diff options
Diffstat (limited to 'lib/model.rb')
| -rw-r--r-- | lib/model.rb | 31 |
1 files changed, 16 insertions, 15 deletions
diff --git a/lib/model.rb b/lib/model.rb index 227d4d3..44b36e6 100644 --- a/lib/model.rb +++ b/lib/model.rb @@ -76,22 +76,23 @@ module OpenTox t = Time.new neighbors = compound.send(neighbor_algorithm, neighbor_algorithm_parameters) - # add activities - # TODO: improve efficiency, takes 3 times longer than previous version - 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 - acts.empty? ? nil : n << acts - end - neighbors.compact! # remove neighbors without training activities + # remove neighbors without prediction_feature + # check for database activities (neighbors may include query compound) + database_activities = nil + if neighbors.collect{|n| n["_id"]}.include? compound.id - database_activities = training_dataset.values(compound,prediction_feature) - if use_database_values and 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 + database_activities = neighbors.select{|n| n["_id"] == compound.id}.first["features"][prediction_feature.id.to_s] + neighbors.delete_if{|n| n["_id"] == compound.id} + end + neighbors.delete_if{|n| n['features'].empty? or n['features'][prediction_feature.id.to_s] == [nil] } + if neighbors.empty? + prediction = {:value => nil,:confidence => nil,:warning => "Cound not find similar compounds."} + else + prediction = Algorithm.run(prediction_algorithm, compound, {:neighbors => neighbors,:training_dataset_id=> training_dataset.id,:prediction_feature_id => prediction_feature.id}) end - predictions << Algorithm.run(prediction_algorithm, compound, {:neighbors => neighbors,:training_dataset_size => training_dataset.data_entries.size}) + prediction[:database_activities] = database_activities + predictions << prediction + =begin # TODO scaled dataset for physchem p neighbor_algorithm_parameters @@ -126,7 +127,7 @@ module OpenTox warning_feature = OpenTox::NominalFeature.find_or_create_by("name" => "Warnings") prediction_dataset.features = [ prediction_feature, confidence_feature, warning_feature ] prediction_dataset.compounds = compounds - prediction_dataset.data_entries = predictions.collect{|p| [p[:value], p[:confidence], p[:warning]]} + prediction_dataset.data_entries = predictions.collect{|p| [p[:value], p[:database_activities] ? "measured" : p[:confidence] , p[:warning]]} prediction_dataset.save_all return prediction_dataset end |