Kalin Nonchev
@nonchev.bsky.social
PhD at ETH Zurich, machine learning and biomedical data https://kalinnonchev.github.io
This project, based on Glib Manaiev’s Master’s thesis, was carried out in close partnership between the Biomedical Informatics Group at @ethz.ch (Gunnar Rätsch @gxxxr.bsky.social), the Computational and Translational Pathology Lab at @UZH.ch and the @unibas.ch (Viktor H. Koelzer).
October 1, 2025 at 3:31 PM
This project, based on Glib Manaiev’s Master’s thesis, was carried out in close partnership between the Biomedical Informatics Group at @ethz.ch (Gunnar Rätsch @gxxxr.bsky.social), the Computational and Translational Pathology Lab at @UZH.ch and the @unibas.ch (Viktor H. Koelzer).
🎉 DeepSpot2Cell will be presented at NeurIPS 2025 Imageomics!
October 1, 2025 at 3:29 PM
🎉 DeepSpot2Cell will be presented at NeurIPS 2025 Imageomics!
The idea: model each spot as a bag of cells. 🧬
DeepSpot2Cell combines pathology foundation models + DeepSets neural networks to extract single-cell–level insights from spot data—keeping past experiments relevant and enabling precise cellular analyses.
DeepSpot2Cell combines pathology foundation models + DeepSets neural networks to extract single-cell–level insights from spot data—keeping past experiments relevant and enabling precise cellular analyses.
October 1, 2025 at 3:28 PM
The idea: model each spot as a bag of cells. 🧬
DeepSpot2Cell combines pathology foundation models + DeepSets neural networks to extract single-cell–level insights from spot data—keeping past experiments relevant and enabling precise cellular analyses.
DeepSpot2Cell combines pathology foundation models + DeepSets neural networks to extract single-cell–level insights from spot data—keeping past experiments relevant and enabling precise cellular analyses.
PS: We also have exciting MSc thesis and semester projects bmi.inf.ethz.ch/opportunitie...
Internships
bmi.inf.ethz.ch
August 18, 2025 at 8:46 PM
PS: We also have exciting MSc thesis and semester projects bmi.inf.ethz.ch/opportunitie...
✉️Full job description and how to apply: bmi.inf.ethz.ch/opportunitie...
Application
❗️Applications will be considered only if submitted through the specified process, and incomplete applications will not be considered.
Application
❗️Applications will be considered only if submitted through the specified process, and incomplete applications will not be considered.
bmi.inf.ethz.ch
August 18, 2025 at 8:46 PM
✉️Full job description and how to apply: bmi.inf.ethz.ch/opportunitie...
Application
❗️Applications will be considered only if submitted through the specified process, and incomplete applications will not be considered.
Application
❗️Applications will be considered only if submitted through the specified process, and incomplete applications will not be considered.
Join us for an exciting internship where cutting-edge machine learning research meets real-world biomedical data!
📍Biomedical Informatics Group of Prof. Gunnar Rätsch @gxxxr.bsky.social, ETH Zürich, Switzerland
⏰ Start: ASAP, full time
💼 Completed PhD in Machine Learning or relevant experience
📍Biomedical Informatics Group of Prof. Gunnar Rätsch @gxxxr.bsky.social, ETH Zürich, Switzerland
⏰ Start: ASAP, full time
💼 Completed PhD in Machine Learning or relevant experience
August 18, 2025 at 8:43 PM
Join us for an exciting internship where cutting-edge machine learning research meets real-world biomedical data!
📍Biomedical Informatics Group of Prof. Gunnar Rätsch @gxxxr.bsky.social, ETH Zürich, Switzerland
⏰ Start: ASAP, full time
💼 Completed PhD in Machine Learning or relevant experience
📍Biomedical Informatics Group of Prof. Gunnar Rätsch @gxxxr.bsky.social, ETH Zürich, Switzerland
⏰ Start: ASAP, full time
💼 Completed PhD in Machine Learning or relevant experience
Reposted by Kalin Nonchev
🤝 Great collaboration between @bocklab.bsky.social (@moritzbaio.bsky.social, Animesh, Jake), @nonchev.bsky.social, @gxxxr.bsky.social, and pathologist Viktor Kölzer.
