lazar 0.0.7 → 0.0.9

data/test/lazar-long.rb

@@ -3,37 +3,40 @@ require_relative "setup.rb"
 class LazarExtendedTest < MiniTest::Test
 
   def test_lazar_bbrc_ham_minfreq
+    skip
     dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"hamster_carcinogenicity.csv")
-    model = OpenTox::Model::Lazar.create dataset, OpenTox::Algorithm::Fminer.bbrc(dataset, :min_frequency => 5)
-    feature_dataset = OpenTox::Dataset.find model.feature_dataset_id
+    model = Model::LazarFminerClassification.create(dataset, :min_frequency => 5)
+    feature_dataset = Dataset.find model.neighbor_algorithm_parameters[:feature_dataset_id]
     assert_equal dataset.compounds.size, feature_dataset.compounds.size
-    assert_equal 41, feature_dataset.features.size
-    assert_equal 'N-C=N', feature_dataset.features.first.smarts
+    assert_equal model.feature_calculation_parameters, {"min_frequency"=>5}
+    #TODO check frequencies, features and confidence
+    #assert_equal 41, feature_dataset.features.size
+    #assert_equal 'N-C=N', feature_dataset.features.first.smarts
     compound = OpenTox::Compound.from_inchi("InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H")
     prediction = model.predict compound
     assert_equal "false", prediction[:value]
-    assert_equal 0.12380952380952381, prediction[:confidence]
+    #assert_equal 0.12380952380952381, prediction[:confidence]
     dataset.delete
     model.delete
     feature_dataset.delete
   end
 
   def test_lazar_bbrc_large_ds
-    # TODO fminer crashes with these settings
-    skip "it seems that fminer aborts without further notice"
+    skip
     dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"multi_cell_call_no_dup.csv")
-    feature_dataset = OpenTox::Algorithm::Fminer.bbrc dataset#, :min_frequency => 15)
-    model = OpenTox::Model::Lazar.create dataset, feature_dataset
+    model = Model::LazarFminerClassification.create dataset
+    feature_dataset = Dataset.find model.neighbor_algorithm_parameters[:feature_dataset_id]
     model.save
     p model.id
-    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 52, feature_dataset.features.size
+    #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
-    assert_in_delta 0.025, prediction[:confidence], 0.001
+    prediction = model.predict compound
+    assert_equal "1", prediction[:value]
+    #p prediction
+    #prediction = prediction_dataset.data_entries.first
+    #assert_in_delta 0.025, prediction[:confidence], 0.001
     #assert_equal 0.025885845574483608, prediction[:confidence]
     # with compound change in training_dataset see:
     # https://github.com/opentox/opentox-test/commit/0e78c9c59d087adbd4cc58bab60fb29cbe0c1da0
@@ -41,32 +44,49 @@ class LazarExtendedTest < MiniTest::Test
     dataset.delete
     model.delete
     feature_dataset.delete
-    prediction_dataset.delete
   end
 
-  def test_lazar_kazius
+  def test_lazar_fminer_kazius
+    skip
     t = Time.now
     dataset = Dataset.from_csv_file File.join(DATA_DIR,"kazius.csv")
     p "Dataset upload: #{Time.now-t}"
     t = Time.now
-    feature_dataset = Algorithm::Fminer.bbrc(dataset, :min_frequency => 100)
+    model = Model::LazarFminerClassification.create(dataset, :min_frequency => 100)
     p "Feature mining: #{Time.now-t}"
     t = Time.now
+    feature_dataset = Dataset.find model.neighbor_algorithm_parameters[:feature_dataset_id]
     assert_equal feature_dataset.compounds.size, dataset.compounds.size
-    model = Model::Lazar.create dataset, feature_dataset
-=begin
-=end
     #model = Model::Lazar.find('55bcf5bf7a7838381200017e')
     #p model.id
     #prediction_times = []
     2.times do
       compound = Compound.from_smiles("Clc1ccccc1NN")
       prediction = model.predict compound
-      assert_equal "1", prediction[:value]
-      assert_in_delta 0.019858401199860445, prediction[:confidence], 0.001
+      p prediction
+      #assert_equal "1", prediction[:value]
+      #assert_in_delta 0.019858401199860445, prediction[:confidence], 0.001
     end
     #dataset.delete
     #feature_dataset.delete
   end
 
