Difference between revisions of "DOCK GA Development Goals"

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(To Do List)
(To Do List)
Line 23: Line 23:
==To Do List==
==To Do List==
#-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)
#nonexhaustive xover (pick subset of xover based on probability)
#2-3 point xover at once
#2-3 point xover at once

Revision as of 11:23, 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

To Do List

  1. -xover (guided based on score) - Good v Good ; Bad v Good ; Bad v Bad
  2. nonexhaustive xover (pick subset of xover based on probability)
  3. 2-3 point xover at once
  4. adaptive maintenance ensemble based on ensemble convergence
  5. bring in new parents based on convergence
  6. Mutations-
  7. adaptive mutation rate
  8. pick location of mutation based on something
  9. pick mutation type based on behavior of esemble
  10. too large boost deletion
  11. too small more add
  12. change ...boost replace/sub
  13. mutation type selection based on probability vs ensemble
  14. complete x # y mutation so far so less prevalent etc
  15. 3 layer subs do no work so don't do them
  16. replace > 1 segment
  17. fitness-
  18. turn on and off niching adaptive/extinction
  19. reduce boost of fragments and all poor mols with niching
  20. pareto/mulitobjective ga
  21. selection-
  22. metropolis selection for tournament/roulette
  23. adaptive keep #p and #o
  24. extinction-
  25. automated vs on convergence
  26. stop-
  27. convergence
  28. which molecules are best-
  29. best first pruning - now uses descriptor score even if niching ned to delta to fitness/niching when used