From 355f2f97e3323ba8b60109e6c9524ef1f692ea1a Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Fri, 27 May 2011 09:40:39 +0200
Subject: Added prop models

---
 lazar.rb | 48 +++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 47 insertions(+), 1 deletion(-)

(limited to 'lazar.rb')

diff --git a/lazar.rb b/lazar.rb
index a8b8de9..a88801d 100644
--- a/lazar.rb
+++ b/lazar.rb
@@ -25,7 +25,7 @@ class LazarTest < Test::Unit::TestCase
 =end
   def test_create_regression_model
     model_uri = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => @@regression_training_dataset.uri, :subjectid => @@subjectid}).to_s
-    puts model_uri
+    #puts model_uri
     validate_owl model_uri,@@subjectid
     lazar = OpenTox::Model::Lazar.find model_uri, @@subjectid
     @models << lazar
@@ -41,6 +41,24 @@ class LazarTest < Test::Unit::TestCase
     assert_equal prediction.neighbors(compound).size, 61
   end
 
+  def test_create_regression_prop_model
+    model_uri = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => @@regression_training_dataset.uri, :subjectid => @@subjectid, :local_svm_kernel => "propositionalized"}).to_s
+    #puts model_uri
+    validate_owl model_uri,@@subjectid
+    lazar = OpenTox::Model::Lazar.find model_uri, @@subjectid
+    @models << lazar
+    assert_equal 219, lazar.features.size
+    compound = OpenTox::Compound.from_smiles("c1ccccc1NN")
+    prediction_uri = lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid).to_s
+    prediction = OpenTox::LazarPrediction.find(prediction_uri, @@subjectid)
+    @predictions << prediction
+    assert_equal prediction.value(compound).round_to(1),0.1.round_to(1)
+    assert_equal prediction.confidence(compound).round_to(3), 0.276.round_to(3)
+    #assert_equal prediction.value(compound).round_to(4), 0.2847.round_to(4)
+    #assert_equal prediction.confidence(compound).round_to(4), 0.3223.round_to(4)
+    assert_equal prediction.neighbors(compound).size, 61
+  end
+
   def test_classification_model
 
     # create model
@@ -96,6 +114,34 @@ class LazarTest < Test::Unit::TestCase
     assert_equal prediction.confidence(compound).round_to(4), 0.4131.round_to(4)
     assert_equal prediction.neighbors(compound).size, 14
 
+    # dataset prediction
+    test_dataset = OpenTox::Dataset.create_from_csv_file("data/multicolumn.csv", @@subjectid)
+    prediction = OpenTox::LazarPrediction.find lazar.run(:dataset_uri => test_dataset.uri, :subjectid => @@subjectid), @@subjectid
+    @predictions << prediction
+    assert_equal prediction.compounds.size, 4
+    compound = OpenTox::Compound.from_smiles "CC(=Nc1ccc2c(c1)Cc1ccccc21)O"
+    assert_equal prediction.value(compound), nil
+    assert_equal prediction.measured_activities(compound).first, true
+ end
+
+  def test_classification_svm_prop_model
+
+
+    # create model
+    model_uri = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => @@classification_training_dataset.uri, :subjectid => @@subjectid, :prediction_algorithm => "local_svm_classification", :local_svm_kernel => "propositionalized"}).to_s
+    lazar = OpenTox::Model::Lazar.find model_uri, @@subjectid
+    @models << lazar
+    assert_equal lazar.features.size, 52
+
+    # single prediction
+    compound = OpenTox::Compound.from_smiles("c1ccccc1NN")
+    prediction_uri = lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid)
+    prediction = OpenTox::LazarPrediction.find(prediction_uri, @@subjectid)
+    @predictions << prediction
+    assert_equal prediction.value(compound), false
+    assert_equal prediction.confidence(compound).round_to(4), 0.4131.round_to(4)
+    assert_equal prediction.neighbors(compound).size, 14
+
     # dataset prediction
     test_dataset = OpenTox::Dataset.create_from_csv_file("data/multicolumn.csv", @@subjectid)
     prediction = OpenTox::LazarPrediction.find lazar.run(:dataset_uri => test_dataset.uri, :subjectid => @@subjectid), @@subjectid
-- 
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