🚀 #NatureMachineIntelligence 🚀 Conditional Monge Gap: a lightweight method for generalizable Optimal Transport across perturbations. Works well on unseen drugs, doses & time points. <1M params! Paper: ibm.biz/conditional-monge-gap Code: ibm.biz/conditional-monge-gap-code @marianna-raps.bsky.social

Conditional Monge Gap enables generalizable single-cell perturbation modelling - Nature Machine Intelligence

Driessen et al. present a conditional optimal transport method that can model the distribution shift between perturbed and unperturbed cell transcriptomes and that can generalize to unseen contexts.

ibm.biz

New preprint 🧫🧬 Spatial transcriptomics (~550,000 cells, 2,432 patient-derived organoids): we map gene expression, shape, and function in space to understand cancer biology and drug response. w/ @marianna-raps.bsky.social @khomicsko.bsky.social and Maxim Norkin www.biorxiv.org/content/10.6...

Looking to start your lab in generative biology / AI? Come join us at the @sangerinstitute.bsky.social Sanger is core-funded so you can generate data at scale to train the next generation of models and understanding. Design/Engineering/Chemistry/Proteins/Pathways! pls RT tinyurl.com/GenGenFaculty

📢 4 #PhD positions in #Quantitative #Biology are available! ⚠️ Application deadline: 30.11.2025 More info 👉 career5.successfactors.eu/career?compa... @ciriellolab.bsky.social @marianna-raps.bsky.social

🔥 18-19/9/25 🔥 Computational Biology Symposium in Lausanne! Meet the speakers: Mo Lotfollahi @sangerinstitute.bsky.social is expert of cutting-edge #AI approaches to study #singlecell biology , #generativeAI, and #spatialbiology lotfollahi.com

🎤 It’s a pleasure to welcome @stephaniehicks.bsky.social from the @jhubiostat.bsky.social to present at the [BC]2 conference. 🔹Session chairs: @marianna-raps.bsky.social (@unil.bsky.social, CHUV) & @julienroux.bsky.social (@unibas.ch) 👉Register: tinyurl.com/3edr5hy6 #bc2basel

🚨 Our new paper: Conditional Optimal Transport generalizes well to unseen drugs. Big step forward, thanks to conditional Monge Gap! Even better: conditional models often beat local, non-conditional ones. arxiv.org/abs/2504.08328. Code public! Thanks to all co-authors @marianna-raps.bsky.social

Towards generalizable single-cell perturbation modeling via the Conditional Monge Gap

Learning the response of single-cells to various treatments offers great potential to enable targeted therapies. In this context, neural optimal transport (OT) has emerged as a principled methodologic...

arxiv.org

Looking forward to 2 days full of exciting CompBio research @unil.bsky.social this September 🧬🧫🔬 Hurry up and register!

Giovanni Ciriello@ciriellolab.bsky.social · 2y ago

After 6 (healthy) months of hiatus from social media, first post with a brand new conference announcement!! 🔥COMPUTATIONAL BIOLOGY IS EVERYWHERE! Join us in Lausanne for the first international Computational Biology Symposium! 18-19 September 2025 Registrations are OPEN! cbiosymposium.unil.ch

#IDWGS — Day of Women and Girls in Science 👩‍🔬 🚀 🏛️ To strengthen the leadership qualities of women researchers, the SNSF ran the #PRIMA #Leadership Programme for five years. Now, some of the participants have written a book to share some of their stories. 📆 Book launch: 29 September 2025

Precision Dermatology 2.0: #DataScience + #Immunology + #Genomics + #Clinical Science. Interdisciplinary collaboration at its best at the @CHUV. www.chuv.ch/fr/chuv-home... Paper on @naturecomms.bsky.social www.nature.com/articles/s41...

If you're @neuripsconf.bsky.social and into #OptimalTransport & bio, dont miss on Alice Driessen's spotlight talk on #ConditionalMongeGap for modeling CAR Response. Today #AIDrugX workshop! Positive results on OOD perturbations -> accurate gene expression prediction. Paper: ibm.biz/carot-pre

We are hiring (resharing appreciated)! Given recent successful grant applications (I got my SNSF Starting Grant 🚀), we are extending the LIAC team with multiple openings (PhD/postdoc) for 2025. Apply now (deadline: December 20th) by filling in this form: forms.fillout.com/t/eq5ADAw3kkus. #ChemSky

Hiring! I'm looking for a postdoc in machine learning of spatial single-cell data. Exciting project to develop methods for modelling cellular circuits in disease and regeneration of heart, liver and bone marrow using Xenium data from our lab. tinyurl.com/ymkvk7vn

Preprint alert! We profiled immune organization in sentinel lymph nodes (sLNs) of melanoma patients using spatial proteomics and spatial transcriptomics, and found that it is prognostic of distant metastases. biorxiv.org/cgi/content/...

