From 4ee96cefffb0792308a9d56134b8a4c4f9395115 Mon Sep 17 00:00:00 2001 From: davor Date: Mon, 27 Feb 2012 11:51:59 +0100 Subject: Added/updated validation scripts. --- cv/scripts/CV_ds_pctype_algo_rseed.rb | 14 +++-- cv/scripts/CV_ds_pctype_algo_rseed_FHM.rb | 62 ++++++++++++++++++++++ cv/scripts/CV_ds_pctype_algo_rseed_LOAEL.rb | 62 ++++++++++++++++++++++ cv/scripts/CV_ds_pctype_algo_rseed_LOAEL_loo.rb | 61 ++++++++++++++++++++++ cv/scripts/CV_ds_pctype_algo_rseed_MOU_ttv.rb | 68 +++++++++++++++++++++++++ cv/scripts/CV_ds_pctype_algo_rseed_RAT_ttv.rb | 68 +++++++++++++++++++++++++ cv/scripts/factors_config | 22 ++++++-- cv/scripts/factors_config_FHM | 31 +++++++++++ cv/scripts/factors_config_LOAEL | 31 +++++++++++ cv/scripts/factors_config_LOAEL_loo | 31 +++++++++++ cv/scripts/factors_config_MOU | 31 +++++++++++ cv/scripts/factors_config_RAT | 31 +++++++++++ cv/scripts/wrapper_pc_cv_FHM.sh | 45 ++++++++++++++++ cv/scripts/wrapper_pc_cv_LOAEL.sh | 45 ++++++++++++++++ cv/scripts/wrapper_pc_cv_LOAEL_loo.sh | 45 ++++++++++++++++ cv/scripts/wrapper_pc_cv_MOU_ttv.sh | 45 ++++++++++++++++ cv/scripts/wrapper_pc_cv_RAT_ttv.sh | 45 ++++++++++++++++ 17 files changed, 728 insertions(+), 9 deletions(-) create mode 100644 cv/scripts/CV_ds_pctype_algo_rseed_FHM.rb create mode 100644 cv/scripts/CV_ds_pctype_algo_rseed_LOAEL.rb create mode 100644 cv/scripts/CV_ds_pctype_algo_rseed_LOAEL_loo.rb create mode 100644 cv/scripts/CV_ds_pctype_algo_rseed_MOU_ttv.rb create mode 100644 cv/scripts/CV_ds_pctype_algo_rseed_RAT_ttv.rb create mode 100644 cv/scripts/factors_config_FHM create mode 100644 cv/scripts/factors_config_LOAEL create mode 100644 cv/scripts/factors_config_LOAEL_loo create mode 100644 cv/scripts/factors_config_MOU create mode 100644 cv/scripts/factors_config_RAT create mode 100755 cv/scripts/wrapper_pc_cv_FHM.sh create mode 100755 cv/scripts/wrapper_pc_cv_LOAEL.sh create mode 100755 cv/scripts/wrapper_pc_cv_LOAEL_loo.sh create mode 100755 cv/scripts/wrapper_pc_cv_MOU_ttv.sh create mode 100755 cv/scripts/wrapper_pc_cv_RAT_ttv.sh diff --git a/cv/scripts/CV_ds_pctype_algo_rseed.rb b/cv/scripts/CV_ds_pctype_algo_rseed.rb index 36adb6f..bd86579 100644 --- a/cv/scripts/CV_ds_pctype_algo_rseed.rb +++ b/cv/scripts/CV_ds_pctype_algo_rseed.rb @@ -36,6 +36,10 @@ pc_ds_uri = ds[ds_name][pc_type] algo_params = "prediction_algorithm=#{algo}" algo_params += ";pc_type=#{pc_type}" unless pc_type == "nil" algo_params += ";feature_dataset_uri=#{pc_ds_uri}" unless pc_type == "nil" +#algo_params += ";min_chisq_significance=0.9" +#algo_params += ";min_frequency=6" +#algo_params += ";feature_type=trees" + puts algo_params.to_yaml prediction_feature = OpenTox::Dataset.find(ds_uri).features.keys.first @@ -45,14 +49,14 @@ prediction_feature = OpenTox::Dataset.find(ds_uri).features.keys.first cv_args = {} cv_args[:dataset_uri] = ds_uri cv_args[:prediction_feature] = prediction_feature -cv_args[:algorithm_uri] = "http://toxcreate3.in-silico.ch:80XX/algorithm/lazar" +cv_args[:algorithm_uri] = "http://toxcreate3.in-silico.ch:8080/algorithm/lazar" cv_args[:algorithm_params] = algo_params cv_args[:stratified] = false cv_args[:random_seed] = r_seed puts cv_args.to_yaml -#cv = OpenTox::Crossvalidation.create(cv_args).uri -#puts cv +cv = OpenTox::Crossvalidation.create(cv_args).uri +puts cv -#cvr = OpenTox::CrossvalidationReport.create( cv , subjectid).uri -#puts cvr +cvr = OpenTox::CrossvalidationReport.create( cv , subjectid).uri +puts cvr diff --git a/cv/scripts/CV_ds_pctype_algo_rseed_FHM.rb b/cv/scripts/CV_ds_pctype_algo_rseed_FHM.rb new