+  def test_lazar_kazius
+    t = Time.now
+    dataset = Dataset.from_csv_file File.join(DATA_DIR,"kazius.csv")
+    p "Dataset upload: #{Time.now-t}"
+    t = Time.now
+    model = Model::LazarClassification.create(dataset)
+    p "Feature mining: #{Time.now-t}"
+    t = Time.now
+    2.times do
+      compound = Compound.from_smiles("Clc1ccccc1NN")
+      prediction = model.predict compound
+      #p prediction
+      assert_equal "1", prediction[:value]
+      #assert_in_delta 0.019858401199860445, prediction[:confidence], 0.001
+    end
+    dataset.delete
+  end
+
 end

data/test/lazar-physchem-short.rb

@@ -2,27 +2,30 @@ require_relative "setup.rb"
 
 class LazarPhyschemDescriptorTest < MiniTest::Test
   def test_epafhm
-    skip "Physchem Regression not yet implemented."
-    # check available descriptors
-    @descriptors = OpenTox::Algorithm::Descriptor::DESCRIPTORS.keys
-    assert_equal 111,@descriptors.size,"wrong number of physchem descriptors"
-    @descriptor_values = OpenTox::Algorithm::Descriptor::DESCRIPTOR_VALUES
 
-    # select descriptors for test
-    @num_features_offset = 0
-    @descriptors.keep_if{|x| x=~/^Openbabel\./}
-    @descriptors.delete("Openbabel.L5") # TODO Openbabel.L5 does not work, investigate!!!
-    puts "Descriptors: #{@descriptors}"
+    skip
+    @descriptors = OpenTox::Algorithm::Descriptor::OBDESCRIPTORS.keys
+    refute_empty @descriptors
 
     # UPLOAD DATA
     training_dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.medi.csv")
-    puts "Dataset: "+training_dataset.id
-#    feature_dataset = Algorithm::Descriptor.physchem training_dataset, @descriptors
-    model = Model::LazarRegression.create training_dataset#, feature_dataset
-    #p model
+    feature_dataset = Algorithm::Descriptor.physchem training_dataset, @descriptors
+    scaled_feature_dataset = feature_dataset.scale
+    model = Model::LazarRegression.create training_dataset
+    model.neighbor_algorithm = "physchem_neighbors"
+    model.neighbor_algorithm_parameters = {
+      :feature_calculation_algorithm => "OpenTox::Algorithm::Descriptor.physchem",
+      :descriptors => @descriptors,
+      :feature_dataset_id => scaled_feature_dataset.id,
+      :min_sim => 0.3
+    }
+    model.save
     compound = Compound.from_smiles "CC(C)(C)CN"
     prediction = model.predict compound
-    p prediction
-
+    refute_nil prediction[:value]
+    refute_nil prediction[:confidence]
+    prediction[:neighbors].each do |line|
+      assert_operator line[1], :>, 0.3
+    end
   end
 end

data/test/prediction_models.rb

@@ -0,0 +1,20 @@
+require_relative "setup.rb"
+
+class PredictionModelTest < MiniTest::Test
+
+  def test_prediction_model
+    pm = Model::Prediction.from_csv_file "#{DATA_DIR}/hamster_carcinogenicity.csv"
+    [:endpoint,:species,:source].each do |p|
+      refute_empty pm[p]
+    end
+    assert pm.classification?
+    refute pm.regression?
+    pm.crossvalidations.each do |cv|
+      p cv
+      assert cv.accuracy > 0.74, "Crossvalidation accuracy (#{cv.accuracy}) should be larger than 0.75. This may happen due to an unfavorable training/test set split."
+    end
+    prediction = pm.predict Compound.from_smiles("CCCC(NN)C")
+    assert_equal "true", prediction[:value]
+    pm.delete
+  end
+end

data/test/regression.rb

@@ -0,0 +1,43 @@
+require_relative "setup.rb"
+
+class LazarRegressionTest < MiniTest::Test
+
+  def test_weighted_average
+    training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv"
+    model = Model::LazarRegression.create training_dataset, {:neighbor_algorithm_parameters => {:min_sim => 0}, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_weighted_average"}
+    compound = Compound.from_smiles "CC(C)(C)CN"
+    prediction = model.predict compound
+    assert_equal 7.2, prediction[:value].round(1)
+    assert_equal 88, prediction[:neighbors].size
+  end
+
+  def test_mpd_fingerprints
+    training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv"
+    model = Model::LazarRegression.create training_dataset
+    model.neighbor_algorithm_parameters[:type] = "MP2D"
+    compound = Compound.from_smiles "CCCSCCSCC"
+    prediction = model.predict compound
+    assert_equal 0.04, prediction[:value].round(2)
+    assert_equal 3, prediction[:neighbors].size
+  end
+
+  def test_local_fingerprint_regression
+    training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv"
+    model = Model::LazarRegression.create(training_dataset, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_fingerprint_regression")
+    compound = Compound.from_smiles "NC(=O)OCCC"
+    prediction = model.predict compound
+    p prediction
+    refute_nil prediction[:value]
+    refute_nil prediction[:prediction_interval]
+    refute_empty prediction[:neighbors]
+  end
+
+  def test_local_physchem_regression
+    training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv"
+    model = Model::LazarRegression.create(training_dataset, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_physchem_regression")
+    compound = Compound.from_smiles "NC(=O)OCCC"
+    prediction = model.predict compound
+    refute_nil prediction[:value]
+  end
+
+end

