layers.py

import math
import numpy as np
import torch
import scipy.sparse as sp
from torch.nn.parameter import Parameter
from torch.nn.modules.module import Module
import torch.nn.functional as F
import torch.nn as nn
from utils_file import utils
import tqdm
from typing import Tuple, Union

import torch.nn.functional as F
from torch import Tensor
from torch_sparse import SparseTensor, matmul

from torch_geometric.nn.conv import MessagePassing
from torch_geometric.nn.dense.linear import Linear
from torch_geometric.typing import Adj, OptPairTensor, Size
from typing import Optional, Tuple
from torch_geometric.typing import Adj, OptTensor, PairTensor

class GraphConvolution(Module):
    """GCN layers

    Simple GCN layer, similar to https://arxiv.org/abs/1609.02907

    forward:
    H: x feature matrix
    A: norm adjacent matrix
    W: weight matrix 
    """

    def __init__(self, in_features, out_features, bias=True):
        super(GraphConvolution, self).__init__()
        self.in_features = in_features
        self.out_features = out_features
        self.weight = Parameter(torch.FloatTensor(in_features, out_features))
        if bias:
            self.bias = Parameter(torch.FloatTensor(out_features))
        else:
            self.register_parameter('bias', None)
        self.reset_parameters()

    def reset_parameters(self):
        stdv = 1. / math.sqrt(self.weight.size(1))
        self.weight.data.uniform_(-stdv, stdv)
        if self.bias is not None:
            self.bias.data.uniform_(-stdv, stdv)

    def forward(self,H,A):
        W = self.weight
        b = self.bias

        HW = torch.mm(H,W)

        # D^{-1/2}AD^{-1/2}XW
        AHW = torch.sparse.mm(A,HW)
        if self.bias is not None:
            return AHW + b
        else:
            return AHW

    def __repr__(self):
        return self.__class__.__name__ + ' (' \
               + str(self.in_features) + ' -> ' \
               + str(self.out_features) + ')'   
        
class SAGEConv(MessagePassing):
    r"""The GraphSAGE operator from the `"Inductive Representation Learning on
    Large Graphs" <https://arxiv.org/abs/1706.02216>`_ paper

    .. math::
        \mathbf{x}^{\prime}_i = \mathbf{W}_1 \mathbf{x}_i + \mathbf{W}_2 \cdot
        \mathrm{mean}_{j \in \mathcal{N(i)}} \mathbf{x}_j

    Args:
        in_channels (int or tuple): Size of each input sample, or :obj:`-1` to
            derive the size from the first input(s) to the forward method.
            A tuple corresponds to the sizes of source and target
            dimensionalities.
        out_channels (int): Size of each output sample.
        normalize (bool, optional): If set to :obj:`True`, output features
            will be :math:`\ell_2`-normalized, *i.e.*,
            :math:`\frac{\mathbf{x}^{\prime}_i}
            {\| \mathbf{x}^{\prime}_i \|_2}`.
            (default: :obj:`False`)
        root_weight (bool, optional): If set to :obj:`False`, the layer will
            not add transformed root node features to the output.
            (default: :obj:`True`)
        bias (bool, optional): If set to :obj:`False`, the layer will not learn
            an additive bias. (default: :obj:`True`)
        **kwargs (optional): Additional arguments of
            :class:`torch_geometric.nn.conv.MessagePassing`.

    Shapes:
        - **inputs:**
          node features :math:`(|\mathcal{V}|, F_{in})` or
          :math:`((|\mathcal{V_s}|, F_{s}), (|\mathcal{V_t}|, F_{t}))`
          if bipartite,
          edge indices :math:`(2, |\mathcal{E}|)`
        - **outputs:** node features :math:`(|\mathcal{V}|, F_{out})` or
          :math:`(|\mathcal{V_t}|, F_{out})` if bipartite
    """
    def __init__(self, in_channels: Union[int, Tuple[int, int]],
                 out_channels: int, normalize: bool = False,
                 root_weight: bool = True, bias: bool = True, **kwargs):
        kwargs.setdefault('aggr', 'mean')
        super().__init__(**kwargs)

        self.in_channels = in_channels
        self.out_channels = out_channels
        self.normalize = normalize
        self.root_weight = root_weight

        if isinstance(in_channels, int):
            in_channels = (in_channels, in_channels)

        self.lin_l = Linear(in_channels[0], out_channels, bias=bias)
        if self.root_weight:
            self.lin_r = Linear(in_channels[1], out_channels, bias=False)

        self.reset_parameters()

    def reset_parameters(self):
        self.lin_l.reset_parameters()
        if self.root_weight:
            self.lin_r.reset_parameters()

    def forward(self, x: Union[Tensor, OptPairTensor], edge_index: Adj,
                size: Size = None) -> Tensor:
        """"""
        if isinstance(x, Tensor):
            x: OptPairTensor = (x, x)

        # propagate_type: (x: OptPairTensor)
        out = self.propagate(edge_index, x=x, size=size)
        out = self.lin_l(out)

        x_r = x[1]
        if self.root_weight and x_r is not None:
            out += self.lin_r(x_r)

        if self.normalize:
            out = F.normalize(out, p=2., dim=-1)

        return out

    def message(self, x_j: Tensor) -> Tensor:
        return x_j

    def message_and_aggregate(self, adj_t: SparseTensor,
                              x: OptPairTensor) -> Tensor:
        adj_t = adj_t.set_value(None, layout=None)
        return matmul(adj_t, x[0], reduce=self.aggr)

class GCNConv(MessagePassing):
    r"""The graph convolutional operator from the `"Semi-supervised
    Classification with Graph Convolutional Networks"
    <https://arxiv.org/abs/1609.02907>`_ paper

    .. math::
        \mathbf{X}^{\prime} = \mathbf{\hat{D}}^{-1/2} \mathbf{\hat{A}}
        \mathbf{\hat{D}}^{-1/2} \mathbf{X} \mathbf{\Theta},

    where :math:`\mathbf{\hat{A}} = \mathbf{A} + \mathbf{I}` denotes the
    adjacency matrix with inserted self-loops and
    :math:`\hat{D}_{ii} = \sum_{j=0} \hat{A}_{ij}` its diagonal degree matrix.
    The adjacency matrix can include other values than :obj:`1` representing
    edge weights via the optional :obj:`edge_weight` tensor.

