Dominique Beaini
@dom-beaini.bsky.social
Research Lead at @valenceai.bsky.social, Adjunct prof at @UMontreal and @Mila_quebec, interested in AI, deep learning, drug discovery, graphs, geometry, biology, chemistry, physics, philosophy, and the origin of life 🧠🦠
Aims to become a crazy scientist 👨🔬
Aims to become a crazy scientist 👨🔬
Pinned
Dominique Beaini
@dom-beaini.bsky.social
· Dec 15
Excited to be presenting MolPhenix today as an #oral presentation at the @neuripsconf.bsky.social workshop: Foundation Models for Science!
3 out the 6 oral presentations in that workshop are from @valenceai.bsky.social / @recursionpharma.bsky.social
Join us in West Meeting Room 202-204 at 12pm
3 out the 6 oral presentations in that workshop are from @valenceai.bsky.social / @recursionpharma.bsky.social
Join us in West Meeting Room 202-204 at 12pm
Very excited by this work! Simultaneously learn the DFT and sample the Boltzmann distribution by using two GPUs concurrently.
Amazing stuff!
Amazing stuff!
(1/n)🚨Train a model solving DFT for any geometry with almost no training data
Introducing Self-Refining Training for Amortized DFT: a variational method that predicts ground-state solutions across geometries and generates its own training data!
📜 arxiv.org/abs/2506.01225
💻 github.com/majhas/self-...
Introducing Self-Refining Training for Amortized DFT: a variational method that predicts ground-state solutions across geometries and generates its own training data!
📜 arxiv.org/abs/2506.01225
💻 github.com/majhas/self-...
June 10, 2025 at 9:00 PM
Very excited by this work! Simultaneously learn the DFT and sample the Boltzmann distribution by using two GPUs concurrently.
Amazing stuff!
Amazing stuff!
🤯 We can now directly interact with biology via this new foundational knowledge graph. A must read 🧵
1/ Introducing TxPert: a new model that predicts transcriptional responses across diverse biological contexts
It’s designed to generalize across unseen single-gene perturbations, novel combinations of gene perturbations, and even new cell types 🧵
www.valencelabs.com/txpert-predi...
It’s designed to generalize across unseen single-gene perturbations, novel combinations of gene perturbations, and even new cell types 🧵
www.valencelabs.com/txpert-predi...
TxPert: Predicting Cellular Responses to Unseen Genetic Perturbations - Valence Labs
We introduce TxPert: a state-of-the-art model that leverages multiple biological knowledge networks to accurately predict transcriptional responses under OOD scenarios.
www.valencelabs.com
May 22, 2025 at 2:28 PM
🤯 We can now directly interact with biology via this new foundational knowledge graph. A must read 🧵
Everyone’s chasing AGI - but what’s the #DrugDiscovery equivalent?
Meet the Virtual Cell: our bold roadmap to curing any disease by simulating the building block of human biology
Check out @valenceai.bsky.social vision of curing diseases with GPU-based scientific discovery
Meet the Virtual Cell: our bold roadmap to curing any disease by simulating the building block of human biology
Check out @valenceai.bsky.social vision of curing diseases with GPU-based scientific discovery
1/ At Valence Labs, @recursionpharma.bsky.social's AI research engine, we’re focused on advancing drug discovery outcomes through cutting-edge computational methods
Today, we're excited to share our vision for building virtual cells, guided by the predict-explain-discover framework 🧵
Today, we're excited to share our vision for building virtual cells, guided by the predict-explain-discover framework 🧵
May 20, 2025 at 5:59 PM
Everyone’s chasing AGI - but what’s the #DrugDiscovery equivalent?
Meet the Virtual Cell: our bold roadmap to curing any disease by simulating the building block of human biology
Check out @valenceai.bsky.social vision of curing diseases with GPU-based scientific discovery
Meet the Virtual Cell: our bold roadmap to curing any disease by simulating the building block of human biology
Check out @valenceai.bsky.social vision of curing diseases with GPU-based scientific discovery
Submit a 1-page abstract of your Neurips work to present it to the MoML conference on June 18th in Montreal
(1/3)The poster submission deadline for MoML 2025 has been extended to May 20th, 2025.
Don’t miss an opportunity to share your work at this years conference.