data/test/setup.rb

@@ -1,6 +1,8 @@
+ENV["LAZAR_ENV"] = "development"
 require 'minitest/autorun'
 require_relative '../lib/lazar.rb'
 include OpenTox
 TEST_DIR ||= File.expand_path(File.dirname(__FILE__))
 DATA_DIR ||= File.join(TEST_DIR,"data")
-#$mongo.database.drop
+$mongo.database.drop
+$gridfs = $mongo.database.fs

data/test/test_environment.rb

@@ -0,0 +1,10 @@
+require_relative "setup.rb"
+
+class EnvironmentTest < MiniTest::Test
+  def test_lazar_environment
+    assert_equal "development", ENV["LAZAR_ENV"]
+    assert_equal "development", ENV["MONGOID_ENV"]
+    assert_equal "development", ENV["RACK_ENV"]
+    assert_equal "development", Mongoid.clients["default"]["database"]
+  end
+end

data/test/validation.rb

@@ -2,41 +2,107 @@ require_relative "setup.rb"
 
 class ValidationTest < MiniTest::Test
 
-  def test_fminer_crossvalidation
+  # defaults
+  
+  def test_default_classification_crossvalidation
     dataset = Dataset.from_csv_file "#{DATA_DIR}/hamster_carcinogenicity.csv"
-    model = Model::LazarFminerClassification.create dataset
+    model = Model::LazarClassification.create dataset
     cv = ClassificationCrossValidation.create model
-    p cv.accuracy
-    p cv.weighted_accuracy
-    refute_empty cv.validation_ids
-    assert cv.accuracy > 0.8
-    assert cv.weighted_accuracy > cv.accuracy, "Weighted accuracy (#{cv.weighted_accuracy}) larger than unweighted accuracy(#{cv.accuracy}) "
+    assert cv.accuracy > 0.7, "Accuracy (#{cv.accuracy}) should be larger than 0.7"
   end
 
-  def test_classification_crossvalidation
+  def test_default_regression_crossvalidation
+    dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv"
+    model = Model::LazarRegression.create dataset
+    cv = RegressionCrossValidation.create model
+    assert cv.rmse < 1.5, "RMSE > 1.5"
+    assert cv.mae < 1
+  end
+
+  # parameters
+
+  def test_classification_crossvalidation_parameters
     dataset = Dataset.from_csv_file "#{DATA_DIR}/hamster_carcinogenicity.csv"
-    model = Model::LazarClassification.create dataset#, features
+    params = {
+        :training_dataset_id => dataset.id,
+      :neighbor_algorithm_parameters => {
+        :min_sim => 0.3,
+        :type => "FP3"
+      }
+    }
+    model = Model::LazarClassification.create dataset, params
+    model.save
     cv = ClassificationCrossValidation.create model
-    p cv.accuracy
-    p cv.weighted_accuracy
-    assert cv.accuracy > 0.7
-    assert cv.weighted_accuracy > cv.accuracy, "Weighted accuracy should be larger than unweighted accuracy."
-  end
+    params = model.neighbor_algorithm_parameters
+    params.delete :training_dataset_id
+    params = Hash[params.map{ |k, v| [k.to_s, v] }] # convert symbols to string
 
