[Tech] AlphaFold - Demis Hassabis

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the CEO and co-founder of DeepMind explains how they solved protein folding.
From Lex Fridman: https://lexfridman.com/demis-hassabis/
Transcripts from Karpathy's https://karpathy.ai/lexicap/0299-large.html
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So let's go to the basic building blocks of biology
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that I think is another angle at which you can start
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to understand the human mind, the human body,
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which is quite fascinating,
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which is from the basic building blocks,
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start to simulate, start to model
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how from those building blocks,
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you can construct bigger and bigger, more complex systems,
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maybe one day the entirety of the human biology.
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So here's another problem that thought
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to be impossible to solve, which is protein folding.
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And Alpha Fold or specifically Alpha Fold 2 did just that.
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It solved protein folding.
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I think it's one of the biggest breakthroughs,
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certainly in the history of structural biology,
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but in general in science,
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maybe from a high level, what is it and how does it work?
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And then we can ask some fascinating questions after.
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Sure.
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So maybe to explain it to people not familiar
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with protein folding is, you know,
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first of all, explain proteins, which is, you know,
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proteins are essential to all life.
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Every function in your body depends on proteins.
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Sometimes they're called the workhorses of biology.
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And if you look into them and I've, you know,
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obviously as part of Alpha Fold,
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I've been researching proteins and structural biology
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for the last few years, you know,
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they're amazing little bio nano machines proteins.
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They're incredible if you actually watch little videos
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of how they work, animations of how they work.
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And proteins are specified by their genetic sequence
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called the amino acid sequence.
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So you can think of it as their genetic makeup.
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And then in the body in nature,
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they fold up into a 3D structure.
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So you can think of it as a string of beads
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and then they fold up into a ball.
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Now, the key thing is you want to know
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what that 3D structure is because the structure,
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the 3D structure of a protein is what helps to determine
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what does it do, the function it does in your body.
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And also if you're interested in drugs or disease,
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you need to understand that 3D structure
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because if you want to target something
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with a drug compound about to block something
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the protein's doing, you need to understand
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where it's gonna bind on the surface of the protein.
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So obviously in order to do that,
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you need to understand the 3D structure.
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So the structure is mapped to the function.
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The structure is mapped to the function
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and the structure is obviously somehow specified
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by the amino acid sequence.
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And that's the, in essence, the protein folding problem is,
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can you just from the amino acid sequence,
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the one dimensional string of letters,
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can you immediately computationally predict
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the 3D structure?
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And this has been a grand challenge in biology
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for over 50 years.
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So I think it was first articulated by Christian Anfinsen,
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a Nobel prize winner in 1972,
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as part of his Nobel prize winning lecture.
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And he just speculated this should be possible
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to go from the amino acid sequence to the 3D structure,
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but he didn't say how.
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So it's been described to me as equivalent
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to Fermat's last theorem, but for biology.
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You should, as somebody that very well might win
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the Nobel prize in the future.
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But outside of that, you should do more
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of that kind of thing.
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In the margin, just put random things
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that will take like 200 years to solve.
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Set people off for 200 years.
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It should be possible.
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And just don't give any details.
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Exactly.
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I think everyone exactly should be,
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I'll have to remember that for future.
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So yeah, so he set off, you know,
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with this one throwaway remark, just like Fermat,
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you know, he set off this whole 50 year field really
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of computational biology.
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And they had, you know, they got stuck.
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They hadn't really got very far with doing this.
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And until now, until AlphaFold came along,
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this is done experimentally, right?
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Very painstakingly.
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So the rule of thumb is, and you have to like
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crystallize the protein, which is really difficult.
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Some proteins can't be crystallized like membrane proteins.
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And then you have to use very expensive electron microscopes
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or X ray crystallography machines.
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Really painstaking work to get the 3D structure
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and visualize the 3D structure.
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So the rule of thumb in experimental biology
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is that it takes one PhD student,
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their entire PhD to do one protein.
