Carlo suggested that I submit this (edited) to the ifeffit list... gb
---------- Forwarded message ----------
Date: Thu, 2 Dec 2004 21:40:54 -0600 (CST)
From: Grant Bunker
To: Carlo U. Segre
Cc: Bruce Ravel ,
Grant Bunker
Subject: Re: differential evolution algorithm
Hi, Carlo - DE is a very nice and simple genetic algorithm for finding
global minima. As far as I know I have been the only person applying it to
XAFS. It might be overkill for the application though - is this just for
finding maximum in the edge derivative? If it is, it's probably simpler
just to smooth the data (e.g. with binomial smoothing which you can do by
repeated convolution Y(n)=y(n+1)+2*y(n)+y(n-1))/4), followed by a
derivative. I've done it that way before (or use smoothing splines) in the
distant past and it worked fine. In the edge-finding hack in the mathematica
notebook (for automated data reduction) I sent you I just used differential
evolution out of laziness, but it's very good for more difficult fitting
problems like the stuff we have been doing with the ab initio DWFs in enzymes.
It's arguable whether using the max derivative is the best way to
choose E0 anyway, but that's a different story.
thanks - grant
ps I googled "differential evolution" and uncovered a good web site at
berkeley. Probably it has references to the original article by storn and
price. A couple of years ago I implemented it in Mathematica code for
global fitting calling feff as an external "function". The intrinsic
NMinimize function in Mathematica also has it available as a minimization
method in purely numerical (nonsymbolic) calculations.
http://www.icsi.berkeley.edu/~storn/code.html
On Thu, 2 Dec 2004, Carlo U. Segre wrote:
I am somewhat ignorant. Grant uses the builtin function from Mathematica.
Perhaps he can give a bit more information. Grant?
Carlo
On Thu, 2 Dec 2004, Bruce Ravel wrote:
Grant has been using a differential evolution algorithm to take case of
noisy data. Perhaps this could help?
Carlo,
Is there a reference for this in the exafs conmtext? I'd like to read
up on it.
B
--
Carlo U. Segre -- Professor of Physics
Associate Dean for Special Projects, Graduate College
Illinois Institute of Technology
Voice: 312.567.3498 Fax: 312.567.3494
Carlo.Segre@iit.edu http://www.iit.edu/~segre
