Jérémie Kalfon

Doing a Ph.D. AI in Bio. | Ex @WhiteLabGx @BroadInstitute @MIT | Built @PiPleteam | ML, Cancer, Genomics, Data Sci, Entrepreneur, FullStack Dev | All Views Mine

[Jérémie Kalfon @jkobject]

🧑‍🎄🎄 Christmas Foundation Model Release: scPRINT-2

*One-liner:* a 20M-active-param single-cell foundation model trained on **350M cells / 16 species / 300 tissues / 500 cell types**.

[Jérémie Kalfon @jkobject]

Biology for you. This is showing you what we need more of and less of.

[Matt Kaeberlein @mkaeberlein]

Pretty interesting story in @ScienceMagazine this week on what looks like a serious problem in the senescence field. More than 400 papers apparently used the wrong antibody for p16-INK4a — an antibody that actually recognizes a completely different, unrelated protein (a component of the actin cytoskeleton). This affects work on senescent cell accumulation in aging and disease, and most critically, some of the evidence base for senolytic drug research.

What concerns me most is that many of these papers somehow got the "right" answer using the wrong antibody. That's not just an innocent reagent mix-up — it raises real questions about data fabrication or selective reporting in at least some of these labs. I've commented before about how ignoring data that doesn't fit the narrative is a major problem in certain areas of the longevity literature (e.g. sirtuins and NAD), and here a potentially widespread example in senescence.

Hopefully journals will investigate and retract as necessary, but based on my experience that seems optimistic. One concrete fix is that journals should flag problematic antibody product codes at submission so reviewers can catch this before publication. Reviewers should absolutely be on the lookout for this going forward.

However, these fixes won't address the larger problem. We need to understand how these scientists got the results they wanted and published them over 400 times (!!!): whether through intentional deception, incompetence, accident, or some legitimate explanation.

Credit for discovering this goes to @addictedtoigno1 who wrote about it first on his blog: For Better Science

https://t.co/BfuALVZCGn?

[Arnaud Bertrand @RnaudBertrand]

As someone who partially grew up among European elite kids like him, this reminds me just how incredibly hollow some of them are.

For a quick background, I went to one of the poshest high schools in France (Janson de Sailly, for those who know) and, afterwards, to what was at the time - and probably still is - the most expensive undergraduate school in Europe (EHL in Lausanne, Switzerland).

Needless to say, many of my classmates were from unbelievably privileged backgrounds. Just in my classroom in Lausanne I had the son of a (very famous) Russian oligarch, the son of Italy's largest real estate developer and the son of Spain's largest real estate developer (funnily, the latter two were flat mates).

Another classmate of mine came from the richest family in Naples, Italy and - while we were at school - his father (known in Naples under the nickname "Il Sultano") got arrested for having bribed half of Naples's city council - which, if you know Naples, ought to tell you something.

These were the kids I was doing group projects on business ethics with (literally) 😅

Anyhow, my story, and probably my luck, was that - before going to high school in Paris - I was raised in very normal public schools in the South of France where my friends were anything but wealthy. Their parents were farmers and everyday workers.

Which means - and I'd come to realize this was very important in life - that it was easy for me to understand how big a mistake it is to see money as identity and meaning - and to confuse someone's net worth with their actual worth.

What really struck me at the time was the contrast with my "poor" classmates of earlier in my life. They couldn't define themselves by what they had - by definition - and this forced them to reach deeper for their identity: their skills, knowledge, humor, etc.

Rich kids can skip that entire process, and the tragedy is that most of them do: they reach for the readymade identity that money provides. I remember being incredibly frustrated by many of my classmates, like "ok, I get it, your dad is rich and you own a lot of nice things but who are YOU, what else is there?" The answer, more often than not, was nothing.

To be fair, there were exceptions. One of my classmates I was most impressed by came from one of Zurich's wealthiest families (which, if you know Zurich, means insanely wealthy) yet he was almost OCD in not showing he had money: driving the shittiest car imaginable, living in a small studio, etc. He was very intellectual, very contrarian, and clearly at war with the idea that his family's wealth ought to define who he was.

I only discovered who he actually was when I started my first company and he approached me to invest: to discuss the investment I went to one of his family homes, which it turned out was a literal palatial castle on the shores of Geneva lake. The guy had decided to live in a small rundown studio when he literally had a castle sitting empty a 5-min drive away.

