Difference between revisions of "DOCK GA Development Goals"

Revision as of 10:41, 13 May 2019

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-
   1. adaptive mutation rate
   2. pick location of mutation based on something
   3. pick mutation type based on behavior of ensemble
   4. molecules too large boost deletion
   5. molecules too small, add more groups
   6. change ...boost replace/sub
   7. mutation type selection based on probability vs ensemble
   8. complete x # y mutation so far so less prevalent etc
   9. 3 layer subs do no work so don't do them
   10. replace > 1 segment
7. fitness-
   1. turn on and off niching adaptive/extinction
   2. reduce boost of fragments and all poor mols with niching
   3. pareto/mulitobjective ga
8. selection-
   1. metropolis selection for tournament/roulette
   2. adaptive keep #p and #o
9. extinction-
   1. user defined point vs on-the-fly convergence
10. stop-
    1. convergence
11. which molecules are best-
    1. best first pruning - now uses descriptor score even if niching ned to delta to fitness/niching when used