Commit 21c60d1b authored by Joseph Gomes's avatar Joseph Gomes
Browse files

Update GDB7 example to use CoulombFitTransformer

parent 1195101e
Loading
Loading
Loading
Loading
+5 −3
Original line number Diff line number Diff line
@@ -14,19 +14,21 @@ np.random.seed(123)

gdb7_tasks, datasets, transformers = load_gdb7(featurizer=dc.feat.CoulombMatrix(23))
train_dataset, valid_dataset, test_dataset = datasets
fit_transformers = [dc.trans.CoulombRandomizationFitTransformer(), dc.trans.NormalizationFitTransformer()]
#fit_transformers = [dc.trans.CoulombRandomizationFitTransformer(), dc.trans.NormalizationFitTransformer()]
X = train_dataset.X
fit_transformers = [dc.trans.CoulombFitTransformer(X, num_atoms=23)]

regression_metric = dc.metrics.Metric(dc.metrics.mean_absolute_error, 
                                      mode="regression")
model = dc.models.TensorflowMultiTaskFitTransformRegressor(
    n_tasks=len(gdb7_tasks), n_features=23,
    learning_rate=.0002, momentum=.8, batch_size=512,
    learning_rate=.001, momentum=.8, batch_size=512,
    weight_init_stddevs=[1/np.sqrt(2000),1/np.sqrt(800),1/np.sqrt(800),1/np.sqrt(1000)],
    bias_init_consts=[0.,0.,0.,0.], layer_sizes=[2000,800,800,1000], 
    dropouts=[0.1,0.1,0.1,0.1], fit_transformers=fit_transformers, n_random_samples=10, seed=123)

# Fit trained model
model.fit(train_dataset, nb_epoch=2)
model.fit(train_dataset, nb_epoch=50)
model.save()

train_scores = model.evaluate(train_dataset, [regression_metric], transformers)