Can just anyone enter this challenge, or do you have to be part of a major institution?
AlphaFold: a solution to a 50-year-old grand challenge in biology
271–280 of 683 posts
Re: AlphaFold: a solution to a 50-year-old grand challenge in biology
#272No, they didn't. They approximated a solution to protein folding. The two are different concepts -- this isn't the typical HN pedantry. "Solving" the problem would entail developing an interpretable algorithm for taking a string of amino acids and determining the 3D structure once folded. Approximating a solution would entail simulating that algorithm, which is what their neural network is doing. It is of course usua…
The distinction you're making between "solved" and "closely approximated" makes logical sense to me. However, if I'm interpreting the AlphaFold results correctly, this distinction isn't practically significant, right?
If you can approximate an algorithm with error that is "below the threshold that is considered acceptable in experimental measurements" (to quote another HN comment), then you have something as good as the algorithm itself for all intents and purposes.
Therefore the use of the word "solve" doesn't qualify as hype-rhetoric, and the distinction you're making does seem somewhat pedantic (even if technically true).
(I'm speaking as someone with only the tiniest amount of stats/ML experience, so I could be totally wrong!)
Re: AlphaFold: a solution to a 50-year-old grand challenge in biology
#273 Can just anyone enter this challenge, or do you have to be part of a major institution?
Re: AlphaFold: a solution to a 50-year-old grand challenge in biology
#274Curious, what are the sizes of the training and validation/test datasets (number of structures)?
Re: AlphaFold: a solution to a 50-year-old grand challenge in biology
#275Two years ago, after DeepMind submitted its first set of predictions to CASP (Critical Assessment of protein Structure Prediction), Mohammed AlQuraishi, an expert in the field, asked, "What just happened?" https://moalquraishi.wordpress.com/2018/12/09/alphafold-casp... Now that the problem of static protein structure prediction has been solved (prediction errors are below the threshold that is considered acceptable i…
AlQuraishi's tweet [0] about this: > CASP14 #s just came out and they’re astounding—DeepMind looks to have solved protein structure prediction. Median GDT_TS went from 68.5 (CASP13) to 92.4!!!! Cf. their 2nd best CASP13 struct scored 92.8 (out of 100). Median RMSD is 2.1Å. I think it's over https://predictioncenter.org/casp14/zscores_final.cgi [0]: https://twitter.com/MoAlQuraishi/status/1333383634649313280
What does that Å mean? Never seen our letter been used in a scientific context.
Re: AlphaFold: a solution to a 50-year-old grand challenge in biology
#276Earlier quoted context omitted.
AlQuraishi's tweet [0] about this: > CASP14 #s just came out and they’re astounding—DeepMind looks to have solved protein structure prediction. Median GDT_TS went from 68.5 (CASP13) to 92.4!!!! Cf. their 2nd best CASP13 struct scored 92.8 (out of 100). Median RMSD is 2.1Å. I think it's over https://predictioncenter.org/casp14/zscores_final.cgi [0]: https://twitter.com/MoAlQuraishi/status/1333383634649313280
What does that Å mean? Never seen our letter been used in a scientific context.
Ångström, a length unit. 1 Å = 0.1 nm.
Re: AlphaFold: a solution to a 50-year-old grand challenge in biology
#277Exiting time
Re: AlphaFold: a solution to a 50-year-old grand challenge in biology
#278Earlier quoted context omitted.
Ok, then this is about enzymes which do not yet exist in the organism. You could then modify bacteria so they produce this enzyme and feed on plastic, I see.
Plastic degradation is a thing already in naturally occurring bacteria that evolved a PETase: https://science.sciencemag.org/content/351/6278/1196/tab-fig...
But producing fuel as the fellow suggested would then be another function to be added to the bacterium; and maybe it should work on different kinds of plastic.
Re: AlphaFold: a solution to a 50-year-old grand challenge in biology
#279Earlier quoted context omitted.
AlQuraishi's tweet [0] about this: > CASP14 #s just came out and they’re astounding—DeepMind looks to have solved protein structure prediction. Median GDT_TS went from 68.5 (CASP13) to 92.4!!!! Cf. their 2nd best CASP13 struct scored 92.8 (out of 100). Median RMSD is 2.1Å. I think it's over https://predictioncenter.org/casp14/zscores_final.cgi [0]: https://twitter.com/MoAlQuraishi/status/1333383634649313280
What does that Å mean? Never seen our letter been used in a scientific context.
It's the symbol for Angstrom, a unit of length 10^-10m https://en.wikipedia.org/wiki/Angstrom
Re: AlphaFold: a solution to a 50-year-old grand challenge in biology
#280Not knowing a lot about biotechnology, I read the article and it sounds great, but how big is this as a gamechanger? Can someone comment on how big are the implications of this in, let’s say, 5 years from now, on day to day life? Does this mean that biotech is going to explode? Or just that drugs will come to market faster, perhaps cheaper for rare diseases, but from the same industry structure as always?
One young lady I knew worked on neural algos recognition of X-ray images. They always had single digit, bizarre artifacts, where the program can't sometimes recognise the very data it was trained on with most minute differences. Other artifact was that the most "stereotypical cases" were least reliably recognised, and they hot a lot of flak for screwed up live demos, where a radiologist put a very, very obvious tumor…
I agree. The failures have to be explicable if we are to trust a model.