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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

#91
post #80

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 unrep…

Are you an editor or reviewer?

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

#92

A video summary of why this research is important: https://youtu.be/Mz7Qp73lj9o?si=29vjdQtTtIOk_0CV

Thanks for this informative video summary. As a layperson, with a BS in Chemistry, it was quite helpful in understanding main bulletpoints of this accomplishment.

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

#93

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://norvig.com/chomsky.html), then you'll be quite happy because this is yet another validation of the value of statistical approaches in moving our ability to predict the universe forward.

If you're the sort of person who believes that human brains are capable of understanding the "why" of how things work in all its true detail, you'll find this an interesting challenge- can we actually interpret these models, or are human brains too feeble to understand complex systems without sophisticated models?

If you're the sort of person who likes simple models with as few parameters as possible, you're probably excited because developing more comprehensible or interpretable models that have equivalent predictive ability is a very attractive research subject.

(FWIW, I'm in the camp of "we should simultaneously seek simpler, more interpretable models, while also seeking to improve native human intelligence using computational augmentation")

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

#94
post #48

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 steelman, wouldn't the abundance of infinitely generate-able situations make it _easier_ for us to develop strong theories and models? The bottleneck has always been data. You have to do expensive work in the real world and accurately measure it before you can start fitting lines to it. If we were to birth an e.g. atomically accurate ML model of quantum physics, I bet it wouldn't take long until we have mathemat…

Maybe; AI chess engines have improved human understanding of the game very rapidly, even though humans cannot beat engines.

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

#97

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 suspect that ML will be state-of-the-art at generating human-interpretable theories as well. Just a matter of time.

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

#98

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.

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

Or jumping the gap entirely to move towards more self-driven reinforcement learning.

Could one structure the training setup to be able to design its own experiments, make predictions, collect data, compare results, and adjust weights...? If that loop could be closed, then it feels like that would be a very powerful jump indeed.

In the area of LLMs, the SPAG paper from last week was very interesting on this topic, and I'm very interested in seeing how this can be expanded to other areas:

https://github.com/Linear95/SPAG

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

#99

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?

Thank God! As a person who uses my brain, I think I can say, pretty definitively, that people are bad at understanding things.

If this actually pans out, it means we will have harnessed knowledge/truth as a fundamental force, like fire or electricity. The "black box" as a building block.

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

#100
post #66
post #31

Earlier quoted context omitted.

Sorry, I don’t mean to be dense - do you mean you don’t trust AlphaFolds structures or NMRs?

I don't trust NMR structures in nearly all cases. The reasons are complex enough that I don't think it's worthwhile to discuss on Hacker News.

Hmm, I would say its always worth to share knowledge. Could you paste some links or maybe type a few key-words for anyone willing to reasearch the topic further on his own.
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