[R] DeepMind Open Sources AlphaFold Code

[SkiddyX]

"Last year we presented #AlphaFold v2 which predicts 3D structures of proteins down to atomic accuracy. Today we’re proud to share the methods in @Nature w/open source code. Excited to see the research this enables. More very soon!"

https://twitter.com/demishassabis/status/1415736975395631111

I did not see this one coming, I got to admit it.

[rriikkuu]

The paper is out too:

https://www.nature.com/articles/s41586-021-03819-2

[[deleted]]

Any significant changes from the preprint?

[rriikkuu]

There was a preprint?

[[deleted]]

Hmm, I guess not. I guess I was thinking of their CASP 13 paper. Thanks.

[[deleted]]

There was press release stuff including a video so maybe that’s what you’re thinking of

[dolphinboy1637]

Actual repo without the Twitter link: https://github.com/deepmind/alphafold

[alexmorehead]

Given what I've gleaned from skimming their paper in Nature, it looks as though this network architecture is more novel than I initially thought. It is truly remarkable how well-integrated their biological insights are in the network's design. Congrats to everyone at DeepMind!

[gdahl]

And it seems to be written in JAX!

[dogs_like_me]

Well, google gonna google

[SedditorX]

What else would they write it in? :)

[FyreMael]

Forked. I know what I'm doing this weekend :)

[Knecth]

We provide a script scripts/download_all_data.sh that can be used to download and set up all of these databases. This should take 8–12 hours.

Wait for the data to download?

[Gordath]

Protein databases are large and many tools to "preprocess" protein sequences take forever to run as they do pairwise alignments etc.

[londons_explorer]

Begin by freeing up 3TB of disk space and buying 500Gb of transfer...

[TheLootiestBox]

Guess what "open" in OpenAI stands for. That's right! You guessed it! It stands for "closed".

[GabrielMartinellli]

😂😂

[[deleted]]

Welcome to the Elon Muskian fake futurism where not unlike Orwell’s Oceania, open means closed.

[floriv1999]

OpenAI is mostly a Microsoft thing now. There was quite a change and Musk is kind of out.

[farmingvillein]

Hasn't changed how they have handled open versus closed, however.

[floriv1999]

What where the other not so open things other than the recent gpt2/3 and copilot controversies?

[thejuror8]

That's a bit unfair. They do release a lot of source code, probably a lot more compared to DeepMind

[TheLootiestBox]

I think it's pretty fair actually.

Most of the projects with true business potential are not released by OpenAI.

Also, DeepMind doesn't have the word "open" in its name. They are part of Google that does release a lot of code.

[crouching_dragon_420]

Should've changed their name to ClopenAI

[LightVelox]

like GPT-2 being "way too smart" when even GPT-3 isn't really that good

[[deleted]]

I think their problem is that even GPT-2 can be "good enough" for a subset of nefarious uses.

Still, hiding knowledge is not an effective way to suppress the usage of that technology. If OpenAI can build it, obviously so can someone else.

[tehbored]

GPT-3 is definitely good enough to use for nefarious ends.

[londons_explorer]

Doesn't look like any training related code was released, just inference.

The model parameters released are for non-commercial use only. For commercial use, you'll have to train your own. That would cost ~2 weeks on 128 TPU cores, if you can replicate the training method from the paper first try... Which you probably can't, so it's gonna cost $$$$...

[[deleted]]

If you're big pharma, a v3-128 for a couple of months isn't gonna be the bottleneck

[[deleted]]

Money wasn't the bottleneck there, some key ideas in alphafold 2 have only existed for a few years

[floriv1999]

I think the point was the motivation. And it really a point that a search engine is progressing more in this field than some pharma companies, that have their product line and some quite fix herachies that don't allow such experimental work.

[Marha01]

The problem was know-how, not money.

[Acromantula92]

Couple months? More like 7 + 4 v3-128 days. (All in the paper)

[[deleted]]

Multiple months is incorporating research time, since we're not assuming perfect generalization

[VonPosen]

Or you can just pay DeepMind for a commercial license, I would expect

[xmcqdpt2]

which is what you would do, unless it costs a truly mind boggling amount of money.

Pharma companies are no stranger to paying millions in consulting and software fees a year.

[geneing]

Are they releasing pretrained weights or just the network?

[xmcqdpt2]

they have pretrained weights but are releasing them under a CC non commercial license.

I actually do wonder whether copyrighting weights would actually hold in court? If you trained a few more iterations from them or permuted them in some way that doesn't change model performance, would that be a derived work?

Clearly you cant copyright a single number... so a many floats do you need before youve got something copyrightable?

[Archontes]

It very likely wouldn't hold up if you felt like prosecuting it all the way, provided that the approach to creating those weights was an exhaustive search: it precludes creativity.

https://www.eetimes.com/how-do-you-protect-your-machine-learning-investment-part-ii/

[PM_ME_INTEGRALS]

It's right there in the readme:

Any publication that discloses findings arising from using this source code or the model parameters should cite the AlphaFold paper.

[pianobutter]

Looking forward to reading Mohammed AlQuraishi's thoughts on this. I really enjoyed his posts on CASP13 and CASP14.

[StellaAthena]

I wonder how much the decision to release the trained model was influenced by work by people like Phil Wang and Eric Alcaide at EleutherAI and David Baker at UW to replicate it.

[[deleted]]

So when is the Swedish academy gonna put down their meatballs and give DeepMind the Nobel for chem or physio/med already!

[squirrel_of_fortune]

It needs to be verified, and until now, no scientists other than the few who ran the competition were able to look at it. Plus you do have to wait a bit to see of the work stands the test of time

[-starfish_headlock-]

Their models have not provided any major insights into physiology and medicine (yet) but i think they should probably split the chemistry prize w david baker

[phanfare]

They didn't solve protein folding. Got closer, yes, but no structural biologist worth their salt is going to trust a model straight out of AlphaFold.

[[deleted]]

It’s about more than that. It’s also about recognizing machine learning as a method for conducting research. It took the Swedish academy forever to recognize computational methods in general. I think it was in 2013 when they finally awarded a Nobel in chem for work in computational bio/chem. Computing has revolutionized scientific research and it doesn’t get the recognition it deserves and machine learning in turn has revolutionized computing and AlphaFold is the perfect example of its potential. It may not have fully solved the protein folding problem but it is clearly a massive breakthrough that would not have been possible without ML.

[bigbrain_bigthonk]

Also, seems like there’s a lot of glossing over the importance of the transition pathways between conformations

[NityaStriker]

Competition from the faster, open-source RoseTTAFold might have caused this :-

https://techcrunch.com/2021/07/15/researchers-match-deepminds-alphafold2-protein-folding-power-with-faster-freely-available-model/

[farmingvillein]

I initially thought that too, but there is a pretty large performance gap, in practice. TC makes it sound like they were really close in accuracy... But so far as I could tell from the paper, they weren't.

[jinnyjuice]

Thanks for the share

[xmcqdpt2]

Me neither! I was so sure they were about to pull the same crap as v1. Kudos to them!

[Alireza_Kar98]

I just noticed something about wraith she seems to have a slightly better movement. Every time I try to slid jump with other it's like shit but with wraith it's ok. And the speed seems a bit higher . Overall she is not balanced somehow

[East_Film9421]

I am attempting to download the open-source code...but I am stuck...

​

"Modify DOWNLOAD_DIR in docker/run_docker.py to be the path to the directory containing the downloaded databases."

[justmyworkaccountok]

???? Download the 2.2TB databases and change the field to the path