diff options
Diffstat (limited to 'lib/bbrc.rb')
| -rw-r--r-- | lib/bbrc.rb | 61 |
1 files changed, 42 insertions, 19 deletions
diff --git a/lib/bbrc.rb b/lib/bbrc.rb index 595d712..6b0eb26 100644 --- a/lib/bbrc.rb +++ b/lib/bbrc.rb @@ -1,6 +1,9 @@ module OpenTox module Algorithm class Fminer + TABLE_OF_ELEMENTS = [ +"H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne", "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca", "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb", "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg", "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th", "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt", "Ds", "Rg", "Cn", "Uut", "Fl", "Uup", "Lv", "Uus", "Uuo"] + # # Run bbrc algorithm on dataset # @@ -14,27 +17,40 @@ module OpenTox # - 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 - def self.bbrc dataset, params={} - - table_of_elements = [ -"H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne", "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca", "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb", "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg", "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th", "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt", "Ds", "Rg", "Cn", "Uut", "Fl", "Uup", "Lv", "Uus", "Uuo"] - - @fminer=OpenTox::Algorithm::Fminer.new - @fminer.check_params(dataset,params,5) + def self.bbrc training_dataset, params={} time = Time.now + bad_request_error "More than one prediction feature found in training_dataset #{training_dataset.id}" unless training_dataset.features.size == 1 + + prediction_feature = training_dataset.features.first + if params[:min_frequency] + minfreq = params[:min_frequency] + else + per_mil = 5 # value from latest version + i = training_dataset.feature_ids.index prediction_feature.id + nr_labeled_cmpds = training_dataset.data_entries.select{|de| !de[i].nil?}.size + minfreq = per_mil * nr_labeled_cmpds.to_f / 1000.0 # AM sugg. 8-10 per mil for BBRC, 50 per mil for LAST + minfreq = 2 unless minfreq > 2 + minfreq = minfreq.round + end + + #@fminer=OpenTox::Algorithm::Fminer.new + #@fminer.check_params(dataset,params,5) + #p @fminer.instance_variables + @bbrc = Bbrc::Bbrc.new @bbrc.Reset - if @fminer.prediction_feature.numeric + if prediction_feature.numeric @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.id}' and "\ - "feature '#{@fminer.prediction_feature.id}'" unless @fminer.prediction_feature.accept_values - value_map = @fminer.prediction_feature.accept_values.each_index.inject({}) { |h,idx| h[idx+1]=@fminer.prediction_feature.accept_values[idx]; h } + "dataset '#{training_dataset.id}' and "\ + "feature '#{prediction_feature.id}'" unless prediction_feature.accept_values + act2value = prediction_feature.accept_values.each_index.inject({}) { |h,idx| h[idx+1]=prediction_feature.accept_values[idx]; h } + value2act = act2value.invert end - @bbrc.SetMinfreq(@fminer.minfreq) + @bbrc.SetMinfreq(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] @@ -42,21 +58,28 @@ module OpenTox params[:nr_hits] ? nr_hits = params[:nr_hits] : nr_hits = false feature_dataset = FminerDataset.new( - :training_dataset_id => dataset.id, + :training_dataset_id => training_dataset.id, :training_algorithm => "#{self.to_s}.bbrc", - :training_feature_id => params[:prediction_feature].id , + :training_feature_id => prediction_feature.id , :training_parameters => { - :min_frequency => @fminer.minfreq, + :min_frequency => minfreq, :nr_hits => nr_hits, :backbone => (params[:backbone] == false ? false : true) } ) - feature_dataset.compounds = dataset.compounds + feature_dataset.compounds = training_dataset.compounds + $logger.debug "Setup: #{Time.now-time}" + time = Time.now # Add data to fminer - @fminer.add_fminer_data(@bbrc, value_map) - g_median=@fminer.all_activities.values.to_scale.median + #@fminer.add_fminer_data(@bbrc, value_map) + training_dataset.compounds.each_with_index do |compound,i| + @bbrc.AddCompound(compound.smiles,i+1) + act = value2act[training_dataset.data_entries[i].first] + @bbrc.AddActivity(act,i+1) + end + #g_median=@fminer.all_activities.values.to_scale.median #task.progress 10 #step_width = 80 / @bbrc.GetNoRootNodes().to_f @@ -76,7 +99,7 @@ module OpenTox smarts = f.shift # convert fminer SMARTS representation into a more human readable format smarts.gsub!(%r{\[#(\d+)&(\w)\]}) do - element = table_of_elements[$1.to_i-1] + element = TABLE_OF_ELEMENTS[$1.to_i-1] $2 == "a" ? element.downcase : element end p_value = f.shift |