regression crossvalidation fixed

3 files changed, 8 insertions, 5 deletions

diff --git a/lib/compound.rb b/lib/compound.rb
index 3af6f6c..0a9111b 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -288,7 +288,10 @@ module OpenTox
         training_dataset.compounds.each do |compound|
           candidate_fingerprint = compound.fingerprint params[:type]
           sim = (query_fingerprint & candidate_fingerprint).size/(query_fingerprint | candidate_fingerprint).size.to_f
-          neighbors << {"_id" => compound.id, "toxicities" => {prediction_feature.id.to_s => {training_dataset_id.to_s => compound.toxicities[prediction_feature.id.to_s][training_dataset_id.to_s]}}, "tanimoto" => sim} if sim >= params[:min_sim]
+          fid = prediction_feature.id.to_s
+          did = params[:training_dataset_id].to_s
+          v = compound.toxicities[prediction_feature.id.to_s]
+          neighbors << {"_id" => compound.id, "toxicities" => {fid => {did => v[params[:training_dataset_id].to_s]}}, "tanimoto" => sim} if sim >= params[:min_sim] and v
         end
         neighbors.sort!{|a,b| b["tanimoto"] <=> a["tanimoto"]}
       end
diff --git a/lib/leave-one-out-validation.rb b/lib/leave-one-out-validation.rb
index 2306041..7189617 100644
--- a/lib/leave-one-out-validation.rb
+++ b/lib/leave-one-out-validation.rb
@@ -3,7 +3,6 @@ module OpenTox
   class LeaveOneOutValidation
 
     field :model_id, type: BSON::ObjectId
-    field :dataset_id, type: BSON::ObjectId
     field :nr_instances, type: Integer
     field :nr_unpredicted, type: Integer
     field :predictions, type: Hash
@@ -13,13 +12,14 @@ module OpenTox
       $logger.debug "#{model.name}: LOO validation started"
       t = Time.now
       model.training_dataset.features.first.nominal? ? klass = ClassificationLeaveOneOutValidation : klass = RegressionLeaveOneOutValidation
-      loo = klass.new :model_id => model.id, :dataset_id => model.training_dataset_id
+      loo = klass.new :model_id => model.id
       predictions = model.predict model.training_dataset.compounds
       predictions.each{|cid,p| p.delete(:neighbors)}
       nr_unpredicted = 0
       predictions.each do |cid,prediction|
         if prediction[:value]
-          prediction[:measured] = Substance.find(cid).toxicities[prediction[:prediction_feature_id].to_s][dataset_id.to_s]
+          tox = Substance.find(cid).toxicities[prediction[:prediction_feature_id].to_s]
+          prediction[:measured] = tox[model.training_dataset_id.to_s] if tox
         else
           nr_unpredicted += 1
         end
diff --git a/test/validation.rb b/test/validation.rb
index 021fac5..8ebb52c 100644
--- a/test/validation.rb
+++ b/test/validation.rb
@@ -25,7 +25,6 @@ class ValidationTest < MiniTest::Test
   def test_classification_crossvalidation_parameters
     dataset = Dataset.from_csv_file "#{DATA_DIR}/hamster_carcinogenicity.csv"
     params = {
-        :training_dataset_id => dataset.id,
       :neighbor_algorithm_parameters => {
         :min_sim => 0.3,
         :type => "FP3"
@@ -56,6 +55,7 @@ class ValidationTest < MiniTest::Test
       }
     }
     model = Model::LazarRegression.create dataset.features.first, dataset, params
+    p model
     cv = RegressionCrossValidation.create model
     cv.validation_ids.each do |vid|
       model = Model::Lazar.find(Validation.find(vid).model_id)