From 2dc66aef3b7932105868ee8c7d32ad975e142d1b Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Thu, 13 Oct 2016 19:48:21 +0200
Subject: compound tests fixed

---
 test/validation-classification.rb | 63 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100644 test/validation-classification.rb

(limited to 'test/validation-classification.rb')

diff --git a/test/validation-classification.rb b/test/validation-classification.rb
new file mode 100644
index 0000000..b71e427
--- /dev/null
+++ b/test/validation-classification.rb
@@ -0,0 +1,63 @@
+require_relative "setup.rb"
+
+class ValidationClassificationTest < MiniTest::Test
+  include OpenTox::Validation
+
+  # defaults
+  
+  def test_default_classification_crossvalidation
+    dataset = Dataset.from_csv_file "#{DATA_DIR}/hamster_carcinogenicity.csv"
+    model = Model::Lazar.create training_dataset: dataset
+    cv = ClassificationCrossValidation.create model
+    assert cv.accuracy > 0.7, "Accuracy (#{cv.accuracy}) should be larger than 0.7, this may occur due to an unfavorable training/test set split"
+    assert cv.weighted_accuracy > cv.accuracy, "Weighted accuracy (#{cv.weighted_accuracy}) should be larger than accuracy (#{cv.accuracy})."
+  end
+
+  # parameters
+
+  def test_classification_crossvalidation_parameters
+    dataset = Dataset.from_csv_file "#{DATA_DIR}/hamster_carcinogenicity.csv"
+    algorithms = {
+      :similarity => { :min => 0.3, },
+      :descriptors => { :type => "FP3" }
+    }
+    model = Model::Lazar.create training_dataset: dataset, algorithms: algorithms
+    cv = ClassificationCrossValidation.create model
+    params = model.algorithms
+    params = Hash[params.map{ |k, v| [k.to_s, v] }] # convert symbols to string
+    
+    cv.validations.each do |validation|
+      validation_params = validation.model.algorithms
+      refute_nil model.training_dataset_id
+      refute_nil validation.model.training_dataset_id
+      refute_equal model.training_dataset_id, validation.model.training_dataset_id
+      ["min_sim","type","prediction_feature_id"].each do |k|
+        assert_equal params[k], validation_params[k]
+      end
+    end
+  end
+  
+  # LOO
+
+  def test_classification_loo_validation
+    dataset = Dataset.from_csv_file "#{DATA_DIR}/hamster_carcinogenicity.csv"
+    model = Model::Lazar.create training_dataset: dataset
+    loo = ClassificationLeaveOneOut.create model
+    assert_equal 14, loo.nr_unpredicted
+    refute_empty loo.confusion_matrix
+    assert loo.accuracy > 0.77
+    assert loo.weighted_accuracy > loo.accuracy, "Weighted accuracy (#{loo.weighted_accuracy}) should be larger than accuracy (#{loo.accuracy})."
+  end
+
+  # repeated CV
+
+  def test_repeated_crossvalidation
+    dataset = Dataset.from_csv_file "#{DATA_DIR}/hamster_carcinogenicity.csv"
+    model = Model::Lazar.create training_dataset: dataset
+    repeated_cv = RepeatedCrossValidation.create model
+    repeated_cv.crossvalidations.each do |cv|
+      assert_operator cv.accuracy, :>, 0.7, "model accuracy < 0.7, this may happen by chance due to an unfavorable training/test set split"
+    end
+  end
+
+end
-- 
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