Commit d3c1af62 authored by miaecle's avatar miaecle
Browse files

debugging

parent d8c3c05b

deepchem/models/tensorgraph/graph_layers.py

+2 −0
Original line number Diff line number Diff line
@@ -913,6 +913,8 @@ class MessagePassing(Layer): 
      out = tf.pad(atom_features, ((0, 0), (0, pad_length)), mode='CONSTANT')

    elif n_atom_features > self.n_hidden:

      raise ValueError("Too large initial feature vector")

    else:

      out = atom_features



    for i in range(self.T):

      message = self.message_function.forward(out, atom_to_pair)

deepchem/molnet/load_function/qm8_datasets.py

+2 −1
Original line number Diff line number Diff line
@@ -49,7 +49,8 @@ def load_qm8(featurizer='CoulombMatrix', split='random', reload=True): 
    elif featurizer == 'Raw':

      featurizer = deepchem.feat.RawFeaturizer()

    elif featurizer == 'MP':

      featurizer = deepchem.feat.WeaveFeaturizer(graph_distance=False)

      featurizer = deepchem.feat.WeaveFeaturizer(graph_distance=False,

                                                 explicit_H=True)

    loader = deepchem.data.SDFLoader(

        tasks=qm8_tasks,

        smiles_field="smiles",

deepchem/molnet/load_function/qm9_datasets.py

+2 −1
Original line number Diff line number Diff line
@@ -52,7 +52,8 @@ def load_qm9(featurizer='CoulombMatrix', split='random', reload=True): 
    elif featurizer == 'Raw':

      featurizer = deepchem.feat.RawFeaturizer()

    elif featurizer == 'MP':

      featurizer = deepchem.feat.WeaveFeaturizer(graph_distance=False)

      featurizer = deepchem.feat.WeaveFeaturizer(graph_distance=False,

                                                 explicit_H=True)

    loader = deepchem.data.SDFLoader(

        tasks=qm9_tasks,

        smiles_field="smiles",

deepchem/molnet/preset_hyper_parameters.py

+0 −1
Original line number Diff line number Diff line
@@ -165,7 +165,6 @@ hps['mpnn'] = { 
    'learning_rate': 0.001,

    'T': 5,

    'M': 10,

    'n_hidden': 30,

    'seed': 123

}

deepchem/molnet/run_benchmark_models.py

+1 −2
Original line number Diff line number Diff line
@@ -703,13 +703,12 @@ def benchmark_regression(train_dataset, 
    learning_rate = hyper_parameters['learning_rate']

    T = hyper_parameters['T']

    M = hyper_parameters['M']

    n_hidden = hyper_parameters['n_hidden']



    model = deepchem.models.MPNNTensorGraph(

        len(tasks),

        n_atom_feat=n_features[0],

        n_pair_feat=n_features[1],

        n_hidden=n_hidden,

        n_hidden=n_features[0],

        T=T,

        M=M,

        batch_size=batch_size,

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