Class: Performancer

Inherits:
Object
  • Object
show all
Defined in:
lib/NetAnalyzer/performancer.rb

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Performancer

Returns a new instance of Performancer.



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# File 'lib/NetAnalyzer/performancer.rb', line 4

def initialize()
	@control = {}
end

Instance Method Details

#get_cuts(limits, n_cuts) ⇒ Object 



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# File 'lib/NetAnalyzer/performancer.rb', line 79

def get_cuts(limits, n_cuts)
	cuts = []
	range = (limits.last - limits.first).abs.fdiv(n_cuts)
	range = BigDecimal(range, 10)
	cut = limits.first
	(n_cuts + 1).times do |n|
		cuts << (cut + n * range).to_f
	end
	return cuts
end

#get_pred_rec(predictions, cut_number = 100, top_number = 10000) ⇒ Object

Pandey 2007, Association Analysis-based Transformations for Protein Interaction Networks: A Function Prediction Case Study



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# File 'lib/NetAnalyzer/performancer.rb', line 23

def get_pred_rec(predictions, cut_number = 100, top_number = 10000)
	performance = [] #cut, pred, rec
	preds, limits = load_prediction(predictions)
	cuts = get_cuts(limits, cut_number)
	cuts.each do |cut|
		prec, rec = pred_rec(preds, cut, top_number)
		performance << [cut, prec, rec]
	end
	return performance
end

#get_reliable_labels(labels, scores, cut, top) ⇒ Object 



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# File 'lib/NetAnalyzer/performancer.rb', line 90

def get_reliable_labels(labels, scores, cut, top)
	reliable_labels = []
	scores.each_with_index do |score, i|
		reliable_labels << [labels[i], score] if score >= cut
	end
	reliable_labels = reliable_labels.sort!{|l1,l2| l2.last <=> l1.last}[0..top-1].map{|pred| pred.first}
	return reliable_labels
end

#load_control(ref_array) ⇒ Object 



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# File 'lib/NetAnalyzer/performancer.rb', line 8

def load_control(ref_array)
	ref_array.each do |node1, node2|
		if node2 != '-'
			query = @control[node1]
			if query.nil?
				@control[node1] = [node2]
			else
				query << node2
			end
		end
	end
	return control
end

#load_prediction(pairs_array) ⇒ Object 



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# File 'lib/NetAnalyzer/performancer.rb', line 34

def load_prediction(pairs_array)
	pred = {}
	min = nil
	max = nil
	pairs_array.each do |key, label, score|
		query = pred[key]
		if !min.nil? && !max.nil?
			min = score if score < min
			max = score if score > max
		else
			min = score; max = score
		end
		if query.nil?
			pred[key] = [[label], [score]]
		else
			query.first << label
			query.last << score
		end
	end
	return pred, [min, max]
end

#pred_rec(preds, cut, top) ⇒ Object 



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# File 'lib/NetAnalyzer/performancer.rb', line 56

def pred_rec(preds, cut, top)
	predicted_labels = 0 #m
	true_labels = 0 #n
	common_labels = 0 # k
	@control.each do |key, c_labels|
		true_labels += c_labels.length #n
		pred_info = preds[key]
		if !pred_info.nil?
			labels, scores = pred_info
			reliable_labels = get_reliable_labels(labels, scores, cut, top)
			predicted_labels += reliable_labels.length #m
			common_labels += (c_labels & reliable_labels).length #k
		end
	end
	#puts "cut: #{cut} trueL: #{true_labels} predL: #{predicted_labels} commL: #{common_labels}"
	prec = common_labels.to_f/predicted_labels
	rec = common_labels.to_f/true_labels
	prec = 0.0 if prec.nan?
	rec = 0.0 if rec.nan?
	return prec, rec
end