Fabian Hörst

Fabian Hörst

Team Lead Computer Vision and Computational Pathology

Institute for AI in Medicine, Germany

Fabian is an electrical engineer with a master’s in information engineering. He completed his master’s at the IKIM and subsequently joined the group as a Ph.D. student. In his research, he is working in the field of computational pathology. During his master’s thesis, he implemented an algorithm to predict the therapy outcome of patients with adenocarcinoma in the esophagus, solely based on H&E tissue samples gathered prior to therapy.

Publications

2026

Vessel branching patterns quantified by artificial intelligence as a novel prognostic biomarker in advanced renal cell carcinoma: A post-hoc analysis of the CM914 trial. Hannah Timm, Marieta Toma, Julian Friedrich, Fabian Hörst, Niklas Klümper, Yangping Li, Alexander Effland, Michael Hölzel, Jens Kleesiek, Viktor Grünwald Journal of Clinical Oncology CellViT++: Energy-Efficient and Adaptive Cell Segmentation and Classification Using Foundation Models Fabian Hörst, Moritz Rempe, Helmut Becker, Lukas Heine, Julius Keyl, Jens Kleesiek Computer Methods and Programs in Biomedicine Deep Learning-derived Sarcopenia Marker Predicts Benefit from Anti-EGFR Therapy in Patients with RAS Wild-Type Metastatic Colorectal Cancer Julius Keyl, René Hosch, Fabian Hörst, Philipp Keyl, Amin Dada, Johannes Haubold, Jannis Straus, Jan Egger, Arndt Stahler, Annika Kurreck, Alexej Ballhausen, Sebastian Stintzing, Stefan Fruehauf, Lothar Müller, Annabel H. S. Alig, Tanja Trarbach, Sylvia Hartmann, Felix Nensa, Jens Kleesiek, Stefan Kasper, Martin Schuler, Dominik P. Modest Clinical Cancer Research Efficient Complex-Valued Vision Transformers for MRI Classification Directly from k-Space Moritz Rempe, Lukas Thomas Rotkopf, Marco Schlimbach, Helmut Becker, Fabian Hörst, Johannes Haubold, Philipp Dammann, Kevin Kröninger, Jens Kleesiek arXiv

