Live data from Hacker News

AlphaFold: a solution to a 50-year-old grand challenge in biology

deepmind.com

541–550 of 683 posts

Re: AlphaFold: a solution to a 50-year-old grand challenge in biology

#541
What size was the test set?

From what I gather, training was done on 170,000 Amino Acids (features) and the resultant protein structure (labels). This is out of 200 million possible proteins.

How many examples were in the test set?

EDIT: Looks like N=100 for test set: “Entrants get amino acid sequences for about 100 proteins whose structures are not known” https://www.sciencemag.org/news/2020/11/game-has-changed-ai-...

Re: AlphaFold: a solution to a 50-year-old grand challenge in biology

#542

Earlier quoted context omitted.

It also makes one reconsider the notion that monopolies are entirely bad. This essentially appears to be a vanity project for Google. Though of course they'll benefit from it in many ways, but it's not like they're doing this as the core product of their service. It's a pretty awesome achievement.

You've just describe why many Socialists 100 years were very skeptical of anti-trust as trying to sacrifice modernity to proper up a romanticized notion of the past as disaggregated pure-petit-bourgeois capitalism. Really not that different than the critism of the Luddites 100 years before that. See https://ilr.law.uiowa.edu/print/volume-100-issue-5/all-i-rea...

This line of argument reminds me of Haldane's point that economic planning can often work for the same reasons why large corporations and monopolies often work well too.

Re: AlphaFold: a solution to a 50-year-old grand challenge in biology

#543

Earlier quoted context omitted.

Well, this relies on the assumption that a God also inherently exists outside of time and space, which is debatable even among religious scholars.

I just had a discussion with a friend about this! It's indeed a very difficult question. We ended on the conclusion that God can't possibly exist outside of time and space in the Abrahamic tradition because he precedes the creation of the Universe, but I'm sure there's a twist we missed somewhere.

“God is dead” Marilyn Manson.

Re: AlphaFold: a solution to a 50-year-old grand challenge in biology

#544

What size was the test set? From what I gather, training was done on 170,000 Amino Acids (features) and the resultant protein structure (labels). This is out of 200 million possible proteins. How many examples were in the test set? EDIT: Looks like N=100 for test set: “Entrants get amino acid sequences for about 100 proteins whose structures are not known” https://www.sciencemag.org/news/2020/11/game-has-changed-ai-.…

As usual with ML, I now wonder how “similar” the test set is to the training set, compared to the examples that are neither in the training set, nor the test set:

TODO: 200 million - 170,000 training - 100 test ~= 199.8 million proteins

Re: AlphaFold: a solution to a 50-year-old grand challenge in biology

#545
post #413

What happens when AI is better at everything measurable than humans? Better at conversation. Better at making people laugh, and generate attraction or other emotions, better at motivating them, and organizing movements, etc. Clearly we are not ready for such an efficient system... it would be a big disruption to all human organizations and relations. It would start with Twitter botnets and directing sentiment.

They still suck pretty bad at many physical things. Bipedal robots are a joke. They also dent and rust. It'll be that way for a while. They don't reproduce.

But virtual world, say they're better at math. Say they prove all the Clay Millennium Problems. Say they go way beyond those problems and produce some math far beyond human's ability to understand it.

I've been thinking about that for a while and have decided it's fine. Math as a profession will still exist. Fact is, there's already a proof for everything mathematicians are investigating (or a proof that there's no proof, recursively), out there somewhere. Mathematicians are just searching for it, so that it can be understood and translated to human language. The fact that AI already knows the answers doesn't mean that human mathematicians are useless: they are still required to uncover the meaning of these results and translate them into human language. AI then is still just a tool that mathematicians use to help them in their search. Similar to how biologists will use AlphaFold. I guess.

Or... https://imgur.com/gallery/9KWrH#sv05qpF

Re: AlphaFold: a solution to a 50-year-old grand challenge in biology

#546
post #198

12-13 years ago in a classroom the professor for my intro to bioinformatics class said if you were to solve this problem, you would win a Nobel prize. Congrats to the team! What an achievement.

They will definitely win the Nobel for this.

Re: AlphaFold: a solution to a 50-year-old grand challenge in biology

#547

Earlier quoted context omitted.

"A sufficiently advanced Artificial Intelligence would be indistinguishable from God." (Way Of The Future - AI Church)

That would require the AI to exist outside of time and space.

From the perspective of a human observer, an AI more or less does exist outside of space and time. It can travel at the speed of light through radio broadcast (with some caveats). It can spend the equivalent of a lifetime learning a topic in just a few days.

Re: AlphaFold: a solution to a 50-year-old grand challenge in biology

#548
The vast majority of structures in the protein data bank are determined by crystallography, which involves putting the protein in a chemical cocktail that causes it to crystallize. The cocktail is very different to the chemical environment in which the protein functions, so an open question is whether the protein structure determined by crystallography (and hence learned by AlphaFold) is representative of the structure in it's natural environment.

It would be very interesting if there was a way to use computational techniques to go beyond what crystallography and other experimental techniques (Cryo) can accomplish and determine the protein structure in it's true biological setting. Some research into experimental methods for this include high power X-ray pulses.

Nonetheless, impressive work!

Re: AlphaFold: a solution to a 50-year-old grand challenge in biology

#549

Earlier quoted context omitted.

Well, this relies on the assumption that a God also inherently exists outside of time and space, which is debatable even among religious scholars.

I just had a discussion with a friend about this! It's indeed a very difficult question. We ended on the conclusion that God can't possibly exist outside of time and space in the Abrahamic tradition because he precedes the creation of the Universe, but I'm sure there's a twist we missed somewhere.

I'm confused, because that seems backwards to me? How can He exist within time and space if He created the universe (including time and space)?

Re: AlphaFold: a solution to a 50-year-old grand challenge in biology

#550
post #543

Earlier quoted context omitted.

I just had a discussion with a friend about this! It's indeed a very difficult question. We ended on the conclusion that God can't possibly exist outside of time and space in the Abrahamic tradition because he precedes the creation of the Universe, but I'm sure there's a twist we missed somewhere.

“God is dead” Marilyn Manson.

Hm. Nietzsche would seem to be in the lead there.
Post reply on HN