Experiments added

6 files changed, 44 insertions, 9 deletions

diff --git a/test/dataset.rb b/test/dataset.rb
index 27dba61..b5275d4 100644
--- a/test/dataset.rb
+++ b/test/dataset.rb
@@ -78,7 +78,7 @@ class DatasetTest < MiniTest::Test
     new_dataset = Dataset.find d.id
     # get metadata
     assert_match "multicolumn.csv",  new_dataset.source
-    assert_equal "multicolumn.csv",  new_dataset.title
+    assert_equal "multicolumn.csv",  new_dataset.name
     # get features
     assert_equal 6, new_dataset.features.size
     assert_equal 7, new_dataset.compounds.size
diff --git a/test/experiment.rb b/test/experiment.rb
new file mode 100644
index 0000000..eae7fa0
--- /dev/null
+++ b/test/experiment.rb
@@ -0,0 +1,31 @@
+require_relative "setup.rb"
+
+class ExperimentTest < MiniTest::Test
+
+  def test_regression_experiment
+    datasets = [
+      "EPAFHM.csv",
+      "FDA_v3b_Maximum_Recommended_Daily_Dose_mmol.csv",
+      "LOAEL_log_mmol_corrected_smiles.csv"
+      ]
+    model_algorithms = ["OpenTox::Model::LazarRegression"]
+    neighbor_algorithms = ["OpenTox::Algorithm::Neighbor.fingerprint_similarity"]
+    prediction_algorithms = ["OpenTox::Algorithm::Regression.weighted_average"]
+    neighbor_algorithm_parameters = [{:min_sim => 0.7}]
+    experiment = Experiment.create(
+      :name => "Regression for datasets #{datasets}.",
+      :dataset_ids => datasets.collect{|d| Dataset.from_csv_file(File.join(DATA_DIR, d)).id},
+      :model_algorithms => model_algorithms,
+      :neighbor_algorithms => neighbor_algorithms,
+      :neighbor_algorithm_parameters => neighbor_algorithm_parameters,
+      :prediction_algorithms => prediction_algorithms,
+    )
+    experiment.run
+=begin
+    experiment = Experiment.find "55dc58b32b72ed14a8000008"
+=end
+    p experiment.id
+    experiment.report
+    refute_empty experiment.crossvalidation_ids
+  end
+end
diff --git a/test/lazar-long.rb b/test/lazar-long.rb
index c0deaa2..1b58319 100644
--- a/test/lazar-long.rb
+++ b/test/lazar-long.rb
@@ -29,7 +29,7 @@ class LazarExtendedTest < MiniTest::Test
     feature_dataset = OpenTox::CalculatedDataset.find model.feature_dataset_id
     assert_equal dataset.compounds.size, feature_dataset.compounds.size
     assert_equal 52, feature_dataset.features.size
-    assert_equal '[#17&A]-[#6&A]', feature_dataset.features.first.title
+    assert_equal '[#17&A]-[#6&A]', feature_dataset.features.first.name
     compound = OpenTox::Compound.from_inchi("InChI=1S/C10H9NO2S/c1-8-2-4-9(5-3-8)13-6-10(12)11-7-14/h2-5H,6H2,1H3")
     prediction_dataset = model.predict compound
     prediction = prediction_dataset.data_entries.first
diff --git a/test/lazar-regression.rb b/test/lazar-regression.rb
index c36f521..4062cfd 100644
--- a/test/lazar-regression.rb
+++ b/test/lazar-regression.rb
@@ -12,11 +12,12 @@ class LazarRegressionTest < MiniTest::Test
     assert_equal 1, prediction[:neighbors].size
   end
 
-  def test_weighted_average_with_relevant_fingerprints
+  def test_local_linear_regression
+    skip
     training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv"
     model = Model::LazarRegression.create training_dataset
-    model.update(:prediction_algorithm => "OpenTox::Algorithm::Regression.weighted_average_with_relevant_fingerprints")
-    compound = Compound.from_smiles "CC(C)(C)CN"
+    model.update(:prediction_algorithm => "OpenTox::Algorithm::Regression.local_linear_regression")
+    compound = Compound.from_smiles "NC(=O)OCCC"
     prediction = model.predict compound
     p prediction
     #assert_equal 13.6, prediction[:value].round(1)
diff --git a/test/setup.rb b/test/setup.rb
index 538853d..3dad683 100644
--- a/test/setup.rb
+++ b/test/setup.rb
@@ -3,5 +3,5 @@ require_relative '../lib/lazar.rb'
 include OpenTox
 TEST_DIR ||= File.expand_path(File.dirname(__FILE__))
 DATA_DIR ||= File.join(TEST_DIR,"data")
-$mongo.database.drop
-$gridfs = $mongo.database.fs # recreate GridFS indexes
+#$mongo.database.drop
+#$gridfs = $mongo.database.fs # recreate GridFS indexes
diff --git a/test/validation.rb b/test/validation.rb
index 485769c..009c337 100644
--- a/test/validation.rb
+++ b/test/validation.rb
@@ -24,8 +24,8 @@ class ValidationTest < MiniTest::Test
   end
 
   def test_regression_crossvalidation
-    dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv"
-    #dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.csv"
+    #dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv"
+    dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.csv"
     model = Model::LazarRegression.create dataset
     cv = RegressionCrossValidation.create model
     p cv.rmse 
@@ -33,6 +33,9 @@ class ValidationTest < MiniTest::Test
     p cv.mae
     p cv.weighted_mae
     #`inkview #{cv.plot}`
+    #puts JSON.pretty_generate(cv.misclassifications)#.collect{|l| l.join ", "}.join "\n"
+    p cv.misclassifications.collect{|l| l[:neighbors].size}
+    `inkview #{cv.plot}`
     assert cv.rmse < 30, "RMSE > 30"
     assert cv.weighted_rmse < cv.rmse, "Weighted RMSE (#{cv.weighted_rmse}) larger than unweighted RMSE(#{cv.rmse}) "
     assert cv.mae < 12