Coby Viner (@cobyviner) header
Coby Viner (@cobyviner) profile picture

Postdoc & Penn AI Fellow • Computational Biologist

Philadelphia, PA
Joined September 2014
Photo by Coby Viner (@cobyviner)Photo by Coby Viner (@cobyviner)Photo by Coby Viner (@cobyviner)Photo by Coby Viner (@cobyviner)Photo by Coby Viner (@cobyviner)Photo by Coby Viner (@cobyviner)Photo by Coby Viner (@cobyviner)Photo by Coby Viner (@cobyviner)Photo by Coby Viner (@cobyviner)Photo by Coby Viner (@cobyviner)
Many of you don't understand how serious this is, so let me break it down. In computer science there is a famous kind of puzzle called 3-SAT. You are given a long list of yes-or-no switches and a set of rules about how they must be arranged, and you have to find a combination that satisfies every rule. The obvious way to solve it is to try every combination, but each new switch doubles the number of possibilities, so a puzzle with a few hundred switches would take longer than the age of the universe to brute force. For decades, the smartest people in the field found clever tricks that made this a little faster, but every trick still hit the same wall: the time required kept exploding as the puzzle grew. About 25 years ago, two computer scientists, Russell Impagliazzo and Ramamohan Paturi, working with Francis Zane, turned that wall into a formal idea. They proposed the Exponential Time Hypothesis, which says this explosion is not a failure of human cleverness but a law of nature. No algorithm, however brilliant, will ever solve 3-SAT without the time blowing up exponentially. Nobody could prove it, but almost everyone believed it, and it became one of the foundations of modern computer science. Researchers used it as a measuring stick. If you could show that solving some other problem quickly would also crack 3-SAT quickly, you had shown that problem was hopelessly hard too. Hundreds of papers, across scheduling, graphs, logic and much more, rest on this one assumption. Now an internal AI model at OpenAI claims to have broken it. It says it found an algorithm that solves these puzzles meaningfully faster than the hypothesis allows, and it has checked the proof in a computer verification system called Lean. And here is the remarkable part: the very people who proposed the hypothesis, Impagliazzo and Paturi, along with MIT's Ryan Williams, are now leading the public review of whether a machine has disproved their own idea. So what happens next? If the disproof holds, a large part of theoretical computer science has to be revisited. Every result that said "this problem cannot be solved faster, assuming ETH" loses its foundation, and researchers will have to work out which of those walls were real and which were simply where we stopped looking. It does not mean everything becomes easy. The new algorithm is still slow in absolute terms and this is not the famous P versus NP problem being solved. But it means our map of what is possible was wrong in a place we were very confident about, and it was an AI that redrew it. If the disproof fails, the hypothesis survives and the field breathes out, but we will still have watched an AI produce serious, checkable work on one of the deepest questions in the discipline, closely enough that the founders of the idea had to take it seriously. Either way, something has shifted.
An internal model at OpenAI has produced a claimed refutation of ETH! Russell Impagliazzo, Mohan Paturi, and I have been asked to help organize an open and independent examination of this claim. 1/4
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⁦@cityoftoronto⁩ There's carrion rotting by Queens Park. Would be great if you could alert the correct city service to have this removed. Thanks!
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17/This methodology gives us evidence of the epigenetic modification state of the DNA that is actually bound to OCT4. And, as it turns out, OCT4 motifs are indeed preferentially bound when the sequence is hydroxymethylated!
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13/For OCT4, our expanded alphabet analysis revealed a potential preference for 5-hydroxymethylcytosine. Unlike some of the other preferences described above, we could not find this described in the literature.
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12/FEZF2 appears to have two completely different motifs, one which prefers modified cytosine, and another which prefers unmodified cytosine.
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11/For example, while previous literature reported that JUND is "uniformly inhibited by 5mC", our analysis suggests that a minority of JUND motifs have a slight preference for 5mC.
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4/We developed a method to explicitly model how cytosine modifications on one side of a base pair or the other might affect transcription factor binding. To do this we simply expand the alphabet, adding m for methylcytosine, h for hydroxymethylcytosine, and so on.
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Coby is looking for a postdoc opportunity in the U.S. next and wants to pivot from computational genomics to molecular evolution and has an interest in performant algorithms. If you have any leads I hope you will chat with him! #KSChromatin23 #KSEpigenetics23
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My posters are located next to each-other, with the (fewer) Q8/#KSChromatin23 posters, in the far back of Salon C. Looking forward to chatting about them! #KSChromatin23 #KSEpigenetics23 @KeystoneSymp
My final-year PhD student @cobyviner presents 2 posters #KSchromatin23 #KSepigenetics23 tonight: 2048 Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet 2521 Comparing chromatin accessibility profiles with maximal cliques in temporal graphs
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Stuck in Calgary, due to a long @WestJet delay, on my way to the @KeystoneSymp in Victoria, BC. Looking forward to the conferences! Unfortunately likely to miss tonight's mixer, due to this delay. 😔 Anyone else stuck here too? #KSchromatin23 #KSepigenetics23
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At least we've now boarded. Here's hoping we still make it in time to catch the end of the event!
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Almost every ⁦@WestJet⁩ flight, out of Calgary this evening (YYC) is delayed. The Customer Service lineup, directly below this sign, has a massive line of well over 50 people. What an unfortunate mess.
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Poster #19, this afternoon! #RECOMB2022
Wish I could be at #recomb2022! I hope you will check out my PhD student @cobyviner's poster "Comparing chromatin accessibility profiles with maximal cliques in temporal graphs" at poster session I today at 2:30p!
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Enjoying #recomb2022 so far. If I know you and you're here, or arriving for the main conference, let me know!