Difference between revisions of "DOCK GA Development Goals"
From Rizzo_Lab
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==To Do List== | ==To Do List== | ||
| − | #-xover (guided based on score) - Good v Good ; Bad v Good ; Bad v Bad | + | #-xover (guided based on score) - Good v Good ; Bad v Good ; Bad v Bad THIS |
#nonexhaustive xover (pick subset of xover based on probability) | #nonexhaustive xover (pick subset of xover based on probability) | ||
#2-3 point xover at once | #2-3 point xover at once | ||
| − | #adaptive maintenance ensemble based on ensemble convergence | + | #adaptive maintenance ensemble based on ensemble convergence THIS |
#bring in new parents based on convergence | #bring in new parents based on convergence | ||
#Mutations- | #Mutations- | ||
| − | ##adaptive mutation rate | + | ##adaptive mutation rate THIS |
##pick location of mutation based on something | ##pick location of mutation based on something | ||
##pick mutation type based on behavior of ensemble | ##pick mutation type based on behavior of ensemble | ||
| Line 47: | Line 47: | ||
##adaptive keep #p and #o | ##adaptive keep #p and #o | ||
#extinction- | #extinction- | ||
| − | ##user defined point vs on-the-fly convergence | + | ##user defined point vs on-the-fly convergence THIS |
#stop- | #stop- | ||
##convergence | ##convergence | ||
#which molecules are best- | #which molecules are best- | ||
##best first pruning - now uses descriptor score even if niching ned to delta to fitness/niching when used | ##best first pruning - now uses descriptor score even if niching ned to delta to fitness/niching when used | ||
Revision as of 12:28, 8 October 2019
| 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) - Good v Good ; Bad v Good ; Bad v Bad THIS
- nonexhaustive xover (pick subset of xover based on probability)
- 2-3 point xover at once
- adaptive maintenance ensemble based on ensemble convergence THIS
- bring in new parents based on convergence
- Mutations-
- adaptive mutation rate THIS
- pick location of mutation based on something
- pick mutation type based on behavior of ensemble
- molecules too large boost deletion
- molecules too small, add more groups
- 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-
- user defined point vs on-the-fly convergence THIS
- stop-
- convergence
- which molecules are best-
- best first pruning - now uses descriptor score even if niching ned to delta to fitness/niching when used
