diff options
Diffstat (limited to 'lib/ot_predictions.rb')
-rwxr-xr-x | lib/ot_predictions.rb | 270 |
1 files changed, 145 insertions, 125 deletions
diff --git a/lib/ot_predictions.rb b/lib/ot_predictions.rb index 335fe84..cf0168e 100755 --- a/lib/ot_predictions.rb +++ b/lib/ot_predictions.rb @@ -8,155 +8,175 @@ module Lib CHECK_VALUES = ENV['RACK_ENV'] =~ /debug|test/ def identifier(instance_index) - return compound(instance_index) + compound(instance_index) end def compound(instance_index) - return @compounds[instance_index] + @compounds[instance_index] end - + def initialize( feature_type, test_dataset_uris, test_target_dataset_uris, - prediction_feature, prediction_dataset_uris, predicted_variables, predicted_confidences, subjectid=nil, task=nil) + prediction_feature, prediction_dataset_uris, predicted_variables, predicted_confidences, + subjectid=nil, task=nil ) + + test_dataset_uris = [test_dataset_uris] unless test_dataset_uris.is_a?(Array) + test_target_dataset_uris = [test_target_dataset_uris] unless test_target_dataset_uris.is_a?(Array) + prediction_dataset_uris = [prediction_dataset_uris] unless prediction_dataset_uris.is_a?(Array) + predicted_variables = [predicted_variables] unless predicted_variables.is_a?(Array) + predicted_confidences = [predicted_confidences] unless predicted_confidences.is_a?(Array) + LOGGER.debug "loading prediction -- test-dataset: "+test_dataset_uris.inspect + LOGGER.debug "loading prediction -- test-target-datset: "+test_target_dataset_uris.inspect + LOGGER.debug "loading prediction -- prediction-dataset: "+prediction_dataset_uris.inspect + LOGGER.debug "loading prediction -- predicted_variable: "+predicted_variables.inspect + LOGGER.debug "loading prediction -- predicted_confidence: "+predicted_confidences.inspect + LOGGER.debug "loading prediction -- prediction_feature: "+prediction_feature.to_s + raise "prediction_feature missing" unless prediction_feature + + @compounds = [] + all_predicted_values = [] + all_actual_values = [] + all_confidence_values = [] + accept_values = nil - test_dataset_uris = [test_dataset_uris] unless test_dataset_uris.is_a?(Array) - test_target_dataset_uris = [test_target_dataset_uris] unless test_target_dataset_uris.is_a?(Array) - prediction_dataset_uris = [prediction_dataset_uris] unless prediction_dataset_uris.is_a?(Array) - predicted_variables = [predicted_variables] unless predicted_variables.is_a?(Array) - predicted_confidences = [predicted_confidences] unless predicted_confidences.is_a?(Array) - LOGGER.debug "loading prediction -- test-dataset: "+test_dataset_uris.inspect - LOGGER.debug "loading prediction -- test-target-datset: "+test_target_dataset_uris.inspect - LOGGER.debug "loading prediction -- prediction-dataset: "+prediction_dataset_uris.inspect - LOGGER.debug "loading prediction -- predicted_variable: "+predicted_variables.inspect - LOGGER.debug "loading prediction -- predicted_confidence: "+predicted_confidences.inspect - LOGGER.debug "loading prediction -- prediction_feature: "+prediction_feature.to_s - raise "prediction_feature missing" unless prediction_feature + if task + task_step = 100 / (test_dataset_uris.size*2 + 1) + task_status = 0 + end + + test_dataset_uris.size.times do |i| - @compounds = [] - all_predicted_values = [] - all_actual_values = [] - all_confidence_values = [] - accept_values = nil + test_dataset_uri = test_dataset_uris[i] + test_target_dataset_uri = test_target_dataset_uris[i] + prediction_dataset_uri = prediction_dataset_uris[i] + predicted_variable = predicted_variables[i] + predicted_confidence = predicted_confidences[i] - if task - task_step = 100 / (test_dataset_uris.size*2 + 1) - task_status = 0 + predicted_variable=prediction_feature if predicted_variable==nil + + test_dataset = Lib::DatasetCache.find test_dataset_uri,subjectid + raise "test dataset not found: '"+test_dataset_uri.to_s+"'" unless test_dataset + + if test_target_dataset_uri == nil || test_target_dataset_uri.strip.size==0 || test_target_dataset_uri==test_dataset_uri + test_target_dataset_uri = test_dataset_uri + test_target_dataset = test_dataset + raise "prediction_feature not found in test_dataset, specify a test_target_dataset\n"+ + "prediction_feature: '"+prediction_feature.to_s+"'\n"+ + "test_dataset: '"+test_target_dataset_uri.to_s+"'\n"+ + "available features are: "+test_target_dataset.features.inspect if test_target_dataset.features.keys.index(prediction_feature)==nil + else + test_target_dataset = Lib::DatasetCache.find test_target_dataset_uri,subjectid + raise "test target datset not found: '"+test_target_dataset_uri.to_s+"'" unless test_target_dataset + if CHECK_VALUES + test_dataset.compounds.each do |c| + raise "test compound not found on test class dataset "+c.to_s unless test_target_dataset.compounds.include?