Immune organization in sentinel lymph nodes of melanoma patients is prognostic of distant metastases

Sentinel lymph node (sLN) biopsy is part of melanoma staging, as involved LNs indicate a higher risk of recurrence. However, how the sLN is shaped by the tumor and reciprocally affects metastatic prog...

biorxiv.org

🚀 We're #Hiring #PhD students at #MLBio Lab at @EPFL through the #EDIC Program! 📅 Deadline: Dec 15 💥 We're part of School of Computer Science and School of Life Sciences at EPFL which gives access to excellent collaborators, network, and resources! 👉 Learn more at brbiclab.epfl.ch!

Women are under-represented at senior levels in #academia globally, & across all #science 🧪 disciplines, as shown by these "scissor-shaped curves" ✂️ So how can we ever achieve #gender #equality? We discuss various strategies in this #Cell Commentary #WomeninSTEM www.cell.com/cell/fulltex... 🧵 1/

If you are considering creating a Python package I strongly suggest cookiecutter-scverse by @scverse.bsky.social It’s a template that already incorporates many useful features. github.com/scverse/cook...

Not a #science post but somehow the perfect #firstblueskypost.. Somewhere in the Swiss Alps, the year of our Lord 2024 😎 Ladies, stay classy!

Sign of the times, no more bluebird on the biorxiv engagement tab..

Fist real post here — so pay attention, folks! Below is (yet another) nice study from our neighbours in the Oudelaar lab and peers SPP2202 and SFB1565, to which we added bottom-up MD simulations to further rationalise experimental data. Read on in @mariekeoudelaar.bsky.social ‘s thread!

Marieke Oudelaar@mariekeoudelaar.bsky.social · 2y ago

📣 Preprint alert! We have studied the formation of pair-wise and multi-way enhancer-promoter interactions in the #3Dgenome in a lymphoid-to-myeloid transdifferentiation system and learned interesting new things about their function in #GeneRegulation. 1/10 www.biorxiv.org/content/10.1...

Fresh off the presses: In "Learning on compressed molecular representations" Jan Weinreich and I looked into whether GZIP performed better than Neural Networks in chemical machine learning tasks. Yes, you've read that right. TL;DR: Yes, GZIP can perform better than baseline GNNs and MLPs. It can ..

Learning on compressed molecular representations

Last year, a preprint gained notoriety, proposing that a k-nearest neighbour classifier is able to outperform large-language models using compressed text as input and normalised compression distance (...

pubs.rsc.org

Thank you for this incredible honor! 🙏 A huge shoutout to the trainees in my lab—this achievement is thanks to you. Excited for what’s ahead from our Biomedical #DataScience Center at UNIL/CHUV 🚀 #Teamwork #Innovation #AI #HighlyCited2024 clarivate.com/highly-cited... @unil.bsky.social

Highly Cited Researchers | Clarivate

The Highly Cited Researchers 2024 list identifies and celebrates individuals who have demonstrated significant and broad influence in their fields of research. Through rigorous selection criteria and ...

clarivate.com

Interested in #singlecell and #spatial #metabolomics? Then book your calendar for December 10th! – Our online, free event will summarize major achievements of the field in 2024. #metabolism #omics #MALDI #EPFL With Giovanni D'Angelo and our #PhD students we prepared for you a fantastic lineup. 🧵 1/5

Alma Dal Co was an incredible scientist and a wonderful person who left us far too soon. Last Friday, Sven Bergmann and the Alma Dal Co foundation organized a very special 2nd Memorial Symposium. It was mind-blowing to see how Alma‘s ideas continue to be a huge influence on all of us who knew her.

So many nice starter packs.. I couldn't find one related to spatial biology yet, so I started one 🧬🔬! Here's who I’ve included so far—let me know if you'd like to be added or suggest other must-follow accounts! #SpatialBiology go.bsky.app/SU34ELC

Here is an initial starter pack list on Machine Learning on Graphs: go.bsky.app/HN2MTzp

Machine Learning on Graphs

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Inspired by the other amazing starter packs - here's one for cancer researchers! I tried to make this broad - from immunology to genomics to cell biology and so much more.. This list also includes organizations & institutes supporting cancer researchers 🧪🔬⚕️🩺 Hope its useful! go.bsky.app/FEoaJMc

🧠Le 23 novembre aura lieu la Journée de l’intelligence artificielle organisée par l’UNIL et l’EPFL. L’occasion de parcourir ses bénéfices et risques dans les sciences biomédicales, glaciologiques et criminelles. À lire dans l'uniscope 👉 go.unil.ch/sMZUc

in case this is useful to someone in this massive platform migration: a starting pack for single-cell omics computational methods go.bsky.app/GmS1cH

single-cell computational methods

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go.bsky.app

this is what escaping twitter felt like