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POefficient algorithm instead of looping
 

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    <p>I have a data set where each samples has a structure similar to this</p> <pre><code>X=[ [[],[],[],[]], [[],[]] , [[],[],[]] ,[[][]]] </code></pre> <p>for example:</p> <pre><code>X=np.array([ [ [1,2,3], [2,4,5] ,[2,3,4] ] , [ [5,6], [6,6] ] , [[2,3,1],[2,3,10],[23,1,2],[1,4,5]] ] ,"object") Y=np.array([ [ [12,14,15] ,[12,13,14] ] , [ [15,16], [16,16] ] , [[22,23,21],[32,33,11],[12,44,55]] ] ,"object") </code></pre> <p>so for <strong>every sample</strong> I need to calculate the dot product between every element of x with corresponding element of y of same index and sum the result. i.e:</p> <pre><code>result=0 for i in range(3): for n,m in itertools.product(X[i],Y[i]): print "%s, %s" % (n,m) result+=np.dot(n,m) .....: [1, 2, 3], [12, 14, 15] [1, 2, 3], [12, 13, 14] [2, 4, 5], [12, 14, 15] [2, 4, 5], [12, 13, 14] [2, 3, 4], [12, 14, 15] [2, 3, 4], [12, 13, 14] [5, 6], [15, 16] [5, 6], [16, 16] [6, 6], [15, 16] [6, 6], [16, 16] [2, 3, 1], [22, 23, 21] [2, 3, 1], [32, 33, 11] [2, 3, 1], [12, 44, 55] [2, 3, 10], [22, 23, 21] [2, 3, 10], [32, 33, 11] [2, 3, 10], [12, 44, 55] [23, 1, 2], [22, 23, 21] [23, 1, 2], [32, 33, 11] [23, 1, 2], [12, 44, 55] [1, 4, 5], [22, 23, 21] [1, 4, 5], [32, 33, 11] [1, 4, 5], [12, 44, 55] </code></pre> <p>This is my whole code:</p> <pre><code> print "***build kernel***" K = np.zeros((n_samples, n_samples)) for i in range(n_samples): for j in range(n_samples): K[i,j] = self.kernel(X[i], X[j]) def kernel(x1,x2): N=8 #number of objects result=0 for i in xrange(N): for n,m in itertools.product(x1[i],x2[i]): result+=np.dot(n,m) return result </code></pre> <p>as you can see the complexity of this algorithm is too high and also my samples are much bigger than this. so for even a small data set, i.e. contains 400 samples, I have to wait 4 hours to get the result. I am looking for a better way to implement this algorithm. P.S: I was thinking about multithreading or multiproccessing but I am not sure if it helps?!</p> <p>I appreciate any suggestion!</p>
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    1. COHow does your problem grow? When you say 200 samples takes 4 hours, do you mean that, for example, `X[i]` and `Y[i]` both have 200 vectors?
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    2. COYour "whole code" does not reference `Y`.
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    3. COX and y are just examples.. you see x1 and x2 in code
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