Assistant professor, Wash U in St. Louis, @wusm_pathology

Saint Louis, MO
Joined June 2010
Alexey Sergushichev retweeted
Смотрите, какая актуальная игра по нашим-то временам! (На самом деле там не напрямую про цензуру, а просто хорошее интеллектуальное упражнение.)
📰 Цензурка №1 █████████, ██████ ███████ interoves.com/censorly/1/
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Alexey Sergushichev retweeted
Out today in Immunity! Our pan-atlas of human immune aging: 12.4 million PBMCs from 2,609 people across 8 global cohorts (including new 188 people cohort from UK). cell.com/immunity/fulltext/S… We map shared aging patterns onto 59 key immune populations and link the balance of GZMK+ and GZMB+ CD8 effector memory T cells to health trajectories; show differences in RTEs and Th2s with sex etc; ethnicity associated features. artyomovlab.wustl.edu/human-… How it came to be: in 2023 we published first hierarchically annotatied atlas of human immune aging in PBMC - 166 people, 55 populations, key changes revealed - CD8 naives, KLRC2/NKG2C+ CD8 memory going down, GZMK+ CD8 T cells and Th2 and Tc2 type 2 memory cells going up! (Terekhova et al, Immunity 2023) in 2024 we added major phenotypes within naive cells - SOX4+ RTE cells and their CD38 marker going down. (Bohacova et al, Immunity 2024) In 2025-26 more atlases published with their own annotations making impossible to leverage power of data.. Now we provide unique in its power and consistency resource - 2600 people across ages, sexes, races, continents etc. All annotated in sync and analyzed for what aging looks like globally!
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Alexey Sergushichev retweeted
FYI I wrapped a lot of immuno-informatics predictors so you don't have to: openvax.github.io/mhctools/ (eg NetMHCpan, MHCflurry, Pepsickle, DeepTAP, ERAMER, BigMHC, PRIME, &c)
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Alexey Sergushichev retweeted
🧬 EPIC is open: the Eukaryotic Promoter and transcription Initiation prediction Challenge. The goal: predict where, and how strongly, RNA Pol II starts transcribing, from nothing but DNA sequence. At single-nucleotide, strand-specific resolution. epic.autosome.org 🧵 1/7
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Alexey Sergushichev retweeted
What if fucking web developers started using input html tags with proper type= at least for email/password fields so browser autocompete didn't require AI 😭
what if copy/paste was smart? powered by @typesafeai jev it feels like every computer interaction will get rewritten
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Alexey Sergushichev retweeted
Knuth is a legend, but if P = NP, then we already know explicit polynomial time algorithms that can solve NP-complete problems! Here is a simple (partial) example: 1/7
“My main point, however, is that I don't believe that the equality P=NP will turn out to be helpful even if it is proved, because such a proof will almost surely be nonconstructive.” — Donald Knuth
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Alexey Sergushichev retweeted
meet @mostik_ai! what happens when you put 12 PhDs in one room for four months? first place on the ARC-AGI leaderboard, which I can't say much about while the competition is still running. and this, which I can. everyone's arguing about whether open models will catch up to frontier models. we think it's the wrong question. here's the one we pose: why does a frontier model have to generate your answer at all, when the only thing you need from it is the reasoning? we do this by enabling models to communicate in latent space. through our protocol, hidden states pass straight from a frontier model into a small one running on your infrastructure -- no text between them, and neither model is fine-tuned. two models from different families, sharing reasoning, both left untouched. how do we know it works? we tested it on a setup where a 753B model reads the problem, and a 4B edge-class model writes the answer. with this approach, we get results 80% as accurate as the frontier model, but at 20x faster performance. we're committed to preventing frontier model lock-in and are already partnering with inference providers to accelerate open-weight adoption. we've done this between 15 of us, in four months, 12 PhDs and a Fields medalist, backed by @generalcatalyst WIRED has the first external account of the company and the work: wired.com/story/russian-star… full writeup, the setup, and all the numbers: mostik.ai/read-more
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Alexey Sergushichev retweeted
Humanity has not prevailed ( • ᴖ • 。) AWTF Heuristic is now over and OpenAI has completely demolished human competitors. In the end, humans performed quite well, but the performance of OpenAI was outstanding. I'll post my detailed thoughts about this in a few days, since this deserves a longer commentary.
