From 1aa9a70d20ec00d74c3ba19332ac11afac6fd8d7 Mon Sep 17 00:00:00 2001 From: David Vorgrimmler Date: Wed, 20 Jun 2012 15:27:47 +0200 Subject: Updated scripts and added comments. --- bbrc-sample/bbrc_sample_dv.rb | 404 ++++++++++++++++++++---------------------- bbrc-sample/factors_config_dv | 56 +++--- 2 files changed, 228 insertions(+), 232 deletions(-) diff --git a/bbrc-sample/bbrc_sample_dv.rb b/bbrc-sample/bbrc_sample_dv.rb index 923469e..4f68cd3 100644 --- a/bbrc-sample/bbrc_sample_dv.rb +++ b/bbrc-sample/bbrc_sample_dv.rb @@ -4,8 +4,8 @@ require 'rubygems' require 'opentox-ruby' require 'yaml' -if ARGV.size != 6 - puts "Args: path/to/dataset.yaml ds_name num_boots backbone min_frequency method" +if ARGV.size != 7 + puts "Args: path/to/dataset.yaml ds_name num_boots backbone min_frequency method find_min_frequency" puts ARGV.size exit end @@ -22,11 +22,12 @@ end subjectid = nil -ds_name = ARGV[1] # e.g. MOU -num_boots = ARGV[2] # e.g. electronic,cpsa or nil to disable +ds_name = ARGV[1] # e.g. MOU,RAT +num_boots = ARGV[2] # integer, 100 recommended backbone = ARGV[3] # true/false -min_freq = ARGV[4] # [100, 90, ..., 10] -method = ARGV[5] # MLE, MEAN, BBRC +min_freq = ARGV[4] # integer +method = ARGV[5] # mle, mean, bbrc +find_min_frequency = ARGV[6] # true/false hits = false ds = YAML::load_file("#{path}") @@ -36,218 +37,207 @@ result1 = [] result2 = [] metadata = [] -for i in 1..50 - puts - puts "--------------------------- Round: #{i} ---------------------------" - - # SPLIT - puts " ----- split ds -----" - split_params = {} - split_params["dataset_uri"] = ds_uri - split_params["prediction_feature"] = (ds_uri.to_s + "/feature/1") - split_params["stratified"] = true - split_params["split_ratio"] = 0.5 - split_params["random_seed"] = i - puts "[#{Time.now.iso8601(4).to_s}] Split params: #{split_params.to_yaml}" - - split_result = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-validation"],"plain_training_test_split"), split_params) - datasets = {} - datasets[:training_ds] = split_result.inspect.gsub(/"/,'').split("\\n")[0] - datasets[:test_ds] = split_result.inspect.gsub(/"/,'').split("\\n")[1] - puts "[#{Time.now.iso8601(4).to_s}] Split result: #{datasets.to_yaml}" - puts +begin + for i in 1..50 + puts + puts "--------------------------- Round: #{i} ---------------------------" + + ################################# + # SPLIT + ################################# + puts " ----- split ds -----" + split_params = {} + split_params["dataset_uri"] = ds_uri + split_params["prediction_feature"] = (ds_uri.to_s + "/feature/1") + split_params["stratified"] = true + split_params["split_ratio"] = 0.5 + split_params["random_seed"] = i + puts "[#{Time.now.iso8601(4).to_s}] Split params: #{split_params.to_yaml}" + + split_result = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-validation"],"plain_training_test_split"), split_params) + datasets = {} + datasets[:training_ds] = split_result.inspect.gsub(/"/,'').split("\\n")[0] + datasets[:test_ds] = split_result.inspect.gsub(/"/,'').split("\\n")[1] + puts "[#{Time.now.iso8601(4).to_s}] Split result: #{datasets.to_yaml}" + puts + + ################################# + # FIND "good" min_frequency + ################################# + + if find_min_frequency.to_s == "true" + min_params = {} + min_params["dataset_uri"] = datasets[:training_ds] + + ds = OpenTox::Dataset.find(datasets[:training_ds]) + ds_nr_com = ds.compounds.size + + min_params["backbone"] = backbone + durations = [] + x = ds_nr_com + ds_result_nr_f = 0 + y = x + y_old = 0 + # puts + # puts "----- Initialization: -----" + while ds_result_nr_f < (ds_nr_com/4).to_i do + y_old = y + y = x + x = (x/2).to_i + min_params["min_frequency"] = x + t = Time.now + result_uri = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc/"), min_params ) + durations << Time.now - t + ds_result = OpenTox::Dataset.find(result_uri) + ds_result_nr_f = ds_result.features.size + end + + # puts + # puts "----- Main phase: -----" + max_duration = durations[0] +(ds_nr_com.to_f * 0.003) # this is only an experience value. + min_params["min_frequency"] = y + y = y_old + found = false + cnt = 0 + min_f = min_params["min_frequency"] + # Search for min_frequency with following heuristic procedure. If no good min_frequency found the delivered value(from the arguments) is used. + while found == false || cnt == 4 do + if min_f == min_params["min_frequency"] + cnt = cnt + 1 + end + min_f = min_params["min_frequency"] + t = Time.now + result_uri = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc/"), min_params ) + durations << Time.now - t + ds_result = OpenTox::Dataset.find(result_uri) + ds_result_nr_f = ds_result.features.size + # Check if number of features is max half and min one-tenth of the number of compounds and performed in accaptable amount of time + if ds_result_nr_f.to_i < (ds_nr_com/2).to_i && ds_result_nr_f.to_i > (ds_nr_com/10).to_i + if durations.last < max_duration + found = true + min_freq = min_params["min_frequency"] + else + x = min_params["min_frequency"] + min_params["min_frequency"] = ((min_params["min_frequency"]+y)/2).to_i + end + else + y = min_params["min_frequency"] + min_params["min_frequency"] = ((x+min_params["min_frequency"])/2).to_i + end + end + end + + ################################# + # BBRC SAMPLE + ################################# + puts " ----- bbrc feature calulation -----" + algo_params = {} + algo_params["dataset_uri"] = datasets[:training_ds] + algo_params["backbone"] = backbone + algo_params["min_frequency"] = min_freq + algo_params["nr_hits"] = hits + algo_params["method"] = method - # Find "good" min_frequency - - min_params = {} - min_params["dataset_uri"] = datasets[:training_ds] - - ds = OpenTox::Dataset.find(datasets[:training_ds]) -# ds_nr_de = ds.data_entries.size - ds_nr_com = ds.compounds.size - - min_params["backbone"] = backbone - durations = [] - x = ds_nr_com - ds_result_nr_f = 0 - y = x - y_old = 0 -# puts -# puts "----- Initialization: -----" - while ds_result_nr_f < (ds_nr_com/4).to_i do - y_old = y - y = x - x = (x/2).to_i - min_params["min_frequency"] = x -# puts "[#{Time.now.iso8601(4).to_s}] min_freq #{x}" t = Time.now - result_uri = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc/"), min_params ) - durations << Time.now - t - ds_result = OpenTox::Dataset.find(result_uri) - ds_result_nr_f = ds_result.features.size -# puts "[#{Time.now.iso8601(4).to_s}] nr features #{ds_result_nr_f}" -# puts "[#{Time.now.iso8601(4).to_s}] duration #{durations.last}" -# puts "-------------" -# puts - end - -# puts "----- Main phase: -----" -# puts - max_duration = durations[0] +(ds_nr_com.to_f * 0.003) -# puts "max duration: #{max_duration}" -# puts - min_params["min_frequency"] = y - y = y_old - found = false - cnt = 0 - min_f = min_params["min_frequency"] - while found == false || cnt == 4 do - if min_f == min_params["min_frequency"] - cnt = cnt + 1 + if method == "bbrc" + puts "[#{Time.now.iso8601(4).to_s}] BBRC params: #{algo_params.to_yaml}" + feature_dataset_uri = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc"), algo_params ) + else + algo_params["num_boots"] = num_boots + algo_params["random_seed"] = i + puts "[#{Time.now.iso8601(4).to_s}] BBRC params: #{algo_params.to_yaml}" + feature_dataset_uri = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc/sample"), algo_params ) end - min_f = min_params["min_frequency"] -# puts "[#{Time.now.iso8601(4).to_s}] min_freq #{min_params["min_frequency"]}" - t = Time.now - result_uri = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc/"), min_params ) - durations << Time.now - t - ds_result = OpenTox::Dataset.find(result_uri) - ds_result_nr_f = ds_result.features.size -# ds_result_nr_de = ds_result.data_entries.size -# ds_result_nr_com = ds_result.compounds.size -# puts "[#{Time.now.iso8601(4).to_s}] nr features #{ds_result_nr_f}" -# puts "[#{Time.now.iso8601(4).to_s}] duration #{durations.last}" -# puts "-------------" -# puts -# puts "smaller than #{(ds_nr_com*0.45).to_i} and larger than #{(ds_nr_com/10).to_i}" -# puts "x #{x}, y #{y}, min_freq #{min_params["min_frequency"]}" - if ds_result_nr_f.to_i < (ds_nr_com/2).to_i && ds_result_nr_f.to_i > (ds_nr_com/10).to_i - if durations.last < max_duration - found = true - min_freq = min_params["min_frequency"] - else - x = min_params["min_frequency"] - min_params["min_frequency"] = ((min_params["min_frequency"]+y)/2).to_i + duration = Time.now - t + puts "[#{Time.now.iso8601(4).to_s}] BBRC duration: #{duration}" + puts "[#{Time.now.iso8601(4).to_s}] BBRC result: #{feature_dataset_uri}" + puts + + ################################# + # MATCH + ################################# + puts " ----- bbrc match -----" + match_params = {} + match_params["feature_dataset_uri"] = "#{feature_dataset_uri}" + match_params["dataset_uri"] = datasets[:test_ds] + match_params["min_frequency"] = min_freq + match_params["nr_hits"] = hits + puts "[#{Time.now.iso8601(4).to_s}] Match params: #{match_params.to_yaml}" + + matched_dataset_uri = OpenTox::RestClientWrapper.post(File.join(CONFIG[:services]["opentox-algorithm"],"fminer","bbrc","match"),match_params) + puts "[#{Time.now.iso8601(4).to_s}] BBRC match result: #{matched_dataset_uri}" + puts + + ################################# + # COMPARE pValues + ################################# + puts " ----- pValue comparision -----" + bbrc_ds = OpenTox::Dataset.find(feature_dataset_uri) + bbrc_smarts_pValues = {} + bbrc_ds.features.each do |f, values| + if values[RDF::type].include?(OT.Substructure) + bbrc_smarts_pValues[values[OT::smarts]] = values[OT::pValue] + end + end + + match_ds = OpenTox::Dataset.find(matched_dataset_uri) + matched_smarts_pValues = {} + match_ds.features.each do |f, values| + if values[RDF::type].include?(OT.Substructure) + matched_smarts_pValues[values[OT::smarts]] = values[OT::pValue] end - else - y = min_params["min_frequency"] - min_params["min_frequency"] = ((x+min_params["min_frequency"])/2).to_i end - end - # BBRC sample - puts " ----- bbrc feature calulation -----" - algo_params = {} - algo_params["dataset_uri"] = datasets[:training_ds] - algo_params["backbone"] = backbone - algo_params["min_frequency"] = min_freq - algo_params["nr_hits"] = hits - algo_params["method"] = method - - t = Time.now - if method == "bbrc" - puts "[#{Time.now.iso8601(4).to_s}] BBRC params: #{algo_params.to_yaml}" - feature_dataset_uri = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc"), algo_params ) - else - algo_params["num_boots"] = num_boots - algo_params["random_seed"] = i - puts "[#{Time.now.iso8601(4).to_s}] BBRC params: #{algo_params.to_yaml}" - feature_dataset_uri = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc/sample"), algo_params ) + sum_E1 = 0.0 + sum_E2 = 0.0 + bbrc_smarts_pValues.each do |s, p| + if matched_smarts_pValues.include?