    Its node-wise formulation is given by:

    .. math::
        \mathbf{x}^{\prime}_i = \mathbf{\Theta}^{\top} \sum_{j \in
        \mathcal{N}(v) \cup \{ i \}} \frac{e_{j,i}}{\sqrt{\hat{d}_j
        \hat{d}_i}} \mathbf{x}_j

    with :math:`\hat{d}_i = 1 + \sum_{j \in \mathcal{N}(i)} e_{j,i}`, where
    :math:`e_{j,i}` denotes the edge weight from source node :obj:`j` to target
    node :obj:`i` (default: :obj:`1.0`)

    Args:
        in_channels (int): Size of each input sample, or :obj:`-1` to derive
            the size from the first input(s) to the forward method.
        out_channels (int): Size of each output sample.
        improved (bool, optional): If set to :obj:`True`, the layer computes
            :math:`\mathbf{\hat{A}}` as :math:`\mathbf{A} + 2\mathbf{I}`.
            (default: :obj:`False`)
        cached (bool, optional): If set to :obj:`True`, the layer will cache
            the computation of :math:`\mathbf{\hat{D}}^{-1/2} \mathbf{\hat{A}}
            \mathbf{\hat{D}}^{-1/2}` on first execution, and will use the
            cached version for further executions.
            This parameter should only be set to :obj:`True` in transductive
            learning scenarios. (default: :obj:`False`)
        add_self_loops (bool, optional): If set to :obj:`False`, will not add
            self-loops to the input graph. (default: :obj:`True`)
        normalize (bool, optional): Whether to add self-loops and compute
            symmetric normalization coefficients on the fly.
            (default: :obj:`True`)
        bias (bool, optional): If set to :obj:`False`, the layer will not learn
            an additive bias. (default: :obj:`True`)
        **kwargs (optional): Additional arguments of
            :class:`torch_geometric.nn.conv.MessagePassing`.

    Shapes:
        - **input:**
          node features :math:`(|\mathcal{V}|, F_{in})`,
          edge indices :math:`(2, |\mathcal{E}|)`,
          edge weights :math:`(|\mathcal{E}|)` *(optional)*
        - **output:** node features :math:`(|\mathcal{V}|, F_{out})`
    """

    _cached_edge_index: Optional[Tuple[Tensor, Tensor]]
    _cached_adj_t: Optional[SparseTensor]

    def __init__(self, in_channels: int, out_channels: int,
                 improved: bool = False, cached: bool = False,
                 add_self_loops: bool = True, normalize: bool = True,
                 bias: bool = True, **kwargs):

        kwargs.setdefault('aggr', 'add')
        super().__init__(**kwargs)

        self.in_channels = in_channels
        self.out_channels = out_channels
        self.improved = improved
        self.cached = cached
        self.add_self_loops = add_self_loops
        self.normalize = normalize

        self._cached_edge_index = None
        self._cached_adj_t = None

        self.lin = Linear(in_channels, out_channels, bias=False,
                          weight_initializer='glorot')

        if bias:
            self.bias = Parameter(torch.Tensor(out_channels))
        else:
            self.register_parameter('bias', None)

        self.reset_parameters()

    def reset_parameters(self):
        self.lin.reset_parameters()
        zeros(self.bias)
        self._cached_edge_index = None
        self._cached_adj_t = None

    def forward(self, x: Tensor, edge_index: Adj,
                edge_weight: OptTensor = None) -> Tensor:
        """"""

        if self.normalize:
            if isinstance(edge_index, Tensor):
                cache = self._cached_edge_index
                if cache is None:
                    edge_index, edge_weight = gcn_norm(  # yapf: disable
                        edge_index, edge_weight, x.size(self.node_dim),
                        self.improved, self.add_self_loops)
                    if self.cached:
                        self._cached_edge_index = (edge_index, edge_weight)
                else:
                    edge_index, edge_weight = cache[0], cache[1]

            elif isinstance(edge_index, SparseTensor):
                cache = self._cached_adj_t
                if cache is None:
                    edge_index = gcn_norm(  # yapf: disable
                        edge_index, edge_weight, x.size(self.node_dim),
                        self.improved, self.add_self_loops)
                    if self.cached:
                        self._cached_adj_t = edge_index
                else:
                    edge_index = cache

        x = self.lin(x)

        # propagate_type: (x: Tensor, edge_weight: OptTensor)
        out = self.propagate(edge_index, x=x, edge_weight=edge_weight,
                             size=None)

        if self.bias is not None:
            out += self.bias

        return out

    def message(self, x_j: Tensor, edge_weight: OptTensor) -> Tensor:
        return x_j if edge_weight is None else edge_weight.view(-1, 1) * x_j

    def message_and_aggregate(self, adj_t: SparseTensor, x: Tensor) -> Tensor:
        return matmul(adj_t, x, reduce=self.aggr)