Publications

Franz Baader, and Renata Wassermann. Contractions Based on Optimal Repairs. Proceedings of the TwentyFirst International Conference on Principles of Knowledge Representation and Reasoning, 94–105, International Joint Conferences on Artificial Intelligence Organization, November 2024. [PUMA: topic_knowledge area_methods] URL

Xiaohan Kuang, zhaoqian su, Yunchao Liu, Xiaobo Lin, Jesse Spencer Smith, Tyler Derr, Yinghao Wu, and Jens Meiler. SuperWater: Predicting Water Molecule Positions on Protein Structures by Generative AI. Cold Spring Harbor Laboratory, November 2024. [PUMA: imported topic_lifescience] URL

C.J.R. Murphy-Barltrop, and J.L. Wadsworth. Modelling Non-Stationarity in Asymptotically Independent Extremes. Computational Statistics and Data Analysis, (199):108025, Elsevier BV, November 2024. [PUMA: imported topic_mathfoundation] URL

Shan Jiang, Zhaoqian Su, Nathaniel Bloodworth, Yunchao Liu, Cristina Martina, David G. Harrison, and Jens Meiler. Machine learning application to predict binding affinity between peptide containing non-canonical amino acids and HLA0201. Cold Spring Harbor Laboratory, November 2024. [PUMA: imported topic_lifescience] URL

Chiara Molinari, Leonardo Solaini, Francesca Rebuzzi, Gianluca Tedaldi, Davide Angeli, Elisabetta Petracci, Dusan Prascevic, Jan Ewald, Erhard Rahm, Matteo Canale, Martinelli Giovanni, Anna Tomezzoli, Maria Bencivenga, Maria Raffaella Ambrosio, Daniele Marrelli, Paolo Morgagni, Giorgio Ercolani, Paola Ulivi, and Luca Saragoni. Genomic events stratifying prognosis of early gastric cancer. Gastric Cancer, (27)6:1189--1200, Springer Science and Business Media LLC, November 2024. [PUMA: Prognosis Pen; topic_lifescience EGC; ARID1A area_bigdata LRP1B]

Johannes Pahlke, and Ivo Sbalzarini. Proven Distributed Memory Parallelization of Particle Methods. ACM Trans. Parallel Comput., Association for Computing Machinery, New York, NY, USA, Sep 18, 2024. [PUMA: meshfree definition, software algorithmics, bounds, simulation distributed engineering methods, scalability formal algorithms, topic_lifescience particle memory, parallelization,] URL

C. J. R. Murphy-Barltrop, J. L. Wadsworth, and E. F. Eastoe. Improving Estimation for Asymptotically Independent Bivariate Extremes via Global Estimators for the Angular Dependence Function. Extremes, Aug 13, 2024. [PUMA: imported topic_mathfoundation] URL

Franz Baader, and Filippo De Bortoli. Logics with Concrete Domains: First-Order Properties, Abstract Expressive Power, and (Un)Decidability. SIGAPP Appl. Comput. Rev., (24)3:5–17, Association for Computing Machinery, New York, NY, USA, Oct 8, 2024. [PUMA: imported topic_knowledge] URL

Markus Ulbricht. Formal Argumentation in Symbolic AI. In Kate Larson (Eds.), Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence, IJCAI-24, 8577--8582, International Joint Conferences on Artificial Intelligence Organization, August 2024. [PUMA: topic_knowledge] URL

Maik Fröbe, Jan Heinrich Reimer, Sean MacAvaney, Niklas Deckers, Simon Reich, Janek Bevendorff, Benno Stein, Matthias Hagen, and Martin Potthast. The Information Retrieval Experiment Platform (Extended Abstract). Proceedings of the Thirty-ThirdInternational Joint Conference on Artificial Intelligence, 8405–8410, International Joint Conferences on Artificial Intelligence Organization, August 2024. [PUMA: imported topic_language] URL

Kiet Nguyen Anh, and Markus Ulbricht. Preferred reasoning in ABA by cycle-breaking. Proceedings of the Thirty-ThirdInternational Joint Conference on Artificial Intelligence, International Joint Conferences on Artificial Intelligence Organization, California, August 2024. [PUMA: topic_knowledge]

