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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

#331

Post by pas »

thfuran wrote: post #293
pas wrote: post #291

Earlier quoted context omitted.

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…

>closed forms (and short and elegant proofs) are much coveted luxury items. Yes, but we're taking about roughly the opposite of a proof

but in usual natural sciences we don't have proofs, only data and models, and then we do model selection (and through careful experiments we end up with confidence intervals)

and it seems with these molecular biology problems we constantly have the problem of specificity (model prediction quality) vs sensitivity (model applicability), right? but due to information theory constraints there's also a dimension along model size/complexity.

so if a ML model can push the ROC curve toward the magic left-up corner then likely it's getting more and more complex.

and at one point we simply are left with models that are completely parametrized by data and there's virtually zero (direct) influence of the first principles. (I mean that at one point as we get more data even to do model selection we can't use "first principles" because what we know through that is already incorporated into previous versions of the models. Ie. the information we gained from those principles we already used to make decisions in earlier iterations.)

Of course then in theory we can do model distillation, and if there's some hidden small/elegant theory we can probably find it. (Which would be like a proof through contradiction, because it would mean that we found model with the same predictive power but with smaller complexity than expected.)

// NB: it's 01:30 here, but independent of ignorance-o-clock ... it's quite possible I'm totally wrong about this, happy to read any criticism/replies

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

#332

Post by Jupe »

moconnor wrote: post #32

Stepping back, the high-order bit here is an ML method is beating physically-based methods for accurately predicting the world. What happens when the best methods for computational fluid dynamics, molecular dynamics, nuclear physics are all uninterpretable ML models? Does this decouple progress from our current understanding of the scientific process - moving to better and better models of the world without human-int…

> Does this decouple progress from our current understanding of the scientific process - moving to better and better models of the world without human-interpretable theories and mathematical models / explanations?

Replace "human-interpretable theories" with "every man interpretable theories", and you'll have a pretty good idea of how > 90% of the world feels about modern science. It is indistinguishable from magic, by the common measure.

Obtuse example: My parents were alive when the first nuclear weapon was detonated. They didn't know that they didn't know this weapon was being built, let alone that it might have ignited the atmosphere.

With sophisticated enough ML, that 90% will become 99.9% - save the few who have access to (and can trust) ML tools that can decipher the "logic" from the original ML tools.

Yes, interesting times ahead... indeed.

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

#333

Post by TheBicPen »

moconnor wrote: post #32

Stepping back, the high-order bit here is an ML method is beating physically-based methods for accurately predicting the world. What happens when the best methods for computational fluid dynamics, molecular dynamics, nuclear physics are all uninterpretable ML models? Does this decouple progress from our current understanding of the scientific process - moving to better and better models of the world without human-int…

Perhaps related, the first computer-assisted mathematics proof: https://en.wikipedia.org/wiki/Four_color_theorem

I'm sure that similar arguments for and against the proof apply here as well.

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

#334

Post by OrigamiPastrami »

akira2501 wrote: post #229
bluerooibos wrote: post #180

Earlier quoted context omitted.

That's pretty good. Based on the previous performance improvements of Alpha-- models, it'll be nearing 100% in the next couple of years.

> it'll be nearing 100% in the next couple of years. What are you basing this on? There is no established "moores law" for computational models.

It's the internet. There is no source more cited than "trust me bro"

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

#335

Post by nsoonhui »

Here's something that bugs me about ML: all we have is prediction and no explanation how we come to that prediction, ie: no deeper understanding on the underlying principles.

So despite that we got a good match this time, how can we be sure that the match will be equally good next time? And how to use ML to predict structure that we have no baseline to start with or experimental result to benchmark ? In the absence of physics-like principles, How can we ever be sure that ML results next time is correct ?

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

#336

Post by BriggyDwiggs42 »

falcor84 wrote: post #277
uptownfunk wrote: post #176

Very sad to see they did not make it open source. When you have a technology that has the potential to be a gateway for drug development, to the cures of new diseases, and instead you choose to make it closed, it is a very huge disservice to the community at large. Sure, release your own product alongside it, but making it closed source does not help the scientific community upon which all these innovations were buil…

The closer it gets to enabling full drug discovery, the closer it also gets to enabling bioterrorism. Taking it to the extreme, if they had the theory of everything, I don't think I'd want it to be made available to the whole world as it is today. On a related note, I highly recommend The Talos Principle 2, which really made me think about these questions.

Oh please, like a terrorist cant fork over a couple bucks to do the bioterrorism. This excuse is utter bs, whether its applied to LLMs or to alphafold. The motivator is profit, not safety.

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

#337

Post by throwaway4aday »

nsoonhui wrote: post #335

Here's something that bugs me about ML: all we have is prediction and no explanation how we come to that prediction, ie: no deeper understanding on the underlying principles. So despite that we got a good match this time, how can we be sure that the match will be equally good next time? And how to use ML to predict structure that we have no baseline to start with or experimental result to benchmark ? In the absence o…

Speaking of physics, we should borrow the quote "Shut up and calculate" to describe the situation: it works so use it now and worry about the explanations later.

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

#338

Post by andy_ppp »

moconnor wrote: post #32

Stepping back, the high-order bit here is an ML method is beating physically-based methods for accurately predicting the world. What happens when the best methods for computational fluid dynamics, molecular dynamics, nuclear physics are all uninterpretable ML models? Does this decouple progress from our current understanding of the scientific process - moving to better and better models of the world without human-int…

What happens if we get to the stage of being able to simulate every chemical and electrical reaction in a human brain, is doing this torture or wrong?

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

#339

Post by jasondigitized »

moconnor wrote: post #32

Stepping back, the high-order bit here is an ML method is beating physically-based methods for accurately predicting the world. What happens when the best methods for computational fluid dynamics, molecular dynamics, nuclear physics are all uninterpretable ML models? Does this decouple progress from our current understanding of the scientific process - moving to better and better models of the world without human-int…

All I can see anymore is that March of Progress illustration [1] with a GPU being added to the far right. Interesting times indeed.

[1] https://en.m.wikipedia.org/wiki/March_of_Progress

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

#340

Post by jasondigitized »

andy_ppp wrote: post #338
moconnor wrote: post #32

Stepping back, the high-order bit here is an ML method is beating physically-based methods for accurately predicting the world. What happens when the best methods for computational fluid dynamics, molecular dynamics, nuclear physics are all uninterpretable ML models? Does this decouple progress from our current understanding of the scientific process - moving to better and better models of the world without human-int…

What happens if we get to the stage of being able to simulate every chemical and electrical reaction in a human brain, is doing this torture or wrong?

So the Matrix?
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