From 5b844250a7d3be05e3139e0ca3c819c3da8ee4f6 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Wed, 9 Sep 2015 14:49:35 +0200
Subject: fminer classification fixed

---
 lib/validation.rb | 75 ++++++-------------------------------------------------
 1 file changed, 8 insertions(+), 67 deletions(-)

(limited to 'lib/validation.rb')

diff --git a/lib/validation.rb b/lib/validation.rb
index 445f897..63fbd89 100644
--- a/lib/validation.rb
+++ b/lib/validation.rb
@@ -1,7 +1,6 @@
 module OpenTox
 
   class Validation
-    #include Celluloid
 
     field :prediction_dataset_id, type: BSON::ObjectId
     field :crossvalidation_id, type: BSON::ObjectId
@@ -18,74 +17,9 @@ module OpenTox
       Dataset.find test_dataset_id
     end
 
-  end
-
-  class ClassificationValidation < Validation
-    field :accept_values, type: String
-    field :confusion_matrix, type: Array
-    field :weighted_confusion_matrix, type: Array
-
-    def self.create model, training_set, test_set
-      validation = self.class.new
-      #feature_dataset = Dataset.find model.feature_dataset_id
-      # TODO check and delegate to Algorithm
-      #features = Algorithm.run feature_dataset.training_algorithm, training_set, feature_dataset.training_parameters
-      validation_model = model.class.create training_set#, features
-      test_set_without_activities = Dataset.new(:compound_ids => test_set.compound_ids) # just to be sure that activities cannot be used
-      prediction_dataset = validation_model.predict test_set_without_activities
-      accept_values = prediction_dataset.prediction_feature.accept_values
-      confusion_matrix = Array.new(accept_values.size,0){Array.new(accept_values.size,0)}
-      weighted_confusion_matrix = Array.new(accept_values.size,0){Array.new(accept_values.size,0)}
-      predictions = []
-      nr_unpredicted = 0
-      prediction_dataset.data_entries.each_with_index do |pe,i|
-        if pe[0] and pe[1] and pe[1].numeric? 
-          prediction = pe[0]
-          # TODO prediction_feature, convention??
-          # TODO generalize for multiple classes
-          activity = test_set.data_entries[i].first
-          confidence = prediction_dataset.data_entries[i][1]
-          predictions << [prediction_dataset.compound_ids[i], activity, prediction, confidence]
-          if prediction == activity
-            if prediction == accept_values[0]
-              confusion_matrix[0][0] += 1
-              weighted_confusion_matrix[0][0] += confidence
-            elsif prediction == accept_values[1]
-              confusion_matrix[1][1] += 1
-              weighted_confusion_matrix[1][1] += confidence
-            end
-          elsif prediction != activity
-            if prediction == accept_values[0]
-              confusion_matrix[0][1] += 1
-              weighted_confusion_matrix[0][1] += confidence
-            elsif prediction == accept_values[1]
-              confusion_matrix[1][0] += 1
-              weighted_confusion_matrix[1][0] += confidence
-            end
-          end
-        else
-          nr_unpredicted += 1 if pe[0].nil?
-        end
-      end
-      validation = self.new(
-        :prediction_dataset_id => prediction_dataset.id,
-        :test_dataset_id => test_set.id,
-        :nr_instances => test_set.compound_ids.size,
-        :nr_unpredicted => nr_unpredicted,
-        :accept_values => accept_values,
-        :confusion_matrix => confusion_matrix,
-        :weighted_confusion_matrix => weighted_confusion_matrix,
-        :predictions => predictions.sort{|a,b| b[3] <=> a[3]} # sort according to confidence
-      )
-      validation.save
-      validation
-    end
-  end
-
-  class RegressionValidation < Validation
     def self.create model, training_set, test_set, crossvalidation=nil
       
-      validation_model = Model::LazarRegression.create training_set
+      validation_model = model.class.create training_set#, features
       test_set_without_activities = Dataset.new(:compound_ids => test_set.compound_ids) # just to be sure that activities cannot be used
       prediction_dataset = validation_model.predict test_set_without_activities
       predictions = []
@@ -112,6 +46,13 @@ module OpenTox
       validation.save
       validation
     end
+
+  end
+
+  class ClassificationValidation < Validation
+  end
+
+  class RegressionValidation < Validation
   end
 
 end
-- 
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