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

Saint Louis, MO
I'm happy to present our new web-tool CORESH alserglab.wustl.edu/coresh/ for searching public gene expression datasets using gene signature as a query, developed by @vd_sukhov, which was just published in @NAR_open doi.org/10.1093/nar/gkaf372 1/n
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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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New application note from the lab: "GAMclust: identification of regulated metabolic modules in bulk, single cell and spatial gene expression data" 1/5
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But it can work with spatial Vizium data too: as a case study we analyzed a glioma dataset: alserglab.wustl.edu/GAMclust… There, one of the modules is glycolysis, which localizes nicely to the tumor core 4/5
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I released new 0.4 version of mascarade package with a much improved label placement algorithm. It's a pretty neat algorithm, but it took a while to get there. 1/8
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All of this I did with Claude. It definitely helped trying out new ideas (and I could do it remotely from my phone at random places where I get new ideas), but I wasn't able to make it solve this on its own. And it took a LOT of my guidance to make the code look reasonable. 7/8
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New preprint from my lab with a technical follow up on our work on fast GSEA algorithm: Hash-augmented adaptive multilevel splitting Monte Carlo algorithm for accurate estimation of two-sample permutation test p-values 1/7
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And yes, these issues were happening with FGSEA, so the current implementation uses exactly this algorithm. 6/7
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We provide a reference implementation in a hamstest Python package: github.com/golikov-nik/hamst…, where you can also provide a function to calculate your own statistic. See the preprint for more details: arxiv.org/abs/2607.12853 7/7
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