diff options
Diffstat (limited to 'model.rb')
| -rw-r--r-- | model.rb | 83 |
1 files changed, 0 insertions, 83 deletions
diff --git a/model.rb b/model.rb deleted file mode 100644 index 3a84217..0000000 --- a/model.rb +++ /dev/null @@ -1,83 +0,0 @@ -class Model - - include OpenTox::Utils - attr_accessor :uri, :activity_dataset_uri, :feature_dataset_uri, :name - - def initialize(params) - @uri = params[:uri] - @activity_dataset_uri = params[:activity_dataset_uri] - @feature_dataset_uri = params[:feature_dataset_uri] - begin - @name = URI.split(@uri)[5] - rescue - puts "Bad URI #{@uri}" - end - end - - def self.create(params) - params[:uri] = params[:activity_dataset_uri].sub(/dataset/,'model') - @@redis.set_add "models", params[:uri] - @@redis.set(File.join(params[:uri],"activity_dataset"), params[:activity_dataset_uri]) - @@redis.set(File.join(params[:uri],"feature_dataset"), params[:feature_dataset_uri]) - Model.new(params) - end - - def self.find(uri) - if @@redis.set_member? "models", uri - activity_dataset_uri = @@redis.get File.join(uri,"activity_dataset") - feature_dataset_uri = @@redis.get File.join(uri,"feature_dataset") - Model.new(:uri => uri, :activity_dataset_uri => activity_dataset_uri, :feature_dataset_uri => feature_dataset_uri) - else - nil - end - end - - def self.find_all - @@redis.set_members("models") - end - - def predict(compound) - - training_activities = OpenTox::Dataset.find :uri => @uri.sub(/model/,'dataset') - # find database activities - # find prediction - training_features = OpenTox::Dataset.find(:uri => @feature_dataset_uri) - - prediction_dataset = OpenTox::Dataset.find_or_create(:name => training_activities.name + '_predictions') - prediction_neighbors = OpenTox::Dataset.find_or_create(:name => training_activities.name + '_neighbors') - prediction_features = OpenTox::Dataset.find_or_create(:name => training_activities.name + '_prediction_features') - - feature_uris = compound.match(training_features) - prediction_features.add({compound.uri => feature_uris}) - - conf = 0.0 - neighbors = [] - - training_features.compounds.each do |neighbor| - sim = OpenTox::Algorithm::Similarity.weighted_tanimoto(training_features,neighbor,prediction_features,compound).to_f - if sim > 0.3 - neighbors << neighbor.uri - training_activities.features(neighbor).each do |a| - case OpenTox::Feature.new(:uri => a.uri).value('classification').to_s - when 'true' - conf += OpenTox::Utils.gauss(sim) - when 'false' - conf -= OpenTox::Utils.gauss(sim) - end - end - end - end - conf = conf/neighbors.size - if conf > 0.0 - classification = true - elsif conf < 0.0 - classification = false - end - - prediction_neighbors.add({compound.uri => neighbors}) - prediction_uri = OpenTox::Feature.new(:name => @name, :values => {:classification => classification, :confidence => conf}).uri - prediction_uri - - end - -end |