[HN Gopher] How is AI impacting science?
___________________________________________________________________
How is AI impacting science?
Author : occamschainsaw
Score : 81 points
Date : 2023-12-30 00:10 UTC (22 hours ago)
(HTM) web link (michaelnotebook.com)
(TXT) w3m dump (michaelnotebook.com)
| freetonik wrote:
| Anecdotal, but I've talked to some physicists working in the
| field of quantum computing, and some of them think that it's
| possible that advancements in AI will provide somewhat efficient
| solutions to some computational problems (namely in the NP
| class), and the solutions will be "good enough" for actual
| businesses (e.g. in logistics) and researchers (e.g. in
| chemistry), to a degree that it might negatively affect future
| funding for quantum computing research. And the pace of
| advancement in AI will continue to accelerate, while the pace of
| advancements in quantum computing is notoriously slow.
| ysofunny wrote:
| I think AI and quantum computing are really the same thing, the
| difference being the same as girltalk in contrast with boytalk.
|
| what I'm saying is that there's no quantum computing; but I
| actually mean to say I simply do not understand whatever
| 'quantum' means in the context of computing given my own
| opinions of what computing really is (I have a philosophical
| opinion).
|
| in my view (as distorted and twisted as it is), what quantum
| computing devices really do is sensing or measuring. computing
| is classical in nature and no amount of hand waving will change
| this.
|
| whatever happens to logic in a qubit? if both A and B are
| anything between 0 and 1, what's the negation of such a thing?
| tux3 wrote:
| >whatever happens to logic in a qubit? if both A and B are
| anything between 0 and 1, what's the negation of such a
| thing?
|
| The problem is the pop sci explanation where qbits are
| everything between 0 and 1 at the same time is super wrong
| and misleading.
|
| Your qbits are in states that have "amplitudes". You do
| things that change the amplitudes, and that happens to do
| computation. From the amplitudes of your qbits, you can
| figure out what the _probabilities_ of observing different
| outcomes is.
|
| It's not that the qbit is anything between 0 and 1. It's in a
| precise state, that results in percentage probabilities for
| different outcomes.
|
| The negation of true 80% of the time is false 80% of the
| time.
| firtoz wrote:
| To be fair, in some quantum computers, it does work. For
| example if you count a beam of photons following the same
| path with (almost) all possible polarization combinations
| as a qubit, that is indeed closer to "everything between",
| however it's got limited utility indeed when compared to
| the broader view.
| gcr wrote:
| Apologies in advance--I don't know how to say this in a
| loving way, but I also don't mean to pass judgment--couldn't
| this just be a skill issue? Why not look into how quantum
| computing works and resolve that once and for all?
|
| https://quantum.country/ is a pretty approachable starting
| point if you're curious. The math is no more intimidating
| than any other skilled discipline.
| ysofunny wrote:
| you can just say it, it's not worse than getting downvoted
| for having off colored opinions
|
| "aren't you just too stupid to understand?"
|
| maybe I am... maybe I just think differently with another
| brand of depth
|
| what I wonder now, given another comment about amplitudes,
| is what happens to combinatorics? (and alphabets, and
| languages as sequences of strings from finite alphabets)
| but it's just simpler to dismiss me as foolish idiot.
| wegfawefgawefg wrote:
| People responded with civility which, in retrospect, you
| may not have deserved.
| firtoz wrote:
| Regarding the negation, you can consider it in a few
| different ways, depending on your use case.
|
| If your qubit is "all values", the negation is the lack of
| any value, e.g. "a measurement that results to 0".
|
| However, in most cases, you will have a segment within the
| possibilities. E.g. one qubit can hold "vertically polarised
| light at frequencies between X and Y at phase P", then the
| negation could be one of "horizontally polarised light at
| that frequency and phase", or, more common, same polarization
| and frequency but the phase is 180 degrees off P. That way,
| if you add them together, you get the cancellation. Another
| negation is "all other possible combinations".
|
| However I must note that when you call a qubit "all possible
| combinations" that's not a typical qubit value.
|
| Think of it like this, "binary" is "0 or 1", but a "binary
| value" is only one of either 0 or 1. A qubit value is,
| depending on your interpretation, photons of some
| polarisation, frequency and phase, or electrons of a
| particular spin, or some other combination of those. Some of
| those can have multiple combinations, for example a qubit
| value could be the combination of a bunch of photons at
| different values. Or, an electron with an "unknown spin". Or
| an electron with an unknown spin that's the complement of
| another electron at another unknown spin, but when you
| measure either you will reveal the other, and so on. So, only
| some qubit values will have "all possible combinations" i.e.
