wehub-resource-sync
348 lines
10 KiB
Python
348 lines
10 KiB
Python
"""Torch Module for Principal Neighbourhood Aggregation Convolution Layer"""
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# pylint: disable= no-member, arguments-differ, invalid-name
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import numpy as np
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import torch
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import torch.nn as nn
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def aggregate_mean(h):
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"""mean aggregation"""
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return torch.mean(h, dim=1)
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def aggregate_max(h):
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"""max aggregation"""
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return torch.max(h, dim=1)[0]
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def aggregate_min(h):
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"""min aggregation"""
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return torch.min(h, dim=1)[0]
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def aggregate_sum(h):
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"""sum aggregation"""
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return torch.sum(h, dim=1)
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def aggregate_std(h):
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"""standard deviation aggregation"""
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return torch.sqrt(aggregate_var(h) + 1e-30)
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def aggregate_var(h):
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"""variance aggregation"""
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h_mean_squares = torch.mean(h * h, dim=1)
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h_mean = torch.mean(h, dim=1)
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var = torch.relu(h_mean_squares - h_mean * h_mean)
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return var
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def _aggregate_moment(h, n):
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"""moment aggregation: for each node (E[(X-E[X])^n])^{1/n}"""
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h_mean = torch.mean(h, dim=1, keepdim=True)
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h_n = torch.mean(torch.pow(h - h_mean, n), dim=1)
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rooted_h_n = torch.sign(h_n) * torch.pow(torch.abs(h_n) + 1e-30, 1.0 / n)
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return rooted_h_n
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def aggregate_moment_3(h):
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"""moment aggregation with n=3"""
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return _aggregate_moment(h, n=3)
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def aggregate_moment_4(h):
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"""moment aggregation with n=4"""
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return _aggregate_moment(h, n=4)
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def aggregate_moment_5(h):
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"""moment aggregation with n=5"""
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return _aggregate_moment(h, n=5)
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def scale_identity(h):
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"""identity scaling (no scaling operation)"""
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return h
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def scale_amplification(h, D, delta):
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"""amplification scaling"""
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return h * (np.log(D + 1) / delta)
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def scale_attenuation(h, D, delta):
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"""attenuation scaling"""
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return h * (delta / np.log(D + 1))
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AGGREGATORS = {
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"mean": aggregate_mean,
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"sum": aggregate_sum,
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"max": aggregate_max,
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"min": aggregate_min,
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"std": aggregate_std,
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"var": aggregate_var,
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"moment3": aggregate_moment_3,
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"moment4": aggregate_moment_4,
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"moment5": aggregate_moment_5,
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}
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SCALERS = {
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"identity": scale_identity,
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"amplification": scale_amplification,
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"attenuation": scale_attenuation,
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}
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class PNAConvTower(nn.Module):
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"""A single PNA tower in PNA layers"""
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def __init__(
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self,
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in_size,
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out_size,
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aggregators,
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scalers,
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delta,
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dropout=0.0,
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edge_feat_size=0,
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):
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super(PNAConvTower, self).__init__()
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self.in_size = in_size
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self.out_size = out_size
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self.aggregators = aggregators
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self.scalers = scalers
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self.delta = delta
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self.edge_feat_size = edge_feat_size
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self.M = nn.Linear(2 * in_size + edge_feat_size, in_size)
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self.U = nn.Linear(
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(len(aggregators) * len(scalers) + 1) * in_size, out_size
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)
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self.dropout = nn.Dropout(dropout)
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self.batchnorm = nn.BatchNorm1d(out_size)
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def reduce_func(self, nodes):
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"""reduce function for PNA layer:
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tensordot of multiple aggregation and scaling operations"""
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msg = nodes.mailbox["msg"]
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degree = msg.size(1)
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h = torch.cat(
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[AGGREGATORS[agg](msg) for agg in self.aggregators], dim=1
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)
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h = torch.cat(
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[
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SCALERS[scaler](h, D=degree, delta=self.delta)
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if scaler != "identity"
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else h
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for scaler in self.scalers
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],
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dim=1,
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)
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return {"h_neigh": h}
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def message(self, edges):
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"""message function for PNA layer"""
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if self.edge_feat_size > 0:
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f = torch.cat(
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[edges.src["h"], edges.dst["h"], edges.data["a"]], dim=-1
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)
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else:
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f = torch.cat([edges.src["h"], edges.dst["h"]], dim=-1)
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return {"msg": self.M(f)}
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def forward(self, graph, node_feat, edge_feat=None):
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"""compute the forward pass of a single tower in PNA convolution layer"""
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# calculate graph normalization factors
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snorm_n = torch.cat(
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[
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torch.ones(N, 1).to(node_feat) / N
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for N in graph.batch_num_nodes()
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],
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dim=0,
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).sqrt()
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with graph.local_scope():
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graph.ndata["h"] = node_feat
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if self.edge_feat_size > 0:
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assert edge_feat is not None, "Edge features must be provided."
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graph.edata["a"] = edge_feat
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graph.update_all(self.message, self.reduce_func)
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h = self.U(torch.cat([node_feat, graph.ndata["h_neigh"]], dim=-1))
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h = h * snorm_n
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return self.dropout(self.batchnorm(h))
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class PNAConv(nn.Module):
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r"""Principal Neighbourhood Aggregation Layer from `Principal Neighbourhood Aggregation
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for Graph Nets <https://arxiv.org/abs/2004.05718>`__
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A PNA layer is composed of multiple PNA towers. Each tower takes as input a split of the
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input features, and computes the message passing as below.
