Publications

Brian Groenke, Kristoffer Aalstad, Norbert Pirk, Sebastian Westermann, Jakob Zscheischler, Guillermo Gallego, and Julia Boike. Simulation-based inference as a paradigm for scientific machine learning in the cryosphere and beyond. Copernicus GmbH, March 2024. [PUMA: zno] URL

Ni Li, Wim Thiery, Jakob Zscheischler, Gabriele Messori, Liane Guillou, Joakim Nivre, Olof Görnerup, Seppe Lampe, Clare Flynn, Mariana Madruga de Brito, and Aglae Jezequel. A new climate impact database using generative AI. Copernicus GmbH, November 2024. [PUMA: zno] URL

Daniel Klotz, Martin Gauch, Frederik Kratzert, Grey Nearing, and Jakob Zscheischler. Technical Note: The divide and measure nonconformity – how metrics can mislead when we evaluate on different data partitions. Hydrology and Earth System Sciences, (28)15:3665–3673, Copernicus GmbH, August 2024. [PUMA: zno] URL

Mohit Anand, Friedrich J. Bohn, Gustau Camps-Valls, Rico Fischer, Andreas Huth, Lily-belle Sweet, and Jakob Zscheischler. Identifying compound weather drivers of forest biomass loss with generative deep learning. Environmental Data Science, (3)Cambridge University Press (CUP), 2024. [PUMA: zno] URL

Ni Li, Shorouq Zahra, Mariana Brito, Clare Flynn, Olof Görnerup, Koffi Worou, Murathan Kurfali, Chanjuan Meng, Wim Thiery, Jakob Zscheischler, Gabriele Messori, and Joakim Nivre. Using LLMs to Build a Database of Climate Extreme Impacts. Proceedings of the 1st Workshop on Natural Language Processing Meets Climate Change (ClimateNLP 2024), 93–110, Association for Computational Linguistics, 2024. [PUMA: imported zno] URL

Siavash Ghiasvand, and Florina M. Ciorba. Assessing Data Usefulness for Failure Analysis in Anonymized System Logs. Proceedings of the 17th International Symposium on Parallel and Distributed Computing (ISPDC), 164--171, Geneva, Switzerland, June 2018. [PUMA: zno]

Maximilian Joas, Neringa Jurenaite, Dusan Prascevic, Nico Scherf, and Jan Ewald. A generalized and versatile framework to train and evaluate autoencoders for biological representation learning and beyond: AUTOENCODIX. bioRxiv, Cold Spring Harbor Laboratory, December 2024. [PUMA: xack] URL

Cristian A. Velandia-Huerto, Ali M. Yazbeck, Jana Schor, and Peter F. Stadler. Evolution and Phylogeny of MicroRNAs — Protocols, Pitfalls, and Problems. miRNomics, 211–233, Springer US, February 2012. [PUMA: Evolution MicroRNAs Phylogeny Zno] URL

Chaonan Ji, Tonio Fincke, Vitus Benson, Gustau Camps-Valls, Miguel-Ángel Fernández-Torres, Fabian Gans, Guido Kraemer, Francesco Martinuzzi, David Montero, Karin Mora, Oscar J. Pellicer-Valero, Claire Robin, Maximilian Söchting, Mélanie Weynants, and Miguel D. Mahecha. DeepExtremeCubes: Earth system spatio-temporal data for assessing compound heatwave and drought impacts. Scientific Data, (12)1:149, Jan 25, 2025. [PUMA: Yaff topic_earthenvironment] URL

Evangelia Skoufa, Jixing Zhong, Oliver Kahre, Kelly Hu, Georgios Tsissios, Louise Carrau, Antonio Herrera, Albert Dominguez Mantes, Alejandro Castilla-Ibeas, Hwanseok Jang, Martin Weigert, Gioele La Manno, Matthias Lutolf, Marian Ros, and Can Aztekin. Specialized signaling centers direct cell fate and spatial organization in a limb organoid model. bioRxiv, Cold Spring Harbor Laboratory, 2024. [PUMA: ML_Spatial_Understanding Zno] URL