2025

Automated CT-based sarcopenia assessment for risk stratification of patients undergoing colorectal cancer resection Johannes Vogelsang, Gernot Pucher, Fabian Hörst, René Hosch, Johannes Haubold, Philipp Keyl, Christopher Sauer, David Albers, Peter Markus, Jan P. Neuhaus, Andreas D. Rink, Jürgen Treckmann, Ulf Peter Neumann, Kai Nassenstein, Michael Forsting, Hideo A. Baba, Jan Egger, Stefan Kasper, Martin Schuler, Felix Nensa, Jens Kleesiek, Julius Keyl Clinical Surgical Oncology CT-GRAPH: Hierarchical Graph Attention Network for Anatomy-Guided CT Report Generation Hamza Kalisch, Fabian Hörst, Jens Kleesiek, Ken Herrmann, Constantin Seibold 2025 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW) Three-Dimensional Quantification of Macular OCT Alterations Improves the Diagnostic Performance of Artificial Intelligence Models Lukas Heine, Anna Vahldiek, Benja Vahldiek, Fabian Hörst, Constantin Seibold, Mael Lever, Laurenz Pauleikhoff, Nikolaos Bechrakis, Daniel Pauleikhoff, Jens Kleesiek Translational Vision Science & Technology De-identification of medical imaging data: a comprehensive tool for ensuring patient privacy Moritz Rempe, Lukas Heine, Constantin Seibold, Fabian Hörst, Jens Kleesiek European Radiology PhaseGen: A Diffusion-Based Approach for Complex-Valued MRI Data Generation Moritz Rempe, Fabian Hörst, Helmut Becker, Marco Schlimbach, Lukas Thomas Rotkopf, Kevin Kröninger, Jens Kleesiek arXiv Cracking the PUMA Challenge in 24 Hours with CellViT++ and nnU-Net Negar Shahamiri, Moritz Rempe, Lukas Heine, Jens Kleesiek, Fabian Hörst arXiv MedShapeNet -- A Large-Scale Dataset of 3D Medical Shapes for Computer Vision Jianning Li, Antonio Pepe, Christina Gsaxner, Gijs Luijten, Yuan Jin, Narmada Ambigapathy, Enrico Nasca, Naida Solak, Gian Marco Melito, Afaque Rafique Memon, Xiaojun Chen, Jan Stefan Kirschke, Ezequiel de la Rosa, Patrick Ferdinand Christ, Hongwei Bran Li, David G. Ellis, Michele R. Aizenberg, Sergios Gatidis, Thomas Kuestner, Nadya Shusharina, Nicholas Heller, Vincent Andrearczyk, Adrien Depeursinge, Mathieu Hatt, Anjany Sekuboyina, Maximilian Loeffler, Hans Liebl, Reuben Dorent, Tom Vercauteren, Jonathan Shapey, Aaron Kujawa, Stefan Cornelissen, Patrick Langenhuizen, Achraf Ben-Hamadou, Ahmed Rekik, Sergi Pujades, Edmond Boyer, Federico Bolelli, Costantino Grana, Luca Lumetti, Hamidreza Salehi, Jun Ma, Yao Zhang, Ramtin Gharleghi, Susann Beier, Eduardo A. Garza-Villarreal, Thania Balducci, Diego Angeles-Valdez, Roberto Souza, Leticia Rittner, Richard Frayne, Yuanfeng Ji, Soumick Chatterjee, Andreas Nuernberger, Joao Pedrosa, Carlos Ferreira, Guilherme Aresta, Antonio Cunha, Aurelio Campilho, Yannick Suter, Jose Garcia, Alain Lalande, Emmanuel Audenaert, Claudia Krebs, Timo Van Leeuwen, Evie Vereecke, Rainer Roehrig, Frank Hoelzle, Vahid Badeli, Kathrin Krieger, Matthias Gunzer, Jianxu Chen, Amin Dada, Miriam Balzer, Jana Fragemann, Frederic Jonske, Moritz Rempe, Stanislav Malorodov, Fin Hendrik Bahnsen, Constantin Seibold, Alexander Jaus, Ana Sofia Ferreira Santos, Mariana Lindo, André Ferreira, Victor Alves, Michael Kamp, Amr Abourayya, Felix Nensa, Fabian Hoerst, Alexander Brehmer, Lukas Heine, Lars E. Podleska, Matthias A. Fink, Julius Keyl, Konstantinos Tserpes, Moon-Sung Kim, Shireen Elhabian, Hans Lamecker, Dzenan Zukic, Beatriz Paniagua, Christian Wachinger, Martin Urschler, Luc Duong, Jakob Wasserthal, Peter F. Hoyer, Oliver Basu, Thomas Maal, Max J. H. Witjes, Ping Luo, Björn Menze, Mauricio Reyes, Christos Davatzikos, Behrus Puladi, Jens Kleesiek, Jan Egger, Zongwei Zhou, Jiancheng Yang, Chongyu Qu, Tiezheng Zhang, Xiaoxi Chen, Wenxuan Li, Marek Wodzinski, Paul Friedrich, Kangxian Xie, Viet Duc Vu, Christopher Schlachta, Sandrine De Ribaupierre, Rajnikant Patel, Roy Eagleson, Heinrich Mächler, Thomas Küstner, Arcot Sowmya, Vincenzo Ferrari, Florian Dubost, Stefanie Schreiber, Hendrik Mattern, Oliver Speck, Daniel Haehn, Christoph John, Vicky Vandenbossche, Aline Van Oevelen, Kate Duquesne, Hamza Mekhzoum, Jef Vandemeulebroucke, Hauke Heidemeyer, Rainer Röhrig, Frank Hölzle, Timo van Meegdenburg, Zdravko Marinov, Paul F. Jäger, Rainer Stiefelhagen, Fabian Hörst, Yannik Hanusrichter, Martin Weßling, Marcel Dudda, Gregor Schiele, Ti-chiun Chang, Seyed-Ahmad Ahmadi, Thomas M. Deserno, Pascal Fua, Alan L. Yuille Biomedical Engineering / Biomedizinische Technik Spacewalker: Traversing Representation Spaces for Fast Interactive Exploration and Annotation of Unstructured Data Lukas Heine, Fabian Hörst, Jana Fragemann, Gijs Luijten, Jan Egger, Fin Hendrik Bahnsen, Saquib Sarfraz, Jens Kleesiek, Constantin Seibold, M. Saquib Sarfraz Machine Learning Methods in Visualisation for Big Data (EuroVis Workshop) Three-Dimensional Quantification of Macular OCT Alterations Improves the Diagnostic Performance of Artificial Intelligence Models Lukas Heine, Anna Vahldiek, Benja Vahldiek, Fabian Hörst, Constantin Seibold, Mael Lever, Laurenz Pauleikhoff, Nikolaos Bechrakis, Daniel Pauleikhoff, Jens Kleesiek Translational Vision Science & Technology

