diff options
Diffstat (limited to 'lib/validation.rb')
| -rw-r--r-- | lib/validation.rb | 75 |
1 files changed, 8 insertions, 67 deletions
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 |