Merge pull request #228 from matchms/make_relu_a_setting

Make relu a setting
matchms · Aug 8, 2024 · cd6eb85 · cd6eb85
2 parents 878e359 + 765a53d
commit cd6eb85
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Showing 4 changed files with 16 additions and 15 deletions.
diff --git a/ms2deepscore/SettingsMS2Deepscore.py b/ms2deepscore/SettingsMS2Deepscore.py
@@ -96,6 +96,7 @@ def __init__(self, **settings):
         self.base_dims = (2000, 2000, 2000)
         self.embedding_dim = 400
         self.ionisation_mode = "positive"
+        self.activation_function = "relu"
 
         # additional model structure options
         self.train_binning_layer: bool = False

diff --git a/ms2deepscore/models/SiameseSpectralModel.py b/ms2deepscore/models/SiameseSpectralModel.py
@@ -125,13 +125,13 @@ def __init__(self,
         else:
             input_size = peak_inputs + additional_inputs
         self.dense_layers.append(
-            dense_layer(input_size, settings.base_dims[0], "lrelu")
+            dense_layer(input_size, settings.base_dims[0], settings.activation_function)
         )
         input_dim = settings.base_dims[0]
 
         # Create additional dense layers
         for output_dim in settings.base_dims[1:]:
-            self.dense_layers.append(dense_layer(input_dim, output_dim, "lrelu"))
+            self.dense_layers.append(dense_layer(input_dim, output_dim, settings.activation_function))
             input_dim = output_dim
 
         self.embedding_layer = dense_layer(settings.base_dims[-1], settings.embedding_dim, "tanh")

diff --git a/tests/test_ms2deepscore.py b/tests/test_ms2deepscore.py
@@ -34,7 +34,7 @@ def test_MS2DeepScore_score_pair():
     """Test score calculation using *.pair* method."""
     spectrums, _, similarity_measure = get_test_ms2deepscore_instance()
     score = similarity_measure.pair(spectrums[0], spectrums[1])
-    assert np.allclose(score, 0.99030185, atol=1e-6), "Expected different score."
+    assert np.allclose(score, 0.990366, atol=1e-6), "Expected different score."
     assert isinstance(score, float), "Expected score to be float"
 
 
@@ -44,10 +44,10 @@ def test_MS2DeepScore_score_matrix():
     scores = similarity_measure.matrix(spectrums[:4], spectrums[:3])
 
     expected_scores = np.array([
-        [1.        , 0.99030184, 0.99073977],
-        [0.99030184, 1.        , 0.99394612],
-        [0.99073977, 0.99394612, 1.        ],
-        [0.98800209, 0.96405927, 0.97329062]
+        [1.        , 0.99036639, 0.99084978],
+        [0.99036639, 1.        , 0.99399306],
+        [0.99084978, 0.99399306, 1.        ],
+        [0.98811793, 0.96436209, 0.97351075]
         ])
     assert np.allclose(expected_scores, scores, atol=1e-6), "Expected different scores."
 
@@ -57,10 +57,10 @@ def test_MS2DeepScore_score_matrix_symmetric():
     spectrums, _, similarity_measure = get_test_ms2deepscore_instance()
     scores = similarity_measure.matrix(spectrums[:4], spectrums[:4], is_symmetric=True)
     expected_scores = np.array([
-        [1.        , 0.99030184, 0.99073977, 0.98800209],
-        [0.99030184, 1.        , 0.99394612, 0.96405927],
-        [0.99073977, 0.99394612, 1.        , 0.97329062],
-        [0.98800209, 0.96405927, 0.97329062, 1.        ]])
+        [1.        , 0.99036639, 0.99084978, 0.98811793],
+        [0.99036639, 1.        , 0.99399306, 0.96436209],
+        [0.99084978, 0.99399306, 1.        , 0.97351075],
+        [0.98811793, 0.96436209, 0.97351075, 1.        ]])
     assert np.allclose(expected_scores, scores, atol=1e-6), "Expected different scores."
 
 

diff --git a/tests/test_ms2deepscore_evaluated.py b/tests/test_ms2deepscore_evaluated.py
@@ -39,7 +39,7 @@ def test_MS2DeepScore_score_pair():
     """Test score calculation using *.pair* method."""
     spectrums, similarity_measure = get_test_ms2deepscore_evaluated_instance()
     score = similarity_measure.pair(spectrums[0], spectrums[1])
-    assert np.allclose(score["score"], 0.99030185, atol=1e-6), "Expected different score."
+    assert np.allclose(score["score"], 0.990366, atol=1e-6), "Expected different score."
     assert score["predicted_absolute_error"] > 0
     assert isinstance(score["score"], np.ndarray)
     assert isinstance(score["predicted_absolute_error"], np.ndarray)
@@ -51,9 +51,9 @@ def test_MS2DeepScore_score_matrix():
     scores = similarity_measure.matrix(spectrums[:3], spectrums[:4])
 
     expected_scores = np.array([
-        [1.        , 0.99030185, 0.99073976, 0.98800206],
-        [0.99030185, 1.        , 0.99394614, 0.9640593 ],
-        [0.99073976, 0.99394614, 1.        , 0.9732906 ]
+        [1.        , 0.9903664 , 0.9908498 , 0.98811793],
+        [0.9903664 , 1.        , 0.99399304, 0.9643621 ],
+        [0.9908498 , 0.99399304, 1.        , 0.97351074]
         ])
     assert np.allclose(expected_scores, scores["score"], atol=1e-6), "Expected different scores."
     assert scores["predicted_absolute_error"].shape == (3, 4)