Source code for torch_geometric.graphgym.models.encoder

import torch

import torch_geometric.graphgym.register as register


class IntegerFeatureEncoder(torch.nn.Module):
    """
    Provides an encoder for integer node features.

    Args:
        emb_dim (int): Output embedding dimension
        num_classes (int): the number of classes for the
        embedding mapping to learn from
    """
    def __init__(self, emb_dim, num_classes=None):
        super(IntegerFeatureEncoder, self).__init__()

        self.encoder = torch.nn.Embedding(num_classes, emb_dim)
        torch.nn.init.xavier_uniform_(self.encoder.weight.data)

    def forward(self, batch):
        """"""
        # Encode just the first dimension if more exist
        batch.x = self.encoder(batch.x[:, 0])

        return batch


class AtomEncoder(torch.nn.Module):
    """
    The atom Encoder used in OGB molecule dataset.

    Args:
        emb_dim (int): Output embedding dimension
        num_classes: None
    """
    def __init__(self, emb_dim, num_classes=None):
        super(AtomEncoder, self).__init__()

        from ogb.utils.features import get_atom_feature_dims

        self.atom_embedding_list = torch.nn.ModuleList()

        for i, dim in enumerate(get_atom_feature_dims()):
            emb = torch.nn.Embedding(dim, emb_dim)
            torch.nn.init.xavier_uniform_(emb.weight.data)
            self.atom_embedding_list.append(emb)

    def forward(self, batch):
        """"""
        encoded_features = 0
        for i in range(batch.x.shape[1]):
            encoded_features += self.atom_embedding_list[i](batch.x[:, i])

        batch.x = encoded_features
        return batch


class BondEncoder(torch.nn.Module):
    """
    The bond Encoder used in OGB molecule dataset.

    Args:
        emb_dim (int): Output edge embedding dimension
    """
    def __init__(self, emb_dim):
        super(BondEncoder, self).__init__()

        from ogb.utils.features import get_bond_feature_dims

        self.bond_embedding_list = torch.nn.ModuleList()

        for i, dim in enumerate(get_bond_feature_dims()):
            emb = torch.nn.Embedding(dim, emb_dim)
            torch.nn.init.xavier_uniform_(emb.weight.data)
            self.bond_embedding_list.append(emb)

    def forward(self, batch):
        """"""
        bond_embedding = 0
        for i in range(batch.edge_attr.shape[1]):
            edge_attr = batch.edge_attr
            bond_embedding += self.bond_embedding_list[i](edge_attr[:, i])

        batch.edge_attr = bond_embedding
        return batch


node_encoder_dict = {'Integer': IntegerFeatureEncoder, 'Atom': AtomEncoder}

register.node_encoder_dict = {
    **register.node_encoder_dict,
    **node_encoder_dict
}

edge_encoder_dict = {'Bond': BondEncoder}

register.edge_encoder_dict = {
    **register.edge_encoder_dict,
    **edge_encoder_dict
}