Difference between revisions of "DOCK GA Development Goals"
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==To Do List== | ==To Do List== | ||
-xover- | -xover- | ||
| − | guided based on score | + | -guided based on score |
1. good v good | 1. good v good | ||
2. bad v good | 2. bad v good | ||
3. bad v bad | 3. bad v bad | ||
| − | 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 |
| − | bring in new parents based on convergence | + | -bring in new parents based on convergence |
-Mutations- | -Mutations- | ||
| − | adaptive mutation rate | + | -adaptive mutation rate |
| − | pick location of mutation based on something | + | -pick location of mutation based on something |
| − | pick mutation type based on behavior of esemble | + | -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 | + | -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 | + | -replace > 1 segment |
-fitness- | -fitness- | ||
| − | turn on and off niching adaptive/extinction | + | -turn on and off niching adaptive/extinction |
| − | reduce boost of fragments and all poor mols with niching | + | -reduce boost of fragments and all poor mols with niching |
| − | pareto/mulitobjective ga | + | -pareto/mulitobjective ga |
-selection- | -selection- | ||
| − | metropolis selection for tournament/roulette | + | -metropolis selection for tournament/roulette |
| − | adaptive keep #p and #o | + | -adaptive keep #p and #o |
-extinction- | -extinction- | ||
| − | automated vs on convergence | + | -automated vs on convergence |
-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 11:52, 15 February 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 | No |
| Put in error messages for mut_rate > 1 | conf_gen_ga | LEP | Yes |
| Manual user-defined mutation type | conf_gen_ga | LEP | No |
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
