diff options
Diffstat (limited to 'lib/lazar.rb')
| -rw-r--r-- | lib/lazar.rb | 33 |
1 files changed, 13 insertions, 20 deletions
diff --git a/lib/lazar.rb b/lib/lazar.rb index 2c83f38..19f8cdd 100644 --- a/lib/lazar.rb +++ b/lib/lazar.rb @@ -13,7 +13,7 @@ module OpenTox include OpenTox include Mongoid::Document include Mongoid::Timestamps - store_in collection: "model" + store_in collection: "models" field :title, type: String field :description, type: String @@ -74,8 +74,8 @@ module OpenTox end unless lazar.prediction_algorithm - lazar.prediction_algorithm = :weighted_majority_vote if prediction_feature.nominal - lazar.prediction_algorithm = :local_svm_regression if prediction_feature.numeric + lazar.prediction_algorithm = "OpenTox::Algorithm::Classification.weighted_majority_vote" if prediction_feature.nominal + lazar.prediction_algorithm = "OpenTox::Algorithm::Regression.local_svm_regression" if prediction_feature.numeric end lazar.prediction_algorithm =~ /majority_vote/ ? lazar.propositionalized = false : lazar.propositionalized = true @@ -144,11 +144,7 @@ module OpenTox $logger.debug "Setup: #{Time.now-time}" time = Time.now - # TODO: remove eval - #p ("#{feature_calculation_algorithm}(#{compounds}, #{@feature_dataset.features.collect{|f| f.smarts}})") - #@query_fingerprint = eval("#{feature_calculation_algorithm}(#{compounds}, #{@feature_dataset.features.collect{|f| f.smarts}})") @query_fingerprint = Algorithm.run(feature_calculation_algorithm, compounds, @feature_dataset.features.collect{|f| f.smarts} ) - #p @query_fingerprint $logger.debug "Fingerprint calculation: #{Time.now-time}" time = Time.now @@ -164,7 +160,9 @@ module OpenTox if database_activities and !database_activities.empty? database_activities.each do |database_activity| $logger.debug "do not predict compound, it occurs in dataset with activity #{database_activity}" - prediction_dataset << [compound, database_activity, nil] + prediction_dataset.compound_ids << compound.id + prediction_dataset[c,0] = database_activity + prediction_dataset[c,1] = nil end next else @@ -176,23 +174,16 @@ module OpenTox # find neighbors neighbors = [] - #@feature_dataset.data_entries.each_with_index do |fingerprint, i| - @feature_dataset.compounds.each_with_index do |compound, i| - #p compound - #p @feature_dataset.features.size - fingerprint = @feature_dataset.feature_values(compound) - #fingerprint = @feature_dataset.features(compound) - #p fingerprint - - sim = Algorithm.run(similarity_algorithm,[fingerprint, @query_fingerprint[c]]) + @feature_dataset.data_entries.each_with_index do |fingerprint, i| + + sim = Algorithm.run(similarity_algorithm,fingerprint, @query_fingerprint[c]) # TODO fix for multi feature datasets neighbors << [@feature_dataset.compounds[i],@training_dataset.data_entries[i].first,sim] if sim > self.min_sim end - #p neighbors prediction = Algorithm.run(prediction_algorithm, neighbors) - $logger.debug "Prediction: #{Time.now-time}" + $logger.debug "Prediction time: #{Time.now-time}" time = Time.now # AM: transform to original space (TODO) @@ -201,7 +192,9 @@ module OpenTox $logger.debug "predicted value: #{prediction[:prediction]}, confidence: #{prediction[:confidence]}" end - prediction_dataset << [ compound, prediction[:prediction], prediction[:confidence] ] + prediction_dataset.compound_ids << compound + prediction_dataset[c,0] = prediction[:prediction] + prediction_dataset[c,1] = prediction[:confidence] end prediction_dataset |