Class: OpenTox::RegressionValidation

Inherits:
Validation show all
Defined in:
lib/validation.rb

Instance Method Summary collapse

Methods inherited from Validation

create, #model, #prediction_dataset, #test_dataset

Instance Method Details

#statistics ⇒ Object 



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# File 'lib/validation.rb', line 71

def statistics
  rmse = 0
  weighted_rmse = 0
  rse = 0
  weighted_rse = 0
  mae = 0
  weighted_mae = 0
  confidence_sum = 0
  predictions.each do |pred|
    compound_id,activity,prediction,confidence = pred
    if activity and 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
    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
  end
  x = predictions.collect{|p| p[1].median}
  y = predictions.collect{|p| p[2]}
  R.assign "measurement", x
  R.assign "prediction", y
  R.eval "r <- cor(-log(measurement),-log(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)
  { "R^2" => r**2, "RMSE" => rmse, "MAE" => mae }
end