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…
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
#212Earlier quoted context omitted.
Also no commercial use, from the paper: > AlphaFold 3 will be available as a non-commercial usage only server at https://www.alphafoldserver.com , with restrictions on allowed ligands and covalent modifications. Pseudocode describing the algorithms is available in the Supplementary Information. Code is not provided.
What's the point in that that - I mean who does non-commercial drug research?
Re: AlphaFold 3 predicts the structure and interactions of life's molecules
#213Earlier quoted context omitted.
That's pretty good. Based on the previous performance improvements of Alpha-- models, it'll be nearing 100% in the next couple of years.
Just "Alpha-- models" in general?? That's not a remotely reasonable way to reason about it. Even if it were, why should it stop DeepMind from clearly communicating accuracy?
(I'm not defending this approach, just making an observation)
Re: AlphaFold 3 predicts the structure and interactions of life's molecules
#214Earlier quoted context omitted.
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.
Agreed. At the very least, models of this nature let us iterate/filter our theories a little bit more quickly.
Re: AlphaFold 3 predicts the structure and interactions of life's molecules
#215Stepping 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…
Re: AlphaFold 3 predicts the structure and interactions of life's molecules
#216As a software engineer, I kind of feel uncomfortable about this new model. It outperforms Alphafold 2 at ligand binding, but Alphafold 2 also had some more hardcoded and interpretable structural reasoning baked into the model architecture. There's so many things you can incorporate into a protein folding model such as structural constraints, rotational equivariance, etc, etc This new model simple does away with some…
A bit more comfortable?
Re: AlphaFold 3 predicts the structure and interactions of life's molecules
#217Earlier quoted context omitted.
the R&D of all major pharma is currently using AlphaFold predictions when they don't have experimentally determined structures. I cannot share further details but the results suggest that we will see future pharmaceuticals based on AF predictions. The important thing to recognize is that protein structures are primarily hypothesis-generation machines and tools to stimulate ideas, rather that direct targets of computa…
Sure. If/when we see anything practical, that’ll be the right moment to pay attention. This is much like “quantum computing” where everyone who doesn’t know what it is is excited for some reason, and those that do know can’t even articulate any practical applications
These approaches are now being explored but I haven't seen any smoking guns showing a QC-based simulation exceeding the accuracy of a classical computer for a reasonable investment.
Folks have suggested other areas, such as logistics, where finding small improvements to the best approximations might give a company a small edge, and crypto-breaking, but there has been not that much progress in this area, and the approximate methods have been improving rapidly.
Re: AlphaFold 3 predicts the structure and interactions of life's molecules
#218Important 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...
Edit: I see now that you're probably objecting to the headline that got edited on HN.
Re: AlphaFold 3 predicts the structure and interactions of life's molecules
#219Re: AlphaFold 3 predicts the structure and interactions of life's molecules
#220As a software engineer, I kind of feel uncomfortable about this new model. It outperforms Alphafold 2 at ligand binding, but Alphafold 2 also had some more hardcoded and interpretable structural reasoning baked into the model architecture. There's so many things you can incorporate into a protein folding model such as structural constraints, rotational equivariance, etc, etc This new model simple does away with some…
Why? Do compilers which can't bootstrap themselves also make you uncomfortable due to dependencies on pre-built artifacts? I'm not saying you're unjustified to feel that way, but sometimes more abstracted systems are quicker to build and may have better performance than those built from the ground up. Selecting which one is better depends on your constraints and taste