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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

#71

Post by ldoughty »

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…

My argument is: weather.

I think it is fine & better for society to have applications and models for things we don't fully understand... We can model lots of small aspects of weather, and we have a lot of factors nailed down, but not necessarily all the interactions.. and not all of the factors. (Additional example for the same reason: Gravity)

Used responsibly. Of course. I wouldn't think an AI model designing an airplane that no engineers understand how it works is a good idea :-)

And presumably all of this is followed by people trying to understand the results (expanding potential research areas)

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

#73

Post by GaggiX »

ldoughty wrote: post #71
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…

My argument is: weather. I think it is fine & better for society to have applications and models for things we don't fully understand... We can model lots of small aspects of weather, and we have a lot of factors nailed down, but not necessarily all the interactions.. and not all of the factors. (Additional example for the same reason: Gravity) Used responsibly. Of course. I wouldn't think an AI model designing an ai…

It would be cool to see an airplane made using generative design.

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

#74

Post by t14n »

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…

A new-ish field of "mechanistic interpretability" is trying to poke at weights and activations and find human-interpretable ideas w/in them. Making lots of progress lately, and there are some folks trying to apply ideas from the field to Alphafold 2. There are hopes of learning the ideas about biology/molecular interactions that the model has "discovered".

Perhaps we're in an early stage of Ted Chiang's story "The Evolution of Human Science", where AIs have largely taken over scientific research and a field of "meta-science" developed where humans translate AI research into more human-interpretable artifacts.

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

#75

Post by mensetmanusman »

jeffreyrogers wrote: post #64
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 asked a friend of mine who is chemistry professor at a large research university something along these lines a while ago. He said that so far these models don't work well in regions where either theory or data is scarce, which is where most progress happens. So he felt that until they can start making progress in those areas it won't change things much.

Major breakthroughs happen when clear connections can be made and engineered between the many bits of solved but obscured solutions.

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

#76

Post by nybsjytm »

dekhn wrote: post #18
dopylitty wrote: post #13

This reminds me of Google’s claim that another “AI” discovered millions of new materials. The results turned out to be a lot of useless noise but that was only apparent after actual expert spent hundreds of hours reviewed the results[0] 0: https://www.404media.co/google-says-it-discovered-millions-o...

The alphafold work has been used across the industry (successfully, in the sense of blind prediction), and has been replicated independently. The work on alphafold will likely net Demis and John a Nobel prize in the next few years. (that said, one should always inspect Google publications with a fine-toothed comb and lots of skepticism, as they have a tendency to juice the results)

>The alphafold work has been used across the industry (successfully, in the sense of blind prediction), and has been replicated independently.

This is clearly an overstatement, or at least very incomplete. See for instance https://www.nature.com/articles/s41592-023-02087-4:

"In many cases, AlphaFold predictions matched experimental maps remarkably closely. In other cases, even very high-confidence predictions differed from experimental maps on a global scale through distortion and domain orientation, and on a local scale in backbone and side-chain conformation. We suggest considering AlphaFold predictions as exceptionally useful hypotheses."

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

#77

Post by timschmidt »

gameman144 wrote: post #54
Jerrrry wrote: post #12

Earlier quoted context omitted.

The second amendment prevents the government's overreaching perversion to restrict me from having the ability to print biological weapons from the comfort of my couch. Google has no such restriction.

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.

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

#78

Post by philip1209 »

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…

It makes me think about how Einstein was famous for making falsifiable real-world predictions to accompany his theoretical work. And, sometimes it took years for proper experiments to be run (such as measuring a solar eclipse during the breakout of a world war).

Perhaps the opportunity here is to provide a quicker feedback loop for theory about predictions in the real world. Almost like unit tests.

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

#79

Post by mnky9800n »

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 believe it simply tells us that our understanding of mechanical systems, especially chaotic ones, is not as well defined as we thought.

https://journals.aps.org/prresearch/abstract/10.1103/PhysRev...

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

#80

Post by j7ake »

So it’s okay now to publish a computational paper with no code? I guess Nature’s reporting standards don’t apply to everyone.

> A condition of publication in a Nature Portfolio journal is that authors are required to make materials, data, code, and associated protocols promptly available to readers without undue qualifications.

> Authors must make available upon request, to editors and reviewers, any previously unreported custom computer code or algorithm used to generate results that are reported in the paper and central to its main claims.

https://www.nature.com/nature-portfolio/editorial-policies/r...

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