DOCK GA Development Goals

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Revision as of 11:17, 13 May 2019 by Jbickel (talk | contribs) (To Do List)
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Tasks src Owner Complete?
Fix bug that collapsed atom coordinates everywhere? nowhere? everyone No
Added Delimeter header conf_gen_ga LEP Yes
Fix xover only feature conf_gen_ga LEP Yes
Put in error messages for mut_rate > 1 conf_gen_ga LEP Yes
Manual user-defined mutation type conf_gen_ga LEP Yes
Remove check only option conf_gen_ga LEP Yes

To Do List

-xover- -guided based on score

  1. good v good
  2. bad v good
  3. bad v bad

-nonexhaustive xover (pick subset of xover based on probability) -2-3 point xover at once -adaptive maintenance ensemble based on ensemble convergence -bring in new parents based on convergence -Mutations- -adaptive mutation rate -pick location of mutation based on something -pick mutation type based on behavior of esemble too large boost deletion too small more add change ...boost replace/sub -mutation type selection based on probability vs ensemble -complete x # y mutation so far so less prevalent etc -3 layer subs do no work so don't do them -replace > 1 segment -fitness- -turn on and off niching adaptive/extinction -reduce boost of fragments and all poor mols with niching -pareto/mulitobjective ga -selection- -metropolis selection for tournament/roulette -adaptive keep #p and #o -extinction- -automated vs on convergence -stop- -convergence -which molecules are best- -best first pruning - now uses descriptor score even if niching ned to delta to fitness/niching when used