Fantastic talk by @stanford.edu's @jameszou.bsky.social for the first Innovation Initiative Distinguished Lecture at @whiteheadinstitute.bsky.social. A fascinating look at how to use #AI to build intelligent research teams that can tackle open-ended scientific problems. #WhiteheadInstitute #MIT

🧠Can AI agents predict #Alzheimers? Participate in our DREAM challenge agentic track to find out! We provide unique training + test data for AI agents: snRNA-seq, IHC, stage, etc synapse.org/Synapse:syn6... Also co-submit your agent paper to agents4science.stanford.edu

“Good science happens when we have deep, interdisciplinary collaborations, and often that’s one of the main bottlenecks and challenging parts of research,” said HAI Faculty Affiliate @jameszou.bsky.social who led a study on AI-driven virtual labs: med.stanford.edu/news/all-new...

Nice @stanforduniversity.bsky.social article profiling our #VirtualLab of AI scientists news.stanford.edu/stories/2025...

Case Study by Eric Wu, PhD, Kevin Wu, PhD, and James Zou, PhD: Limitations of Learning New and Updated Medical Knowledge with Commercial Fine-Tuning Large Language Models nejm.ai/4nTx1Np @jameszou.bsky.social #AI #MedSky

⚡️Thrilled that #VirtualLab is published in @nature.com! www.nature.com/articles/s41... We created a team of AI agents to mirror my Stanford lab 🤖. Led by a PI agent, the AI scientists ran their own group meetings and discovered effective binders to new CoVID variants that we validated.

Who do you call when you need to design novel, potent nanobodies vs a pathogen? The virtual lab of A.I. agents @nature.com @jameszou.bsky.social @kylewswanson.bsky.social www.nature.com/articles/s41...

Day 3 of #ISMBECCB2025 started with an excellent talk from @jameszou.bsky.social which presented how AI can form virtual labs to discuss problems, how can AI reanalyse research data to get new biological results, and how we can interpret complex AI predictions 💻🤖

Six frontier large language models evaluated on incorporating newly updated medical knowledge through commercial fine-tuning application programming interfaces struggled to generalize updated information, despite modest gains. Learn more: nejm.ai/4nTx1Np @jameszou.bsky.social

🏆Thrilled that #CollabLLM won the #ICML2025 Outstanding Paper Award! We propose a new approach to optimize human-AI collaboration, which is critical for agents. Congratulations to my fantastic co-authors; great job Shirley Wu and Michel Galley driving the project! 👏 Paper: arxiv.org/pdf/2502.00640

What is it like for scientists to work with AI co-scientists? Excellent @nature.com feature discussing researchers' experience interacting with our #VirtualLab and other tools www.nature.com/articles/d41...

Introducing EvoLM, a model suite with 100+ decoder-only LMs (1B/4B) trained from scratch, across four training stages — 🟦 Pre-training 🟩 Continued Pre-Training (CPT) 🟨 Supervised Fine-Tuning (SFT) 🟥 Reinforcement Learning (RL)

💡IMO one of the best use of AI Scientist is to reanalyze data to find new insights. Introducing #CellVoyager: AI Compbio Agent that makes new discoveries by autonomously analyzing papers/data, which we then validate🚀 New findings on aging, Covid, scRNAseq etc. Open source!

Very cool work from James Zou. Link to paper: www.nature.com/articles/s41...

Excited that nuclei.io is featured on the cover of Nature BME! AI-clinician collaboration paper rdcu.be/dLgV1

We discuss how to conduct intersectional analysis in science and technology in @nature.com nature.com/articles/s41... I learned a ton from working w/ dream team co-authors! Great job by Londa Schiebinger + Mathias Nielson leading this project 👏 Also thanks @meharpist.bsky.social for guidance!

Here's the non-paywall version of our #TextGrad paper rdcu.be/efRp4! 📜

SCI member @jameszou.bsky.social & others present a method for genAI self-improvement via a new calculus of text. They show TextGrad’s power in optimizing agents, molecules, code, treatments, & more, solving PhD-level problems and enabling impactful #AI development. www.nature.com/articles/s41...

Scholars developed a versatile framework called TextGrad to improve complex AI systems by leveraging natural language feedback. @jameszou.bsky.social Read more about this research supported by @stanfordhai.bsky.social in a new paper published in Nature: www.nature.com/articles/s41...

I had a lot of fun discussing #textgrad on the @nature.com podcast with @climateadam.bsky.social! It starts at around 12 minutes here www.nature.com/articles/d41...

Thrilled to be back on The @nature.com Podcast! Covering a nifty approach to give feedback to AI systems using normal speech. www.nature.com/articles/d41...

⚡️Really thrilled that #textgrad is published in @nature.com today!⚡️ We present a general method for genAI to self-improve via our new *calculus of text*. We show how this optimizes agents🤖, molecules🧬, code🖥️, treatments💊, non-differentiable systems🤯 + more!

Great review by @jameszou.bsky.social & colleagues from @stanfordmedicine.bsky.social on how integrating #iPSC technology with #AI can accelerate therapeutic discovery, enhance drug screening & advance personalized medicine. 🧪 #medsky www.annualreviews.org/content/jour...

