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

deepmind.com

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

#631

Post by complexmango »

sudosysgen wrote: post #586
drdeca wrote: post #549

Earlier quoted context omitted.

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)?

The conclusion we came to is that such a being would have to have it's own, metaphysically superior, time and space, and our time would be a subtime of it as well as our space would be a subspace of it. The concept of a being subject to causality presupposes something akin to time.

No. The concept is that there is an infinite, indescribable void from which emerges consciousness manifested in matter.

And conscious matter creates universes constantly, that appear out of the void, hence creating time and space. This would also imply that its possible not only to change the future, but also the past.

The masters advise, however, that these are distractions and that the journey inevitably leads to experiencing the void itself, hence stepping out of time and space, and consciously experiencing any aspect of time and space and consciousness one wishes to, while always remembering that one is beyond it.

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

#632

Post by lambdamore »

softwaredoug wrote: post #487
cs702 wrote: post #118

Two 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…

> I don’t think we would do ourselves a service by not recognizing that what just happened presents a serious indictment of academic science. Much like other fields, I do begin to question the academic structure to making advances. It appears something is rotten in the state of academia. Oddly it's academia doing incremental improvements to existing methods but industry making novel leaps and bounds... The other majo…

Deepmind does not foster its future PhD, but, yes, they offer a better rewarding environment for those PhDs to flourish after they get the basic training.

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

#633

Post by dqpb »

complexmango wrote: post #630
drusepth wrote: post #535

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.

There is an in depth explanation in Zen, Buddhism and Hinduism of this phenomenon. I would suggest reading anything by Nisargadatta Maharaj, who expanded on this in detail to questioners from all over the world who came to his humble dwellings in a Mumbai tenement to observe him. I’d suggest starting with ‘I am That’, available on Amazon, iBooks etc. He claimed to be outside of time and space himself.

Anybody can say anything

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

#634

Post by Ar-Curunir »

codingslave wrote: post #497
softwaredoug wrote: post #487

Earlier quoted context omitted.

> I don’t think we would do ourselves a service by not recognizing that what just happened presents a serious indictment of academic science. Much like other fields, I do begin to question the academic structure to making advances. It appears something is rotten in the state of academia. Oddly it's academia doing incremental improvements to existing methods but industry making novel leaps and bounds... The other majo…

Academia keeps employing people who have done well in classes and within fine bounds. Its a careerist track. Industry cares about results, its more meritocratic

I wish people would stop making reductive and false statements. Life isn't this simple.

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

#635

Post by drdeca »

sudosysgen wrote: post #586
drdeca wrote: post #549

Earlier quoted context omitted.

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)?

The conclusion we came to is that such a being would have to have it's own, metaphysically superior, time and space, and our time would be a subtime of it as well as our space would be a subspace of it. The concept of a being subject to causality presupposes something akin to time.

Ah, ok. My thought is to distinguish between “logically prior” or “causally prior” or something like that, and “prior in time”, But, I suppose one might consider those things to be a kind of “time” in some sense.

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

#636

Post by gamegoblin »

CJefferson wrote: post #607
gamegoblin wrote: post #539

Earlier quoted context omitted.

The "dodgy experiments" (setting the per-turn computation time to a fixed value) in the chess system were only in the pre-print. In the actual publication, they allowed for full time control of the most up-to-date version of stockfish.

I will admit I may not have kept up to date. Did they also restore the opening and endings, and use the latest Stockfish?

Yes, and then Leela Chess Zero, an open source implementation of AlphaZero, beat the latest Stockfish in the de facto engine championship (TCEC). Since AlphaZero, the TCEC finals have been traded back and forth between Stockfish and LCZero.

This last season, Stockfish won by using NNUE, a neural network based evaluation function.

https://en.wikipedia.org/wiki/Top_Chess_Engine_Championship#...

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

#637

Post by snovv_crash »

adw wrote: post #575
Polygator wrote: post #573

Earlier quoted context omitted.

Not really. Using a statistical approach to text modelling, specifically using Markov Chains, was proposed by Shannon in 1948. But yeah, there's a point in the 2000s where generative grammar/ symbolic approaches were pretty much left behind by NN methods. When we discuss Google's input in NLP, the most important contribution is certainly the "Attention is all you Need" paper, which paved the way for BERT and GTP (Alp…

> generative grammar/ symbolic approaches were pretty much left behind by NN methods Which is the same thing as hand-engineered feature stacks being left behind in vision problems, really. The story in every field is more or less "you're not clever enough to engineer good features"; "you might be clever enough to define good symmetries for the feature space in which the features live... maybe" (convolutional neural n…

The hand generated features are still superior for SfM style problems, where the geometry is well defined but would need to be learned by the NN from scratch.

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

#639

Post by drdeca »

_0w8t wrote: post #613
sudosysgen wrote: post #540

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.

One cannot define the notion of “exist” without explicitly or implicitly referring to time. So the question of existence without time reduces to absurdity like can one exist without existing?

Huh? How is it necessary to speak of time when discussing whether there exists e.g. a solution to a set of equations?

Or whether there is a finite simple group with given number of elements, or the like?

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

#640

Post by kovek »

dang wrote: post #516
nathancahill wrote: post #495

Earlier quoted context omitted.

Also, what do the traffic stats look like for the second/third pages of big threads like this one? Pretty steep falloff?

I assume so, but haven't looked recently. I'll try to do that and report back here later. Feel free to ping me at hn@ycombinator.com if I forget. Edit: ok, for this thread so far, 95% of views are page 1, 4% are page 2, 1% are page 3. For https://news.ycombinator.com/item?id=25065026 , which had a "more pages" comment at the top: 93% of views were page 1, 5% page 2, 2% viewed page 3. For https://news.ycombinator.com/…

If you are fine serving more data, you could trigger a "More" automatically when the user minimizes a comment thread, and add the "More" comments to the bottom of the page?

Also, to encourage people exploring "More" comments, maybe some comments inside the 2-3 megathreads showing in the first page can be minimized at first?

I wonder what are the thoughts on these design. I really like how Hacker News is designed, thank you!

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