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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

#311

Post by abledon »

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…

Next decade we will focus on building out debugging and visualization tools for deep learning , to glance inside the current black box

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

#312

Post by hyperthesis »

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…

Engineering often precedes Science. It's just more data.

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

#313

Post by LouisSayers »

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 do you need AI for bioterrorism? There are plenty of well known biological organisms that can kill us today...

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

#314

Post by heyoni »

dekhn wrote: post #23
joshuamcginnis wrote: post #17

Earlier quoted context omitted.

Accuracy can be assessed two main ways: computationally and experimentally. Computationally, they would compare the predicted structures and interactions with known data from databases like PDB (Protein Database). Experimentally, they can use tools like x-ray crystallography and NMR (nuclear magnetic resonance) to obtain the actual molecule structure and compare it to the predicted result. The outcomes of each approa…

AlphaFold very explicitly (unless something has changed) removes NMR structures as references because they are not accurate enough. I have a PhD in NMR biomolecular structure and I wouldn't trust. the structures for anything.

Nice to see you on this thread as well! :)

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

#315

Post by TaupeRanger »

qwertox wrote: post #44

> Thrilled to announce AlphaFold 3 which can predict the structures and interactions of nearly all of life’s molecules with state-of-the-art accuracy including proteins, DNA and RNA. [1] There's a slight mismatch between the blog's title and Demis Hassabis' tweet, where he uses "nearly all". The blog's title suggests that it's a 100% solved problem. [1] https://twitter.com/demishassabis/status/1788229162563420560

First time reading a Deep Mind PR? This is literally their modus operandi.

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

#316

Post by salty_biscuits »

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…

I'd say it's not new. Take fluid dynamics as an example, the navier stokes equations predict the motion of fluids very well but you need to approximately solve them on a computer in order to get useful predictions for most setups. I guess the difference is the equation is compact and the derivation from continuum mechanics is easy enough to follow. People still rely on heuristics to answer "how does a wing produce lift?". These heuristic models are completely useless at "how much lift will this particular wing produce under these conditions?". Seems like the same kind of situation. Maybe progress forward will look like producing compact models or tooling to reason about why a particular thing happened.

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

#317

Post by ranger_danger »

dekhn wrote: post #36
ranger_danger wrote: post #26

Earlier quoted context omitted.

Not just unfortunate, but doesn't this make it completely untrustable? How can you be sure the data was not modified in any way? How can you verify any results?

You determine a crystal structure of a known protein which does not previously have a known structure, and compare the prediction to the experimentally determined structure. There is a biennial (biannual?) competition known as CASP where some new structures, not yet published, are used for testing predictions from a wide range of protein structure prediction (so, basically blind predictions which are then compared wh…

By data I meant between the client and server, nothing actually related to how the program itself works, but just the fact that it's controlled by a proprietary third party.

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

#318

Post by ramon156 »

pythonguython wrote: post #301
falcor84 wrote: post #277

Earlier quoted context omitted.

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.

Any organization/country that has the ability to use a tool like this to create a bio weapon is already sophisticated enough to do bioterrorism today.

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

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

#319

Post by Brian_K_White »

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 an ai can be made to produce the work as well as a final answer, even if it has to reconstruct or invent the work backwards rather than explain it's own internal inscrutable process.

"produce a process that arrives at this result" should be just another answer it can spit out. We don't necessarily care if the answer it produces is actually the same as what originally happened inside itself. All we need is that the answer checks out when we try it.

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

#320

Post by JacobThreeThree »

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…

As a tool people will use it as any other tool, by experimenting, testing, tweaking and iterating.

As a scientific theory for fundamentally explaining the nature of the universe, maybe it won't be as useful.

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