diff options
-rw-r--r-- | lib/model.rb | 63 | ||||
-rw-r--r-- | test/model-classification.rb (renamed from test/classification.rb) | 16 | ||||
-rw-r--r-- | test/model.rb | 7 | ||||
-rw-r--r-- | test/nanoparticles.rb | 13 |
4 files changed, 60 insertions, 39 deletions
diff --git a/lib/model.rb b/lib/model.rb index 7029c31..b949042 100644 --- a/lib/model.rb +++ b/lib/model.rb @@ -57,7 +57,10 @@ module OpenTox if substance_classes.first == "OpenTox::Compound" model.algorithms = { - :descriptors => ['MP2D'], + :descriptors => { + :method => "fingerprint", + :type => "MP2D", + }, :similarity => { :method => "Algorithm::Similarity.tanimoto", :min => 0.1 @@ -77,7 +80,10 @@ module OpenTox elsif substance_classes.first == "OpenTox::Nanoparticle" model.algorithms = { - :descriptors => ["P-CHEM"], + :descriptors => { + :method => "properties", + :category => "P-CHEM", + }, #:descriptors => ["P-CHEM","Proteomics"], :similarity => { :method => "Algorithm::Similarity.weighted_cosine", @@ -115,34 +121,41 @@ module OpenTox end if values end + descriptor_method = model.algorithms[:descriptors][:method] + case descriptor_method # parse fingerprints - if model.fingerprints? - model.algorithms[:descriptors].each do |type| - model.substances.each_with_index do |s,i| - model.fingerprints[i] ||= [] - model.fingerprints[i] += s.fingerprint(type) - model.fingerprints[i].uniq! - end + when "fingerprint" + type = model.algorithms[:descriptors][:type] + model.substances.each_with_index do |s,i| + model.fingerprints[i] ||= [] + model.fingerprints[i] += s.fingerprint(type) + model.fingerprints[i].uniq! end model.descriptor_ids = model.fingerprints.flatten.uniq model.descriptor_ids.each do |d| - # resulting model may break BSON size limit (e.g. f Kazius dataset + # resulting model may break BSON size limit (e.g. f Kazius dataset) model.independent_variables << model.substance_ids.collect_with_index{|s,i| model.fingerprints[i].include? d} if model.algorithms[:prediction][:method].match /Caret/ end - else - # parse independent_variables - if (model.algorithms[:descriptors] & [PhysChem::OPENBABEL,PhysChem::CDK,PhysChem::JOELIB]).empty? - properties = model.substances.collect { |s| s.properties } - all_property_ids = properties.collect{|p| p.keys}.flatten.uniq - model.descriptor_ids = all_property_ids.select{|id| model.algorithms[:descriptors].include? Feature.find(id).category } - model.independent_variables = model.descriptor_ids.collect{|i| properties.collect{|p| p[i] ? p[i].median : nil}} - - # calculate physchem properties - else - properties = model.substances.collect { |s| s.calculate_properties(model.algorithms[:descriptors]) } - model.descriptor_ids = properties.collect{|p| p.keys}.flatten.uniq - model.independent_variables = model.descriptor_ids.collect{|i| properties.collect{|p| p[i]}} + # calculate physchem properties + when "calculate_properties" + features = model.algorithms[:descriptors][:features] + model.descriptor_ids = features.collect{|f| f.id.to_s} + model.algorithms[:descriptors].delete(:features) + model.algorithms[:descriptors].delete(:type) + model.substances.each_with_index do |s,i| + s.calculate_properties(features).each_with_index do |v,j| + model.independent_variables[j] ||= [] + model.independent_variables[j][i] = v + end end + # parse independent_variables + when "properties" + properties = model.substances.collect { |s| s.properties } + all_property_ids = properties.collect{|p| p.keys}.flatten.uniq + model.descriptor_ids = all_property_ids.select{|id| model.algorithms[:descriptors].include? Feature.find(id).category } + model.independent_variables = model.descriptor_ids.collect{|i| properties.collect{|p| p[i] ? p[i].median : nil}} + else + bad_request_error "Descriptor method '#{descriptor_method}' not implemented." end if model.algorithms[:feature_selection] and