From 1b44e0cd76f2ead93b8b3fa0f970c85ef32a4b14 Mon Sep 17 00:00:00 2001
From: "helma@in-silico.ch" <helma@in-silico.ch>
Date: Fri, 16 Nov 2018 22:45:17 +0100
Subject: confidence for prediction datasets

---
 lib/dataset.rb | 11 +++++++++--
 lib/feature.rb |  5 +++++
 lib/model.rb   |  5 +++--
 3 files changed, 17 insertions(+), 4 deletions(-)

(limited to 'lib')

diff --git a/lib/dataset.rb b/lib/dataset.rb
index 3979105..df17569 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -70,6 +70,12 @@ module OpenTox
       features.select{|f| f.is_a?(Warnings)}
     end
 
+    # Get Confidence feature
+    # @return [OpenTox::Confidence] confidence feature
+    def confidence_feature
+      features.select{|f| f.is_a?(Confidence)}.first
+    end
+
     # Get nominal and numeric bioactivity features
     # @return [Array<OpenTox::NominalBioActivity,OpenTox::NumericBioActivity>]
     def bioactivity_features
@@ -392,8 +398,9 @@ module OpenTox
         predictions[s] ||= {}
         prediction_feature = prediction_features.first
         predictions[s][:value] = values(s,prediction_feature).first
-        predictions[s][:warnings] = []
-        warnings_features.each { |w| predictions[s][:warnings] += values(s,w) }
+        #predictions[s][:warnings] = []
+        #warnings_features.each { |w| predictions[s][:warnings] += values(s,w) }
+        predictions[s][:confidence] = values(s,confidence_feature).first
         if predictions[s][:value] and prediction_feature.is_a? NominalLazarPrediction
           prediction_feature.accept_values.each do |v|
             f = LazarPredictionProbability.find_by(:name => v, :model_id => prediction_feature.model_id, :training_feature_id => prediction_feature.training_feature_id)
diff --git a/lib/feature.rb b/lib/feature.rb
index b474398..72c26d7 100644
--- a/lib/feature.rb
+++ b/lib/feature.rb
@@ -15,6 +15,11 @@ module OpenTox
     field :dataset_id, type: BSON::ObjectId
   end
 
+  # Confidence
+  class Confidence < Feature
+    field :dataset_id, type: BSON::ObjectId
+  end
+
   # Categorical variables
   class NominalFeature < Feature
     field :accept_values, type: Array
diff --git a/lib/model.rb b/lib/model.rb
index 08ca07e..cbfefe3 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -338,7 +338,8 @@ module OpenTox
           return predictions
         elsif object.is_a? Dataset
           d = object.copy
-          warning_feature = Warnings.find_or_create_by(:dataset_id => d.id)
+          #warning_feature = Warnings.find_or_create_by(:dataset_id => d.id)
+          confidence_feature = Confidence.find_or_create_by(:dataset_id => d.id)
           if prediction_feature.is_a? NominalBioActivity
             f = NominalLazarPrediction.find_or_create_by(:name => prediction_feature.name, :accept_values => prediction_feature.accept_values, :model_id => self.id, :training_feature_id => prediction_feature.id)
             probability_features = {}
@@ -356,7 +357,7 @@ module OpenTox
           # add predictions to dataset
           predictions.each do |substance_id,p|
             substance_id = BSON::ObjectId.from_string(substance_id)
-            d.add substance_id,warning_feature,p[:warnings].join(" ") unless p[:warnings].empty?
+            d.add substance_id,confidence_feature,p[:confidence]
             unless p[:value].nil?
               d.add substance_id,f,p[:value]
               p[:probabilities].each {|name,p| d.add substance_id,probability_features[name],p} if p[:probabilities]
-- 
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