tag:blogger.com,1999:blog-22973357.post6262247185383471089..comments2023-09-27T07:44:19.769-04:00Comments on Sabine Hossenfelder: Backreaction: Has Protein Folding Been Solved?Sabine Hossenfelderhttp://www.blogger.com/profile/06151209308084588985noreply@blogger.comBlogger45125tag:blogger.com,1999:blog-22973357.post-60321775859032676462021-02-08T14:21:33.349-05:002021-02-08T14:21:33.349-05:00This great advancement in protein folding predicti...This great advancement in protein folding prediction will also have a very strong impact on genomics. We have, at the present time, a huge number of sequenced genomes, containing a huge number of protein-coding genes (there are also genes which do not code for proteins). These gene sequences are also predicted by computer programs. The algorithms used to compare linear protein sequences are not Mario Altierihttps://www.blogger.com/profile/09210470482212989895noreply@blogger.comtag:blogger.com,1999:blog-22973357.post-59029679796293862362021-02-07T11:10:19.781-05:002021-02-07T11:10:19.781-05:00A good resource for contemplating the effectivenes...A good resource for contemplating the effectiveness of neural networks is the documentary film that won a couple of Oscars last year – “My Octopus Teacher.” <br /><br />Two thirds of an octopus’s neurons are located in its arms and there is beautiful footage of how that translates into amazingly adaptive and seemingly sentient behavior in what is essentially a mollusk. <br /><br />An excellent Don Fosterhttps://www.blogger.com/profile/04814669413022486958noreply@blogger.comtag:blogger.com,1999:blog-22973357.post-30986709507009489302021-02-06T02:16:05.966-05:002021-02-06T02:16:05.966-05:00The only technical information currently publicly ...The only technical information currently publicly available on the design of AlphaFold2 is pages 22-24 of the CASP14 Abstract Book [1].<br /><br />AlphaFold2 begins with three vast databases (UniRef90, BFD, and MGnify clusters) of experimentally determined DNA-to-protein mapping data. This profound reliance on lab-collected data distinguishes AlphaFold2 sharply from AlphaGo Zero and MuZero since Terry Bollingerhttps://www.blogger.com/profile/03915136249111338024noreply@blogger.comtag:blogger.com,1999:blog-22973357.post-38780130276786301142021-02-05T09:24:34.477-05:002021-02-05T09:24:34.477-05:00@Terry Bollinger,
From what I understand, machine...@Terry Bollinger,<br /><br />From what I understand, machine learning began with expert systems modelling knowledge and then with neural networks.<br /><br />I don't see that quantum computing heralds anything new in terms of what it can compute since the quantum Turing machine can be related to the classical version. It merely represents a computational speedup of certain algorithms. Of Moziburhttps://www.blogger.com/profile/11836761141351221660noreply@blogger.comtag:blogger.com,1999:blog-22973357.post-64146863590393831952021-02-05T08:19:47.267-05:002021-02-05T08:19:47.267-05:00Alas, the most straightforward answer is no, but I...Alas, the most straightforward answer is no, but I will look around a bit. These are events I lived through rather than read about, e.g., the above quote is from a couple of decades ago from an old-timer (then!) talking about the lack of progress. I was surprised at first, but I could not show any examples that contradicted his assertion after looking into it.<br /><br />The history is complex. Terry Bollingerhttps://www.blogger.com/profile/03915136249111338024noreply@blogger.comtag:blogger.com,1999:blog-22973357.post-7085599217108743052021-02-04T12:52:43.270-05:002021-02-04T12:52:43.270-05:00"Most of the seminal theoretical work in the ... "Most of the seminal theoretical work in the area was done in the 1960s and 1970s, and everything since then has been far more a consequence of adding hardware than new insights."<br /><br /> I'm interested in learning the basics of AI. Do you know of references that would describe the field at the seminal level you mentioned?<br /><br /> Robert ClarkRobert Clarkhttps://www.blogger.com/profile/16114043697010364282noreply@blogger.comtag:blogger.com,1999:blog-22973357.post-75094236475355462222021-02-04T04:44:36.231-05:002021-02-04T04:44:36.231-05:00Steve, though it was someone else who brought up c...Steve, though it was someone else who brought up chicken strips, I like your nicely poetic metaphor. We sure could use some cooler-climate time to enable a bit of quantum political annealing!Terry Bollingerhttps://www.blogger.com/profile/03915136249111338024noreply@blogger.comtag:blogger.com,1999:blog-22973357.post-69951692008675421332021-02-03T18:07:55.842-05:002021-02-03T18:07:55.842-05:00Terry,
I think you may have been the one who made ...Terry,<br />I think you may have been the one who made the comment a day or so ago about cooking chicken strips. I spent a good part of that day asking myself why the leftover chicken strips didn't uncook them selves later on in the fridge. But I was stuck on the idea that the heat of cooking just refolded the chicken proteins into a different shape. I finally realized that stuff doesn'Steve Bullfoxhttps://www.blogger.com/profile/13990244011256349875noreply@blogger.comtag:blogger.com,1999:blog-22973357.post-58992427347714198092021-02-03T09:42:13.856-05:002021-02-03T09:42:13.856-05:00Moziber,
