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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

#271

Post by AtlasBarfed »

dekhn wrote: post #25
weregiraffe wrote: post #3

s/predicts/attempts to predict

AlphaFold has been widely validated- it's now appreciated that its predictions are pretty damn good, with a few important exceptions, instances of which are addressed with the newer implementation.

"pretty damn good"

So... what percentage of the time? If you made an AI to pilot an airplane, how would you verify its edge conditions, you know, like plummeting out of the sky because it thought it had to nosedive?

Because these AIs are black box neural networks, how do you know they are predicting things correctly for things that aren't in the training dataset?

AI has so many weasel words.

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

#272

Post by gameman144 »

timschmidt wrote: post #77
gameman144 wrote: post #54

Earlier quoted context omitted.

I know this is tongue in cheek, but you absolutely can be restricted from having a biological weapons factory in your basement (similar to not being able to pick "nuclear bombs" as your arms to bear).

Seems like the recipe for independence, and agreed upon borders, and thus whatever interpretation of the second amendment one wants involves exactly choosing nuclear bombs, and managing to stockpile enough of them before being bombed oneself. At least at the nation state scale. Sealand certainly resorted to arms at several points in it's history.

The second amendment only applies to the United States -- it's totally normal to have one set of rights for citizens and another set for the government itself.

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

#273

Post by mistermann »

refulgentis wrote: post #269
dekhn wrote: post #203

Earlier quoted context omitted.

Then we should dedicate large fractions of human engineering towards finding ethical ways to improve human intelligence so that we can appreciate the underlying principles better.

I spend about 30 minutes reading this thread and links from it: I don't really follow your line of argument. I find it fascinating and well-communicated, the lack of understanding is on me: my attention flits around like a butterfly, in a way that makes it hard for me to follow people writing original content. High level, I see a distinction between theory and practice, between an oracle predicting without explanatio…

There's a much easier route: consciousness is not included in the discussion...what a coincidence.

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

#274

Post by [deleted] »

dekhn wrote: post #93
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…

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…

[deleted]

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

#275

Post by itissid »

Noob here. Can one make the following deduction:

In transformer based architectures, where one typically uses variation of attention mechanism to model interactions, even if one does not consider the autoregressive assumption of the domain's "nodes"(amino acids, words, image patches), if the number of final states that nodes take eventually can be permuted only in a finite way(i.e. they have sparse interactions between them), then these architectures are efficient way of modeling such domains.

In plain english the final state of words in a sentence and amino acids in a protein have only so many ways they can be arranged and transformers do a good job of modeling it.

Also can one assume this won't do well for domains where there is, say, sensitivity to initial conditions, like chaotic systems like wheather where the # final states just explodes?

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

#276

Post by mikeyouse »

nkingsy wrote: post #267
thfuran wrote: post #258

Earlier quoted context omitted.

>there is no way to confirm you have discovered underlying principles unless they have some predictive power. Yes, but a perfect oracle has no explanatory power, only predictive.

increasing the volume of predictions produces patterns that often lead to underlying principles.

And much of the 20th century was characterized by a very similar progression - we had no clue what the actual mechanism of action was for hundreds of life saving drugs until relatively recently, and we still only have best guesses for many.

That doesn’t diminish the value that patients received in any way even though it would be more satisfying to make predictions and design something to interact in a way that exactly matches your theory.

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

#277

Post by falcor84 »

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.

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

#278

Post by panabee »

dekhn wrote: post #186
nybsjytm wrote: post #172

Earlier quoted context omitted.

Thanks, those look helpful. Whenever I meet someone with relevant PhDs I ask their thoughts on AlphaFold, and I've gotten a wide variety of responses, from responses like yours to people who acknowledge its usefulness but are rather dismissive about its ultimate contribution.

The people who are most likely to deprecate AlphaFold are the ones whose job viability is directly affected by its existence. Let me be clear: DM only "solved" (and really didn't "solve") a subset of a much larger problem: creating a highly accurate model of the process by which real proteins adopt their folded conformations, or how some proteins don't adopt folded conformations without assistance, or how some protei…

this is very astute, not only about deepmind but about science and humanity overall.

what CASP did was narrowly scope a hard problem, provided clear rules and metrics for evaluating participants, and offered a regular forum in which candidates can showcase skills -- they created a "game" or competition.

in doing so, they advanced the state of knowledge regarding protein structure.

how can we apply this to cancer and deepen our understanding?

specifically, what parts of cancer can we narrowly scope that are still broadly applicable to a complex heterogenous disease and evaluate with objective metrics?

[edited to stress the goal of advancing cancer knowledge, not to "gamify" cancer science but to create structures that inivte more ways to increase our understanding of cancer.]

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

#279

Post by mistermann »

ajuc wrote: post #246
jvanderbot wrote: post #210

Earlier quoted context omitted.

A human mind is perfectly capable of following the same instructions as the computer did. Computers are stupidly simple and completely deterministic. The concern is about "holding it all in your head", and depending on your preferred level of abstraction, "all" can perfectly reasonably be held in your head. For example: "This program generates the most likely outputs" makes perfect sense to me, even if I don't unders…

Abstraction isn't the silver bullet. Not everything is abstractable. "This program generates the most likely outputs" isn't a scientific explanation, it's teleology.

What is an example of something that isn't abstractable?

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

#280

Post by theGnuMe »

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…

The models are learning an encoding based on evolutionary related and known structures. We should be able to derive fundamental properties from those encodings eventually. Or at least our biophysical programmed models should map into that encoding. That might be a reasonable approach to look at the folding energy landscape.
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