Multinomial capability for Fminer and Lazar

2 files changed, 56 insertions, 67 deletions

diff --git a/fminer.rb b/fminer.rb
index ee031ff..8c6451c 100644
--- a/fminer.rb
+++ b/fminer.rb
@@ -138,8 +138,8 @@ post '/fminer/bbrc/?' do
 
     id = 1 # fminer start id is not 0
     compounds = []
-    nr_active=0
-    nr_inactive=0
+    nr_classes={}
+    nr_total=0
     all_activities = Hash.new# DV: for effect calculation in regression part
 
     training_dataset.data_entries.each do |compound,entry|
@@ -160,7 +160,7 @@ post '/fminer/bbrc/?' do
       entry.each do |feature,values|
          values.each do |value|
             if prediction_feature.feature_type == "regression"
-               if (! value.nil?) && (value.to_f < 1)
+               if (! value.nil?) && (value.to_f <= 0)
                  take_logs=false
                end
             end
@@ -170,26 +170,13 @@ post '/fminer/bbrc/?' do
         if feature == prediction_feature.uri
           values.each do |value|
             if value.nil? 
-              LOGGER.warn "No #{feature} activiity for #{compound.to_s}."
+              LOGGER.warn "No #{feature} activity for #{compound.to_s}."
             else
               if prediction_feature.feature_type == "classification"
-                case value.to_s
-                when "true"
-                  nr_active += 1
-                  activity = 1
-                when "false"
-                  nr_inactive += 1
-                  activity = 0
-                when /#{@training_classes.last}/
-                  nr_active += 1
-                  activity = 1
-                when /#{@training_classes.first}/
-                  nr_inactive += 1
-                  activity = 0
-                else
-                  LOGGER.warn "Unknown class \"#{value.to_s}\"."
-                end
-              elsif prediction_feature.feature_type == "regression"
+                activity= value.to_f 
+                nr_classes[activity].nil? ? nr_classes[activity]=0 : nr_classes[activity]+=1
+                nr_total+=1
+             elsif prediction_feature.feature_type == "regression"
                 activity= take_logs ? Math.log10(value.to_f) : value.to_f 
               end
               begin
@@ -223,14 +210,22 @@ post '/fminer/bbrc/?' do
         p_value = f[1]
 
         if (!@@bbrc.GetRegression) 
-          ids = f[2] + f[3]
-          if f[2].size.to_f/ids.size > nr_active.to_f/(nr_active+nr_inactive)
-            effect = 'activating'
-          else
-            effect = 'deactivating'
-          end
+          id_arrs = f[2..-1].flatten
+          max=nil
+          max_value=0
+          f[2..-1].reverse.each_with_index { |id,i| # fminer outputs occurrences sorted reverse by activity.
+            actual = id.size.to_f/id_arrs.size
+            expected = nr_classes[i].to_f/nr_total
+            if actual > expected
+              if ((actual - expected) / actual) > max_value
+                max_value = (actual - expected) / actual # 'Schleppzeiger'
+                max = i
+              end
+            end
+          }
+          effect = max.to_s
         else #regression part
-          ids = f[2]
+          id_arrs = f[2]
           # DV: effect calculation
           f_arr=Array.new
           f[2].each do |id|
@@ -261,7 +256,7 @@ post '/fminer/bbrc/?' do
           feature_dataset.add_feature feature_uri, metadata
           #feature_dataset.add_feature_parameters feature_uri, feature_dataset.parameters
         end
-        ids.each { |id| feature_dataset.add(compounds[id], feature_uri, true)}
+        id_arrs.each { |id| feature_dataset.add(compounds[id], feature_uri, true)}
       end
     end
     feature_dataset.save(@subjectid) 
@@ -328,8 +323,8 @@ post '/fminer/last/?' do
     id = 1 # fminer start id is not 0
     compounds = []
     smi = [] # AM LAST: needed for matching the patterns back
-    nr_active=0
-    nr_inactive=0
+    nr_classes = []
+    nr_total=0
     all_activities = Hash.new #DV: for effect calculation (class and regr)
 
