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author | helma@in-silico.ch <helma@in-silico.ch> | 2018-11-16 18:42:42 +0100 |
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committer | helma@in-silico.ch <helma@in-silico.ch> | 2018-11-16 18:42:42 +0100 |
commit | 0882c2cd0de934d7377fc9d08c306be98612c88a (patch) | |
tree | 683da6042a5cc4d1786c79fa94d02111ca4af67a /test/regression-validation.rb | |
parent | 7e547fd4a296f497615a7805d565b378cb1bd7cd (diff) |
real datasets for testing, test data cleanup, Daphnia import, upper and lower similarity thresholds
Diffstat (limited to 'test/regression-validation.rb')
-rw-r--r-- | test/regression-validation.rb | 9 |
1 files changed, 5 insertions, 4 deletions
diff --git a/test/regression-validation.rb b/test/regression-validation.rb index afa4278..7dbe354 100644 --- a/test/regression-validation.rb +++ b/test/regression-validation.rb @@ -6,7 +6,8 @@ class RegressionValidationTest < MiniTest::Test # defaults def test_default_regression_crossvalidation - dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM_log10.csv" + training_dataset = Dataset.from_csv_file File.join(Download::DATA, "Acute_toxicity-Fathead_minnow.csv") + dataset = Dataset.from_csv_file File.join(Download::DATA, "Acute_toxicity-Fathead_minnow.csv") model = Model::Lazar.create training_dataset: dataset cv = RegressionCrossValidation.create model assert cv.rmse[:all] < 1.5, "RMSE #{cv.rmse[:all]} should be smaller than 1.5, this may occur due to unfavorable training/test set splits" @@ -21,7 +22,7 @@ class RegressionValidationTest < MiniTest::Test algorithms = { :prediction => { :method => "OpenTox::Algorithm::Regression.weighted_average" }, :descriptors => { :type => "MACCS", }, - :similarity => {:min => 0.7} + :similarity => {:min => [0.9,0.1]} } model = Model::Lazar.create training_dataset: dataset, algorithms: algorithms assert_equal algorithms[:descriptors][:type], model.algorithms[:descriptors][:type] @@ -64,7 +65,7 @@ class RegressionValidationTest < MiniTest::Test }, :similarity => { :method => "Algorithm::Similarity.weighted_cosine", - :min => 0.5 + :min => [0.5,0.1] }, :feature_selection => { :method => "Algorithm::FeatureSelection.correlation_filter", @@ -83,7 +84,7 @@ class RegressionValidationTest < MiniTest::Test model = Model::Lazar.create training_dataset: dataset repeated_cv = RepeatedCrossValidation.create model repeated_cv.crossvalidations.each do |cv| - assert cv.r_squared[:all] > 0.34, "R^2 (#{cv.r_squared[:all]}) should be larger than 0.034" + assert cv.r_squared[:all] > 0.34, "R^2 (#{cv.r_squared[:all]}) should be larger than 0.34" assert cv.rmse[:all] < 1.5, "RMSE (#{cv.rmse[:all]}) should be smaller than 0.5" end end |