Introducing MedArena medarena.ai/app/?__theme... for clinicians to ask medical questions and compare results of LLM models @jameszou.bsky.social @doximity.bsky.social

📢Thrilled to introduce #MedArena medarena.ai 🏥, a platform for clinicians to try frontier #LLMs for free (o3, Gemini, Perplexity + more). Compare and rank medical chatbots and help shape the future of medical AI! 🏆 Current leaderboard👇 Please share #MedSky

Incredibly grateful and honored to receive the 2025 Overton Prize ♥️ Surreal to follow the steps of my science heroes🙏 Truly, credit goes to my amazing students, collaborators and mentors who make research so inspiring! Also underscores the value of open academic environment that make this possible

New A.I. models in spatial omics —singe cell GPT @bowang87.bsky.social www.biorxiv.org/content/10.1... —CORAL @jameszou.bsky.social www.biorxiv.org/content/10.1... These are coming along incredibly fast and helping us learn the language of life www.science.org/doi/10.1126/... @science.org

Thrilled to introduce #CORAL🪸—a deep probabilistic graphical model that integrates spatial multiomics data! 🔹Resolves spatial resolution discrepancies across modalities 🔹Deconvolutes low-res data to achieve single-cell granularity 🔹Enables parallel integrative analysis 1/🪸

The shift from AI as tools to AI as agents has tremendous implications for medicine and healthcare. @erictopol.bsky.social and I share our perspective on new possibilities and how to prepare for this shift in @thelancet.bsky.social thelancet.com/journals/lan...

Our new piece in The Lancet on the potential of AI agents in medicine www.thelancet.com/journals/lan... @jameszou.bsky.social

Our new paper in Circulation shows how #ADMET-AI predicts cardiotoxicity of drugs and generates interpretable insights www.ahajournals.org/doi/abs/10.1...

#AAAI Spring Symposium on #AgenticAI for Science is calling for papers. We will have a fun 2.5-day event with speakers and participants from #agents, #LLM and #science communities in #SanFrancisco from Mar 31 to Apr 2, 2025.

@anusri.bsky.social first author & developer of ChromBPNet is looking for opportunities in industry in ML for bio/genomics. She is an excellent rigorous scientist (as u can see from the paper). Very strongly recommend her. Plz reach out to her if u have openings. Plz forward.

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

The 2024 Good Tech Awards, spotlighted by @kevinroose.com for #AI/Science nytimes.com/2024/12/30/t... congrats! @arcinstitute.org @brianhie.bsky.social @patrickhsuu.bsky.social @jameszou.bsky.social and the others for well deserved recognition

🎆 #SyntheMol AI is recognized for a 2024 Good Tech Award in @nytimes.com! Very excited about using AI to design new antibiotics and other drugs. Thank you @kevinroose.bsky.social for the nice shoutout! www.nytimes.com/2024/12/30/t...

My @stanfordhai.bsky.social colleagues and I predict #AI trends in 2025 hai.stanford.edu/news/predict... My take: we will see many more multi-agent AI teams, instead of individual models, for tackling complex problems like those in science.

Thank you Stanford Knight Initiative for highlighting our new brain aging paper with @brunetlab.bsky.social! brainresilience.stanford.edu/news/blight-...

🎆4 years in the making! Thrilled to share the 1st spatial single cell aging clock ⏰ www.nature.com/articles/s41... We use #AI + spatial transcriptomics to discover what makes some cells age faster/slower in the brain 🧠 Led by Eric Sun and awesome collaboration w/ @brunetlab.bsky.social🧵

It's so wonderful collaborating with @brunetlab.bsky.social on this project! Amazing work by Eric Sun leading this big effort👏 Really excited about the power of AI to help us understand how cell-cell interactions affect biological age + rejuvenation!

Thrilled to see this paper out!! 🧪 Spatial transcriptomics of brain aging and 'spatial aging clocks' identify cells that have pro-aging or pro-rejuvenating effects on their neighbors! Huge CONGRATS to Eric Sun and all authors! Fantastic collaboration with @jameszou.bsky.social! rdcu.be/d33uQ 🧵

🎆4 years in the making! Thrilled to share the 1st spatial single cell aging clock ⏰ www.nature.com/articles/s41... We use #AI + spatial transcriptomics to discover what makes some cells age faster/slower in the brain 🧠 Led by Eric Sun and awesome collaboration w/ @brunetlab.bsky.social🧵

Excited to share several works w/ fantastic students + collaborators at #NeurIPS2024 this week! ✈️ Look forward to meeting old and new friends in Vancouver; let me know if you'd like to chat!

📢 Excited that #unitox is selected as a #NeurIPS2024 spotlight!💡 We created #LLM agent to analyze >100K pages of FDA docs from all approved drugs ➡️ new database annotating 8 toxicity types for 2400 drugs. Validated by clinicians. openreview.net/pdf?id=Vb1vV...

🎉Thrilled that #GenePT is published! We show how to create #ChatGPT embeddings of genes and #singlecell --> improve gene function prediction + cell annotation/analyses🧬 📰 www.nature.com/articles/s41... 🌐 github.com/yiqunchen/Ge... Great job Yiqun Chen! #LLM for bio.

If you use SHAP, LIME or Data Shapley, you might be interested in our new #neurips2024 paper. We introduce stochastic amortization to speed up feature + data attribution by 10x-100x 🚀 #XML Surprisingly we can "learn to attribute" cheaply from noisy explanations! arxiv.org/abs/2401.15866

Excited to join the Bluesky community!