Clément Weinreich
@clement-wh.bsky.social
Reposted by Clément Weinreich
Happy to share STORIES out now on Nature Methods
STORIES learns cell fate landscapes from spatial tramscripromics data profiled at several time points, thus allowing prediction of future cell states.
Led by Geert-Jan Huizing and Jules Samaran
www.nature.com/articles/s41...
@pasteur.fr
STORIES learns cell fate landscapes from spatial tramscripromics data profiled at several time points, thus allowing prediction of future cell states.
Led by Geert-Jan Huizing and Jules Samaran
www.nature.com/articles/s41...
@pasteur.fr
STORIES: learning cell fate landscapes from spatial transcriptomics using optimal transport - Nature Methods
By learning a differentiation potential using an optimal transport-based approach, STORIES models and infers cell fate trajectories using spatiotemporal omics data.
www.nature.com
November 4, 2025 at 7:25 AM
Happy to share STORIES out now on Nature Methods
STORIES learns cell fate landscapes from spatial tramscripromics data profiled at several time points, thus allowing prediction of future cell states.
Led by Geert-Jan Huizing and Jules Samaran
www.nature.com/articles/s41...
@pasteur.fr
STORIES learns cell fate landscapes from spatial tramscripromics data profiled at several time points, thus allowing prediction of future cell states.
Led by Geert-Jan Huizing and Jules Samaran
www.nature.com/articles/s41...
@pasteur.fr
Reposted by Clément Weinreich
I'm presenting #CIRCE, a Python package to infer co-accessible DNA region networks 🧬
Based on #Cicero 's algorithm (Pliner et al.), it runs ~150x faster, processing an atlas of 700k cells in less than 40 min! ⛷️
Short paper: doi.org/10.1101/2025...
Code: github.com/cantinilab/CIRCE
1/5 ⬇️
Based on #Cicero 's algorithm (Pliner et al.), it runs ~150x faster, processing an atlas of 700k cells in less than 40 min! ⛷️
Short paper: doi.org/10.1101/2025...
Code: github.com/cantinilab/CIRCE
1/5 ⬇️
September 30, 2025 at 12:23 PM
I'm presenting #CIRCE, a Python package to infer co-accessible DNA region networks 🧬
Based on #Cicero 's algorithm (Pliner et al.), it runs ~150x faster, processing an atlas of 700k cells in less than 40 min! ⛷️
Short paper: doi.org/10.1101/2025...
Code: github.com/cantinilab/CIRCE
1/5 ⬇️
Based on #Cicero 's algorithm (Pliner et al.), it runs ~150x faster, processing an atlas of 700k cells in less than 40 min! ⛷️
Short paper: doi.org/10.1101/2025...
Code: github.com/cantinilab/CIRCE
1/5 ⬇️
Reposted by Clément Weinreich
It was received quite enthusiastically here so time to share it again!!!
Our #ICLR2025 blog post on Flow Matching was published yesterday : iclr-blogposts.github.io/2025/blog/co...
My PhD student @annegnx.bsky.social will present it tomorrow in ICLR, 👉poster session 4, 3 pm, #549 in Hall 3/2B 👈
Our #ICLR2025 blog post on Flow Matching was published yesterday : iclr-blogposts.github.io/2025/blog/co...
My PhD student @annegnx.bsky.social will present it tomorrow in ICLR, 👉poster session 4, 3 pm, #549 in Hall 3/2B 👈
A Visual Dive into Conditional Flow Matching | ICLR Blogposts 2025
Conditional flow matching (CFM) was introduced by three simultaneous papers at ICLR 2023, through different approaches (conditional matching, rectifying flows and stochastic interpolants). <br/> The m...
iclr-blogposts.github.io
April 24, 2025 at 1:45 PM
It was received quite enthusiastically here so time to share it again!!!
Our #ICLR2025 blog post on Flow Matching was published yesterday : iclr-blogposts.github.io/2025/blog/co...
My PhD student @annegnx.bsky.social will present it tomorrow in ICLR, 👉poster session 4, 3 pm, #549 in Hall 3/2B 👈
Our #ICLR2025 blog post on Flow Matching was published yesterday : iclr-blogposts.github.io/2025/blog/co...
My PhD student @annegnx.bsky.social will present it tomorrow in ICLR, 👉poster session 4, 3 pm, #549 in Hall 3/2B 👈
Reposted by Clément Weinreich
Excited to see scPRINT published in @natcomms.nature.com ! scPRINT is a large cell model for the inference of gene networks pre-trained on 50Mcells with innovative pretraining tasks inspired from biology. Work led by @jkobject.com
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! 🎉🧬
www.nature.com/artic...
www.nature.com/artic...
scPRINT: pre-training on 50 million cells allows robust gene network predictions
Nature Communications - Authors present a state-of-the-art cell foundation model trained on 50 million cells. They show that the model generates a meaningful gene network and has zero-shot...
www.nature.com
April 16, 2025 at 1:16 PM
Excited to see scPRINT published in @natcomms.nature.com ! scPRINT is a large cell model for the inference of gene networks pre-trained on 50Mcells with innovative pretraining tasks inspired from biology. Work led by @jkobject.com
Reposted by Clément Weinreich
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! 🎉🧬
www.nature.com/artic...
www.nature.com/artic...
scPRINT: pre-training on 50 million cells allows robust gene network predictions
Nature Communications - Authors present a state-of-the-art cell foundation model trained on 50 million cells. They show that the model generates a meaningful gene network and has zero-shot...
www.nature.com
April 16, 2025 at 12:53 PM
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! 🎉🧬
www.nature.com/artic...
www.nature.com/artic...