Yep, the deep dark secret is that blinki...Moziber,<br /><br />Yep, the deep dark secret is that blinkin' near <i>all</i> of the most interesting advanced research in artificial intelligence over the past decade or so has been intensely based on hard physics concepts and mathematics.<br /><br />It all started as a wild hypothesis, "free energy" and such, but quickly developed into a large and remarkably effective research Terry Bollingerhttps://www.blogger.com/profile/03915136249111338024noreply@blogger.comtag:blogger.com,1999:blog-22973357.post-48255714866973350032021-02-03T07:39:17.397-05:002021-02-03T07:39:17.397-05:00I fully agree. Thanks for pointing this out. It ne...I fully agree. Thanks for pointing this out. It needs to be said given just how much hype surrounds so-called 'machine learning' and 'artificial intelligence'. They're not intelligence as we know it. <br /><br />Socrates was once called the wisest man in Athens for admitting what he didn't know and for affirming that a man should know himself. It seems AI doesn't know Moziburhttps://www.blogger.com/profile/11836761141351221660noreply@blogger.comtag:blogger.com,1999:blog-22973357.post-53508197474899833862021-02-03T07:34:43.204-05:002021-02-03T07:34:43.204-05:00Whilst researching somethimg completely unrelated,...Whilst researching somethimg completely unrelated, I stumbled upon an article on Wikipedia about helix folding. They say that the Zimm-Bragg model, which gives a reasonable prediction of fractional helicity, is equivalent to the Ising model, familiar from condensed matter theory! Moreover, there is a refinement called the Lifson-Roig model which can be exactly solved via transfer matrices. These Moziburhttps://www.blogger.com/profile/11836761141351221660noreply@blogger.comtag:blogger.com,1999:blog-22973357.post-28577228497803777072021-02-03T05:05:19.657-05:002021-02-03T05:05:19.657-05:00>... "from what I've read, the technol...>... "from what I've read, the technology did originally arise from studying human games."<br /><br />For the first AlphaGo that is true. For the subsequent AlphaGo Zero it is flatly false. AlphaGo Zero created a virtual reality world in which it began literally with zero knowledge (hence the name) of any human Go strategies. It then began playing against itself within its Terry Bollingerhttps://www.blogger.com/profile/03915136249111338024noreply@blogger.comtag:blogger.com,1999:blog-22973357.post-304344903430335092021-02-02T21:45:56.560-05:002021-02-02T21:45:56.560-05:00I'm a former software engineer. I never worked...I'm a former software engineer. I never worked on "AI" and there's obviously been a lot of progress on it since I retired. What I do understand, though, is that while it now uses new data structures and algorithms called "neural networks" to evaluate results against the criteria for success, it's still using more-or-less brute force methods of trial and error to jim_hhttps://www.blogger.com/profile/10618326446656475641noreply@blogger.comtag:blogger.com,1999:blog-22973357.post-64965078081062655322021-02-02T18:12:23.922-05:002021-02-02T18:12:23.922-05:00Personally, I expect human players to improve agai...<i>Personally, I expect human players to improve against AlphaGo by studying AlphaGo's game. After all, although AlphaGo doesn't use a training set of games, from what I've read, the technology did originally arise from studying human games. It seems to be that humans ought to be given a chance to learn by playing against AlphaGo.</i><br /><br />Unlikely this will happen. When Deep Scotthttps://www.blogger.com/profile/16914985126761335721noreply@blogger.comtag:blogger.com,1999:blog-22973357.post-42077055228422306422021-02-01T19:21:37.192-05:002021-02-01T19:21:37.192-05:00Proteins that are created by ribosomes fold as the...Proteins that are created by ribosomes fold as they are constructed one amino acid at a time so it's a sequential process. Parts will be folded inside "knots" where they are no longer pushed around by the electrostatic forces of the surrounding water molecules in the way a free linear protein would. (You can't tweak the inner blocks of a lego spaceship.) An unfolded protein Jim Birchhttps://www.blogger.com/profile/07415199338332642534noreply@blogger.comtag:blogger.com,1999:blog-22973357.post-10125368665363230862021-02-01T10:41:17.795-05:002021-02-01T10:41:17.795-05:00Hello Empischon,
