Publications

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;]

Chiara Maria Lavinia Loeffler, Nadina Ortiz Bruechle, Max Jung, Lancelot Seillier, Michael Rose, Narmin Ghaffari Laleh, Ruth Knuechel, Titus J Brinker, Christian Trautwein, Nadine T Gaisa, and Jakob N Kather. Artificial intelligence-based detection of FGFR3 mutational status directly from routine histology in bladder cancer: A possible preselection for molecular testing?. Eur. Urol. Focus, (8)2:472--479, Elsevier BV, March 2022. [PUMA: topic_lifescience Artificial Bladder Deep FGFR3 Molecular cancer; factor fibroblast for growth intelligence; learning; mutations; receptor testing therapy]

David Nam, Julius Chapiro, Valerie Paradis, Tobias Paul Seraphin, and Jakob Nikolas Kather. Artificial intelligence in liver diseases: Improving diagnostics, prognostics and response prediction. JHEP Rep., (4)4:100443, Elsevier BV, April 2022. [PUMA: topic_lifescience AI, Artificial CNN, Communications DICOM, Diagnosis; Digital HCC, Imaging Individual ML, MVI, Medicine; NAFLD, NASH, Prognosis Reporting TACE, TRIPOD, Transparent WSIs, a and artificial carcinoma; chemoembolisation; convolutional data deep diagnostic disease; fatty for hepatocellular images; imaging; in integration intelligence; invasion; learning; liver machine microvascular model multimodal multivariable network; neural non-alcoholic of or prediction slide steatohepatitis; support system; transarterial whole]

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

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,]