[HN Gopher] AI is changing chemical discovery
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AI is changing chemical discovery
Author : andreyk
Score : 57 points
Date : 2022-02-14 20:03 UTC (2 hours ago)
(HTM) web link (thegradient.pub)
(TXT) w3m dump (thegradient.pub)
| uejfiweun wrote:
| Don't mean to sound cynical here, but is AI _actually_ gonna
| change chemical discovery? Or is AI gonna "change chemical
| discovery" in the same way that it will "make radiologists
| obsolete", or "revolutionize healthcare with Watson", or "put
| millions of truckers out of business"? There's certainly a lot of
| marketing, technical talent, and hope behind modern "AI", but I'm
| not really aware of any major part of our economy that's been
| THAT changed by it.
| shoguning wrote:
| Advertising and media? Robots bid on the ads that billions see
| every day, and decide what videos billions of people watch.
| fock wrote:
| I don't know if I have missed the big thing here (was supposed to
| do exactly the same flowery thing described there for crystals
| around 2019-2020), but the graphic with the Autoencoder is
| roughly what people did in 2018 (Gomez-Bombarelli,
| https://pubs.acs.org/doi/10.1021/acscentsci.7b00572), I think the
| review cited reproduced this. Also notice: it has the MLP in the
| middle, the performance of which was/is not really helping either
| - especially if your model should actually produce novel stuff,
| e.g. extrapolate.
|
| Finally: every kid can draw up novel structures. Then: how do you
| actually fabricate these (in the case of real novel chemistry and
| not some building-block stuff). Noone has a clue!
|
| I for myself have decided that for now (with the data at hand and
| non-Alphafold-budgets) the 2 keys areas, where you can actually
| help computational chemistry are:
|
| - creating really robust and generally applicable ML-MD-
| potentials, potentially using graphs
| https://arxiv.org/abs/2106.08903 (or a traditional approach:
| https://www.nature.com/articles/s41467-020-20427-2). Facebook is
| also working in this area:
| https://pubs.acs.org/doi/10.1021/acscatal.0c04525
|
| - and approximating exchange correlation functionals (... Google
| and some guys at Oxford, which got stomped over by the deepmind-
| PR machine https://arxiv.org/pdf/2102.04229.pdf):
| https://www.science.org/doi/10.1126/science.abj6511
|
| If anyone can tell me how those generative models spit out graphs
| which look like reality (actually this is imho part of
| AlphaFold), wake me up.
| busyant wrote:
| > every kid can draw up novel structures. Then: how do you
| actually fabricate these (in the case of real novel chemistry
| and not some building-block stuff). Noone has a clue!
|
| Yep. I worked at a biotech startup in the early/mid 2000s.
|
| We had a 2-pronged approach to finding small molecule drugs: 1)
| traditional medicinal chemistry based on simple SAR (structure-
| activity relationships) and 2) predictive modeling (before ML
| was hot).
|
| The traditional med chemists were, in my opinion, rightfully
| skeptical of the suggestions coming out of the predictive
| modeling group ( _" That's a great suggestion, but can you tell
| me how to synthesize it?"_).
|
| As one of my co-workers said to me: _" The predictions made by
| the modeling group range from pretty bad to ... completely
| worthless."_
|
| It's possible that things have gotten better, though, as I
| haven't done that type of work since about 2008.
| dbodin11 wrote:
| TLDR https://www.kontxt.io/document/d/JIEEx-
| DeuipovrgBJ1vzDzC5X4v...
| Mizza wrote:
| I have an AI chemistry project that appears to work on my test
| data, but I had to put it on the backburner because I simply
| can't (couldn't) find a 3070/80 anywhere! I stopped looking 6
| months ago, does anybody know a reliable place where I can snag
| one?
| hobs wrote:
| I dont know if it has enough ram for your purposes but I also
| gave up and just bought an entire computer to get a 3080 and
| got it in 3 weeks before Christmas
| https://skytechgaming.com/product/shiva-amd-ryzen-5-5600x-nv...
| hervature wrote:
| If you don't mind having a gaming PC (stupid RGB lights and
| fans) then Build Redux [1] is not price gouging. You can
| basically just think of the GPU markup as a builder fee. They
| are incredibly slow to ship but the lead time is something like
| a month which beats your 6 months. At this point, it would take
| bitcoin dropping below 10k for the market not to be silly.
|
| [1] - https://buildredux.com/
| Mizza wrote:
| You know what, this might actually be the guy. Good tip. It's
| a bummer to pay for a Windows license I don't want, but the
| fee for that is less than the markup I'd pay to some scalper
| just to get the card.
| hervature wrote:
| If you don't want Windows, you can remove it!
| KerrAvon wrote:
| Isn't it Ethereum driving the GPU shortage? I thought Bitcoin
| was not really profitable without an ASIC rig.
| umvi wrote:
| Have you considered renting cloud GPUs by the minute? You can
| rent some pretty powerful GPUs from cloud providers (i.e.
| https://cloud.google.com/compute/docs/gpus)
| whymauri wrote:
| What about moving to the cloud? Something like CoLab?
| Mizza wrote:
| Yeah, I guess I could go down that route, I've used the AWS
| Gx instances for projects before, but this dataset would
| justttt fit in memory for a 3080, which really simplified the
| rest of the code, and the speed of iteration, and, at the end
| of the day, quite frankly I just want one. I'll do more weird
| stuff if I don't have the meter of how much I'm paying to
| Jeff Bezos running in my head every time I run an experiment.
| tehsauce wrote:
| vast.ai, nothing else is remotely as cheap
| kukx wrote:
| The price is great, the downside is that you do not know
| whether the server owner reads your data. The "jobs" run in a
| Docker container on somebody's machine.
| fock wrote:
| I wonder why you've not teamed up with some uni-lab, they
| usually have some hardware and also some free labor if you
| share credits. A single GPU also means, whatever your idea, it
| probably would have finished already on a CPU ;).
| munchbunny wrote:
| If you're willing to pay scalper prices, there's a relatively
| consistent availability. If you're looking for closer to MSRP,
| they're in short supply and your choices are either waiting
| lists or racing other people for online restocks. I got a 3080
| a month ago only after waiting on EVGA's wait list for just
| over a year.
|
| Why do you need a 3070/3080 specifically? If it's to run
| something like Tensorflow or CUDA code more generally, could
| you do it with an older card, or the more available 3060s?
| chaosbutters314 wrote:
| just bought one with a PC from falcon northwest. Not sure about
| buying it standalone but they sell them with their PCs
| cheonic8492 wrote:
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