diff options
| author | gebele <gebele@in-silico.ch> | 2016-09-23 12:26:08 +0000 |
|---|---|---|
| committer | gebele <gebele@in-silico.ch> | 2016-09-23 12:26:08 +0000 |
| commit | f4b457653ae3aa2001e2edb178a61e246fa90009 (patch) | |
| tree | e8c6803c0b182bbfdfc3d08e2758227e97b55dbe /application.rb | |
| parent | f2912140b930dbedd4dde5dfbf955a47e32e84a3 (diff) | |
example selection by training dataset and relevant features;added links for core, coating and keywords
Diffstat (limited to 'application.rb')
| -rw-r--r-- | application.rb | 20 |
1 files changed, 13 insertions, 7 deletions
diff --git a/application.rb b/application.rb index 5df466c..ea0684e 100644 --- a/application.rb +++ b/application.rb @@ -22,14 +22,18 @@ get '/predict/?' do prediction_models = OpenTox::Model::NanoPrediction.all prediction_models.each{|m| m.model[:feature_selection_algorithm_parameters]["category"] == "P-CHEM" ? @prediction_models[0] = m : @prediction_models[1] = m} @prediction_models.each_with_index{|m,idx| idx == 0 ? m[:pc_model] = true : m[:pcp_model] = true} - nanoparticles = OpenTox::Nanoparticle.all.select{|n| n.core["name"] == "Au" || n.core["name"] == "Ag"} - ## helper for preselect nanos with more than 12 pc_descriptors but take too much time for now - #example = nanoparticles.collect{|n| n if n.physchem_descriptors.size > 16 && (arr = n.physchem_descriptors.collect{|k,v| OpenTox::Feature.find(k).category == "P-CHEM"}; arr.size > 12 )}.compact - example = nanoparticles.collect{|n| n if n.physchem_descriptors.size > 16}.compact - pcp = example.sample + + # collect nanoparticles by training dataset (Ag + Au) + dataset = OpenTox::Dataset.find_by(:name=> "Protein Corona Fingerprinting Predicts the Cellular Interaction of Gold and Silver Nanoparticles") + nanoparticles = dataset.nanoparticles + # select physchem_parameters by relevant_features out of each model + @@pc_relevant_features = @prediction_models[0].model.relevant_features.collect{|id, v| OpenTox::Feature.find(id)} + @@pcp_relevant_features = @prediction_models[1].model.relevant_features.collect{|id, v| OpenTox::Feature.find(id)} + pcp = nanoparticles.sample + pcp.physchem_descriptors.delete_if{|id,v| !@@pcp_relevant_features.include?(OpenTox::Feature.find(id))} @example_pcp = pcp - pc = example.sample - pc.physchem_descriptors.delete_if{|k,v| feature = OpenTox::Feature.find_by(:id => k); feature.category != "P-CHEM"} + pc = nanoparticles.sample + pc.physchem_descriptors.delete_if{|id,v| !@@pc_relevant_features.include?(OpenTox::Feature.find(id))} @example_pc = pc haml :predict @@ -41,6 +45,8 @@ get '/license' do end post '/predict/?' do + + # choose the right prediction model prediction_model = OpenTox::Model::NanoPrediction.find(params[:prediction_model]) size = params[:size].to_i @type = params[:type] |