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-rw-r--r--lib/similarity.rb65
1 files changed, 65 insertions, 0 deletions
diff --git a/lib/similarity.rb b/lib/similarity.rb
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+++ b/lib/similarity.rb
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+module OpenTox
+ module Algorithm
+
+ class Vector
+ def self.dot_product(a, b)
+ products = a.zip(b).map{|a, b| a * b}
+ products.inject(0) {|s,p| s + p}
+ end
+
+ def self.magnitude(point)
+ squares = point.map{|x| x ** 2}
+ Math.sqrt(squares.inject(0) {|s, c| s + c})
+ end
+ end
+
+ class Similarity
+
+ def self.tanimoto fingerprints
+ ( fingerprints[0] & fingerprints[1]).size/(fingerprints[0]|fingerprints[1]).size.to_f
+ end
+
+ #def self.weighted_tanimoto fingerprints
+ #( fingerprints[0] & fingerprints[1]).size/(fingerprints[0]|fingerprints[1]).size.to_f
+ #end
+
+ def self.euclid scaled_properties
+ sq = scaled_properties[0].zip(scaled_properties[1]).map{|a,b| (a - b) ** 2}
+ Math.sqrt(sq.inject(0) {|s,c| s + c})
+ end
+
+ # http://stackoverflow.com/questions/1838806/euclidean-distance-vs-pearson-correlation-vs-cosine-similarity
+ def self.cosine scaled_properties
+ scaled_properties = remove_nils scaled_properties
+ Algorithm::Vector.dot_product(scaled_properties[0], scaled_properties[1]) / (Algorithm::Vector.magnitude(scaled_properties[0]) * Algorithm::Vector.magnitude(scaled_properties[1]))
+ end
+
+ def self.weighted_cosine scaled_properties # [a,b,weights]
+ a,b,w = remove_nils scaled_properties
+ return cosine(scaled_properties) if w.uniq.size == 1
+ dot_product = 0
+ magnitude_a = 0
+ magnitude_b = 0
+ (0..a.size-1).each do |i|
+ dot_product += w[i].abs*a[i]*b[i]
+ magnitude_a += w[i].abs*a[i]**2
+ magnitude_b += w[i].abs*b[i]**2
+ end
+ dot_product/(Math.sqrt(magnitude_a)*Math.sqrt(magnitude_b))
+ end
+
+ def self.remove_nils scaled_properties
+ a =[]; b = []; w = []
+ (0..scaled_properties.first.size-1).each do |i|
+ if scaled_properties[0][i] and scaled_properties[1][i] and !scaled_properties[0][i].nan? and !scaled_properties[1][i].nan?
+ a << scaled_properties[0][i]
+ b << scaled_properties[1][i]
+ w << scaled_properties[2][i]
+ end
+ end
+ [a,b,w]
+ end
+
+ end
+ end
+end