THAT I was impressed by: it's easy to see that money isn't meaning when you don't have any. To see it when you have more than almost anyone - when everyone around you is organized around the opposite assumption - is much harder. But to actually live it, to choose the studio when you have the castle keys in your pockets - with no audience to applaud you for that - that shows real depth.

At the end of the day, I think, the real distinction isn't between rich and poor but between people who exist from the inside out and people who exist from the outside in.

Wealth just happens to make it incredibly easy to be the latter, to skip the work of becoming someone and settle for a borrowed identity that glitters from the outside but is hollow all the way through. A Potemkin village identity.

This is actually a real societal issue, and magnified by social media (with idiotic posts like this one 👇): the more "outside in" folks out there, the less people with genuine internal anchors, the more fragile everything becomes.

When you think about it, everything that genuinely matters in a society is built by people who think for themselves: they take the world in, pass it through something genuinely their own, and give back something that didn't exist before: an idea, a conviction, a stand.

Every reform, every invention, every act of moral courage in history came from someone with an internal anchor strong enough to resist the current. Remove those people and all you have left is the current.

This isn't new, by the way. Most ancient traditions warn against exactly this, from the Bible (the golden calf story) to Confucius, who built his entire ethics around the distinction between the exemplary person (the Junzi, 君子) - oriented around internal cultivation and righteousness - and the petty person (Xiaoren, 小人), oriented around profit and gain. The junzi builds himself from the inside, the xiaoren chases what's outside.

So please, do not make the mistake of being impressed by wealthy people flaunting their wealth. Don't focus on the glitter, focus on the hollowness it's trying to hide.

[Until @untillabs]

Did you catch our latest blog post on our rewarming machine? 👀


With our magnet, a kidney can successfully traverse the danger zone of ice formation in under a minute, using only a few kilowatts. That means it can operate off of standard hospital outlets⚡️

All of our devices are designed with the patient and care team in mind. 
Check out the writeup!

1/5🧵

[Watt The Duck @sjowall69]

Bon, puisqu'à l'appui du programme économique délirant de Mélenchon, on nous ressort régulièrement l'argument d'autorité des 300 "économistes" qui l'auraient validé, il est temps de réanalyser en détail cette fameuse liste.

Spoiler : c'est du flan.

↩️

https://t.co/dG4a73Ifxk

[Dindon Fiscal @LeDindonFiscal]

Je viens de me taper le programme de Mélenchon sur le SMIC à 1 700 €.

Bravo déjà aux insoumis : contrairement à avant, c’est enfin complet et je peux en mesurer l’impact.

Par contre, je vais debunk le truc, car c’est un enfumage incroyable pour vos électeurs.

[Alan Murphy @Al_Murphy_]

1/ We built the Genomics × AI blog so the genomics + ML community can share work fast and actually discuss it — incremental results, negative results, tutorials — without waiting on a publisher. Posts are live, more landing over the coming weeks: https://t.co/a4YY6avrda

[John Arnold @johnarnold]

America's cultural ideal has been the self-made entrepreneur while Europe's was rooted in aristocracy, with status inherited rather than earned. Europe's inheritance laws show this divide.

Many European countries have "forced heirship" laws that require people to leave 50-75% of their estates to their children. Want to leave the majority of your wealth to charity? not allowed. Your kids are estranged from you, struggling with addiction, or irresponsible? still required to give them the money. Want your kids to avoid a life of entitlement? tough.

Incredibly, these laws look back at transfers made during your lifetime. If you have 3 children in France, you're required to bequeath them a minimum of 75% of your estate. Because French law calculates this based on your assets at death plus all lifetime gifts, giving away more than 25% of your wealth while alive means your heirs can legally sue to force charities or foundations to return the funds. This has limited the development of the nonprofit sector on the continent.

The cultural gap between an entrepreneurial society and one shaped by dynastic wealth is enormous. If you make it yourself, you tend to want your kids to do the same. If you inherit it, the primary goal is protecting the estate for the next gen.

Countries like Spain, France, and Italy legally entrench family dynasties, while America has historically sought to limit them through estate taxes. The result is not only a weaker culture of philanthropy and civil society in Europe, but also less economic dynamism.

[Anshul Kundaje @anshulkundaje]

Academic labs continue to lead on next generation tech dev for powering AI models for biology.

