Jeremie Kalfon 👨💻🧬🤖🚀
@jkobject.com
Doing a Ph.D. AI in Bio. | Ex @WhiteLabGx @BroadInstitute @MIT | Built @PiPleteam | ML, Cancer, Genomics, Data Sci, Entrepreneur, FullStack Dev | All views are mine
We prefer some people to get cancer, MS, parkinson than to give a virus to people that will get the virus anyway. Many people might volunteer! Indeed, we give so much to associations against cancer, MS, and dementia, but when it comes time to do something about it, it seems no one wants to.
6/6
6/6
January 29, 2026 at 8:40 AM
We prefer some people to get cancer, MS, parkinson than to give a virus to people that will get the virus anyway. Many people might volunteer! Indeed, we give so much to associations against cancer, MS, and dementia, but when it comes time to do something about it, it seems no one wants to.
6/6
6/6
← Nowadays, no regulatory agency, even less in Europe, would let you do that.
5/6
5/6
January 29, 2026 at 8:40 AM
← Nowadays, no regulatory agency, even less in Europe, would let you do that.
5/6
5/6
You could recruit kids, give them the vaccine, and infect them with EBV directly, since you know that almost all of them will be at some point, then check if they get infected or not using sequencing (PCR tests, B-cell antigen sequencing), and accept this as the endpoint of the trial.
4/6
4/6
January 29, 2026 at 8:40 AM
You could recruit kids, give them the vaccine, and infect them with EBV directly, since you know that almost all of them will be at some point, then check if they get infected or not using sequencing (PCR tests, B-cell antigen sequencing), and accept this as the endpoint of the trial.
4/6
4/6
Because you need to recruit tens of thousands of young kids, test them often for infection, and wait decades to see symptoms of other diseases appear in some of them. The statistics are terrible.
But it could be cheap...
3/6
But it could be cheap...
3/6
January 29, 2026 at 8:40 AM
Because you need to recruit tens of thousands of young kids, test them often for infection, and wait decades to see symptoms of other diseases appear in some of them. The statistics are terrible.
But it could be cheap...
3/6
But it could be cheap...
3/6
From different cancers, skin diseases, dementia, parkinson and more.
The reason why there is no vaccine yet in 2026 is very interesting.
Basically, it is super expensive. But why is it so?
2/6
The reason why there is no vaccine yet in 2026 is very interesting.
Basically, it is super expensive. But why is it so?
2/6
January 29, 2026 at 8:40 AM
From different cancers, skin diseases, dementia, parkinson and more.
The reason why there is no vaccine yet in 2026 is very interesting.
Basically, it is super expensive. But why is it so?
2/6
The reason why there is no vaccine yet in 2026 is very interesting.
Basically, it is super expensive. But why is it so?
2/6
Reposted by Jeremie Kalfon 👨💻🧬🤖🚀
And then lucky to pursue through an atlas of cells of many types and species, with a focus on quality and diversity mattering more than quantity with @jkobject.com
January 27, 2026 at 1:10 PM
And then lucky to pursue through an atlas of cells of many types and species, with a focus on quality and diversity mattering more than quantity with @jkobject.com
December 17, 2025 at 7:08 AM
Paper: www.biorxiv.org/cont... • Code: github.com/cantinila...
Curious: **what’s the one benchmark you wish every single-cell foundation model reported by default?**
6/6
Curious: **what’s the one benchmark you wish every single-cell foundation model reported by default?**
6/6
scPRINT-2: Towards the next-generation of cell foundation models and benchmarks
Cell biology has been booming with foundation models trained on large single-cell RNA-seq databases, but benchmarks and capabilities remain unclear. We propose an additive benchmark across a gymnasium of tasks to discover which features improve performance. From these findings, we present scPRINT-2, a single-cell Foundation Model pre-trained across 350 million cells and 16 organisms. Our contributions in pre-training tasks, tokenization, and losses made scPRINT-2 state-of-the-art in expression denoising, cell embedding, and cell type prediction. Furthermore, with our cell-level architecture, scPRINT-2 becomes generative, as demonstrated by our expression imputation and counterfactual reasoning results. Finally, thanks to our pre-training database, we uncover generalization to unseen modalities and organisms. These studies, together with improved abilities in gene embeddings and gene network inference, place scPRINT-2 as a next-generation cell foundation model.
