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How can i speed up this part of my code?

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I have this part of code that i apply for different indns (which are different vectors each time):
phi1=phi(indn1);
p1=p(indn1,indn1);
rtn1=(phi1'*(p1*phi1));
Ctn1=((rtn1*ep2)/(st*(1+rtn1)));
Ctn1=max(Ctn1,0);
Sn1=gammainc(Ctn1*0.5,0.5) ;
Sn1=1-Sn1;
phi2=phi(indn2);
....
....
I tried cellfun and structfun but it was slower. Is there something more i can do to improve the speed?
  5 Comments
amanita
amanita on 16 Jun 2013
The problem was solved by creating mex files and calling them through the GA btw.

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Accepted Answer

Roger Stafford
Roger Stafford on 17 Jun 2013
In your code the multiplication part of doing
phi1'*p1*phi1
is being repeated over and over again as you select different index combinations. Perhaps you could speed up things, even in your mex method, by doing things in the following way. (I am assuming phi is a column vector: one column, with the same number of rows as there are rows and columns in p.)
First, compute, one time only, the matrix
A = (phi*phi').*p;
Then for each new indn vector as it comes along do only this
rtn = sum(sum(A(indn,indn)));
or
rtn = sum(reshape(A(indn,indn),[],1));
whichever is faster. This step requires only addition operations rather than the multiplications plus additions required for matrix multiplication, and gives the same result.
Also in gammainc use the 'upper' option instead of doing Sn1=1-Sn1.
  1 Comment
amanita
amanita on 17 Jun 2013
Thanx Roger! This really helped.
Sum sum was faster than reshape, the 'upper' though i think makes it a little bit slower.

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