Cleaned Weighted Majority Vote

2 files changed, 18 insertions, 10 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index 529cffb..a355647 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -622,12 +622,13 @@ module OpenTox
         confidence = 0.0
         prediction = nil
 
-        params[:neighbors].each do |neighbor|
-          neighbor_weight = neighbor[:similarity].to_f
-          neighbor_contribution += neighbor[:activity].to_f * neighbor_weight
+        LOGGER.debug "Weighted Majority Vote Classification."
+        params[:acts].each_index do |idx|
+          neighbor_weight = params[:sims][1][idx]
+          neighbor_contribution += params[:acts][idx] * neighbor_weight
 
           if params[:value_map].size == 2 # AM: provide compat to binary classification: 1=>false 2=>true
-            case neighbor[:activity]
+            case params[:acts][idx]
             when 1
               confidence_sum -= neighbor_weight
             when 2
@@ -640,19 +641,21 @@ module OpenTox
 
         if params[:value_map].size == 2 
           if confidence_sum >= 0.0
-            prediction = 2 unless params[:neighbors].size==0
+            prediction = 2 unless params[:acts].size==0
           elsif confidence_sum < 0.0
-            prediction = 1 unless params[:neighbors].size==0
+            prediction = 1 unless params[:acts].size==0
           end
         else 
-          prediction = (neighbor_contribution/confidence_sum).round  unless params[:neighbors].size==0  # AM: new multinomial prediction
+          prediction = (neighbor_contribution/confidence_sum).round  unless params[:acts].size==0  # AM: new multinomial prediction
         end 
         LOGGER.debug "Prediction is: '" + prediction.to_s + "'." unless prediction.nil?
-        confidence = confidence_sum/params[:neighbors].size if params[:neighbors].size > 0
+        confidence = confidence_sum/params[:acts].size if params[:acts].size > 0
         LOGGER.debug "Confidence is: '" + confidence.to_s + "'." unless prediction.nil?
         return {:prediction => prediction, :confidence => confidence.abs}
       end
 
+
+
       # Local support vector regression from neighbors 
       # @param [Hash] params Keys `:neighbors,:compound,:features,:p_values,:similarity_algorithm,:prop_kernel,:value_map` are required
       # @return [Numeric] A prediction value.
diff --git a/lib/model.rb b/lib/model.rb
index 191f732..1aa9cf7 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -266,9 +266,14 @@ module OpenTox
 
           neighbors
           prediction_fingerprints = @fingerprints.merge({@compound.uri => @compound_fingerprints})
+          
+          # props
           props = OpenTox::Algorithm::Neighbors.get_props_fingerprints({:neighbors => @neighbors, :features => @features, :fingerprints => prediction_fingerprints, :compound => @compound})
+
+          # acts
           acts = @neighbors.collect { |n| n[:activity] }
 
+          # sims
           gram_matrix = []
           @neighbors.each_index do |i|
             gram_matrix[i] = [] unless gram_matrix[i]
@@ -287,12 +292,12 @@ module OpenTox
           end
           sims = [ gram_matrix, @neighbors.collect { |n| n[:similarity] } ] 
 
+          # prediction
           prediction = eval("#{@prediction_algorithm} ( { :props => props,
                                                           :acts => acts,
                                                           :sims => sims,
-                                                          :p_values => @p_values, 
-                                                          :similarity_algorithm => @similarity_algorithm, 
                                                           :prop_kernel => @prop_kernel,
+                                                          :value_map => @value_map,
                                                           :conf_stdev => @conf_stdev
                                                          } ) ")