diff options
Diffstat (limited to 'lib/model.rb')
| -rw-r--r-- | lib/model.rb | 24 |
1 files changed, 18 insertions, 6 deletions
diff --git a/lib/model.rb b/lib/model.rb index ddb69e4..9892f64 100644 --- a/lib/model.rb +++ b/lib/model.rb @@ -39,6 +39,7 @@ module OpenTox prediction_feature = training_dataset.features.first prediction_feature.nominal ? lazar = OpenTox::Model::LazarClassification.new : lazar = OpenTox::Model::LazarRegression.new lazar.training_dataset_id = training_dataset.id + lazar.neighbor_algorithm_parameters[:training_dataset_id] = training_dataset.id lazar.prediction_feature_id = prediction_feature.id lazar.name = "#{training_dataset.name} #{prediction_feature.name}" @@ -78,7 +79,8 @@ module OpenTox predictions << {:compound => compound, :value => database_activities, :confidence => "measured", :warning => "Compound #{compound.smiles} occurs in training dataset with activity '#{database_activities}'."} next end - neighbors = Algorithm.run(neighbor_algorithm, compound, neighbor_algorithm_parameters) + 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| @@ -129,8 +131,12 @@ module OpenTox def initialize super self.prediction_algorithm = "OpenTox::Algorithm::Classification.weighted_majority_vote" - self.neighbor_algorithm = "OpenTox::Algorithm::Neighbor.fingerprint_similarity" - self.neighbor_algorithm_parameters = {:min_sim => 0.7} + self.neighbor_algorithm = "fingerprint_neighbors" + self.neighbor_algorithm_parameters = { + :type => "FP4", + :training_dataset_id => training_dataset_id, + :min_sim => 0.7 + } end end @@ -141,7 +147,7 @@ module OpenTox model = super(training_dataset) model.update "_type" => self.to_s # adjust class model = self.find model.id # adjust class - model.neighbor_algorithm = "OpenTox::Algorithm::Neighbor.fminer_similarity" + model.neighbor_algorithm = "fminer_neighbors" model.neighbor_algorithm_parameters = { :feature_calculation_algorithm => "OpenTox::Algorithm::Descriptor.smarts_match", :feature_dataset_id => Algorithm::Fminer.bbrc(training_dataset,fminer_params).id, @@ -154,11 +160,17 @@ module OpenTox end class LazarRegression < Lazar + def initialize super - self.neighbor_algorithm = "OpenTox::Algorithm::Neighbor.fingerprint_similarity" + #self.neighbor_algorithm = "OpenTox::Algorithm::Neighbor.fingerprint_similarity" + self.neighbor_algorithm = "fingerprint_neighbors" self.prediction_algorithm = "OpenTox::Algorithm::Regression.weighted_average" - self.neighbor_algorithm_parameters = {:min_sim => 0.7} + self.neighbor_algorithm_parameters = { + :type => "FP4", + :training_dataset_id => self.training_dataset_id, + :min_sim => 0.7 + } end end |