Mauro Gwerder, Cansaran Saygili Demir, Hannah L Williams, Alessandro Lugli, Cristina Graham Martinez, Joanna Kowal, Amjad Khan, Philipp Kirchner, Thibaud Koessler, Martin D Berger, and others. Morpho-molecular features of Epithelial Mesenchymal Transition associate with clinical outcome in patients with rectal cancer. bioRxiv, 2024--11, Cold Spring Harbor Laboratory, 2024. [PUMA: ML_Spatial_Understanding Yaff]

Simon Graham, Quoc Dang Vu, Mostafa Jahanifar, Martin Weigert, Uwe Schmidt, Wenhua Zhang, Jun Zhang, Sen Yang, Jinxi Xiang, Xiyue Wang, and others. CoNIC Challenge: Pushing the Frontiers of Nuclear Detection, Segmentation, Classification and Counting. arXiv preprint arXiv:2303.06274, (92):103047, 2023. [PUMA: Computational_pathology Deep_learning ML_Spatial_Understanding Nuclear_recognition Zno] URL

Andreas Müller, Deborah Schmidt, Jan Philipp Albrecht, Lucas Rieckert, Maximilian Otto, Leticia Elizabeth Galicia Garcia, Gunar Fabig, Michele Solimena, and Martin Weigert. Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets. Nature Protocols, 1--31, Nature Publishing Group UK London, 2024. [PUMA: ML_Spatial_Understanding Zno]

Benjamin Gallusser, and Martin Weigert. Trackastra: Transformer-based cell tracking for live-cell microscopy. European Conference on Computer Vision, 467--484, 2025. [PUMA: ML_Spatial_Understanding imported]

Rhea Sanjay Sukthanker, Arber Zela, Benedikt Staffler, Aaron Klein, Lennart Purucker, Joerg K. H. Franke, and Frank Hutter. HW-GPT-Bench: Hardware-Aware Architecture Benchmark for Language Models. The Thirty-eight Conference on Neural Information Processing Systems Datasets and Benchmarks Track (NeurIPS'24), 2024. [PUMA: AutoML Xack Yaff large_language_models neural_architecture_search]

Antonia Stubenvoll, Maria Schmidt, Johanna Moeller, Max Alexander Lingner Chango, Carolyn Schultz, Olga Antoniadou, Henry Loeffler-Wirth, Stephan Bernhart, Florian Peter Große, Beatrice Thier, Annette Paschen, Ulf Anderegg, Jan C. Simon, Mirjana Ziemer, Clara T. Schoeder, Hans Binder, and Manfred Kunz. Single-cell transcriptomics and epigenomics point to CD58-CD2 interaction in controlling primary melanoma growth and immunity. Cancer Communications, (n/a)n/aJohn Wiley & Sons, Ltd, January 2025. [PUMA: Yaff melanoma myown single-cell topic_lifescience transcriptomics] URL

Byung Ho Lee, Kana Fuji, Heike Petzold, Phil Seymour, Siham Yennek, Coline Schewin, Allison Lewis, Daniel Riveline, Tetsuya Hiraiwa, Masaki Sano, and Anne Grapin-Botton. Control of lumen geometry and topology by the interplay between pressure and cell proliferation rate in pancreatic organoids. bioRxiv, Cold Spring Harbor Laboratory, 2024. [PUMA: Yaff imported] URL

Yuvaraj Natarajan, Gitanjali Wadhwa, Sri Preethaa K R, Karthic Sundaram, and Rama Abirami K. Advancing Sustainable IoT Appliance Load Monitoring Through Edge-Enabled Federated Transfer Learning. 2024 International Conference on Green Energy, Computing and Sustainable Technology (GECOST), 386-391, January 2024. [PUMA: Yaff imported]

Reza Nicknam, Seyyed Rouhollah Hadj Zargarbashi, and Abtin Safavipour. AI Development in Germany After the Publication of German Nation AI Strategy, Problems and Solutions. Journal of Humanities and Education Development, (6)5:68–81, AI Publications, 2024. [PUMA: Zno imported] URL

Prakash Gondode, Sakshi Duggal, and Vaishali Mahor. Artificial intelligence hallucinations in anaesthesia: Causes, consequences and countermeasures. Indian Journal of Anaesthesia, (68)7:658–661, Medknow, June 2024. [PUMA: Zno imported] URL