Submit here: portal.ml4dd.com/moml-2025-po...
Don’t miss an opportunity to share your work at this years conference.
Submit here: portal.ml4dd.com/moml-2025-po...
May 14, 2025 at 12:32 AM
Submit a 1-page abstract of your Neurips work to present it to the MoML conference on June 18th in Montreal
MoML conference is back on June 18th!
(1/5) The Molecular Machine Learning Conference (MoML) is back @mila-quebec.bsky.social this June 18th.
Join researchers advancing machine learning, molecular modeling, and therapeutic design.
Tickets are free for students.
Register Today: portal.ml4dd.com/events/molec...
Join researchers advancing machine learning, molecular modeling, and therapeutic design.
Tickets are free for students.
Register Today: portal.ml4dd.com/events/molec...
April 17, 2025 at 2:54 PM
MoML conference is back on June 18th!
We're currently looking for a PostDoc position at @umontreal.ca and @mila-quebec.bsky.social to build a multimodal bacterial representation for anti-biotic with biologists from brunlab.com using:
- Phenomics
- Transcriptiomics
- Structural bio
- Viability
- ADME
DM me for more info
- Phenomics
- Transcriptiomics
- Structural bio
- Viability
- ADME
DM me for more info
Brun Lab – Université de Montréal
brunlab.com
February 6, 2025 at 4:47 PM
We're currently looking for a PostDoc position at @umontreal.ca and @mila-quebec.bsky.social to build a multimodal bacterial representation for anti-biotic with biologists from brunlab.com using:
- Phenomics
- Transcriptiomics
- Structural bio
- Viability
- ADME
DM me for more info
- Phenomics
- Transcriptiomics
- Structural bio
- Viability
- ADME
DM me for more info
Reposted by Dominique Beaini
We’re absolutely thrilled to have an exciting lineup of speakers this year covering a wide range of topics, including @pseudomanifold.topology.rocks @dom-beaini.bsky.social @mathildepapillon.bsky.social Dhananjay Bhaskar, Naoki Saito!
January 26, 2025 at 1:54 PM
We’re absolutely thrilled to have an exciting lineup of speakers this year covering a wide range of topics, including @pseudomanifold.topology.rocks @dom-beaini.bsky.social @mathildepapillon.bsky.social Dhananjay Bhaskar, Naoki Saito!
Reposted by Dominique Beaini
First place: “How Molecules Impact Cells: Unlocking Contrastive PhenoMolecular Retrieval”
Predicting the effect of molecules on cells with MolPhenix
Paper: www.arxiv.org/abs/2409.08302
@dom-beaini.bsky.social
Predicting the effect of molecules on cells with MolPhenix
Paper: www.arxiv.org/abs/2409.08302
@dom-beaini.bsky.social
December 20, 2024 at 6:25 PM
First place: “How Molecules Impact Cells: Unlocking Contrastive PhenoMolecular Retrieval”
Predicting the effect of molecules on cells with MolPhenix
Paper: www.arxiv.org/abs/2409.08302
@dom-beaini.bsky.social
Predicting the effect of molecules on cells with MolPhenix
Paper: www.arxiv.org/abs/2409.08302
@dom-beaini.bsky.social
Reposted by Dominique Beaini
Thanks to the FM4Science workshop at #Neurips for recognizing MolPhenix as best paper!
We had so much fun working on this with Puria (co-first author), @karush17.bsky.social, Frederik and co-supervised by Maciej and @dom-beaini.bsky.social
arxiv.org/abs/2409.08302
@valenceai.bsky.social
We had so much fun working on this with Puria (co-first author), @karush17.bsky.social, Frederik and co-supervised by Maciej and @dom-beaini.bsky.social
arxiv.org/abs/2409.08302
@valenceai.bsky.social
December 17, 2024 at 2:47 AM
Thanks to the FM4Science workshop at #Neurips for recognizing MolPhenix as best paper!
