lazar 0.9.3 → 1.0.0

data/lib/crossvalidation.rb

@@ -1,301 +1,102 @@
 module OpenTox
 
-  class CrossValidation
-    field :validation_ids, type: Array, default: []
-    field :model_id, type: BSON::ObjectId
-    field :folds, type: Integer
-    field :nr_instances, type: Integer
-    field :nr_unpredicted, type: Integer
-    field :predictions, type: Array, default: []
-    field :finished_at, type: Time 
-
-    def time
-      finished_at - created_at
-    end
-
-    def validations
-      validation_ids.collect{|vid| Validation.find vid}
-    end
-
-    def model
-      Model::Lazar.find model_id
-    end
-
-    def self.create model, n=10
-      model.training_dataset.features.first.nominal? ? klass = ClassificationCrossValidation : klass = RegressionCrossValidation
-      bad_request_error "#{dataset.features.first} is neither nominal nor numeric." unless klass
-      cv = klass.new(
-        name: model.name,
-        model_id: model.id,
-        folds: n
-      )
-      cv.save # set created_at
-      nr_instances = 0
-      nr_unpredicted = 0
-      predictions = []
-      training_dataset = Dataset.find model.training_dataset_id
-      training_dataset.folds(n).each_with_index do |fold,fold_nr|
-        #fork do # parallel execution of validations
-          $logger.debug "Dataset #{training_dataset.name}: Fold #{fold_nr} started"
-          t = Time.now
-          validation = Validation.create(model, fold[0], fold[1],cv)
-          $logger.debug "Dataset #{training_dataset.name}, Fold #{fold_nr}:  #{Time.now-t} seconds"
-        #end
-      end
-      #Process.waitall
-      cv.validation_ids = Validation.where(:crossvalidation_id => cv.id).distinct(:_id)
-      cv.validations.each do |validation|
-        nr_instances += validation.nr_instances
-        nr_unpredicted += validation.nr_unpredicted
-        predictions += validation.predictions
-      end
-      cv.update_attributes(
-        nr_instances: nr_instances,
-        nr_unpredicted: nr_unpredicted,
-        predictions: predictions#.sort{|a,b| b[3] <=> a[3]} # sort according to confidence
-      )
-      $logger.debug "Nr unpredicted: #{nr_unpredicted}"
-      cv.statistics
-      cv
-    end
-  end
-
-  class ClassificationCrossValidation < CrossValidation
-
-    field :accept_values, type: Array
-    field :confusion_matrix, type: Array
-    field :weighted_confusion_matrix, type: Array
-    field :accuracy, type: Float
-    field :weighted_accuracy, type: Float
-    field :true_rate, type: Hash
-    field :predictivity, type: Hash
-    field :confidence_plot_id, type: BSON::ObjectId
-    # TODO auc, f-measure (usability??)
-
-    def statistics
-      accept_values = Feature.find(model.prediction_feature_id).accept_values
-      confusion_matrix = Array.new(accept_values.size,0){Array.new(accept_values.size,0)}
-      weighted_confusion_matrix = Array.new(accept_values.size,0){Array.new(accept_values.size,0)}
-      true_rate = {}
-      predictivity = {}
-      predictions.each do |pred|
-        compound_id,activities,prediction,confidence = pred
-        if activities and prediction #and confidence.numeric? 
-          if activities.uniq.size == 1
-            activity = activities.uniq.first
-            if prediction == activity
-              if prediction == accept_values[0]
-                confusion_matrix[0][0] += 1
-                #weighted_confusion_matrix[0][0] += confidence
-              elsif prediction == accept_values[1]
-                confusion_matrix[1][1] += 1
-                #weighted_confusion_matrix[1][1] += confidence
-              end
