Bug in `models.MessagePassingNeuralNetwork` regarding `layers.Set2Set`

[jasperhyp]

Line 58 in mpnn.py:

self.readout = layers.Set2Set(feature_dim, num_s2s_step)

Whereas the initiation of Set2Set requires specification of type (line 166 in readout.py):

def __init__(self, input_dim, type="node", num_step=3, num_lstm_layer=1):
        super(Set2Set, self).__init__(type)
        self.input_dim = input_dim
        self.output_dim = self.input_dim * 2
        self.num_step = num_step
        self.lstm = nn.LSTM(input_dim * 2, input_dim, num_lstm_layer)
        self.softmax = Softmax(type)

[jasperhyp]

Potential fix: Specify "node" for line 58 in mpnn.py.

[jasperhyp]

Btw is there a way to automatically add "node_position" to PackedMolecule object given SMILES strings?

[Oxer11]

Thanks for reporting this bug. It has been fixed in ed17610.

For the second question, I think node_position cannot be inferred directly from SMILES strings.