We had so much fun working on this with Puria (co-first author), @karush17.bsky.social, Frederik and co-supervised by Maciej and @dom-beaini.bsky.social
arxiv.org/abs/2409.08302
@valenceai.bsky.social
We had so much fun working on this with Puria (co-first author), @karush17.bsky.social, Frederik and co-supervised by Maciej and @dom-beaini.bsky.social
arxiv.org/abs/2409.08302
@valenceai.bsky.social
Definitely a career highlight to be awarded a best paper award at @neuripsconf.bsky.social FM4Science 🤩🤩
But even more exciting is that the 2nd and 3rd awards are given to colleagues Kian and Mohit, a podium sweep from @valenceai.bsky.social / @recursionpharma.bsky.social 🥇🥈🥉
But even more exciting is that the 2nd and 3rd awards are given to colleagues Kian and Mohit, a podium sweep from @valenceai.bsky.social / @recursionpharma.bsky.social 🥇🥈🥉
December 15, 2024 at 9:50 PM
Definitely a career highlight to be awarded a best paper award at @neuripsconf.bsky.social FM4Science 🤩🤩
But even more exciting is that the 2nd and 3rd awards are given to colleagues Kian and Mohit, a podium sweep from @valenceai.bsky.social / @recursionpharma.bsky.social 🥇🥈🥉
But even more exciting is that the 2nd and 3rd awards are given to colleagues Kian and Mohit, a podium sweep from @valenceai.bsky.social / @recursionpharma.bsky.social 🥇🥈🥉
Excited to be presenting MolPhenix today as an #oral presentation at the @neuripsconf.bsky.social workshop: Foundation Models for Science!
3 out the 6 oral presentations in that workshop are from @valenceai.bsky.social / @recursionpharma.bsky.social
Join us in West Meeting Room 202-204 at 12pm
3 out the 6 oral presentations in that workshop are from @valenceai.bsky.social / @recursionpharma.bsky.social
Join us in West Meeting Room 202-204 at 12pm
December 15, 2024 at 3:53 PM
Excited to be presenting MolPhenix today as an #oral presentation at the @neuripsconf.bsky.social workshop: Foundation Models for Science!
3 out the 6 oral presentations in that workshop are from @valenceai.bsky.social / @recursionpharma.bsky.social
Join us in West Meeting Room 202-204 at 12pm
3 out the 6 oral presentations in that workshop are from @valenceai.bsky.social / @recursionpharma.bsky.social
Join us in West Meeting Room 202-204 at 12pm
We're hiringggggg
Interested? Come find me at @neuripsconf.bsky.social :)
valencelabs.com/careers
#machinelearning #AI #drugdiscovery
Interested? Come find me at @neuripsconf.bsky.social :)
valencelabs.com/careers
#machinelearning #AI #drugdiscovery
December 14, 2024 at 12:18 AM
We're hiringggggg
Interested? Come find me at @neuripsconf.bsky.social :)
valencelabs.com/careers
#machinelearning #AI #drugdiscovery
Interested? Come find me at @neuripsconf.bsky.social :)
valencelabs.com/careers
#machinelearning #AI #drugdiscovery
Reposted by Dominique Beaini
Special delivery from @neuripsconf.bsky.social! We just released our latest certified dataset, RxRx3-core, which includes labeled images of 735 genetic knockouts & 1,674 small-molecule perturbations. The related benchmark evaluates the zero-shot prediction of compound-gene activity. #NeurIPS
👇
👇
🛡️ New certified dataset and benchmark from
@recursionpharma.bsky.social!
Did you know that high-dimensional data like cell images (i.e. phenomics) can help us understand the relationship between compounds and genes? 🧵
Dataset: polarishub.io/datasets/rec...
Benchmark: polarishub.io/benchmarks/r...
@recursionpharma.bsky.social!
Did you know that high-dimensional data like cell images (i.e. phenomics) can help us understand the relationship between compounds and genes? 🧵
Dataset: polarishub.io/datasets/rec...
Benchmark: polarishub.io/benchmarks/r...