very interesting and informative ...Hello Empischon,<br />very interesting and informative comment.<br />Greetings StefanStefan Freundthttps://www.blogger.com/profile/04834262116439292657noreply@blogger.comtag:blogger.com,1999:blog-22973357.post-69588671258027271272021-02-01T06:47:45.205-05:002021-02-01T06:47:45.205-05:00There was a Swedish physicist who was doing someth...There was a Swedish physicist who was doing something kinda similar to what you describe around 2010-2015, I think his name was Anti Niemi or sth like that, he was cooperating with A. Liwo from UNRES group.Empischonhttps://www.blogger.com/profile/04409688265238003404noreply@blogger.comtag:blogger.com,1999:blog-22973357.post-52122756251049818932021-02-01T05:57:57.177-05:002021-02-01T05:57:57.177-05:00This might be compared to trying to use FFT to com...This might be compared to trying to use FFT to compute Shor's algorithm. It might work, but the problem grows exponentially in size. Quantum computing can overcome some of those limitations. <br /><br />These AI deep learning algorithms are neural networks and this approach is to extremize neural net work connections in a way that minimizes their energy. At this time it is evident this is theLawrence Crowellhttps://www.blogger.com/profile/12090839464038445335noreply@blogger.comtag:blogger.com,1999:blog-22973357.post-82932451112529347552021-02-01T05:22:30.229-05:002021-02-01T05:22:30.229-05:00Protein biochemist / bioinformatician specializing...Protein biochemist / bioinformatician specializing in protein structure here:<br /><br />AI structure prediction may be useful for downstream users, like wet biochemists who investigate how a protein works or interacts, but it gives us absolutely nothing about protein folding.<br />What we need to know are pathways a protein takes from completely extended conformation in which it begins its life Empischonhttps://www.blogger.com/profile/04409688265238003404noreply@blogger.comtag:blogger.com,1999:blog-22973357.post-52083082381404836452021-02-01T04:24:41.653-05:002021-02-01T04:24:41.653-05:00Hi MikeS,
Mysticism is blind faith that "sla...Hi MikeS,<br /><br />Mysticism is blind faith that "slathering some o' that there software stuff onto a computer" (the actual ancient origin of Houston's Manned Spaceflight Center) is all you need to make everything work.<br /><br />Actually <i>figuring out how to write the software</i>, say to implement a working general artificial intelligence, is a lot tougher. Instead of &Terry Bollingerhttps://www.blogger.com/profile/03915136249111338024noreply@blogger.comtag:blogger.com,1999:blog-22973357.post-39618780961986291382021-02-01T03:42:16.504-05:002021-02-01T03:42:16.504-05:00Terry Bollinger
“While human knowledge does indeed...Terry Bollinger<br />“While human knowledge does indeed have a close relationship to collecting and validating patterns, human intelligence differs in at least one major way: Patterns don’t ask questions like you just did.”<br /><br />I am extremely wary of the assertion that sentience and ‘true’ intelligence is something humans have but AI systems self-evidently do not / can never have. Wary MikeShttps://www.blogger.com/profile/01927171078192729219noreply@blogger.comtag:blogger.com,1999:blog-22973357.post-62307256112795839332021-01-31T23:45:20.137-05:002021-01-31T23:45:20.137-05:00A 90% sucess rate is pretty remarkable. What we ne...A 90% sucess rate is pretty remarkable. What we need is *machine explaining* that actually explains to humans the reasoning by which machine learning achieved its high score. I don't expect this to be solved anytime soon, even if machine learning is set on the task ...<br /><br />An experiment I'd like to try with AlphaGo is to see how well it does when the board size is increased from 19Moziburhttps://www.blogger.com/profile/11836761141351221660noreply@blogger.comtag:blogger.com,1999:blog-22973357.post-3275710750641488752021-01-31T21:35:00.271-05:002021-01-31T21:35:00.271-05:00DougOnBlogger,
>… “What else has human knowled...DougOnBlogger,<br /><br />>… “What else has human knowledge got going for it besides patterns? I’d happily characterize the entire project of understanding as patterns.”<br /><br />While human <i>knowledge</i> does indeed have a close relationship to collecting and validating patterns, human <i>intelligence</i> differs in at least one major way: Patterns don’t ask questions like you just did.<Terry Bollingerhttps://www.blogger.com/profile/03915136249111338024noreply@blogger.comtag:blogger.com,1999:blog-22973357.post-78206219668289927032021-01-31T21:27:34.046-05:002021-01-31T21:27:34.046-05:00where and when did you learn biology ? were you pr...where and when did you learn biology ? were you premedneohttps://www.blogger.com/profile/16769182614452171312noreply@blogger.comtag:blogger.com,1999:blog-22973357.post-56121941376609252912021-01-31T15:09:48.150-05:002021-01-31T15:09:48.150-05:00Just to remind people who point out that poorly-tr...Just to remind people who point out that poorly-trained neural-networks produce poor results, and we can never be sure we have found all the relevant data to train them with: human brains have exactly the same problem.<br /><br />Also, call it just a parameter fit, but how do you know that's qualitatively different than what your neurons and synapses are doing? (Albeit at a scale factor of JimVhttps://www.blogger.com/profile/10198704789965278981noreply@blogger.com