| "when observed, it could literally be anything".
|
| The internal of "what was the value before you observe it"
| is, well, controversial, and to most people, almost
| irrelevant, and even, "not good to consider".
| wegfawefgawefg wrote:
| Im just as ignorant as you about it. The quantum part to me
| doesnt seem to matter. I don't see why its any fundamentally
| different from making a computer out of any other substrate.
| Light, sand, chemicals, at the end of the day you compute a
| function by following a set of steps which may or may not
| have constraints of seriality.
|
| I think von neumann cant handle purely parralel algorithms
| efficiently. Even gpus. I think thats whats where the "all
| qbits interacting simultaniously for n steps after being put
| in initial conditions" is about. Its purely parralel.
|
| It could be the case that information cant be extracted
| before it is computed, and that for some algorithms the peak
| efficiency serial version is equal to the best efficiency
| purely parralel version. It could also be the case thats not
| true and that classes of quantum algorithms could be better.
|
| At the end if the day the way i see it substrate is just an
| engineered means of applied ops per time.
| RandomLensman wrote:
| The quantum part does matter in the sense that certain
| kinds of "maths" are not directly accessible in a classical
| computer. You can sort of simulate Shor's algorithm on a
| classical computer but you cannot get the same low
| complexity. Of course, whether the quantum computer uses
| substrate A or B doesn't matter (other than practically).
|
| The only way I ever found an access to understanding
| quantum computing is by doing the math, as other pop-sci
| explanations don't really reflect what is happening (at
| least for me).
| moffkalast wrote:
| Well that sounds like good news, are there any practical
| applications for quantum computing other than breaking commonly
| used encryption that would push the modern world even further
| towards a complete surveillance state?
| firtoz wrote:
| I'm not in the field but in my understanding it's going to
| make it easier to do parallel competitions and also will
| allow us to find the inputs that can lead to a particular
| output in some types of equations. Factoring numbers is only
| one of the "practical" equations.
|
| Materials science and chemistry (e.g. predicting how drugs
| may behave in our bodies) will benefit, or other
| computationally heavy "try out many permutations and see
| which ones fall though" tasks may become a bit easier.
| Climate modelling, supply chain logistics, financial
| modelling, and of course AI.
| dragontamer wrote:
| The #1 proposed use of quantum computers is... simulating
| quantum effects.
|
| Modern quantum simulators running on supercomputers is an
| exponential (O(k^n)) kind of operation. But a quantum
| computer can simulate any quantum effect in just one step,
| O(1) time. Because ya know... a quantum computer is just a
| computer that has isolated quantum effects and allows a
| programmer to control them easily.
| canjobear wrote:
| Quantum doesn't help for NP problems.
|
| In the case of codebreaking, where QC may have an advantage, AI
| is unlikely to provide an alternative because modern AI is all
| based on finding probabilistic patterns and cryptography is
| explicitly designed to be resistant to that kind of attack.
| firtoz wrote:
| Can you please elaborate?
| canjobear wrote:
| The class of this problems where quantum computing gives an
| advantage is called BQP and it includes things like
| factoring but it is not known to include NP complete
| problems like the traveling salesman.
| firtoz wrote:
| Thank you!
| wegfawefgawefg wrote:
| I have not programmed a quantum computer before. My current
| state of ignorance, and so im relying only on intuition here,
| is that it is massively parralel in the same way that the
| surface of water in your cup is massively parralel.
|
| To program a serial algorithm in a quantum computer would be
| to miss the point. You could encode the interactions between
| clumps of qbits to function as nodes in a wave simulation.
|
| There would be few enough nodes in the wave that it would be
| not equivalent to a true wave simulation. It would be a
| discretization, but now it functions as an analog asic like
| proxy for the real thing. If the groups of qbits are smaller
| than the true nodes in a wave surface your computation would
| be faster than the real thing, but lower precision.
|
| In a classical computer this would have to be done with
| buffers, or a very narrow set of parralel deterministic
| programs, otherwise impossible. (examples: a subset of
| cellular automata rules, gravity sort)
|
| Is any of that right or am i completely off base.
| TachyonicBytes wrote:
| One of the challenges of quantum computing is getting the
| useful results back into "classical" mode, where you can
| use them. Theoretically that's one of the hurdles of
| getting better theoretical performance than a classical
| computer. What you describe is more akin to how a GPU
| works, but in this case, you can't "just get" the result
| from the GPU.