December 13, 2024 at 7:53 PM
Special delivery from @neuripsconf.bsky.social! We just released our latest certified dataset, RxRx3-core, which includes labeled images of 735 genetic knockouts & 1,674 small-molecule perturbations. The related benchmark evaluates the zero-shot prediction of compound-gene activity. #NeurIPS
👇
👇
Huge crowd at the Molphenix paper 🤩🤩 presented by @phil-fradkin.bsky.social and Puria
Follow us to our spotlight paper on MolPhenix at
@neuripsconf.bsky.social - the foundation model that can predict the effect of any given molecule & concentration pair on phenotypic cell assays and cell morphology -- presented by researchers at @valenceai.bsky.social. 🧵
@neuripsconf.bsky.social - the foundation model that can predict the effect of any given molecule & concentration pair on phenotypic cell assays and cell morphology -- presented by researchers at @valenceai.bsky.social. 🧵
December 12, 2024 at 3:36 AM
Huge crowd at the Molphenix paper 🤩🤩 presented by @phil-fradkin.bsky.social and Puria
Great news from Recursion! Getting closer to industrialization of drug discovery
December 11, 2024 at 1:13 AM
Great news from Recursion! Getting closer to industrialization of drug discovery
Super excited to be flying to @neuripsconf.bsky.social to present 3 awesome papers! Including an oral presentation 📣!
Check out MolGPS, MolPhenix, and ET-Flow.
You can find us Wednesday and Friday at the posters, and Sunday for the oral!
Thanks to an amazing team of co-authors in the thread 🧵
Check out MolGPS, MolPhenix, and ET-Flow.
You can find us Wednesday and Friday at the posters, and Sunday for the oral!
Thanks to an amazing team of co-authors in the thread 🧵
December 9, 2024 at 7:20 PM
Super excited to be flying to @neuripsconf.bsky.social to present 3 awesome papers! Including an oral presentation 📣!
Check out MolGPS, MolPhenix, and ET-Flow.
You can find us Wednesday and Friday at the posters, and Sunday for the oral!
Thanks to an amazing team of co-authors in the thread 🧵
Check out MolGPS, MolPhenix, and ET-Flow.
You can find us Wednesday and Friday at the posters, and Sunday for the oral!
Thanks to an amazing team of co-authors in the thread 🧵
My students @majhas.bsky.social and @jyoonlee.bsky.social are now on bluesky!
They're new in the field, but they're assuming BIG! You should follow them to not miss out on their work.
Already a @neuripsconf.bsky.social paper only a few months after they started.
They're new in the field, but they're assuming BIG! You should follow them to not miss out on their work.
Already a @neuripsconf.bsky.social paper only a few months after they started.
We’re excited to present ET-Flow at #NeurIPS 2024—an Equivariant Flow Matching model that combines simplicity, efficiency, and precision to set a new standard for 3D molecular conformer generation.
🔖Paper: arxiv.org/abs/2410.22388
🔗Github: github.com/shenoynikhil...
🔖Paper: arxiv.org/abs/2410.22388
🔗Github: github.com/shenoynikhil...
December 7, 2024 at 6:57 PM
My students @majhas.bsky.social and @jyoonlee.bsky.social are now on bluesky!
They're new in the field, but they're assuming BIG! You should follow them to not miss out on their work.
Already a @neuripsconf.bsky.social paper only a few months after they started.
They're new in the field, but they're assuming BIG! You should follow them to not miss out on their work.
Already a @neuripsconf.bsky.social paper only a few months after they started.
ET-Flow shows, once again, that equivariance is better than Transformer when physical precision matters!
come see us at @neuripsconf.bsky.social !!
come see us at @neuripsconf.bsky.social !!
December 7, 2024 at 3:57 PM
ET-Flow shows, once again, that equivariance is better than Transformer when physical precision matters!
come see us at @neuripsconf.bsky.social !!
come see us at @neuripsconf.bsky.social !!
Reposted by Dominique Beaini
I'll be at #NeurIPS2024 next week presenting 4 papers all on generative models!
Happy to meet old friends and new ones at all the fun events!
Papers in thread 🧵
Happy to meet old friends and new ones at all the fun events!
Papers in thread 🧵
December 7, 2024 at 2:39 AM
I'll be at #NeurIPS2024 next week presenting 4 papers all on generative models!
Happy to meet old friends and new ones at all the fun events!
Papers in thread 🧵
Happy to meet old friends and new ones at all the fun events!
Papers in thread 🧵
That's exactly how I feel about science. There's just too many papers on too many things and too much science going on to keep up.
There's probably 100x more scientists in 2025 than there was during Einstein's time in 1925.
There's probably 100x more scientists in 2025 than there was during Einstein's time in 1925.