file mode 100644 index 0000000..bd86579 --- /dev/null +++ b/cv/scripts/CV_ds_pctype_algo_rseed_FHM.rb @@ -0,0 +1,62 @@ +# Do a 10-fold crossvalidation +# # Author: Andreas Maunz, David Vorgrimmler +# # @params: Dataset_name(see dataset_nestle.yaml), pc_type(electronic,cpsa or constitutional ... or nil to disable), prediction_algorithm(local_mlr_prop or local_svm_regression ...) + +if ARGV.size != 4 + puts "Args: ds_name, pc_type, algo, random_seed" + puts ARGV.size + exit +end + +ds_file = "datasets.yaml" +pwd=`pwd` +path = "#{pwd.chop}/../data/#{ds_file}" +if File.exists?(path) + puts "#{ds_file} exists" +else + puts "#{ds_file} does not exist." + exit +end + +require 'rubygems' +require 'opentox-ruby' +require 'yaml' + +subjectid = nil + +ds_name = ARGV[0] # e.g. MOU +pc_type = ARGV[1] # e.g. electronic,cpsa or nil to disable +algo = ARGV[2] # e.g. local_svm_regression, local_mlr_prop +r_seed = ARGV[3] # 1, 2, ..., 10 + +ds = YAML::load_file("../data/datasets.yaml") +ds_uri = ds[ds_name]["dataset"] +pc_ds_uri = ds[ds_name][pc_type] + +algo_params = "prediction_algorithm=#{algo}" +algo_params += ";pc_type=#{pc_type}" unless pc_type == "nil" +algo_params += ";feature_dataset_uri=#{pc_ds_uri}" unless pc_type == "nil" +#algo_params += ";min_chisq_significance=0.9" +#algo_params += ";min_frequency=6" +#algo_params += ";feature_type=trees" + +puts algo_params.to_yaml + +prediction_feature = OpenTox::Dataset.find(ds_uri).features.keys.first + + +# Ready +cv_args = {} +cv_args[:dataset_uri] = ds_uri +cv_args[:prediction_feature] = prediction_feature +cv_args[:algorithm_uri] = "http://toxcreate3.in-silico.ch:8080/algorithm/lazar" +cv_args[:algorithm_params] = algo_params +cv_args[:stratified] = false +cv_args[:random_seed] = r_seed +puts cv_args.to_yaml + +cv = OpenTox::Crossvalidation.create(cv_args).uri +puts cv + +cvr = OpenTox::CrossvalidationReport.create( cv , subjectid).uri +puts cvr diff --git a/cv/scripts/CV_ds_pctype_algo_rseed_LOAEL.rb b/cv/scripts/CV_ds_pctype_algo_rseed_LOAEL.rb new file mode 100644 index 0000000..bd86579 --- /dev/null +++ b/cv/scripts/CV_ds_pctype_algo_rseed_LOAEL.rb @@ -0,0 +1,62 @@ +# Do a 10-fold crossvalidation +# # Author: Andreas Maunz, David Vorgrimmler +# # @params: Dataset_name(see dataset_nestle.yaml), pc_type(electronic,cpsa or constitutional ... or nil to disable), prediction_algorithm(local_mlr_prop or local_svm_regression ...) + +if ARGV.size != 4 + puts "Args: ds_name, pc_type, algo, random_seed" + puts ARGV.size + exit +end + +ds_file = "datasets.yaml" +pwd=`pwd` +path = "#{pwd.chop}/../data/#{ds_file}" +if File.exists?(path) + puts "#{ds_file} exists" +else + puts "#{ds_file} does not exist." + exit +end + +require 'rubygems' +require 'opentox-ruby' +require 'yaml' + +subjectid = nil + +ds_name = ARGV[0] # e.g. MOU +pc_type = ARGV[1] # e.g. electronic,cpsa or nil to disable +algo = ARGV[2] # e.g. local_svm_regression, local_mlr_prop +r_seed = ARGV[3] # 1, 2, ..., 10 + +ds = YAML::load_file("../data/datasets.yaml") +ds_uri = ds[ds_name]["dataset"] +pc_ds_uri = ds[ds_name][pc_type] + +algo_params = "prediction_algorithm=#{algo}" +algo_params += ";pc_type=#{pc_type}" unless pc_type == "nil" +algo_params += ";feature_dataset_uri=#{pc_ds_uri}" unless pc_type == "nil" +#algo_params += ";min_chisq_significance=0.9" +#algo_params += ";min_frequency=6" +#algo_params += ";feature_type=trees" + +puts algo_params.to_yaml + +prediction_feature = OpenTox::Dataset.find(ds_uri).features.keys.first + + +# Ready +cv_args = {} +cv_args[:dataset_uri] = ds_uri +cv_args[:prediction_feature] = prediction_feature +cv_args[:algorithm_uri] = "http://toxcreate3.in-silico.ch:8080/algorithm/lazar" +cv_args[:algorithm_params] = algo_params +cv_args[:stratified] = false +cv_args[:random_seed] = r_seed +puts cv_args.to_yaml + +cv = OpenTox::Crossvalidation.create(cv_args).uri +puts cv + +cvr = OpenTox::CrossvalidationReport.create( cv , subjectid).uri +puts cvr diff --git a/cv/scripts/CV_ds_pctype_algo_rseed_LOAEL_loo.rb b/cv/scripts/CV_ds_pctype_algo_rseed_LOAEL_loo.rb new file mode 100644 index 0000000..88adac2 --- /dev/null +++ b/cv/scripts/CV_ds_pctype_algo_rseed_LOAEL_loo.rb @@ -0,0 +1,61 @@ +# Do a 10-fold crossvalidation +# # Author: Andreas Maunz, David Vorgrimmler +# # @params: Dataset_name(see dataset_nestle.yaml), pc_type(electronic,cpsa or constitutional ... or nil to disable), prediction_algorithm(local_mlr_prop or local_svm_regression ...) + +if ARGV.size != 4 + puts "Args: ds_name, pc_type, algo, random_seed" + puts ARGV.size + exit +end + +ds_file = "datasets.yaml" +pwd=`pwd` +path = "#{pwd.chop}/../data/#{ds_file}" +if File.exists?(path) + puts "#{ds_file} exists" +else + puts "#{ds_file} does not exist." + exit +end + +require 'rubygems' +require 'opentox-ruby' +require 'yaml' + +subjectid = nil + +ds_name = ARGV[0] # e.g. MOU +pc_type = ARGV[1] # e.g. electronic,cpsa or nil to disable +algo = ARGV[2] # e.g. local_svm_regression, local_mlr_prop +r_seed = ARGV[3] # 1, 2, ..., 10 + +ds = YAML::load_file("../data/datasets.yaml") +ds_uri = ds[ds_name]["dataset"] +pc_ds_uri = ds[ds_name][pc_type] + +algo_params = "prediction_algorithm=#{algo}" +algo_params += ";pc_type=#{pc_type}" unless pc_type == "nil" +algo_params += ";feature_dataset_uri=#{pc_ds_uri}" unless pc_type == "nil" +#algo_params += ";min_chisq_significance=0.9" +#algo_params += ";min_frequency=6" +#algo_params += ";feature_type=trees" + +puts algo_params.to_yaml + +prediction_feature = OpenTox::Dataset.find(ds_uri).features.keys.first + + +# Ready +cv_args = {} +cv_args[:dataset_uri] = ds_uri +cv_args[:prediction_feature] = prediction_feature +cv_args[:algorithm_uri] = "http://toxcreate3.in-silico.ch:8080/algorithm/lazar" +cv_args[:algorithm_params] = algo_params +cv_args[:loo] = true +puts cv_args.to_yaml + +loo = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-validation"],"crossvalidation/loo"), cv_args ) +puts loo + +cvr = OpenTox::CrossvalidationReport.create( loo , subjectid).uri +puts cvr diff --git a/cv/scripts/CV_ds_pctype_algo_rseed_MOU_ttv.rb b/cv/scripts/CV_ds_pctype_algo_rseed_MOU_ttv.rb new file mode 100644 index 0000000..5fc7661 --- /dev/null +++ b/cv/scripts/CV_ds_pctype_algo_rseed_MOU_ttv.rb @@ -0,0 +1,68 @@ +# Do a 10-fold crossvalidation +# # Author: Andreas Maunz, David Vorgrimmler +# # @params: Dataset_name(see dataset_nestle.yaml), pc_type(electronic,cpsa or constitutional ... or nil to disable), prediction_algorithm(local_mlr_prop or local_svm_regression ...) + +if ARGV.size != 4 + puts "Args: ds_name, pc_type, algo, random_seed" + puts ARGV.size + exit +end + +ds_file = "datasets.yaml" +pwd=`pwd` +path = "#{pwd.chop}/../data/#{ds_file}" +if File.exists?