### Competing Interest Statement
The authors have declared no competing interest.
www.biorxiv.org
December 16, 2025 at 7:49 PM
Paper: www.biorxiv.org/cont... • Code: github.com/cantinila...
Curious: **what’s the one benchmark you wish every single-cell foundation model reported by default?**
6/6
Curious: **what’s the one benchmark you wish every single-cell foundation model reported by default?**
6/6
4. **Generalization:** evaluation on **unseen organisms, tasks, and modalities.** It is also a push to rethink some evaluation of scFM; **SOTA on many tasks**. 🥇 🏃 ⛷️ ⛹️♀️
🎁 If you’re reading papers over the break, I hope this is useful.
5/6
🎁 If you’re reading papers over the break, I hope this is useful.
5/6
December 16, 2025 at 7:49 PM
4. **Generalization:** evaluation on **unseen organisms, tasks, and modalities.** It is also a push to rethink some evaluation of scFM; **SOTA on many tasks**. 🥇 🏃 ⛷️ ⛹️♀️
🎁 If you’re reading papers over the break, I hope this is useful.
5/6
🎁 If you’re reading papers over the break, I hope this is useful.
5/6
3. **Data + pipeline:** unified **scBaseCount + Tahoe-100M + CELLxGENE**, with consistent preprocessing + weighted random sampling ****(and other practical bits that usually stay hidden) → **350M cells, 16 species, ~300 tissues, ~500 cell types**. 🌍🫁🐭
4/6
4/6
December 16, 2025 at 7:48 PM
3. **Data + pipeline:** unified **scBaseCount + Tahoe-100M + CELLxGENE**, with consistent preprocessing + weighted random sampling ****(and other practical bits that usually stay hidden) → **350M cells, 16 species, ~300 tissues, ~500 cell types**. 🌍🫁🐭
4/6
4/6
1. **Benchmark:** **42 components** of scFMs across a gymnasium of tasks; looking at dataset size, encoding, training, architectures, losses, etc. 📊
2. **Model:** **scPRINT-2** — *small but mighty* with **~20M active parameters**, built from the strongest ingredients we found. 🤖🧬
3/6
2. **Model:** **scPRINT-2** — *small but mighty* with **~20M active parameters**, built from the strongest ingredients we found. 🤖🧬
3/6
December 16, 2025 at 7:48 PM
1. **Benchmark:** **42 components** of scFMs across a gymnasium of tasks; looking at dataset size, encoding, training, architectures, losses, etc. 📊
2. **Model:** **scPRINT-2** — *small but mighty* with **~20M active parameters**, built from the strongest ingredients we found. 🤖🧬
3/6
2. **Model:** **scPRINT-2** — *small but mighty* with **~20M active parameters**, built from the strongest ingredients we found. 🤖🧬
3/6
After a few years building scFMs (scPRINT, Xpressor, scPRINT-2…), I wanted to do something more “complete” than just shipping a new model: understand what matters, train the best version we can, and stress-test generalization properly.
So this work is a 4-in-1 release:
2/6
So this work is a 4-in-1 release:
2/6
December 16, 2025 at 7:48 PM
After a few years building scFMs (scPRINT, Xpressor, scPRINT-2…), I wanted to do something more “complete” than just shipping a new model: understand what matters, train the best version we can, and stress-test generalization properly.
So this work is a 4-in-1 release:
2/6
So this work is a 4-in-1 release:
2/6
Thanks to Future4Care, Timothé Cynober, Whitelab Genomics, and Scienta Lab for organizing the event, and to Matteo Marengo, Clara Brouaux, and Gabriel Michaux for helping me manage the round table.
