Difference between revisions of "DOCK GA Development Goals"

Revision as of 12:40, 13 March 2020

To Do List

1. slow down molecular evolution so there are less drastic canges between each successive generation
2. tanimoto coefficient percent change - might be inaccurate due to tan coef behavior
3. Rotatable bond changes
4. Number of aromatic rings
5. -xover (guided based on score) - Good v Good ; Bad v Good ; Bad v Bad THIS
6. nonexhaustive xover (pick subset of xover based on probability)
7. 2-3 point xover at once
8. adaptive maintenance ensemble based on ensemble convergence THIS
9. bring in new parents based on convergence
10. Mutations-
    1. adaptive mutation rate THIS
    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
11. fitness-
    1. turn on and off niching adaptive/extinction
    2. reduce boost of fragments and all poor mols with niching
    3. pareto/mulitobjective ga
12. selection-
    1. metropolis selection for tournament/roulette
    2. adaptive keep #p and #o
13. extinction-
    1. user defined point vs on-the-fly convergence THIS
14. stop-
    1. convergence
15. which molecules are best-
    1. best first pruning - now uses descriptor score even if niching ned to delta to fitness/niching when used
    2. geometric diversity using Hingarian and Tan pruning