Difference between revisions of "DOCK GA Development Goals"
From Rizzo_Lab
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# bad v good | # bad v good | ||
# bad v bad | # 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 large boost deletion |
| − | too small more add | + | #too small more add |
| − | change ...boost replace/sub | + | #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 | |
Revision as of 10:18, 13 May 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
- 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