As someone who actually would love to write fiction, following writers on this site is intensely demotivating. There are just *so many* books out there, even in relatively niche genres, and it feels like no one is reading them and each one represents so much work!
December 6, 2024 at 2:55 AM
That's exactly how I feel about science. There's just too many papers on too many things and too much science going on to keep up.
There's probably 100x more scientists in 2025 than there was during Einstein's time in 1925.
There's probably 100x more scientists in 2025 than there was during Einstein's time in 1925.
Reposted by Dominique Beaini
Hey 👋 I'm new here and I did my best to compile some starter packs to help other new people in the same community!
I probably missed some people so please help me update my lists :)
1/6 Machine learning for drug discovery
go.bsky.app/2PpxWLc
More in the thread! 🧵
I probably missed some people so please help me update my lists :)
1/6 Machine learning for drug discovery
go.bsky.app/2PpxWLc
More in the thread! 🧵
December 5, 2024 at 8:27 PM
Hey 👋 I'm new here and I did my best to compile some starter packs to help other new people in the same community!
I probably missed some people so please help me update my lists :)
1/6 Machine learning for drug discovery
go.bsky.app/2PpxWLc
More in the thread! 🧵
I probably missed some people so please help me update my lists :)
1/6 Machine learning for drug discovery
go.bsky.app/2PpxWLc
More in the thread! 🧵
Reposted by Dominique Beaini
For the structural biology enthusiasts of our followers!
2/6 AlphaFold and ML for structural bio
Regrouping various people working on ML for proteins and other structural problems in biology
go.bsky.app/KuXyaAM
Regrouping various people working on ML for proteins and other structural problems in biology
go.bsky.app/KuXyaAM
December 5, 2024 at 9:22 PM
For the structural biology enthusiasts of our followers!
Hey 👋 I'm new here and I did my best to compile some starter packs to help other new people in the same community!
I probably missed some people so please help me update my lists :)
1/6 Machine learning for drug discovery
go.bsky.app/2PpxWLc
More in the thread! 🧵
I probably missed some people so please help me update my lists :)
1/6 Machine learning for drug discovery
go.bsky.app/2PpxWLc
More in the thread! 🧵
December 5, 2024 at 8:27 PM
Hey 👋 I'm new here and I did my best to compile some starter packs to help other new people in the same community!
I probably missed some people so please help me update my lists :)
1/6 Machine learning for drug discovery
go.bsky.app/2PpxWLc
More in the thread! 🧵
I probably missed some people so please help me update my lists :)
1/6 Machine learning for drug discovery
go.bsky.app/2PpxWLc
More in the thread! 🧵
I'm genuinely excited for this competition! 🤩
I'm glad that the field is moving towards being able to test our models in real-world settings, rather than optimize an obscure test set!
I'm glad that the field is moving towards being able to test our models in real-world settings, rather than optimize an obscure test set!
🦠 We’re excited to announce our first competition in partnership with @asapdiscovery.bsky.social and @omsf.io!
Test your skills across three sub-challenges revolving around SARS-CoV-2 and MERS-CoV Mpro🧵
Full details: polarishub.io/competitions
Blog: polarishub.io/blog/antivir...
Test your skills across three sub-challenges revolving around SARS-CoV-2 and MERS-CoV Mpro🧵
Full details: polarishub.io/competitions
Blog: polarishub.io/blog/antivir...
December 3, 2024 at 6:47 PM
I'm genuinely excited for this competition! 🤩
I'm glad that the field is moving towards being able to test our models in real-world settings, rather than optimize an obscure test set!
I'm glad that the field is moving towards being able to test our models in real-world settings, rather than optimize an obscure test set!
Reposted by Dominique Beaini
📣 Announcing the first patient dosed in our Phase 1/2 clinical study of REC-1245 - a potential first-in-class RBM39 degrader for biomarker-enriched solid tumors and lymphoma and the first program to emerge from end-to-end use of the RecursionOS. #techbio More: ir.recursion.com/news-release...
December 3, 2024 at 1:41 PM
📣 Announcing the first patient dosed in our Phase 1/2 clinical study of REC-1245 - a potential first-in-class RBM39 degrader for biomarker-enriched solid tumors and lymphoma and the first program to emerge from end-to-end use of the RecursionOS. #techbio More: ir.recursion.com/news-release...