(path) + puts "#{ds_file} exists" +else + puts "#{ds_file} does not exist." + exit +end + +require 'rubygems' +require 'opentox-ruby' +require 'yaml' + +subjectid = nil + +ds_name = ARGV[0] # e.g. MOU +pc_type = ARGV[1] # e.g. electronic,cpsa or nil to disable +algo = ARGV[2] # e.g. local_svm_regression, local_mlr_prop +r_seed = ARGV[3] # 1, 2, ..., 10 + +ds = YAML::load_file("../data/datasets.yaml") +ds_uri = ds[ds_name]["dataset"] +#ds_test_target_uri = ds[ds_name]["dataset"] +ds_test_uri = ds[ds_name]["test"] +ds_training_uri = ds[ds_name]["training"] +pc_ds_uri = ds[ds_name][pc_type] + +algo_params = "prediction_algorithm=#{algo}" +algo_params += ";pc_type=#{pc_type}" unless pc_type == "nil" +algo_params += ";feature_dataset_uri=#{pc_ds_uri}" unless pc_type == "nil" +#algo_params += ";min_chisq_significance=0.9" +#algo_params += ";min_frequency=6" +#algo_params += ";feature_type=trees" + +puts algo_params.to_yaml + +prediction_feature = OpenTox::Dataset.find(ds_training_uri).features.keys.first + + +# Ready +cv_args = {} +#cv_args[:dataset_uri] = ds_uri +cv_args[:test_dataset_uri] = ds_test_uri +cv_args[:training_dataset_uri] = ds_training_uri +#cv_args[:test_target_dataset_uri] = ds_test_target_uri +cv_args[:prediction_feature] = prediction_feature +cv_args[:algorithm_uri] = "http://toxcreate3.in-silico.ch:8080/algorithm/lazar" +cv_args[:algorithm_params] = algo_params +#cv_args[:stratified] = false +#cv_args[:random_seed] = r_seed +puts cv_args.to_yaml + +ttv = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-validation"],"training_test_validation"), cv_args ) +puts ttv + +vr = OpenTox::ValidationReport.create( ttv , subjectid).uri +puts vr diff --git a/cv/scripts/CV_ds_pctype_algo_rseed_RAT_ttv.rb b/cv/scripts/CV_ds_pctype_algo_rseed_RAT_ttv.rb new file mode 100644 index 0000000..5fc7661 --- /dev/null +++ b/cv/scripts/CV_ds_pctype_algo_rseed_RAT_ttv.rb @@ -0,0 +1,68 @@ +# Do a 10-fold crossvalidation +# # Author: Andreas Maunz, David Vorgrimmler +# # @params: Dataset_name(see dataset_nestle.yaml), pc_type(electronic,cpsa or constitutional ... or nil to disable), prediction_algorithm(local_mlr_prop or local_svm_regression ...) + +if ARGV.size != 4 + puts "Args: ds_name, pc_type, algo, random_seed" + puts ARGV.size + exit +end + +ds_file = "datasets.yaml" +pwd=`pwd` +path = "#{pwd.chop}/../data/#{ds_file}" +if File.exists?(path) + puts "#{ds_file} exists" +else + puts "#{ds_file} does not exist." + exit +end + +require 'rubygems' +require 'opentox-ruby' +require 'yaml' + +subjectid = nil + +ds_name = ARGV[0] # e.g. MOU +pc_type = ARGV[1] # e.g. electronic,cpsa or nil to disable +algo = ARGV[2] # e.g. local_svm_regression, local_mlr_prop +r_seed = ARGV[3] # 1, 2, ..., 10 + +ds = YAML::load_file("../data/datasets.yaml") +ds_uri = ds[ds_name]["dataset"] +#ds_test_target_uri = ds[ds_name]["dataset"] +ds_test_uri = ds[ds_name]["test"] +ds_training_uri = ds[ds_name]["training"] +pc_ds_uri = ds[ds_name][pc_type] + +algo_params = "prediction_algorithm=#{algo}" +algo_params += ";pc_type=#{pc_type}" unless pc_type == "nil" +algo_params += ";feature_dataset_uri=#{pc_ds_uri}" unless pc_type == "nil" +#algo_params += ";min_chisq_significance=0.9" +#algo_params += ";min_frequency=6" +#algo_params += ";feature_type=trees" + +puts algo_params.to_yaml + +prediction_feature = OpenTox::Dataset.find(ds_training_uri).features.keys.first + + +# Ready +cv_args = {} +#cv_args[:dataset_uri] = ds_uri +cv_args[:test_dataset_uri] = ds_test_uri +cv_args[:training_dataset_uri] = ds_training_uri +#cv_args[:test_target_dataset_uri] = ds_test_target_uri +cv_args[:prediction_feature] = prediction_feature +cv_args[:algorithm_uri] = "http://toxcreate3.in-silico.ch:8080/algorithm/lazar" +cv_args[:algorithm_params] = algo_params +#cv_args[:stratified] = false +#cv_args[:random_seed] = r_seed +puts cv_args.to_yaml + +ttv = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-validation"],"training_test_validation"), cv_args ) +puts ttv + +vr = OpenTox::ValidationReport.create( ttv , subjectid).uri +puts vr diff --git a/cv/scripts/factors_config b/cv/scripts/factors_config index 83bb54c..b2588ff 100644 --- a/cv/scripts/factors_config +++ b/cv/scripts/factors_config @@ -1,17 +1,31 @@ #Dataset pc_type prediction_algorithm -MDD constitutional local_svm_regression -MDD electronic,cpsa local_svm_regression -MDD topological local_svm_regression -MDD nil local_svm_regression +#MDD constitutional local_svm_regression +#MDD electronic,cpsa local_svm_regression +#MDD topological local_svm_regression +#MDD hybrid local_svm_regression +#MDD joelib local_svm_regression +#MDD nil local_svm_regression #FHM constitutional local_svm_regression #FHM electronic,cpsa local_svm_regression #FHM topological local_svm_regression +#FHM hybrid local_svm_regression +#FHM joelib local_svm_regression #FHM nil local_svm_regression #RAT constitutional local_svm_regression #RAT electronic,cpsa local_svm_regression #RAT topological local_svm_regression +#RAT hybrid local_svm_regression +#RAT joelib local_svm_regression #RAT nil local_svm_regression #MOU constitutional local_svm_regression #MOU electronic,cpsa local_svm_regression #MOU topological local_svm_regression +#MOU hybrid local_svm_regression +#MOU joelib local_svm_regression #MOU nil local_svm_regression +#LOAEL constitutional local_svm_regression +#LOAEL electronic,cpsa local_svm_regression +#LOAEL topological local_svm_regression +#LOAEL hybrid local_svm_regression +#LOAEL joelib local_svm_regression +#LOAEL nil local_svm_regressioni diff --git a/cv/scripts/factors_config_FHM b/cv/scripts/factors_config_FHM new file mode 100644 index 0000000..2b840bd --- /dev/null +++ b/cv/scripts/factors_config_FHM @@ -0,0 +1,31 @@ +#Dataset pc_type prediction_algorithm +#MDD constitutional local_svm_regression +#MDD electronic,cpsa local_svm_regression +#MDD topological local_svm_regression +#MDD hybrid local_svm_regression +#MDD joelib local_svm_regression +#MDD nil local_svm_regression +FHM constitutional local_svm_regression +FHM electronic,cpsa local_svm_regression +FHM topological local_svm_regression +FHM hybrid local_svm_regression +FHM joelib local_svm_regression +FHM nil local_svm_regression +#RAT constitutional local_svm_regression +#RAT electronic,cpsa local_svm_regression +#RAT topological local_svm_regression +#RAT hybrid local_svm_regression +#RAT joelib local_svm_regression +#RAT nil local_svm_regression +#MOU constitutional local_svm_regression +#MOU electronic,cpsa local_svm_regression +#MOU topological local_svm_regression +#MOU hybrid local_svm_regression +#MOU joelib local_svm_regression +#MOU nil local_svm_regression +#LOAEL constitutional local_svm_regression +#LOAEL electronic,cpsa local_svm_regression +#LOAEL topological local_svm_regression +#LOAEL hybrid local_svm_regression +#LOAEL joelib local_svm_regression +#LOAEL nil local_svm_regressioni diff --git a/cv/scripts/factors_config_LOAEL b/cv/scripts/factors_config_LOAEL new file mode 100644 index 0000000..91294e7 --- /dev/null +++ b/cv/scripts/factors_config_LOAEL @@ -0,0 +1,31 @@ +#Dataset pc_type prediction_algorithm +#MDD constitutional local_svm_regression +#MDD electronic,cpsa local_svm_regression +#MDD topological local_svm_regression +#MDD hybrid local_svm_regression +#MDD joelib local_svm_regression +#MDD nil local_svm_regression +#FHM constitutional local_svm_regression +#FHM electronic,cpsa local_svm_regression +#FHM topological local_svm_regression +#FHM hybrid local_svm_regression +#FHM joelib local_svm_regression +#FHM nil local_svm_regression +#RAT constitutional local_svm_regression +#RAT electronic,cpsa local_svm_regression +#RAT topological local_svm_regression +#RAT hybrid local_svm_regression +#RAT joelib local_svm_regression +#RAT nil local_svm_regression +#MOU constitutional local_svm_regression +#MOU electronic,cpsa local_svm_regression +#MOU topological local_svm_regression +#MOU hybrid local_svm_regression +#MOU joelib local_svm_regression +#MOU nil local_svm_regression +LOAEL constitutional local_svm_regression +LOAEL electronic,cpsa local_svm_regression +LOAEL topological local_svm_regression +LOAEL hybrid local_svm_regression +LOAEL joelib local_svm_regression +LOAEL nil local_svm_regressioni diff --git a/cv/scripts/factors_config_LOAEL_loo b/cv/scripts/factors_config_LOAEL_loo new file mode 100644 index 0000000..91294e7 --- /dev/null +++ b/cv/scripts/factors_config_LOAEL_loo @@ -0,0 +1,31 @@ +#Dataset pc_type prediction_algorithm +#MDD constitutional local_svm_regression +#MDD electronic,cpsa local_svm_regression +#MDD topological local_svm_regression +#MDD hybrid local_svm_regression +#MDD joelib local_svm_regression +#MDD nil local_svm_regression +#FHM constitutional local_svm_regression +#FHM electronic,cpsa local_svm_regression +#FHM topological local_svm_regression +#FHM hybrid local_svm_regression +#FHM joelib local_svm_regression +#FHM nil local_svm_regression +#RAT constitutional local_svm_regression +#RAT electronic,cpsa local_svm_regression +#RAT topological local_svm_regression +#RAT hybrid local_svm_regression +#RAT joelib local_svm_regression +#RAT nil local_svm_regression +#MOU constitutional local_svm_regression +#MOU electronic,cpsa local_svm_regression +#MOU topological local_svm_regression +#MOU hybrid local_svm_regression +#MOU joelib local_svm_regression +#MOU nil local_svm_regression +LOAEL constitutional local_svm_regression +LOAEL electronic,cpsa local_svm_regression +LOAEL topological local_svm_regression +LOAEL hybrid local_svm_regression +LOAEL joelib local_svm_regression +LOAEL nil local_svm_regressioni diff --git a/cv/scripts/factors_config_MOU b/cv/scripts/factors_config_MOU new file mode 100644 index 0000000..e839067 --- /dev/null +++ b/cv/scripts/factors_config_MOU @@ -0,0 +1,31 @@ +#Dataset pc_type prediction_algorithm +#MDD constitutional local_svm_regression +#MDD electronic,cpsa local_svm_regression +#MDD topological local_svm_regression +#MDD hybrid local_svm_regression +#MDD joelib local_svm_regression +#MDD nil local_svm_regression +#FHM constitutional local_svm_regression +#FHM electronic,cpsa local_svm_regression +#FHM topological local_svm_regression +#FHM hybrid local_svm_regression +#FHM joelib local_svm_regression +#FHM nil local_svm_regression +#RAT constitutional local_svm_regression +#RAT electronic,cpsa local_svm_regression +#RAT topological local_svm_regression +#RAT hybrid local_svm_regression +#RAT joelib local_svm_regression +#RAT nil local_svm_regression +MOU constitutional local_svm_regression +MOU electronic,cpsa local_svm_regression +MOU topological local_svm_regression +MOU hybrid local_svm_regression +MOU joelib local_svm_regression +MOU nil local_svm_regression +#LOAEL constitutional local_svm_regression +#LOAEL electronic,cpsa local_svm_regression +#LOAEL topological local_svm_regression +#LOAEL hybrid local_svm_regression +#LOAEL joelib local_svm_regression +#LOAEL nil local_svm_regressioni diff --git a/cv/scripts/factors_config_RAT b/cv/scripts/factors_config_RAT new file mode 100644 index 0000000..8d7f102 --- /dev/null +++ b/cv/scripts/factors_config_RAT @@ -0,0 +1,31 @@ +#Dataset pc_type prediction_algorithm +#MDD constitutional local_svm_regression +#MDD electronic,cpsa local_svm_regression +#MDD topological local_svm_regression +#MDD hybrid local_svm_regression +#MDD joelib local_svm_regression +#MDD nil local_svm_regression +#FHM constitutional local_svm_regression +#FHM electronic,cpsa local_svm_regression +#FHM topological local_svm_regression +#FHM hybrid local_svm_regression +#FHM joelib local_svm_regression +#FHM nil local_svm_regression +RAT constitutional local_svm_regression +RAT electronic,cpsa local_svm_regression +RAT topological local_svm_regression +RAT hybrid local_svm_regression +RAT joelib local_svm_regression +RAT nil local_svm_regression +#MOU constitutional local_svm_regression +#MOU electronic,cpsa local_svm_regression +#MOU topological local_svm_regression +#MOU hybrid local_svm_regression +#MOU joelib local_svm_regression +#MOU nil local_svm_regression +#LOAEL constitutional local_svm_regression +#LOAEL electronic,cpsa local_svm_regression +#LOAEL topological local_svm_regression +#LOAEL hybrid local_svm_regression +#LOAEL joelib local_svm_regression +#LOAEL nil local_svm_regressioni diff --git a/cv/scripts/wrapper_pc_cv_FHM.sh b/cv/scripts/wrapper_pc_cv_FHM.sh new file mode 100755 index 0000000..4415062 --- /dev/null +++ b/cv/scripts/wrapper_pc_cv_FHM.sh @@ -0,0 +1,45 @@ +#!/bin/bash +# Wrapper Skript for CV +# Reads factors_config, ../data/datasets.yaml and performs cv's +# Andreas Maunz, David Vorgrimmler, 2012 + +if [ $# -lt 1 ]; then + echo "Usage: $0 factors" + exit +fi + +PWD=`pwd` +echo $PWD +if [ ! -f $PWD/../data/datasets.yaml ] +then + echo "datasets.yaml does not exist." + exit +fi + +# Configure basics +source $HOME/.bash_aliases +otconfig +THIS_DATE=`date +%Y%m%d_%H_` +CV="CV_ds_pctype_algo_rseed_FHM.rb" +FACTORS="$1" + +# Don't start when running +while ps x | grep $CV | grep -v grep >/dev/null 2>&1; do sleep 3; done + +LOGFILE="$THIS_DATE""$USER""_wrapper_pc_cv_FHM.log" +rm "$LOGFILE" >/dev/null 2>&1 + + +cat $FACTORS | while read factor; do + if ! [[ "$factor" =~ "#" ]]; then # allow comments + for r_seed in 1 #2 3 4 5 + do + factor="$factor $r_seed" + echo "${THIS_DATE}: $factor" >> $LOGFILE>&1 + echo "ruby $CV $factor" >> $LOGFILE 2>&1 + ruby $CV $factor >> $LOGFILE 2>&1 + echo >> $LOGFILE 2>&1 + done + fi +done + diff --git a/cv/scripts/wrapper_pc_cv_LOAEL.sh b/cv/scripts/wrapper_pc_cv_LOAEL.sh new file mode 100755 index 0000000..4d74596 --- /dev/null +++ b/cv/scripts/wrapper_pc_cv_LOAEL.sh @@ -0,0 +1,45 @@ +#!/bin/bash +# Wrapper Skript for CV +# Reads factors_config, ../data/datasets.yaml and performs cv's +# Andreas Maunz, David Vorgrimmler, 2012 + +if [ $# -lt 1 ]; then + echo "Usage: $0 factors" + exit +fi + +PWD=`pwd` +echo $PWD +if [ ! -f $PWD/../data/datasets.yaml ] +then + echo "datasets.yaml does not exist." + exit +fi + +# Configure basics +source $HOME/.bash_aliases +otconfig +THIS_DATE=`date +%Y%m%d_%H_` +CV="CV_ds_pctype_algo_rseed_LOAEL.rb" +FACTORS="$1" + +# Don't start when running +while ps x | grep $CV | grep -v grep >/dev/null 2>&1; do sleep 3; done + +LOGFILE="$THIS_DATE""$USER""_wrapper_pc_cv_LOAEL.log" +rm "$LOGFILE" >/dev/null 2>&1 + + +cat $FACTORS | while read factor; do + if ! [[ "$factor" =~ "#" ]]; then # allow comments + for r_seed in 1 #2 3 4 5 + do + factor="$factor $r_seed" + echo "${THIS_DATE}: $factor" >> $LOGFILE>&1 + echo "ruby $CV $factor" >> $LOGFILE 2>&1 + ruby $CV $factor >> $LOGFILE 2>&1 + echo >> $LOGFILE 2>&1 + done + fi +done + diff --git a/cv/scripts/wrapper_pc_cv_LOAEL_loo.sh b/cv/scripts/wrapper_pc_cv_LOAEL_loo.sh new file mode 100755 index 0000000..be3e6df --- /dev/null +++ b/cv/scripts/wrapper_pc_cv_LOAEL_loo.sh @@ -0,0 +1,45 @@ +#!