Difference between revisions of "DOCK GA Development Goals"

Revision as of 10:23, 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

-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

@@ Line 23: / Line 23: @@
 ==To Do List==
--xover-
+#-xover (guided based on score) - Good v Good ; Bad v Good ; Bad v Bad
--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