Darwin: a genomics co-processor provides up to 15,000x acceleration
1–10 of 51 posts
Re: Darwin: a genomics co-processor provides up to 15,000x acceleration
#2Oh no, someone should tell them that darwin is the name for the kernel inside of iOS/MacOS.
Re: Darwin: a genomics co-processor provides up to 15,000x acceleration
#3Very interesting write up too! I often read that computational biology is a different beast than the rest of the computational landscape (which usually revolve around solving PDE's fundamentally) and this was a nice picture into at least one problem on that side of the pond. A "best substring" search to me sounds closer to the kind of problems CS people think about than what computational cats do.
Re: Darwin: a genomics co-processor provides up to 15,000x acceleration
#4Oh no, someone should tell them that darwin is the name for the kernel inside of iOS/MacOS.
... as well as a british biologist.
Re: Darwin: a genomics co-processor provides up to 15,000x acceleration
#5Serious question: if the processing problems are classified as NP, then couldn't that processing be outsourced to a blockchain? Why have miners solve for useless problems that have no long lasting impact like "number of zeros in a SHA string" instead of processing data such as this? I can easily see it being the case that the mining problem in a given blockchain could be based on real scientific problems that needs solving.
I'm looking for someone to help me understand why the above isn't possible.
Re: Darwin: a genomics co-processor provides up to 15,000x acceleration
#6Serious question: if the processing problems are classified as NP, then couldn't that processing be outsourced to a blockchain? Why have miners solve for useless problems that have no long lasting impact like "number of zeros in a SHA string" instead of processing data such as this? I can easily see it being the case that the mining problem in a given blockchain could be based on real scientific problems that needs s…
Would the solving of the problem have a "difficulty" that could be adjusted to ensure that blocks appeared approximately every ten minutes?
Is checking that the solution is valid a very fast operation?
Are we sure that there is no "final" answer which would make the calculation unusable at some point?
(Those are the three main factors for choosing what kind of work to do, as far as I can see)
Re: Darwin: a genomics co-processor provides up to 15,000x acceleration
#7Serious question: if the processing problems are classified as NP, then couldn't that processing be outsourced to a blockchain? Why have miners solve for useless problems that have no long lasting impact like "number of zeros in a SHA string" instead of processing data such as this? I can easily see it being the case that the mining problem in a given blockchain could be based on real scientific problems that needs s…
Generally, blockchain "mining" requires a problem that is hard to solve, easy to verify. If I understand it correctly, the genome sequencing problem is hard to solve, hard to verify.
Re: Darwin: a genomics co-processor provides up to 15,000x acceleration
#8Serious question: if the processing problems are classified as NP, then couldn't that processing be outsourced to a blockchain? Why have miners solve for useless problems that have no long lasting impact like "number of zeros in a SHA string" instead of processing data such as this? I can easily see it being the case that the mining problem in a given blockchain could be based on real scientific problems that needs s…
I thought about this as well before, but the problem is that you don't want just ANY NP-problem: You want an NP problem (it doesn't even have to be NP-complete) that you can easily adjust the difficulty.
How do you adjust the difficulty on something like this?
Also, you always have to calculate the "hashes" of the blocks. I guess you could encode a block as a graph and it's "hash" could be the smallest path that visited all the edges, but how useful would that be?
When I looked into this in the past, I stumbled into Gridcoin[1], but I don't know how they deal with the difficulty/usefulness of the solutions.
Re: Darwin: a genomics co-processor provides up to 15,000x acceleration
#9Serious question: if the processing problems are classified as NP, then couldn't that processing be outsourced to a blockchain? Why have miners solve for useless problems that have no long lasting impact like "number of zeros in a SHA string" instead of processing data such as this? I can easily see it being the case that the mining problem in a given blockchain could be based on real scientific problems that needs s…
Generally, blockchain "mining" requires a problem that is hard to solve, easy to verify. If I understand it correctly, the genome sequencing problem is hard to solve, hard to verify.
What you just said is the "definition" of NP problems which is why I had it in my question to begin with. Even if genome sequencing is not a good problem for mining. There are plenty of other scientific problems that are. Yet mining today is not tackling any of them :/
Re: Darwin: a genomics co-processor provides up to 15,000x acceleration
#10Serious question: if the processing problems are classified as NP, then couldn't that processing be outsourced to a blockchain? Why have miners solve for useless problems that have no long lasting impact like "number of zeros in a SHA string" instead of processing data such as this? I can easily see it being the case that the mining problem in a given blockchain could be based on real scientific problems that needs s…
It's difficult to generate hard instances of problems. Many (all?) NP complete problems are easy on average. For example almost all uniform random SAT instances can be solved quite easily.