[Strategy market] Deep blue Vienna

I would like to give our little monster (the ensemble algorithm) the same ability as us – that of reading the positional entropy in Vienna RNA fold.

Jeehyung just reminded me: RNAFold’s numbers can’t capture everything. Note that ViennaRNA = RNAFold.

With that he meant, the vienna bot that has trouble solving our puzzles :slight_smile:

So Vienna is clearly not perfect – I regulary forget – I love my only half-seing guide.

With that in mind now, I only want our algorithm to spot the most clearest warning sign of something being wrong. That is dark blue nucleotides in the graphics of positional entropy.

As two dark blue are often allowed, even in the best of the designs, let the first two pass without penalty.

Graphics of positional entropy in Vienna RNA fold of Mat – Asymmetry V1, (100%)

Jerryfu, one of the programmers, once asked if I would want my strategy to penalize linear or exponential. The last option hadn’t crossed my mind. But now I would like to use it. Thanks for asking, Jerryfu!

First two dark nucleotides go unpunished. If more than two dark blue nt’s, penalize the next with -1 and let the penalty grow exponential with the numbers of dark blue. Blue entropy is evil. :slight_smile:

Dear Eli,

Your strategy has been added to our implementation queue with task id 48. You can check the schedule of the implementation here.

Unfortunately, we don’t have entropy calculation integrated with our strategy system yet, so this may take longer to implement. We’ll update with an ETA once we get better idea.

Thanks for sharing your thoughts!