| dragontamer wrote:
| Quantum is not parallel.
|
| Quantum is quantum. We did a few quantum gate simulations
| in my college back in the day.
|
| The gist is that entangling bits (say b0, b1, b2, b3 are
| all entangled), has special properties. You can almost
| perform retroactive computing. you can send these values to
| quantum gates to define properties, like b0 + b1 = b2 * b3.
|
| Later, you unentangled the values and they will 'snap' into
| some true state. Like b0,b1,b2,b3 == 1111, but the values
| 0001 or 0010 are also possible.
|
| There is nothing 'parallel' about this. It's just a quantum
| operator using the properties of entanglement /
| disentanglement for the purposes of computation.
|
| -------
|
| I'd say that quantum is closer to retroactive computing
| than parallel. Operations seemingly go backwards in time
| thanks to entanglement.
|
| That doesn't mean quantum is useful in all algorithms, but
| it seemingly has applications in cryptography and 3SAT / NP
| Complete and... Lol simulations of quantum effects.
|
| --------
|
| Ultimately, Quantum is only useful if you get enough bits
| at a time entangled. For now, it's faster for standard
| computers to brute-force all 2^32 bit combinations rather
| than using lasers+diamonds to entangle 32-bits and perform
| the operations.
|
| Quantum needs more entanglement and at lower costs to
| become competitive. But maybe it happens. At very least,
| quantum computers do exist but who knows how long it will
| be before they are competitive.
| daveed wrote:
| ^ Just pointing out, the parent didn't say NP-hard or
| -complete, so they weren't wrong (but could be
| misunderstood). But saying Quantum doesn't help for NP isn't
| right either.
| canjobear wrote:
| Fair enough!
| marcosdumay wrote:
| > Quantum doesn't help for NP problems.
|
| Notice that the GP is about the other way around. Solving NP-
| hard problems will absolutely make quantum computers useless.
|
| And in the case of physics simulation (the actually valuable
| use for a quantum computer), there's no guarantee that you
| can't find a probabilistic solution.
| sanderjd wrote:
| Yep, I'm very interested in "good enough" optimization
| techniques using ML, to massively speed up optimization
| problems that require a lot of computation that doesn't
| parallelize easily. I'm not an expert in it, but I work
| adjacent to it, and it seems like a promising direction to me.
| nickpsecurity wrote:
| They've always gotten lots of funding in quantum for techniques
| with big promises that haven't delivered yet. I'm not even
| saying they're misleading us so much as it has had basically no
| payoff compared to HPC, FPGA's, and even analog computing.
|
| The bigger concern of companies like that is if someone
| bankrolls dirt-cheap FPGA's or Adapteva-style cores with open
| architectures targeted by a toolchain like Synflow's or Cray's
| Chapel. From there, domain-specific applications (esp optimized
| kernels) targeting those tools. Then, MPP-style hardware as
| cheap as commodity servers to scale it up and out. I'm talking
| engineering the thing by combining proven strategies, not doing
| new research.
|
| Even $100 million put into such systems would deliver more
| value in more areas than $1 billion put into quantum computing.
| If not, we'd at least get huge speed-ups with the parallel
| architectures for a while and then the QC folks eventually
| deliver something better in some areas. I'd be happy both ways
| so long as one is in my building or it's in the cloud for
| $2.30/hr. :)
| t_mann wrote:
| It's from May, pity, it would have been really interesting if the
| author had discussed DeepMind's recent FunSearch paper as well:
| https://www.nature.com/articles/s41586-023-06924-6
|
| But it goes to show just how fast we are currently progressing.
| nickpsecurity wrote:
| Someone needs to host an event where those people, others doing
| genetic programming, and those doing executable synthesis are
| all in the same place. Let them bounce ideas off each other.
| All their brainstorming is recorded to be published into the
| public domain.
|
| We might see some interesting combos.
|
| EDIT: Maybe use a sample from the Humies as benchmarks for the
| techniques, including new LLM's. Let people try every approach
| in parallel mixing the best of each.
|
| https://human-competitive.org/awards
| vouaobrasil wrote:
| > how to predict the 3-dimensional structure of a protein from
| the sequence of amino acids making up that protein
|
| Keep in mind that proteins and deducing the structure of them
| (which in turn would help deduce their function) may not be a
| good thing. Proteins can also be poisons, prions, etc.
