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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

#431

Post by [deleted] »

refulgentis wrote: post #269
dekhn wrote: post #203

Earlier quoted context omitted.

Then we should dedicate large fractions of human engineering towards finding ethical ways to improve human intelligence so that we can appreciate the underlying principles better.

I spend about 30 minutes reading this thread and links from it: I don't really follow your line of argument. I find it fascinating and well-communicated, the lack of understanding is on me: my attention flits around like a butterfly, in a way that makes it hard for me to follow people writing original content. High level, I see a distinction between theory and practice, between an oracle predicting without explanatio…

[deleted]

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

#432

Post by d0mine »

drdeca wrote: post #400
d0mine wrote: post #385

Earlier quoted context omitted.

Why do you think systems of partial differential equations (common in physics) are somehow provide more understanding than the corresponding ML math (at the end of the day both can produce results using a lots of matrix multiplications).

... because people understand things about what is described when dealing with such systems in physics, and people don't understand how the weights in ML learned NNs produce the overall behavior? (For one thing, the number of parameters is much greater with the NNs)

Looking at Navier-Stokes equations tells you very little about the weather tomorrow.

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

#433

Post by bluerooibos »

akira2501 wrote: post #229
bluerooibos wrote: post #180

Earlier 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.

> it'll be nearing 100% in the next couple of years. What are you basing this on? There is no established "moores law" for computational models.

Computational models have been shown to improve with computing power though, right?

It's a tongue in cheek comment about how fast models have been improving over the last few years, but I forgot HN scrutinizes every comment like it's a scientific paper.

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

#434

Post by FeepingCreature »

BriggyDwiggs42 wrote: post #411
hackernewds wrote: post #405

Earlier quoted context omitted.

These are very specific ideas you have..

It’s very frustrating when people consider the possession of information equivalent to malice. It suggests that the right way to run society is to keep people stupid and harmless.

Okay, I'll live in the harmless society, you go live in the harmful society.

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

#435

Post by DrScientist »

uptownfunk wrote: post #176

Very sad to see they did not make it open source. When you have a technology that has the potential to be a gateway for drug development, to the cures of new diseases, and instead you choose to make it closed, it is a very huge disservice to the community at large. Sure, release your own product alongside it, but making it closed source does not help the scientific community upon which all these innovations were buil…

I suspect https://www.isomorphiclabs.com/ is the reason.

There are 3 basic ways to fund research.

- Taxes - most academic research

- begging - research charities

- profits - companies like Google.

Sometimes the lines get blurred - but I don't think you can expect Google to release as much of their work for free as people who are paid via central taxes.

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

#436

Post by DrScientist »

tsimionescu wrote: post #401
ramon156 wrote: post #318

Earlier quoted context omitted.

Alright, but now picture this: it's now open to the masses, meaning an individual could probably even do it.

The problem of producing bio weapons is not computational, it's physical in nature. Even if predictions from these tools become 100% accurate and encompassed 100% of the chemistry, you still need to actually do the manual steps to breed the bioagents. And, very importantly, you need to do so without getting you and your co-workers deadly ill long before finishing the thing. Which requires extremely sophisticated mach…

To be honest, apart from the containment systems you mentioned, much of biology basic research doesn't actually need that much sophisticated kit for basic cloning and genetic manipulation.

A lot of the key reagents can just be bought - and BTW it's why code like Screepy exist ( https://edinburgh-genome-foundry.github.io/ ),.

I think the real thing that stops it - it not that you can't make stuff that kills people, but the problem of specificity - ie how do you stop it killing yourself.

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

#437

Post by DrScientist »

rolph wrote: post #39
renonce wrote: post #5

> What is different about the new AlphaFold3 model compared to AlphaFold2? > AlphaFold3 can predict many biomolecules in addition to proteins. AlphaFold2 predicts structures of proteins and protein-protein complexes. AlphaFold3 can generate predictions containing proteins, DNA, RNA, ions,ligands, and chemical modifications. The new model also improves the protein complex modelling accuracy. Please refer to our paper…

problem is biomolecules, are "chaperoned" to fold properly, only specific regions such as, alpha helix, or beta pleatedsheet will fold de novo. Chaperone (protein) https://en.wikipedia.org/wiki/Chaperone_(protein)

Chaperones exist - however many proteins will quite happily fold in isolation without any external help.

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

#438

Post by abecedarius »

RUnconcerned wrote: post #420
kriro wrote: post #419

Earlier quoted context omitted.

I think Alphazero is a lot more interesting than Stockfish though. Most notably it lead me to reevaluate positional play. Iirc A0 at around 2-3 ply is still above SuperGM Level which is pretty mind-blowing. Based on this I have increased my strategy to tactics ratio quite a bit. FWIW Stockfish is always evolving and adapting and has incorporated ideas from A0.

Stockfish has not incorporated ideas from AlphaZero. Stockfish's NN eval technology, NNUE, comes from Shogi and it predates Alphazero there. The 2nd strongest engine, Leela Chess Zero, is indeed directly inspired by AlphaZero, though, and did surpass Stockfish until NNUE was introduced.

Hmm: NNUE was introduced in 2018, the AlphaZero preprint 2017, AlphaGo 2015-2016. I checked this because my memory claimed that it was AlphaGo's success that sparked the new level of interest in NN evaluation.

Wouldn't surprise me if AlphaZero's improvements had no influence in that timeline, but for AlphaGo it would.

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

#439

Post by carlsborg »

dekhn wrote: post #23
joshuamcginnis wrote: post #17

Earlier quoted context omitted.

Accuracy can be assessed two main ways: computationally and experimentally. Computationally, they would compare the predicted structures and interactions with known data from databases like PDB (Protein Database). Experimentally, they can use tools like x-ray crystallography and NMR (nuclear magnetic resonance) to obtain the actual molecule structure and compare it to the predicted result. The outcomes of each approa…

AlphaFold very explicitly (unless something has changed) removes NMR structures as references because they are not accurate enough. I have a PhD in NMR biomolecular structure and I wouldn't trust. the structures for anything.

Would you trust the CryoEM structures more?

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

#440

Post by bronco21016 »

FeepingCreature wrote: post #434
BriggyDwiggs42 wrote: post #411

Earlier quoted context omitted.

It’s very frustrating when people consider the possession of information equivalent to malice. It suggests that the right way to run society is to keep people stupid and harmless.

Okay, I'll live in the harmless society, you go live in the harmful society.

We all live in the harmful society already right? I’m not aware of where to find this harmless society.

Suffering of finite beings is inevitable. While a very worthwhile goal, creating a harmless civilization isn’t possible. There are some common sense things we should do to prevent harm like negative consequences (prison etc) for needlessly harming each other. However, locking up knowledge doesn’t make much sense to me.

I’d rather explore the bounds of this world than mindlessly collect my drip of Soma and live comatose. To me that sounds more harmful.

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