validation statistic fixes

1 files changed, 0 insertions, 91 deletions

diff --git a/test/validation-regression.rb b/test/validation-regression.rb
deleted file mode 100644
index 0328c88..0000000
--- a/test/validation-regression.rb
+++ /dev/null
@@ -1,91 +0,0 @@
-require_relative "setup.rb"
-
-class ValidationRegressionTest < MiniTest::Test
-  include OpenTox::Validation
-
-  # defaults
-  
-  def test_default_regression_crossvalidation
-    dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi_log10.csv"
-    model = Model::Lazar.create training_dataset: dataset
-    cv = RegressionCrossValidation.create model
-    assert cv.rmse < 1.5, "RMSE #{cv.rmse} should be smaller than 1.5, this may occur due to unfavorable training/test set splits"
-    assert cv.mae < 1.1, "MAE #{cv.mae} should be smaller than 1.1, this may occur due to unfavorable training/test set splits"
-    assert cv.percent_within_prediction_interval > 80, "Only #{cv.percent_within_prediction_interval.round(2)}% of measurement within prediction interval. This may occur due to unfavorable training/test set splits"
-  end
-
-  # parameters
-  
-  def test_regression_crossvalidation_params
-    dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi_log10.csv"
-    algorithms = {
-      :prediction => { :method => "OpenTox::Algorithm::Regression.weighted_average" },
-      :descriptors => { :type => "MACCS", },
-      :similarity => {:min => 0.7}
-    }
-    model = Model::Lazar.create training_dataset: dataset, algorithms: algorithms
-    assert_equal algorithms[:descriptors][:type], model.algorithms[:descriptors][:type]
-    cv = RegressionCrossValidation.create model
-    cv.validation_ids.each do |vid|
-      model = Model::Lazar.find(Validation.find(vid).model_id)
-      assert_equal algorithms[:descriptors][:type], model.algorithms[:descriptors][:type]
-      assert_equal algorithms[:similarity][:min], model.algorithms[:similarity][:min]
-      refute_nil model.training_dataset_id
-      refute_equal dataset.id, model.training_dataset_id
-    end
-
-    refute_nil cv.rmse
-    refute_nil cv.mae 
-  end
-
-  def test_physchem_regression_crossvalidation
-    training_dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.medi_log10.csv")
-    model = Model::Lazar.create training_dataset:training_dataset
-    cv = RegressionCrossValidation.create model
-    refute_nil cv.rmse
-    refute_nil cv.mae 
-  end
-
-  # LOO
-
-  def test_regression_loo_validation
-    dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.medi_log10.csv")
-    model = Model::Lazar.create training_dataset: dataset
-    loo = RegressionLeaveOneOut.create model
-    assert loo.r_squared > 0.34, "R^2 (#{loo.r_squared}) should be larger than 0.034"
-  end
-
-  def test_regression_loo_validation_with_feature_selection
-    dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.medi_log10.csv")
-    algorithms = {
-      :descriptors => {
-        :method => "calculate_properties",
-        :features => PhysChem.openbabel_descriptors,
-      },
-      :similarity => {
-        :method => "Algorithm::Similarity.weighted_cosine",
-        :min => 0.5
-      },
-      :feature_selection => {
-        :method => "Algorithm::FeatureSelection.correlation_filter",
-      },
-    }
-    model = Model::Lazar.create training_dataset: dataset, algorithms: algorithms
-    assert_raises OpenTox::BadRequestError do
-      loo = RegressionLeaveOneOut.create model
-    end
-  end
-
-  # repeated CV
-
-  def test_repeated_crossvalidation
-    dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.medi_log10.csv")
-    model = Model::Lazar.create training_dataset: dataset
-    repeated_cv = RepeatedCrossValidation.create model
-    repeated_cv.crossvalidations.each do |cv|
-      assert cv.r_squared > 0.34, "R^2 (#{cv.r_squared}) should be larger than 0.034"
-      assert cv.rmse < 1.5, "RMSE (#{cv.rmse}) should be smaller than 0.5"
-    end
-  end
-
-end