Dear all,
is it possible, that something fundamental changed in the optimizers, steepest descent as well as conjugate gradients? I try to fit a protein to an em density, simulated from another conformational state using the em restraint and plenty of harmonic restraints. With an older version (revision 7018) it moves towards the density, whereas with the revision 9277 the score and the positions barely change, irrespective of the number of steps, threshold, stepsize and different weights of restraints. More importantly, i did compare the optimization results of v 7018 and 9277 of conjugate gradient optimization and steepest descent from identical starting positions with identical restraints and optimizer settings. the initial scores are identical, but then the problem starts: For example, with v7018 my model improves from a score of 1835 to 1101 after 100 steps of steepest descent optimization. However, with v9277 my score increases (!) to 1836. behavior of conjugate gradients similarly deteriorates for v9277, albeit i did not observe increases of scores. nevertheless, improvements in score were disappointingly low. Does someone know, why the optimizers behave so differently, for my purposes worse?
Thanks a lot!
Regards,
Pia
I suspect it is an issue with em::FitRestraint as the derivatives returned by that restraint are currently broken (the direction is fine, but the magnitude off by quite a bit). As a result derivative-using optimizers don't perform well with it.
Keren, Ben, is there a plan for fixing it? --Daniel
On May 18, 2011, at 6:31 AM, Pia Unverdorben wrote:
> Dear all, > > is it possible, that something fundamental changed in the optimizers, steepest descent as well as conjugate gradients? > I try to fit a protein to an em density, simulated from another conformational state using the em restraint and plenty of harmonic restraints. With an older version (revision 7018) it moves towards the density, whereas with the revision 9277 the score and the positions barely change, irrespective of the number of steps, threshold, stepsize and different weights of restraints. > More importantly, i did compare the optimization results of v 7018 and 9277 of conjugate gradient optimization and steepest descent from identical starting positions with identical restraints and optimizer settings. the initial scores are identical, but then the problem starts: > For example, with v7018 my model improves from a score of 1835 to 1101 after 100 steps of steepest descent optimization. However, with v9277 my score increases (!) to 1836. behavior of conjugate gradients similarly deteriorates for v9277, albeit i did not observe increases of scores. nevertheless, improvements in score were disappointingly low. > Does someone know, why the optimizers behave so differently, for my purposes worse? > > Thanks a lot! > > Regards, > > Pia > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
Major changes to the code from my part were in verion 7212 in class CoarseCC, which mainly dealt with rigid bodies support. I am not sure if that is the reason for Pia's problem, but as she needs to use EM based optimization relatively soon, i will take a look again. In any case - Pia - it would be useful if you can write a test case that I can check things against. keren. On May 18, 2011, at 7:43 AM, Daniel Russel wrote:
> I suspect it is an issue with em::FitRestraint as the derivatives returned by that restraint are currently broken (the direction is fine, but the magnitude off by quite a bit). As a result derivative-using optimizers don't perform well with it. > > Keren, Ben, is there a plan for fixing it? > --Daniel > > On May 18, 2011, at 6:31 AM, Pia Unverdorben wrote: > >> Dear all, >> >> is it possible, that something fundamental changed in the optimizers, steepest descent as well as conjugate gradients? >> I try to fit a protein to an em density, simulated from another conformational state using the em restraint and plenty of harmonic restraints. With an older version (revision 7018) it moves towards the density, whereas with the revision 9277 the score and the positions barely change, irrespective of the number of steps, threshold, stepsize and different weights of restraints. >> More importantly, i did compare the optimization results of v 7018 and 9277 of conjugate gradient optimization and steepest descent from identical starting positions with identical restraints and optimizer settings. the initial scores are identical, but then the problem starts: >> For example, with v7018 my model improves from a score of 1835 to 1101 after 100 steps of steepest descent optimization. However, with v9277 my score increases (!) to 1836. behavior of conjugate gradients similarly deteriorates for v9277, albeit i did not observe increases of scores. nevertheless, improvements in score were disappointingly low. >> Does someone know, why the optimizers behave so differently, for my purposes worse? >> >> Thanks a lot! >> >> Regards, >> >> Pia >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >
Hi Pia: Please check version 9494. Derivatives problems should be resolved. Please let me know if you still experience any problems. Keren. On May 18, 2011, at 6:31 AM, Pia Unverdorben wrote:
> Dear all, > > is it possible, that something fundamental changed in the optimizers, steepest descent as well as conjugate gradients? > I try to fit a protein to an em density, simulated from another conformational state using the em restraint and plenty of harmonic restraints. With an older version (revision 7018) it moves towards the density, whereas with the revision 9277 the score and the positions barely change, irrespective of the number of steps, threshold, stepsize and different weights of restraints. > More importantly, i did compare the optimization results of v 7018 and 9277 of conjugate gradient optimization and steepest descent from identical starting positions with identical restraints and optimizer settings. the initial scores are identical, but then the problem starts: > For example, with v7018 my model improves from a score of 1835 to 1101 after 100 steps of steepest descent optimization. However, with v9277 my score increases (!) to 1836. behavior of conjugate gradients similarly deteriorates for v9277, albeit i did not observe increases of scores. nevertheless, improvements in score were disappointingly low. > Does someone know, why the optimizers behave so differently, for my purposes worse? > > Thanks a lot! > > Regards, > > Pia > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
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Daniel Russel -
Keren Lasker -
Pia Unverdorben