Reading: File:Nchembio.689.pdf Efficient discovery of anti-inflammatory small-molecule combinations using evolutionary computing – Zeke to lead
Administrativa
- Merging updates with master: Since I (Tom) am pushing a lot of Clojush updates recently, I’d be happy to do the actual merging etc. as well. This would probably involve Lee giving an ok to the merge before it happens.
Things Tom wants to Discuss
- Bloat theory and uniform operators
- Real-time graphing and statistics of cluster runs.
Notes:
article:
this paper was about innate immunity rather than that which you develop in response to pathogens
There are certain white bloodcells that just respond to patterns of bad.
Ther white blood cells they looked at respond to certain things and signal other cells to act with IL1beta
The drug company wanted to use drugs synergistically to control IL1beta, because using a lot will kill you
they had 33 drugs and wanted to combine them in order to attempt to produce a specific amount of IL1betta in response to LPS
note that the drugs can kill the macrophages, so they were trying to get low macrophage death for low IL1betta production
they used a simple binary GA with the fitness in the real world
the trick to it is the way you treat multiple objectives for fitness in parents. There's a lot of talk about hypervolume in attempting to improve this. Most are pareto based. This one wasn't.
LEE!!! ~ Contact UCon guy. Invite him to come discuss projects with us.
UMASS may have automated labs that could do the wet side of some cool gp stuff.
we should have a blackboard of ideas —>> we could build a space —>> we could have a google doc, Oh, ya great. Coool, now we have one.
Experiment idea: Lexicase selection is a way of making parents that are talented as specific aspects of problems. Similarly if any parent that is capable of solving a novel combination of answers it should be valued. Perhaps scaled lexical selection should be pursued. The two together (lexical and gsgp) could be mashed up so they might hit on answers and then blend success.
quasi-gsgp where instead of (if ___ A B), you do (if ______ (chunk A) (chunk B)) even better if you can do it intelligently. The goal of this is to use gsgp ideas to increase modularity, rather than acting towards hitting the geometric mean.
You can have a GP program which is a bunch of numbers and they follow lists choosing options and diving down to deeper lists.
code could be executed on it’s own scope <— relating to chunk gsgp
why do people mutate so stuff adds and removes in the same spot in push, why even do both?
there are some papers which believe they have conclusively stated that bloat as defense against cross over and mutation have been disprove. Lee doesn’t believe them. There’s lot’s of stuff that causes bloat, it’s context dependent.
Thomass and Zeke: a web page that is displaying graphs and logfiles of the generations as they’re run
currently only outputting population data should test to see how much it's slowing things down you could link children to parents to get genealogies