@PracheeAC There might also be less citation bias if these journals did not randomly limit the number of citations allowed (unbelievable that this is still a thing in the age of the internet)

I hate reference limits of journals so much. I'm sitting here trying to find a few more references to remove despite me knowing that I'll either remove context & evidence for scientific conclusions or not mention tools that very much deserve to be mentioned and cited.

📡 Join us for the next session in the Foundation Models for Biology Seminar Series (FM4Bio) on May 16 at 10 AM PT, featuring @jkobject. Jérémie will introduce scPRINT, a large-scale foundation model trained on 50M single cells from the cellxgene database. The model infers gene

I am super happy to annonce that after 9 months under review the first paper of my PhD: scPRINT is finally available on Nature Comms! 🎉🧬 https://t.co/xAMMsbSYZ7

On Tuesday at 2025-02-04 18:00 CET, @jkobject will talk about scPrint, a transformer model that infers gene networks from scRNA-seq data, at our 2nd community meeting of 2025! For more information, check out the GitHub: https://t.co/1DPZAT63Zu & pre-print

Groundbreaking work, congrats to the team!! 🎉 When I started my PhD 3 years ago, our tabular benchmark showed tree-based models miles ahead of neural networks. On the same benchmark, TabPFN v2 now reaches in 10s what CatBoost achieves in 4h of tuning 🤯

Merci pour l’opportunité d’avoir échangé sur mes recherches et mes expériences ! Merci à mes directeurs de thèse @gabrielpeyre et @RemiGribonval pour votre supervision 😊

I had the opportunity to present #HuMMuS at @ECCBinfo — amazing experience! Huge thanks to the organisers for their formidable job. 🫶 And special mention for the food and fresh hummus! Perfectly on-point snack reminder 😋🧆

After a very constructive back and forth with editors and reviewers of @NatureComms, scConfluence has now been published @LauCan88 @gabrielpeyre ! I'll present it this afternoon at the poster session of @ECCBinfo (P296) Published version:

𝗕𝗔𝗖𝗞 𝗧𝗢 𝗕𝗔𝗖𝗞 🥋 L'équipe de France 🇫🇷 de #Judo conserve son titre de champion olympique par équipe mixte 🥇 #JeuxOlympiques | #Paris2024

🚨🚨 AI in Bio release 🧬  Very happy to share my work on a Large Cell Model for Gene Network Inference. It is for now just a preprint and more is to come. We are asking the question: “What can 50M cells tell us about gene networks?” ❓Behind it, other questions arose like:

🎉 New preprint! https://t.co/XXspy6nlwX STORIES learns a differentiation potential from spatial transcriptomics profiled at several time points using Fused Gromov-Wasserstein, an extension of Optimal Transport. @gabrielpeyre @LauCan88

STORIES: Learning cell fate landscapes from spatial transcriptomics using Fused Gromov-Wasserstein https://t.co/JYdsFiGrfX

Come to our #ICML2024 poster presentation tomorrow at 1:30 pm (Poster #903)!

🚨🚨New ICML 2024 Paper: https://t.co/X0YczCtZ9k How do Transformers perform In-Context Autoregressive Learning? We investigate how causal Transformers learn simple autoregressive processes or order 1. with @RGiryes, @btreetaiji, @mblondel_ml and @gabrielpeyre 🙏

Are you interested in cis-regulatory DNA interactions? In 2018, #Cicero introduced an algorithm for inferring cis-coaccessible networks from scATAC I’m excited to share #Circe, a Python implementation that is 100x faster and uses 5x less memory! @LauCan88 @JulioSaezRod 1/5

There is still time to apply for this postdoc position! If you have a machine learning background and you are interested in applications to genomics/health, do not hesitate to reach out! #postdocall #openposition #recruiting

If you like ResNet and enjoy Optimal Transport, you might enjoy this paper with Raphaël Barboni and F-X Vialard. We show that infinite width/depth ResNet are ("conditional") Wasserstein flows.

HuMMuS is finally out in Bioinformatics ! 🥳 https://t.co/LsTRgZ2yxj We provide new insights, notably on HuMMuS robustness, and methylation data contribution in identifying driver TFs. The revision was a very interesting journey, thanks everyone for all the great feedbacks !😊

scConfluence is available as an open-source Python package extensively documented and seamlessly integrated within the @scverse_team workflow. Visit https://t.co/KmbpNF0maP to try it!