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

Patricia Evelyn Schlosser. Klangwelten neu gedacht : Zur Nutzung und Rolle von Künstlicher Intelligenz in der Musikproduktion. Universitäts- und Landesbibliothek Sachsen-Anhalt, 2024. [PUMA: Zno imported] URL

Gishnu Harikumar Parvathy, Dhananjay Bhandiwad, Lars Eggers, Linda von Borstel, Jochen Behrends, Martina Hein, David Hertz, Jaqueline Marschner, Zane Orinska, Stefan H E Kaufmann, Mario Alberto Flores-Valdez, Hanna Lotter, and Bianca E Schneider. Sex differences in vaccine induced immunity and protection againstMycobacterium tuberculosis. Cold Spring Harbor Laboratory, April 2024. [PUMA: Yaff imported] URL

Atharva Naik. On the Limitations of Embedding Based Methods for Measuring Functional Correctness for Code Generation. 2024. [PUMA: Zno imported] URL

Meysam Alishahi, and Jeff M. Phillips. No Dimensional Sampling Coresets for Classification. 2024. [PUMA: Yaff imported] URL

Aldo Acevedo, Yue Wu, Fabio Lorenzo Traversa, and Carlo Vittorio Cannistraci. Geometric separability of mesoscale patterns in embedding representation and visualization of multidimensional data and complex networks. PLOS Complex Systems, (1)2:1-28, Public Library of Science, October 2024. [PUMA: Yaff imported] URL

Jakob Rehof. LIPIcs, Volume 299, FSCD 2024, Complete Volume. Schloss Dagstuhl – Leibniz-Zentrum für Informatik, 2024. [PUMA: Xack Yaff imported] URL

C. Molinari, J. Bulgarelli, F. Rebuzzi, R. Camara, V. Kokala Dimitropoulou, E. Petracci, J. Ewald, D. Prascevic, P. Ulivi, M. Canale, M. Monti, S. Tamberi, and A. Derventzi. 16P The role of systemic immunity in locally advanced gastric cancer patients treated with neoadjuvant chemotherapy. ESMO Open, (9):103762, 2024. [PUMA: Yaff imported] URL

Patrick Ebel, Rochelle Schneider, Massimo Bonavita, Mariana Clare, Anna Jungbluth, Maryam Pourshamsi, Matthew Chantry, Mihai Alexe, Alessandro Sebastianelli, and Marcin Chrust. 2024 ESA-ECMWF workshop report: current status, progress and opportunities in machine learning for Earth system observation and prediction. npj Climate and Atmospheric Science, (7)1:241, Oct 9, 2024. [PUMA: Zno imported] URL

Maria Wyrzykowska, Gabriel della Maggiora, Nikita Deshpande, Ashkan Mokarian, and Artur Yakimovich. A Benchmark for Virus Infection Reporter Virtual Staining in Fluorescence and Brightfield Microscopy. Cold Spring Harbor Laboratory, September 2024. [PUMA: Xack imported] URL

Vaibhav Sharma, and Artur Yakimovich. A deep learning dataset for sample preparation artefacts detection in multispectral high-content microscopy. Scientific Data, (11)1:232, Feb 23, 2024. [PUMA: Xack imported] URL

Mariana Madruga de Brito, Jan Sodoge, Zora Reckhaus, Miguel Mahecha, and Christian Kuhlicke. Analyzing impact cascades: an integrative approach for assessing the interconnected effects of extreme events across sectors and systems. EGU General Assembly Conference Abstracts, 1496, April 2024. [PUMA: Yaff imported]

Gabriela Araujo-Pardo, Marston Conder, Natalia García-Colín, György Kiss, and Dimitri Leemans. A note on girth-diameter cages. 2024. [PUMA: Yaff imported] URL

Nicolas-Domenic Reiter, Jonas Wahl, Gabriele C. Hegerl, and Jakob Runge. Asymptotic Uncertainty in the Estimation of Frequency Domain Causal Effects for Linear Processes. 2024. [PUMA: Yaff imported] URL

Michael Faerber, David Lamprecht, and Yuni Susanti. AutoRDF2GML: Facilitating RDF Integration in Graph Machine Learning. In Gianluca Demartini, Katja Hose, Maribel Acosta, Matteo Palmonari, Gong Cheng, Hala Skaf-Molli, Nicolas Ferranti, Daniel Hernández, and Aidan Hogan (Eds.), The Semantic Web -- ISWC 2024, 115--133, Springer Nature Switzerland, Cham, 2025. [PUMA: Yaff imported]

Jens Lehmann, Dhananjay Bhandiwad, Preetam Gattogi, and Sahar Vahdati. Beyond Boundaries: A Human-like Approach for Question Answering over Structured and Unstructured Information Sources. Transactions of the Association for Computational Linguistics, (12):786--802, MIT Press, Cambridge, MA, 2024. [PUMA: Yaff imported] URL

Greg Eisenhauer, Norbert Podhorszki, Ana Gainaru, Scott Klasky, Philip E. Davis, Manish Parashar, Matthew Wolf, Eric Suchtya, Erick Fredj, Vicente Bolea, Franz Pöschel, Klaus Steiniger, Michael Bussmann, Richard Pausch, and Sunita Chandrasekaran. Streaming Data in HPC Workflows Using ADIOS. 2024. [PUMA: Zno imported] URL

