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Generative A.I. arrives in the gene editing world of CRISPR

nytimes.com

51–60 of 69 posts

Re: Generative A.I. arrives in the gene editing world of CRISPR

#51
post #16

I still consider biological life as the best ‘robot’ because it can create more of itself. As long as robots are incapable of recreation I don’t see the threat. One could say all maschines today are infertile.

What about computer viruses?

I think of robots as being physically embodied somehow. I don't think of a software program like a virus as being a robot.

Re: Generative A.I. arrives in the gene editing world of CRISPR

#52
post #40
post #23

Earlier quoted context omitted.

You mean exactly what 23andMe tried to do, and failed miserably at.

We are still early. Eventually you'll be able to change your race, gender, add reptile eyes, regrow limbs etc. Has to start somewhere. Need more data.

I can already change my race. I just check a different box on government forms...

Re: Generative A.I. arrives in the gene editing world of CRISPR

#53

Reading their blog post I wonder if an LLMs is really the best way to do this. If I got it right, they used the LLM to enumerate potential protein DNA sequences. Does that really need an LLM? Enumeration is not novel, nor are LLMs particularily good at it. If you want to computationally parallelize the search in a large enumeration space it would be much easier to simply, well, do that instead of taking a detour via…

I don't have a direct answer to your question. My guess is that LLMs are too limited to make truly great solutions in biology but sequential modelling is a key component that will not be replaced any time soon. For example, transformers were key to AlphaFold's success, but they still needed many other steps to make accurate predictions.

I worked on a predecessor to LLMs - HMMs for protein modelling. They were, and still are for most people the best way to model protein sequences. It's usually done as prediction, rather than generation (IE, you use the model to classify an unknown sequence into a known category, rather than asking the model to generate new instances of a category). HMMs for proteins are a bit stuffy, and they model local changes well, but struggle with long-range interactions that LLMs seem to excel at (for example, an HMM will do a good job of letting you stuff a few more residues into a protein in a localized region such as a hinge, but are not so great at modelling groups of residues that are located far-apart in sequence space but close in protein space).

One detail of the bitter lesson is, imho, that statistical parrots are better than they "should" be, probably for the same reason that mathematics is unexpectedly proficient in modelling physics: to some degree, the models recapitulate the true latent space of the underlying system well enough to generalize outside the original observation space.

Re: Generative A.I. arrives in the gene editing world of CRISPR

#54
post #17

Reading their blog post I wonder if an LLMs is really the best way to do this. If I got it right, they used the LLM to enumerate potential protein DNA sequences. Does that really need an LLM? Enumeration is not novel, nor are LLMs particularily good at it. If you want to computationally parallelize the search in a large enumeration space it would be much easier to simply, well, do that instead of taking a detour via…

It's not an English LLM, but a "protein" language model, where tokens represent amino acids or nucleotides. Learning a transformer language model on such data simply learns a distribution over sequences of tokens. It's a fine approach conceptually that in many ways is the "right" way or most elegant method, and not a stretch at all.

> Learning a transformer language model on such data simply learns a distribution over sequences of tokens.

If statistical distributions can model higher level polypeptide structure, then it could be useful.

Re: Generative A.I. arrives in the gene editing world of CRISPR

#55
post #40

Earlier quoted context omitted.

We are still early. Eventually you'll be able to change your race, gender, add reptile eyes, regrow limbs etc. Has to start somewhere. Need more data.

Exactly. We should start building global database connecting DNA with medical history.

You mean, like UKBB and All of Us already do, but less nationally focused? The approach seems fraught with complexity due to the complexity of medical ethics, the variation of national laws, and strongly-held nationalist positions.

Re: Generative A.I. arrives in the gene editing world of CRISPR

#57
post #40
post #23

Earlier quoted context omitted.

You mean exactly what 23andMe tried to do, and failed miserably at.

We are still early. Eventually you'll be able to change your race, gender, add reptile eyes, regrow limbs etc. Has to start somewhere. Need more data.

I really, really wanted to see a new generation of tattoo technology based on fluorescence and squid chromatophores. However, for the time being, the vast majority of gene editing will be for well-understood medical conditions where all the alternatives have been excluded. Germline (or even somatic) modification for recreational purposes or for non-urgent medical reasons is definitely still considered highly suspect by society as a whole, and I don't see that changing overnight. Somethings still work better in scifi than reality.

Re: Generative A.I. arrives in the gene editing world of CRISPR

#58
post #17

Earlier quoted context omitted.

It's not an English LLM, but a "protein" language model, where tokens represent amino acids or nucleotides. Learning a transformer language model on such data simply learns a distribution over sequences of tokens. It's a fine approach conceptually that in many ways is the "right" way or most elegant method, and not a stretch at all.

I enjoyed the feeling when I made this connection talking with a startup doing this a while back. It's just a different "language" and although it's not a given that LLMs can operate in it, it's a reasonable thing to try, and it turns out they can.

Personally I think it was obvious that LLMs were going to be useful for protein modelling since the previous generation used HMMs very successfully. Pfam (a library of HMMs for classifying proteins into preexisting known families) is one of the most important resources we have because of the power of HMMs to model sequential language.

I suspect we will need to move from sequential modelling to graphical modelling to level-up again, though.

Re: Generative A.I. arrives in the gene editing world of CRISPR

#59

Reading their blog post I wonder if an LLMs is really the best way to do this. If I got it right, they used the LLM to enumerate potential protein DNA sequences. Does that really need an LLM? Enumeration is not novel, nor are LLMs particularily good at it. If you want to computationally parallelize the search in a large enumeration space it would be much easier to simply, well, do that instead of taking a detour via…

First the search space is way too large for brute force enumeration. We’re talking like 10^300 combinations. Also the hard part isn’t just listing amino acid sequences, its finding ones that do what you want them to. The only way to figure that out is by testing them, which is difficult and expensive. So you need an algorithm that is good at only listing sequences that are likely to work. That’s precisely what LLM’s are good at: finding patterns and sequences that are correlated in a useful way

Re: Generative A.I. arrives in the gene editing world of CRISPR

#60
post #23
post #21

Imagine an AI learning from photos/videos of a person and their DNA sequence? And also a list of diseases, health records, etc. Then asking it for predictions while giving it feedback afterwards so it can tune itself. You could even guarantee privacy. That would be some really useful data.

You mean exactly what 23andMe tried to do, and failed miserably at.

There was no privacy there
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