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AlphaFold 3 predicts the structure and interactions of life's molecules

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Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#351

Post by hereme888 »

nybsjytm wrote: post #62

Important caveat: it's only about 70% accurate. Why doesn't the press release say this explicitly? It seems intentionally misleading to only report accuracy relative to existing methods, which apparently are just not so good (30%, 50% in various settings). https://www.fastcompany.com/91120456/deepmind-alphafold-3-dn...

That's what I thought. They go from "predicting all of life's molecules" to "it's a 50% improvement...and we HOPE to...transform drug discovery..."

Seems unfortunately typical of Google these days: "Gemini will destroy GPT-4..."

Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#352

Post by [deleted] »

pas wrote: post #291
chasd00 wrote: post #270

Earlier quoted context omitted.

If all you can do is predict an outcome without being able to explain how then what have you really discovered? Asking someone to just believe you can predict outcomes without any reasoning as to how, even if you're always right, sounds like the concept of faith in religion.

it's still an extremely valuable tool. just as we see in mathematics, closed forms (and short and elegant proofs) are much coveted luxury items. for many basic/fundamental mathematical objects we don't (yet) have simple mechanistic ways to compute them. so if a probabilistic model spits out something very useful, we can slap a nice label on it and call it a day. that's how engineering works anyway. and then hopefully…

[deleted]

Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#353

Post by empath-nirvana »

jprete wrote: post #194
dekhn wrote: post #93

Earlier quoted context omitted.

If you're a scientist who works in protein folding (or one of those other areas) and strongly believe that science's goal is to produce falsifiable hypotheses, these new approaches will be extremely depressing, especially if you aren't proficient enough with ML to reproduce this work in your own hands. If you're a scientist who accepts that probabilist models beat interpretable ones (articulated well here: https://no…

The goal of science has always been to discover underlying principles and not merely to predict the outcome of experiments. I don't see any way to classify an opaque ML model as a scientific artifact since by definition it can't reveal the underlying principles. Maybe one could claim the ML model itself is the scientist and everyone else is just feeding it data. I doubt human scientists would be comfortable with that…

If have an oracle that can predict the outcome of experiments does it _matter_ if you understand why?

Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#354

Post by empath-nirvana »

SJC_Hacker wrote: post #290
jprete wrote: post #194

Earlier quoted context omitted.

The goal of science has always been to discover underlying principles and not merely to predict the outcome of experiments. I don't see any way to classify an opaque ML model as a scientific artifact since by definition it can't reveal the underlying principles. Maybe one could claim the ML model itself is the scientist and everyone else is just feeding it data. I doubt human scientists would be comfortable with that…

What if it turns out that nature simply doesn't have nice, neat models that humans can comprehend for many observable phenomena?

I read an article about the "unreasonable effectiveness of mathematics" that it was basically the result of a drunk looking for his keys under a lamp post because that's where the light is. We know how to use math to model parts of the world, and every where we look, there's _something_ we can model with math, but that doesn't mean that there's all there is to the universe. We could be understanding .0000001% of what's out there to understand, and it's the stuff that's amenable to mathematical analysis.

Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#355

Post by bongodongobob »

uptownfunk wrote: post #323
ramon156 wrote: post #318

Earlier quoted context omitted.

Alright, but now picture this: it's now open to the masses, meaning an individual could probably even do it.

The risks don't exceed what is already out there. If someone wants to do damage, especially in America, there are more than enough ways they can do it already. The technology should be made free. I also wonder how much the claims are being exaggerated and are marketing-speak vs. real results. Is there any benchmark for this that they have published?

No. I love to be egalitarian as well but this AI thing really feels different. We didn't just invent a better plow or a more durable sword. We're working on making a better brain. I think social media shows us a pretty good slice of the average person and it's not great. Now imagine they can manipulate the smartest person in the world to do dangerous, dumb shit.

Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#356

Post by bongodongobob »

pythonguython wrote: post #327
ramon156 wrote: post #318

Earlier quoted context omitted.