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.. math::
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h_i^(l+1) = U(h_i^l, \oplus_{(i,j)\in E}M(h_i^l, e_{i,j}, h_j^l))
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where :math:`h_i` and :math:`e_{i,j}` are node features and edge features, respectively.
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:math:`M` and :math:`U` are MLPs, taking the concatenation of input for computing
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output features. :math:`\oplus` represents the combination of various aggregators
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and scalers. Aggregators aggregate messages from neighbours and scalers scale the
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aggregated messages in different ways. :math:`\oplus` concatenates the output features
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of each combination.
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The output of multiple towers are concatenated and fed into a linear mixing layer for the
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final output.
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Parameters
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----------
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in_size : int
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Input feature size; i.e. the size of :math:`h_i^l`.
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out_size : int
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Output feature size; i.e. the size of :math:`h_i^{l+1}`.
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aggregators : list of str
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List of aggregation function names(each aggregator specifies a way to aggregate
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messages from neighbours), selected from:
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* ``mean``: the mean of neighbour messages
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* ``max``: the maximum of neighbour messages
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* ``min``: the minimum of neighbour messages
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* ``std``: the standard deviation of neighbour messages
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* ``var``: the variance of neighbour messages
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* ``sum``: the sum of neighbour messages
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* ``moment3``, ``moment4``, ``moment5``: the normalized moments aggregation
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:math:`(E[(X-E[X])^n])^{1/n}`
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scalers: list of str
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List of scaler function names, selected from:
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* ``identity``: no scaling
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* ``amplification``: multiply the aggregated message by :math:`\log(d+1)/\delta`,
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where :math:`d` is the degree of the node.
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* ``attenuation``: multiply the aggregated message by :math:`\delta/\log(d+1)`
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delta: float
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The degree-related normalization factor computed over the training set, used by scalers
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for normalization. :math:`E[\log(d+1)]`, where :math:`d` is the degree for each node
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in the training set.
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dropout: float, optional
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The dropout ratio. Default: 0.0.
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num_towers: int, optional
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The number of towers used. Default: 1. Note that in_size and out_size must be divisible
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by num_towers.
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edge_feat_size: int, optional
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The edge feature size. Default: 0.
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residual : bool, optional
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The bool flag that determines whether to add a residual connection for the
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output. Default: True. If in_size and out_size of the PNA conv layer are not
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the same, this flag will be set as False forcibly.
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Example
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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 PNAConv
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>>>
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>>> g = dgl.graph(([0,1,2,3,2,5], [1,2,3,4,0,3]))
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>>> feat = th.ones(6, 10)
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>>> conv = PNAConv(10, 10, ['mean', 'max', 'sum'], ['identity', 'amplification'], 2.5)
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>>> ret = conv(g, feat)
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"""
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def __init__(
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self,
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in_size,
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out_size,
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aggregators,
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scalers,
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delta,
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dropout=0.0,
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num_towers=1,
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edge_feat_size=0,
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residual=True,
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):
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super(PNAConv, self).__init__()
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self.in_size = in_size
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self.out_size = out_size
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assert (
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in_size % num_towers == 0
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), "in_size must be divisible by num_towers"
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assert (
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out_size % num_towers == 0
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), "out_size must be divisible by num_towers"
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self.tower_in_size = in_size // num_towers
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self.tower_out_size = out_size // num_towers
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self.edge_feat_size = edge_feat_size
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self.residual = residual
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if self.in_size != self.out_size:
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self.residual = False
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self.towers = nn.ModuleList(
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[
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PNAConvTower(
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self.tower_in_size,
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self.tower_out_size,
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aggregators,
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scalers,
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delta,
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dropout=dropout,
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edge_feat_size=edge_feat_size,
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)
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for _ in range(num_towers)
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]
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)
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self.mixing_layer = nn.Sequential(
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nn.Linear(out_size, out_size), nn.LeakyReLU()
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)
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def forward(self, graph, node_feat, edge_feat=None):
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r"""
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Description
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-----------
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Compute PNA layer.
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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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node_feat : torch.Tensor
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The input feature of shape :math:`(N, h_n)`. :math:`N` is the number of
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nodes, and :math:`h_n` must be the same as in_size.
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edge_feat : torch.Tensor, optional
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The edge feature of shape :math:`(M, h_e)`. :math:`M` is the number of
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edges, and :math:`h_e` must be the same as edge_feat_size.
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Returns
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-------
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torch.Tensor
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The output node feature of shape :math:`(N, h_n')` where :math:`h_n'`
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should be the same as out_size.
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"""
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h_cat = torch.cat(
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[
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tower(
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graph,
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node_feat[
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:,
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ti * self.tower_in_size : (ti + 1) * self.tower_in_size,
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],
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edge_feat,
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)
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for ti, tower in enumerate(self.towers)
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],
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dim=1,
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)
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h_out = self.mixing_layer(h_cat)
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# add residual connection
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if self.residual:
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h_out = h_out + node_feat
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return h_out
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