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authorhelma@in-silico.ch <helma@in-silico.ch>2018-11-16 18:42:42 +0100
committerhelma@in-silico.ch <helma@in-silico.ch>2018-11-16 18:42:42 +0100
commit0882c2cd0de934d7377fc9d08c306be98612c88a (patch)
tree683da6042a5cc4d1786c79fa94d02111ca4af67a /test/regression-validation.rb
parent7e547fd4a296f497615a7805d565b378cb1bd7cd (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.rb9
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