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And with AlphaFold 2, we were able to predict
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the 3D structure in a matter of seconds.
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And so we were, you know, over Christmas,
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we did the whole human proteome
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or every protein in the human body or 20,000 proteins.
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So the human proteomes like the equivalent
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of the human genome, but on protein space.
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And sort of revolutionized really
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what a structural biologist can do.
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Because now they don't have to worry
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about these painstaking experimental,
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should they put all of that effort in or not?
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They can almost just look up the structure
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of their proteins like a Google search.
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And so there's a data set on which it's trained
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and how to map this amino acid sequence.
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First of all, it's incredible that a protein,
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this little chemical computer is able to do
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that computation itself in some kind of distributed way
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and do it very quickly.
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That's a weird thing.
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And they evolve that way because, you know,
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in the beginning, I mean, that's a great invention,
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just the protein itself.
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And then there's, I think, probably a history
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of like they evolved to have many of these proteins
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and those proteins figure out how to be computers themselves
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in such a way that you can create structures
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that can interact in complexes with each other
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in order to form high level functions.
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I mean, it's a weird system that they figured it out.
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Well, for sure.
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I mean, you know, maybe we should talk
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about the origins of life too,
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but proteins themselves, I think are magical
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and incredible, as I said, little bio nano machines.
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And actually Leventhal, who was another scientist,
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a contemporary of Amphinson, he coined this Leventhal,
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what became known as Leventhal's paradox,
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which is exactly what you're saying.
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He calculated roughly an average protein,
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which is maybe 2000 amino acids base as long,
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is can fold in maybe 10 to the power 300
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different confirmations.
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So there's 10 to the power 300 different ways
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that protein could fold up.
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And yet somehow in nature, physics solves this,
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solves this in a matter of milliseconds.
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So proteins fold up in your body in, you know,
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sometimes in fractions of a second.
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So physics is somehow solving that search problem.
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And just to be clear, in many of these cases,
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maybe you can correct me if I'm wrong,
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there's often a unique way for that sequence to form itself.
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So among that huge number of possibilities,
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it figures out a way how to stably,
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in some cases there might be a misfunction, so on,
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which leads to a lot of the disorders and stuff like that.
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But most of the time it's a unique mapping
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and that unique mapping is not obvious.
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No, exactly.
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Which is what the problem is.
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Exactly, so there's a unique mapping usually in a healthy,
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if it's healthy, and as you say in disease,
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so for example, Alzheimer's,
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one conjecture is that it's because of misfolded protein,
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a protein that folds in the wrong way, amyloid beta protein.
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So, and then because it folds in the wrong way,
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it gets tangled up, right, in your neurons.
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So it's super important to understand
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both healthy functioning and also disease
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is to understand, you know, what these things are doing
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and how they're structuring.
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Of course, the next step is sometimes proteins change shape
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when they interact with something.
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So they're not just static necessarily in biology.
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Maybe you can give some interesting,
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so beautiful things to you about these early days
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of AlphaFold, of solving this problem,
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because unlike games, this is real physical systems
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that are less amenable to self play type of mechanisms.
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Sure.
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The size of the data set is smaller
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than you might otherwise like,
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so you have to be very clever about certain things.
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Is there something you could speak to
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what was very hard to solve
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and what are some beautiful aspects about the solution?
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Yeah, I would say AlphaFold is the most complex
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and also probably most meaningful system
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we've built so far.
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So it's been an amazing time actually in the last,
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you know, two, three years to see that come through
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because as we talked about earlier, you know,
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games is what we started on
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building things like AlphaGo and AlphaZero,
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but really the ultimate goal was to,
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not just to crack games,
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it was just to build,
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use them to bootstrap general learning systems
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we could then apply to real world challenges.
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Specifically, my passion is scientific challenges
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like protein folding.
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And then AlphaFold of course
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is our first big proof point of that.
