From 9d17895ab9e8cd31e0f32e8e622e13612ea5ff77 Mon Sep 17 00:00:00 2001
From: "helma@in-silico.ch" <helma@in-silico.ch>
Date: Fri, 12 Oct 2018 21:58:36 +0200
Subject: validation statistic fixes

---
 test/nanomaterial-model-validation.rb~ | 54 ++++++++++++++++++++++++++++++++++
 1 file changed, 54 insertions(+)
 create mode 100644 test/nanomaterial-model-validation.rb~

(limited to 'test/nanomaterial-model-validation.rb~')

diff --git a/test/nanomaterial-model-validation.rb~ b/test/nanomaterial-model-validation.rb~
new file mode 100644
index 0000000..9eaa17d
--- /dev/null
+++ b/test/nanomaterial-model-validation.rb~
@@ -0,0 +1,54 @@
+require_relative "setup.rb"
+
+class NanomaterialValidationModelTest < MiniTest::Test
+
+  def setup
+    @training_dataset = Dataset.where(:name => "Protein Corona Fingerprinting Predicts the Cellular Interaction of Gold and Silver Nanoparticles").first
+    @prediction_feature = @training_dataset.features.select{|f| f["name"] == 'log2(Net cell association)'}.first
+  end
+
+  def test_default_nanomaterial_validation_model
+    validation_model = Model::Validation.from_enanomapper
+    [:endpoint,:species,:source].each do |p|
+      refute_empty validation_model[p]
+    end
+    assert validation_model.regression?
+    refute validation_model.classification?
+    validation_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 = validation_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."
+    validation_model.delete
+  end
+
+  def test_nanomaterial_validation_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
+    }
+    validation_model = Model::Validation.from_enanomapper algorithms: algorithms
+    assert validation_model.regression?
+    refute validation_model.classification?
+    validation_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 = validation_model.predict nanoparticle
+    refute_nil prediction[:value]
+  end
+end
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