optimize matlab,Optimize MATLAB code (nested for loop to compute similarity matrix)

The function to do so in matlab is called pdist. Unfortunately it is painfully slow and doesnt take Matlabs vectorization abilities into account.

The following is code I wrote for a project. Let me know what kind of speed up you get.

Qx=repmat(dot(x,x,2),1,size(x,1));

D=sqrt(Qx+Qx'-2*x*x');

Note though that this will only work if your data points are in the rows and your dimensions the columns. So for example lets say I have 256 data points and 100000 dimensions then on my mac using x=rand(256,100000) and the above code produces a 256x256 matrix in about half a second.