diff options
Diffstat (limited to 'lib/model.rb')
| -rw-r--r-- | lib/model.rb | 42 |
1 files changed, 23 insertions, 19 deletions
diff --git a/lib/model.rb b/lib/model.rb index 817a61e..cd88e0c 100644 --- a/lib/model.rb +++ b/lib/model.rb @@ -82,7 +82,6 @@ module OpenTox end neighbors = compound.send(neighbor_algorithm, neighbor_algorithm_parameters) - #neighbors = Algorithm.run(neighbor_algorithm, compound, neighbor_algorithm_parameters) # add activities # TODO: improve efficiency, takes 3 times longer than previous version neighbors.collect! do |n| @@ -145,12 +144,12 @@ module OpenTox def self.create training_dataset, params={} model = self.new training_dataset, params model.prediction_algorithm = "OpenTox::Algorithm::Classification.weighted_majority_vote" unless model.prediction_algorithm - model.neighbor_algorithm |= "fingerprint_neighbors" + model.neighbor_algorithm ||= "fingerprint_neighbors" model.neighbor_algorithm_parameters ||= {} { - :type => "FP4", + :type => "MP2D", :training_dataset_id => training_dataset.id, - :min_sim => 0.7 + :min_sim => 0.1 }.each do |key,value| model.neighbor_algorithm_parameters[key] ||= value end @@ -163,16 +162,19 @@ module OpenTox def self.create training_dataset, params={} model = self.new training_dataset, params - #model.neighbor_algorithm ||= "fingerprint_neighbors" - #model.prediction_algorithm ||= "OpenTox::Algorithm::Regression.weighted_average" - #model.neighbor_algorithm_parameters ||= {} - #{ + model.neighbor_algorithm ||= "fingerprint_neighbors" + model.prediction_algorithm ||= "OpenTox::Algorithm::Regression.weighted_average" + model.neighbor_algorithm_parameters ||= {} + { + :type => "MP2D", + :training_dataset_id => training_dataset.id, + :min_sim => 0.1 #:type => "FP4", #:training_dataset_id => training_dataset.id, #:min_sim => 0.7 - #}.each do |key,value| - #model.neighbor_algorithm_parameters[key] ||= value - #end + }.each do |key,value| + model.neighbor_algorithm_parameters[key] ||= value + end model.save model end @@ -209,7 +211,7 @@ module OpenTox field :source, type: String field :unit, type: String field :model_id, type: BSON::ObjectId - field :crossvalidation_id, type: BSON::ObjectId + field :repeated_crossvalidation_id, type: BSON::ObjectId def predict object Lazar.find(model_id).predict object @@ -223,8 +225,12 @@ module OpenTox Lazar.find model_id end - def crossvalidation - CrossValidation.find crossvalidation_id + def repeated_crossvalidation + RepeatedCrossValidation.find repeated_crossvalidation_id + end + + def crossvalidations + repeated_crossvalidation.crossvalidations end def regression? @@ -241,16 +247,14 @@ module OpenTox prediction_model = self.new JSON.parse(File.read(metadata_file)) training_dataset = Dataset.from_csv_file file model = nil - cv = nil if training_dataset.features.first.nominal? - model = LazarFminerClassification.create training_dataset - cv = ClassificationCrossValidation.create model + #model = LazarFminerClassification.create training_dataset + model = LazarClassification.create training_dataset elsif training_dataset.features.first.numeric? model = LazarRegression.create training_dataset - cv = RegressionCrossValidation.create model end prediction_model[:model_id] = model.id - prediction_model[:crossvalidation_id] = cv.id + prediction_model[:repeated_crossvalidation_id] = RepeatedCrossValidation.create(model).id prediction_model.save prediction_model end |