Stefan Bonn

23 papers Journal 17Unranked 6
YearRankTypeTitle / Venue / Authors
2026 J jnl
A systematic analysis of the impact of data variation on AI-based histopathological grading of prostate cancer.
Medical Image Anal.
Patrick Fuhlert, Fabian Westhaeusser, Esther Dietrich, Maximilian Lennartz, Robin Khatri, Nico Kaiser, Pontus Röbeck, Roman David Bülow, Saskia Von Stillfried, Anja Witte, Sam Ladjevardi, Anders Drotte, Peter Severgårdh, Jan Baumbach, Victor G. Puelles, Michael Häggman, Michael Brehler, Peter Boor, Peter Walhagen, Anca Dragomir, Christer Busch, Markus Graefen, Ewert Bengtsson, Guido Sauter, Marina Zimmermann, Stefan Bonn
2026 J jnl
On the power and limits of foundation model image embeddings for privacy-preserving federated learning.
Array
Jens Johann Georg Lohmann, Anja Witte, Andreas Maier, Christina Caroline Saak, Guido Sauter, Marina Zimmermann, Stefan Bonn, Jan Baumbach
2025 J jnl
PCA-based spatial domain identification with state-of-the-art performance.
Bioinform.
Darius P. Schaub, Behnam Yousefi, Nico Kaiser, Robin Khatri, Victor G. Puelles, Christian F. Krebs, Ulf Panzer, Stefan Bonn
2024 J jnl
A comprehensive comparison of deep learning-based compound-target interaction prediction models to unveil guiding design principles.
J. Cheminformatics
Sina Abdollahi, Darius P. Schaub, Madalena Barroso, Nora C. Laubach, Wiebke Hutwelker, Ulf Panzer, Søren W. Gersting, Stefan Bonn
2024 J jnl
Gene count estimation with pytximport enables reproducible analysis of bulk RNA sequencing data in Python.
Bioinform.
Malte Kuehl, Milagros N. Wong, Nicola Wanner, Stefan Bonn, Victor G. Puelles
2023 J jnl
Pathogen detection in RNA-seq data with Pathonoia.
BMC Bioinform.
Anna-Maria Liebhoff, Kevin Menden, Alena Laschtowitz, Andre Franke, Christoph Schramm, Stefan Bonn
2022 — conf
Deep Learning-Based Discrete Calibrated Survival Prediction.
ICDH
Patrick Fuhlert, Anne Ernst, Esther Dietrich, Fabian Westhaeusser, Karin Kloiber, Stefan Bonn
2022 J jnl
Deep Learning-Based Discrete Calibrated Survival Prediction.
CoRR
Patrick Fuhlert, Anne Ernst, Esther Dietrich, Fabian Westhaeusser, Karin Kloiber, Stefan Bonn
2022 — conf
Uncertainty Estimation for Single-cell Label Transfer.
COPA
Robin Khatri, Stefan Bonn
2021 — conf
Deep Learning-Based Bias Transfer for Overcoming Laboratory Differences of Microscopic Images.
MIUA
Ann-Katrin Thebille, Esther Dietrich, Martin Klaus, Lukas Gernhold, Maximilian Lennartz, Christoph Kuppe, Rafael Kramann, Tobias B. Huber, Guido Sauter, Victor G. Puelles, Marina Zimmermann, Stefan Bonn
2021 J jnl
Deep learning-based bias transfer for overcoming laboratory differences of microscopic images.
CoRR
Ann-Katrin Thebille, Esther Dietrich, Martin Klaus, Lukas Gernhold, Maximilian Lennartz, Christoph Kuppe, Rafael Kramann, Tobias B. Huber, Guido Sauter, Victor G. Puelles, Marina Zimmermann, Stefan Bonn
2021 J jnl
Interactive gene networks with KNIT.
Bioinform.
Daniel Sumner Magruder, Anna-Maria Liebhoff, Jörn Bethune, Stefan Bonn
2021 — conf
Towards Explainable End-to-End Prostate Cancer Relapse Prediction from H&E Images Combining Self-Attention Multiple Instance Learning with a Recurrent Neural Network.
ML4H@NeurIPS
Esther Dietrich, Patrick Fuhlert, Anne Ernst, Guido Sauter, Maximilian Lennartz, H. Siegfried Stiehl, Marina Zimmermann, Stefan Bonn
2021 J jnl
Towards Explainable End-to-End Prostate Cancer Relapse Prediction from H&E Images Combining Self-Attention Multiple Instance Learning with a Recurrent Neural Network.
CoRR
Esther Dietrich, Patrick Fuhlert, Anne Ernst, Guido Sauter, Maximilian Lennartz, H. Siegfried Stiehl, Marina Zimmermann, Stefan Bonn
2020 J jnl
Explainable Deep Learning for Augmentation of Small RNA Expression Profiles.
J. Comput. Biol.
Jelena Fiosina, Maksims Fiosins, Stefan Bonn
2020 J jnl
SEAweb: the small RNA Expression Atlas web application.
Nucleic Acids Res.
Raza-Ur Rahman, Anna-Maria Liebhoff, Vikas Bansal, Maksims Fiosins, Ashish Rajput, Abdul Sattar, Daniel Sumner Magruder, Sumit Madan, Ting Sun, Abhivyakti Gautam, Sven Heins, Timur Liwinski, Jörn Bethune, Claudia Trenkwalder, Juliane Fluck, Brit Mollenhauer, Stefan Bonn
2019 — conf
Deep Learning and Random Forest-Based Augmentation of sRNA Expression Profiles.
ISBRA
Jelena Fiosina, Maksims Fiosins, Stefan Bonn
2019 J jnl
Deep Learning and Random Forest-Based Augmentation of sRNA Expression Profiles.
CoRR
Jelena Fiosina, Maksims Fiosins, Stefan Bonn
2019 J jnl
Explainable Deep Learning for Augmentation of sRNA Expression Profiles.
CoRR
Jelena Fiosina, Maksims Fiosins, Stefan Bonn
2018 — conf
A semantic data integration methodology for translational neurodegenerative disease research.
SWAT4LS
Sumit Madan, Maksims Fiosins, Stefan Bonn, Juliane Fluck
2018 J jnl
Oasis 2: improved online analysis of small RNA-seq data.
BMC Bioinform.
Raza-Ur Rahman, Abhivyakti Gautam, Jörn Bethune, Abdul Sattar, Maksims Fiosins, Daniel Sumner Magruder, Vincenzo Capece, Orr Shomroni, Stefan Bonn
2017 J jnl
Root demotion: efficient post-processing of layered graphs to reduce dummy vertices for hierarchical graph drawing.
J. Graph Algorithms Appl.
Daniel Sumner Magruder, Stefan Bonn
2015 J jnl
Oasis: online analysis of small RNA deep sequencing data.
Bioinform.
Vincenzo Capece, Julio C. Garcia Vizcaino, Ramon Vidal, Raza-Ur Rahman, Tonatiuh Pena Centeno, Orr Shomroni, Irantzu Suberviola, André Fischer, Stefan Bonn