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Diffstat (limited to 'model.rb')
| -rw-r--r-- | model.rb | 83 |
1 files changed, 83 insertions, 0 deletions
diff --git a/model.rb b/model.rb new file mode 100644 index 0000000..3a84217 --- /dev/null +++ b/model.rb @@ -0,0 +1,83 @@ +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 |