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Alexey Sergushichev retweeted
My nuanced predictions for the AWTF heuristic human vs AI: You may think that since OpenAI took 2nd place in 2025 and the progress over the last year has been insane this should be an easy win for the AI. It's not. At least not an easy one. There are a lot of things that I need to cover so let me briefly go over everything that's important. Where AI agents are today: - Produce code at insane speeds; a single agent is probably one-two orders of magnitude faster than the fastest humans - Excellent at finding relevant and applicable knowledge - Good at reasoning about problems that are easily explainable via text - Code quality and expressiveness is much better but still behind very good coders, this mostly matters in larger projects so it's unclear if this will have any impact here - Standard autoresearch tends to easily get stuck in local minima - Surprisingly bad at code optimization. If you believe otherwise... I'm sorry. Performing well in complex optimization problems requires the following: - Very good and thorough problem understanding. For common problems it's enough to apply and tweak existing knowledge, but with truly unique problems you really need some form of continual learning. - Being able to quickly implement all ideas. Solving those complex problems is an iterative process: each time you test a new idea, you gain new knowledge that improves your understanding of the problem. The quicker you go, the more information you'll be able to extract. - Squeezing the maximum performance out of your idea. This often requires performing many tests with minor tweaks. It's also worth noting that IMHO humans heavily underperformed (including me, due to lack of sleep) in 2025. If I competed in isolation (without a leaderboard), my guess would be that I'd probably finish around 4-6th place. Based on everything above we can say that the main advantage of AI is insane speed and the ability to parallelize work, but its main weakness is that as time goes on it won't be much smarter about the problem it's trying to solve. If you need a simple analogy: AI here is like 100 okay-ish programmers heavily cooperating with each other. The longer the contest goes and the more unique the problem is, the higher the chances for humans are. On the other hand, if the problem is very heavy on the implementation side and/or we can arrive at great solution by performing small tweaks (i.e. the gradient from "random solution" to a very good one is smooth), humans won't have much of a chance. In 2025, problem setters assumed that AI is not that good yet and the problem wasn't "AI-proofed". I'm pretty sure that this year there was a lot of thought put into problem design and we can expect something truly unique. I'm sure that there exists many different problems where humans have a good chance of winning vs AI, but finding them might be very tricky and obviously AtCoder cannot test against the best in-house model that OpenAI currently has. On the other hand, one might ask yourself why in 2026 OpenAI decided to compete again vs humans. In 2025 they had a very strong result in IMO, got the 2nd place at AWTF heuristic and solved all of the problems at the ICPC. That would be a huge narrative violation if in 2026 they didn't easily win, right? Considering this, I expect that OpenAI put some actual effort into it and this is not just the same thing they did in 2025 with a stronger underlying model. A lot of current AI downsides can be alleviated by better harness (in order to improve exploration of different ideas) and massive parallelization. Since it's OpenAI official participation, we can safely assume that OpenAI has infinite inference at its disposal here. With massive inference issues like "bad at code optimization" should mostly disappear. Ok, that's a lot of text, so what's my actual prediction? I do believe that OpenAI put significant effort and expects to win. If they were consistently winning online 10-day contests then winning 2-day finals should be easy. I'm also sure that AtCoder's final problem is going to be very unique and completely unrelated to any of the past problems. Unless OpenAI slowplays their advantage, we should expect that once again they will have a crushing lead right from the start. Once again humans will be playing a catch-up game. We might expect some tweets from OpenAI if their advantage is huge near the end of the competition, but I wouldn't be surprised if they wait till they get their full sweep with both heuristic & algo. In the end, I think I give humans around 20-25% chance of winning. Either way, this should be both entertaining and educational since we rarely get a chance to see any of the frontier AI labs trying to put their best in-house models to the test.
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Alexey Sergushichev retweeted
The most important* human vs AI programming competition of 2026 starts in 8 hours: - another edition of AWTF heuristic, where AI placed 2nd in 2025 - the 12 best human heuristic competitors vs whatever OpenAI has been cooking and probably won't see the light of day for at least a few months - a single complex optimization problem made specifically for the competition - the contest lasts two days: on day one only the leaderboard is available to avoid spoilers for competitors; day two will feature a full 10-hour live commentary with analysis, interviews and a lot of awkward silence *surprisingly not hyperbole links in the comments ⬇️ Note: I'll be tweeting a lot about the tournament over the next few days. If you don't want to see it, feel free to mute "AWTF"
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Alexey Sergushichev retweeted
AI is a tinkerer, not an engineer. Writing a complicated piece of code with AI is somewhat like evolution. You can get to a local minima with such a bad architecture that the only way out is to scratch it and start again. Like the unfixable left recurrent laryngeal nerve route.
