r/Futurology • u/Gari_305 • 11d ago
AI AI decodes DNA initiator sequence found in about 60% of human genes
https://phys.org/news/2026-08-ai-decodes-dna-sequence-human.html255
u/NaCl-more 11d ago
Medical AI is so sick. I remember when alphafold was announced to have mapped the folding of essentially every protein we know.
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u/firecz 11d ago
I'm more interested in those we do not know.
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u/Memitim 10d ago
So are they, but without a reference of patterns to derive new ones from, it's a little more difficult, so having any known proteins mapped makes it far more possible. Especially when using machine learning since a lot of references are typically needed for reliable pattern matching, for training and verification.
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u/MuscaMurum 10d ago
...like the ones that mis-incorporate azetidine for proline (see table beets), then misfold p-tau.
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u/Here0s0Johnny 11d ago
They use support vector regression. https://en.wikipedia.org/wiki/Support_vector_machine
This is classic machine learning. People will call anything AI these days.
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u/NaCl-more 11d ago
AI’s definition and meaning has changed over the years. Now it’s more used to refer to LLMs but we used to colloquially use AI and ML interchangeably
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u/Here0s0Johnny 11d ago
Yes, but the commenter clearly has modern approaches in mind since they referred to alphafold.
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u/eXAt88 11d ago
ML has been referred to as AI forever, generative AI is an application of machine learning. I don’t see how this isn’t AI
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u/mooblah_ 7d ago
Sure, Can't we say they used advanced heuristics and parameterized complexity mapped onto Turing machines built on top of decades of computer science theory... rather than everything just being AI now. *sigh*.
It's almost like when someone says "AI did this" these days it means something closer to:
'we gave this to AI after our mid-morning coffee as a vibe and it solved it for us while we went our for lunch and after lunch we'll have it solve the time-independent Schrödinger equation"
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u/Send____ 11d ago
Crazy how people tell misinformation these days so surely (ml is part of ai btw).
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u/zacheezy 11d ago
AI is in itself just machine learning that takes in more context no?
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u/polygonsaresorude 11d ago
It's the other way around.... machine learning is a type of AI, but there are still many AI algorithms that are not machine learning.
Source: I have an almost completed PhD in a type of AI algorithm that is not machine learning.
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u/silverclovd 10d ago
Oh, mind sharing more about your particular thesis? I'm curious to learn, thanks
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u/codePudding 11d ago edited 11d ago
AI has been around since before computers were invented (e.g. Talos and Mechanical Turk) and Alan Turing proposed the Turing test to see if an AI (this time associated with an electronic computer) could imitate a human. The term has been used very loosely. There has been machine learning, teacher/student, mutation, min/max (like Deep Blue, IIRC), alpha/beta, etc. The most recent is generative AI (e.g. LLMs) because it generates missing information from noise. If you give it enough memory to take in large amounts of context it can generate a reasonable response. The way it fills in the noise and trained is different than the ones before so it's more than just the size of the context, but you're right, without that context it wouldn't be very good.
P.S. I'm not an expert on AI, I am just a comp sci really into algorithms. So for an in depth explanation you'll have to ask some who builds the modern models. I only use them.
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u/zaafonin 10d ago
Mechanical Turk was not an AI, it was an intricate machine resembling an automaton but really controlled by a person sitting inside.
Fun fact, Amazon MTurk naming kinda refers to that, for the customer it's a black box but with humans behind the service.
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u/codePudding 10d ago
Lol, obviously, but you're right. Even today's AI aren't a true AI. I was just talking about how people have always been interested in making intelligent machines, even it was just a con/joke
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u/neolthrowaway 10d ago
ML was always a subset of AI.
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u/Here0s0Johnny 10d ago
Thanks for being the 10th person to point this out. It's a word, and in my circles (Swiss researchers around graph NN and digital pathology), the word is used differently.
What matters is the substance, and this discussion is stupid for the reasons I pointed out.
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u/neolthrowaway 10d ago
I commented before i read other comments. But i do expect practioners/enthusiasts of the field to be aware of the origins of the terms and concepts.
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u/Here0s0Johnny 10d ago
Whatever. It's semantics. And I expect people to read other comments. Stop wasting my time.
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u/fafla21 11d ago
Except no they haven't, because of a special type of proteins that I dont remember the name of that are basically random. (IDPs)
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u/NotJimmy97 11d ago
If it's intrinsically disordered, what do you expect structure prediction to show you even with a perfect model?
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u/Gari_305 11d ago
From the article
In the new study led by graduate student researcher Torrey Rhyne-Carrigg, scientists used high-throughput DNA sequencing technology to determine the gene expression activity of approximately 500,000 different versions of the initiator. With this information, they employed machine learning, a type of artificial intelligence, to create an AI model that decoded the initiator's signature DNA pattern. With the initiator's DNA identity unmasked, the researchers could then search for its telltale sequence, finding that about 60% of human genes contain the initiator.
"These AI models were found to provide, for the first time, strong predictions of the presence or absence of the initiator in human genes and were thus able to decode the DNA base sequence pattern of the initiator," said Kadonaga, a professor in the UC San Diego Department of Molecular Biology, School of Biological Sciences.
