They trained on 170k sequences/ structures/ proteins, each sequence has 10s to 100s or even 1000s amino acids. Structure is much more conserved than sequence. Out of the 100 targets, roughly 1/4th have no similarity to known structures, so there shouldn't be an overlap for those with the training set. They did very well on those targets.
There are different categories of samples, namely FM and TBM targets. FM targets don't have any similarity to known structures. Roughly a quarter were FM targets. I think the more interesting thing to look at is the size of the multiple sequence alignments (MSAs) which is the basis of this and essentially all methods. They seem to do very well with few MSAs, which bodes well for other targets, although there are families of proteins with few MSAs.
There are other experimental methods that are much cheaper that can be used to assist validation. Also the models look damn impressive, even down to the sidechain packing.
How do you define enormous? "It uses approximately 128 TPUv3 cores (roughly equivalent to ~100-200 GPUs) run over a few weeks". Also last time it took about a year for good replications to pop up.
A year is a fast time to replication in many scientific fields.
While substantial, the resources here are well within reach of many labs, research institutes, and organizations. For this result this big, I'd guess we'll have 2-6 additional implementations in the next 18 months. The problem has been 'open' for 40+ years, so that's lightening fast!
A couple of hundred GPU's is well within the reach of many even moderately well heeled research institutes. It'd seem that about 3 weeks of compute time with 128 TPU v3's would be about $170,311.68.
But of course that cost would only be for the final model. Anyway, I think I am just living in a different world... :-) We could never compete with that
Yah, big grant money. Now the grad students programming the open source clones will only make approximately $0.56, or 4.2 Ramen packs, for their effort. ;)
Also with keeping in mind that once a good open source model is available, researchers with less resources can still use it to fine tune and get new results for far cheaper than training a new model from scratch.
A lot of labs have access to the various strategic supercomputers of the USA.
Ex: Summit has 27,648 V100 GPUs (and those V100s have Tensor units). If you're saying that only 200 GPUs are needed to replicate the experiment, that doesn't even use up 1% of Summit's available utilization.
The targets are completely unknown. They were experimentally solved, but not submitted to the Protein Data Bank. You basically get a target every day (meaning sequence of amino acids) and then depending on the category, you have three days to predict it (I think upto two weeks for "human" servers). In the modeling category they participated in, you can submit 5 models. A model is a fully predicted 3d structure of the protein. The targets are mostly independent. Some targets were split over a few days. But in principle, a target on day X has no connection to a target on day Y. The targets have varying difficulty. There are two categories: TBM (templated based) and FM (free modeling). You don't know which protein corresponds to which category, you can just guess by looking at the available template data. They focused on FM targets. Meaning there are no homologous available. It's hard to say how good of an indicator the results are. Looking at the contact prediction results, many methods are getting very good at constructing MSAs (gathering similar sequences). We already saw this at CASP12 - I think the FM targets are getting "easier" in that sense. There is basically zero feedback throughout the whole competition. Some targets are released after the deadline (because of publications), but in general, you don't know anything until the CASP meeting, which currently takes place. The competition ended in August.
Did the supplement contain pepper? AFAIK you need to consume turmeric together with black pepper to make it effective (blocks something in the liver IIRC). Maybe that was the reason?
I used to get a lot of sinus infections, to remedy this, I drank for an extended period of my life cooled "onion juice" (onion + water + honey, cooked for ~1h). My whole family was disgusted by it, but I somehow enjoyed it.
I'm very interested in fasting. I have been doing IF for 4 months and it works out great. Has anyone experience with prolonged fasting (3 days+) and auto immune diseases, specifically Alopecia?