|
| But beyond that, we should not have such easy to access
| knowledge. It's just too much power for our current greedy,
| short-term thinking.
| JackFr wrote:
| Chipping flints into sharpened edges may not be a good thing.
| Sharpened flints can also be stone axes, spear heads, etc.
|
| But beyond that, we should not have such easy to access cutting
| technology. It's just too much power for our current greedy,
| short-term thinking.
| vouaobrasil wrote:
| Glib analogy, but there's got to be a limit to everything.
| Beyond resorting to superficial analogies, we should give
| serious thought into what level of technology is simply too
| much.
|
| Moreover, I actually agree with you in some ways, even though
| you meant to be sarcastic. Modern cutting technology, which
| certainly should include deep-well oil drilling, IS too much.
|
| In fact, all technology has a limit beyond which we should
| not go. We just have to apply deep thinking to figure out
| what it is, or at least do our best to try.
|
| You
| _factor wrote:
| You're more likely to get cut with a dull knife. It can
| cause it to slip.
|
| Technology is fine. It's this artificial cookie-cutter
| society we're forcing on everyone. We have a mental health
| and education problem.
|
| The tech isn't the issue, it's the people who feel the need
| to use it for negative purposes.
|
| Limiting tech is just a bandaid.
| vouaobrasil wrote:
| People will always use technology for negative purposes
| as long as it can help them get ahead in the short term
| and they aren't held accountable for the long-term
| consequences.
|
| Technology is not fine. Not all of it is bad, but to say
| all of it is fine makes no sense. Yes, we have a mental
| and health education problem, but it's reasonable to have
| rules for all societies. Limiting technology that makes
| getting ahead too easy makes sense because even in the
| most utopian and good societies, if gaining something is
| TOO EASY, then it WILL be taken.
|
| It's much too simplistic to frame technology as fine. If
| all technology is fine, perhaps every corner store should
| sell automatic weapons? Can you imagine a society, ANY
| society, in which this makes sense?
| jabradoodle wrote:
| Nowhere did OP suggest limiting tech, they suggested we
| are not ready to handle the powers we are gaining
| responsibily.
|
| Your point seems in agreement with this to a degree.
|
| More importantly, you claim it to be a mental
| health/education issue; yet you can't show me a period of
| human history without wars and power struggles.
| JackFr wrote:
| I was being sarcastic, I don't think I was necessarily
| being glib.
|
| I suppose the deeper point I was trying to make was that
| "this time is different/special" is shallow thinking, as is
| believing that the real issue is with our "current greedy
| short term thinking".
|
| The real issue is the human condition, which remains
| largely as it has throughout our history. We need to choose
| a way to live knowing we will die, and then live that way.
| vouaobrasil wrote:
| This time is different....highest CO2 level in 800,000
| years, highest human population ever. Seems like a bit of
| uniqueness there.
| wegfawefgawefg wrote:
| Cars can be used to ram people. But most people simply dont
| want to do that.
|
| What is different about cars and new tech is that new tech
| comes with the ability to track and monitor all users. So
| historically we didnt mind if one in ten million people
| wanted to ram people with their truck on purpose. But now
| the power to monitor everyone all the time to prevent these
| "one in ten million" crimes exists.
|
| Its up to you to decide if the trade off is worth it.
| wegfawefgawefg wrote:
| I want to become a von neumann probe, fill the universe
| with my offspring and go to war.
|
| Until tech can do that it hasnt gone far enough.
| johngossman wrote:
| How do you feel about antibiotics? How do you feel about
| medical advances that reduced infant mortality from more than
| 20% in the 19th century to less than 1%? How about the
| elimination of smallpox or how fertilizer and other
| agricultural technologies have eliminated most famines. Now how
| about possible cures for cancer or alzheimer's? You need a much
| more nuanced answer than "we should not have such easy access
| to knowledge."
| vouaobrasil wrote:
| > How do you feel about antibiotics? How do you feel about
| medical advances that reduced infant mortality from more than
| 20% in the 19th century to less than 1%? How about the
| elimination of smallpox or how fertilizer and other
| agricultural technologies have eliminated most famines. Now
| how about possible cures for cancer or alzheimer's?
|
| Like everything else, it's only good up to a point!
|
| - I believe in basic medical care, but medical technology
| that permits immortality is bad.
|
| - Likewise, is reducing mortality always good? Now we have
| extreme overpopulation. In short, reducing OUR mortality has
| also INCREASED the mortality of non-human animals, which I
| believe have just as much right to live as us.
