Message Passing Neural Network (MPNN)

class DeepPurpose.models.MPNN(nn.Sequential)

Message Passing Neural Network (MPNN) (Source) encode drug in its graph representation.

constructor create an instance of MPNN class.

__init__(self, mpnn_hidden_size, mpnn_depth)

• mpnn_hidden_size (int) - specify dimension of hidden layer in MPNN, e.g, mpnn_hidden_size = 256.
• mpnn_depth (int) - specify depth of MPNN, e.g., mpnn_depth = 3.

Calling functions implement the feedforward procedure of MPNN.

forward(self, feature)

• feature (tuple of length 5)

  • feature[0] (torch.Tensor) - atom-level feature
  • feature[1] (torch.Tensor) - bond-level feature
  • feature[2] (torch.Tensor) - neighbor information of every atom
  • feature[3] (torch.Tensor) - neighbor information of every bond
  • feature[4] (torch.Tensor) - store number of atoms and bonds for each molecule in a batch