2024

Early versus late response to PD-1-based immunotherapy in metastatic melanoma Georg C. Lodde, Fang Zhao, Rudolf Herbst, Patrick Terheyden, Jochen Utikal, Claudia Pföhler, Jens Ulrich, Alexander Kreuter, Peter Mohr, Ralf Gutzmer, Friedegund Meier, Edgar Dippel, Michael Weichenthal, Philipp Jansen, Bernd Kowall, Wolfgang Galetzka, Fabian Hörst, Jens Kleesiek, Birte Hellwig, Jörg Rahnenführer, Luisa Rajcsanyi, Triinu Peters, Anke Hinney, Jan-Malte Placke, Antje Sucker, Annette Paschen, Jürgen C. Becker, Elisabeth Livingstone, Lisa Zimmer, Alpaslan Tasdogan, Alexander Roesch, Eva Hadaschik, Dirk Schadendorf, Klaus Griewank, Selma Ugurel European Journal of Cancer Cyto R-CNN and CytoNuke Dataset: Towards reliable whole-cell segmentation in bright-field histological images Johannes Raufeisen, Kunpeng Xie, Fabian Hörst, Till Braunschweig, Jianning Li, Jens Kleesiek, Rainer Röhrig, Jan Egger, Bastian Leibe, Frank Hölzle, Alexander Hermans, Behrus Puladi Computer Methods and Programs in Biomedicine Tumor likelihood estimation on MRI prostate data by utilizing k-Space information Moritz Rempe, Fabian Hörst, Constantin Seibold, Boris Hadaschik, Marco Schlimbach, Jan Egger, Kevin Kröninger, Felix Breuer, Martin Blaimer, Jens Kleesiek arXiv Accelerating Artificial Intelligence-based Whole Slide Image Analysis with an Optimized Preprocessing Pipeline Fabian Hörst, Sajad H. Schaheer, Giulia Baldini, Fin Hendrik Bahnsen, Jan Egger, Jens Kleesiek Bildverarbeitung für die Medizin 2024 CytoNuke Dataset: Towards reliable whole-cell segmentation in bright-field histological images Johannes Raufeisen, Kunpeng Xie, Fabian Hörst, Till Braunschweig, Jianning Li, Jens Kleesiek, Rainer Röhrig, Jan Egger, Bastian Leibe, Frank Hölzle, Alexander Hermans, Behrus Puladi Zenodo

2023

Histology-Based Prediction of Therapy Response to Neoadjuvant Chemotherapy for Esophageal and Esophagogastric Junction Adenocarcinomas Using Deep Learning Fabian Hörst, Saskia Ting, Sven-Thorsten Liffers, Kelsey L. Pomykala, Katja Steiger, Markus Albertsmeier, Martin K. Angele, Sylvie Lorenzen, Michael Quante, Wilko Weichert, Jan Egger, Jens T. Siveke, Jens Kleesiek JCO Clinical Cancer Informatics CellViT: Vision Transformers for Precise Cell Segmentation and Classification Fabian Hörst, Moritz Rempe, Lukas Heine, Constantin Seibold, Julius Keyl, Giulia Baldini, Selma Ugurel, Jens T. Siveke, Barbara Grünwald, Jan Egger, Jens Kleesiek arXiv Valuing vicinity: Memory attention framework for context-based semantic segmentation in histopathology Oliver Ester, Fabian Hörst, Constantin Seibold, Julius Keyl, Saskia Ting, Nikolaos Vasileiadis, Jessica Schmitz, Philipp Ivanyi, Viktor Grünwald, Jan Hinrich Bräsen, Jan Egger, Jens Kleesiek Computerized Medical Imaging and Graphics Histology-based Prediction of Therapy Response to Neoadjuvant Chemotherapy for Esophageal and Esophagogastric Junction Adenocarcinomas Using Deep Learning Fabian Hörst, Saskia Ting, Sven-Thorsten Liffers, Kelsey L. Pomykala, Katja Steiger, Markus Albertsmeier, Marting K. Angele, Sylvie Lorenzen, Michael Quante, Wilko Weichert, Jan Egger, Jens T. Siveke, Jens Kleesiek medRxiv Lean Study Host: Towards an Automated Pipeline for Multi-Center Study Hosting Lukas Heine, Fabian Hörst, Enrico Nasca, Jens T. Siveke, Jan Egger, Moon-Sung Kim, Fin Hendrik Bahnsen, Jens Kleesiek Proceedings of the 57th Hawaii International Conference on System Sciences

2022

Valuing Vicinity: Memory attention framework for context-based semantic segmentation in histopathology Oliver Ester, Fabian Hörst, Constantin Seibold, Julius Keyl, Saskia Ting, Nikolaos Vasileiadis, Jessica Schmitz, Philipp Ivanyi, Viktor Grünwald, Jan Hinrich Bräsen, Jan Egger, Jens Kleesiek arXiv