Publications

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: 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]

Bian Li, Jeffrey Mendenhall, John A Capra, and Jens Meiler. A multitask deep-learning method for predicting membrane associations and secondary structures of proteins. J. Proteome Res., (20)8:4089--4100, American Chemical Society (ACS), August 2021. [PUMA: convolutional deep learning; long memory multitask networks; neural prediction prediction; secondary short-term structure topic_lifescience topology transmembrane]

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: Artificial Computational Convolutional Learning; Multiple-Instance Vision Weakly-supervised deep intelligence; learning networks; neural pathology; transformers;]

Benjamin P Brown, Oanh Vu, Alexander R Geanes, Sandeepkumar Kothiwale, Mariusz Butkiewicz, Edward W Lowe, Jr, Ralf Mueller, Richard Pape, Jeffrey Mendenhall, and Jens Meiler. Introduction to the BioChemical Library (BCL): An application-based open-source toolkit for integrated cheminformatics and machine learning in computer-aided drug discovery. Front. Pharmacol., (13):833099, Frontiers Media SA, February 2022. [PUMA: BCL; QSAR; biochemical cheminformatics; deep design; discovery; drug library; network; neural open-source topic_lifescience]