DOCK GA Development Goals

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Revision as of 11:18, 13 May 2019 by Jbickel (talk | contribs) (To Do List)
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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

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