chemprop.nn.agg

Module Contents

Classes

Aggregation	An Aggregation aggregates the node-level representations of a batch of graphs into
MeanAggregation	Average the graph-level representation:
SumAggregation	Sum the graph-level representation:
NormAggregation	Sum the graph-level representation and divide by a normalization constant:
AttentiveAggregation	An Aggregation aggregates the node-level representations of a batch of graphs into

Attributes

AggregationRegistry

class chemprop.nn.agg.Aggregation(dim=0, *args, **kwargs)

Bases: torch.nn.Module, chemprop.nn.hparams.HasHParams

An Aggregation aggregates the node-level representations of a batch of graphs into a batch of graph-level representations

Note

this class is abstract and cannot be instantiated.

See also

MeanAggregation, SumAggregation, NormAggregation

Parameters:

dim (int)

abstract forward(H, batch)

Aggregate the graph-level representations of a batch of graphs into their respective global representations

NOTE: it is possible for a graph to have 0 nodes. In this case, the representation will be a zero vector of length d in the final output.

Parameters:

• H (Tensor) – a tensor of shape V x d containing the batched node-level representations of b graphs

• batch (Tensor) – a tensor of shape V containing the index of the graph a given vertex corresponds to

Returns:

a tensor of shape b x d containing the graph-level representations

Return type:

Tensor

chemprop.nn.agg.AggregationRegistry

class chemprop.nn.agg.MeanAggregation(dim=0, *args, **kwargs)

Bases: Aggregation

Average the graph-level representation:

\[\mathbf h = \frac{1}{|V|} \sum_{v \in V} \mathbf h_v\]

Parameters:

dim (int)

forward(H, batch)

Aggregate the graph-level representations of a batch of graphs into their respective global representations

NOTE: it is possible for a graph to have 0 nodes. In this case, the representation will be a zero vector of length d in the final output.

Parameters:

• H (Tensor) – a tensor of shape V x d containing the batched node-level representations of b graphs

• batch (Tensor) – a tensor of shape V containing the index of the graph a given vertex corresponds to

Returns:

a tensor of shape b x d containing the graph-level representations

Return type:

Tensor

class chemprop.nn.agg.SumAggregation(dim=0, *args, **kwargs)

Bases: Aggregation

Sum the graph-level representation:

\[\mathbf h = \sum_{v \in V} \mathbf h_v\]

Parameters:

dim (int)

forward(H, batch)

Aggregate the graph-level representations of a batch of graphs into their respective global representations

NOTE: it is possible for a graph to have 0 nodes. In this case, the representation will be a zero vector of length d in the final output.

Parameters:

• H (Tensor) – a tensor of shape V x d containing the batched node-level representations of b graphs

• batch (Tensor) – a tensor of shape V containing the index of the graph a given vertex corresponds to

Returns:

a tensor of shape b x d containing the graph-level representations

Return type:

Tensor

class chemprop.nn.agg.NormAggregation(dim=0, *args, norm=100.0, **kwargs)

Bases: SumAggregation

Sum the graph-level representation and divide by a normalization constant:

\[\mathbf h = \frac{1}{c} \sum_{v \in V} \mathbf h_v\]

Parameters:

• dim (int)

• norm (float)

forward(H, batch)

Aggregate the graph-level representations of a batch of graphs into their respective global representations

NOTE: it is possible for a graph to have 0 nodes. In this case, the representation will be a zero vector of length d in the final output.

Parameters:

• H (Tensor) – a tensor of shape V x d containing the batched node-level representations of b graphs

• batch (Tensor) – a tensor of shape V containing the index of the graph a given vertex corresponds to

Returns:

a tensor of shape b x d containing the graph-level representations

Return type:

Tensor

class chemprop.nn.agg.AttentiveAggregation(dim=0, *args, output_size, **kwargs)

Bases: Aggregation

An Aggregation aggregates the node-level representations of a batch of graphs into a batch of graph-level representations

Note

this class is abstract and cannot be instantiated.

See also

MeanAggregation, SumAggregation, NormAggregation

Parameters:

• dim (int)

• output_size (int)

forward(H, batch)

Aggregate the graph-level representations of a batch of graphs into their respective global representations

NOTE: it is possible for a graph to have 0 nodes. In this case, the representation will be a zero vector of length d in the final output.

Parameters:

• H (Tensor) – a tensor of shape V x d containing the batched node-level representations of b graphs

• batch (Tensor) – a tensor of shape V containing the index of the graph a given vertex corresponds to

Returns:

a tensor of shape b x d containing the graph-level representations

Return type:

Tensor