-  def test_regression_crossvalidation
+    cv.validations.each do |validation|
+      validation_params = validation.model.neighbor_algorithm_parameters
+      validation_params.delete "training_dataset_id"
+      assert_equal params, validation_params
+    end
+  end
+  
+  def test_regression_crossvalidation_params
     dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv"
-    #dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.csv"
-    model = Model::LazarRegression.create dataset
+    params = {
+      :prediction_algorithm => "OpenTox::Algorithm::Regression.local_weighted_average",
+      :neighbor_algorithm => "fingerprint_neighbors",
+      :neighbor_algorithm_parameters => {
+        :type => "MACCS",
+        :min_sim => 0.7,
+      }
+    }
+    model = Model::LazarRegression.create dataset, params
     cv = RegressionCrossValidation.create model
-    p cv.rmse 
-    p cv.weighted_rmse
-    p cv.mae
-    p cv.weighted_mae
-    #`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
-    assert cv.weighted_mae < cv.mae
+    cv.validation_ids.each do |vid|
+      model = Model::Lazar.find(Validation.find(vid).model_id)
+      assert_equal params[:neighbor_algorithm_parameters][:type], model[:neighbor_algorithm_parameters][:type]
+      assert_equal params[:neighbor_algorithm_parameters][:min_sim], model[:neighbor_algorithm_parameters][:min_sim]
+      refute_equal params[:neighbor_algorithm_parameters][:training_dataset_id], model[:neighbor_algorithm_parameters][:training_dataset_id]
+    end
+
+    refute_nil cv.rmse
+    refute_nil cv.mae 
+  end
+
+  def test_physchem_regression_crossvalidation
+
+    training_dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.medi.csv")
+    model = Model::LazarRegression.create(training_dataset, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_physchem_regression")
+    cv = RegressionCrossValidation.create model
+    refute_nil cv.rmse
+    refute_nil cv.mae 
+  end
+
+  # LOO
+
+  def test_classification_loo_validation
+    dataset = Dataset.from_csv_file "#{DATA_DIR}/hamster_carcinogenicity.csv"
+    model = Model::LazarClassification.create dataset
+    loo = ClassificationLeaveOneOutValidation.create model
+    assert_equal 14, loo.nr_unpredicted
+    refute_empty loo.confusion_matrix
+    assert loo.accuracy > 0.77
+  end
+
+  def test_regression_loo_validation
+    dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.medi.csv")
+    model = Model::LazarRegression.create dataset
+    loo = RegressionLeaveOneOutValidation.create model
+    assert loo.r_squared > 0.34
+  end
+
+  # repeated CV
+
+  def test_repeated_crossvalidation
+    dataset = Dataset.from_csv_file "#{DATA_DIR}/hamster_carcinogenicity.csv"
+    model = Model::LazarClassification.create 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

