diff options
Diffstat (limited to 'test/test_examples.rb')
-rwxr-xr-x | test/test_examples.rb | 234 |
1 files changed, 231 insertions, 3 deletions
diff --git a/test/test_examples.rb b/test/test_examples.rb index 49d7838..f3c0b7e 100755 --- a/test/test_examples.rb +++ b/test/test_examples.rb @@ -74,6 +74,14 @@ module ValidationExamples end end + class LazarLastEPAFHMSplit < LazarEPAFHMSplit + def initialize + super + @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/last") + end + end + + class MajorityEPAFHMSplit < EPAFHMSplit def initialize @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/regr/algorithm") @@ -81,11 +89,18 @@ module ValidationExamples end end + class MajorityRandomEPAFHMSplit < MajorityEPAFHMSplit + def initialize + @algorithm_params = "random=true" + super + end + end + ######################################################################################################## class EPAFHMCrossvalidation < CrossValidation def initialize - @dataset_file = File.new("data/EPAFHM.mini.csv","r") + @dataset_file = File.new("data/EPAFHM.csv","r") #@prediction_feature = "http://ot-dev.in-silico.ch/toxcreate/feature#IRIS%20unit%20risk" @num_folds = 10 end @@ -93,11 +108,20 @@ module ValidationExamples class MajorityEPAFHMCrossvalidation < EPAFHMCrossvalidation def initialize + #@dataset_uri = "http://local-ot/dataset/2366" + #@prediction_feature = "http://local-ot/dataset/2366/feature/LC50_mmol" @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/regr/algorithm") super end end + class MajorityRandomEPAFHMCrossvalidation < MajorityEPAFHMCrossvalidation + def initialize + @algorithm_params = "random=true" + super + end + end + class LazarEPAFHMCrossvalidation < EPAFHMCrossvalidation def initialize @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar") @@ -125,6 +149,14 @@ module ValidationExamples super end end + + class LazarLastHamsterSplit < LazarHamsterSplit + def initialize + super + @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/last") + end + end + class MajorityHamsterSplit < HamsterSplit def initialize @@ -133,6 +165,13 @@ module ValidationExamples end end + class MajorityRandomHamsterSplit < MajorityHamsterSplit + def initialize + @algorithm_params = "random=true" + super + end + end + ######################################################################################################## class HamsterBootstrapping < BootstrappingValidation @@ -212,6 +251,13 @@ module ValidationExamples super end end + + class MajorityRandomHamsterCrossvalidation < MajorityHamsterCrossvalidation + def initialize + @algorithm_params = "random=true" + super + end + end class LazarHamsterCrossvalidation < HamsterCrossvalidation def initialize @@ -221,6 +267,45 @@ module ValidationExamples end end + class LazarLastHamsterCrossvalidation < LazarHamsterCrossvalidation + def initialize + super + @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/last") + end + end + + ######################################################################################################## + + class LazarHamsterMiniCrossvalidation < CrossValidation + def initialize + @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar") + @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc") + @dataset_file = File.new("data/hamster_carcinogenicity.mini.csv","r") + @num_folds = 2 + end + end + + class ISSCANStratifiedCrossvalidation < CrossValidation + def initialize + @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar") + @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc") + @dataset_file = File.new("data/ISSCAN_v3a_canc-red.csv","r") + @stratified = true + @num_folds = 10 + end + end + + class ISSCAN2StratifiedCrossvalidation < CrossValidation + def initialize + @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar") + @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc") + @dataset_file = File.new("data/ISSCAN_v3a_sal.csv","r") + @stratified = true + @num_folds = 10 + end + end + + ######################################################################################################## class ISTHamsterCrossvalidation < CrossValidation @@ -368,6 +453,94 @@ module ValidationExamples end end + class NtuaModel2 < ModelValidation + def initialize + @model_uri = "http://opentox.ntua.gr:8080/model/11093fbc-3b8b-41e2-bfe3-d83f5f529efc" + @test_dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/54" + @prediction_feature="http://apps.ideaconsult.net:8080/ambit2/feature/579820" + end + end + + class NtuaModel3 < ModelValidation + def initialize + @model_uri = "http://opentox.ntua.gr:8080/model/bbab3714-e90b-4990-bef9-8e7d3a30eece" + @test_dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/R545" + #@prediction_feature="http://apps.ideaconsult.net:8080/ambit2/feature/579820" + end + end + + ######################################################################################################## + + class NtuaTrainingTest < TrainingTestValidation + def initialize + @algorithm_uri = "http://opentox.ntua.gr:8080/algorithm/mlr" + @training_dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/R545" + @test_dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/R545" + @prediction_feature="http://apps.ideaconsult.net:8080/ambit2/feature/22200" + end + end + + class NtuaTrainingTestSplit < SplitTestValidation + def initialize + @algorithm_uri = "http://opentox.ntua.gr:8080/algorithm/mlr" + @dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/R545" + @prediction_feature="http://apps.ideaconsult.net:8080/ambit2/feature/22200" + end + end + + class NtuaCrossvalidation < CrossValidation + def initialize + @algorithm_uri = "http://opentox.ntua.gr:8080/algorithm/mlr" + @dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/R545" + @prediction_feature="http://apps.ideaconsult.net:8080/ambit2/feature/22200" + end + end + + class AmbitVsNtuaTrainingTest < TrainingTestValidation + def initialize + @algorithm_uri = "http://apps.ideaconsult.net:8080/ambit2/algorithm/LR" + @training_dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/R545" + @test_dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/R545" + @prediction_feature="http://apps.ideaconsult.net:8080/ambit2/feature/22200" + end + end + + class AnotherAmbitJ48TrainingTest < TrainingTestValidation + def initialize + @algorithm_uri = "http://apps.ideaconsult.net:8080/ambit2/algorithm/J48" + @training_dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/585758" + @test_dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/585758" + @prediction_feature= "http://apps.ideaconsult.net:8080/ambit2/feature/111148" + end + end + + class TumTrainingTest < TrainingTestValidation + def initialize + @algorithm_uri = "http://lxkramer34.informatik.tu-muenchen.de:8080/OpenTox-dev/algorithm/kNNclassification" + @training_dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/585758" + @test_dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/585758" + @prediction_feature= "http://apps.ideaconsult.net:8080/ambit2/feature/111148" + end + end + + + + + class LazarVsNtuaCrossvalidation < CrossValidation + def initialize + @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar") + @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc") + @dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/R545" + @prediction_feature="http://apps.ideaconsult.net:8080/ambit2/feature/22200" + @num_folds=3 + end + end + + +# loading prediciton via test-dataset:'http://apps.ideaconsult.net:8080/ambit2/dataset/R545', +# test-target-datset:'', prediction-dataset:'http://apps.ideaconsult.net:8080/ambit2/dataset/584389', +# prediction_feature: 'http://apps.ideaconsult.net:8080/ambit2/feature/22200' ', predicted_variable: 'http://apps.ideaconsult.net:8080/ambit2/feature/627667' :: /ot_predictions.rb:21:in `initialize' +#D, [2011-05-11T13:47:26.631628 #22952] DEBUG -- : validation :: ######################################################################################################## class TumModel < ModelValidation @@ -402,6 +575,23 @@ module ValidationExamples end end + class AmbitXYModelValidation < ModelValidation + def initialize + @model_uri = "http://apps.ideaconsult.net:8080/ambit2/model/237692" + @test_dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/R736156" + @prediction_feature = "http://apps.ideaconsult.net:8080/ambit2/feature/430905" + end + end + + class AmbitXYZModelValidation < ModelValidation + def initialize + @model_uri = "http://apps.ideaconsult.net:8080/ambit2/model/238008" + @test_dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/R736396" + #@prediction_feature = "http://apps.ideaconsult.net:8080/ambit2/feature/430905" ?? + end + end + + class AmbitTrainingTest < TrainingTestValidation def initialize @training_dataset_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/R401560" @@ -528,20 +718,36 @@ module ValidationExamples end end + ######################################################################################################## + + class TumCrossValidation < CrossValidation + def initialize + @dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/124963" + @algorithm_uri = "http://opentox:8080/OpenTox/algorithm/kNNregression" + @prediction_feature = "http://apps.ideaconsult.net:8080/ambit2/feature/121905" + @num_folds=2 + super + end + end + ######################################################################################################## @@list = { - "1" => [ LazarHamsterSplit, MajorityHamsterSplit ], + "1" => [ LazarHamsterSplit, MajorityHamsterSplit, MajorityRandomHamsterSplit ], "1a" => [ LazarHamsterSplit ], "1b" => [ MajorityHamsterSplit ], + "1c" => [ MajorityRandomHamsterSplit ], + "1d" => [ LazarLastHamsterSplit ], "2" => [ LazarHamsterTrainingTest, MajorityHamsterTrainingTest ], "2a" => [ LazarHamsterTrainingTest ], "2b" => [ MajorityHamsterTrainingTest ], - "3" => [ LazarHamsterCrossvalidation, MajorityHamsterCrossvalidation ], + "3" => [ LazarHamsterCrossvalidation, MajorityHamsterCrossvalidation, MajorityRandomHamsterCrossvalidation ], "3a" => [ LazarHamsterCrossvalidation ], "3b" => [ MajorityHamsterCrossvalidation ], + "3c" => [ MajorityRandomHamsterCrossvalidation ], + "3d" => [ LazarLastHamsterCrossvalidation ], "4" => [ MajorityISTHamsterCrossvalidation, LazarISTHamsterCrossvalidation, ISTLazarISTHamsterCrossvalidation ], "4a" => [ MajorityISTHamsterCrossvalidation ], @@ -574,11 +780,17 @@ module ValidationExamples "13a" => [ LazarEPAFHMSplit ], "13b" => [ MajorityEPAFHMSplit ], + "13c" => [ MajorityRandomEPAFHMSplit ], + "13d" => [ LazarLastEPAFHMSplit ], + "14" => [ LazarEPAFHMCrossvalidation, MajorityEPAFHMCrossvalidation, MajorityRandomEPAFHMCrossvalidation ], "14a" => [ LazarEPAFHMCrossvalidation ], "14b" => [ MajorityEPAFHMCrossvalidation ], + "14c" => [ MajorityRandomEPAFHMCrossvalidation ], "15a" => [ NtuaModel ], + "15b" => [ NtuaModel2 ], + "15c" => [ NtuaModel3 ], "16" => [ LazarRepdoseSplit, MajorityRepdoseSplit ], "16a" => [ LazarRepdoseSplit ], @@ -599,7 +811,23 @@ module ValidationExamples "19g" => [ AmbitJ48TrainingTest ], "19h" => [ AmbitJ48TrainingTestSplit ], "19i" => [ AmbitAquaticModelValidation ], + "19j" => [ AmbitXYModelValidation ], + "20a" => [ TumCrossValidation ], + + "21a" => [ LazarHamsterMiniCrossvalidation ], + "21b" => [ ISSCANStratifiedCrossvalidation ], + "21c" => [ ISSCAN2StratifiedCrossvalidation ], + + "22a" => [ NtuaTrainingTest ], + "22b" => [ NtuaTrainingTestSplit ], + "22c" => [ NtuaCrossvalidation ], + "22d" => [ LazarVsNtuaCrossvalidation ], + + #impt + "22e" => [ AmbitVsNtuaTrainingTest ], + "22f" => [ AnotherAmbitJ48TrainingTest ], + "22g" => [ TumTrainingTest ], } |