Fabian Theis

scConcept: Contrastive pretraining for technology-agnostic single-cell representations beyond reconstruction Recent large-scale single-cell foundation models have shown promise for exploring cellular states, yet they often underperform compared to simpler, domain-specific methods, raising concerns about…

🚀 Excited to share our preprint scConcept: a contrastive pretraining framework for technology-agnostic single-cell representations.
We move beyond reconstruction to learn rich, cell-level embeddings for diverse omics.
📘 www.biorxiv.org/content/10.1...

Breaking down walls in #PrecisionHealth at #FallingWalls 2025! Great exchange with Frank Laukien, Caroline Gubser-Keller, Eicke Latz & Steve Quake on how AI & molecular analytics reshape medicine.
Our goal: virtual twin cells, tissues & patients.
#AIinMedicine #HelmholtzMunich

🚀 Prophet v3 is out!
AI that predicts how cells respond to genetic & chemical perturbations across readouts.
Now scales to 1.9 M molecules + in vitro validation of melanoma-specific hits 🧬💊
📄 biorxiv.org/content/10.1...
#AI #Biology #DeepLearning

EU commissioner Henna Virkkunen officially launching EU‘s RAISE project - its Resource for AI Science in Europe at AIS25 in Copenhagen. includes training programs, data hubs, funding and compute. Exciting & important for Europe and beyond. 🇪🇺

The next generation of startup ecosystems: a benchmarking This report is the conclusion of a data-driven analysis of 201 tech ecosystems. This set of actionable benchmarks is meant as a tool to help ecosystems understand and measure their maturity and…

Munich is now the #2 AI ecosystem in Europe (after Paris) and #11 globally, per Dealroom’s Global Tech Ecosystem Index 2025! 🇩🇪🤖🇫🇷
Proud of the growing strength of the Bavarian AI ecosystem 👉 baiosphere.org
�� dealroom.co/tech-ecosystem-index-2025�5
#AI #Munich #baiosphere

Nicheformer: a foundation model for single-cell and spatial omics - Nature Methods Pretrained on SpatialCorpus-110M, a curated resource of vast and diverse transcriptomes of dissociated and spatially resolved cells from both human and mouse, Nicheformer advances toward building foun...

🔗 To the original publication in Nature Methods: t1p.de/ba2gx

@fabiantheis.bsky.social @comphealthmunich.bsky.social

🎃 Happy Halloween from our Lab! 👻🧬
No bad computational tricks — only treats! 🧫💻✨

Aliee Group - Cancer Research UK Cambridge Institute Explain. Predict. Outsmart cancer.

Looking for a PhD/postdoc position in Cambridge UK in comp bio? Check out Hana Aliee's new lab at CRUK: www.cruk.cam.ac.uk/research-gro...

🧬 Excited to share Nicheformer out now in Nature Methods!

A transformer foundation model linking single-cell & spatial omics, learning spatial context from gene expression to map tissue organization.

Led by Ale Tejada & Anna Schaar 👏
👉 www.nature.com/articles/s41...

At the Staatskanzlei Munich for the State Reception celebrating Bavaria’s Excellence Clusters — great to see so much scientific excellence and innovation recognized and supported across disciplines. 🚀🇩🇪 #Wissenschaft #Innovation #Bayern

scPortrait integrates single-cell images into multimodal modeling Machine learning increasingly uncovers rules of biology directly from data, enabled by large, standardized datasets. Microscopy images provide rich information on cellular architecture and are accessi...

Our preprint on scPortrait is out! We built a framework + format to turn microscopy into standardized single-cell image datasets. #scPortrait scales >100M cells, integrates with @scverse.bsky.social, & enables cross-modality modeling from morphology to transcriptomics
doi.org/10.1101/2025...

Prof. Eric Topol at Helmholtz Munich

Roundtable with Prof. Eric Topol at Helmholtz Munich on the Virtual Human

✨ Prof. Eric Topol visited #HelmholtzMunich for a roundtable on the future of #AI in healthcare. The discussion focused on the concept of the #VirtualHuman.

👉Read more: t1p.de/5wthc

#AIinMedicine #DigitalHuman #PrecisionMedicine

Björn Schuller from TUM and Imperial talking about deep learning on mobile sensor data at scale. Wonder how and when we get all these scales together. #BavarianAcademy #MedicalAIConference

Eric Topol giving evening keynote at our Bavarian Conference on AI in medicine, amongst other on AI for prevention and super aging. A true visionary and communicator! see eg erictopol.substack.com/p/dawn-of-a-...
@eriktopol

Inspiring evening w/ Eric Topol, Matthias Tschöp & Markus Schwaiger. Key message: unite scientists and data across institutions to make AI medicine real — starting with prevention. 🧬🤝
Excited for the Bavarian AI in Medicine Conference tomorrow.