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And so, you know, in terms of the data
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and the amount of innovations that had to go into it,
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we, you know, it was like
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more than 30 different component algorithms
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needed to be put together to crack the protein folding.
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I think some of the big innovations were that
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kind of building in some hard coded constraints
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around physics and evolutionary biology
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to constrain sort of things like the bond angles
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in the protein and things like that,
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a lot, but not to impact the learning system.
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So still allowing the system to be able to learn
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the physics itself from the examples that we had.
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And the examples, as you say,
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there are only about 150,000 proteins,
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even after 40 years of experimental biology,
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only around 150,000 proteins have been,
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the structures have been found out about.
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So that was our training set,
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which is much less than normally we would like to use,
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but using various tricks, things like self distillation.
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So actually using AlphaFold predictions,
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some of the best predictions
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that it thought was highly confident in,
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we put them back into the training set, right?
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To make the training set bigger,
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that was critical to AlphaFold working.
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So there was actually a huge number
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of different innovations like that,
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that were required to ultimately crack the problem.
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AlphaFold one, what it produced was a distrogram.
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So a kind of a matrix of the pairwise distances
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between all of the molecules in the protein.
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And then there had to be a separate optimization process
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to create the 3D structure.
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And what we did for AlphaFold two
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is make it truly end to end.
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So we went straight from the amino acid sequence of bases
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to the 3D structure directly
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without going through this intermediate step.
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And in machine learning, what we've always found is
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that the more end to end you can make it,
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the better the system.
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And it's probably because in the end,
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the system's better at learning what the constraints are
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than we are as the human designers of specifying it.
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So anytime you can let it flow end to end
00:47:54.040">link |
00:47:54.040 
and actually just generate what it is
00:47:55.400">link |
00:47:55.400 
you're really looking for, in this case, the 3D structure,
00:47:58.440">link |
00:47:58.440 
you're better off than having this intermediate step,
00:48:00.560">link |
00:48:00.560 
which you then have to handcraft the next step for.
00:48:03.360">link |
00:48:03.360 
So it's better to let the gradients and the learning
00:48:06.160">link |
00:48:06.160 
flow all the way through the system from the end point,
00:48:09.000">link |
00:48:09.000 
the end output you want to the inputs.
00:48:10.880">link |
00:48:10.880 
So that's a good way to start on a new problem.
00:48:13.040">link |
00:48:13.040 
Handcraft a bunch of stuff,
00:48:14.360">link |
00:48:14.360 
add a bunch of manual constraints
00:48:16.640">link |
00:48:16.640 
with a small end to end learning piece
00:48:18.640">link |
00:48:18.640 
or a small learning piece and grow that learning piece
00:48:21.560">link |
00:48:21.560 
until it consumes the whole thing.
00:48:22.840">link |
00:48:22.840 
That's right.
00:48:23.680">link |
00:48:23.680 
And so you can also see,
00:48:25.320">link |
00:48:25.320 
this is a bit of a method we've developed
00:48:26.960">link |
00:48:26.960 
over doing many sort of successful alpha,
00:48:29.640">link |
00:48:29.640 
we call them alpha X projects, right?
00:48:32.200">link |
00:48:32.200 
And the easiest way to see that is the evolution
00:48:34.600">link |
00:48:34.600 
of alpha go to alpha zero.
00:48:36.720">link |
00:48:36.720 
So alpha go was a learning system,
00:48:39.640">link |
00:48:39.640 
but it was specifically trained to only play go, right?
00:48:42.280">link |
00:48:42.280 
So, and what we wanted to do with first version of alpha go
00:48:45.360">link |
00:48:45.360 
is just get to world champion performance
00:48:47.520">link |
00:48:47.520 
no matter how we did it, right?
00:48:49.200">link |
00:48:49.200 
And then of course, alpha go zero,
00:48:51.400">link |
00:48:51.400 
we remove the need to use human games as a starting point,
00:48:55.280">link |
00:48:55.280 
right?
