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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

#411

Post by BriggyDwiggs42 »

hackernewds wrote: post #405
tsimionescu wrote: post #401

Earlier quoted context omitted.

The problem of producing bio weapons is not computational, it's physical in nature. Even if predictions from these tools become 100% accurate and encompassed 100% of the chemistry, you still need to actually do the manual steps to breed the bioagents. And, very importantly, you need to do so without getting you and your co-workers deadly ill long before finishing the thing. Which requires extremely sophisticated mach…

These are very specific ideas you have..

It’s very frustrating when people consider the possession of information equivalent to malice. It suggests that the right way to run society is to keep people stupid and harmless.

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

#412

Post by TylerLives »

searealist wrote: post #406
stouset wrote: post #403

Earlier quoted context omitted.

Yes, I understand how chess engines work. Ignore the existence of engines for a moment. The reason a particular line works, at the end of the day, is simply because it does . Just because we have heuristics that help us skip a lot of evaluation doesn’t mean the heuristics have intrinsic meaning within the game. They don’t. They’re shortcuts that let us skip having to do the impossible. The heuristics will always lose…

So your point is that we are not omnipotent? Ok.

Because of our limitations, we have to compress reality more in order to reason about it. This means we're blind to some ideas that computers are not. Just like a depth 1 chess engine can't see what's happening at depth 3 but has to make an imperfect guess.

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

#413

Post by ajuc »

mistermann wrote: post #279
ajuc wrote: post #246

Earlier quoted context omitted.

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?

Stuff that we can't program directly, but can program using machine learning.

Speech recognition. OCR. Reccomendation engines.

You don't write OCR by going "if there's a line at this angle going for this long and it crosses another line at this angle then it's an A".

There's too many variables and influence of each of them is too small and too tightly coupled with others to be able to abstract it into something that is understandeable to a human brain.

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

#414

Post by coriny »

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…

There is a biannual structural prediction contest called CASP [1], in which a set of newly determined structures is used to benchmark the prediction methods. Some of these structures will be "novel", and so can be used to estimate the performance of current methods on predicting "structure that we have no baseline to start with".

CASP-style assessments are something that should done for more research fields, but it's really hard to persuade funders and researchers to put up the money and embargo the data as required.

[1] https://en.wikipedia.org/wiki/CASP

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

#415

Post by robertlagrant »

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 community at large

Which community? Not any I'm part of.

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

#416

Post by datadeft »

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.

Why on Earth would any terrorist want to invest into this when you can just purchase guns and explosives much easier?

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

#417

Post by fsloth »

tsimionescu wrote: post #384
fsloth wrote: post #379

Earlier quoted context omitted.

AFAIK in wet science you need (or needed) to do tons of experimentations with liquids with specific molar compositions and temperatures splurging in and out of test tubes - basically just physically navigating a search space. I would view an AI model with super powerful guestimation capability as a much faster way of A) cutting through search space B) providing accidental discoveries while at it Now, if we look at hi…

> singularity? That’s just a word for “we don’t know what’s gonna happen” - not a specific concrete forecasted scenario It's more specific than you make it out. The singularity idea is that smart AIs working on improving AI will produce smarter AIs, leading to an ever increasing curve that at some point hits a mathematical singularity.

No it's not specific at all in predicting technological progress, which was the point of my comment.

Nobody knows what singularity would actually mean from the point of view of specific technological development.

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

#418

Post by narrator »

dekhn wrote: post #161
narrator wrote: post #140

Earlier quoted context omitted.

What if our understanding of the laws of the natural sciences are subtly flawed and AI just corrects perfectly for our flawed understanding without telling us what the error in our theory was? Forget trying to understand dark matter. Just use this model to correct for how the universe works. What is actually wrong with our current model and if dark matter exists or not or something else is causing things doesn't matt…

All models are wrong, but some models are useful.

The black box AI models could calculate epicycles perfectly so the middle ages Catholic Church could say just use those instead of being a geocentrrism denier.

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

#419

Post by kriro »

porphyra wrote: post #381
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...

They also had a headline for Alphazero that convinced everyone that they crushed Stockfish and that classical chess engines were stuff of the past, when in fact it was about 50 elo better than the Stockfish version they were testing against, or roughly the same as how much Stockfish improves each year.

I think Alphazero is a lot more interesting than Stockfish though. Most notably it lead me to reevaluate positional play. Iirc A0 at around 2-3 ply is still above SuperGM Level which is pretty mind-blowing. Based on this I have increased my strategy to tactics ratio quite a bit. FWIW Stockfish is always evolving and adapting and has incorporated ideas from A0.

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

#420

Post by RUnconcerned »

kriro wrote: post #419
porphyra wrote: post #381

Earlier quoted context omitted.

They also had a headline for Alphazero that convinced everyone that they crushed Stockfish and that classical chess engines were stuff of the past, when in fact it was about 50 elo better than the Stockfish version they were testing against, or roughly the same as how much Stockfish improves each year.

I think Alphazero is a lot more interesting than Stockfish though. Most notably it lead me to reevaluate positional play. Iirc A0 at around 2-3 ply is still above SuperGM Level which is pretty mind-blowing. Based on this I have increased my strategy to tactics ratio quite a bit. FWIW Stockfish is always evolving and adapting and has incorporated ideas from A0.

Stockfish has not incorporated ideas from AlphaZero. Stockfish's NN eval technology, NNUE, comes from Shogi and it predates Alphazero there.

The 2nd strongest engine, Leela Chess Zero, is indeed directly inspired by AlphaZero, though, and did surpass Stockfish until NNUE was introduced.

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