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authorChristoph Helma <helma@in-silico.ch>2016-02-29 14:11:30 +0100
committerChristoph Helma <helma@in-silico.ch>2016-02-29 14:11:30 +0100
commit003332ad95dd4c63d0b7c00d22c73f460b163139 (patch)
tree5d0e442e3ccbebd9623a089812989682afb42631 /test/lazar-regression.rb
parentc4b56b22fd6e65633deb7e52bd99865e3bee8f00 (diff)
modular regression algorithms
Diffstat (limited to 'test/lazar-regression.rb')
-rw-r--r--test/lazar-regression.rb51
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diff --git a/test/lazar-regression.rb b/test/lazar-regression.rb
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-require_relative "setup.rb"
-
-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.weighted_average"}
- compound = Compound.from_smiles "CC(C)(C)CN"
- prediction = model.predict compound
- assert_equal 7.2, prediction[:value].round(1)
- assert_equal 88, prediction[:neighbors].size
- end
-
- def test_mpd_fingerprints
- training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv"
- model = Model::LazarRegression.create training_dataset
- 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 3, prediction[:neighbors].size
- end
-
- def test_local_pls_regression
- training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv"
- model = Model::LazarRegression.create training_dataset
- compound = Compound.from_smiles "NC(=O)OCCC"
- prediction = model.predict compound
- p prediction
- model.update(:prediction_algorithm => "OpenTox::Algorithm::Regression.local_pls_regression")
- prediction = model.predict compound
- p prediction
- #assert_equal 13.6, prediction[:value].round(1)
- #assert_equal 0.83, prediction[:confidence].round(2)
- #assert_equal 1, prediction[:neighbors].size
- end
-
- 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")
- compound = Compound.from_smiles "NC(=O)OCCC"
- prediction = model.predict compound
- model.update(:prediction_algorithm => "OpenTox::Algorithm::Regression.local_pls_regression")
- prediction = model.predict compound
- # TODO assertions
- #assert_equal 13.6, prediction[:value].round(1)
- #assert_equal 0.83, prediction[:confidence].round(2)
- #assert_equal 1, prediction[:neighbors].size
- end
-
-end