Reposted by Clément Weinreich
AI for life sciences day 2 started!
@m-albert.bsky.social is now teaching AI for image analysis. Felipe Llinares from Bioptimus will then talk about LLMs, with short talks from @jkobject.com from my team and @emordret.bsky.social from @audeber.bsky.social team.
@pasteur.fr @pasteuredu.bsky.social
@m-albert.bsky.social is now teaching AI for image analysis. Felipe Llinares from Bioptimus will then talk about LLMs, with short talks from @jkobject.com from my team and @emordret.bsky.social from @audeber.bsky.social team.
@pasteur.fr @pasteuredu.bsky.social
March 18, 2025 at 8:50 AM
AI for life sciences day 2 started!
@m-albert.bsky.social is now teaching AI for image analysis. Felipe Llinares from Bioptimus will then talk about LLMs, with short talks from @jkobject.com from my team and @emordret.bsky.social from @audeber.bsky.social team.
@pasteur.fr @pasteuredu.bsky.social
@m-albert.bsky.social is now teaching AI for image analysis. Felipe Llinares from Bioptimus will then talk about LLMs, with short talks from @jkobject.com from my team and @emordret.bsky.social from @audeber.bsky.social team.
@pasteur.fr @pasteuredu.bsky.social
Very happy to start this new journey!!
Welcome to two new lab members @clement-wh.bsky.social (cosupervision @lucapinello.bsky.social )and Anna Audit (cosupervision @gabrielpeyre.bsky.social )! Recruited on the ERC StG MULTI-viewCELL to work on GRN inference and cell trajectory inference from temporal single-cell RNA data, respectively
December 2, 2024 at 4:54 PM
Very happy to start this new journey!!
Reposted by Clément Weinreich
I wrote a summary of the main ingredients of the neat proof by Hugo Lavenant that diffusion models do not generally define optimal transport. github.com/mathematical...
November 30, 2024 at 8:35 AM
I wrote a summary of the main ingredients of the neat proof by Hugo Lavenant that diffusion models do not generally define optimal transport. github.com/mathematical...
Reposted by Clément Weinreich
Anne Gagneux, Ségolène Martin, @quentinbertrand.bsky.social Remi Emonet and I wrote a tutorial blog post on flow matching: dl.heeere.com/conditional-... with lots of illustrations and intuition!
We got this idea after their cool work on improving Plug and Play with FM: arxiv.org/abs/2410.02423
We got this idea after their cool work on improving Plug and Play with FM: arxiv.org/abs/2410.02423
November 27, 2024 at 9:00 AM
Anne Gagneux, Ségolène Martin, @quentinbertrand.bsky.social Remi Emonet and I wrote a tutorial blog post on flow matching: dl.heeere.com/conditional-... with lots of illustrations and intuition!
We got this idea after their cool work on improving Plug and Play with FM: arxiv.org/abs/2410.02423
We got this idea after their cool work on improving Plug and Play with FM: arxiv.org/abs/2410.02423
Reposted by Clément Weinreich
Johnson-Lindenstrauss lemma in action:
it is possible to embed any cloud of N points from R^d into R^k without distorting their respective distances too much, provided k is not too small (independently of d!)
Better: any random Gaussian embedding works with high proba!
it is possible to embed any cloud of N points from R^d into R^k without distorting their respective distances too much, provided k is not too small (independently of d!)
Better: any random Gaussian embedding works with high proba!
November 25, 2024 at 9:58 AM
Johnson-Lindenstrauss lemma in action:
it is possible to embed any cloud of N points from R^d into R^k without distorting their respective distances too much, provided k is not too small (independently of d!)
Better: any random Gaussian embedding works with high proba!
it is possible to embed any cloud of N points from R^d into R^k without distorting their respective distances too much, provided k is not too small (independently of d!)
Better: any random Gaussian embedding works with high proba!
Reposted by Clément Weinreich
Looking for a postdoc in comp bio, single cell, ml and data science in an amazing city like Paris? 🗼
Come join the Cantinilab!
emploi.cnrs.fr/Offres/CDD/U... (better english version coming up soon)
Come join the Cantinilab!
emploi.cnrs.fr/Offres/CDD/U... (better english version coming up soon)
Portail Emploi CNRS - Offre d'emploi - Post-doctorat (H/F) en développement de méthodes d'apprentissage automatique pour les données omiques unicellulaires
emploi.cnrs.fr
November 20, 2024 at 2:20 PM
Looking for a postdoc in comp bio, single cell, ml and data science in an amazing city like Paris? 🗼
Come join the Cantinilab!
emploi.cnrs.fr/Offres/CDD/U... (better english version coming up soon)
Come join the Cantinilab!
emploi.cnrs.fr/Offres/CDD/U... (better english version coming up soon)