
Postdoc Fellow @IdoAmitLab. Interested in deciphering the complex cell-cell interactions in tumors
Rehovot, Israel
Joined October 2022
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Excited to share our fun journey through time with the amazing team @D_Birschenkaum @FlorianIngelfi1 Yonathan @kathleenabadie @AssafWeiner from the @IdoAmitLab, measuring the temporal dynamics of immune cells in the GBM!
We are very excited to present the development of Zman-seq (“Zman”, Hebrew for “time”), the 1st technology that measures single-cell transcriptomes and physical time in vivo, led by @D_Birschenkaum, @CuriousKX, @FlorianIngelfi1, @AssafWeiner
sciencedirect.com/science/ar…. (1/19)
Ken Xie retweeted
Google DeepMind researchers argue that LLMs will NEVER reach AGI.
It is mathematically impossible.
Every major AI model today, from ChatGPT to Claude, is built on the exact same foundation: statistical learning.
That means they don't actually learn how to think.
They just learn how to guess.
They train on massive datasets and optimize for average performance. They find shortcuts. They memorize patterns.
But a new paper just proved that this approach has a hard, impenetrable ceiling.
The paper, titled Beyond Statistical Learning: Exact Learning Is Essential for General Intelligence, exposes a fatal flaw in the entire AI industry.
Statistical learning works perfectly for drafting marketing emails or summarizing meetings.
But it fails catastrophically at strict, logical deduction.
If an AI learns rules statistically, it will always break when faced with a truly novel scenario. It can never guarantee flawless reasoning.
It will always, eventually, hallucinate.
For businesses deploying these models into zero-tolerance workflows, like financial analysis, legal compliance, or complex operations, this is a massive warning sign. You are building on a foundation that is mathematically guaranteed to crack.
The researchers proved that current models are fundamentally incapable of "Exact Learning"—the ability to learn and apply underlying rules perfectly across all possible inputs.
And here is the most crushing part.
You cannot fix this with more data. You cannot fix this by paying for larger models.
The researchers demonstrated that the fundamental math of how we train AI today physically prevents exact learning.
We spent the last five years scaling up our models, assuming that if we just made the statistical guesser big enough, it would magically turn into a logical reasoner.
This paper just shattered that illusion.
If we want AI that we can actually trust to run our operations, we have to completely rethink how algorithms are designed.
Ken Xie retweeted
Thrilled to share my freshly "baked" Baker lab paper. We took a bottom-up approach to designing transcriptional regulators. Instead of relying on natural activation domains, we designed compact proteins that recruit specific cofactors. Activators for now, repressors to come!
Ken Xie retweeted
I’ve spent years watching T cells kill cancer cells through the microscope. The failed attacks are just as fascinating as the successes.
Can you spot the failed attack halfway through this video? 👀🔬🦠
Ken Xie retweeted
What if a single RNA transfection could program human stem cell fate or enable functional biosensing for more than a month?
Our new @CellRepMethods paper explores how self-amplifying RNA makes this possible, without genomic integration. 1/n :🧵
Self-amplifying RNA enables rapid, durable, integration-free programming of hiPSCs dlvr.it/TVWHCk
Ken Xie retweeted
Nature paper...
CANCER is evil...it prepares distant organs for metastasis BEFORE tumor cells arrive
Suppressive myeloid cells helped build lung premetastatic niches.
Epigenetic therapy disrupted this process and reduced metastases
nature.com/articles/s41586-0…
Ken Xie retweeted
Transcription factor specificity isn’t encoded by DNA motifs alone. Live-cell single-molecule imaging shows that unstructured transcription factor interactions enable emergent specificity.
science.org/doi/10.1126/scie…
Ken Xie retweeted
Review @JExpMed
Turning cold tumors hot: Strategies to enhance antitumor immunity
rupress.org/jem/article/223/…
Ken Xie retweeted
Congrats to Ke Shen and Zhi Wang on our new paper (doi.org/10.1002/jccs.70260),
presenting a CNN model, which is beyond previous PWM/PSAM models, and trained by our high-throughput Kd measurements (biorxiv.org/content/10.64898…), in collaboration with Mingchen Chen and Jian Yan's teams!
Ken Xie retweeted
Integrating RNA-seq, metabolomics & proteomics, @GeraldineMaier mapped how exercise rewires metabolism across tissues:
• Glycolysis
• Fat oxidation
• Ketone use
• BCAA metabolism
@WuTsaiAlliance
cell.com/cell/abstract/S0092…
Ken Xie retweeted
1/8 🧬 Have you ever been frustrated by the highcost and limited throughput of single-cell Hi-C?
We have too!