|
| - Fertilizer and agriculture? Most industrial fertilizer
| poisons the land and agriculture has eliminated millions of
| acres of wild forest and destroyed a lot of ecosystem.
| Agriculture is also responsible for the huge population
| growth that is causing global warming.
|
| - Cure for cancer? Maybe good, maybe bad IF that cure results
| in significantly extended lifetimes due to how it works.
|
| I do have MANY more nuanced answers. That is why I believe in
| looking at each of your points AND others individually. My
| answer was specifically directed at AI, which I believe to be
| universally bad.
|
| Most of the technologies you listed have significant negative
| consequences, and it's not clear to me that those are
| outweighed by the positives, especially if our modern society
| results in the destruction of the phytoplankton of the ocean
| producing half our oxygen.
|
| I suspect in the long term, it would be better to have more
| mortality, smaller populations, and less technology than our
| current world. It's not a popular view because people are
| emotional about such things, but it's hard to imagine how a
| world with 8+billion and mass eco-destruction to be better IN
| THE LONG TERM.
| BrainBacon wrote:
| I wholeheartedly disagree with your assertions on
| mortality. Global population growth is slowing and is set
| to peak in the 2060s and will decline afterwards. We're
| more at risk of not having enough hands to take care of an
| aging population. An educated populace has fewer children
| and many countries are already feeling the strain of being
| below the replacement rate.
| johngossman wrote:
| Yes, strangely, people get emotional about being asked to
| let their kids die of scarlet fever and other bacterial
| infections. I'm a birder too, but some new luddism isn't
| going to save the environment. If we stop where we're at,
| we're stuck burning fossil fuels, stuck with slash-and-
| burning the Amazon. If you want save to animals, you need
| better messaging than "maybe cancer isn't bad." Look around
| the world, places with great longevity have lower
| population growth, not higher. Places with better economies
| and more technology are also greener. When you say things
| like "AI is universally bad" you're making an ethical
| judgement about a means rather than an end and ruling out
| many possible good ends. You've read Peter Singer, now go
| read Hans Rosling.
| vouaobrasil wrote:
| My message isn't that "cancer isn't bad". It's that
| medical research into cancer may lead to other outcomes
| which are definitely not good.
|
| Yes, I am making an ethical judgment about the means of
| AI, because after some analysis I do believe that the
| negative effects will be far worse than the positive.
| True, there are good applications of it. I never denied
| that.
|
| Of course, my line of reasoning is far more vast than
| what I wrote here. I'm just arguing a specific point
| here, not presenting a thesis. I do think there is more
| to saving animals than arguing against human growth. Of
| course, people need incentives.
| nick__m wrote:
| You says you have nuanced view yet you make universal
| statement don't you see a contradiction?
|
| Take your stand on AI, which is more diverse than the LLMs
| and diffusion models that are currently making the news.
| Would it be bad to replace peoples by computer vision and
| robotics in a waste sorting center, enabling more recycling
| and less microplastics in the environment due to a better
| sorting of the waste stream ?
|
| I see that as a good thing enabled by AI.
| vouaobrasil wrote:
| AI for me is an exception to my nuance, simply because
| it's too powerful and has too many horrible consequences.
| Yes, your application could be considered good. But what
| happens if there are people at the waste recycling plant
| who can't get other jobs? It's not a nice job but we have
| to first figure out what those people can do.
| pixl97 wrote:
| How do you feel about extremes?
|
| Antibiotics have saved billions of peoples lives from an
| early death. But use of antibiotics in farm animals is
| putting us at risk again via resistant superbugs that are
| sending us scrambling for new drugs to combat them.
|
| Or, to take the analogy to 11, should each individual on the
| planet have access to a button that if pushed would cause the
| planet to explode? I seems reasonable the answer would be no,
| but now how do you set up a system of rules limiting who has
| access to the technology to make that button?
| wegfawefgawefg wrote:
| 1. These are not even comparable dangers. Reduction in
| infant mortalty by 98% versus what.. some hormone issues
| sometimes in some people??
|
| 2. The laws of physics have so far prevented us from making
| technology like a tiny portable button that blows up a
| planet. Id assume a universe with weak energy constraints
| like that would have yielded much larger scale organisms,
| or perhaps none at all.
| pixl97 wrote:
| Uh you don't comprehend 1 then.
|
| 1 is you get a scratch then die because your body rots
| and you can do nothing about it. May want to spend some
| time learning about antibiotics resistance.