-            elsif prediction != activity
-              if prediction == accept_values[0]
-                confusion_matrix[0][1] += 1
-                #weighted_confusion_matrix[0][1] += confidence
-              elsif prediction == accept_values[1]
-                confusion_matrix[1][0] += 1
-                #weighted_confusion_matrix[1][0] += confidence
-              end
-            end
-          end
-        else
-          nr_unpredicted += 1 if prediction.nil?
+  module Validation
+    class CrossValidation < Validation
+      field :validation_ids, type: Array, default: []
+      field :folds, type: Integer, default: 10
+
+      def self.create model, n=10
+        $logger.debug model.algorithms
+        klass = ClassificationCrossValidation if model.is_a? Model::LazarClassification
+        klass = RegressionCrossValidation if model.is_a? Model::LazarRegression
+        bad_request_error "Unknown model class #{model.class}." unless klass
+
+        cv = klass.new(
+          name: model.name,
+          model_id: model.id,
+          folds: n
+        )
+        cv.save # set created_at
+
+        nr_instances = 0
+        nr_unpredicted = 0
+        training_dataset = model.training_dataset
+        training_dataset.folds(n).each_with_index do |fold,fold_nr|
+          #fork do # parallel execution of validations can lead to Rserve and memory problems
+            $logger.debug "Dataset #{training_dataset.name}: Fold #{fold_nr} started"
+            t = Time.now
+            validation = TrainTest.create(model, fold[0], fold[1])
+            cv.validation_ids << validation.id
+            cv.nr_instances += validation.nr_instances
+            cv.nr_unpredicted += validation.nr_unpredicted
+            #cv.predictions.merge! validation.predictions
+            $logger.debug "Dataset #{training_dataset.name}, Fold #{fold_nr}:  #{Time.now-t} seconds"
+          #end
         end
+        #Process.waitall
+        cv.save
+        $logger.debug "Nr unpredicted: #{nr_unpredicted}"
+        cv.statistics
+        cv.update_attributes(finished_at: Time.now)
+        cv
       end
-      true_rate = {}
-      predictivity = {}
-      accept_values.each_with_index do |v,i|
-        true_rate[v] = confusion_matrix[i][i]/confusion_matrix[i].reduce(:+).to_f
-        predictivity[v] = confusion_matrix[i][i]/confusion_matrix.collect{|n| n[i]}.reduce(:+).to_f
-      end
-      confidence_sum = 0
-      #weighted_confusion_matrix.each do |r|
-        #r.each do |c|
-          #confidence_sum += c
-        #end
-      #end
-      update_attributes(
-        accept_values: accept_values,
-        confusion_matrix: confusion_matrix,
-        #weighted_confusion_matrix: weighted_confusion_matrix,
-        accuracy: (confusion_matrix[0][0]+confusion_matrix[1][1])/(nr_instances-nr_unpredicted).to_f,
-        #weighted_accuracy: (weighted_confusion_matrix[0][0]+weighted_confusion_matrix[1][1])/confidence_sum.to_f,
-        true_rate: true_rate,
-        predictivity: predictivity,
-        finished_at: Time.now
-      )
-      $logger.debug "Accuracy #{accuracy}"
-    end
-
-    def confidence_plot
-      unless confidence_plot_id
-        tmpfile = "/tmp/#{id.to_s}_confidence.png"
-        accuracies = []
-        confidences = []
-        correct_predictions = 0
-        incorrect_predictions = 0
-        predictions.each do |p|
-          if p[1] and p[2]
-            p[1] == p[2] ? correct_predictions += 1 : incorrect_predictions += 1
-            accuracies << correct_predictions/(correct_predictions+incorrect_predictions).to_f
-            confidences << p[3]
 