(c) + end + end + raise "prediction_feature not found in test_target_dataset\n"+ + "prediction_feature: '"+prediction_feature.to_s+"'\n"+ + "test_target_dataset: '"+test_target_dataset_uri.to_s+"'\n"+ + "available features are: "+test_target_dataset.features.inspect if test_target_dataset.features.keys.index(prediction_feature)==nil end - - test_dataset_uris.size.times do |i| - - test_dataset_uri = test_dataset_uris[i] - test_target_dataset_uri = test_target_dataset_uris[i] - prediction_dataset_uri = prediction_dataset_uris[i] - predicted_variable = predicted_variables[i] - predicted_confidence = predicted_confidences[i] - - predicted_variable=prediction_feature if predicted_variable==nil - test_dataset = Lib::DatasetCache.find test_dataset_uri,subjectid - raise "test dataset not found: '"+test_dataset_uri.to_s+"'" unless test_dataset + compounds = test_dataset.compounds + LOGGER.debug "test dataset size: "+compounds.size.to_s + raise "test dataset is empty "+test_dataset_uri.to_s unless compounds.size>0 - if test_target_dataset_uri == nil || test_target_dataset_uri.strip.size==0 || test_target_dataset_uri==test_dataset_uri - test_target_dataset_uri = test_dataset_uri - test_target_dataset = test_dataset - raise "prediction_feature not found in test_dataset, specify a test_target_dataset\n"+ - "prediction_feature: '"+prediction_feature.to_s+"'\n"+ - "test_dataset: '"+test_target_dataset_uri.to_s+"'\n"+ - "available features are: "+test_target_dataset.features.inspect if test_target_dataset.features.keys.index(prediction_feature)==nil + if feature_type=="classification" + av = test_target_dataset.accept_values(prediction_feature) + raise "'"+OT.acceptValue.to_s+"' missing/invalid for feature '"+prediction_feature.to_s+"' in dataset '"+ + test_target_dataset_uri.to_s+"', acceptValues are: '"+av.inspect+"'" if av==nil or av.length<2 + if accept_values==nil + accept_values=av else - test_target_dataset = Lib::DatasetCache.find test_target_dataset_uri,subjectid - raise "test target datset not found: '"+test_target_dataset_uri.to_s+"'" unless test_target_dataset - if CHECK_VALUES - test_dataset.compounds.each do |c| - raise "test compound not found on test class dataset "+c.to_s unless test_target_dataset.compounds.include?(c) - end - end - raise "prediction_feature not found in test_target_dataset\n"+ - "prediction_feature: '"+prediction_feature.to_s+"'\n"+ - "test_target_dataset: '"+test_target_dataset_uri.to_s+"'\n"+ - "available features are: "+test_target_dataset.features.inspect if test_target_dataset.features.keys.index(prediction_feature)==nil + raise "accept values (in folds) differ "+av.inspect+" != "+accept_values.inspect if av!=accept_values end - - compounds = test_dataset.compounds - LOGGER.debug "test dataset size: "+compounds.size.to_s - raise "test dataset is empty "+test_dataset_uri.to_s unless compounds.size>0 - - if feature_type=="classification" - av = test_target_dataset.accept_values(prediction_feature) - raise "'"+OT.acceptValue.to_s+"' missing/invalid for feature '"+prediction_feature.to_s+"' in dataset '"+ - test_target_dataset_uri.to_s+"', acceptValues are: '"+av.inspect+"'" if av==nil or av.length<2 - if accept_values==nil - accept_values=av - else - raise "accept values (in folds) differ "+av.inspect+" != "+accept_values.inspect if av!=accept_values - end + end + + actual_values = [] + compounds.each do |c| + case feature_type + when "classification" + actual_values << classification_val(test_target_dataset, c, prediction_feature, accept_values) + when "regression" + actual_values << regression_val(test_target_dataset, c, prediction_feature) end - - actual_values = [] - compounds.each do |c| + end + task.progress( task_status += task_step ) if task # loaded actual values + + prediction_dataset = Lib::DatasetCache.find prediction_dataset_uri,subjectid + raise "prediction dataset not found: '"+prediction_dataset_uri.to_s+"'" unless prediction_dataset + + # allow missing prediction feature if there are no compounds in the prediction dataset + raise "predicted_variable not found in prediction_dataset\n"+ + "predicted_variable '"+predicted_variable.to_s+"'\n"+ + "prediction_dataset: '"+prediction_dataset_uri.to_s+"'\n"+ + "available features are: "+prediction_dataset.features.inspect if prediction_dataset.features.keys.index(predicted_variable)==nil and prediction_dataset.compounds.size>0 + raise "predicted_confidence not found in prediction_dataset\n"+ + "predicted_confidence '"+predicted_confidence.to_s+"'\n"+ + "prediction_dataset: '"+prediction_dataset_uri.to_s+"'\n"+ + "available features are: "+prediction_dataset.features.inspect if predicted_confidence and prediction_dataset.features.keys.index(predicted_confidence)==nil and prediction_dataset.compounds.size>0 + + raise "more predicted than test compounds, #test: "+compounds.size.to_s+" < #prediction: "+ + prediction_dataset.compounds.size.to_s+", test-dataset: "+test_dataset_uri.to_s+", prediction-dataset: "+ + prediction_dataset_uri if compounds.size < prediction_dataset.compounds.size + if CHECK_VALUES + prediction_dataset.compounds.each do |c| + raise "predicted compound not found in test dataset:\n"+c+"\ntest-compounds:\n"+ + compounds.collect{|c| c.to_s}.join("\n") if compounds.index(c)==nil + end + end + + predicted_values = [] + confidence_values = [] + count = 0 + compounds.each do |c| + if prediction_dataset.compounds.index(c)==nil + predicted_values << nil + confidence_values << nil + else case feature_type when "classification" - actual_values << classification_val(test_target_dataset, c, prediction_feature, accept_values) + predicted_values << classification_val(prediction_dataset, c, predicted_variable, accept_values) when "regression" - actual_values << regression_val(test_target_dataset, c, prediction_feature) + predicted_values << regression_val(prediction_dataset, c, predicted_variable) end - end - task.progress( task_status += task_step ) if task # loaded actual values - - prediction_dataset = Lib::DatasetCache.find prediction_dataset_uri,subjectid - raise "prediction dataset not found: '"+prediction_dataset_uri.to_s+"'" unless prediction_dataset - - # allow missing prediction feature if there are no compounds in the prediction dataset - raise "predicted_variable not found in prediction_dataset\n"+ - "predicted_variable '"+predicted_variable.to_s+"'\n"+ - "prediction_dataset: '"+prediction_dataset_uri.to_s+"'\n"+ - "available features are: "+prediction_dataset.features.inspect if prediction_dataset.features.keys.index(predicted_variable)==nil and prediction_dataset.compounds.size>0 - raise "predicted_confidence not found in prediction_dataset\n"+ - "predicted_confidence '"+predicted_confidence.to_s+"'\n"+ - "prediction_dataset: '"+prediction_dataset_uri.to_s+"'\n"+ - "available features are: "+prediction_dataset.features.inspect if predicted_confidence and prediction_dataset.features.keys.index(predicted_confidence)==nil and prediction_dataset.compounds.size>0 - - raise "more predicted than test compounds, #test: "+compounds.size.to_s+" < #prediction: "+ - prediction_dataset.compounds.size.to_s+", test-dataset: "+test_dataset_uri.to_s+", prediction-dataset: "+ - prediction_dataset_uri if compounds.size < prediction_dataset.compounds.size - if CHECK_VALUES - prediction_dataset.compounds.each do |c| - raise "predicted compound not found in test dataset:\n"+c+"\ntest-compounds:\n"+ - compounds.collect{|c| c.to_s}.join("\n") if compounds.index(c)==nil - end - end - - predicted_values = [] - confidence_values = [] - count = 0 - compounds.each do |c| - if prediction_dataset.compounds.index(c)==nil - predicted_values << nil - confidence_values << nil + if predicted_confidence + confidence_values << confidence_val(prediction_dataset, c, predicted_confidence) else - case feature_type - when "classification" - predicted_values << classification_val(prediction_dataset, c, predicted_variable, accept_values) - when "regression" - predicted_values << regression_val(prediction_dataset, c, predicted_variable) - end - if predicted_confidence - confidence_values << confidence_val(prediction_dataset, c, predicted_confidence) - else - confidence_values << nil - end + confidence_values << nil end - count += 1 end - @compounds += compounds - all_predicted_values += predicted_values - all_actual_values += actual_values - all_confidence_values += confidence_values - - task.progress( task_status += task_step ) if task # loaded predicted values and confidence + count += 1 end + @compounds += compounds + all_predicted_values += predicted_values + all_actual_values += actual_values + all_confidence_values += confidence_values + task.progress( task_status += task_step ) if task # loaded predicted values and confidence + end + + #sort according to confidence if available + if all_confidence_values.compact.size>0 + values = [] + all_predicted_values.size.times do |i| + values << [all_predicted_values[i], all_actual_values[i], all_confidence_values[i], @compounds[i]] + end + values = values.sort_by{ |v| v[2] || 0 }.reverse # sorting by confidence + all_predicted_values = [] + all_actual_values = [] + all_confidence_values = [] + @compounds = [] + values.each do |v| + all_predicted_values << v[0] + all_actual_values << v[1] + all_confidence_values << v[2] + @compounds << v[3] + end + end + super(all_predicted_values, all_actual_values, all_confidence_values, feature_type, accept_values) - raise "illegal num compounds "+num_info if @compounds.size != @predicted_values.size + raise "illegal num compounds "+num_info if @compounds.size != @predicted_values.size task.progress(100) if task # done with the mathmatics end |