| johngossman wrote:
| Funnily enough, I wrote a sci-fi story a long time ago
| where there was a machine like the replicator in Star Trek
| that could make anything, but it was easy to turn it into a
| gigaton bomb.
| BiasRegularizer wrote:
| Although the article focused primarily on AlphaFold, many other
| ML approaches are making impactful contributions in the general
| scientific field. One example is the diffusion model and its use
| of stochastic differential equations (SDEs).
|
| Microsoft has an initiative called AI4Sciencie
| (https://www.microsoft.com/en-us/research/lab/microsoft-resea...)
| which published a fair amount of SDE/diffusion-based method to
| solve scientific problems
| justinl33 wrote:
| Are there any molecular biologists here? I'm curious: what
| happens to society if/when we figure out protein folding?
| Hypothetically, how does the world change if we had a 100%
| accurate way to model quaternary structure from primary
| structure?
| namibj wrote:
| We could do computer-only search for enzymes that catalyze
| desired reactions in enzyme-friendly reaction environments.
| Assuming that the way that makes the above 100% accurate also
| yields us the tooling to simulate the candidates in operation
| accurate enough to let the search/optimizer learn from the
| simulation feedback.
| alevskaya wrote:
| The static shape of a protein doesn't automatically give you a
| prediction of its functional properties. There's a hell of a
| lot more biophysics going on that we have no predictive models
| for that are needed to understand catalysis, allostery,
| assembly, etc etc etc. We don't even have good comprehensive
| data for any of that (compared to sequences or structure) to
| model with.
|
| Fold prediction is an incredibly useful tool for scientists and
| genetic engineers to help design new proteins, but it doesn't
| magically solve molecular or cell biology. Designing new
| functions and mechanisms is still going to involve a huge
| amount of labor and brute-force experimentation.
| LeonardoTolstoy wrote:
| My brother worked in protein folding (although his statement
| about specifically AlphaFold was years after he left that
| field) but I showed him the AlphaFold results from like 5 years
| ago and his reaction was "oh ... Yeah they solved protein
| folding"
|
| So at least according to him we've lived in that world for the
| last 5 years.
|
| As a person working with / tangentially to people in the same
| field I would say that it's made things faster and more
| scalable, but protein structure isn't the be all end all of
| things. Researchers use AlphaFold a lot for filtering potential
| candidates, but that is only one step in a lot of steps. A SNP
| mutation -> protein structure change -> functional change is
| already difficult without then considering that the vast
| majority of mutations that create function change in humans are
| not in exons, so something like AlphaFold (in the form I'm
| familiar with) would be useless for those as well.
|
| Eventually though an AI system that can go mutation->function
| change is entirely possible, although it is much much further
| in the future. In that case though I think you'll be quite
| close to a future where combined with things like CRISPR
| therapeutic treatment for all heritable disease would be
| possible.
| kiba wrote:
| I heard a lot of different opinion about AlphaFolding, how
| it's not revolutionary or not revolutionary, or something
| like that.
| sigmoid10 wrote:
| It _is_ revolutionary in what it does. There 's no question
| about it. The problem is that a lot of people think it does
| something different or more practical, like creating new
| drugs. That is one of the ultimate goals, but it's way down
| the road.
| selimthegrim wrote:
| Counting down to dekhn appearance in 3...
| dekhn wrote:
| Uh ok. Now I feel obliged to say that AlphaFold is the
| obvious outcome you'd get from having a company dedicated
| to winning games deciding to win at CASP.
|
| To me, "solving" structure prediction (explicitly
| acknowledging there are areas where AF doesn't make
| accurate predictions), is a clear and satisfying win,
| although it still doesn't answer some of the fundamental
| physics questions around folding.
|
| I am glad to see the existence proof but want to see more
| outcomes; in particular, I'd like to see a lab-in-the-loop
| that actually produces something of high value (higher than
| the cost of building the lab-in-the-loop).
| carbocation wrote:
| AlphaFold did not solve protein folding. You can tell this is
| the case because it doesn't correctly model structures with
| missense variants.
|
| AlphaFold is a huge advance and people are extending it to
| try to tackle this (eg AlphaMissense) but to say it solved
| protein folding is hyperbolic.
| ProllyInfamous wrote:
| >"AlphaFold can do in TEN MINUTES what a PhD dissertation
| required, fifteen years ago."
|
| Quoting a PhD immunologist from Texas, who uses AlphaFold
| daily.
