4 ms·

> Will be interesting to see how ML and CRISPR converge I've been seeing similar comments a lot lately, and I don't understand why. As someone with a backgroun

> Will be interesting to see how ML and CRISPR converge I've been seeing similar comments a lot lately, and I don't understand why. As someone with a background in ML that is now studying biochemistry I'd be the first person to jump at something like that, but I'm just not seeing any big ML potential that directly has to do with CRISPR. Is it just two hyped technologies being thrown in a pot? Is there something I'm missing?

shpongled 6y ago
As someone about to graduate with a PhD in biochemistry who has been programming for ~10 years and personally used CRISPR/Cas9 ... the parent comment gave me a good laugh. That being said, I can see some applications to using ML to analyze the results of CRISPR/Cas9 screens or better predict functional editing sites - but that's not exactly exclusive to Cas9.
- hobofan 6y ago
  Exactly what I had in mind. ML has its place in bioinformatics (and is being applied to a huge amount of sub-problems there), but it almost always is an incremental improvement for that niche rather than transforming the whole landscape.
  - jcims 6y ago
    I'm talking precisely about what this guy worked on - https://news.ycombinator.com/item?id=23540564 https://news.ycombinator.com/item?id=23540564 ML provides predictive capabilities over large fugly datasets. CRISPR gives us the ability to test those predictions. These are both essentially commodity technologies at this point and not everyone is going to take a disciplined approach to experimentation.
nisten 6y ago
I know you what you're missing. You gotta put AI in the Blockchain before adding CRISPER and applying for funding. EDIT: And don't forget Kubernetes.
- choeger 6y ago
  Serverless Gene editing!
  - nisten 6y ago
    CRISPRAAS
    - jcims 6y ago
      You laugh but... https://www.genscript.com/crispr-services.html https://www.genscript.com/crispr-services.html https://canopybiosciences.com/custom-cell-line-engineering-2/ https://canopybiosciences.com/custom-cell-line-engineering-2... https://www.reprocell.com/gene-editing-services-i174 https://www.reprocell.com/gene-editing-services-i174 etc. etc. This guy lifestreams some really interesting work - https://www.youtube.com/user/TheChemlife/videos https://www.youtube.com/user/TheChemlife/videos
- grawprog 6y ago
  It's not complete though until someone rewrites the whole thing from the ground up entirely in rust and declares it now safe to actually use.
akiselev 6y ago
I've only heard of the two topics seriously discussed together in the context of directed evolution. Instead of using radiation to increase the rate of mutation, use (semi) randomized snippets injected via CRISPR with a feedback loop that includes your optimization function (i.e. increasing temperature range for a protein). The conclusion was that the data would be far too sparse for the algorithm to really learn anything.

shpongled 6y ago

As someone about to graduate with a PhD in biochemistry who has been programming for ~10 years and personally used CRISPR/Cas9 ... the parent comment gave me a good laugh. That being said, I can see some applications to using ML to analyze the results of CRISPR/Cas9 screens or better predict functional editing sites - but that's not exactly exclusive to Cas9.

hobofan 6y ago
Exactly what I had in mind. ML has its place in bioinformatics (and is being applied to a huge amount of sub-problems there), but it almost always is an incremental improvement for that niche rather than transforming the whole landscape.
- jcims 6y ago
  I'm talking precisely about what this guy worked on - https://news.ycombinator.com/item?id=23540564 https://news.ycombinator.com/item?id=23540564 ML provides predictive capabilities over large fugly datasets. CRISPR gives us the ability to test those predictions. These are both essentially commodity technologies at this point and not everyone is going to take a disciplined approach to experimentation.

nisten 6y ago

I know you what you're missing. You gotta put AI in the Blockchain before adding CRISPER and applying for funding. EDIT: And don't forget Kubernetes.

choeger 6y ago
Serverless Gene editing!
- nisten 6y ago
  CRISPRAAS
  - jcims 6y ago
    You laugh but... https://www.genscript.com/crispr-services.html https://www.genscript.com/crispr-services.html https://canopybiosciences.com/custom-cell-line-engineering-2/ https://canopybiosciences.com/custom-cell-line-engineering-2... https://www.reprocell.com/gene-editing-services-i174 https://www.reprocell.com/gene-editing-services-i174 etc. etc. This guy lifestreams some really interesting work - https://www.youtube.com/user/TheChemlife/videos https://www.youtube.com/user/TheChemlife/videos
grawprog 6y ago
It's not complete though until someone rewrites the whole thing from the ground up entirely in rust and declares it now safe to actually use.

akiselev 6y ago

I've only heard of the two topics seriously discussed together in the context of directed evolution. Instead of using radiation to increase the rate of mutation, use (semi) randomized snippets injected via CRISPR with a feedback loop that includes your optimization function (i.e. increasing temperature range for a protein). The conclusion was that the data would be far too sparse for the algorithm to really learn anything.