We recently published Metagraph [1] & polished the website to made it usable/stable/efficient for more users. Check out AI summary/tax. id feature [2]. Search in 17PB indexed sequences takes ≈3min on single server. Try!
[1] www.nature.com/articles/s41...
[2] metagraph.ethz.ch/results?sear...
[1] www.nature.com/articles/s41...
[2] metagraph.ethz.ch/results?sear...
November 7, 2025 at 8:02 PM
We recently published Metagraph [1] & polished the website to made it usable/stable/efficient for more users. Check out AI summary/tax. id feature [2]. Search in 17PB indexed sequences takes ≈3min on single server. Try!
[1] www.nature.com/articles/s41...
[2] metagraph.ethz.ch/results?sear...
[1] www.nature.com/articles/s41...
[2] metagraph.ethz.ch/results?sear...
Reposted by Gunnar Rätsch
The Metagraph paper is out in Nature; it showed up in my feeds today! Congratulations to Mikhail Karasikov, @gxxxr.bsky.social, @akkah21.bsky.social and all of the other authors (whom I'd love to follow on Bluesky if I can find you ;P) www.nature.com/articles/s41...
Efficient and accurate search in petabase-scale sequence repositories - Nature
MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.
www.nature.com
October 9, 2025 at 2:40 PM
The Metagraph paper is out in Nature; it showed up in my feeds today! Congratulations to Mikhail Karasikov, @gxxxr.bsky.social, @akkah21.bsky.social and all of the other authors (whom I'd love to follow on Bluesky if I can find you ;P) www.nature.com/articles/s41...
Reposted by Gunnar Rätsch
After years of research and continuous refinement, we’re thrilled to share that our paper on the MetaGraph framework — enabling Petabase-scale search across sequencing data — has been published today in Nature (www.nature.com/articles/s41...)
Efficient and accurate search in petabase-scale sequence repositories - Nature
MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.
www.nature.com
October 8, 2025 at 8:56 PM
After years of research and continuous refinement, we’re thrilled to share that our paper on the MetaGraph framework — enabling Petabase-scale search across sequencing data — has been published today in Nature (www.nature.com/articles/s41...)
This manuscript on the reproducibility of splicing neoepitope prediction took us a while. We find that subtle choices in how one exactly generates and filters neoepitope candidates, creates major differences in the number and identity of the neoepitopes.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Splicing neoepitope prediction is sensitive to methodological differences
Motivation: Cancer-specific neoepitopes may arise from abnormal splicing in the transcriptomic landscape (alternative splicing neoepitopes, ASNs), leading to divergent proteins with high potential imm...
www.biorxiv.org
September 16, 2025 at 1:05 PM
This manuscript on the reproducibility of splicing neoepitope prediction took us a while. We find that subtle choices in how one exactly generates and filters neoepitope candidates, creates major differences in the number and identity of the neoepitopes.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Gunnar Rätsch
🔬 Toward histopathology 2.0: spatial transcriptomes inferred from routine diagnostic H&E images + a chat interface for cell-resolution histopathology through English language. (1/6)
July 18, 2025 at 10:40 PM
🔬 Toward histopathology 2.0: spatial transcriptomes inferred from routine diagnostic H&E images + a chat interface for cell-resolution histopathology through English language. (1/6)
Reposted by Gunnar Rätsch
Just presented our new multimodal histopathology method "SpotWhisperer" at ICML, one of the largest AI conference.
SpotWhisperer enables spatially resolved annotation of histopathology images using natural language. We achieved this by "transferring" annotations from transcriptomic data. More soon!
SpotWhisperer enables spatially resolved annotation of histopathology images using natural language. We achieved this by "transferring" annotations from transcriptomic data. More soon!
July 21, 2025 at 1:24 AM
Just presented our new multimodal histopathology method "SpotWhisperer" at ICML, one of the largest AI conference.
SpotWhisperer enables spatially resolved annotation of histopathology images using natural language. We achieved this by "transferring" annotations from transcriptomic data. More soon!
SpotWhisperer enables spatially resolved annotation of histopathology images using natural language. We achieved this by "transferring" annotations from transcriptomic data. More soon!
Congrats, great work!
The DeepSpot project was carried out in close partnership between the Biomedical Informatics Group at ETH Zurich @gxxxr.bsky.social, the Computational and Translational Pathology Lab at UZH
and @unibas.ch, and the Silina Group at the Institute of Pharmaceutical Sciences, @ethzurich.bsky.social
and @unibas.ch, and the Silina Group at the Institute of Pharmaceutical Sciences, @ethzurich.bsky.social
March 20, 2025 at 7:04 AM
Congrats, great work!
Reposted by Gunnar Rätsch
🎉 Yesterday, @alizeepace.bsky.social, our first PhD Fellow of the @eth-ai-center.bsky.social, graduated! She was supervised by ETH AI Center Faculty members Prof. Rätsch @gxxxr.bsky.social and Prof. Schölkopf. Congrats, Dr. Pace! Next, she will join Google DeepMind in Zurich as a Research Scientist.
