diff options
Diffstat (limited to '5x_cv')
-rw-r--r-- | 5x_cv/CV_ds_pctype_prop_algo_rseed.rb | 60 | ||||
-rw-r--r-- | 5x_cv/factors_config | 38 | ||||
-rwxr-xr-x | 5x_cv/wrapper_pc_cv.sh | 45 |
3 files changed, 0 insertions, 143 deletions
diff --git a/5x_cv/CV_ds_pctype_prop_algo_rseed.rb b/5x_cv/CV_ds_pctype_prop_algo_rseed.rb deleted file mode 100644 index b9c55dd..0000000 --- a/5x_cv/CV_ds_pctype_prop_algo_rseed.rb +++ /dev/null @@ -1,60 +0,0 @@ -# Do a 10-fold crossvalidation -# # Author: Andreas Maunz, David Vorgrimmler -# # @params: Dataset_name(see dataset_nestle.yaml), pc_type(electronic,cpsa or constitutional ...), prop(true or false), prediction_algorithm(local_mlr_prop or local_svm_regression ...) - -if ARGV.size != 5 - puts "Args: ds_name, pc_type, prop, algo, random_seed" - puts ARGV.size - exit -end - -ds_file = "datasets_nestle.yaml" -pwd=`pwd` -path = "#{pwd.chop}/#{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 -prop = ARGV[2] # true or false -algo = ARGV[3] # e.g. local_svm_regression, local_mlr_prop -r_seed = ARGV[4] # 1, 2, ..., 10 - -ds = YAML::load_file("datasets_nestle.yaml") -ds_uri = ds[ds_name]["dataset"] -pc_ds_uri = ds[ds_name][pc_type] - -algo_params = "pc_type=#{pc_type}"; -algo_params += ";feature_dataset_uri=#{pc_ds_uri}" -algo_params += ";propositionalized=#{prop}" -algo_params += ";prediction_algorithm=#{algo}" -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:8087/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/5x_cv/factors_config b/5x_cv/factors_config deleted file mode 100644 index 604ca45..0000000 --- a/5x_cv/factors_config +++ /dev/null @@ -1,38 +0,0 @@ -#Dataset pc_type prop prediction_algorithm -MDD constitutional false local_svm_regression -MDD constitutional true local_svm_regression -MDD electronic,cpsa false local_svm_regression -MDD electronic,cpsa true local_svm_regression -MDD constitutional,electronic,cpsa false local_svm_regression -MDD constitutional,electronic,cpsa true local_svm_regression -#MDD constitutional true local_mlr_prop -#MDD electronic,cpsa true local_mlr_prop -#MDD constitutional,electronic,cpsa true local_mlr_prop -FHM2 constitutional false local_svm_regression -FHM2 constitutional true local_svm_regression -FHM2 electronic,cpsa false local_svm_regression -FHM2 electronic,cpsa true local_svm_regression -FHM2 constitutional,electronic,cpsa false local_svm_regression -FHM2 constitutional,electronic,cpsa true local_svm_regression -#MOU constitutional true local_mlr_prop -#MOU electronic,cpsa true local_mlr_prop -#MOU constitutional,electronic,cpsa true local_mlr_prop -RAT2 constitutional false local_svm_regression -RAT2 constitutional true local_svm_regression -RAT2 electronic,cpsa false local_svm_regression -RAT2 electronic,cpsa true local_svm_regression -RAT2 constitutional,electronic,cpsa false local_svm_regression -RAT2 constitutional,electronic,cpsa true local_svm_regression -#MOU constitutional true local_mlr_prop -#MOU electronic,cpsa true local_mlr_prop -#MOU constitutional,electronic,cpsa true local_mlr_prop -MOU2 constitutional false local_svm_regression -MOU2 constitutional true local_svm_regression -MOU2 electronic,cpsa false local_svm_regression -MOU2 electronic,cpsa true local_svm_regression -MOU2 constitutional,electronic,cpsa false local_svm_regression -MOU2 constitutional,electronic,cpsa true local_svm_regression -#MOU constitutional true local_mlr_prop -#MOU electronic,cpsa true local_mlr_prop -#MOU constitutional,electronic,cpsa true local_mlr_prop - diff --git a/5x_cv/wrapper_pc_cv.sh b/5x_cv/wrapper_pc_cv.sh deleted file mode 100755 index 719885a..0000000 --- a/5x_cv/wrapper_pc_cv.sh +++ /dev/null @@ -1,45 +0,0 @@ -#!/bin/bash -# Wrapper Skript for CV -# Reads factors_config, dataset_nestle.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/datasets_nestle.yaml ] -then - echo "datasets_nestle.yaml does not exist." - exit -fi - -# Configure basics -source $HOME/.bash_aliases -otconfig -THIS_DATE=`date +%Y%m%d_%H_` -CV="CV_ds_pctype_prop_algo_rseed.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""$USER""_wrapper_pc_cv.log" -rm "$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 - |