diff options
Diffstat (limited to 'paper/rmse.rb')
| -rw-r--r-- | paper/rmse.rb | 59 |
1 files changed, 38 insertions, 21 deletions
diff --git a/paper/rmse.rb b/paper/rmse.rb index 0d5ac11..90245eb 100644 --- a/paper/rmse.rb +++ b/paper/rmse.rb @@ -4,12 +4,33 @@ include OpenTox old = Dataset.from_csv_file File.join(File.dirname(__FILE__),"..","regression","LOAEL_mg_corrected_smiles_mmol.csv") new = Dataset.from_csv_file File.join(File.dirname(__FILE__),"..","regression","swissRat_chron_LOAEL_mmol.csv") -[old,new].each do |dataset| +File.open("rmse.R","w+") do |result| + + names = {old => "mazzatorta",new => "swiss"} + + [old,new].each do |dataset| + rmse = 0 + nr = 0 + dataset.compound_ids.each do |cid| + c = Compound.find cid + values = dataset.values(c,dataset.features.first) + if values.size > 1 + median = -Math.log(values.mean) + values.each do |v| + rmse += (-Math.log(v) - median)**2 + nr += 1 + end + end + end + rmse = Math.sqrt(rmse/nr) + result.puts "#{names[dataset]}.rmse <- #{rmse}" + end + rmse = 0 nr = 0 - dataset.compound_ids.each do |cid| + (old.compound_ids & new.compound_ids).each do |cid| c = Compound.find cid - values = dataset.values(c,dataset.features.first) + values = old.values(c,old.features.first) + new.values(c,new.features.first) if values.size > 1 median = -Math.log(values.mean) values.each do |v| @@ -18,29 +39,25 @@ new = Dataset.from_csv_file File.join(File.dirname(__FILE__),"..","regression"," end end end - p nr rmse = Math.sqrt(rmse/nr) - p "#{dataset.name}: #{rmse}" -end - + result.puts "common.rmse <- #{rmse}" -rmse = 0 -nr = 0 -(old.compound_ids & new.compound_ids).each do |cid| - c = Compound.find cid - values = old.values(c,old.features.first) + new.values(c,new.features.first) - p values.size - if values.size > 1 - median = -Math.log(values.mean) - values.each do |v| - rmse += (-Math.log(v) - median)**2 - nr += 1 + rmse = 0 + nr = 0 + (old.compound_ids + new.compound_ids).uniq.each do |cid| + c = Compound.find cid + values = old.values(c,old.features.first) + new.values(c,new.features.first) + if values.size > 1 + median = -Math.log(values.mean) + values.each do |v| + rmse += (-Math.log(v) - median)**2 + nr += 1 + end end end -end -p nr rmse = Math.sqrt(rmse/nr) - p "combined: #{rmse}" + result.puts "combined.rmse <- #{rmse}" +end #combined_rmse = Math.sqrt(combined_rmse/combined_nr) #p "combined: #{combined_rmse}" |