| carbocation wrote:
| Agreed - and this is not in tension with my comment
| whatsoever.
| maxlamb wrote:
| It would not have a huge practical impact in the short term.
| There are many steps from figuring out protein folding to
| figuring out new, effective and safe drugs. Here's a good
| Nature article discussing just that: https://archive.is/4QNKy
| pama wrote:
| A lot of things become simpler, but hard problems remain. In
| the cell, a structure of a protein is the result of its
| sequence and all the other environmental conditions (cofactors,
| ligands, binding partners, lipids,...), and furthermore, the
| structure is a dynamical construct, so it can change over time.
| So the main advance for society is when we can accurately
| predict how to jam or unblock a machine in a cell without
| influencing all the other machines in a cell. The essential
| pieces of this puzzle are the possible shapes of the pieces
| that make up the machines and AF2 gives you those. But the
| puzzle is huge. And very important.
| wegfawefgawefg wrote:
| Even if we had a perfect library of useful proteins and their
| utilities, the composition of these protiens, and the emergent
| behaviour within "machines" made by them, would be complex
| enough to be handfuls of classes of new engineering altogethor.
|
| I think its like saying "we know how to make bricks and iron
| and bolts now, shouldnt it be easy to make a full scale
| functioning replica of the greater tokyo metropolitan area?"
|
| Even if you came up with a spec for a complex tissue or just a
| fluid that functions as a standalone chemical factory, you
| would need to fabricate it. However many specific protiens from
| your library, in specific ratios, mixed and maybe even...
| positioned.
|
| In short protein folding is just the first fundamental step
| towards this print any biological design out of proteins world
| that I guessed you are alluding to.
| arccy wrote:
| there was a talk about this a few days ago
| https://media.ccc.de/v/37c3-12061-alphafold_how_machine_lear...
| justinl33 wrote:
| okay so the prevailing sentiment seems to be: a) We kind of
| already have b) it's a big deal but not that big of a deal
| because knowing the precise protein structure does not become
| useful until you know how that structure interacts
|
| So my takeaway is that we just need sufficiently advanced
| quantum computers that can do molecule-level simulation on a
| large cell, THEN we'll be there.
| Erratic6576 wrote:
| I'm not a scientist but I enjoy reading the literary genre they
| write (the headlines). Most of the time, the articles themselves
| are hard or impossible to understand.
|
| ChatGPT can lend a helping hand
| amelius wrote:
| Anyone here who knows a good project that attempts to solve large
| sparse linear systems using ML, preferably in Python?
| Balgair wrote:
| I know the article focused on the deeper/code-ier aspects of AI.
| However, I think that it's mundane aspects are going to be huge.
|
| I once had a co-researcher that asked for help with his Matlab
| code. We were in a smell-lab together working on mice. His code
| was about controlling some scent valves in response to a mouse
| putting it's nose in a hole and breaking a laser beam.
| Importantly, this code was running his thesis, essentially, and
| he had no coding experience prior to this experiment.
|
| I said sure, I'd love to help, but you owe me a six-pack. So we
| sat down one day and started going through his Matlab code. After
| the 18th nested 'if' statement, I had to up the payment to a case
| of beer.
|
| LLMs would have helped my co-researcher out a _lot_. He might
| have actually gotten the code working at least.
|
| Most HNers don't appreciate, I think, how difficult coding is
| most people. AIs are already helping bridge that gap.
|
| Another more mundane area is in communication. Research papers
| are notorious for being obtuse and jargon filled, to the point
| where many fields are nearly speaking another language entirely.
| AIs can help with that as well. Not only in the writing side, but
| also in the reading side. Can can put a paper into them and ask
| for summaries, you can put multiple papers in and ask for review
| papers. You must be very careful, of course, but the speed
| increase is just amazing.
| boredtofears wrote:
| How would they know if the code produced by ChatGPT had a side
| effect that effected their research? Isn't it risky to not
| fully understand the behavior of your experiment?
| kian wrote:
| I think in this case that problem even exists in their own
| code that they don't fully understand.
| _giorgio_ wrote:
| Breaking down code in cells and asking chatGPT for help is
| quite easy and mostly foolproof, if you have enough will to
| learn things.
| dpflan wrote:
| Indeed, build up the complexity from smaller, verifiable
| code components.
| Balgair wrote:
| I get what you're saying, but the reality is that most
| researchers aren't any more code literate than the average
| person. Which is to say, they know just enough to make things
| worse. Hopefully those errors are removed before publication,
| but in my experience, they are not. Especially when it comes
| to coding.
