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At the last AI Safety reading group meeting, we discussed the Decision Theory section of MIRI's Embedded Agency post.
We had some confusion over the idea of an agent being 'bigger than the world' or 'smaller than the world'. This is a braindump of my thoughts on the spectrum of 'small' vs 'big' worlds.

It's a Small World
At one extreme, there are problems that are completely computable, such that the agent can hold a complete and precise map of the game 'in their head'. Examples include very simple discrete games like tic-tac-toe. You can also think of simple utility-maximization problems you'd see in basic microeconomics, optimizing a differentiable f(x1,x2) subject to differentiable constraints g(x1,x2) = C, h(x1,x2) = D. (At the continuous limit, where f, g, h become integrals over a continuous variable x, this is solved by one of my favorite tools, the Euler-Lagrange equation.)

At first blush, this class of problems seems pretty irrelevant compared to those that, yknow, require actual intellectual work. On reflection, that's not completely true. What's in this class is determined by what we have tractable algorithms for, so it's widened over time as theory and computing power have advanced. Also, difficult problems are often solved in part by approximating them as a solved-out problem. (Example: generate a game tree N moves out, evaluate game-states at time N, then choose the best move the same way you would in tic-tac-toe.)

A Little Bit Taller
Moving up the ladder, we have worlds that we can construct good representations or approximate solutions for. Often a solution is found through iteration over approximate solutions, with the convergence to some 'good' solution usually only empirically supported. At the simpler end, there may be theoretical convergence guarantees. Examples: finding the thermodynamic distribution of a molecular system through molecular modeling; playing chess or Go; playing Atari games.

Lots of useful problems lie around here. If I knew more computational complexity stuff, there would probably be useful things to say about polynomial vs exponential time.

Playing Ball
Now we introduce the second aspect of 'bigness': how good of a representation the world has of the agent. At the simplest level, the world may be able to approximate the agent as aiming for some fixed (i.e. non-agent-dependent) utility function. For example, most chess or Go algorithms will implicitly assume the agent is optimizing for the algorithm's own position-evaluation function. This could also matter when the agent plays against imperfect players of solvable games like Tic-Tac-Toe. In either case, it's possible to do better by modeling opponents correctly. There's probably some interesting stuff in this modeling-of-capacity question. Note that the basic game theory solution of computing Nash equilibria assumes the opponent is capable of computing Nash, will choose to pursue Nash (simulating the agent as a Nash player), and that there is a common-knowledge map of game rewards to each player's utility (each agent assuming the other's utility function).

Things get more complicated when the representation of the agent is parameterized in some way, such that the agent's actions provide information about its goals. In the simplest case, the agent knows exactly how its actions affect other players, and can tractably include this in its game-tree or utility function. In reality, the details of others' thinking is often complex, though we can hope that a simplified representation captures most of the information. A trading algorithm, for example, might be able to accurately model the market impact of its buy and sell orders, and use this information to maximize expected profits. However, in a real market, it usually has no way to learn that trader N has become more skittish in the X market, at least until it sees evidence that its trades there are having more impact than usual. Trading is a useful model here because the simulation effect varies continuously with trader size. Small traders in liquid markets can generally assume their trades have effectively no impact, and so are free to simply optimize on price + trader-models. In contrast, traders who provide a substantial portion of liquidity must assume that others are modeling them, opening the door to the potentially infinite hierarchy of models-of-models.

A very simple version of simulation is in cooperative coordination games, such as the Stag Hunt. For a slightly more sophisticated example, consider the Cross Game: each player chooses Left, Right, Top, Bottom, or Middle. If they both choose the same square, they get reward 1; else, reward 0. I like this model because it's easy to tweak in interesting ways, by changing the symmetry of the actions and introducing asymmetry in the rewards. You can introduce penalties for guessing wrong, or penalties for choosing the obvious Schelling point. What's 'correct' might depend a lot on what the players know about each other's mental structure, or what they think is deducible from first principles. What if the game is to choose a 5-digit decimal between .00001 and .99999, not inclusive? As with all things, this leads back to Solomonoff Induction, which relates to some neat ideas. And it's also pretty fun to think about humans rather than algorithms playing these games, though I make no claim that it's especially useful.

Head Games
At the extreme, of course, you get worlds with simulations of the agent. The simple end of this is Newcomb's problem. Functional Decision Theory is an attempt to deal with this, and I think it makes sense, but apparently it's not as concretely specified as traditional decision theorists would like. Not sure what the gaps are there, but that's an obvious place to look for deep conceptual difficulties/needs.

Before that point, though, there's a lot of fun, meaty stuff with regards to co-simulation. I'm no expert, but my sense is that this stuff is quite difficult to handle analytically, since you can't use your clean optimization tools as easily. A lot can depend on the precise level of the agent's ability to simulate the opponents, and vice-versa. One neat post is Scott Garrabrant on The Prisoners' Dilemma With Modeling Costs. It seems like the literature on bounded rationality and the like would be useful here. Anecdotally, it seems like a lot of rationalist advice for humans rests on tools that assume arbitrary computing power and world-knowledge (Solomonoff Induction, Bayes, expected-utility-maximization); that might lead us pretty far astray, so it would be nice to have tools for bounded agents. That notion seems to be at the heart of the Embedded Agency post.

