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Kalin Nonchev

@nonchev.bsky.social

48 followers 81 following 44 posts

PhD at ETH Zurich, machine learning and biomedical data https://kalinnonchev.github.io

kalinnonchev.github.io

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Kalin Nonchev @nonchev.bsky.social · Feb 24

How can we predict spatial transcriptomics from histology images to enable simple, affordable, and reliable analysis of spatially resolved gene expression in routine clinical use? 🤔 Introducing DeepSpot – a deep learning model designed to tackle this! 🧵👇 www.medrxiv.org/content/10.1...

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Reposted by Kalin Nonchev

Andre Kahles @akkah21.bsky.social · 3d

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

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Kalin Nonchev @nonchev.bsky.social · 10d

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).

Kalin Nonchev @nonchev.bsky.social · 10d

Preprint: www.biorxiv.org/content/10.1...
Code: github.com/ratschlab/De...

DeepSpot2Cell: Predicting Virtual Single-Cell Spatial Transcriptomics from H&E images using Spot-Level Supervision

Spot-based spatial transcriptomics (ST) technologies like 10x Visium quantify genome-wide gene expression and preserve spatial tissue organization. However, their coarse spot-level resolution aggregat...

www.biorxiv.org

Kalin Nonchev @nonchev.bsky.social · 10d

🎉 DeepSpot2Cell will be presented at NeurIPS 2025 Imageomics!

Kalin Nonchev @nonchev.bsky.social · 10d

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.

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Kalin Nonchev @nonchev.bsky.social · 10d

Older spot-level spatial transcriptomics datasets shouldn't be forgotten now that new single-cell methods exist. 🧬

Instead of discarding this rich resource, we can bridge the gap.
DeepSpot2Cell helps bridge the gap 👇

Reposted by Kalin Nonchev

AI x Bio Discovery @aixbiobot.bsky.social · 16d

DeepSpot2Cell: Predicting Virtual Single-Cell Spatial Transcriptomics from H&E images using Spot-Level Supervision [new]
Pred. sc gene expr. via DeepSet & spot sup. for spatial transcriptomics.

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Kalin Nonchev @nonchev.bsky.social · Aug 18

PS: We also have exciting MSc thesis and semester projects bmi.inf.ethz.ch/opportunitie...

Internships

bmi.inf.ethz.ch

Kalin Nonchev @nonchev.bsky.social · Aug 18

✉️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.

bmi.inf.ethz.ch

Kalin Nonchev @nonchev.bsky.social · Aug 18

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

Kalin Nonchev @nonchev.bsky.social · Aug 18

Internship Opportunity: Multimodal AI Research Scientist at the Biomedical Informatics Group at ETH Zurich 🚀

Interested in working at the intersection of computational pathology, spatial transcriptomics, LLM representation learning, and tissue generation?

Reposted by Kalin Nonchev

Moritz Schaefer @moritzbaio.bsky.social · Jul 21

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!

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Reposted by Kalin Nonchev

Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · Jul 18

🤝 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)

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Reposted by Kalin Nonchev

Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · Jul 18

🔬 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)

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Reposted by Kalin Nonchev

Peter Koo @pkoo562.bsky.social · May 23

Excited to share an update to D3 (DNA Discrete Diffusion) — an application of score-entropy discrete diffusion model for regulatory genomics!

🧬 Paper: biorxiv.org/content/10.110…

(See thread below 👇) (1/n)

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Kalin Nonchev @nonchev.bsky.social · May 12

#pathology #spatialtranscriptomics #machinelearning

Kalin Nonchev @nonchev.bsky.social · May 12

Explore the dataset: huggingface.co/datasets/non...
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

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Kalin Nonchev @nonchev.bsky.social · May 12

💡 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.

Kalin Nonchev @nonchev.bsky.social · May 12

🚀 Excited to share that we've generated the largest digital spatial transcriptomics dataset using DeepSpot - over 56 million spatial transcriptomics spots from 3 780 TCGA samples across skin melanoma, renal cell carcinoma, lung adenocarcinoma, and lung squamous cell carcinoma cohorts. #pathology

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Kalin Nonchev @nonchev.bsky.social · Mar 20

Glad that you find it exciting too!

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Kalin Nonchev @nonchev.bsky.social · Mar 20

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

Kalin Nonchev @nonchev.bsky.social · Mar 20

More about the competition: www.youtube.com/watch?v=GUXi...

Leaderboard: hub.crunchdao.com/competitions...

Autoimmune Disease Machine Learning Challenge Overview

YouTube video by Broad Institute

www.youtube.com

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Kalin Nonchev @nonchev.bsky.social · Mar 20

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

Kalin Nonchev @nonchev.bsky.social · Mar 20

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!

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Kalin Nonchev @nonchev.bsky.social · Mar 20

First place award at the Autoimmune Disease Machine Learning Challenge organized by the @broadinstitute.org and CrunchDAO. Our approach outperformed competitors worldwide in predicting single-cell spatial transcriptomics from H&E images. 🎉

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