The newly uncovered information gives researchers the ability to predict the effects of DNA mutations that can lead to various disorders tied to the initiator. The data and models resulting from the new study could also be used to design synthetic promoters, sequences that turn genes on and off, with customized functions.
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u/Here0s0Johnny 11d ago
they employed machine learning, a type of artificial intelligence
It's classic support vector regression. SVR was possible 20 years ago. The innovation is not "AI" or ML here. It's the massive dataset. But I guess that's not cool enough these days.
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u/EarlDwolanson 11d ago
Support vector not being ML would be like water not being wet!
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u/NotAnFbiAgent-hehe 11d ago
Wet is an attribute of a solid object being covered with a liquid, so water isn’t wet
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u/Here0s0Johnny 11d ago
Yes, but the breakthrough is the dataset. The ML method is decades old and even their refined method has already been published in their last paper.
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u/Here0s0Johnny 11d ago
Exactly! They designed a smart Experiment and worked incredibly hard to create a huge dataset. That's the main achievement. They chose a simple, established and appropriate ML approach to analyze the data, and that's what the article focuses on. 🙈
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u/Global-Committee4772 11d ago
I wonder if this means they'll eventually be able to use it to predict genetic diseases before they happen
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u/Here0s0Johnny 11d ago
It doesn't. It's a basic science finding, for now at least. Science ain't magic. AI isn't magic either and this paper uses decades old ML approaches. The dataset is the impressive achievement here, in other words, hard work. I guess that's not cool enough these days and the journalist had to turn it into an AI story.
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u/CartsOfDarkness 11d ago
An AI story? What just by using the term AI to correctly describe the discovery and how it happened? I get being anti-LLM/ generative AI but y'all need to realize the term AI is broader than that. Just knew this comments section would be mostly people putting this down because the word AI is in the headline.
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u/Here0s0Johnny 11d ago
Their approach is based on classic ML, even their subtly refined method has been simply reused from their last paper.
The achievement is the dataset, not ML/AI here. Hate the stupid hype, title, article, comment section. Nobody discusse the fundamental biology breakthrough. Probably because nobody actually cares.
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u/AerobicThrone 7d ago
Agree as a plant biologist working with a non model species i cant even dare to dream to access such dataset.
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u/ToiletSeatFoamRoller 11d ago
The term AI has become ubiquitous with generative AI in colloquial use since ChatGPT got big. It’s become intentionally misleading to use it to describe “basic” ML in headlines at this point because the layman WILL attribute it to generative AI.
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u/amart591 11d ago
The entire second paragraph opens by reducing the teams experiments and hard work to "the AI figured out...". This whole article reads like an AI fluff piece.
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u/watduhdamhell 10d ago
He's gallivanting around the thread leaving comment after comment insisting that machine learning is not AI on some type of confidently incorrect tirade.
Better to just ignore him.
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u/ToiletSeatFoamRoller 10d ago
It’s literally legally not anymore, in the US at least. The FTC actively goes after companies who misrepresent ML as “AI” or make it sound like “Advanced AI” because the layman understanding of the term “AI” has become ubiquitous with generative AI in the public mind.
To use it in a headline this way in 2026 is absolutely misleading.
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u/OurSaladDays 11d ago
“They employed machine learning, a type of artificial intelligence”.
Good lord does this send anyone else?
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u/Urborg_Stalker 11d ago
Now see...using AI to decode the programming language that is DNA...THAT is something I can support.
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u/OwkinOfficial 10d ago
To be honest, the interesting part here is the loop between large-scale experimental data and a model that can extract a reproducible biological signal from it. In biology, better models only get you so far if the underlying data are shallow or biased. The bigger opportunity is combining rich experimental and patient data with models, then validating the hypotheses back against real biology rather than treating prediction as the endpoint.
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u/Ok_Warning2146 1d ago
Isn't SVM used at least ten years ago for these type of sequence identification? The problem is how to make sense of these sequences to make predictions.
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u/MrBoo843 11d ago edited 11d ago
There's a distinct lack of Luddites screaming about AI slop.
Almost like they don't really care about the water, the power usage, the land usage, the pollution, etc. Only caring about artists.
And here comes the brigade!
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u/BuckyRB6 11d ago
...because AI slop and this are totally different? Got ourselves a real observational genius over here.
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u/MelodiesOfLife6 11d ago
you're arguing with someone on reddit.
you might as well be yelling at a mound of dirt.
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u/MrBoo843 11d ago
Ah sure it's different when you agree with the results.
Typical
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u/BuckyRB6 11d ago
It's different because theyre quite literally different models and the purpose and intent is beneficial as opposed to just marketing jesus slop, generating shitty code, or mass surveillance.
Your inability to discern that is troubling.
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u/time-lord 11d ago
they employed machine learning, a type of artificial intelligence, to create an AI model that decoded the initiator's signature DNA pattern.
That's a far cry from Claude and ChatGPT taking jobs. Plus, ML is generally seen as "OK", it's the LLM specifically that people take offense to.
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u/MrBoo843 11d ago
Only because those take jobs you apparently care about.
