diff options
Diffstat (limited to 'lib')
| -rw-r--r-- | lib/crossvalidation.rb | 17 | ||||
| -rw-r--r-- | lib/dataset.rb | 2 | ||||
| -rw-r--r-- | lib/lazar.rb | 2 | ||||
| -rw-r--r-- | lib/model.rb (renamed from lib/lazar-model.rb) | 13 | ||||
| -rw-r--r-- | lib/regression.rb | 24 |
5 files changed, 50 insertions, 8 deletions
diff --git a/lib/crossvalidation.rb b/lib/crossvalidation.rb index d926cc4..d0ad324 100644 --- a/lib/crossvalidation.rb +++ b/lib/crossvalidation.rb @@ -2,11 +2,16 @@ module OpenTox class CrossValidation field :validation_ids, type: Array, default: [] + field :model_id, type: BSON::ObjectId field :folds, type: Integer field :nr_instances, type: Integer field :nr_unpredicted, type: Integer field :predictions, type: Array field :finished_at, type: Time + + def time + finished_at - created_at + end end class ClassificationCrossValidation < CrossValidation @@ -22,6 +27,7 @@ module OpenTox def self.create model, n=10 cv = self.new + cv.save # set created_at validation_ids = [] nr_instances = 0 nr_unpredicted = 0 @@ -64,6 +70,10 @@ module OpenTox end end cv.update_attributes( + name: model.name, + model_id: model.id, + folds: n, + validation_ids: validation_ids, nr_instances: nr_instances, nr_unpredicted: nr_unpredicted, accept_values: accept_values, @@ -85,10 +95,8 @@ module OpenTox #F measure carcinogen: 0.769, noncarcinogen: 0.348 end - class RegressionCrossValidation < Validation + class RegressionCrossValidation < CrossValidation - field :validation_ids, type: Array, default: [] - field :folds, type: Integer field :rmse, type: Float field :mae, type: Float field :weighted_rmse, type: Float @@ -96,6 +104,7 @@ module OpenTox def self.create model, n=10 cv = self.new + cv.save # set created_at validation_ids = [] nr_instances = 0 nr_unpredicted = 0 @@ -145,6 +154,8 @@ module OpenTox rmse = Math.sqrt(rmse/n) weighted_rmse = Math.sqrt(weighted_rmse/confidence_sum) cv.update_attributes( + name: model.name, + model_id: model.id, folds: n, validation_ids: validation_ids, nr_instances: nr_instances, diff --git a/lib/dataset.rb b/lib/dataset.rb index 8c5ffc0..5850c3d 100644 --- a/lib/dataset.rb +++ b/lib/dataset.rb @@ -49,7 +49,7 @@ module OpenTox @data_entries = Marshal.load(data_entry_file.data) bad_request_error "Data entries (#{data_entries_id}) are not a 2D-Array" unless @data_entries.is_a? Array and @data_entries.first.is_a? Array bad_request_error "Data entries (#{data_entries_id}) have #{@data_entries.size} rows, but dataset (#{id}) has #{compound_ids.size} compounds" unless @data_entries.size == compound_ids.size - bad_request_error "Data entries (#{data_entries_id}) have #{@data_entries..first.size} columns, but dataset (#{id}) has #{feature_ids.size} features" unless @data_entries.first.size == feature_ids.size + bad_request_error "Data entries (#{data_entries_id}) have #{@data_entries.first.size} columns, but dataset (#{id}) has #{feature_ids.size} features" unless @data_entries.first.size == feature_ids.size $logger.debug "Retrieving data: #{Time.now-t}" end end diff --git a/lib/lazar.rb b/lib/lazar.rb index 2ea8cba..174fb2c 100644 --- a/lib/lazar.rb +++ b/lib/lazar.rb @@ -58,7 +58,7 @@ CLASSES = ["Feature","Compound","Dataset","Validation","CrossValidation"]# Algor "algorithm.rb", "descriptor.rb", "bbrc.rb", - "lazar-model.rb", + "model.rb", "similarity.rb", "neighbor.rb", "classification.rb", diff --git a/lib/lazar-model.rb b/lib/model.rb index 1970401..bf8c549 100644 --- a/lib/lazar-model.rb +++ b/lib/model.rb @@ -8,7 +8,7 @@ module OpenTox include Mongoid::Timestamps store_in collection: "models" - field :title, type: String + field :title, as: :name, type: String field :creator, type: String, default: __FILE__ # datasets field :training_dataset_id, type: BSON::ObjectId @@ -156,9 +156,16 @@ module OpenTox end - class PredictionModel < Lazar - field :category, type: String + class PredictionModel + include OpenTox + include Mongoid::Document + include Mongoid::Timestamps + store_in collection: "models" + + # TODO field Validations field :endpoint, type: String + field :species, type: String + field :source, type: String field :unit, type: String field :model_id, type: BSON::ObjectId field :crossvalidation_id, type: BSON::ObjectId diff --git a/lib/regression.rb b/lib/regression.rb index 8a52e7d..0bc6547 100644 --- a/lib/regression.rb +++ b/lib/regression.rb @@ -34,6 +34,30 @@ module OpenTox {:value => prediction,:confidence => confidence} end + def self.weighted_average_with_relevant_fingerprints neighbors + weighted_sum = 0.0 + sim_sum = 0.0 + fingerprint_features = [] + neighbors.each do |row| + n,sim,acts = row + neighbor = Compound.find n + fingerprint_features += neighbor.fp4 + end + fingerprint_features.uniq! + p fingerprint_features +=begin + p n + acts.each do |act| + weighted_sum += sim*Math.log10(act) + sim_sum += sim + end + end +=end + confidence = sim_sum/neighbors.size.to_f + sim_sum == 0 ? prediction = nil : prediction = 10**(weighted_sum/sim_sum) + {:value => prediction,:confidence => confidence} + end + # Local support vector regression from neighbors # @param [Hash] params Keys `:props, :activities, :sims, :min_train_performance` are required # @return [Numeric] A prediction value. |