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Alexey Sergushichev retweeted
Earlier this week I posted an example of a fake western blot provided by ThermoFisher to demonstrate the validity of a p53 antibody. I considered it an amusing curiosity. In fact ThermoFisher has systematically manipulated antibody validation data. Short Thread... 🧵
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Alexey Sergushichev retweeted
Interested in single cell and spatial genomics? Check out the agenda for our 10th Single Cell Genomics Day on Friday 6/12. Speakers: Aviv Regev @anshulkundaje @junyue_cao @xinjin + many more! All talks are free and live-streamed at satijalab.org/scgd
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Alexey Sergushichev retweeted
In 2021 we identified GZMK+ CD8 T cells as Taa - age-associated subset of cells in mice. How they developed remained unclear. Today, our latest work on the mechanism of development of age-associated GZMK+ CD8 Taa cells in old mice is now out! cell.com/cell-reports/fullte… "Inflammaging in aged tissues drives remodeling of the CD8+ T cell compartment" let by Irina Shchukina and co-supervised by Gwendalyn Randolph with a huge team that helped to make it happen. We definitively show that: 1. GZMK+ Taa cell development is cell extrinsic and requires antigen exposure in aged tissues. 2. We introduce major new model that accelerates immune aging in CD8 T cells and show that low-grade inflammation accelerates CD8+ T cell aging and Taa cell accumulation. 3. Aged adipose tissue acts as a niche that supports progenitor Taa cells and overall development of these cells.
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Alexey Sergushichev retweeted
#aging #rejuvenation #outlook #Community @NatureAging just published a very nice piece describing the view on the field of aging from ~30 experts in the field, humbly yours including: nature.com/articles/s43587-0… In addition to reading the key messages that were nicely assembled by Sebastien Thuault and Hannah Walters, i strongly recommend to read supplementary material to that article, where each of the authors more extensively asnwers to these 10 questions - it is incredible source for discussions, debates and raw insights: 1. Is there one advance in aging or age-related disease research from the past 5 to 10 years that changed how you think about the field, and why? 2. What have we learned about translating geroscience from model organisms to humans, and where do the biggest gaps remain? 3. The field of aging is very broad, covering biology, clinical, public health and social sciences. Has your work or thinking been inspired by approaches or findings from separate disciplines? 4. Which single shared resource (e.g. dataset, biobank, model, tool) would most accelerate progress in your field? 5. How should we balance large, collaborative team science efforts and the focus and agility of individual labs to drive research forward? Should there be more big-team science in aging research? 6. Where do you see research on aging and age-related diseases having the biggest impact on clinical care and public health now and in the future? 7. If you could change one funding or regulatory policy to speed up progress, what would it be and why? 8. There is growing public interest in aging and age-related disease research. What can researchers do to ensure that aging science can be trusted and benefits everyone? 9. What advice would you give to researchers entering the field now? 10. Where do you see your field heading in the next 5 to 10 years?
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Alexey Sergushichev retweeted
Very excited to announce our latest paper in Nucleic Acids Research: "Accurate chromatin marks peak calling with Omnipeak." NAR Nucleic Acids Research lead by Oleg Shpynov lnkd.in/gqTJ4k5D For years, we all have been forced to swap between different tools depending on their data: MACS2 for sharp peaks or SICER for broad domains. Furthermore, the same methods could give vastly different numbers of peaks for the same mark when the quality varies a bit. Omnipeak changes the game: ✅Unlike MACS2, which struggles with broad histone modifications, Omnipeak captures the full architecture of the epigenome—from razor-sharp H3K4me3 peaks to expansive H3K27me3 domains—within a single framework. ✅ Better Biological Signal: Our method demonstrates higher consistency across biological replicates, ensuring that the "peaks" you find are real biological features, not technical noise. ✅ Superior Boundary Precision: In our benchmarking against ENCODE and Roadmap datasets, Omnipeak consistently outperformed existing methods in defining exact peak start/end coordinates. ✅ Consistency at a low-quality peak calling and no dependency on the control samples. This also provides unique systematic approach for any large-scale epigenetic analysis of many studies and samples. Stop juggling multiple pipelines. Switch to a universal, unsupervised solution that brings mathematical rigor to your ChIP-seq and ATAC-seq analysis.
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Alexey Sergushichev retweeted
1/ New in @NatureComms: A scalable method for non-additive GWAS reduces computational cost 700-fold and uncovers 781 novel disease loci in @FinnGen_FI . Led by @ivan_molotkov_ , this work opens large-scale dominant/recessive analysis for large biobanks. nature.com/articles/s41467-0…
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Alexey Sergushichev retweeted
🚀 New preprint! The Human Cytokine Dictionary - 9.7M cells, 12 donors, 90 cytokines - our largest human single-cell perturbation atlas yet. Users can map cytokine activity in their own data. Huge thanks to Lukas, Sören, Larsen, Parse Bio & Seelig lab! 🔗 biorxiv.org/content/10.64898…
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