Excited to share ChromE-seq, our new method for jointly profiling 3D genome architecture and gene expression, at massive scale!
And biology is even more exciting!
Ken Xie retweeted
A beautiful reminder of the importance of dynamics.
Glad to have contributed to this tour de force.
🎉 Our paper is out today in @ScienceMagazine!
How does the intestine maintain the right balance of cell types? We find that signalling rhythms matter!
So proud of our three shared first authors, Sonja Weterings, @HiromuneEto & @jddeleede!
🔗 science.org/doi/10.1126/scie…
Ken Xie retweeted
#NeurIPS2026 To align or not to align?
Building on our Aristotelian Representation Hypothesis, we turn shared local neighborhoods into a practical guide for choosing compatible model pairs.
We introduce C🧭MPASS, a cheap diagnostic that estimates model-pair compatibility before alignment or merging. It helps decide what to do next: act now, invest more compute, switch training paradigms, or deprioritize a pair.
Across 72 vision-language alignment experiments and 392 model merges, COMPASS correlates downstream success:
• Alignment: 0.91 correlation
• Model merging: 0.70 correlation
Check your C🧭MPASS before you train.
Kudos to @FabianGroger and Petar Damjanovic 🙌
Paper: arxiv.org/abs/2610.18638
Webpage: brbiclab.epfl.ch/projects/co…
Code: github.com/mlbio-epfl/COMPAS…
Ken Xie retweeted
Are weak TF motifs important? @ZeitlingerLab use deep learning to systematically map low-affinity pioneer binding sites in mESCs and show that they cooperate with strong motifs to open chromatin. Preview w/ @gracecbower: cell.com/cell-genomics/fullt… Paper: cell.com/cell-genomics/fullt…
Ken Xie retweeted
When you look at the teamwork behind work like what was just published here, you realize the coordination required across teams, datasets, and time.
Will AI help us with this coordination? What if we took the same dataset and findings here... and asked AI to coordinate the data, find overlooked relationships, and uncover additional insights? What happens when you add to this the work of thousands of other papers in the space? Mere mortals cannot encompass the range of expertise required to fully plumb the opportunities.
That's an AI/SI goal worth pondering. But what resources would it take to make it happen?
Congratulations to Patel et al., the other authors, and the rest of the team without whose effort a work of this complexity could not come to the aid of patients with dire diseases such as those represented in this publication. And, of course, thanks to the patients and family members whose lives are represented in papers like this.
SCI member @GarryPNolan & others map cellular states across 54 #neuroblastoma tumors, uncovering ADRN and MES tumor cells. Crucially, high MES gene expression predicts worse survival, independent of clinical risk factors. brnw.ch/21x6p9L
Ken Xie retweeted
I’m excited to share MeRN, our new method for inferring single-cell metabolic states from transcriptomic data that enables the discovery of metabolic data-driven pathways! 🧵 1/
Preprint: biorxiv.org/content/10.64898…
GitHub: github.com/wagnerlab-berkele…
Tutorial: wagnerlab-berkeley.github.io…
Ken Xie retweeted
Our Nature Medicine paper is out: menopause isn't a slow slope. Across 300M+ lab tests from 1M+ women, many body systems jump at the final menstrual period. Men show no such jump. 1/4
nature.com/articles/s41591-0…
Ken Xie retweeted
Yale researchers have unveiled a new imaging platform that can measure the metabolic activity of individual cells and identify their specific cell type, all within a single slice of intact human tissue. The method, called REDCAT (Raman Enhanced Delineation of Cell Atlases in Tissues), bridges a long-standing gap in biology by connecting what a cell is genetically programmed to do with its actual physical behavior. Reported in the journal Nature Methods, the technology was developed by a collaborative team led by professors from Yale University, the University of California, San Diego, Columbia University, and the University of Pennsylvania.
"By combining technologies, REDCAT provides an exciting and powerful advance that allows users to connect cell type or state to metabolic function," said Allison Doerr, chief editor of Nature Methods.
Read here: medicine.yale.edu/news-artic…
#REDCAT #metabolism #cellimaging
Ken Xie retweeted
Using a new method inspired by astronomy, Weizmann Institute researchers led by @UriAlonWeizmann analyzed 300 million lab tests and uncovered a sharp physiological turning point at menopause >> bit.ly/Menopause-ENG
Ken Xie retweeted
How does a single cell become a mouse? 🐭 Our new paper reconstructs mouse development in a timed tree of 1.28M cells from the zygote using DNA Typewriter! 🌳
My favorite part: <5% founder cells at day 7 contribute >50% of cells at 13.5 - clonal dominance during gastrulation!
































