What if LLMs could “read” & “write” biology? 🤔 Introducing C2S‑Scale—a Yale and Google collab: we scaled LLMs (up to 27B!) to analyze & generate single‑cell data 🧬 ➡️ 📝 🔗 Blog: research.google/blog/teachin... 🔗 Preprint: biorxiv.org/content/10.1...

Excited to share our new preprint: COAST: Intelligent Time-Adaptive Neural Operators! 🌊 We introduce a novel neural operator that learns to dynamically and intelligently adjust time step sizes for modeling dynamical systems from data. 🚀 doi.org/10.48550/arX...

🔥🧠🌌 Now accepted at #ICLR2025 ! How does complexity shape intelligence? 🤔 In our new paper "Intelligence at the Edge of Chaos", we explore the relationship between complex systems and the emergence of intelligence in AI models. Can complexity alone unlock smarter systems? arxiv.org/abs/2410.02536

Can we learn protein biology from a language model? In new work led by @liambai.bsky.social and me, we explore how sparse autoencoders can help us understand biology—going from mechanistic interpretability to mechanistic biology.

scGPT-spatial: Continual Pretraining of Single-Cell Foundation Model for Spatial Transcriptomics https://www.biorxiv.org/content/10.1101/2025.02.05.636714v1 🧬🖥️🧪 https://github.com/bowang-lab/scGPT-spatial

Excited to post my first #skySplain about our recent work published yesterday in Nature Genetics! www.nature.com/articles/s41.... One of the first authors of this study - Annika Vannan – actually wrote this breakdown, but she's not yet over here on bluesky and asked me to post!

New: The largest medical A.I. randomized controlled trial yet performed, enrolling >100,000 women undergoing mammography screening The use of AI led to 29% higher detection of cancer, no increase of false positives, and reduced workload compared with radiologists w/o AI thelancet.com/journals/lan...

Very cool work showing the promise of integrating several sources of data to directly address human health conditions. Synchronized long-read genome, methylome, epigenome and transcriptome profiling resolve a Mendelian condition www.nature.com/articles/s41...

Omega-3 fatty acids had a small protective effect of slowing biological aging (via multiple epigenetic clocks, Figure) nature.com/articles/s43... Exercise and Vit D were also assessed with some additive benefits but not significant on their own

Benchmarking gene embeddings from sequence, expression, network, and text models for functional prediction tasks https://www.biorxiv.org/content/10.1101/2025.01.29.635607v1 🧬🖥️🧪 https://github.com/ylaboratory/gene-embedding-benchmarks

Fruitful collaboration between our team & Sven Jager/Ziv Bar Joseph's team @Sanofi published today @narjournal.bsky.social: a language model that learns the grammar of all regions of an mRNA from head to tail!! Can be fine-tuned on all of your favorite mRNA-related tasks -- a successor of CodonBERT.

Our op-ed @nytopinion.nytimes.com today addresses the surprising results of recent medical studies that showed A.I. alone outperformed physicians using A.I. W/@rajpurkar.bsky.social Here is a summary Table, an overview, and a gift link to the op-ed erictopol.substack.com/p/when-docto...

We do see strong scaling laws in single cell foundation models

A month ago we @vevotherapeutics.bsky.social announced that we have generated the largest single-cell perturbation atlas in history, Tahoe-100M. Today, we announce that we will fully open-source Tahoe-100M in Feb, as part of a collaboration with NVidia health to train cell state models.

Excited to share our new study of #genomics🧬, #EHR📈 + treatment outcomes of 78K patients across 20 #cancers! We identified >700 mutations predicting which drugs💊 are effective for individual patients. Our #ML model predicts who responds well to immunotherapies. #precisioncancer

Our ChromBPNet preprint out! www.biorxiv.org/content/10.1... Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/

First 🦋 post! Very excited to share our lab's latest work exploring the shared and divergent aspects of human astrocyte development and glioblastoma. This effort spans many fields from developmental #glial biology to #stem cells and #tumor biology. rdcu.be/d5ADz A 🧵

Out today in @naturegenet.bsky.social -- PERFF-seq! With @tsionabay.bsky.social , @ronanchaligne.bsky.social, Bob Stickels, Meril Takizawa, + Ansu Satpathy, we describe this new assay to study rare populations with programmable nucleic acid cytometry. 1/n www.nature.com/articles/s41...

Seeking pioneering scientists in immunology, neuroscience, and machine learning! Join Arc Institute as a Core Investigator + Stanford Bioengineering as Associate/Full Professor. Full lab funding and cutting-edge facilities in Palo Alto. Apply by Jan 15 for full consideration: shorturl.at/CuH1K