fitting with dynafit?
mendes at vt.edu
Fri Aug 10 10:13:27 EST 2001
At the risk of making some publicity to my own work:
Least squares problems, especially with many data points and many
variables, have many local minima in the error surface. This makes
solving these problems with Levenberg-Marquardt (or other gradient
descent methods) a challange. You need to be really close to the
solution for these methods to converge. With the program GEPASI
(which I am the author of), you can do the fitting with many different
algorithms, including Levenberg-Marquardt . Importantly Gepasi contains
Genetic Algoriths, Evolutionary programming and Multistart (with L-M)
which all have a much bigger chance of solving your fitting problem.
The only drawback to these methods is that they will take longer time
Gepasi is available for free at http://www.gepasi.org
There is also a paper in the journal Bioinformatics discussing these issues
(and optimisation in general):
Mendes & Kell (1998) "Non-linear optimization of biochemical pathways:
applications to metabolic engineering and parameter estimation."
Abstract in PubMed:
Disclaimer: I am the author of both the software and the paper that I
mentioned above, so my opinion is definitly biased...
Assistant Research Professor
Virginia Bioinformatics Institute
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