SpotWhisperer is at #ICML25 FM4LS workshop. Visit our poster on Saturday (19 July 2025) if you're interested & attending ICML. (6/6)
SpotWhisperer is at #ICML25 FM4LS workshop. Visit our poster on Saturday (19 July 2025) if you're interested & attending ICML. (6/6)
July 18, 2025 at 10:40 PM
🤝 Great collaboration between @bocklab.bsky.social (@moritzbaio.bsky.social, Animesh, Jake), @nonchev.bsky.social, @gxxxr.bsky.social, and pathologist Viktor Kölzer.
SpotWhisperer is at #ICML25 FM4LS workshop. Visit our poster on Saturday (19 July 2025) if you're interested & attending ICML. (6/6)
SpotWhisperer is at #ICML25 FM4LS workshop. Visit our poster on Saturday (19 July 2025) if you're interested & attending ICML. (6/6)
Explore the dataset: huggingface.co/datasets/non...
Manuscript: www.medrxiv.org/content/10.1...
GitHub: github.com/ratschlab/De...
Manuscript: www.medrxiv.org/content/10.1...
GitHub: github.com/ratschlab/De...
nonchev/TCGA_digital_spatial_transcriptomics · Datasets at Hugging Face
We’re on a journey to advance and democratize artificial intelligence through open source and open science.
huggingface.co
May 12, 2025 at 5:08 AM
Explore the dataset: huggingface.co/datasets/non...
Manuscript: www.medrxiv.org/content/10.1...
GitHub: github.com/ratschlab/De...
Manuscript: www.medrxiv.org/content/10.1...
GitHub: github.com/ratschlab/De...
💡 This resource unlocks exciting opportunities for developing new multi-modal deep learning methods, benchmarking existing ones, and accelerating biological discoveries in cancer research using digital spatial transcriptomics.
May 12, 2025 at 5:08 AM
💡 This resource unlocks exciting opportunities for developing new multi-modal deep learning methods, benchmarking existing ones, and accelerating biological discoveries in cancer research using digital spatial transcriptomics.
Glad that you find it exciting too!
March 20, 2025 at 11:51 AM
Glad that you find it exciting too!
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 6:43 AM
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
More about the competition: www.youtube.com/watch?v=GUXi...
Leaderboard: hub.crunchdao.com/competitions...
Leaderboard: hub.crunchdao.com/competitions...
Autoimmune Disease Machine Learning Challenge Overview
YouTube video by Broad Institute
www.youtube.com
March 20, 2025 at 6:38 AM
More about the competition: www.youtube.com/watch?v=GUXi...
Leaderboard: hub.crunchdao.com/competitions...
Leaderboard: hub.crunchdao.com/competitions...
Learn more about DeepSpot, developed at @ethzurich.bsky.social: www.medrxiv.org/content/10.1...
DeepSpot: Leveraging Spatial Context for Enhanced Spatial Transcriptomics Prediction from H&E Images
Spatial transcriptomics technology remains resource-intensive and unlikely to be routinely adopted for patient care soon. This hinders the development of novel precision medicine solutions and, more i...
www.medrxiv.org
March 20, 2025 at 6:38 AM
Learn more about DeepSpot, developed at @ethzurich.bsky.social: www.medrxiv.org/content/10.1...
By extending our recent deep learning method, DeepSpot, to support 10x Genomics Xenium data, we significantly improved single-cell gene expression predictions in patients with Inflammatory Bowel Disease. It is exciting to see its performance validated in an independent evaluation!
March 20, 2025 at 6:36 AM
By extending our recent deep learning method, DeepSpot, to support 10x Genomics Xenium data, we significantly improved single-cell gene expression predictions in patients with Inflammatory Bowel Disease. It is exciting to see its performance validated in an independent evaluation!