diff options
Diffstat (limited to 'test/model.rb')
| -rw-r--r-- | test/model.rb | 41 |
1 files changed, 15 insertions, 26 deletions
diff --git a/test/model.rb b/test/model.rb index 02b8e73..9f30928 100644 --- a/test/model.rb +++ b/test/model.rb @@ -4,17 +4,13 @@ class ModelTest < MiniTest::Test def test_default_regression algorithms = { - :descriptors => { - :method => "fingerprint", - :type => "MP2D" - }, + :descriptors => [ "MP2D" ], :similarity => { :method => "Algorithm::Similarity.tanimoto", :min => 0.1 }, :prediction => { - :method => "Algorithm::Caret.regression", - :parameters => "pls", + :method => "Algorithm::Caret.pls", }, :feature_selection => nil, } @@ -29,17 +25,13 @@ class ModelTest < MiniTest::Test def test_regression_parameters algorithms = { - :descriptors => { - :method => "fingerprint", - :type => "MP2D" - }, + :descriptors => [ "MP2D" ], :similarity => { :method => "Algorithm::Similarity.tanimoto", :min => 0.3 }, :prediction => { :method => "Algorithm::Regression.weighted_average", - :parameters => "rf", }, :feature_selection => nil, } @@ -57,18 +49,22 @@ class ModelTest < MiniTest::Test def test_physchem_regression algorithms = { - :descriptors => "physchem", + :descriptors => ["PhysChem::OPENBABEL"], :similarity => { - :method => "Algorithm::Similarity.weighted_cosine", + :method => "Algorithm::Similarity.cosine", } } training_dataset = Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.mini_log10.csv") model = Model::Lazar.create training_dataset: training_dataset, algorithms: algorithms assert_kind_of Model::LazarRegression, model - assert_equal "Algorithm::Caret.regression", model.algorithms[:prediction][:method] - assert_equal "Algorithm::Similarity.weighted_cosine", model.algorithms[:similarity][:method] + assert_equal "Algorithm::Caret.pls", model.algorithms[:prediction][:method] + assert_equal "Algorithm::Similarity.cosine", model.algorithms[:similarity][:method] assert_equal 0.1, model.algorithms[:similarity][:min] assert_equal algorithms[:descriptors], model.algorithms[:descriptors] + prediction = model.predict training_dataset.substances[10] + p prediction + refute_nil prediction[:value] + # TODO test predictin end def test_nanoparticle_default @@ -78,8 +74,7 @@ class ModelTest < MiniTest::Test training_dataset = Dataset.where(name: "Protein Corona Fingerprinting Predicts the Cellular Interaction of Gold and Silver Nanoparticles").first end model = Model::Lazar.create training_dataset: training_dataset - assert_equal "Algorithm::Caret.regression", model.algorithms[:prediction][:method] - assert_equal "rf", model.algorithms[:prediction][:parameters] + assert_equal "Algorithm::Caret.rf", model.algorithms[:prediction][:method] assert_equal "Algorithm::Similarity.weighted_cosine", model.algorithms[:similarity][:method] prediction = model.predict training_dataset.substances[14] assert_includes prediction[:prediction_interval][0]..prediction[:prediction_interval][1], prediction[:measurements].median, "This assertion assures that measured values are within the prediction interval. It may fail in 5% of the predictions." @@ -99,7 +94,7 @@ class ModelTest < MiniTest::Test training_dataset = Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.mini_log10.csv") model = Model::Lazar.create training_dataset: training_dataset, algorithms: algorithms assert_kind_of Model::LazarRegression, model - assert_equal "Algorithm::Caret.regression", model.algorithms[:prediction][:method] + assert_equal "Algorithm::Caret.pls", model.algorithms[:prediction][:method] assert_equal "Algorithm::Similarity.tanimoto", model.algorithms[:similarity][:method] assert_equal 0.1, model.algorithms[:similarity][:min] assert_equal algorithms[:feature_selection][:method], model.algorithms[:feature_selection][:method] @@ -111,10 +106,7 @@ class ModelTest < MiniTest::Test def test_default_classification algorithms = { - :descriptors => { - :method => "fingerprint", - :type => 'MP2D', - }, + :descriptors => [ "MP2D" ], :similarity => { :method => "Algorithm::Similarity.tanimoto", :min => 0.1 @@ -135,10 +127,7 @@ class ModelTest < MiniTest::Test def test_classification_parameters algorithms = { - :descriptors => { - :method => "fingerprint", - :type => 'MACCS', - }, + :descriptors => ['MACCS'], :similarity => { :min => 0.4 }, |