The next big leap in models of gene regulation will be when they truly master the long range functional architecture of the genome. 1/

[NewLimit @newlimit]

Following breakthrough results, we’re bringing longevity medicine to human trials.

We’ve raised a $435M Series C led by @foundersfund to make it happen.

Reprogramming cell age has the potential to create more healthy years for everyone. We're closer than ever to realizing it.

[Jérémie Kalfon @jkobject]

@labs_mann @ProteinAtlas @CarolineWeiss30 We're you a le to find cell states using the proteomic data that you couldn't with similar amount of scRNAseq data?

[Simon Maechling @simonmaechling]

You live in France, one of the most electrified and low-carbon countries on Earth.

The technology exists.
The comfort exists.
The power exists.

And yet people are told to sit in overheated apartments and “adapt.”

Not because we can’t solve the problem.

But because some decided discomfort is morally superior to abundance.

A strange ideology has emerged:
suffering as climate policy.

It’s almost like people think that sweating in the dark makes the planet cooler.

[Ed Krassenstein @EdKrassen]

BREAKING: @NYCMayor just announced COGE (Commission of Government Efficiency) and he takes a shot at Elon Musk in the process.

"COGE, COGE, yes. Now, Elon Musk manipulated the fact that so many people across this country want to see a government that is more efficient. He used that as a justification to simply slash and burn so much of the services that Americans rely on. What we are speaking about is a sincere fulfillment of a vision that ensures that city government is operating with the same level of focus that a working class New Yorker is when they're trying to balance their bills. And that means looking at the processes we have, that means looking at the procedures of city government, and that means looking at anything we can do to deliver a more efficient and more excellent government... It's just the name and what it should have been. I think government efficiency, these are words that somehow have been understood as if they are Republican priorities when in fact they are the priorities of anyone who believes in the public sector. And yet Elon Musk took that language and used it to cut as many jobs that were as critical as possible for so many of the neediest people across the country and across the world. Ours is going to be a focus on actually delivering efficiency, not as a byword for cutting services, but actually a sincere commitment to efficiency."

[Jérémie Kalfon @jkobject]

@ebetica We're you able to make a version of this plot with more orders of magnitudes available? 10**18-10**21

[Jérémie Kalfon @jkobject]

Pour ceux qui travaillent gratuitement aujourd'hui par solidarité pour rembourser les retraites du public, sachez que pour les fonctionnaires aujourd'hui c'est souvent férié: mairie, bibliothèque, ...

[Jérémie Kalfon @jkobject]

Thanks to Cécile Laurent & Lorette Noiret for the invite, and to Chloé-Agathe Azencott for opening the Omics session before me. (and thanks Paul Steinmetz, my conference pal 📸)
2/2

[Jérémie Kalfon @jkobject]

This morning I had the chance to present my research at the Cancéropôle IDF "AI & Cancer" day.
Talking single-cell foundation models to cancer researchers and clinicians was a great exercise! 😅
1/2

[Jérémie Kalfon @jkobject]

@bloodandtime1 Hi grant, Is there an open access version?

[Georgia Channing @cgeorgiaw]

Hugging Science just got a whole lot more huggier 🤗🤗🤗

Today, we’re releasing a family of genomics models, which we call Carbon

[Max Marchione @maxmarchione]

In some very real sense, Ozempic was invented in 1990. Pfizer ran the human trials and just never published them.

They showed it lowered blood glucose in diabetics, slowed gastric emptying, and killed hunger; the same 3 things that make Ozempic work today.

The joint venture agreement said internal data stayed internal, and that was that. Pfizer killed the program in 1991. The reasoning, as far as I can tell, was that nobody would ever want an injectable diabetes drug besides insulin.

So, the license went back to the hospital in Boston that held the patents.

Novo picked it up in 1992 and spent the next two decades building liraglutide, then semaglutide.

It's insane that data sat in a filing cabinet for 30+ years.

I only know this because Jeffrey Flier, one of the Harvard scientists in the room, finally wrote it up. He's in his late 70s and didn't want the history to die with him.

This makes you wonder what else is in those filing cabinets.

Ozempic could've existed 27 years ago.

[Thag Simmons @d_h_sanders]

It effectively illustrates that you could not commit a mass shooting with technology from the 18th century