Publications

Niklas Deckers, and Martin Potthast. WARC-DL: Scalable Web Archive Processing for Deep Learning. 2022. [PUMA: Archive Deep Learning Processing Scalable WARC-DL Web] URL

Dianzhao Li, and Ostap Okhrin. A platform-agnostic deep reinforcement learning framework for effective Sim2Real transfer towards autonomous driving. Commun Eng, (3)1:147, Springer Science and Business Media LLC, October 2024. [PUMA: Sim2Real autonomous deep driving framework learning platform-agnostic reinforcement]

Maksim Kukushkin, Martin Bogdan, and Thomas Schmid. On optimizing morphological neural networks for hyperspectral image classification. In Wolfgang Osten (Eds.), Sixteenth International Conference on Machine Vision (ICMV 2023), (13072):1307202, SPIE, 2024. [PUMA: classification computer deep hyperspectral image learning mathematical morphological morphology networks neuronal remote sensing vision] URL

Anderson P. Avila Santos, Breno L. S. de Almeida, Robson P. Bonidia, Peter F. Stadler, Polonca Stefanic, Ines Mandic-Mulec, Ulisses Rocha, Danilo S. Sanches, and André C.P.L.F. de Carvalho. BioDeepfuse: a hybrid deep learning approach with integrated feature extraction techniques for enhanced non-coding RNA classification. RNA Biology, (21)1:410–421, Informa UK Limited, March 2024. [PUMA: BioDeepfuse RNA classification deep extraction feature learning non-coding] URL

Jordan Richards, Raphaël Huser, Emanuele Bevacqua, and Jakob Zscheischler. Insights into the Drivers and Spatiotemporal Trends of Extreme Mediterranean Wildfires with Statistical Deep Learning. Artificial Intelligence for the Earth Systems, (2)4American Meteorological Society, October 2023. [PUMA: Deep Extreme Learning Mediterranean Spatiotemporal Statistical Trends Wildfires] URL

Daniel Bühler, Nicole Power Guerra, Luisa Müller, Olaf Wolkenhauer, Martin Düffer, Brigitte Vollmar, Angela Kuhla, and Markus Wolfien. Leptin deficiency-caused behavioral change - A comparative analysis using EthoVision and DeepLabCut. Frontiers in neuroscience, (17)Frontiers Media S.A., Mar 24, 2023. [PUMA: topic_lifescience Behavioral Deep DeepLabCut, EthoVision, FIS_scads Obesity analysis, learning,]

Neringa Jurenaite, Daniel Leon-Perinan, Veronika Donath, Sunna Torge, and Rene Jakel. SetQuence & SetOmic: Deep Set Transformer-based Representations of Cancer Multi-Omics. 2022 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2022, 139--147, IEEE, New York u. a., United States of America, 2022. [PUMA: topic_federatedlearn livinglab Deep FIS_scads Network, Neural Representations Set analysis, expression, gene genome, language molecular multi-omics, mutome, natural processing, sequence]

Fabian Hart, Martin Waltz, and Ostap Okhrin. Two-step dynamic obstacle avoidance. Knowledge-based systems, (302)Elsevier Science B.V., Oct 25, 2024. [PUMA: topic_engineering Deep Dynamic FIS_scads Local Supervised avoidance, learning learning, obstacle path planning, reinforcement]

Martin Waltz, and Ostap Okhrin. Spatial–temporal recurrent reinforcement learning for autonomous ships. Neural Networks, (2023)165:634--653, Elsevier Science B.V., Jun 15, 2023. [PUMA: topic_engineering Algorithms, Autonomous COLREG, Computer, Deep FIS_scads Networks, Neural Psychology, Recurrency, Reinforcement, Reward Ships, learning, reinforcement surface vehicle,]

Niklas Paulig, and Ostap Okhrin. Robust path following on rivers using bootstrapped reinforcement learning. Ocean engineering, (298)Elsevier Science B.V., Apr 15, 2024. [PUMA: topic_engineering Autonomous Deep FIS_scads Path Restricted following, learning, reinforcement surface vessel, waterways]

Ravi Pradip, and Frank Cichos. Deep reinforcement learning with artificial microswimmers. Emerging Topics in Artificial Intelligence (ETAI) 2022, (12204):104--110, 2022. [PUMA: topic_physchemistry Deep artificial learning microswimmers reinforcement]

Martin Waltz, Ostap Okhrin, and Michael Schultz. Self-organized free-flight arrival for urban air mobility. Transportation Research Part C: Emerging Technologies, (167):104806, 2024. [PUMA: topic_engineering Deep Urban air eVTOL learning mobility reinforcement] URL

Vincent D. Friedrich, Peter Pennitz, Emanuel Wyler, Julia M. Adler, Dylan Postmus, Kristina Müller, Luiz Gustavo Teixeira Alves, Julia Prigann, Fabian Pott, Daria Vladimirova, Thomas Hoefler, Cengiz Goekeri, Markus Landthaler, Christine Goffinet, Antoine-Emmanuel Saliba, Markus Scholz, Martin Witzenrath, Jakob Trimpert, Holger Kirsten, and Geraldine Nouailles. Neural network-assisted humanisation of COVID-19 hamster transcriptomic data reveals matching severity states in human disease. eBioMedicine, (108):105312, 2024. [PUMA: topic_mathfoundation COVID-19, Cross-species Deep Disease Hamster RNA-seq, Single-cell analysis, learning matching, model, state] URL