Jeremy J. Williams, Daniel Medeiros, Stefan Costea, David Tskhakaya, Franz Poeschel, René Widera, Axel Huebl, Scott Klasky, Norbert Podhorszki, Leon Kos, Ales Podolnik, Jakub Hromadka, Tapish Narwal, Klaus Steiniger, Michael Bussmann, Erwin Laure, and Stefano Markidis. Enabling High- Throughput Parallel I/O in Particle-in-Cell Monte Carlo Simulations with openPMD and Darshan I/O Monitoring. 2024 IEEE International Conference on Cluster Computing Workshops (CLUSTER Workshops), 86-95, September 2024. [PUMA: Zno imported]

Anshu Ankolekar, Sebastian Boie, Maryam Abdollahyan, Emanuela Gadaleta, Seyed Alireza Hasheminasab, Guang Yang, Charles Beauville, Nikolaos Dikaios, George Anthony Kastis, Michael Bussmann, Sara Khalid, Hagen Kruger, Philippe Lambin, and Giorgos Papanastasiou. Advancing oncology with federated learning: transcending boundaries in breast, lung, and prostate cancer. A systematic review. 2024. [PUMA: Zno imported] URL

Dieter Weber, Simeon Ehrig, Andreas Schropp, Alexander Clausen, Silvio Achilles, Nico Hoffmann, Michael Bussmann, Rafal E Dunin-Borkowski, and Christian G Schroer. Live Iterative Ptychography. Microscopy and Microanalysis, (30)1:103–117, Oxford University Press (OUP), February 2024. [PUMA: Iterative Live Ptychography Zno imported] URL

Beth Russell, Katharina Beyer, Ailbhe Lawlor, Monique J. Roobol, Lionne D.F. Venderbos, Sebastiaan Remmers, Erik Briers, Sara J. MacLennan, Steven MacLennan, Muhammad Imran Omar, Mieke Van Hemelrijck, Emma Smith, James N’Dow, Karin Plass, Maria Ribal, Nicolas Mottet, Robert Shepherd, Tom Abbott, Ken Mastris, Lisa Moris, Michael Lardas, Thomas Van den Broeck, Peter-Paul Willemse, Nicola Fossati, Karl Pang, Riccardo Campi, Isabella Greco, Mauro Gacci, Sergio Serni, Anders Bjartell, Ragnar Lonnerbro, Alberto Briganti, Daniele Crosti, Roberto Garzonio, Giorgio Gandaglia, Martina Faticoni, Grant office, Chris Bangma, Maria Jongerden, Derya Tilki, Anssi Auvinen, Teemu Murtola, Tapio Visakorpi, Kirsi Talala, Teuvo Tammela, Aino Siltari, Stephane Lejeune, Laurence Colette, Simona Caputova, Delielena Poli, Sophie Byrne, Luz Fialho, Ashley Rowland, Neo Tapela, Nicola Di Flora, Kathi Apostolidis, Valerie Lemair, Bertrand De Meulder, Charles Auffray, Nesrine Taibi, Ayman Hijazy, Albert Saporta, Kai Sun, Shaun Power, Nazanin Zounemat Kermani, Kees van Bochove, Azadeh Tafreshiha, Chiara Bernini, Denis Horgan, Louise Fullwood, Marc Holtorf, Doron Lancet, Gabi Bernstein, Sheela Tripathee, Manfred Wirth, Michael Froehner, Beate Brenner, Angelika Borkowetz, Christian Thomas, Friedemann Horn, Kristin Reiche, Markus Kreuz, Andreas Josefsson, Delila Gasi Tandefelt, Jonas Hugosson, Jack Schalken, Henkjan Huisman, Thomas Hofmarcher, Peter Lindgren, Emelie Andersson, Adam Fridhammar, Monica Tames Grijalva, Susan Evans-Axelsson, Frank Verholen, Jihong Zong, John-Edward Butler-Ransohoff, Todd Williamson, Reg Waldeck, Amanda Bruno, Ekaterina Nevedomskaya, Samuel Fatoba, Niculae Constantinovici, Carl Steinbeisser, Monika Maass, Patrizia Torremante, Emmanuelle Dochy, Federica Pisa, Marc Dietrich Voss, Kishore Papineni, Jing Wang silvanto, Robert Snijder, Xuewei Wang, Mark Lambrecht, Russ Wolfinger, Sherinne Eid, Soundarya Palanisamy, Samiul Haque, Laurent Antoni, Angela Servan, Katie Pascoe, Paul Robinson, Joana Lencart, Bertrand Jaton, Heidi Turunen, Olavi Kilkku, Pasi Pohjanjousi, Olli Voima, Liina Nevalaita, Keijo Punakivi, Sarah Seager, Shilpa Ratwani, Katarzyna Grzeslak, James Brash, Elaine Longden-Chapman, Danny Burke, Muriel Licour, Sarah Payne, Alan Yong, Flavia Lujan, Sophia Le Mare, Jan Hendrich, Michael Bussmann, Juckeland, Kotik, Delielena Poli, and Christian Reich. Survivorship Data in Prostate Cancer: Where Are We and Where Do We Need To Be?. European Urology Open Science, (59):27–29, Elsevier BV, January 2024. [PUMA: Cancer: Data Prostate Survivorship Zno imported] URL