February 27, 2025 at 10:39 AM
🎉 Yesterday, @alizeepace.bsky.social, our first PhD Fellow of the @eth-ai-center.bsky.social, graduated! She was supervised by ETH AI Center Faculty members Prof. Rätsch @gxxxr.bsky.social and Prof. Schölkopf. Congrats, Dr. Pace! Next, she will join Google DeepMind in Zurich as a Research Scientist.
Reposted by Gunnar Rätsch
This is joint work with Bernhard Schölkopf, @gxxxr.bsky.social, and @gioramponi.bsky.social, which we will also be presenting at ICLR 2025 🎉
Link: arxiv.org/abs/2406.18450
Link: arxiv.org/abs/2406.18450
Preference Elicitation for Offline Reinforcement Learning
Applying reinforcement learning (RL) to real-world problems is often made challenging by the inability to interact with the environment and the difficulty of designing reward functions. Offline RL...
arxiv.org
February 13, 2025 at 10:48 AM
This is joint work with Bernhard Schölkopf, @gxxxr.bsky.social, and @gioramponi.bsky.social, which we will also be presenting at ICLR 2025 🎉
Link: arxiv.org/abs/2406.18450
Link: arxiv.org/abs/2406.18450
I'm excited about a meeting on RNA + AI together with @quaidmorris.bsky.social and @hagentilgner.bsky.social in Ascona, Ticino on May 4-8. We have a great line-up of speakers and room for you to present your work. Please join us if you are into RNA & AI. Registration open www.rna-ai.org.
January 30, 2025 at 7:41 PM
I'm excited about a meeting on RNA + AI together with @quaidmorris.bsky.social and @hagentilgner.bsky.social in Ascona, Ticino on May 4-8. We have a great line-up of speakers and room for you to present your work. Please join us if you are into RNA & AI. Registration open www.rna-ai.org.
Great to see ELLIS and EMBL getting closer and working together!
January 30, 2025 at 4:36 PM
Great to see ELLIS and EMBL getting closer and working together!
Where RNA Science Meets AI, May 4–8, 2025, Ascona. Invited speakers: @evamarianovoa.bsky.social @fabiantheis.bsky.social @rivaselenarivas.bsky.social, Sterling Churchman, Barbara Treutlein, Rahul Satijia,
Registration open www.rna-ai.org
@hagentilgner.bsky.social @quaidmorris.bsky.social
Registration open www.rna-ai.org
@hagentilgner.bsky.social @quaidmorris.bsky.social
RNA-AI 2025
www.rna-ai.org
December 18, 2024 at 8:22 AM
Where RNA Science Meets AI, May 4–8, 2025, Ascona. Invited speakers: @evamarianovoa.bsky.social @fabiantheis.bsky.social @rivaselenarivas.bsky.social, Sterling Churchman, Barbara Treutlein, Rahul Satijia,
Registration open www.rna-ai.org
@hagentilgner.bsky.social @quaidmorris.bsky.social
Registration open www.rna-ai.org
@hagentilgner.bsky.social @quaidmorris.bsky.social
Reposted by Gunnar Rätsch
Very honored to have been elected an @ellis.eu Scholar in the program for Robust Machine Learning: ellis.eu/programs/rob...
What better way to celebrate it than to speak at the ELLIS UnConference in Bad Teinach?
What better way to celebrate it than to speak at the ELLIS UnConference in Bad Teinach?
December 10, 2024 at 10:04 PM
Very honored to have been elected an @ellis.eu Scholar in the program for Robust Machine Learning: ellis.eu/programs/rob...
What better way to celebrate it than to speak at the ELLIS UnConference in Bad Teinach?
What better way to celebrate it than to speak at the ELLIS UnConference in Bad Teinach?
Reposted by Gunnar Rätsch
My group is hiring postdoc(s) and I will be at #NeurIPS2024 if you want to talk - send me a DM or find me on Whova!
UK-based, 2 year position. We work on AI/ML for health, specifically building and *understanding/explaining* deep (multimodal) models on healthcare data, especially medical imaging.
UK-based, 2 year position. We work on AI/ML for health, specifically building and *understanding/explaining* deep (multimodal) models on healthcare data, especially medical imaging.
December 9, 2024 at 4:53 PM
My group is hiring postdoc(s) and I will be at #NeurIPS2024 if you want to talk - send me a DM or find me on Whova!
UK-based, 2 year position. We work on AI/ML for health, specifically building and *understanding/explaining* deep (multimodal) models on healthcare data, especially medical imaging.
UK-based, 2 year position. We work on AI/ML for health, specifically building and *understanding/explaining* deep (multimodal) models on healthcare data, especially medical imaging.
Reposted by Gunnar Rätsch
November 23, 2024 at 7:01 PM
Reposted by Gunnar Rätsch
Generative AI’s environmental costs are soaring — and mostly secret
Generative AI’s environmental costs are soaring — and mostly secret
First-of-its-kind US bill would address the environmental costs of the technology, but there’s a long way to go.
buff.ly
November 24, 2024 at 8:48 AM
Generative AI’s environmental costs are soaring — and mostly secret