(s) + dif = (p.to_f - matched_smarts_pValues[s].to_f).abs + sum_E1 = sum_E1 + dif + sum_E2 = sum_E2 + dif**2 + end + end + puts "[#{Time.now.iso8601(4).to_s}] Sum pValue difference (E1): #{sum_E1}" + puts "[#{Time.now.iso8601(4).to_s}] Squared sum pValue difference (E2): #{sum_E2}" + + ################################# + # SAVE data + ################################# + result1 << sum_E1 + result2 << sum_E2 + + info = [] + info << { :ds_name => ds_name, :nr_features => bbrc_ds.features.size} + info << split_params + info << algo_params + info << match_params + + metadata << info + puts end - duration = Time.now - t - puts "[#{Time.now.iso8601(4).to_s}] BBRC duration: #{duration}" - puts "[#{Time.now.iso8601(4).to_s}] BBRC result: #{feature_dataset_uri}" - puts - # Match - puts " ----- bbrc match -----" - match_params = {} - match_params["feature_dataset_uri"] = "#{feature_dataset_uri}" - match_params["dataset_uri"] = datasets[:test_ds] - match_params["min_frequency"] = min_freq - match_params["nr_hits"] = hits - puts "[#{Time.now.iso8601(4).to_s}] Match params: #{match_params.to_yaml}" - - matched_dataset_uri = OpenTox::RestClientWrapper.post(File.join(CONFIG[:services]["opentox-algorithm"],"fminer","bbrc","match"),match_params) - puts "[#{Time.now.iso8601(4).to_s}] BBRC match result: #{matched_dataset_uri}" + puts "############################################" + puts "############# FINAL RESULTS ################" + puts "############################################" puts + puts "[#{Time.now.iso8601(4).to_s}] metadata: #{metadata.to_yaml}" + puts + puts "[#{Time.now.iso8601(4).to_s}] result1: #{result1.to_yaml}" + puts + puts "[#{Time.now.iso8601(4).to_s}] result2: #{result2.to_yaml}" - # Compare pValues - puts " ----- pValue comparision -----" - bbrc_ds = OpenTox::Dataset.find(feature_dataset_uri) - bbrc_smarts_pValues = {} - bbrc_ds.features.each do |f, values| - if values[RDF::type].include?(OT.Substructure) - bbrc_smarts_pValues[values[OT::smarts]] = values[OT::pValue] - end - end - - match_ds = OpenTox::Dataset.find(matched_dataset_uri) - matched_smarts_pValues = {} - match_ds.features.each do |f, values| - if values[RDF::type].include?(OT.Substructure) - matched_smarts_pValues[values[OT::smarts]] = values[OT::pValue] - end - end - - sum_E1 = 0.0 - sum_E2 = 0.0 - bbrc_smarts_pValues.each do |s, p| - if matched_smarts_pValues.include?(s) - dif = (p.to_f - matched_smarts_pValues[s].to_f).abs - sum_E1 = sum_E1 + dif - sum_E2 = sum_E1 + dif**2 - end - end - puts "[#{Time.now.iso8601(4).to_s}] Sum pValue difference (E1): #{sum_E1}" - puts "[#{Time.now.iso8601(4).to_s}] Squared sum pValue difference (E2): #{sum_E2}" - - # Save data - result1 << sum_E1 - result2 << sum_E2 - - info = [] - info << { :ds_name => ds_name, :nr_features => bbrc_ds.features.size} - info << split_params - info << algo_params - info << match_params - - metadata << info - - # ds = OpenTox::Dataset.find(datasets[:training_ds]) - # ds_nr_de = ds.data_entries.size - # ds_nr_com = ds.compounds.size - # - # ds_result = OpenTox::Dataset.find(result_uri) - # ds_result_nr_de = ds_result.data_entries.size - # ds_result_nr_com = ds_result.compounds.size - # ds_result_nr_f = ds_result.features.size - # - # min_sampling_support = ds_result.metadata[OT::parameters][2][OT::paramValue] - # num_boots = ds_result.metadata[OT::parameters][3][OT::paramValue] - # min_frequency_per_sample = ds_result.metadata[OT::parameters][4][OT::paramValue] - # nr_hits = ds_result.metadata[OT::parameters][5][OT::paramValue] - # merge_time = ds_result.metadata[OT::parameters][6][OT::paramValue] - # n_stripped_mss = ds_result.metadata[OT::parameters][7][OT::paramValue] - # n_stripped_cst = ds_result.metadata[OT::parameters][8][OT::paramValue] - # random_seed = ds_result.metadata[OT::parameters][9][OT::paramValue] - # - # puts "[#{Time.now.iso8601(4).to_s}] nr dataentries: #{ds_result_nr_de} , (of #{ds_nr_de} )" - # puts "[#{Time.now.iso8601(4).to_s}] nr dataentries: #{ds_result_nr_com} , (of #{ds_nr_com} )" - # puts "[#{Time.now.iso8601(4).to_s}] nr features: #{ds_result_nr_f}" - # puts "[#{Time.now.iso8601(4).to_s}] Merge time: #{merge_time}" - # - # puts "=hyperlink(\"#{ds_uri}\";\"#{ds_name}\"),#{num_boots},#{min_sampling_support},#{min_frequency_per_sample},#{nr_hits},=hyperlink(\"#{result_uri}\";\"bbrc_result\"),#{ds_result_nr_com},#{ds_nr_com},#{ds_result_nr_f},#{duration},#{merge_time},#{n_stripped_mss},#{n_stripped_cst},#{random_seed}" +rescue Exception => e + LOGGER.debug "#{e.class}: #{e.message}" + LOGGER.debug "Backtrace:\n\t#{e.backtrace.join("\n\t")}" + puts "############################################" + puts "############ RESULTS befor error ###########" + puts "############################################" puts - + puts "[#{Time.now.iso8601(4).to_s}] metadata: #{metadata.to_yaml}" + puts + puts "[#{Time.now.iso8601(4).to_s}] result1: #{result1.to_yaml}" + puts + puts "[#{Time.now.iso8601(4).to_s}] result2: #{result2.to_yaml}" end -puts "############################################" -puts "############# FINAL RESULTS ################" -puts "############################################" -puts -puts "[#{Time.now.iso8601(4).to_s}] metadata: #{metadata.to_yaml}" -puts -puts "[#{Time.now.iso8601(4).to_s}] result1: #{result1.to_yaml}" -puts -puts "[#{Time.now.iso8601(4).to_s}] result2: #{result2.to_yaml}" diff --git a/bbrc-sample/factors_config_dv b/bbrc-sample/factors_config_dv index 41fe9a9..76e089e 100644 --- a/bbrc-sample/factors_config_dv +++ b/bbrc-sample/factors_config_dv @@ -1,25 +1,31 @@ -#Dataset num_boots backbone min_frequence -#MOU 100 true -#MOU 100 false -#RAT 100 true -#RAT 100 false -#MCC 100 true -#MCC 100 false -SAL 100 true 40pm mle -SAL 100 true 40pm mean -SAL 100 true 40pm bbrc -#SAL 100 false -#KAZ 100 true -#KAZ 100 false -#BB 300 -#BB 200 -#BB 150 -#BB 100 -#NCT 300 -#NCT 200 -#NCT 150 -#NCT 100 -#YOSH 300 -#YOSH 200 -#YOSH 150 -#YOSH 100 +#Dataset num_boots backbone min_frequence method find_min_frequency +#MOU 100 true 20pm mle true +#MOU 100 true 20pm mean true +#MOU 100 true 20pm bbrc true +#MOU 100 false 30pm mle true +#MOU 100 false 30pm mean true +#MOU 100 false 30pm bbrc true +#RAT 100 true 20pm mle true +#RAT 100 true 20pm mean true +#RAT 100 true 20pm bbrc true +#RAT 100 false 40pm mle true +#RAT 100 false 40pm mean true +#RAT 100 false 40pm bbrc true +#MCC 100 true 20pm mle true +#MCC 100 true 20pm mean true +#MCC 100 true 20pm bbrc true +#MCC 100 false 50pm mle true +#MCC 100 false 50pm mean true +#MCC 100 false 50pm bbrc true +#SAL 100 true 40pm mle true +#SAL 100 true 40pm mean true +#SAL 100 true 40pm bbrc true +#SAL 100 false 70pm mle true +#SAL 100 false 70pm mean true +#SAL 100 false 70pm bbrc true +#KAZ 100 true 30pm mle true +#KAZ 100 true 30pm mean true +#KAZ 100 true 30pm bbrc true +#KAZ 100 false 90pm mle true +#KAZ 100 false 90pm mean true +#KAZ 100 false 90pm bbrc true -- cgit v1.2.3