Klaus Steiniger, Rene Widera, Sergei Bastrakov, Michael Bussmann, Sunita Chandrasekaran, Benjamin Hernandez, Kristina Holsapple, Axel Huebl, Guido Juckeland, Jeffrey Kelling, Matt Leinhauser, Richard Pausch, David Rogers, Ulrich Schramm, Jeff Young, and Alexander Debus. EZ: An efficient, charge conserving current deposition algorithm for electromagnetic particle-in-cell simulations. Computer Physics Communications, (291):108849, 2023. [PUMA: Charge Current EZ PIConGPU Particle-in-cell Zno conservation deposition imported] URL

Wael Elwasif, William Godoy, Nick Hagerty, J. Austin Harris, Oscar Hernandez, Balint Joo, Paul Kent, Damien Lebrun-Grandie, Elijah Maccarthy, Veronica Melesse Vergara, Bronson Messer, Ross Miller, Sarp Oral, Sergei Bastrakov, Michael Bussmann, Alexander Debus, Klaus Steiniger, Jan Stephan, Rene Widera, Spencer Bryngelson, Henry Le Berre, Anand Radhakrishnan, Jeffrey Young, Sunita Chandrasekaran, Florina Ciorba, Osman Simsek, Kate Clark, Filippo Spiga, Jeff Hammond, Stone John, David Hardy, Sebastian Keller, Jean-Guillaume Piccinali, and Christian Trott. Application Experiences on a GPU-Accelerated Arm-based HPC Testbed. Proceedings of the HPC Asia 2023 Workshops, 35–49, Association for Computing Machinery, New York, NY, USA, 2023. [PUMA: Zno imported] URL

Anna Willmann, Jurjen Couperus Cabadağ, Yen-Yu Chang, Richard Pausch, Amin Ghaith, Alexander Debus, Arie Irman, Michael Bussmann, Ulrich Schramm, and Nico Hoffmann. Learning Electron Bunch Distribution along a FEL Beamline by Normalising Flows. 2023. [PUMA: Bunch Distribution Electron Learning Zno imported] URL

Brian Edward Marré, Ulrich Schramm, Michael Bussmann, Thomas Kluge, Thomas Cowan, René Widera, Sergei Bastrakov, and Axel Huebl. Atomic population kinetics for Particle in Cell. 2023. [PUMA: Atomic Zno imported kinetics population]

Peer-Timo Bremer, Brian Spears, Tom Gibbs, and Michael Bussmann. AI-Augmented Facilities: Bridging Experiment and Simulation with ML (Dagstuhl Seminar 23132). Schloss Dagstuhl – Leibniz-Zentrum für Informatik, 2023. [PUMA: AI-Augmented Facilities Zno imported] URL

Bernhard Manfred Gruber, Guilherme Amadio, Jakob Blomer, Alexander Matthes, René Widera, and Michael Bussmann. LLAMA: The low‐level abstraction for memory access. Software: Practice and Experience, (53)1:115–141, Wiley, March 2022. [PUMA: LLAMA Zno access imported memory] URL

Patrick Stiller, Varun Makdani, Franz Pöschel, Richard Pausch, Alexander Debus, Michael Bussmann, and Nico Hoffmann. Continual learning autoencoder training for a particle-in-cell simulation via streaming. 2022. [PUMA: Continual Zno autoencoder imported learning particle-in-cell simulation training] URL

J. N’Dow, E.J. Smith, K. Polychronopoulos, A. Cannon, M. Roobol, S. Auweter, M. Thomas, A. Kremer, B. De Meulder, D. Dellamonica, D.P. Alhambra, A. Asiimwe, M. Bussmann, X. Ji, P. Torremante, S. Keller, F. Kube, and H. Krueger. 917P OPTIMA: Improve care for patients with prostate, breast, and lung cancer through artificial intelligence. Annals of Oncology, (33):S966, Elsevier BV, September 2022. [PUMA: 917P OPTIMA Zno imported] URL

Accelerator Programming Using Directives: 8th International Workshop, WACCPD 2021, Virtual Event, November 14, 2021, Proceedings. In Sridutt Bhalachandra, Christopher Daley, and Verónica Melesse Vergara (Eds.), Springer-Verlag, Berlin, Heidelberg, 2021. [PUMA: 2021 Accelerator Programming WACCPD Zno imported]

George Markomanolis, Aksel Alpay, Jeffrey Young, Michael Klemm, Nicholas Malaya, Aniello Esposito, Jussi Heikonen, Sergei Bastrakov, Alexander Debus, Thomas Kluge, Klaus Steiniger, Jan Stephan, Rene Widera, and Michael Bussmann. Evaluating GPU Programming Models for the LUMI Supercomputer. 79-101, January 2022. [PUMA: GPU LUMI Programming Supercomputer Zno]