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Diffstat (limited to 'bbrc-sample/bbrc_sample_dv.rb')
| -rw-r--r-- | bbrc-sample/bbrc_sample_dv.rb | 318 |
1 files changed, 318 insertions, 0 deletions
diff --git a/bbrc-sample/bbrc_sample_dv.rb b/bbrc-sample/bbrc_sample_dv.rb new file mode 100644 index 0000000..e3c268d --- /dev/null +++ b/bbrc-sample/bbrc_sample_dv.rb @@ -0,0 +1,318 @@ +# # Author: Andreas Maunz, David Vorgrimmler + +require 'rubygems' +require 'opentox-ruby' +require 'yaml' + +if ARGV.size != 9 + puts "Args: path/to/dataset.yaml ds_name num_boots backbone min_frequency method find_min_frequency start_seed end_seed" + puts ARGV.size + exit +end + +path = ARGV[0] +ds_file = path.split("/").last + +if File.exists?(path) + puts "[#{Time.now.iso8601(4).to_s}] #{ds_file} exists." +else + puts "#{ds_file} does not exist." + exit +end + +subjectid = nil + +ds_name = ARGV[1] # e.g. MOU,RAT +num_boots = ARGV[2] # integer, 100 recommended +backbone = ARGV[3] # true/false +min_freq = ARGV[4] # integer +method = ARGV[5] # mle, mean, bbrc +find_min_frequency = ARGV[6] # true/false +start_seed = ARGV[7] # integer (< end_seed) +end_seed = ARGV[8] #integer (> start_seed) +hits = false + +if start_seed > end_seed + puts "Start_seed has to be smaller than end_seed. " +end + +ds = YAML::load_file("#{path}") +ds_uri = ds[ds_name]["dataset"] + +result1 = [] +result2 = [] +metadata = [] + +statistics = {} +statistics[:t_ds_nr_com] = [] +statistics[:bbrc_ds_nr_com] = [] +statistics[:bbrc_ds_nr_f] = [] +statistics[:min_sampling_support] = [] +statistics[:min_frequency_per_sample] = [] +statistics[:duration] = [] +statistics[:merge_time] = [] +statistics[:n_stripped_mss] = [] +statistics[:n_stripped_cst] = [] + +begin + for i in start_seed..end_seed + 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 + + 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 ) + end + bbrc_duration = Time.now - t + puts "[#{Time.now.iso8601(4).to_s}] BBRC duration: #{bbrc_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 + 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_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 + + # save statistics + t_ds = OpenTox::Dataset.find(datasets[:training_ds]) + statistics[:t_ds_nr_com] << ds.compounds.size.to_f + + statistics[:bbrc_ds_nr_com] << bbrc_ds.compounds.size.to_f + statistics[:bbrc_ds_nr_f] << bbrc_ds.features.size.to_f + statistics[:duration] << bbrc_duration + + if !method.to_s.include?("bbrc") + statistics[:min_sampling_support] << bbrc_ds.metadata[OT::parameters][2][OT::paramValue].to_f #ToDo get values by params name + statistics[:min_frequency_per_sample] << bbrc_ds.metadata[OT::parameters][4][OT::paramValue].to_f + statistics[:merge_time] << bbrc_ds.metadata[OT::parameters][6][OT::paramValue].to_f + statistics[:n_stripped_mss] << bbrc_ds.metadata[OT::parameters][7][OT::paramValue].to_f + statistics[:n_stripped_cst] << bbrc_ds.metadata[OT::parameters][8][OT::paramValue].to_f + end + + # save params + 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 + + min_sampling_support = (statistics[:min_sampling_support].inject{|sum,x| sum + x })/(statistics[:min_sampling_support].size) unless statistics[:min_sampling_support].compact.empty? + min_frequency_per_sample = (statistics[:min_frequency_per_sample].inject{|sum,x| sum + x })/(statistics[:min_frequency_per_sample].size) unless statistics[:min_frequency_per_sample].compact.empty? + bbrc_ds_nr_com = (statistics[:bbrc_ds_nr_com].inject{|sum,x| sum + x })/(statistics[:bbrc_ds_nr_com].size) unless statistics[:bbrc_ds_nr_com].compact.empty? + ds_nr_com = (statistics[:t_ds_nr_com].inject{|sum,x| sum + x })/(statistics[:t_ds_nr_com].size) unless statistics[:t_ds_nr_com].compact.empty? + bbrc_ds_nr_f = (statistics[:bbrc_ds_nr_f].inject{|sum,x| sum + x })/(statistics[:bbrc_ds_nr_f].size) unless statistics[:bbrc_ds_nr_f].compact.empty? + duration = (statistics[:duration].inject{|sum,x| sum + x })/(statistics[:duration].size) unless statistics[:duration].compact.empty? + merge_time = (statistics[:merge_time].inject{|sum,x| sum + x })/(statistics[:merge_time].size) unless statistics[:merge_time].compact.empty? + n_stripped_mss = (statistics[:n_stripped_mss].inject{|sum,x| sum + x })/(statistics[:n_stripped_mss].size) unless statistics[:n_stripped_mss].compact.empty? + n_stripped_cst = (statistics[:n_stripped_cst].inject{|sum,x| sum + x })/(statistics[:n_stripped_cst].size) unless statistics[:n_stripped_cst].compact.empty? + + if method.to_s.include?("bbrc") + metadata << "Dataset,num_boot,nr_hits,bbrc_ds_nr_com,ds_nr_com,bbrc_ds_nr_f,duration" + gdoc_input = "=hyperlink(\"#{ds_uri}\";\"#{ds_name}\"),#{num_boots},#{hits},#{bbrc_ds_nr_com},#{ds_nr_com},#{bbrc_ds_nr_f},#{duration}" + metadata << gdoc_input + else + metadata << "Dataset,num_boot,min_sampling_support,min_frequency,nr_hits,bbrc_ds_nr_com,ds_nr_com,bbrc_ds_nr_f,duration,merge_time,n_stripped_mss,n_stripped_cst" + gdoc_input = "=hyperlink(\"#{ds_uri}\";\"#{ds_name}\"),#{num_boots},#{min_sampling_support},#{min_frequency_per_sample},#{hits},#{bbrc_ds_nr_com},#{ds_nr_com},#{bbrc_ds_nr_f},#{duration},#{merge_time},#{n_stripped_mss},#{n_stripped_cst}" + metadata << gdoc_input + 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}" + +rescue Exception => e + LOGGER.debug "#{e.class}: #{e.message}" + LOGGER.debug "Backtrace:\n\t#{e.backtrace.join("\n\t")}" + + min_sampling_support = (statistics[:min_sampling_support].inject{|sum,x| sum + x })/(statistics[:min_sampling_support].size) unless statistics[:min_sampling_support].compact.empty? + min_frequency_per_sample = (statistics[:min_frequency_per_sample].inject{|sum,x| sum + x })/(statistics[:min_frequency_per_sample].size) unless statistics[:min_frequency_per_sample].compact.empty? + bbrc_ds_nr_com = (statistics[:bbrc_ds_nr_com].inject{|sum,x| sum + x })/(statistics[:bbrc_ds_nr_com].size) unless statistics[:bbrc_ds_nr_com].compact.empty? + ds_nr_com = (statistics[:t_ds_nr_com].inject{|sum,x| sum + x })/(statistics[:t_ds_nr_com].size) unless statistics[:t_ds_nr_com].compact.empty? + bbrc_ds_nr_f = (statistics[:bbrc_ds_nr_f].inject{|sum,x| sum + x })/(statistics[:bbrc_ds_nr_f].size) unless statistics[:bbrc_ds_nr_f].compact.empty? + duration = (statistics[:duration].inject{|sum,x| sum + x })/(statistics[:duration].size) unless statistics[:duration].compact.empty? + merge_time = (statistics[:merge_time].inject{|sum,x| sum + x })/(statistics[:merge_time].size) unless statistics[:merge_time].compact.empty? + n_stripped_mss = (statistics[:n_stripped_mss].inject{|sum,x| sum + x })/(statistics[:n_stripped_mss].size) unless statistics[:n_stripped_mss].compact.empty? + n_stripped_cst = (statistics[:n_stripped_cst].inject{|sum,x| sum + x })/(statistics[:n_stripped_cst].size) unless statistics[:n_stripped_cst].compact.empty? + + if method.to_s.include?("bbrc") + metadata << "Dataset,num_boot,nr_hits,bbrc_ds_nr_com,ds_nr_com,bbrc_ds_nr_f,duration" + gdoc_input = "=hyperlink(\"#{ds_uri}\";\"#{ds_name}\"),#{num_boots},#{hits},#{bbrc_ds_nr_com},#{ds_nr_com},#{bbrc_ds_nr_f},#{duration}" + metadata << gdoc_input + else + metadata << "Dataset,num_boot,min_sampling_support,min_frequency,nr_hits,bbrc_ds_nr_com,ds_nr_com,bbrc_ds_nr_f,duration,merge_time,n_stripped_mss,n_stripped_cst" + gdoc_input = "=hyperlink(\"#{ds_uri}\";\"#{ds_name}\"),#{num_boots},#{min_sampling_support},#{min_frequency_per_sample},#{hits},#{bbrc_ds_nr_com},#{ds_nr_com},#{bbrc_ds_nr_f},#{duration},#{merge_time},#{n_stripped_mss},#{n_stripped_cst}" + metadata << gdoc_input + end + + 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 + |