diff options
Diffstat (limited to 'lib/lazar-model.rb')
| -rw-r--r-- | lib/lazar-model.rb | 21 |
1 files changed, 17 insertions, 4 deletions
diff --git a/lib/lazar-model.rb b/lib/lazar-model.rb index 4ca3403..aeaa515 100644 --- a/lib/lazar-model.rb +++ b/lib/lazar-model.rb @@ -9,7 +9,6 @@ module OpenTox store_in collection: "models" field :title, type: String - field :endpoint, type: String field :creator, type: String, default: __FILE__ # datasets field :training_dataset_id, type: BSON::ObjectId @@ -64,12 +63,18 @@ module OpenTox # make predictions predictions = [] + neighbors = [] compounds.each_with_index do |compound,c| t = Time.new + database_activities = training_dataset.values(compound,prediction_feature) + if database_activities and !database_activities.empty? + database_activities = database_activities.first if database_activities.size == 1 + 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) # add activities # TODO: improve efficiency, takes 3 times longer than previous version - # TODO database activity?? neighbors.collect! do |n| rows = training_dataset.compound_ids.each_index.select{|i| training_dataset.compound_ids[i] == n.first} acts = rows.collect{|row| training_dataset.data_entries[row][0]}.compact @@ -82,7 +87,9 @@ module OpenTox # serialize result case object.class.to_s when "OpenTox::Compound" - return predictions.first + prediction = predictions.first + prediction[:neighbors] = neighbors.sort{|a,b| b[1] <=> a[1]} # sort according to similarity + return prediction when "Array" return predictions when "OpenTox::Dataset" @@ -98,7 +105,7 @@ module OpenTox warning_feature = OpenTox::NominalFeature.find_or_create_by("title" => "Warnings") prediction_dataset.features = [ prediction_feature, confidence_feature, warning_feature ] prediction_dataset.compounds = compounds - prediction_dataset.data_entries = predictions + prediction_dataset.data_entries = predictions.collect{|p| [p[:value], p[:confidence], p[:warning]]} prediction_dataset.save_all return prediction_dataset end @@ -281,6 +288,12 @@ module OpenTox end + class PredictionModel < Lazar + field :category, type: String + field :endpoint, type: String + field :crossvalidation_id, type: BSON::ObjectId + end + end end |