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module OpenTox
class Experiment
field :dataset_ids, type: Array
field :model_algorithms, type: Array
field :model_ids, type: Array, default: []
field :crossvalidation_ids, type: Array, default: []
field :prediction_algorithms, type: Array
field :neighbor_algorithms, type: Array
field :neighbor_algorithm_parameters, type: Array
end
# TODO more sophisticated experimental design
def run
dataset_ids.each do |dataset_id|
dataset = Dataset.find(dataset_id)
model_algorithms.each do |model_algorithm|
prediction_algorithms.each do |prediction_algorithm|
neighbor_algorithms.each do |neighbor_algorithm|
neighbor_algorithm_parameters.each do |neighbor_algorithm_parameter|
$logger.debug "Creating #{model_algorithm} model for dataset #{dataset.name}, with prediction_algorithm #{prediction_algorithm}, neighbor_algorithm #{neighbor_algorithm}, neighbor_algorithm_parameters #{neighbor_algorithm_parameter}."
model = Object.const_get(model_algorithm).create dataset
model.prediction_algorithm = prediction_algorithm
model.neighbor_algorithm = neighbor_algorithm
model.neighbor_algorithm_parameters = neighbor_algorithm_parameter
model.save
model_ids << model.id
cv = nil
if dataset.features.first.nominal
cv = ClassificationCrossValidation
elsif dataset.features.first.numeric
cv = RegressionCrossValidation
end
if cv
$logger.debug "Creating #{cv} for #{model_algorithm}, dataset #{dataset.name}, with prediction_algorithm #{prediction_algorithm}, neighbor_algorithm #{neighbor_algorithm}, neighbor_algorithm_parameters #{neighbor_algorithm_parameter}."
crossvalidation = cv.create model
self.crossvalidation_ids << crossvalidation.id
else
$logger.warn "#{dataset.features.first} is neither nominal nor numeric."
end
end
end
end
end
end
save
end
def self.create params
experiment = self.new
$logge.debug "Experiment started ..."
experiment.run params
experiment
end
def report
# TODO create ggplot2 report
self.crossvalidation_ids.each do |id|
cv = CrossValidation.find(id)
file = "/tmp/#{id}.svg"
File.open(file,"w+"){|f| f.puts cv.correlation_plot}
`inkview '#{file}'`
end
end
end
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