Source code for dgllife.model.model_zoo.weave_predictor

# -*- coding: utf-8 -*-
# Copyright, Inc. or its affiliates. All Rights Reserved.
# SPDX-License-Identifier: Apache-2.0
# Weave
# pylint: disable= no-member, arguments-differ, invalid-name

import torch.nn as nn
import torch.nn.functional as F

from ..gnn import WeaveGNN
from ..readout import WeaveGather

__all__ = ['WeavePredictor']

# pylint: disable=W0221
[docs]class WeavePredictor(nn.Module): r"""Weave for regression and classification on graphs. Weave is introduced in `Molecular Graph Convolutions: Moving Beyond Fingerprints <>`__ Parameters ---------- node_in_feats : int Size for the input node features. edge_in_feats : int Size for the input edge features. num_gnn_layers : int Number of GNN (Weave) layers to use. Default to 2. gnn_hidden_feats : int Size for the hidden node and edge representations. Default to 50. gnn_activation : callable Activation function to be used in GNN (Weave) layers. Default to ReLU. graph_feats : int Size for the hidden graph representations. Default to 50. gaussian_expand : bool Whether to expand each dimension of node features by gaussian histogram in computing graph representations. Default to True. gaussian_memberships : list of 2-tuples For each tuple, the first and second element separately specifies the mean and std for constructing a normal distribution. This argument comes into effect only when ``gaussian_expand==True``. By default, we set this to be a list consisting of ``(-1.645, 0.283)``, ``(-1.080, 0.170)``, ``(-0.739, 0.134)``, ``(-0.468, 0.118)``, ``(-0.228, 0.114)``, ``(0., 0.114)``, ``(0.228, 0.114)``, ``(0.468, 0.118)``, ``(0.739, 0.134)``, ``(1.080, 0.170)``, ``(1.645, 0.283)``. readout_activation : callable Activation function to be used in computing graph representations out of node representations. Default to Tanh. n_tasks : int Number of tasks, which is also the output size. Default to 1. """ def __init__(self, node_in_feats, edge_in_feats, num_gnn_layers=2, gnn_hidden_feats=50, gnn_activation=F.relu, graph_feats=128, gaussian_expand=True, gaussian_memberships=None, readout_activation=nn.Tanh(), n_tasks=1): super(WeavePredictor, self).__init__() self.gnn = WeaveGNN(node_in_feats=node_in_feats, edge_in_feats=edge_in_feats, num_layers=num_gnn_layers, hidden_feats=gnn_hidden_feats, activation=gnn_activation) self.node_to_graph = nn.Sequential( nn.Linear(gnn_hidden_feats, graph_feats), readout_activation, nn.BatchNorm1d(graph_feats) ) self.readout = WeaveGather(node_in_feats=graph_feats, gaussian_expand=gaussian_expand, gaussian_memberships=gaussian_memberships, activation=readout_activation) self.predict = nn.Linear(graph_feats, n_tasks)
[docs] def forward(self, g, node_feats, edge_feats): """Graph-level regression/soft classification. Parameters ---------- g : DGLGraph DGLGraph for a batch of graphs. node_feats : float32 tensor of shape (V, node_in_feats) Input node features. V for the number of nodes. edge_feats : float32 tensor of shape (E, edge_in_feats) Input edge features. E for the number of edges. Returns ------- float32 tensor of shape (G, n_tasks) Prediction for the graphs in the batch. G for the number of graphs. """ node_feats = self.gnn(g, node_feats, edge_feats, node_only=True) node_feats = self.node_to_graph(node_feats) g_feats = self.readout(g, node_feats) return self.predict(g_feats)