-          end
-        end
-        R.assign "accuracy", accuracies
-        R.assign "confidence", confidences
-        R.eval "image = qplot(confidence,accuracy)+ylab('accumulated accuracy')+scale_x_reverse()"
-        R.eval "ggsave(file='#{tmpfile}', plot=image)"
-        file = Mongo::Grid::File.new(File.read(tmpfile), :filename => "#{self.id.to_s}_confidence_plot.png")
-        plot_id = $gridfs.insert_one(file)
-        update(:confidence_plot_id => plot_id)
+      def time
+        finished_at - created_at
       end
-      $gridfs.find_one(_id: confidence_plot_id).data
-    end
-
-    #Average area under roc  0.646
-    #Area under roc  0.646
-    #F measure carcinogen: 0.769, noncarcinogen: 0.348
-  end
 
-  class RegressionCrossValidation < CrossValidation
-
-    field :rmse, type: Float
-    field :mae, type: Float
-    field :r_squared, type: Float
-    field :correlation_plot_id, type: BSON::ObjectId
-
-    def statistics
-      rmse = 0
-      mae = 0
-      x = []
-      y = []
-      predictions.each do |pred|
-        compound_id,activity,prediction,confidence = pred
-        if activity and prediction 
-          unless activity == [nil]
-            x << -Math.log10(activity.median)
-            y << -Math.log10(prediction)
-            error = Math.log10(prediction)-Math.log10(activity.median)
-            rmse += error**2
-            #weighted_rmse += confidence*error**2
-            mae += error.abs
-            #weighted_mae += confidence*error.abs
-            #confidence_sum += confidence
-          end
-        else
-          warnings << "No training activities for #{Compound.find(compound_id).smiles} in training dataset #{model.training_dataset_id}."
-          $logger.debug "No training activities for #{Compound.find(compound_id).smiles} in training dataset #{model.training_dataset_id}."
-        end
+      def validations
+        validation_ids.collect{|vid| TrainTest.find vid}
       end
-      R.assign "measurement", x
-      R.assign "prediction", y
-      R.eval "r <- cor(measurement,prediction,use='complete')"
-      r = R.eval("r").to_ruby
 
-      mae = mae/predictions.size
-      #weighted_mae = weighted_mae/confidence_sum
-      rmse = Math.sqrt(rmse/predictions.size)
-      #weighted_rmse = Math.sqrt(weighted_rmse/confidence_sum)
-      update_attributes(
-        mae: mae,
-        rmse: rmse,
-        #weighted_mae: weighted_mae,
-        #weighted_rmse: weighted_rmse,
-        r_squared: r**2,
-        finished_at: Time.now
-      )
-      $logger.debug "R^2 #{r**2}"
-      $logger.debug "RMSE #{rmse}"
-      $logger.debug "MAE #{mae}"
+      def predictions
+        predictions = {}
+        validations.each{|v| predictions.merge!(v.predictions)}
+        predictions
+      end
     end
 
-    def misclassifications n=nil
-      #n = predictions.size unless n
-      n ||= 10 
-      model = Model::Lazar.find(self.model_id)
-      training_dataset = Dataset.find(model.training_dataset_id)
-      prediction_feature = training_dataset.features.first
-      predictions.collect do |p|
-        unless p.include? nil
-          compound = Compound.find(p[0])
-          neighbors = compound.send(model.neighbor_algorithm,model.neighbor_algorithm_parameters)
-          neighbors.collect! do |n|
-            neighbor = Compound.find(n[0])
-            values = training_dataset.values(neighbor,prediction_feature)
-            { :smiles => neighbor.smiles, :similarity => n[1], :measurements => values}
-          end
-          {
-            :smiles => compound.smiles, 
-            #:fingerprint => compound.fp4.collect{|id|  Smarts.find(id).name},
-            :measured => p[1],
-            :predicted => p[2],
-            #:relative_error => (Math.log10(p[1])-Math.log10(p[2])).abs/Math.log10(p[1]).to_f.abs,
-            :log_error => (Math.log10(p[1])-Math.log10(p[2])).abs,
-            :relative_error => (p[1]-p[2]).abs/p[1],
-            :confidence => p[3],
-            :neighbors => neighbors
-          }
-        end
-      end.compact.sort{|a,b| b[:relative_error] <=> a[:relative_error]}[0..n-1]
+    class ClassificationCrossValidation < CrossValidation
+      include ClassificationStatistics
+      field :accept_values, type: Array
+      field :confusion_matrix, type: Array
+      field :weighted_confusion_matrix, type: Array
+      field :accuracy, type: Float
+      field :weighted_accuracy, type: Float
+      field :true_rate, type: Hash
+      field :predictivity, type: Hash
+      field :probability_plot_id, type: BSON::ObjectId
     end
 