And thanks to my all-star panel: Yann Fleureau, Jeremy Besnard, Sofia Dahoune, and Steven Jerome
And thanks to my all-star panel: Yann Fleureau, Jeremy Besnard, Sofia Dahoune, and Steven Jerome
December 5, 2025 at 9:30 AM
Thanks to Future4Care, Timothé Cynober, Whitelab Genomics, and Scienta Lab for organizing the event, and to Matteo Marengo, Clara Brouaux, and Gabriel Michaux for helping me manage the round table.
And thanks to my all-star panel: Yann Fleureau, Jeremy Besnard, Sofia Dahoune, and Steven Jerome
And thanks to my all-star panel: Yann Fleureau, Jeremy Besnard, Sofia Dahoune, and Steven Jerome
Without double-talk and with amazing panelists🧑🔬:
- Yann Fleureau, CEO, Blossom Life Sci & Founder of Cardiologs
- Steven Jerome, Director, Lead of Hit Discovery, Schrödinger
- Jérémy Besnard, Advisor, InFocusTx & Co-founder of Exsciencia
- Sofia Dahoune, Partner at Daphni
2/3
- Yann Fleureau, CEO, Blossom Life Sci & Founder of Cardiologs
- Steven Jerome, Director, Lead of Hit Discovery, Schrödinger
- Jérémy Besnard, Advisor, InFocusTx & Co-founder of Exsciencia
- Sofia Dahoune, Partner at Daphni
2/3
November 7, 2025 at 9:15 AM
Without double-talk and with amazing panelists🧑🔬:
- Yann Fleureau, CEO, Blossom Life Sci & Founder of Cardiologs
- Steven Jerome, Director, Lead of Hit Discovery, Schrödinger
- Jérémy Besnard, Advisor, InFocusTx & Co-founder of Exsciencia
- Sofia Dahoune, Partner at Daphni
2/3
- Yann Fleureau, CEO, Blossom Life Sci & Founder of Cardiologs
- Steven Jerome, Director, Lead of Hit Discovery, Schrödinger
- Jérémy Besnard, Advisor, InFocusTx & Co-founder of Exsciencia
- Sofia Dahoune, Partner at Daphni
2/3
👉Learn more & apply:
LinkedIn
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lnkd.in
October 6, 2025 at 8:46 AM
👉Learn more & apply:
🔷 Alnylam BioVenture Challenge — one day at Alnylam HQ, one shot at $100K in non-dilutive funding. Apply by Oct 17.
And — we’re also recruiting the next generation of Nucleate Leaders. If you’re ready to build biotech and strengthen the community behind it, apply today.
And — we’re also recruiting the next generation of Nucleate Leaders. If you’re ready to build biotech and strengthen the community behind it, apply today.
October 6, 2025 at 8:46 AM
🔷 Alnylam BioVenture Challenge — one day at Alnylam HQ, one shot at $100K in non-dilutive funding. Apply by Oct 17.
And — we’re also recruiting the next generation of Nucleate Leaders. If you’re ready to build biotech and strengthen the community behind it, apply today.
And — we’re also recruiting the next generation of Nucleate Leaders. If you’re ready to build biotech and strengthen the community behind it, apply today.
It’s about growth, collaboration, and the chance to give back by lifting others.
Two flagship opportunities are now open:
🔷 Activator 2026
— our equity-free accelerator equipping scientific founders with the tools to launch biotech ventures. Apply by Oct 20.
Two flagship opportunities are now open:
🔷 Activator 2026
— our equity-free accelerator equipping scientific founders with the tools to launch biotech ventures. Apply by Oct 20.
October 6, 2025 at 8:46 AM
It’s about growth, collaboration, and the chance to give back by lifting others.
Two flagship opportunities are now open:
🔷 Activator 2026
— our equity-free accelerator equipping scientific founders with the tools to launch biotech ventures. Apply by Oct 20.
Two flagship opportunities are now open:
🔷 Activator 2026
— our equity-free accelerator equipping scientific founders with the tools to launch biotech ventures. Apply by Oct 20.