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Based on reading this post by Harvard biologist Mo Al-Quraishi.


What was the direct scientific benefit of AlphaFold's folding results? Did they, as Kelsey says, 'break the problem open'?

The CASP contest happens every two years, and for the past couple years improvements on the GDT_TS distance metric have been fairly constant. Comparing their GDT_TS to the previous CASP, AlphaFold was about 1.8x the average improvement; the second-place team this year was at just about the average improvement. This metric went from 40% to ~ 58%, meaning there are only ~2 improvements of comparable size to make before the metric hits 100% (meaning complete accuracy to within 1 angstrom). MaQ notes that this could require some new revolutionary insights, though.

Further, the GDT_HA (high accuracy) metric shows again that AlphaFold was ~2x as big an improvement as usual, but has a lot further to go - AlphaFold took it from 27% to 40%.

What about the underlying methods/insights?

Here's my understanding of MaQ's "AlphaFold" section. AlphaFold used MSAs (sets of corresponding, aligned protein + RNA + DNA sequences) as training data. Protein residues (amino acids) were considered 'similar' if the genes for them tended to appear together and mutate together. They used a neural net to map similarity into a discrete probability distribution of residue distance (with a few bins). Used smoothing and some physics knowledge ('reference potentials') to turn these into pairwise potentials, then did gradient descent on these. [I assume there were constraints to ensure physicality. Maybe just pairwise constraints on nearby residues is enough to enforce that the protein chain is realistic, if your at-a-distance potentials are reasonable? Probably some Van der Waals and dipole stuff to ensure too-close residues get penalized.] I think their training involved backpropping over the gradient descent steps, presumably taking the (error) gradient of the potential function elements at each step.

This seems straightforward, and MaQ says it seems that way to biologists too. The use of pairwise potentials rather than binary 'in contact / out of contact' indicators is somewhat new, but another team (Xu) was also doing this. Meanwhile, the second-place Zhang team used binary contact data but a better protein folding model. MaQ says "AlphaFold's preliminary results indicate" they wouldn't gain much from using a better folder; maybe they tried this and didn't see much benefit? If so, maybe the field would have gotten about as far by combining Xu and Zhang labs' results after the contest this year. (Note that it would have to be after the contest because protein-folding labs are highly competitive and secretive in the leadup to the contest, so the field only has global updates every two years. MaQ attributes these norms to the needs of a much less developed field, and thinks they should change now that the field is more sophisticated about training/test splits, has some public benchmark data, and has enough secular progress that they don't have to worry about charlatans faking it.) MaQ claims AlphaFold's methods are more elegant, though, which might be true.

One thing worth noting is that AlphaFold's 'energy functions' aren't constrained by real physics; they're 'the function such that, on the training set, gradient descent yielded structures with the highest GDT_TS". And from what MaQ says, they're not universal, but specific to the set of proteins whose info is given in a single MSA. [One thing I don't get; how do they determine how to analyze a protein that's outside any of the structural families they have MSAs for? I should revisit this when the AlphaFold paper is up.] In fact I suppose there's no reason they have to act as a pairwise additive force, though it sounds like they do work this way; I guess it's easier to calculate, plus it's suggested by the physics.

What are the implications?


MaQ says unclear. If high accuracy is needed for useful folding predictions, many new insights might be necessary. And unlike in other ML fields, there isn't a ton of increase in dataset size over time, so that can't be relied on to feed algorithmic improvement. But there's a new player in town, and it's possible protein folding will eventually get eaten by ML.

He does see AlphaFold's success here as an indictment of protein folding academic culture, and especially of pharma lab culture, which (he says) talks a big game about fundamental research but is almost entirely focused on incremental practical work.

He highlights the further subproblems that still need to be figured out. AlphaFold type methods are fairly specific to protein 'families' and struggle to deal with novel structures (mutations, engineered proteins). Even within families, sub-angstrom precision is important for designing small targeted drugs, and such precision is still far beyond us. And there's the 'holy grail' of actual folding dynamics, which would be really useful for predicting protein function. So there's a long way to go, and protein folding researchers should think about what problems they can best approach from a high-insight but lower-compute angle.

--

This was a neat, accessible blog post. It's nice to read things by people honest enough to admit things like "we were all really worried at first that DeepMind made some amazing insight and we'd all be out of a job, then read their preprint, breathed a sigh of relief, and started sneering about how incremental their advances were". A little inaccessible for sure--MaQ seems to be writing for people somewhat outside the field, but also doesn't explain what an MSA is--so I've probably missed some things, but quick lookups gave me enough context to feel like I get it. It's also nice to hear about molecular modeling-y things from time to time; they're like missives from a life I'm glad I don't live, but enjoy visiting.

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