From 79238bddb59607aa9f759caa9e3c8db176709703 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Thu, 28 Apr 2016 12:19:48 +0200 Subject: compound validations fixed --- test/regression.rb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) (limited to 'test/regression.rb') diff --git a/test/regression.rb b/test/regression.rb index ad460b5..6d461ed 100644 --- a/test/regression.rb +++ b/test/regression.rb @@ -4,7 +4,7 @@ class LazarRegressionTest < MiniTest::Test def test_weighted_average training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv" - model = Model::LazarRegression.create training_dataset, {:neighbor_algorithm_parameters => {:min_sim => 0}, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_weighted_average"} + model = Model::LazarRegression.create training_dataset.features.first, training_dataset, {:neighbor_algorithm_parameters => {:min_sim => 0}, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_weighted_average"} compound = Compound.from_smiles "CC(C)(C)CN" prediction = model.predict compound assert_equal 7.2, prediction[:value].round(1) @@ -13,7 +13,7 @@ class LazarRegressionTest < MiniTest::Test def test_mpd_fingerprints training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv" - model = Model::LazarRegression.create training_dataset + model = Model::LazarRegression.create training_dataset.features.first, training_dataset model.neighbor_algorithm_parameters[:type] = "MP2D" compound = Compound.from_smiles "CCCSCCSCC" prediction = model.predict compound @@ -23,10 +23,9 @@ class LazarRegressionTest < MiniTest::Test def test_local_fingerprint_regression training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv" - model = Model::LazarRegression.create(training_dataset, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_fingerprint_regression") + model = Model::LazarRegression.create(training_dataset.features.first, training_dataset, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_fingerprint_regression") compound = Compound.from_smiles "NC(=O)OCCC" prediction = model.predict compound - p prediction refute_nil prediction[:value] refute_nil prediction[:prediction_interval] refute_empty prediction[:neighbors] @@ -34,7 +33,7 @@ class LazarRegressionTest < MiniTest::Test def test_local_physchem_regression training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv" - model = Model::LazarRegression.create(training_dataset, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_physchem_regression") + model = Model::LazarRegression.create(training_dataset.features.first, training_dataset, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_physchem_regression") compound = Compound.from_smiles "NC(=O)OCCC" prediction = model.predict compound refute_nil prediction[:value] -- cgit v1.2.3 From 48234554ea99b972a01718ac36c4e8332dd9159b Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Sat, 7 May 2016 10:34:03 +0200 Subject: -log10 for regression datasets, test cleanups --- test/regression.rb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'test/regression.rb') diff --git a/test/regression.rb b/test/regression.rb index 6d461ed..8ed8789 100644 --- a/test/regression.rb +++ b/test/regression.rb @@ -3,7 +3,7 @@ require_relative "setup.rb" class LazarRegressionTest < MiniTest::Test def test_weighted_average - training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv" + training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi_log10.csv" model = Model::LazarRegression.create training_dataset.features.first, training_dataset, {:neighbor_algorithm_parameters => {:min_sim => 0}, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_weighted_average"} compound = Compound.from_smiles "CC(C)(C)CN" prediction = model.predict compound @@ -12,7 +12,7 @@ class LazarRegressionTest < MiniTest::Test end def test_mpd_fingerprints - training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv" + training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi_log10.csv" model = Model::LazarRegression.create training_dataset.features.first, training_dataset model.neighbor_algorithm_parameters[:type] = "MP2D" compound = Compound.from_smiles "CCCSCCSCC" @@ -22,7 +22,7 @@ class LazarRegressionTest < MiniTest::Test end def test_local_fingerprint_regression - training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv" + training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi_log10.csv" model = Model::LazarRegression.create(training_dataset.features.first, training_dataset, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_fingerprint_regression") compound = Compound.from_smiles "NC(=O)OCCC" prediction = model.predict compound @@ -32,7 +32,7 @@ class LazarRegressionTest < MiniTest::Test end def test_local_physchem_regression - training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv" + training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi_log10.csv" model = Model::LazarRegression.create(training_dataset.features.first, training_dataset, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_physchem_regression") compound = Compound.from_smiles "NC(=O)OCCC" prediction = model.predict compound -- cgit v1.2.3 From 06fc914653face2c58fd4e6c47161cb03e217582 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Sun, 8 May 2016 12:22:58 +0200 Subject: default validations fixed --- test/regression.rb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'test/regression.rb') diff --git a/test/regression.rb b/test/regression.rb index 8ed8789..c0782c4 100644 --- a/test/regression.rb +++ b/test/regression.rb @@ -7,7 +7,7 @@ class LazarRegressionTest < MiniTest::Test model = Model::LazarRegression.create training_dataset.features.first, training_dataset, {:neighbor_algorithm_parameters => {:min_sim => 0}, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_weighted_average"} compound = Compound.from_smiles "CC(C)(C)CN" prediction = model.predict compound - assert_equal 7.2, prediction[:value].round(1) + assert_equal -0.86, prediction[:value].round(2) assert_equal 88, prediction[:neighbors].size end @@ -17,7 +17,7 @@ class LazarRegressionTest < MiniTest::Test model.neighbor_algorithm_parameters[:type] = "MP2D" compound = Compound.from_smiles "CCCSCCSCC" prediction = model.predict compound - assert_equal 0.04, prediction[:value].round(2) + assert_equal 1.37, prediction[:value].round(2) assert_equal 3, prediction[:neighbors].size end -- cgit v1.2.3 From b8bb12c8a163c238d7d4387c1914e2100bb660df Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Thu, 12 May 2016 15:23:01 +0200 Subject: enm study import fixed --- test/regression.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'test/regression.rb') diff --git a/test/regression.rb b/test/regression.rb index c0782c4..799650f 100644 --- a/test/regression.rb +++ b/test/regression.rb @@ -17,7 +17,7 @@ class LazarRegressionTest < MiniTest::Test model.neighbor_algorithm_parameters[:type] = "MP2D" compound = Compound.from_smiles "CCCSCCSCC" prediction = model.predict compound - assert_equal 1.37, prediction[:value].round(2) + assert_equal 1.26, prediction[:value].round(2) assert_equal 3, prediction[:neighbors].size end -- cgit v1.2.3 From cc08e6beda7f7d70ebf6c6929a22d1a0cd7c1a20 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Tue, 24 May 2016 15:41:24 +0200 Subject: tests fixed. DescriptorTest#test_compound_all may fail within all.rb --- test/regression.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'test/regression.rb') diff --git a/test/regression.rb b/test/regression.rb index 799650f..c0782c4 100644 --- a/test/regression.rb +++ b/test/regression.rb @@ -17,7 +17,7 @@ class LazarRegressionTest < MiniTest::Test model.neighbor_algorithm_parameters[:type] = "MP2D" compound = Compound.from_smiles "CCCSCCSCC" prediction = model.predict compound - assert_equal 1.26, prediction[:value].round(2) + assert_equal 1.37, prediction[:value].round(2) assert_equal 3, prediction[:neighbors].size end -- cgit v1.2.3 From 0f31c884d1bcfa448a1bf43a41d8fd6cf88bfc52 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Wed, 8 Jun 2016 18:26:07 +0200 Subject: compound tests fixed --- test/regression.rb | 1 + 1 file changed, 1 insertion(+) (limited to 'test/regression.rb') diff --git a/test/regression.rb b/test/regression.rb index c0782c4..dff0518 100644 --- a/test/regression.rb +++ b/test/regression.rb @@ -32,6 +32,7 @@ class LazarRegressionTest < MiniTest::Test end def test_local_physchem_regression + skip # TODO: fix training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi_log10.csv" model = Model::LazarRegression.create(training_dataset.features.first, training_dataset, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_physchem_regression") compound = Compound.from_smiles "NC(=O)OCCC" -- cgit v1.2.3 From ec87f7e079f3a7ef8ea6a0fa57f3b40e81ecaed0 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Wed, 5 Oct 2016 14:43:18 +0200 Subject: classification and regression tests --- test/regression.rb | 25 +++++++++++++++++++------ 1 file changed, 19 insertions(+), 6 deletions(-) (limited to 'test/regression.rb') diff --git a/test/regression.rb b/test/regression.rb index dff0518..4c21450 100644 --- a/test/regression.rb +++ b/test/regression.rb @@ -4,7 +4,15 @@ class LazarRegressionTest < MiniTest::Test def test_weighted_average training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi_log10.csv" - model = Model::LazarRegression.create training_dataset.features.first, training_dataset, {:neighbor_algorithm_parameters => {:min_sim => 0}, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_weighted_average"} + algorithms = { + :similarity => { + :min => 0 + }, + :prediction => { + :method => "Algorithm::Regression.weighted_average", + }, + } + model = Model::Lazar.create training_dataset: training_dataset, algorithms: algorithms compound = Compound.from_smiles "CC(C)(C)CN" prediction = model.predict compound assert_equal -0.86, prediction[:value].round(2) @@ -13,17 +21,22 @@ class LazarRegressionTest < MiniTest::Test def test_mpd_fingerprints training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi_log10.csv" - model = Model::LazarRegression.create training_dataset.features.first, training_dataset - model.neighbor_algorithm_parameters[:type] = "MP2D" + algorithms = { + :descriptors => { + :method => "fingerprint", + :type => "MP2D" + } + } + model = Model::Lazar.create training_dataset: training_dataset, algorithms: algorithms compound = Compound.from_smiles "CCCSCCSCC" prediction = model.predict compound - assert_equal 1.37, prediction[:value].round(2) assert_equal 3, prediction[:neighbors].size + assert_equal 1.37, prediction[:value].round(2) end def test_local_fingerprint_regression training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi_log10.csv" - model = Model::LazarRegression.create(training_dataset.features.first, training_dataset, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_fingerprint_regression") + model = Model::Lazar.create training_dataset: training_dataset compound = Compound.from_smiles "NC(=O)OCCC" prediction = model.predict compound refute_nil prediction[:value] @@ -34,7 +47,7 @@ class LazarRegressionTest < MiniTest::Test def test_local_physchem_regression skip # TODO: fix training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi_log10.csv" - model = Model::LazarRegression.create(training_dataset.features.first, training_dataset, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_physchem_regression") + model = Model::Lazar.create(training_dataset.features.first, training_dataset, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_physchem_regression") compound = Compound.from_smiles "NC(=O)OCCC" prediction = model.predict compound refute_nil prediction[:value] -- cgit v1.2.3 From dc4ab1f4e64d738d6c0b70f0b690a2359685080f Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Wed, 12 Oct 2016 21:32:27 +0200 Subject: physchem regression, correlation_filter for fingerprints --- test/regression.rb | 37 +++++++++++++++++++++++++++++++++++-- 1 file changed, 35 insertions(+), 2 deletions(-) (limited to 'test/regression.rb') diff --git a/test/regression.rb b/test/regression.rb index 4c21450..aad4195 100644 --- a/test/regression.rb +++ b/test/regression.rb @@ -45,12 +45,45 @@ class LazarRegressionTest < MiniTest::Test end def test_local_physchem_regression - skip # TODO: fix training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi_log10.csv" - model = Model::Lazar.create(training_dataset.features.first, training_dataset, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_physchem_regression") + algorithms = { + :descriptors => ["PhysChem::OPENBABEL"], + :similarity => { + :method => "Algorithm::Similarity.weighted_cosine", + :min => 0.5 + }, + } + model = Model::Lazar.create(training_dataset:training_dataset, algorithms:algorithms) + p model compound = Compound.from_smiles "NC(=O)OCCC" prediction = model.predict compound refute_nil prediction[:value] end + def test_local_physchem_regression_with_feature_selection + training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi_log10.csv" + algorithms = { + :descriptors => { + :method => "calculated_properties", + :types => ["OPENBABEL"] + }, + :similarity => { + :method => "Algorithm::Similarity.weighted_cosine", + :min => 0.5 + }, + :feature_selection => { + :method => "Algorithm::FeatureSelection.correlation_filter", + }, + } + model = Model::Lazar.create(training_dataset.features.first, training_dataset, algorithms) + p model + compound = Compound.from_smiles "NC(=O)OCCC" + prediction = model.predict compound + refute_nil prediction[:value] + end + + def test_local_physchem_classification + skip + end + end -- cgit v1.2.3 From 8d325866dd7cacdd04bd2306a9144a5e7300c7c8 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Thu, 13 Oct 2016 10:11:09 +0200 Subject: molecular_weight fixed --- test/regression.rb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) (limited to 'test/regression.rb') diff --git a/test/regression.rb b/test/regression.rb index aad4195..b1051f1 100644 --- a/test/regression.rb +++ b/test/regression.rb @@ -22,10 +22,7 @@ class LazarRegressionTest < MiniTest::Test def test_mpd_fingerprints training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi_log10.csv" algorithms = { - :descriptors => { - :method => "fingerprint", - :type => "MP2D" - } + :descriptors => [ "MP2D" ] } model = Model::Lazar.create training_dataset: training_dataset, algorithms: algorithms compound = Compound.from_smiles "CCCSCCSCC" -- cgit v1.2.3 From 9e99495ecbff147218023c136bade9e56a502fed Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Thu, 13 Oct 2016 14:39:04 +0200 Subject: descriptor tests fixed --- test/regression.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'test/regression.rb') diff --git a/test/regression.rb b/test/regression.rb index b1051f1..cdbac4b 100644 --- a/test/regression.rb +++ b/test/regression.rb @@ -44,7 +44,7 @@ class LazarRegressionTest < MiniTest::Test def test_local_physchem_regression training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi_log10.csv" algorithms = { - :descriptors => ["PhysChem::OPENBABEL"], + :descriptors => [PhysChem::OPENBABEL], :similarity => { :method => "Algorithm::Similarity.weighted_cosine", :min => 0.5 -- cgit v1.2.3 From 160e75e696452ac61e651664ac56d16ce1c9c4b6 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Thu, 13 Oct 2016 19:17:03 +0200 Subject: model tests separated and cleaned --- test/regression.rb | 86 ------------------------------------------------------ 1 file changed, 86 deletions(-) delete mode 100644 test/regression.rb (limited to 'test/regression.rb') diff --git a/test/regression.rb b/test/regression.rb deleted file mode 100644 index cdbac4b..0000000 --- a/test/regression.rb +++ /dev/null @@ -1,86 +0,0 @@ -require_relative "setup.rb" - -class LazarRegressionTest < MiniTest::Test - - def test_weighted_average - training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi_log10.csv" - algorithms = { - :similarity => { - :min => 0 - }, - :prediction => { - :method => "Algorithm::Regression.weighted_average", - }, - } - model = Model::Lazar.create training_dataset: training_dataset, algorithms: algorithms - compound = Compound.from_smiles "CC(C)(C)CN" - prediction = model.predict compound - assert_equal -0.86, prediction[:value].round(2) - assert_equal 88, prediction[:neighbors].size - end - - def test_mpd_fingerprints - training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi_log10.csv" - algorithms = { - :descriptors => [ "MP2D" ] - } - model = Model::Lazar.create training_dataset: training_dataset, algorithms: algorithms - compound = Compound.from_smiles "CCCSCCSCC" - prediction = model.predict compound - assert_equal 3, prediction[:neighbors].size - assert_equal 1.37, prediction[:value].round(2) - end - - def test_local_fingerprint_regression - training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi_log10.csv" - model = Model::Lazar.create training_dataset: training_dataset - compound = Compound.from_smiles "NC(=O)OCCC" - prediction = model.predict compound - refute_nil prediction[:value] - refute_nil prediction[:prediction_interval] - refute_empty prediction[:neighbors] - end - - def test_local_physchem_regression - training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi_log10.csv" - algorithms = { - :descriptors => [PhysChem::OPENBABEL], - :similarity => { - :method => "Algorithm::Similarity.weighted_cosine", - :min => 0.5 - }, - } - model = Model::Lazar.create(training_dataset:training_dataset, algorithms:algorithms) - p model - compound = Compound.from_smiles "NC(=O)OCCC" - prediction = model.predict compound - refute_nil prediction[:value] - end - - def test_local_physchem_regression_with_feature_selection - training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi_log10.csv" - algorithms = { - :descriptors => { - :method => "calculated_properties", - :types => ["OPENBABEL"] - }, - :similarity => { - :method => "Algorithm::Similarity.weighted_cosine", - :min => 0.5 - }, - :feature_selection => { - :method => "Algorithm::FeatureSelection.correlation_filter", - }, - } - model = Model::Lazar.create(training_dataset.features.first, training_dataset, algorithms) - p model - compound = Compound.from_smiles "NC(=O)OCCC" - prediction = model.predict compound - refute_nil prediction[:value] - end - - def test_local_physchem_classification - skip - end - -end -- cgit v1.2.3