|
| Also, a larger point is that this was fundamental research. A
| very hard thing. You're supposed to be getting it wrong most
| of the time. Then when you think you've got it right, you try
| to publish. Then you hope the reviewers actually read
| anything you wrote and catch all the errors [0]. But a lot of
| the time, errors sneak through and really only get discovered
| after a few years/decades. That's fine in the end, as science
| is a 'strongest-link' system where we really only care about
| the big and correct discoveries. 'Weak-link' systems are the
| opposite, they are governed by the small little falsehoods
| and errors.
|
| [0] Very unlikely, reviews almost always only review to see
| if the paper is of a high enough quality for the journal to
| include. I want to be clear on this point: Reviewers do not
| re-do experiments and typically do not go back through your
| math, let alone the code you used. Now, each field is
| different and has different standards, and those vary wildly.
| But generally, reviewers aren't there to make sure the
| science is right.
| kiba wrote:
| It sounds like that researchers should just learn to
| properly code.
| sdenton4 wrote:
| If the set theorists knew how to farm, then we wouldn't
| need the NSF to give them money.
| nitwit005 wrote:
| You have to understand the code the AI emits, to be able to
| check if it's done what you wanted. That's sometimes more
| challenging than writing it yourself, as it may use features
| you're not familiar with.
|
| Which is not to say it can't be useful, but don't expect a cure
| all.
| IanCal wrote:
| What they're describing is dealing with a person who already
| doesn't understand what their code does.
| mettamage wrote:
| Reading code is easier than starting from scratch. Not sure
| how that is for a researcher though, just my SWE perspective
| sdenton4 wrote:
| They're different kinds of easy...
|
| Writing fresh code is easy because you just express your
| ideas. What's hard is hitting all the contingencies
| appropriately; it can take years of 'burn in' to get right.
|
| Reading code is easy - especially if you don't know the
| language well - because someone has already assembled all
| the correct syntax, etc. What's hard is that the code may
| be convoluted from years of monkey-patches to handle all
| those inconvenient contingencies, to the point of obscuring
| the core ideas. eg, making you search through ten nested
| indirections to figure out how something actually
| executes...
|
| On the writing side, LLM's make it much easier to have the
| idiomatics of the language easily on hand. (eg, I never
| ever remember the exact way to use 'super' in python... but
| ML assistance is happy to fill in the parens as soon as I
| start them.)
| block_dagger wrote:
| I think the gap is quickly narrowing on the need to fully
| comprehend most computer programs for most use cases,
| especially if bugs and changes can all be managed through
| natural language by the primary stakeholders.
| CJefferson wrote:
| I can tell you one impact -- there are huge amounts of ChatGPT
| helped, or entirely written, junk papers appearing at
| conferences, which is causing serious problems getting reviewers.
| Some large events have introduced a pre-review phase to filter
| out junk, but it's getting harder, as LLMs are good at producing
| plausable looking nonsense.
|
| Honestly, I'm not sure of the long term solution here.
| Conferences and journals may have to introduce a system where you
| need an existing member of the community to "vouch" for your work
| to be allowed to submit (they don't have to say it should be
| published, just worth reviewing).
| fastneutron wrote:
| LLM-written content has a certain gestalt to it that's pretty
| easy to sniff out once you've seen it a few times, just look at
| Quora and LinkedIn these days.
|
| While I think it's probably fair for people with English as a
| second language to use LLMs as a writing assistant (for
| example), there definitely needs to be some kind of author
| disclosure statement at the very least. This could be similar
| to how more papers are now including contribution statements
| when there are many coauthors.
| corethree wrote:
| That gestalt can easily be smoothed out. You simply need to
| prompt LLM to do so in your query. Tell the LLM to depart
| from its default style. Say _make your response more brief,
| well written and add a witty conclusion at the end_
|
| Then you say rewrite the final paragraph to be slightly
| shorter and incorporate a certain example. Yada yada.
|
| Likely you can even do this "write your response in a style
| that is not typical for an LLM"
| throwup238 wrote:
| It's easier to illustrate with prose: ask it to write in
| the style of Terry Pratchett or Hunter S Thompson and the
| style changes drastically. You can even ask it to rewrite
| your scientific paper in the style of Shakespeare: https://
| chat.openai.com/share/498804da-6d59-4a0c-91d1-da4cea...
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