model.algorithms[:feature_selection][:method] @@ -165,7 +178,7 @@ module OpenTox case algorithms[:similarity][:method] when /tanimoto/ # binary features - similarity_descriptors = algorithms[:descriptors].collect{|type| substance.fingerprint(type)}.flatten.uniq + similarity_descriptors = substance.fingerprint algorithms[:descriptors][:type] # TODO this excludes descriptors only present in the query substance query_descriptors = descriptor_ids.collect{|id| similarity_descriptors.include? id} when /euclid|cosine/ # quantitative features @@ -295,7 +308,7 @@ module OpenTox end def fingerprints? - algorithms[:similarity][:method].match("tanimoto") ? true : false + algorithms[:descriptors][:method] == "fingerprint" ? true : false end end diff --git a/test/classification.rb b/test/model-classification.rb index c670bb5..1424f6a 100644 --- a/test/classification.rb +++ b/test/model-classification.rb @@ -4,7 +4,10 @@ class LazarClassificationTest < MiniTest::Test def test_classification_default algorithms = { - :descriptors => [ "MP2D" ], + :descriptors => { + :method => "fingerprint", + :type => "MP2D" + }, :similarity => { :method => "Algorithm::Similarity.tanimoto", :min => 0.1 @@ -55,7 +58,10 @@ class LazarClassificationTest < MiniTest::Test def test_classification_parameters algorithms = { - :descriptors => ['MACCS'], + :descriptors => { + :method => "fingerprint", + :type => "MACCS" + }, :similarity => { :min => 0.4 }, @@ -86,7 +92,11 @@ class LazarClassificationTest < MiniTest::Test training_dataset.delete end - def test_fingerprint_feature_selection + def test_caret_classification + skip + end + + def test_fingerprint_chisq_feature_selection skip end diff --git a/test/model.rb b/test/model.rb index 322ad90..027efe4 100644 --- a/test/model.rb +++ b/test/model.rb @@ -49,7 +49,10 @@ class ModelTest < MiniTest::Test def test_physchem_regression algorithms = { - :descriptors => [PhysChem::OPENBABEL], + :descriptors => { + :method => "calculate_properties", + :features => PhysChem.openbabel_descriptors, + }, :similarity => { :method => "Algorithm::Similarity.cosine", } @@ -60,9 +63,9 @@ class ModelTest < MiniTest::Test assert_equal "Algorithm::Caret.pls", model.algorithms[:prediction][:method] assert_equal "Algorithm::Similarity.cosine", model.algorithms[:similarity][:method] assert_equal 0.1, model.algorithms[:similarity][:min] + algorithms[:descriptors].delete :features assert_equal algorithms[:descriptors], model.algorithms[:descriptors] prediction = model.predict training_dataset.substances[10] - p prediction refute_nil prediction[:value] # TODO test predictin end diff --git a/test/nanoparticles.rb b/test/nanoparticles.rb index c489cb7..9a67e63 100644 --- a/test/nanoparticles.rb +++ b/test/nanoparticles.rb @@ -1,6 +1,5 @@ require_relative "setup.rb" - class NanoparticleTest < MiniTest::Test include OpenTox::Validation @@ -13,7 +12,7 @@ class NanoparticleTest < MiniTest::Test @prediction_feature = @training_dataset.features.select{|f| f["name"] == 'log2(Net cell association)'}.first end - def test_create_model + def test_nanoparticle_model model = Model::Lazar.create training_dataset: @training_dataset, prediction_feature: @prediction_feature nanoparticle = @training_dataset.nanoparticles[-34] prediction = model.predict nanoparticle @@ -23,6 +22,8 @@ class NanoparticleTest < MiniTest::Test model.delete end + # validations + def test_validate_default_nanoparticle_model model = Model::Lazar.create training_dataset: @training_dataset, prediction_feature: @prediction_feature cv = CrossValidation.create model @@ -77,15 +78,9 @@ class NanoparticleTest < MiniTest::Test refute_nil cv.rmse end - def test_export - skip - Dataset.all.each do |d| - puts d.to_csv - end - end def test_import_ld - skip + skip # Ambit JSON-LD export defunct dataset_ids = Import::Enanomapper.import_ld end end |