Commit 44a841ca authored by Bharath Ramsundar's avatar Bharath Ramsundar
Browse files

potential fix

parent 59a229a5
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+7 −0
Original line number Diff line number Diff line
@@ -277,6 +277,13 @@ class TensorGraph(Model):
          result = np.array(sess.run(out_tensors, feed_dict=feed_dict))
          if len(result.shape) == 3:
            result = np.transpose(result, axes=[1, 0, 2])
          elif len(result.shape) == 4:
            # Shape is (n_output_tensors, n_samples, n_tasks, n_classes)

            # Support having only one output if we call predict_proba_on_generator()
            # TODO: Might want to generalize by having an explicit output argument.
            assert result.shape[0] == 1
            result = np.squeeze(result, axis=0)
          result = undo_transforms(result, transformers)
          results.append(result)
        return np.concatenate(results, axis=0)
+4 −4
Original line number Diff line number Diff line
@@ -14,18 +14,18 @@ np.random.seed(123)

# Load Tox21 dataset
n_features = 1024
tox21_tasks, tox21_datasets, transformers = load_tox21()
tox21_tasks, tox21_datasets, transformers = dc.molnet.load_tox21()
train_dataset, valid_dataset, test_dataset = tox21_datasets

# Fit models
metric = dc.metrics.Metric(dc.metrics.roc_auc_score, np.mean)

model = dc.models.TensorflowMultiTaskClassifier(
model = dc.models.TensorGraphMultiTaskClassifier(
    len(tox21_tasks), n_features, layer_sizes=[1000], dropouts=[.25],
    learning_rate=0.001, batch_size=50)
    learning_rate=0.001, batch_size=50, use_queue=False)

# Fit trained model
model.fit(train_dataset)
model.fit(train_dataset, nb_epoch=1)
model.save()

print("Evaluating model")