diff options
Diffstat (limited to 'fminer.rb')
| -rw-r--r-- | fminer.rb | 172 |
1 files changed, 0 insertions, 172 deletions
@@ -107,178 +107,6 @@ module OpenTox end - # Run bbrc algorithm on dataset - # - # @param [String] dataset_uri URI of the training dataset - # @param [String] prediction_feature URI of the prediction feature (i.e. dependent variable) - # @param [optional] parameters BBRC parameters, accepted parameters are - # - min_frequency Minimum frequency (default 5) - # - feature_type Feature type, can be 'paths' or 'trees' (default "trees") - # - backbone BBRC classes, pass 'false' to switch off mining for BBRC representatives. (default "true") - # - min_chisq_significance Significance threshold (between 0 and 1) - # - nr_hits Set to "true" to get hit count instead of presence - # - get_target Set to "true" to obtain target variable as feature - # @return [text/uri-list] Task URI - post '/fminer/bbrc/?' do - - @@fminer=OpenTox::Algorithm::Fminer.new(to('/fminer/bbrc',:full)) - @@fminer.check_params(params,5) - - task = OpenTox::Task.run("Mining BBRC features", uri('/fminer/bbrc')) do |task| - - time = Time.now - - @@bbrc.Reset - if @@fminer.prediction_feature.feature_type == "regression" - @@bbrc.SetRegression(true) # AM: DO NOT MOVE DOWN! Must happen before the other Set... operations! - else - bad_request_error "No accept values for "\ - "dataset '#{@@fminer.training_dataset.uri}' and "\ - "feature '#{@@fminer.prediction_feature.uri}'" unless - @@fminer.prediction_feature.accept_values - value_map=@@fminer.prediction_feature.value_map - end - @@bbrc.SetMinfreq(@@fminer.minfreq) - @@bbrc.SetType(1) if params[:feature_type] == "paths" - @@bbrc.SetBackbone(false) if params[:backbone] == "false" - @@bbrc.SetChisqSig(params[:min_chisq_significance].to_f) if params[:min_chisq_significance] - @@bbrc.SetConsoleOut(false) - - feature_dataset = OpenTox::Dataset.new - feature_dataset.metadata = { - RDF::DC.title => "BBRC representatives", - RDF::DC.creator => to('/fminer/bbrc',:full), - RDF::OT.hasSource => to('/fminer/bbrc', :full), - } - feature_dataset.parameters = [ - { RDF::DC.title => "dataset_uri", RDF::OT.paramValue => params[:dataset_uri] }, - { RDF::DC.title => "prediction_feature", RDF::OT.paramValue => params[:prediction_feature] }, - { RDF::DC.title => "min_frequency", RDF::OT.paramValue => @@fminer.minfreq }, - { RDF::DC.title => "nr_hits", RDF::OT.paramValue => (params[:nr_hits] == "true" ? "true" : "false") }, - { RDF::DC.title => "backbone", RDF::OT.paramValue => (params[:backbone] == "false" ? "false" : "true") } - ] - - @@fminer.compounds = [] - @@fminer.db_class_sizes = Array.new # AM: effect - @@fminer.all_activities = Hash.new # DV: for effect calculation in regression part - @@fminer.smi = [] # AM LAST: needed for matching the patterns back - - # Add data to fminer - @@fminer.add_fminer_data(@@bbrc, value_map) - g_median=@@fminer.all_activities.values.to_scale.median - - #task.progress 10 - step_width = 80 / @@bbrc.GetNoRootNodes().to_f - features_smarts = Set.new - features = Array.new - - puts "Setup: #{Time.now-time}" - time = Time.now - ftime = 0 - - # run @@bbrc - - # prepare to receive results as hash { c => [ [f,v], ... ] } - fminer_results = {} - - (0 .. @@bbrc.GetNoRootNodes()-1).each do |j| - results = @@bbrc.MineRoot(j) - #task.progress 10+step_width*(j+1) - results.each do |result| - f = YAML.load(result)[0] - smarts = f[0] - p_value = f[1] - - if (!@@bbrc.GetRegression) - id_arrs = f[2..-1].flatten - max = OpenTox::Algorithm::Fminer.effect(f[2..-1].reverse, @@fminer.db_class_sizes) # f needs reversal for bbrc - effect = max+1 - else #regression part - id_arrs = f[2] - # DV: effect calculation - f_arr=Array.new - f[2].each do |id| - id=id.keys[0] # extract id from hit count hash - f_arr.push(@@fminer.all_activities[id]) - end - f_median=f_arr.to_scale.median - if g_median >= f_median - effect = 'activating' - else - effect = 'deactivating' - end - end - - ft = Time.now - unless features_smarts.include? smarts - features_smarts << smarts - feature = OpenTox::Feature.find_or_create({ - RDF::DC.title => smarts.dup, - RDF::OT.hasSource => to('/fminer/bbrc', :full), - RDF.type => [RDF::OT.Feature, RDF::OT.Substructure, RDF::OT.NumericFeature], - RDF::OT.smarts => smarts.dup, - RDF::OT.pValue => p_value.to_f.abs.round(5), - RDF::OT.effect => effect - }) - features << feature - end - ftime += Time.now - ft - - id_arrs.each { |id_count_hash| - id=id_count_hash.keys[0].to_i - count=id_count_hash.values[0].to_i - fminer_results[@@fminer.compounds[id]] || fminer_results[@@fminer.compounds[id]] = {} - if params[:nr_hits] == "true" - fminer_results[@@fminer.compounds[id]][feature.uri] = count - else - fminer_results[@@fminer.compounds[id]][feature.uri] = 1 - end - } - - end # end of - end # feature parsing - - - puts "Fminer: #{Time.now-time} (find/create Features: #{ftime})" - time = Time.now - - fminer_compounds = @@fminer.training_dataset.compounds - prediction_feature_idx = @@fminer.training_dataset.features.collect{|f| f.uri}.index @@fminer.prediction_feature.uri - prediction_feature_all_acts = fminer_compounds.each_with_index.collect { |c,idx| - @@fminer.training_dataset.data_entries[idx][prediction_feature_idx] - } - fminer_noact_compounds = fminer_compounds - @@fminer.compounds - - feature_dataset.features = features - feature_dataset.features = [ @@fminer.prediction_feature ] + feature_dataset.features if params[:get_target] == "true" - feature_dataset.compounds = fminer_compounds - fminer_compounds.each_with_index { |c,idx| - # TODO: reenable option - #if (params[:get_target] == "true") - #row = row + [ prediction_feature_all_acts[idx] ] - #end - features.each { |f| - v = fminer_results[c][f.uri] if fminer_results[c] - unless fminer_noact_compounds.include? c - v = 0 if v.nil? - end - feature_dataset.add_data_entry c, f, v.to_i - } - } - - puts "Prepare save: #{Time.now-time}" - time = Time.now - feature_dataset.put - - puts "Save: #{Time.now-time}" - feature_dataset.uri - - - end - response['Content-Type'] = 'text/uri-list' - halt 202,task.uri - end - |