From 3927fb1ed8e7c49b82d2609f18ea68986bffa088 Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Thu, 8 Aug 2024 12:06:14 +0200 Subject: [PATCH 1/2] Add relu to SettingsMS2Deepscore.py --- ms2deepscore/SettingsMS2Deepscore.py | 1 + 1 file changed, 1 insertion(+) diff --git a/ms2deepscore/SettingsMS2Deepscore.py b/ms2deepscore/SettingsMS2Deepscore.py index 9756828e..d882f6b0 100644 --- 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 From 765a53dab409de66ba1b5be7251951d9b77688cd Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Thu, 8 Aug 2024 12:06:47 +0200 Subject: [PATCH 2/2] Replace "lrelu" with setting.activation_function and revert test results --- ms2deepscore/models/SiameseSpectralModel.py | 4 ++-- tests/test_ms2deepscore.py | 18 +++++++++--------- tests/test_ms2deepscore_evaluated.py | 8 ++++---- 3 files changed, 15 insertions(+), 15 deletions(-) diff --git a/ms2deepscore/models/SiameseSpectralModel.py b/ms2deepscore/models/SiameseSpectralModel.py index 8371f356..e7cb3618 100644 --- 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 index 80196db5..f8161b8b 100644 --- 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 index 22cad687..60ecd154 100644 --- 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)