Readout for Computing Graph Representations¶
After updating node/edge representations with graph neural networks (GNNs), a common operation is to compute graph representations out of updated node/edge representations. For example, we need to compute molecular representations out of atom/bond representations in molecular property prediction. We call the various modules for computing graphlevel representations readout as in Neural Message Passing for Quantum Chemistry and this section lists the readout modules implemented in DGLLifeSci.
AttentiveFP Readout¶

class
dgllife.model.readout.attentivefp_readout.
AttentiveFPReadout
(feat_size, num_timesteps=2, dropout=0.0)[source]¶ Readout in AttentiveFP
AttentiveFP is introduced in Pushing the Boundaries of Molecular Representation for Drug Discovery with the Graph Attention Mechanism
This class computes graph representations out of node features.
 Parameters

forward
(g, node_feats, get_node_weight=False)[source]¶ Computes graph representations out of node features.
 Parameters
g (DGLGraph) – DGLGraph for a batch of graphs.
node_feats (float32 tensor of shape (V, node_feat_size)) – Input node features. V for the number of nodes.
get_node_weight (bool) – Whether to get the weights of nodes in readout. Default to False.
 Returns
g_feats (float32 tensor of shape (G, graph_feat_size)) – Graph representations computed. G for the number of graphs.
node_weights (list of float32 tensor of shape (V, 1), optional) – This is returned when
get_node_weight
isTrue
. The list has a lengthnum_timesteps
andnode_weights[i]
gives the node weights in the ith update.
MLP Readout¶

class
dgllife.model.readout.mlp_readout.
MLPNodeReadout
(node_feats, hidden_feats, graph_feats, activation=None, mode='sum')[source]¶ MLPbased Readout.
This layer updates node representations with a MLP and computes graph representations out of node representations with max, mean or sum.
 Parameters
node_feats (int) – Size for the input node features.
hidden_feats (int) – Size for the hidden representations.
graph_feats (int) – Size for the output graph representations.
activation (callable) – Activation function. Default to None.
mode ('max' or 'mean' or 'sum') – Whether to compute elementwise maximum, mean or sum of the node representations.

forward
(g, node_feats)[source]¶ Computes graph representations out of node features.
 Parameters
g (DGLGraph) – DGLGraph for a batch of graphs.
node_feats (float32 tensor of shape (V, node_feats)) – Input node features, V for the number of nodes.
 Returns
graph_feats – Graph representations computed. G for the number of graphs.
 Return type
float32 tensor of shape (G, graph_feats)
Weighted Sum and Max Readout¶

class
dgllife.model.readout.weighted_sum_and_max.
WeightedSumAndMax
(in_feats)[source]¶ Apply weighted sum and max pooling to the node representations and concatenate the results.
 Parameters
in_feats (int) – Input node feature size

forward
(bg, feats)[source]¶ Readout
 Parameters
bg (DGLGraph) – DGLGraph for a batch of graphs.
feats (FloatTensor of shape (N, M1)) –
N is the total number of nodes in the batch of graphs
M1 is the input node feature size, which must match in_feats in initialization
 Returns
h_g –
B is the number of graphs in the batch
M1 is the input node feature size, which must match in_feats in initialization
 Return type
FloatTensor of shape (B, 2 * M1)
Weave Readout¶

class
dgllife.model.readout.weave_readout.
WeaveGather
(node_in_feats, gaussian_expand=True, gaussian_memberships=None, activation=Tanh())[source]¶ Readout in Weave
 Parameters
node_in_feats (int) – Size for the input node features.
gaussian_expand (bool) – Whether to expand each dimension of node features by gaussian histogram. Default to True.
gaussian_memberships (list of 2tuples) – 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)
.activation (callable) – Activation function to apply. Default to tanh.

forward
(g, node_feats)[source]¶ Computes graph representations out of node representations.
 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 in the batch of graphs.
 Returns
g_feats – Output graph representations. G for the number of graphs in the batch.
 Return type
float32 tensor of shape (G, node_in_feats)

gaussian_histogram
(node_feats)[source]¶ Constructs a gaussian histogram to capture the distribution of features
 Parameters
node_feats (float32 tensor of shape (V, node_in_feats)) – Input node features. V for the number of nodes in the batch of graphs.
 Returns
Updated node representations
 Return type
float32 tensor of shape (V, node_in_feats * len(self.means))