diff options
| author | davor <vorgrimmlerdavid@gmx.de> | 2011-12-07 14:24:49 +0100 |
|---|---|---|
| committer | davor <vorgrimmlerdavid@gmx.de> | 2011-12-07 14:24:49 +0100 |
| commit | 5212f57c0dc6b8c5a7fa98b3e06eecd8bb5b4513 (patch) | |
| tree | 7f3ab3cc8c3dd75a918f3797673d5bf7d758d03c | |
| parent | d45afcc81db71801773eeb68b0de1417ae28e478 (diff) | |
Modified structure of log file.
| -rw-r--r-- | 5x_cv/5x_crossvalidation.rb | 9 | ||||
| -rw-r--r-- | 5x_cv/dataset_config | 10 | ||||
| -rw-r--r-- | 5x_cv/factors_config | 6 | ||||
| -rw-r--r-- | 5x_cv/lib/cv_am.rb | 6 |
4 files changed, 18 insertions, 13 deletions
diff --git a/5x_cv/5x_crossvalidation.rb b/5x_cv/5x_crossvalidation.rb index 7f465d8..9473df2 100644 --- a/5x_cv/5x_crossvalidation.rb +++ b/5x_cv/5x_crossvalidation.rb @@ -48,8 +48,8 @@ if ! exception_config[params[0]].nil? } end -i=1 -#for i in 1..5 +#i=1 +for i in 1..5 begin puts puts "Round #{i.to_s}." @@ -58,4 +58,7 @@ i=1 rescue Exception => e puts "Error in 5xCV: #{e.message}: #{e.backtrace}" end -#end +end +puts +puts "--- Validation of dataset (#{params[0]}) finished." +puts diff --git a/5x_cv/dataset_config b/5x_cv/dataset_config index b8bb45e..9bc011e 100644 --- a/5x_cv/dataset_config +++ b/5x_cv/dataset_config @@ -1,9 +1,11 @@ +#FDA v3b Maximum Recommended Daily Dose mmol +http://toxcreate3.in-silico.ch:8080/dataset/2366 +#EPA v4b Fathead Minnow Acute Toxicity LC50_mmol +#http://toxcreate3.in-silico.ch:8080/dataset/2133 #CPDBAS_v5d_20Nov2008_rat_TD50 -http://toxcreate3.in-silico.ch:8080/dataset/1408 +#http://toxcreate3.in-silico.ch:8080/dataset/1408 #CPDBAS_v5d_20Nov2008_mouse_TD50 -http://toxcreate3.in-silico.ch:8080/dataset/1384 -#EPA v4b Fathead Minnow Acute Toxicity LC50_mmol -#http://toxcreate3.in-silico.ch:8080/dataset/2093 +#http://toxcreate3.in-silico.ch:8080/dataset/1384 #MultiCellCall: DSSTox Carcinogenic Potency DBS MultiCellCall_no_duplicates.csv #http://toxcreate3.in-silico.ch:8080/dataset/130 #Bloodbarr: bloodbarr_no_duplicate.csv diff --git a/5x_cv/factors_config b/5x_cv/factors_config index 5ea1c57..d4ac1b3 100644 --- a/5x_cv/factors_config +++ b/5x_cv/factors_config @@ -1,4 +1,2 @@ -feature_generation_uri=http://toxcreate3.in-silico.ch:8082/algorithm/fminer/bbrc;prediction_algorithm=local_mlr_prop;pc_type=electronic -feature_generation_uri=http://toxcreate3.in-silico.ch:8082/algorithm/fminer/bbrc;prediction_algorithm=local_mlr_prop;pc_type=topological -feature_generation_uri=http://toxcreate3.in-silico.ch:8082/algorithm/fminer/bbrc;prediction_algorithm=local_mlr_prop;pc_type=geometrical -feature_generation_uri=http://toxcreate3.in-silico.ch:8082/algorithm/fminer/bbrc;prediction_algorithm=local_mlr_prop;pc_type=constitutional +feature_generation_uri=http://toxcreate3.in-silico.ch:8083/algorithm/fminer/bbrc +#feature_generation_uri=http://toxcreate3.in-silico.ch:8082/algorithm/fminer/bbrc;prediction_algorithm=local_mlr_prop;pc_type=electronic;max_perc_neighbors=20 diff --git a/5x_cv/lib/cv_am.rb b/5x_cv/lib/cv_am.rb index c2ce55f..625011f 100644 --- a/5x_cv/lib/cv_am.rb +++ b/5x_cv/lib/cv_am.rb @@ -125,7 +125,7 @@ def cv (args) prediction_feature = OpenTox::Dataset.find(training_dataset_uri).features.keys.first puts prediction_feature # end - puts training_dataset_uri + #puts training_dataset_uri # Crossvalidation @@ -146,7 +146,9 @@ def cv (args) cv_args = {:dataset_uri => training_dataset_uri, :prediction_feature => prediction_feature, :algorithm_uri => args[1].split('fminer')[0] + "lazar", :algorithm_params => alg_params, :stratified => stratified_param } cv_args[:random_seed] = random_seed_param unless random_seed_param == "" - puts file + #puts file + puts + puts "Crossvalidation parameters:" puts cv_args.to_yaml puts begin |