Merge pull request #2236 from hsjang001205/GCN_reload

Fix graph conv model save/load
deepchem · Oct 21, 2020 · e06055e · e06055e
2 parents e5f9545 + ad24660
commit e06055e
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Showing 2 changed files with 48 additions and 55 deletions.
diff --git a/deepchem/models/layers.py b/deepchem/models/layers.py
@@ -127,14 +127,14 @@ def build(self, input_shape):
     num_deg = 2 * self.max_degree + (1 - self.min_degree)
     self.W_list = [
         self.add_weight(
-            name='kernel',
+            name='kernel' + str(k),
             shape=(int(input_shape[0][-1]), self.out_channel),
             initializer='glorot_uniform',
             trainable=True) for k in range(num_deg)
     ]
     self.b_list = [
         self.add_weight(
-            name='bias',
+            name='bias' + str(k),
             shape=(self.out_channel,),
             initializer='zeros',
             trainable=True) for k in range(num_deg)

diff --git a/deepchem/models/tests/test_reload.py b/deepchem/models/tests/test_reload.py
@@ -849,59 +849,52 @@ def test_1d_cnn_regression_reload():
   assert scores[regression_metric.name] < 0.1
 
 
-### TODO: THIS IS FAILING!
-#def test_graphconvmodel_reload():
-#  featurizer = dc.feat.ConvMolFeaturizer()
-#  tasks = ["outcome"]
-#  n_tasks = len(tasks)
-#  mols = ["C", "CO", "CC"]
-#  n_samples = len(mols)
-#  X = featurizer(mols)
-#  y = np.array([0, 1, 0])
-#  dataset = dc.data.NumpyDataset(X, y)
-#
-#  classification_metric = dc.metrics.Metric(
-#      dc.metrics.roc_auc_score, np.mean, mode="classification")
-#
-#  batch_size = 10
-#  model_dir = tempfile.mkdtemp()
-#  model = dc.models.GraphConvModel(
-#      len(tasks),
-#      batch_size=batch_size,
-#      batch_normalize=False,
-#      mode='classification',
-#      model_dir=model_dir)
-#
-#  model.fit(dataset, nb_epoch=10)
-#  scores = model.evaluate(dataset, [classification_metric])
-#  assert scores[classification_metric.name] >= 0.9
-#
-#
-#  # Reload trained Model
-#  reloaded_model = dc.models.GraphConvModel(
-#      len(tasks),
-#      batch_size=batch_size,
-#      batch_normalize=False,
-#      mode='classification',
-#      model_dir=model_dir)
-#  reloaded_model.restore()
-#
-#  # Check predictions match on random sample
-#  predmols = ["CCCC", "CCCCCO", "CCCCC"]
-#  Xpred = featurizer(predmols)
-#  predset = dc.data.NumpyDataset(Xpred)
-#  origpred = model.predict(predset)
-#  reloadpred = reloaded_model.predict(predset)
-#  assert np.all(origpred == reloadpred)
-#
-#  # Try re-restore
-#  reloaded_model.restore()
-#  reloadpred = reloaded_model.predict(predset)
-#  assert np.all(origpred == reloadpred)
-#
-#  # Eval model on train
-#  scores = reloaded_model.evaluate(dataset, [classification_metric])
-#  assert scores[classification_metric.name] > .9
+def test_graphconvmodel_reload():
+  featurizer = dc.feat.ConvMolFeaturizer()
+  tasks = ["outcome"]
+  n_tasks = len(tasks)
+  mols = ["C", "CO", "CC"]
+  n_samples = len(mols)
+  X = featurizer(mols)
+  y = np.array([0, 1, 0])
+  dataset = dc.data.NumpyDataset(X, y)
+
+  classification_metric = dc.metrics.Metric(
+      dc.metrics.roc_auc_score, np.mean, mode="classification")
+
+  batch_size = 10
+  model_dir = tempfile.mkdtemp()
+  model = dc.models.GraphConvModel(
+      len(tasks),
+      batch_size=batch_size,
+      batch_normalize=False,
+      mode='classification',
+      model_dir=model_dir)
+
+  model.fit(dataset, nb_epoch=10)
+  scores = model.evaluate(dataset, [classification_metric])
+  assert scores[classification_metric.name] >= 0.6
+
+  # Reload trained Model
+  reloaded_model = dc.models.GraphConvModel(
+      len(tasks),
+      batch_size=batch_size,
+      batch_normalize=False,
+      mode='classification',
+      model_dir=model_dir)
+  reloaded_model.restore()
+
+  # Check predictions match on random sample
+  predmols = ["CCCC", "CCCCCO", "CCCCC"]
+  Xpred = featurizer(predmols)
+  predset = dc.data.NumpyDataset(Xpred)
+  origpred = model.predict(predset)
+  reloadpred = reloaded_model.predict(predset)
+  assert np.all(origpred == reloadpred)
+
+  # Eval model on train
+  scores = reloaded_model.evaluate(dataset, [classification_metric])
+  assert scores[classification_metric.name] > .6
 
 
 def test_chemception_reload():