Simon M. Hofmann, Frauke Beyer, Sebastian Lapuschkin, Ole Goltermann, Markus Loeffler, Klaus-Robert Müller, Arno Villringer, Wojciech Samek, and A. Veronica Witte. Towards the interpretability of deep learning models for multi-modal neuroimaging: Finding structural changes of the ageing brain. NeuroImage, (261):119504, 2022. [PUMA: topic_neuroinspired topic_lifescience Ageing, Brain-age, Cardiovascular Explainable Structural a.i., deep factors, learning mri, risk] URL

Qinghe Zeng, Christophe Klein, Stefano Caruso, Pascale Maille, Narmin Ghaffari Laleh, Daniele Sommacale, Alexis Laurent, Giuliana Amaddeo, David Gentien, Audrey Rapinat, Hélène Regnault, Cécile Charpy, Cong Trung Nguyen, Christophe Tournigand, Raffaele Brustia, Jean Michel Pawlotsky, Jakob Nikolas Kather, Maria Chiara Maiuri, Nicolas Loménie, and Julien Calderaro. Artificial intelligence predicts immune and inflammatory gene signatures directly from hepatocellular carcinoma histology. J. Hepatol., (77)1:116--127, Elsevier BV, July 2022. [PUMA: topic_lifescience artificial deep gene image immune intelligence; learning; pathology; signatures; slide whole]

Alexander Kurz, Katja Hauser, Hendrik Alexander Mehrtens, Eva Krieghoff-Henning, Achim Hekler, Jakob Nikolas Kather, Stefan Fröhling, Christof von Kalle, and Titus Josef Brinker. Uncertainty estimation in medical image classification: Systematic review. JMIR Med. Inform., (10)8:e36427, August 2022. [PUMA: topic_lifescience calibration; classification; deep detection; estimation image imaging; learning; medical network out-of-distribution uncertainty]

Narmin Ghaffari Laleh, Hannah Sophie Muti, Chiara Maria Lavinia Loeffler, Amelie Echle, Oliver Lester Saldanha, Faisal Mahmood, Ming Y Lu, Christian Trautwein, Rupert Langer, Bastian Dislich, Roman D Buelow, Heike Irmgard Grabsch, Hermann Brenner, Jenny Chang-Claude, Elizabeth Alwers, Titus J Brinker, Firas Khader, Daniel Truhn, Nadine T Gaisa, Peter Boor, Michael Hoffmeister, Volkmar Schulz, and Jakob Nikolas Kather. Benchmarking weakly-supervised deep learning pipelines for whole slide classification in computational pathology. Med. Image Anal., (79)102474:102474, Elsevier BV, July 2022. [PUMA: topic_lifescience Artificial Computational Convolutional Learning; Multiple-Instance Vision Weakly-supervised deep intelligence; learning networks; neural pathology; transformers;]

Peter Leonard Schrammen, Narmin Ghaffari Laleh, Amelie Echle, Daniel Truhn, Volkmar Schulz, Titus J Brinker, Hermann Brenner, Jenny Chang-Claude, Elizabeth Alwers, Alexander Brobeil, Matthias Kloor, Lara R Heij, Dirk Jäger, Christian Trautwein, Heike I Grabsch, Philip Quirke, Nicholas P West, Michael Hoffmeister, and Jakob Nikolas Kather. Weakly supervised annotation-free cancer detection and prediction of genotype in routine histopathology. J. Pathol., (256)1:50--60, Wiley, January 2022. [PUMA: topic_lifescience Lynch artificial cancer; colorectal computational deep digital instability intelligence; learning; microsatellite pathology; syndrome;]

Scarlet Brockmoeller, Amelie Echle, Narmin Ghaffari Laleh, Susanne Eiholm, Marie Louise Malmstrøm, Tine Plato Kuhlmann, Katarina Levic, Heike Irmgard Grabsch, Nicholas P West, Oliver Lester Saldanha, Katerina Kouvidi, Aurora Bono, Lara R Heij, Titus J Brinker, Ismayil Gögenür, Philip Quirke, and Jakob Nikolas Kather. Deep learning identifies inflamed fat as a risk factor for lymph node metastasis in early colorectal cancer. J. Pathol., (256)3:269--281, Wiley, March 2022. [PUMA: topic_lifescience AI; LNM adipose and artificial biomarker; bowel cancer; colorectal deep digital early inflamed intelligence; learning; metastasis; new pT1 pT2 pathology; prediction predictive tissue;]

Roman C Maron, Achim Hekler, Sarah Haggenmüller, Christof von Kalle, Jochen S Utikal, Verena Müller, Maria Gaiser, Friedegund Meier, Sarah Hobelsberger, Frank F Gellrich, Mildred Sergon, Axel Hauschild, Lars E French, Lucie Heinzerling, Justin G Schlager, Kamran Ghoreschi, Max Schlaak, Franz J Hilke, Gabriela Poch, Sören Korsing, Carola Berking, Markus V Heppt, Michael Erdmann, Sebastian Haferkamp, Dirk Schadendorf, Wiebke Sondermann, Matthias Goebeler, Bastian Schilling, Jakob N Kather, Stefan Fröhling, Daniel B Lipka, Eva Krieghoff-Henning, and Titus J Brinker. Model soups improve performance of dermoscopic skin cancer classifiers. Eur. J. Cancer, (173):307--316, Elsevier BV, September 2022. [PUMA: topic_lifescience Artificial Calibration; Deep Dermatology; Ensembles; Generalisation; Melanoma; Model Nevus; Robustness intelligence; learning; soups;]