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: lazar
 version: !ruby/object:Gem::Version
-  version: 0.0.7
+  version: 0.0.9
 platform: ruby
 authors:
 - Christoph Helma, Martin Guetlein, Andreas Maunz, Micha Rautenberg, David Vorgrimmler,
@@ -9,78 +9,92 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-08-20 00:00:00.000000000 Z
+date: 2016-03-31 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '1.11'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '1.11'
 - !ruby/object:Gem::Dependency
   name: rest-client
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '1.8'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '1.8'
 - !ruby/object:Gem::Dependency
   name: nokogiri
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '1.6'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '1.6'
 - !ruby/object:Gem::Dependency
   name: rserve-client
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.3'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.3'
 - !ruby/object:Gem::Dependency
   name: mongoid
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 5.0beta
+        version: '5.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.0'
+- !ruby/object:Gem::Dependency
+  name: openbabel> 2.3.2.2
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 5.0beta
+        version: '0'
 description: Libraries for lazy structure-activity relationships and read-across.
 email:
 - helma@in-silico.ch
@@ -98,6 +112,7 @@ files:
 - VERSION
 - ext/lazar/Makefile
 - ext/lazar/extconf.rb
+- ext/lazar/rinstall.R
 - java/CdkDescriptorInfo.class
 - java/CdkDescriptorInfo.java
 - java/CdkDescriptors.class
@@ -112,28 +127,26 @@ files:
 - java/joelib2.jar
 - java/log4j.jar
 - lazar.gemspec
-- lib/SMARTS_InteLigand.txt
 - lib/algorithm.rb
-- lib/bbrc.rb
 - lib/classification.rb
 - lib/compound.rb
 - lib/crossvalidation.rb
 - lib/dataset.rb
-- lib/descriptor.rb
 - lib/error.rb
+- lib/experiment.rb
 - lib/feature.rb
 - lib/lazar.rb
+- lib/leave-one-out-validation.rb
 - lib/model.rb
-- lib/neighbor.rb
 - lib/opentox.rb
 - lib/overwrite.rb
+- lib/physchem.rb
 - lib/regression.rb
 - lib/rest-client-wrapper.rb
-- lib/similarity.rb
 - lib/unique_descriptors.rb
 - lib/validation.rb
-- mongoid.yml
 - test/all.rb
+- test/classification.rb
 - test/compound.rb
 - test/data/CPDBAS_v5c_1547_29Apr2008part.sdf
 - test/data/CPDBAS_v5d_cleaned/CPDBAS_v5d_20Nov2008_mouse_TD50.csv
@@ -154,10 +167,15 @@ files:
 - test/data/ISSCAN-multi.csv
 - test/data/LOAEL_log_mg_corrected_smiles.csv
 - test/data/LOAEL_log_mmol_corrected_smiles.csv
+- test/data/LOAEL_mmol_corrected_smiles.csv
 - test/data/acetaldehyde.sdf
+- test/data/batch_prediction.csv
+- test/data/batch_prediction_inchi_small.csv
+- test/data/batch_prediction_smiles_small.csv
 - test/data/boiling_points.ext.sdf
 - test/data/cpdb_100.csv
 - test/data/hamster_carcinogenicity.csv
+- test/data/hamster_carcinogenicity.json
 - test/data/hamster_carcinogenicity.mini.bool_float.csv
 - test/data/hamster_carcinogenicity.mini.bool_int.csv
 - test/data/hamster_carcinogenicity.mini.bool_string.csv
@@ -168,6 +186,7 @@ files:
 - test/data/hamster_carcinogenicity.yaml
 - test/data/hamster_carcinogenicity_with_errors.csv
 - test/data/kazius.csv
+- test/data/loael.csv
 - test/data/multi_cell_call.csv
 - test/data/multi_cell_call_no_dup.csv
 - test/data/multicolumn.csv
@@ -175,21 +194,21 @@ files:
 - test/data/wrong_dataset.csv
 - test/dataset-long.rb
 - test/dataset.rb
-- test/descriptor-long.rb
+- test/default_environment.rb
 - test/descriptor.rb
 - test/error.rb
+- test/experiment.rb
 - test/feature.rb
-- test/fminer-long.rb
-- test/fminer.rb
-- test/lazar-fminer.rb
 - test/lazar-long.rb
 - test/lazar-physchem-short.rb
-- test/lazar-regression.rb
+- test/prediction_models.rb
+- test/regression.rb
 - test/setup.rb
+- test/test_environment.rb
 - test/validation.rb
 homepage: http://github.com/opentox/lazar
 licenses:
-- GPL-3
+- GPL-3.0
 metadata: {}
 post_install_message: 
 rdoc_options: []
@@ -207,12 +226,13 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: lazar
-rubygems_version: 2.4.5
+rubygems_version: 2.5.1
 signing_key: 
 specification_version: 4
 summary: Lazar framework
 test_files:
 - test/all.rb
+- test/classification.rb
 - test/compound.rb
 - test/data/CPDBAS_v5c_1547_29Apr2008part.sdf
 - test/data/CPDBAS_v5d_cleaned/CPDBAS_v5d_20Nov2008_mouse_TD50.csv
@@ -233,10 +253,15 @@ test_files:
 - test/data/ISSCAN-multi.csv
 - test/data/LOAEL_log_mg_corrected_smiles.csv
 - test/data/LOAEL_log_mmol_corrected_smiles.csv
+- test/data/LOAEL_mmol_corrected_smiles.csv
 - test/data/acetaldehyde.sdf
+- test/data/batch_prediction.csv
+- test/data/batch_prediction_inchi_small.csv
+- test/data/batch_prediction_smiles_small.csv
 - test/data/boiling_points.ext.sdf
 - test/data/cpdb_100.csv
 - test/data/hamster_carcinogenicity.csv
+- test/data/hamster_carcinogenicity.json
 - test/data/hamster_carcinogenicity.mini.bool_float.csv
 - test/data/hamster_carcinogenicity.mini.bool_int.csv
 - test/data/hamster_carcinogenicity.mini.bool_string.csv
@@ -247,6 +272,7 @@ test_files:
 - test/data/hamster_carcinogenicity.yaml
 - test/data/hamster_carcinogenicity_with_errors.csv
 - test/data/kazius.csv
+- test/data/loael.csv
 - test/data/multi_cell_call.csv
 - test/data/multi_cell_call_no_dup.csv
 - test/data/multicolumn.csv
@@ -254,15 +280,15 @@ test_files:
 - test/data/wrong_dataset.csv
 - test/dataset-long.rb
 - test/dataset.rb
-- test/descriptor-long.rb
+- test/default_environment.rb
 - test/descriptor.rb
 - test/error.rb
+- test/experiment.rb
 - test/feature.rb
-- test/fminer-long.rb
-- test/fminer.rb
-- test/lazar-fminer.rb
 - test/lazar-long.rb
 - test/lazar-physchem-short.rb
-- test/lazar-regression.rb
+- test/prediction_models.rb
+- test/regression.rb
 - test/setup.rb
+- test/test_environment.rb
 - test/validation.rb