     training_dataset.data_entries.each do |compound,entry|
@@ -343,38 +338,38 @@ post '/fminer/last/?' do
         LOGGER.warn "Cannot find smiles for #{compound.to_s}."
         next
       end
+
+      # AM: take log if appropriate
+      take_logs=true
+      entry.each do |feature,values|
+         values.each do |value|
+            if prediction_feature.feature_type == "regression"
+               if (! value.nil?) && (value.to_f <= 0)
+                 take_logs=false
+               end
+            end
+         end
+      end
+
       entry.each do |feature,values|
         if feature == prediction_feature.uri
           values.each do |value|
             if value.nil? 
-              LOGGER.warn "No #{feature} activiity for #{compound.to_s}."
+              LOGGER.warn "No #{feature} activity for #{compound.to_s}."
             else
               if prediction_feature.feature_type == "classification"
-                case value.to_s
-                when "true"
-                  nr_active += 1
-                  activity = 1
-                when "false"
-                  nr_inactive += 1
-                  activity = 0
-                when /#{@training_classes.last}/
-                  nr_active += 1
-                  activity = 1
-                when /#{@training_classes.first}/
-                  nr_inactive += 1
-                  activity = 0
-                else
-                  LOGGER.warn "Unknown class \"#{value.to_s}."
-                end
+                activity= value.to_f
+                nr_classes[activity].nil? ? nr_classes[activity]=0 : nr_classes[activity]+=1
+                nr_total+=1
               elsif prediction_feature.feature_type == "regression"
-                activity = value.to_f
+                activity= take_logs ? Math.log10(value.to_f) : value.to_f
               end
               begin
                 @@last.AddCompound(smiles,id)
                 @@last.AddActivity(activity, id)
                 all_activities[id]=activity # DV: insert global information
                 compounds[id] = compound
-		smi[id] = smiles # AM LAST: changed this to store SMILES.
+                smi[id] = smiles # AM LAST: changed this to store SMILES.
                 id += 1
               rescue
                 LOGGER.warn "Could not add " + smiles + "\t" + value.to_s + " to fminer"
@@ -404,10 +399,13 @@ post '/fminer/last/?' do
     instances=lu.match_rb(smi,smarts)       # AM LAST: creates instantiations
     instances.each do |smarts, ids|
       feat_hash = Hash[*(all_activities.select { |k,v| ids.include?(k) }.flatten)] # AM LAST: get activities of feature occurrences; see http://www.softiesonrails.com/2007/9/18/ruby-201-weird-hash-syntax
-      @@last.GetRegression() ? p_value = @@last.KSTest(all_activities.values, feat_hash.values).to_f : p_value = @@last.ChisqTest(all_activities.values, feat_hash.values).to_f # AM LAST: use internal function for test
-
-
-      effect = (p_value > 0) ? "activating" : "deactivating"
+      if @@last.GetRegression() 
+        p_value = @@last.KSTest(all_activities.values, feat_hash.values).to_f # AM LAST: use internal function for test
+        effect = (p_value > 0) ? "activating" : "deactivating"
+      else
+        p_value = @@last.ChisqTest(all_activities.values, feat_hash.values).to_f
+        effect = "unknown"
+      end
       feature_uri = File.join feature_dataset.uri,"feature","last", features.size.to_s
       unless features.include? smarts
         features << smarts
diff --git a/lazar.rb b/lazar.rb
index 4441726..31cdd4d 100644
--- a/lazar.rb
+++ b/lazar.rb
@@ -131,7 +131,9 @@ post '/lazar/?' do
 
     if prediction_feature.feature_type == "classification"
       @training_classes = training_activities.accept_values(prediction_feature.uri).sort
-      lazar.value_map = { true => @training_classes.last, false => @training_classes.first }
+      @training_classes.each_with_index { |c,i|
+        lazar.value_map[i] = c
+      }
     elsif  prediction_feature.feature_type == "regression"
       lazar.prediction_algorithm = "Neighbors.local_svm_regression" 
     end
@@ -145,18 +147,7 @@ post '/lazar/?' do
       unless entry[prediction_feature.uri].empty?
         entry[prediction_feature.uri].each do |value|
           if prediction_feature.feature_type == "classification"
-            case value.to_s
-            when "true"
-              lazar.activities[compound] << true
-            when "false"
-              lazar.activities[compound] << false
-            when /#{@training_classes.last}/
-              lazar.activities[compound] << true
-            when /#{@training_classes.first}/
-              lazar.activities[compound] << false
-            else
-              LOGGER.warn "Unknown class \"#{value.to_s}\"."
-            end
+            lazar.activities[compound] << lazar.value_map.invert[value] # insert mapped values, not originals
           elsif prediction_feature.feature_type == "regression"
             #never use halt in tasks, do not raise exception when, print warning instead
             if value.to_f==0