim=0, dim_size=batch.size(0), reduce="mean"
        )
        out = (
            torch.cat([x, out, u[batch]], dim=1)
            if u.shape != torch.Size([0])
            else torch.cat([x, out], dim=1)
        )
 
        out = self.nonlin_function(self.lin_in(out))
        out = F.dropout(out, self.dropout_prob, training=self.training)
 
        out_skip = out
 
        for lin_hid in self.lins_hid:
            out = self.nonlin_function(lin_hid(out))
            out = F.dropout(out, self.dropout_prob, training=self.training)
 
        if self.num_hid_layers > 1:
            out += out_skip
 
        if self.normalize:
            out = self.nonlin_function(self.norm(self.lin_out(out)))
        else:
            out = self.nonlin_function(self.lin_out(out))
 
        return out
 
 
class GlobalLayer(nn.Module):
    """
    Updates node features in MetaLayer:
 
    .. math::
        u_{i}^{'} = \\phi^{u}(\\rho^{e \\to u}(e), \\rho^{v \\to u}(v), u)
 
    with
 
    .. math::
        \\rho^{e \\to u}(e) = \\frac{\\sum_{i,j=1,\\ i \\neq j}^{N} e_{ij}}{N \\cdot (N-1)},\\\\
        \\rho^{v \\to u}(e) = \\frac{\\sum_{i=1}^{N} v_{i}}{N},
 
    where :math:`\\phi^{u}` is a neural network of the form
 
    .. figure:: figs/MLP_structure.png
        :width: 42em
        :align: center
 
    Args:
        nfeat_in_dim (int): Node features input dimension (number of node features in input).
        efeat_in_dim (int): Edge features input dimension (number of edge features in input).
        gfeat_in_dim (int): Gloabl features input dimension (number of global features in input).
        nfeat_hid_dim (int): Global features dimension in hidden layers.
        nfeat_out_dim (int): Global features output dimension.
        num_hid_layers (int): Number of hidden layers.
        dropout (float): Dropout rate :math:`r \\in [0,1]`.
        normalize (str): Type of normalization (batch/layer).
 
    :return: Updated global features tensor.
    :rtype: `Tensor <https://pytorch.org/docs/stable/tensors.html#torch.Tensor>`_
    """
 
    def __init__(
        self,
        nfeat_in_dim,
        efeat_in_dim,
        gfeat_in_dim,
        gfeat_hid_dim,
        gfeat_out_dim,
        num_hid_layers,
        dropout,
        normalize=True,
    ):
        """
        Initialization.
        """
        super(GlobalLayer, self).__init__()
 
        
        self.nonlin_function = F.elu
        
        self.num_hid_layers = num_hid_layers
        
        self.dropout_prob = dropout
        
        self.normalize = normalize
 
        
        self.lin_in = nn.Linear(
            nfeat_in_dim + efeat_in_dim + gfeat_in_dim, gfeat_hid_dim
        )
        
        self.lins_hid = nn.ModuleList(
            [
                nn.Linear(gfeat_hid_dim, gfeat_hid_dim)
                for _ in range(self.num_hid_layers)
            ]
        )
        
        self.lin_out = nn.Linear(gfeat_hid_dim, gfeat_out_dim, bias=not normalize)
 
        if normalize:
            
            self.norm = nn.BatchNorm1d(gfeat_out_dim)
 
        _init_weights(self, normalize)
 
    def forward(self, x, edge_index, edge_attr, u, batch):
        """
        Called internally by Pytorch to propagate the input through the network.
         - x: [N, F_x], where N is the number of nodes.
         - edge_index: [2, E] with max entry N - 1.
         - edge_attr: [E, F_e]
         - u: [B, F_u]
         - batch: [N] with max entry B - 1.
 
        Nodes are averaged over graph
        """
        node_mean = scatter(
            x, batch, dim=0, reduce="mean"
        )
        # Edges are averaged over nodes
        edge_mean = scatter(
            edge_attr, edge_index[1], dim=0, reduce="mean"
        )
        # Edges are averaged over graph
        edge_mean = scatter(
            edge_mean, batch, dim=0, reduce="mean"
        )
        out = (
            torch.cat([u, node_mean, edge_mean], dim=1)
            if u.shape != torch.Size([0])
            else torch.cat([node_mean, edge_mean], dim=1)
        )
 
        out = self.nonlin_function(self.lin_in(out))
        out = F.dropout(out, self.dropout_prob, training=self.training)
 
        out_skip = out
 
        for lin_hid in self.lins_hid:
            out = self.nonlin_function(lin_hid(out))
            out = F.dropout(out, self.dropout_prob, training=self.training)
 
        if self.num_hid_layers > 1:
            out += out_skip
 
        if self.normalize:
            out = self.nonlin_function(self.norm(self.lin_out(out)))
        else:
            out = self.lin_out(out)
 
        return out