Forum: Quantum Bioinformatics ahead?
gravatar for Michael Dondrup
4.3 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

We have heard about the advent of quantum computing since some years or decades. With some seemingly real quantum computers around the corner (Google's D-Wave, IBM quantum experience), what are the prospects of quantum bioinformatics? Which are the fields in bioinformatics that would profit most from quantum computation?

Just yesterday IBM has released what they call IBM quantum experience, a cloud service that provides interested users access to 5 (real?) qbits. I am eager to try this out, but which toy bioinformatics problem (if any) can be tackled with 5 qbits?

Given that my understanding is right, these states would be able to encode 2.5 nucleotides, and then, using Grover's algorithm, I could find the 'A' in 'AT' with always 1 2-qbit lookup instead of having to look at all bits?
This feels like I had just learned how to build and connect a series of NAND gates to build my first arithmetic unit, then asking myself how to use this machine by connecting logic gates directly to solve bioinformatics problems. There are at least two layers of abstraction missing.

ADD COMMENTlink modified 4.3 years ago by Damian Kao15k • written 4.3 years ago by Michael Dondrup47k

Don't we already use quantum bioinformatics?

Sometimes it works, sometimes it doesn't.

ADD REPLYlink written 4.3 years ago by Istvan Albert ♦♦ 84k

"I can tell you exactly how far along our in-house pipeline your data is, but not exactly where it is - or I can tell you exactly where your data is, but not whether it's been through all the necessary pipelines."

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by John12k

John and Istvan, I propose we should entangle our pipelines.

ADD REPLYlink written 4.3 years ago by Michael Dondrup47k

Just no spooky action at a distance on the cluster, please.

ADD REPLYlink written 4.3 years ago by Devon Ryan96k
gravatar for Damian Kao
4.3 years ago by
Damian Kao15k
Damian Kao15k wrote:

From the little I understand about quantum computing, it is only really good for certain types of problems (traveling salesman type problems) where some kind of simulated annealing is used? I don't think it is just a speedier swap-in replacement for traditional cpus.

I guess one usage in bioinformatics would be graph processing like finding optimal paths through an assembly graph.

ADD COMMENTlink written 4.3 years ago by Damian Kao15k
gravatar for DG
4.3 years ago by
DG7.1k wrote:

I don't think the systems are at that level yet, and there is still some controversy in the field about whether D-Wave is really doing quantum computation. The data is apparently a little mixed, although I am certainly no expert. But they apparently aren't getting speed-ups over classical algorithms in many of the work I see reported. Given some of the timelines and breakthroughs I have looked at, you need something like 4 qubits just to do factorization of numbers in the 100's so I'm not sure there is anything practical you can do with that yet.

ADD COMMENTlink written 4.3 years ago by DG7.1k

Thank you for your view Dan. How many qbits would one need to encode one DNA letter, my understanding is that I would still need 2 qbits, as many as normal bits?

ADD REPLYlink written 4.3 years ago by Michael Dondrup47k

That I really don't know. I'm by no means an expert on the nuts and bolts of this topic

ADD REPLYlink written 4.3 years ago by DG7.1k
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