/bin/bash +# Wrapper Skript for CV +# Reads factors_config, ../data/datasets.yaml and performs cv's +# Andreas Maunz, David Vorgrimmler, 2012 + +if [ $# -lt 1 ]; then + echo "Usage: $0 factors" + exit +fi + +PWD=`pwd` +echo $PWD +if [ ! -f $PWD/../data/datasets.yaml ] +then + echo "datasets.yaml does not exist." + exit +fi + +# Configure basics +source $HOME/.bash_aliases +otconfig +THIS_DATE=`date +%Y%m%d_%H_` +CV="CV_ds_pctype_algo_rseed_LOAEL_loo.rb" +FACTORS="$1" + +# Don't start when running +while ps x | grep $CV | grep -v grep >/dev/null 2>&1; do sleep 3; done + +LOGFILE="$THIS_DATE""$USER""_wrapper_pc_cv_LOAEL_loo.log" +rm "$LOGFILE" >/dev/null 2>&1 + + +cat $FACTORS | while read factor; do + if ! [[ "$factor" =~ "#" ]]; then # allow comments + for r_seed in 1 #2 3 4 5 + do + factor="$factor $r_seed" + echo "${THIS_DATE}: $factor" >> $LOGFILE>&1 + echo "ruby $CV $factor" >> $LOGFILE 2>&1 + ruby $CV $factor >> $LOGFILE 2>&1 + echo >> $LOGFILE 2>&1 + done + fi +done + diff --git a/cv/scripts/wrapper_pc_cv_MOU_ttv.sh b/cv/scripts/wrapper_pc_cv_MOU_ttv.sh new file mode 100755 index 0000000..2bc8415 --- /dev/null +++ b/cv/scripts/wrapper_pc_cv_MOU_ttv.sh @@ -0,0 +1,45 @@ +#!/bin/bash +# Wrapper Skript for CV +# Reads factors_config, ../data/datasets.yaml and performs cv's +# Andreas Maunz, David Vorgrimmler, 2012 + +if [ $# -lt 1 ]; then + echo "Usage: $0 factors" + exit +fi + +PWD=`pwd` +echo $PWD +if [ ! -f $PWD/../data/datasets.yaml ] +then + echo "datasets.yaml does not exist." + exit +fi + +# Configure basics +source $HOME/.bash_aliases +otconfig +THIS_DATE=`date +%Y%m%d_%H_` +CV="CV_ds_pctype_algo_rseed_MOU_ttv.rb" +FACTORS="$1" + +# Don't start when running +while ps x | grep $CV | grep -v grep >/dev/null 2>&1; do sleep 3; done + +LOGFILE="$THIS_DATE""$USER""_wrapper_pc_cv_MOU_ttv.log" +rm "$LOGFILE" >/dev/null 2>&1 + + +cat $FACTORS | while read factor; do + if ! [[ "$factor" =~ "#" ]]; then # allow comments + for r_seed in 1 #2 3 4 5 + do + factor="$factor $r_seed" + echo "${THIS_DATE}: $factor" >> $LOGFILE>&1 + echo "ruby $CV $factor" >> $LOGFILE 2>&1 + ruby $CV $factor >> $LOGFILE 2>&1 + echo >> $LOGFILE 2>&1 + done + fi +done + diff --git a/cv/scripts/wrapper_pc_cv_RAT_ttv.sh b/cv/scripts/wrapper_pc_cv_RAT_ttv.sh new file mode 100755 index 0000000..fc84f5a --- /dev/null +++ b/cv/scripts/wrapper_pc_cv_RAT_ttv.sh @@ -0,0 +1,45 @@ +#!/bin/bash +# Wrapper Skript for CV +# Reads factors_config, ../data/datasets.yaml and performs cv's +# Andreas Maunz, David Vorgrimmler, 2012 + +if [ $# -lt 1 ]; then + echo "Usage: $0 factors" + exit +fi + +PWD=`pwd` +echo $PWD +if [ ! -f $PWD/../data/datasets.yaml ] +then + echo "datasets.yaml does not exist." + exit +fi + +# Configure basics +source $HOME/.bash_aliases +otconfig +THIS_DATE=`date +%Y%m%d_%H_` +CV="CV_ds_pctype_algo_rseed_RAT_ttv.rb" +FACTORS="$1" + +# Don't start when running +while ps x | grep $CV | grep -v grep >/dev/null 2>&1; do sleep 3; done + +LOGFILE="$THIS_DATE""$USER""_wrapper_pc_cv_RAT_ttv.log" +rm "$LOGFILE" >/dev/null 2>&1 + + +cat $FACTORS | while read factor; do + if ! [[ "$factor" =~ "#" ]]; then # allow comments + for r_seed in 1 #2 3 4 5 + do + factor="$factor $r_seed" + echo "${THIS_DATE}: $factor" >> $LOGFILE>&1 + echo "ruby $CV $factor" >> $LOGFILE 2>&1 + ruby $CV $factor >> $LOGFILE 2>&1 + echo >> $LOGFILE 2>&1 + done + fi +done + -- cgit v1.2.3