Nature of the bots

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  • Updated 7 years ago
I been thinking about why it is the bots fail certain puzzles. When it comes to the strongest bot, INFO-RNA, untill now there is only 3 types of puzzles it fails. It don't like zigzags and it don't like really big, symmetrical puzzles. Then for some reason, half-circles made of circles - Iroppy says about the bots: ”it is like they have no guide to the obvious boost points.” (in the crop circles)

I think the bots dislikes pattern not commonly found in the nature, as this is all their inbuild algorithm knows of so far. The bot generally don't like sharp angles too – by this I mean strings take a very sudden turning. Nature like things smooth and curvy. Even when it comes to rocks - it just takes a lot of a time.

Others have an oppinion on why some of the bots fail certain types of puzzles? This could be an interesting discussion, now the eterna crew wish us to point to lab puzzles that beats Vienna and Nupack.
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Eli Fisker

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Posted 8 years ago

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Edward Lane

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Fair point Eli, but having seen that I made the same change that the labs are undergoing when compared to the player projects

if you take an old 'lab' puzzle and then remove the hook by submitting the same shape as a 'not lab' puzzle

this one with the hook
http://eterna.cmu.edu/eterna_page.php...

this one without the hook
http://eterna.cmu.edu/eterna_page.php...

infoRNA bot failed the first but not second one
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Eli Fisker

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As long as the hook is there, it ads complexity to the to the puzzle, for the algorithm having to solve it.

But this comparison between old lab and new lab, I'm really looking forward to. How similar does the results for those twosame design look in regular lab and player projects? Great idea making this experiment.
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ruch.mscd.edu

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I'm not sure if people know, but you can use INFO-RNA directly at:
http://www.bioinf.uni-freiburg.de/Sof...

Easy to paste in the secondary structure like ((...(....).)) and let it run.

It has several options for its optimization, which make a difference in its "solution".

Which options does eteRNA use? I don't know.

I tried it on Buard's "An actual easy puzzle" a bunch of times, and it got it right about half the time. It almost always got the top part of the puzzle correct, but often butchered the bottom part.

You might enjoy tinkering with your favorite puzzles.
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Eli Fisker

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Hi Ruch!

I just tried this on Edward Lane's Plimsole line.

I copied it's dot bracket structure (secondary structure) into the puzzle maker, threw the same into the link to Info-Rna and submitted it. Then I copied out the "designed sequence" and posted the letter sequence into the puzzle in the puzzle maker. And InfoRNA stabilized the puzzle in one hit. One would still have to fill out the requirements, as Starry rightfully pointed out.

Hehe, wicked!
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Eli Fisker

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I guess this loophole, you Ruch found, is exactly why, we are not allowed dumping letter sequences directly into a puzzle. :)
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paramodic

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I think another thing worth exploring is that the bots seem to do worse on puzzles with many unbonded nucleotides (the exception usually being InfoBot). It may be the case that they have no algorithm for handling those separately, which would offer a partial explanation as to why human players tend to do better.

I'm still trying to precisely define the parameters that cause infobot to fail so that we may then ask why. Once I'm done with that, though, I think I'm going to try and more accurately define the number of bonded to unbonded nucleotides which cause failure in Vienna and SSDbot.