Bavarian Conference on AI in Medicine We are excited to invite you to the Bavarian Conference on AI in Medicine where we will explore the intersection of artificial intelligence and medical research. This event is aimed at Bavarian PhD st...

Looking fwd to Bavarian Conference on AI in Medicine (Oct 27–28) in Munich: events.hifis.net/event/2048
with Eric Topol, Mihaela van der Schaar, & Islem Rekik. Plus prologue with @erictopol at Helmholtz Munich on monday morning. Let’s discuss where AI can really impact medicine. 💡

🚀 Our new Science paper is out (w/ B DeMeo, D Burkhardt, A Shalek, M Cortes): www.science.org/doi/10.1126/...
We show that active learning + transcriptomic perturbations can guide which exps to run next, boosting phenotypic hit rates >13x. AI not just predicting bio, but designing it. 🔁

Our lab together with the Lücken lab is in the mountains for our annual hackathon & retreat ⛰️💻
A great mix of science and community: new project ideas, evening coding, creative drawing, and a group hike.
Inspiring energy & fresh thinking, truly grateful for this awesome team!

🚀 Excited to share scPortrait! Led by Sophia Mädler & Niklas Schmacke w/ the Mann lab — a new @scverse tool for standardized single-cell image data. Enables ML-ready extraction, >1B cell processing, cross-omics, & cancer macrophage insights.
🔗 www.biorxiv.org/content/10.1...

not sure about competition only. think in current times EU needs sovereign AI for quite some fields right ..

Excited to speak today at the EC’s R&I Community event on RAISE – Building the Resource for AI Science in Europe.

We’ll discuss how pooling compute, data, talent & funding can supercharge AI-driven discovery across life sciences & health.

👉 stream: research-innovation-community.ec.europa.eu

¡¡El Flashmob Bohemian Rhapsody más INCREÍBLE que jamás verás!!😍

2nd day of our DLD Baiosphere conference starting out w aim to ‘put on some fairy dust’ (Yossi Vardi’s words) - w supermotivating Bohemian Rhapsody flashmob vid, watch it will make your day ☺️ youtu.be/jO2R_35HhiY

Excited that our DLD Baiosphere conference on AI is starting now - with major political presence from Bavaria & great talks/panels from science and industry! MP Söder with strong commitment on academic freedom & local strength in AI to attract talents.

🚀https://dld-conference.com

New paper in @ScienceMagazine with Schoof & Porse labs: We chart early human hematopoiesis using single-cell proteomics, and amongst others developed a dynamic model linking RNA to protein levels, explaining more proteomic variation.

📄 www.science.org/doi/10.1126/...

Back from the SolvAI Retreat 2025 in Nice — amazing discussions on AI in science. Key themes: LMs alone won’t get us to scientific discovery, what makes a theory, and how AI can help us build them. Thanks to Eric Xing & Yann LeCun for organizing!

So excited to see it out in @science.org. See details below in the 🧵 from stellar former PhD student @bfurtwa.bsky.social.
Many thanks to all involved, especially Blueskyless Nil Uresin and Sabrina Richer and my co-PIs @fabiantheis.bsky.social and @erwinschoof.bsky.social

NSF announces $100 million investment in National Artificial Intelligence Research Institutes awards to secure American leadership in AI The investment will accelerate open innovation, empower an AI-ready workforce and strengthen U.S. global competitiveness...

🚀 NSF just announced a $100M investment in National AI Research Institutes, with medicine & health applications listed first among priority areas, highlighting how biomedical impact continues to lead innovation and real-world benefit! www.nsf.gov/news/nsf-ann... 👩⚕️🔬 #AI #Health

🚀 Exciting opportunity for scientists in the Bavarian AI ecosystem @bAIosphere!
Host your funded retreat or workshop at the beautiful, remote Speinshart Scientific Center for AI & SuperTech🤖.
👉 baiosphere.org/baiosphere-s...
👉 www.speinshart.ai
#AI #Bavaria #ScienceCommunity

Great to host Eric Xing, President & University Professor at MBZUAI, together with Dekyi Liang, Chief of Staff, at our Helmholtz Computational Health Center last Friday 🤖. Inspiring talk on “AI-driven Digital Organism” and engaging discussions with colleagues & PIs 🧬.

thanks Rob - also for staying until end of conference :). enjoyed the discussions a lot!