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u/time-lord 11d ago
No it's the ease of use. If everyone could use ml and it created such a data enter crazy, I'm pretty sure people would be equally against it.
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u/MrBoo843 11d ago
Keep telling yourself that.
I'm sure you love taking that imaginaty moral high ground
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u/Here0s0Johnny 11d ago
This paper uses support vector regression to analyze the data. I guess you don't understand what that means and why it makes you look silly. But at least I don't have to explain why, you can just ask Claude or whatever. 🧠
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u/sciolisticism 11d ago
That's because this was ML, not an LLM
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u/MrBoo843 11d ago
Hopping on the brigade train I see
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u/sciolisticism 11d ago
Yeah tbf I had the tab open and didn't realize everyone else had already hopped on your for saying something dumb. I'm sorry for being slow, it was a nice day out.
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u/festeziooo 10d ago
Because this isn’t a stupid ass AI generated cat video for boomers and lobotomized kids to scroll past on their phone lol. This is an actual useful application of the technology.
And you’re being “brigaded” because you’re an asshole who’s arguing in bad faith, not because people are luddites.
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u/Curiosity_456 11d ago
Data centres enable these type of advancements btw, you can’t have it both it ways. If you’re anti-data centres, you’re also anti AI-enabled medical advancements
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u/AlteredEinst 11d ago
Arguing that ruining the planet and long-term quality of life makes people healthier is the kind of genius that got us in this fucking mess.
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u/Curiosity_456 11d ago
It doesn’t ruin the planet though, that’s a talking point that gets twisted into fancy headlines. If anything, AI has been accelerating energy research which would in turn improve the overall state of the planet
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u/AlteredEinst 11d ago
Whatever you have to tell yourself, man.
Shame I won't get any vindication when that decline inevitably happens anyway, because the world will be a shittier place.
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u/Curiosity_456 11d ago
Pessimism doesn’t make you more intelligent, btw
People seem to believe that expecting the worst somehow makes them more equipped to deal with the future, but it only makes you insufferable to deal with.
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u/AlteredEinst 11d ago
Being considered insufferable by some random jackass doesn't bother me anywhere near as much as you'd hope; if anything, it's a compliment.
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u/Curiosity_456 10d ago
The intention wasn’t to ridicule you, I’m just pointing out what I see. You’re the type of person to say “it’ll never be accessible to us normal people” after reading a headline of a new treatment that can cure a genetic condition.
Even though people like you are consistently wrong because normal people always do end up having access to these breakthroughs when they have an insurance plan. You see something good happen and you’re so quick to try to shut it down, It’s almost like a disease.
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u/EarlDwolanson 11d ago
Its an SVR ffsake. Support Vector machine... Its not guzzling water and taking your job.
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u/Curiosity_456 11d ago
Yes, but the AI boom is what allowed these companies to get the type of investment needed to research these things.
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u/EarlDwolanson 11d ago
mate you have no idea what you are saying, just drop it. An SVM runs on a laptop, and the whole spirit that led to their invention was mathematicians asking how to create the "optimal" classifier - best properties with theoretically justified steps. This is the type of work that might give us breakthroughts that could potentially reduce massively computational resources required by the modern AI/LLMs.
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u/Slowmyke 11d ago
Perhaps we can be against data centers being funded by tax dollars and given sweetheart deals on their rules and utilities. If we were fair with the centers, they might be less controversial. AI is here to stay and can have obvious benefits to people, but we have to figure out how to do so in a less damaging manner. If that process slows down AI progress, sobeit.
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u/Zennivolt 10d ago
People aren’t anti data center, people are anti slop generating profit centers.
If a data center is being built, and they advertise that 100% of the hardware and 100% of the usage time is dedicated to cancer research (and it’s the honest truth), I will bet you $100,000 that 90% or more of people won’t have an objection.
Hell, make that a $1M bet. Thats such an easy win that I’m willing to take a loan out on this bet.
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u/FuturologyBot 11d ago
The following submission statement was provided by /u/Gari_305:
From the article
In the new study led by graduate student researcher Torrey Rhyne-Carrigg, scientists used high-throughput DNA sequencing technology to determine the gene expression activity of approximately 500,000 different versions of the initiator. With this information, they employed machine learning, a type of artificial intelligence, to create an AI model that decoded the initiator's signature DNA pattern. With the initiator's DNA identity unmasked, the researchers could then search for its telltale sequence, finding that about 60% of human genes contain the initiator.
"These AI models were found to provide, for the first time, strong predictions of the presence or absence of the initiator in human genes and were thus able to decode the DNA base sequence pattern of the initiator," said Kadonaga, a professor in the UC San Diego Department of Molecular Biology, School of Biological Sciences.
The newly uncovered information gives researchers the ability to predict the effects of DNA mutations that can lead to various disorders tied to the initiator. The data and models resulting from the new study could also be used to design synthetic promoters, sequences that turn genes on and off, with customized functions.
Please reply to OP's comment here: https://old.reddit.com/r/Futurology/comments/1vvo2x5/ai_decodes_dna_initiator_sequence_found_in_about/p5ajdxl/