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| author | Christoph Helma <helma@in-silico.ch> | 2015-08-13 18:57:11 +0200 |
|---|---|---|
| committer | Christoph Helma <helma@in-silico.ch> | 2015-08-13 18:57:11 +0200 |
| commit | d0850e2983a219da214a67190fe881c7650f532f (patch) | |
| tree | a917334a1a70823dc979a27e453b2598e98c8027 /lib/bbrc.rb | |
| parent | 6ab86c253ba0eb79b9e6a20effa2d18626accf2b (diff) | |
majority of tests working
Diffstat (limited to 'lib/bbrc.rb')
| -rw-r--r-- | lib/bbrc.rb | 12 |
1 files changed, 9 insertions, 3 deletions
diff --git a/lib/bbrc.rb b/lib/bbrc.rb index 6a2eed7..c83b9b3 100644 --- a/lib/bbrc.rb +++ b/lib/bbrc.rb @@ -26,6 +26,7 @@ module OpenTox minfreq = params[:min_frequency] else per_mil = 5 # value from latest version + per_mil = 8 # as suggested below 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 @@ -65,9 +66,11 @@ module OpenTox # add data 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) + if act # TODO check if this works + @bbrc.AddCompound(compound.smiles,i+1) + @bbrc.AddActivity(act,i+1) + end end #g_median=@fminer.all_activities.values.to_scale.median @@ -94,6 +97,9 @@ module OpenTox end p_value = f.shift f.flatten! + compound_idxs = f.collect{|e| e.first.first-1} + # majority class + effect = compound_idxs.collect{|i| training_dataset.data_entries[i].first}.mode =begin if (!@bbrc.GetRegression) @@ -122,7 +128,7 @@ module OpenTox feature = OpenTox::FminerSmarts.find_or_create_by({ "smarts" => smarts, "p_value" => p_value.to_f.abs.round(5), - #"effect" => effect, + "effect" => effect, "dataset_id" => feature_dataset.id }) feature_dataset.feature_ids << feature.id |