3 ms·

As 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 hard

As 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 of that, achieving greater results. And the authors simply use distillation from data outputted from Alphafold2 and Alphafold2-multimer to get those better results for those cases where you wind up with implausible results. You have to run all those previous models, and output their predictions to do the distillation to achieve a real end-to-end training from scratch for this new model! Makes me feel a bit uncomfortable.

amitport 2y ago
Consider that humans also learn from other humans, and sometimes surpass their teachers. A bit more comfortable?
- Balgair 2y ago
  Ahh, but the new young master is able to explain their work and processes to the satisfaction of the old masters. In the 'Science' of our modern times it's a requirement to show your work (yes, yes, I know about the replication crisis and all that terrible jazz). Not being able to ascertain how and why the ML/AI is achieving results is not quite the same and more akin to the alchemists and sorcerers with their cyphers and hidden laboratories.
  - falcor84 2y ago
    > the new young master is able to explain their work and processes to the satisfaction of the old masters Yes, but it's one level deep - in general they wouldn't be able to explain their work to their master's master (note "science advances one funeral at a time").
  - hackerdood 2y ago
    I’ll add that specially when it comes to playing go, professionals who are at the peak of their ability can often find the best move at a given point but be unable to explain why beyond “it feels right” or “it looks right”.
  - borgdefense 2y ago
    [flagged]
sangnoir 2y ago
> Makes me feel a bit uncomfortable. 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
- arjvik 2y ago
  Compilers are deterministic (for the most part, and it's incredibly rare to introduce a compiler bug that self-replicates in future compilers (unless you're Ken Thompson and are reflecting upon trust itself)). Alternatively, AlphaFold 2's output is noisy, and using that to train AlphaFold 3, which presumably may be used to train what becomes AlphaFold 4, results in a cascade of errors.

amitport 2y ago

Consider that humans also learn from other humans, and sometimes surpass their teachers. A bit more comfortable?

Balgair 2y ago
Ahh, but the new young master is able to explain their work and processes to the satisfaction of the old masters. In the 'Science' of our modern times it's a requirement to show your work (yes, yes, I know about the replication crisis and all that terrible jazz). Not being able to ascertain how and why the ML/AI is achieving results is not quite the same and more akin to the alchemists and sorcerers with their cyphers and hidden laboratories.
- falcor84 2y ago
  > the new young master is able to explain their work and processes to the satisfaction of the old masters Yes, but it's one level deep - in general they wouldn't be able to explain their work to their master's master (note "science advances one funeral at a time").
- hackerdood 2y ago
  I’ll add that specially when it comes to playing go, professionals who are at the peak of their ability can often find the best move at a given point but be unable to explain why beyond “it feels right” or “it looks right”.
- borgdefense 2y ago
  [flagged]

sangnoir 2y ago

> Makes me feel a bit uncomfortable. 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

arjvik 2y ago
Compilers are deterministic (for the most part, and it's incredibly rare to introduce a compiler bug that self-replicates in future compilers (unless you're Ken Thompson and are reflecting upon trust itself)). Alternatively, AlphaFold 2's output is noisy, and using that to train AlphaFold 3, which presumably may be used to train what becomes AlphaFold 4, results in a cascade of errors.