00:48:56.120">link |
00:48:56.120 
So it could just play against itself
00:48:57.960">link |
00:48:57.960 
from random starting point from the beginning.
00:49:00.280">link |
00:49:00.280 
So that removed the need for human knowledge about go.
00:49:03.720">link |
00:49:03.720 
And then finally alpha zero then generalized it
00:49:05.960">link |
00:49:05.960 
so that any things we had in there, the system,
00:49:08.920">link |
00:49:08.920 
including things like symmetry of the go board were removed.
00:49:12.240">link |
00:49:12.240 
So the alpha zero could play from scratch
00:49:14.600">link |
00:49:14.600 
any two player game and then mu zero,
00:49:16.440">link |
00:49:16.440 
which is the final, our latest version
00:49:18.360">link |
00:49:18.360 
of that set of things was then extending it
00:49:20.680">link |
00:49:20.680 
so that you didn't even have to give it
00:49:22.120">link |
00:49:22.120 
the rules of the game.
00:49:23.200">link |
00:49:23.200 
It would learn that for itself.
00:49:24.880">link |
00:49:24.880 
So it could also deal with computer games
00:49:26.600">link |
00:49:26.600 
as well as board games.
00:49:27.760">link |
00:49:27.760 
So that line of alpha go, alpha go zero, alpha zero,
00:49:30.400">link |
00:49:30.400 
mu zero, that's the full trajectory
00:49:33.480">link |
00:49:33.480 
of what you can take from imitation learning
00:49:37.200">link |
00:49:37.200 
to full self supervised learning.
00:49:40.440">link |
00:49:40.440 
Yeah, exactly.
00:49:41.640">link |
00:49:41.640 
And learning the entire structure
00:49:44.720">link |
00:49:44.720 
of the environment you're put in from scratch, right?
00:49:47.640">link |
00:49:47.640 
And bootstrapping it through self play yourself.
00:49:51.840">link |
00:49:51.840 
But the thing is it would have been impossible, I think,
00:49:53.720">link |
00:49:53.720 
or very hard for us to build alpha zero
00:49:55.960">link |
00:49:55.960 
or mu zero first out of the box.
00:49:58.600">link |
00:49:58.600 
Even psychologically, because you have to believe
00:50:01.400">link |
00:50:01.400 
in yourself for a very long time.
00:50:03.040">link |
00:50:03.040 
You're constantly dealing with doubt
00:50:04.640">link |
00:50:04.640 
because a lot of people say that it's impossible.
00:50:06.680">link |
00:50:06.680 
Exactly, so it's hard enough just to do go.
00:50:08.640">link |
00:50:08.640 
As you were saying, everyone thought that was impossible
00:50:10.920">link |
00:50:10.920 
or at least a decade away from when we did it
00:50:14.160">link |
00:50:14.160 
back in 2015, 2016.
00:50:17.320">link |
00:50:17.320 
And so yes, it would have been psychologically
00:50:20.960">link |
00:50:20.960 
probably very difficult as well as the fact
00:50:22.960">link |
00:50:22.960 
that of course we learn a lot by building alpha go first.
00:50:26.400">link |
00:50:26.400 
Right, so I think this is why I call AI
00:50:28.520">link |
00:50:28.520 
an engineering science.
00:50:29.880">link |
00:50:29.880 
It's one of the most fascinating science disciplines,
00:50:32.280">link |
00:50:32.280 
but it's also an engineering science in the sense
00:50:34.200">link |
00:50:34.200 
that unlike natural sciences, the phenomenon you're studying
00:50:38.200">link |
00:50:38.200 
doesn't exist out in nature.
00:50:39.440">link |
00:50:39.440 
You have to build it first.
00:50:40.880">link |
00:50:40.880 
So you have to build the artifact first,
00:50:42.480">link |
00:50:42.480 
and then you can study and pull it apart and how it works.
[Tech] AlphaFold - Demis Hassabis
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