-    def confidence_plot
-      tmpfile = "/tmp/#{id.to_s}_confidence.png"
-      sorted_predictions = predictions.collect{|p| [(Math.log10(p[1])-Math.log10(p[2])).abs,p[3]] if p[1] and p[2]}.compact
-      R.assign "error", sorted_predictions.collect{|p| p[0]}
-      R.assign "confidence", sorted_predictions.collect{|p| p[1]}
-      # TODO fix axis names
-      R.eval "image = qplot(confidence,error)"
-      R.eval "image = image + stat_smooth(method='lm', se=FALSE)"
-      R.eval "ggsave(file='#{tmpfile}', plot=image)"
-      file = Mongo::Grid::File.new(File.read(tmpfile), :filename => "#{self.id.to_s}_confidence_plot.png")
-      plot_id = $gridfs.insert_one(file)
-      update(:confidence_plot_id => plot_id)
-      $gridfs.find_one(_id: confidence_plot_id).data
+    class RegressionCrossValidation < CrossValidation
+      include RegressionStatistics
+      field :rmse, type: Float, default:0
+      field :mae, type: Float, default:0
+      field :r_squared, type: Float
+      field :within_prediction_interval, type: Integer, default:0
+      field :out_of_prediction_interval, type: Integer, default:0
+      field :correlation_plot_id, type: BSON::ObjectId
     end
 
-    def correlation_plot
-      unless correlation_plot_id
-        tmpfile = "/tmp/#{id.to_s}_correlation.png"
-        x = predictions.collect{|p| p[1]}
-        y = predictions.collect{|p| p[2]}
-        attributes = Model::Lazar.find(self.model_id).attributes
-        attributes.delete_if{|key,_| key.match(/_id|_at/) or ["_id","creator","name"].include? key}
-        attributes = attributes.values.collect{|v| v.is_a?(String) ? v.sub(/OpenTox::/,'') : v}.join("\n")
-        R.assign "measurement", x
-        R.assign "prediction", y
-        R.eval "all = c(-log(measurement),-log(prediction))"
-        R.eval "range = c(min(all), max(all))"
-        R.eval "image = qplot(-log(prediction),-log(measurement),main='#{self.name}',asp=1,xlim=range, ylim=range)"
-        R.eval "image = image + geom_abline(intercept=0, slope=1)"
-        R.eval "ggsave(file='#{tmpfile}', plot=image)"
-        file = Mongo::Grid::File.new(File.read(tmpfile), :filename => "#{self.id.to_s}_correlation_plot.png")
-        plot_id = $gridfs.insert_one(file)
-        update(:correlation_plot_id => plot_id)
+    class RepeatedCrossValidation < Validation
+      field :crossvalidation_ids, type: Array, default: []
+      field :correlation_plot_id, type: BSON::ObjectId
+
+      def self.create model, folds=10, repeats=3
+        repeated_cross_validation = self.new
+        repeats.times do |n|
+          $logger.debug "Crossvalidation #{n+1} for #{model.name}"
+          repeated_cross_validation.crossvalidation_ids << CrossValidation.create(model, folds).id
+        end
+        repeated_cross_validation.save
+        repeated_cross_validation
       end
-      $gridfs.find_one(_id: correlation_plot_id).data
-    end
-  end
 
-  class RepeatedCrossValidation
-    field :crossvalidation_ids, type: Array, default: []
-    def self.create model, folds=10, repeats=3
-      repeated_cross_validation = self.new
-      repeats.times do |n|
-        $logger.debug "Crossvalidation #{n+1} for #{model.name}"
-        repeated_cross_validation.crossvalidation_ids << CrossValidation.create(model, folds).id
+      def crossvalidations
+        crossvalidation_ids.collect{|id| CrossValidation.find(id)}
       end
-      repeated_cross_validation.save
-      repeated_cross_validation
-    end
-    def crossvalidations
-      crossvalidation_ids.collect{|id| CrossValidation.find(id)}
+
     end
   end
 
-
 end