After reading this I can't stop thinking about a possible future where we have predicted all possible permutations of different diseases and created vaccines for them. Maybe our kids one day will get an all in one vaccine preventing all viral and bacterial disease.
AlphaFold: a solution to a 50-year-old grand challenge in biology
591–600 of 683 posts
Re: AlphaFold: a solution to a 50-year-old grand challenge in biology
#592Earlier quoted context omitted.
> Are there any cases where ML performed decently but then hit a ceiling while expert systems kept improving? Yes, this describes entire history of AI including several boom-bust cycles. In particular the 80's come to mind. Yes the practitioners think that there's no technical barriers stopping them from eating the world, but that's exactly what people thought about other so-called revolutionary advances. Although to…
> We appear to be at the tail end of the maximum hype part of the boom-bust cycle. Thinking that the rapid gains being made by the current deep learning approaches will soon hit a wall is a reasonable outside-view prediction to make: nearly every time we've had a similarly transformative technology in the AI space and elsewhere, hitting the wall is exactly what happened. The onus would be on practitioners to show tha…
It's not asinine to have realistic expectations and not give in to hyperbolic claims.
Re: AlphaFold: a solution to a 50-year-old grand challenge in biology
#593Additional commentary in Science: https://www.sciencemag.org/news/2020/11/game-has-changed-ai-... (submitted by furcyd : https://news.ycombinator.com/item?id=25254888 ).
The most amazing part: > The organizers even worried DeepMind may have been cheating somehow. So Lupas set a special challenge: a membrane protein from a species of archaea, an ancient group of microbes. For 10 years, his research team tried every trick in the book to get an x-ray crystal structure of the protein. “We couldn’t solve it.” > But AlphaFold had no trouble. It returned a detailed image of a three-part pro…
I used to work in scientific HPC and seeing the amount what researchers used computing resources for folding was staggering. Just thinking how much this will speedup the research in coming years is to be seen. I am really hope full.
Re: AlphaFold: a solution to a 50-year-old grand challenge in biology
#594Earlier quoted context omitted.
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
> Industry cares about results, its more meritocratic Industry cares about positive results. If you're not allowed to fail, you will be afraid to explore. That's what Academia is. Then, the industry reaps the fruit of that exploration, which is as it should be.
High impact journals care about positive results and academia very much cares about journals.
You need to win grants to survive.
Re: AlphaFold: a solution to a 50-year-old grand challenge in biology
#595CASP (Critical Assessment of protein Structure Prediction) is calling it a solution. To quote from the article: "We have been stuck on this one problem – how do proteins fold up – for nearly 50 years. To see DeepMind produce a solution for this, having worked personally on this problem for so long and after so many stops and starts, wondering if we’d ever get there, is a very special moment." --Professor John Moult C…
This is an issue of the more subtle aspects of English. "To see DeepMind produce a solution for this" does not imply something is solved. I can produce a bad solution. I can produce a really good solution. All without solving a problem.
Laypersons often use the word "solution" in situations where an academic would say "method" or "approach": we did something useful, but it may not be the best possible way.
In pure math, "solution" means determining whether a logical statement is true or false. For example, in (asymptotic, worst-case) analysis of algorithms, the logical statements take the form "there exists an algorithm to compute X with asymptotic complexity O(f(n)), and no algorithm with lower complexity exists." These are crisp notions with no room for debate.
In this competition, they defined "solved" as achieving 90% accuracy. This is somewhere in between the two definitions. It's technically a valid problem statement, but it can become obsolete in a weird way. If someone else solves the problem of achieving 95% accuracy, then suddenly the 90% solution doesn't look so good. Compare to e.g. sorting. If we add the requirement of a stable sort, it becomes a new problem. Stable sorting algorithms are not automatically "better" than unstable ones.
Re: AlphaFold: a solution to a 50-year-old grand challenge in biology
#596Earlier quoted context omitted.
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
> Industry cares about results, its more meritocratic Industry cares about positive results. If you're not allowed to fail, you will be afraid to explore. That's what Academia is. Then, the industry reaps the fruit of that exploration, which is as it should be.
If academia actually allowed failure we wouldn't be getting so many tiny incremental growth papers just for the sake of it as in deep learning and machine learning.
Re: AlphaFold: a solution to a 50-year-old grand challenge in biology
#597Earlier quoted context omitted.
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
> Industry cares about results, its more meritocratic Industry cares about positive results. If you're not allowed to fail, you will be afraid to explore. That's what Academia is. Then, the industry reaps the fruit of that exploration, which is as it should be.
In my (one point) experience of industry R&D more projects failed than succeeded, but project leaders were not blamed.
How could one predict success or failure in risky project proposals? In both cases you learn something.
Re: AlphaFold: a solution to a 50-year-old grand challenge in biology
#598Earlier 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…
> The other major case in point being NLP Speaking of which, Google Translate was published in 2006, but when did the "learning from data" approach became an accepted idea in machine translation? I think the earlier attempts at machine translation were more about trying to codify grammar rules in software, than doing statistical learning from large text corpuses? I remember in 2002, the approach of leaning protein su…
I think it was with the seq2seq paper of Sutskever, Vinyals and Le in 2014: https://arxiv.org/abs/1409.3215
People were doing a mix of learning from data and hand engineered solutions before this, but this was the first system learned end-to-end, afaik.
Re: AlphaFold: a solution to a 50-year-old grand challenge in biology
#599Now onto the much harder problem of doing the reverse: taking an arbitrary structure and determining an amino-acid sequence that will fold into it.
If you have a good (and even differentiable) forward model, that should help significantly with the inverse problem.
Re: AlphaFold: a solution to a 50-year-old grand challenge in biology
#600Earlier 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.
The answer i've read is that he _logically_ precedes it, not _temporally_. But yes that only makes a tad more sense :)
That's a distinction without a difference though.