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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

#111

Post by tantalor »

sdwr wrote: post #99
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…

> 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.

This type of thing is called an "oracle".

We've had stuff like this for a long time.

Notable examples:

- Temple priestesses

- Tea-leaf reading

- Water scrying

- Palmistry

- Clairvoyance

- Feng shui

- Astrology

The only difference is, the ML model is really quite good at it.

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

#112

Post by scotty79 »

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…

We should be thankful that we live in the universe that obeys math simple enough to comprehend that we were able to reach that level.

Imagine if optis was complex enough that it would require ML model to predict anything.

We'd be in permanent stone age without a way out.

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

#113

Post by mberning »

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 would assume that given enough hints from AI and if it is deemed important enough humans will come in to figure out the “first principles” required to arrive at the conclusion.

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

#114

Post by nybsjytm »

dekhn wrote: post #83
nybsjytm wrote: post #76

Earlier quoted context omitted.

>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 differ…

Yep, I know Paul Adams (used to work with him at Berkeley Lab) and that's exactly the paper he'd publish. If you read that paper carefully (as we all have, since it's the strongest we've seen from the crystallography community so far) they're basically saying the results from AF are absolutely excellent, and fit for purpose. (put another way: if Paul publishes a paper saying your structure predictions have issues, an…

I don't know Paul Adams, so it's hard for me to know how to interpret your post. Is there anything else I can read that discusses the accuracy of AlphaFold?

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

#116

Post by danielmarkbruce »

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…

"better and better models of the world" does not always mean "more accurate" and never has.

We already know how to model the vast majority of things, just not at a speed and cost which makes it worthwhile. There are dimensions of value - one is accuracy, another speed, another cost, and in different domains additional dimensions. There are all kinds of models used in different disciplines which are empirical and not completely understood. Reducing things to the lowest level of physics and building up models from there has never been the only approach. Biology, geology, weather, materials all have models which have hacks in them, known simplifications, statistical approximations, so the result can be calculated. It's just about choosing the best hacks to get the best trade off of time/money/accuracy.

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

#117

Post by dekhn »

11101010001100 wrote: post #67
dekhn wrote: post #18

Earlier quoted context omitted.

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)

Depending on your expected value of quantum computing, the Nobel committee shouldn't wait too long.

Personally I don't expect QC to be a competitor to ML in protein structure prediction for the foreseeable future. After spending more money on molecular dynamics than probably any other human being, I'm really skeptical that physical models of protein structures will compete with ML-based approaches (that exploit homology and other protein sequence similarities).

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

#118

Post by Gimpei »

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…

Might be easier to come up with new models with analytic solutions if you have a probabilistic model at hand. A lot easier to evaluate against data and iterate. Also, I wouldn't be surprised if we develop better tools for introspecting these models over time.

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

#119

Post by karencarits »

perihelions wrote: post #102
l33tman wrote: post #10

Earlier quoted context omitted.

That sucks a bit. I was just wondering why they are touting that 3rd party company in their own blog post, who commercialise research tools, as well. Maybe there are some corporate agreements with them that prevents them from opening the system... Imagine the goodwill for humanity for releasing these pure research systems for free. I just have a hard time understanding how you can motivate to keep it closed. Let's ho…

- "Imagine the goodwill for humanity for releasing these pure research systems for free." The entire point[0] is that they want to sell an API to drug-developer labs, at exclusive-monopoly pricing. Those labs in turn discover life-saving drugs, and recoup their costs from e.g. parents of otherwise-terminally-ill children—again, priced as an exclusive monopoly. [0] As signaled by "it is not possible to obtain structur…

What is the current status of drugs where the major contribution is from AI? Are they protectable like other drugs? Or are they more copyless like AI art and so on?

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

#120

Post by _yb2s »

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 means we now have an accurate surrogate model or "digital twin" that can be experimented on almost instantaneously. So we can massively accelerate the traditional process of developing mechanistic understanding through experiment, while also immediately be able to benefit from the ability to make accurate predictions, even without needing understanding.

In reality, science has already pretty much gone this way long ago, even if people don't like to admit it. Simple, reductionist explanations for complex phenomena in living systems don't really exist. Virtually all of medicine nowadays is empirical: try something, and if you can prove its safe and effective, you keep doing it. We almost never have a meaningful explanation for how it really works, and when we think we do, it gets proven wrong repeatedly, while the treatment keeps working as always.

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