Alright, but now picture this: it's now open to the masses, meaning an individual could probably even do it.

I hear you, but I don't think an individual can. If I gave you $20,000 and an open source 70% accurate protein folding model and told you to develop, mass produce, and develop a deployment mechanism for a highly infectious and deadly pathogen, I don't think you could make that happen. Nor do I think you could do it if you had a PhD in microbiology.

right now

Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#357

Post by melagonster »

jprete wrote: post #194
dekhn wrote: post #93

Earlier quoted context omitted.

If you're a scientist who works in protein folding (or one of those other areas) and strongly believe that science's goal is to produce falsifiable hypotheses, these new approaches will be extremely depressing, especially if you aren't proficient enough with ML to reproduce this work in your own hands. If you're a scientist who accepts that probabilist models beat interpretable ones (articulated well here: https://no…

The goal of science has always been to discover underlying principles and not merely to predict the outcome of experiments. I don't see any way to classify an opaque ML model as a scientific artifact since by definition it can't reveal the underlying principles. Maybe one could claim the ML model itself is the scientist and everyone else is just feeding it data. I doubt human scientists would be comfortable with that…

they offered a good tool for science... so this is a part of science.

Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#358

Post by a_bonobo »

s1artibartfast wrote: post #2

The article was heavy on the free research aspect, but light on the commercial application. I'm curious about the business strategy. Does Google intend to license out tools, partner, or consult for commercial partners?

This version has Isomorphic Labs far more in the focus of the press release, which seems to be now the commercial arm more or less licensing access out.

The new AlphaFold server does not do everything the paper says AlphaFold 3 says it does. You cannot predict docking with the server! That is the main interest of pharma companies, 'does our medication bind to the target protein?'. From the FAQ: 'AlphaFold Server is a web-service that offers customized biomolecular structure prediction. It makes several newer AlphaFold3 capabilities available, including support for a wider range of molecule type' - that's not ALL AlphaFold3 capabilities. Isomorphic prints the money with those additional capabilities.

It's hilarious that Google says they don't allow this for safety reasons, pure OpenAI fluff. It's just money.

Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#359

Post by gandalfthepink »

dekhn wrote: post #200
jprete wrote: post #194

Earlier quoted context omitted.

The goal of science has always been to discover underlying principles and not merely to predict the outcome of experiments. I don't see any way to classify an opaque ML model as a scientific artifact since by definition it can't reveal the underlying principles. Maybe one could claim the ML model itself is the scientist and everyone else is just feeding it data. I doubt human scientists would be comfortable with that…

That's the aspirational goal. And I would say that it's a bit of an inflexible one- for example, if we had an ML that could generate molecules that cure diseases that would pass FDA approval, I wouldn't really care if scientists couldn't explain the underlying principles. But I'm an ex-scientist who is now an engineer, because I care more about tools that produce useful predictions than understanding underlying princ…

Me like thee career path. Interesting.

Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#360

Post by hammock »

dekhn wrote: post #200
jprete wrote: post #194

Earlier quoted context omitted.

The goal of science has always been to discover underlying principles and not merely to predict the outcome of experiments. I don't see any way to classify an opaque ML model as a scientific artifact since by definition it can't reveal the underlying principles. Maybe one could claim the ML model itself is the scientist and everyone else is just feeding it data. I doubt human scientists would be comfortable with that…

That's the aspirational goal. And I would say that it's a bit of an inflexible one- for example, if we had an ML that could generate molecules that cure diseases that would pass FDA approval, I wouldn't really care if scientists couldn't explain the underlying principles. But I'm an ex-scientist who is now an engineer, because I care more about tools that produce useful predictions than understanding underlying princ…

> if we had an ML that could generate molecules that cure diseases that would pass FDA approval, I wouldn't really care if scientists couldn't explain the underlying principles

It’s actually required as part of the submission for FDA approval that you posit a specific Mechanism of Action for why your drug works the way it does. You can’t get approval without it

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