diff options
Diffstat (limited to 'validation/validation_service.rb')
| -rwxr-xr-x | validation/validation_service.rb | 19 |
1 files changed, 10 insertions, 9 deletions
diff --git a/validation/validation_service.rb b/validation/validation_service.rb index 5fded24..1b29630 100755 --- a/validation/validation_service.rb +++ b/validation/validation_service.rb @@ -500,8 +500,8 @@ module Validation meta, self.subjectid ).uri test_dataset_uris << test_dataset_uri end - when /true|super/ - raise "DO NOT USED SUPER-STRATIFICATION FOR VAL-EXPERIMENTS AND CV, IF SO SOLVE _MISSING_VAULE_NA_ PROBLEM" if stratified=="super" + when /^(true|super|super4)$/ + raise "DO NOT USED SUPER-STRATIFICATION FOR VAL-EXPERIMENTS AND CV, IF SO SOLVE _MISSING_VAULE_NA_ PROBLEM" if stratified=~/super/ if stratified=="true" features = [ self.prediction_feature ] else @@ -627,7 +627,7 @@ module Validation # splits a dataset into test and training dataset # returns map with training_dataset_uri and test_dataset_uri def self.train_test_dataset_split( orig_dataset_uri, prediction_feature, subjectid, stratified="false", - split_ratio=nil, random_seed=nil, missing_values=nil, task=nil ) + split_ratio=nil, random_seed=nil, missing_values=nil, task=nil, features=nil ) split_ratio=0.67 unless split_ratio split_ratio = split_ratio.to_f @@ -651,30 +651,31 @@ module Validation meta = { DC.creator => $url_provider.url_for('/training_test_split',:full) } case stratified - when /true|super|anti/ + when /^(true|super|super4|anti)$/ if stratified=="true" raise OpenTox::BadRequestError.new "prediction feature required for stratified splits" unless prediction_feature + LOGGER.warn "split features are ignored for stratified splits (use super instead)" if features features = [prediction_feature] else LOGGER.warn "prediction feature is ignored for super- or anti-stratified splits" if prediction_feature - features = nil end r_util = OpenTox::RUtil.new - train, test = r_util.stratified_split( orig_dataset, meta, missing_values, split_ratio, @subjectid, random_seed, features, stratified=="anti" ) + train, test = r_util.stratified_split( orig_dataset, meta, missing_values, split_ratio, @subjectid, random_seed, features, stratified ) r_util.quit_r result = {:training_dataset_uri => train.uri, :test_dataset_uri => test.uri} when "false" + LOGGER.warn "split features are ignored for non-stratified splits (use super instead)" if features compounds = orig_dataset.compounds raise OpenTox::BadRequestError.new "Cannot split datset, num compounds in dataset < 2 ("+compounds.size.to_s+")" if compounds.size<2 split = (compounds.size*split_ratio).to_i split = [split,1].max split = [split,compounds.size-2].min LOGGER.debug "splitting dataset "+orig_dataset_uri+ - " into train:0-"+split.to_s+" and test:"+(split+1).to_s+"-"+(compounds.size-1).to_s+ + " into train:0-"+(split-1).to_s+" and test:"+split.to_s+"-"+(compounds.size-1).to_s+ " (shuffled with seed "+random_seed.to_s+")" compounds.shuffle!( random_seed ) - training_compounds = compounds[0..split] - test_compounds = compounds[(split+1)..-1] + training_compounds = compounds[0..(split-1)] + test_compounds = compounds[split..-1] task.progress(33) if task meta[DC.title] = "Training dataset split of "+orig_dataset.uri |