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 graph-level representations readout as in Neural Message Passing for Quantum Chemistry and this section lists the readout modules implemented in DGL-LifeSci.

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

  • feat_size (int) – Size for the input node features, graph features and output graph representations.

  • num_timesteps (int) – Times of updating the graph representations with GRU. Default to 2.

  • dropout (float) – The probability for performing dropout. Default to 0.

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 is True. The list has a length num_timesteps and node_weights[i] gives the node weights in the i-th update.

MLP Readout

class dgllife.model.readout.mlp_readout.MLPNodeReadout(node_feats, hidden_feats, graph_feats, activation=None, mode='sum')[source]

MLP-based 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 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).

  • 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))