From 9a06f2ff5ae6bdbe7dc90555599e186f1585e0d2 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Thu, 10 Nov 2016 15:27:26 +0100 Subject: Model::NanoPrediction parameters --- test/model-nanoparticle.rb | 30 +++++++++++++++++ test/nanomaterial-prediction-models.rb | 60 ++++++++++++++++++++++++++++++++++ test/validation-nanoparticle.rb | 19 +++++++++++ 3 files changed, 109 insertions(+) create mode 100644 test/nanomaterial-prediction-models.rb (limited to 'test') diff --git a/test/model-nanoparticle.rb b/test/model-nanoparticle.rb index 88032bc..c5f3223 100644 --- a/test/model-nanoparticle.rb +++ b/test/model-nanoparticle.rb @@ -61,6 +61,36 @@ class NanoparticleModelTest < MiniTest::Test model.delete end + def test_nanoparticle_fingerprint_model_with_feature_selection + assert true, @prediction_feature.measured + algorithms = { + :descriptors => { + :method => "fingerprint", + :type => "MP2D", + }, + :similarity => { + :method => "Algorithm::Similarity.tanimoto", + :min => 0.1 + }, + } + model = Model::Lazar.create training_dataset: @training_dataset, prediction_feature: @prediction_feature, algorithms: algorithms + refute_empty model.algorithms[:feature_selection] + refute_empty model.dependent_variables + refute_empty model.descriptor_ids + refute_empty model.independent_variables + assert_equal "Algorithm::Caret.rf", model.algorithms[:prediction][:method] + assert_equal "Algorithm::Similarity.tanimoto", model.algorithms[:similarity][:method] + nanoparticle = @training_dataset.nanoparticles[-34] + assert_includes nanoparticle.dataset_ids, @training_dataset.id + prediction = model.predict nanoparticle + refute_nil prediction[:value] + 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." + prediction = model.predict @training_dataset.substances[14] + refute_nil prediction[:value] + 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." + model.delete + end + def test_nanoparticle_calculated_properties_model skip "Nanoparticle calculate_properties similarity not yet implemented" assert true, @prediction_feature.measured diff --git a/test/nanomaterial-prediction-models.rb b/test/nanomaterial-prediction-models.rb new file mode 100644 index 0000000..b0c05f3 --- /dev/null +++ b/test/nanomaterial-prediction-models.rb @@ -0,0 +1,60 @@ +require_relative "setup.rb" + +class NanomaterialPredictionModelTest < MiniTest::Test + + def setup + @training_dataset = Dataset.where(:name => "Protein Corona Fingerprinting Predicts the Cellular Interaction of Gold and Silver Nanoparticles").first + unless @training_dataset + Import::Enanomapper.import File.join(File.dirname(__FILE__),"data","enm") + @training_dataset = Dataset.where(name: "Protein Corona Fingerprinting Predicts the Cellular Interaction of Gold and Silver Nanoparticles").first + end + @prediction_feature = @training_dataset.features.select{|f| f["name"] == 'log2(Net cell association)'}.first + end + + def test_default_nanomaterial_prediction_model + prediction_model = Model::NanoPrediction.create + p prediction_model + [:endpoint,:species,:source].each do |p| + refute_empty prediction_model[p] + end + assert prediction_model.regression? + refute prediction_model.classification? + prediction_model.crossvalidations.each do |cv| + refute_nil cv.r_squared + refute_nil cv.rmse + end + nanoparticle = @training_dataset.nanoparticles[-34] + assert_includes nanoparticle.dataset_ids, @training_dataset.id + prediction = prediction_model.predict nanoparticle + refute_nil prediction[:value] + 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." + prediction_model.delete + end + + def test_nanomaterial_prediction_model_parameters + algorithms = { + :descriptors => { + :method => "fingerprint", + :type => "MP2D", + }, + :similarity => { + :method => "Algorithm::Similarity.tanimoto", + :min => 0.1 + }, + :prediction => { :method => "OpenTox::Algorithm::Regression.weighted_average" }, + :feature_selection => nil + } + prediction_model = Model::NanoPrediction.create algorithms: algorithms + assert prediction_model.regression? + refute prediction_model.classification? + prediction_model.crossvalidations.each do |cv| + refute_nil cv.r_squared + refute_nil cv.rmse + end + nanoparticle = @training_dataset.nanoparticles[-34] + assert_includes nanoparticle.dataset_ids, @training_dataset.id + prediction = prediction_model.predict nanoparticle + refute_nil prediction[:value] + 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." + end +end diff --git a/test/validation-nanoparticle.rb b/test/validation-nanoparticle.rb index 7391f21..5ed70f2 100644 --- a/test/validation-nanoparticle.rb +++ b/test/validation-nanoparticle.rb @@ -113,4 +113,23 @@ class NanoparticleValidationTest < MiniTest::Test refute_nil cv.rmse end + def test_nanoparticle_fingerprint_model_with_feature_selection + algorithms = { + :descriptors => { + :method => "fingerprint", + :type => "MP2D", + }, + :similarity => { + :method => "Algorithm::Similarity.tanimoto", + :min => 0.1 + }, + } + model = Model::Lazar.create prediction_feature: @prediction_feature, training_dataset: @training_dataset, algorithms: algorithms + cv = CrossValidation.create model + p cv.rmse + p cv.r_squared + refute_nil cv.r_squared + refute_nil cv.rmse + end + end -- cgit v1.2.3