Giovanni Buraglio, Wolfgang Dvorak, Matthias König, and Markus Ulbricht. Justifying argument acceptance with collective attacks: Discussions and disputes. Proceedings of the Thirty-ThirdInternational Joint Conference on Artificial Intelligence, International Joint Conferences on Artificial Intelligence Organization, California, August 2024. [PUMA: topic_knowledge]

Christopher W. Moth, Jonathan H. Sheehan, Abdullah Al Mamun, R. Michael Sivley, Alican Gulsevin, David Rinker, John A. Capra, and Jens Meiler. VUStruct: a compute pipeline for high throughput and personalized structural biology. Cold Spring Harbor Laboratory, August 2024. [PUMA: imported topic_lifescience] URL

Theresa Elstner, Bärbel Hanle, Frank Loebe, Maik Fröbe, Nikolay Kolyada, Janis Mohr, Jörg Frochte, Sven Hofmann, Benno Stein, and Martin Potthast. Classification of shared tasks used in teaching. Proceedings of the 2024 on Innovation and Technology in Computer Science Education V. 1, ACM, New York, NY, USA, July 2024. [PUMA: topic_knowledge topic_language]

Nandan Thakur, Luiz Bonifacio, Maik Fröbe, Alexander Bondarenko, Ehsan Kamalloo, Martin Potthast, Matthias Hagen, and Jimmy Lin. Systematic evaluation of neural retrieval models on the touché 2020 argument retrieval subset of BEIR. Proceedings of the 47th International ACM SIGIR Conference on Research and Development in Information Retrieval, (618):1420--1430, ACM, New York, NY, USA, July 2024. [PUMA: topic_language]

Christian Genest, Ostap Okhrin, and Taras Bodnar. Copula modeling from Abe Sklar to the present day. J. Multivar. Anal., (201)CAcademic Press, Inc., USA, July 2024. [PUMA: 62H05 Copula models modeling Dependence 62G32 62H20 62H10 topic_engineering 62H12 62H15] URL

Maik Fröbe, Harrisen Scells, Theresa Elstner, Christopher Akiki, Lukas Gienapp, Jan Heinrich Reimer, Sean MacAvaney, Benno Stein, Matthias Hagen, and Martin Potthast. Resources for Combining Teaching and Research in Information Retrieval Coursework. Proceedings of the 47th International ACM SIGIR Conference on Research and Development in Information Retrieval, 1115–1125, ACM, July 2024. [PUMA: imported topic_language] URL

Lukas Gienapp, Harrisen Scells, Niklas Deckers, Janek Bevendorff, Shuai Wang, Johannes Kiesel, Shahbaz Syed, Maik Fröbe, Guido Zuccon, Benno Stein, Matthias Hagen, and Martin Potthast. Evaluating Generative Ad Hoc Information Retrieval. Proceedings of the 47th International ACM SIGIR Conference on Research and Development in Information Retrieval, 1916–1929, ACM, July 2024. [PUMA: imported topic_language] URL

Ostap Okhrin, and Alexander Ristig. Penalized estimation of hierarchical Archimedean copula. J. Multivar. Anal., (201)CAcademic Press, Inc., USA, July 2024. [PUMA: Hierarchical estimation 62G07 Stage-wise copula likelihood Archimedean topic_engineering 62H12 Maximum] URL

Carsten Lutz, and Quentin Manière. Adding Circumscription to Decidable Fragments of First-Order Logic: A Complexity Rollercoaster. July 2024. [PUMA: imported topic_knowledge]

Maik Fröbe, Joel Mackenzie, Bhaskar Mitra, Franco Maria Nardini, and Martin Potthast. ReNeuIR at SIGIR 2024: The third workshop on reaching efficiency in neural information retrieval. Proceedings of the 47th International ACM SIGIR Conference on Research and Development in Information Retrieval, (31):3051--3054, ACM, New York, NY, USA, July 2024. [PUMA: topic_language]

Nandan Thakur, Luiz Bonifacio, Maik Fröbe, Alexander Bondarenko, Ehsan Kamalloo, Martin Potthast, Matthias Hagen, and Jimmy Lin. Systematic Evaluation of Neural Retrieval Models on the Touché 2020 Argument Retrieval Subset of BEIR. Proceedings of the 47th International ACM SIGIR Conference on Research and Development in Information Retrieval, 1420–1430, ACM, July 2024. [PUMA: imported topic_language] URL

Jan Ewald, Ziyang He, Wassili Dimitriew, and Stefan Schuster. Including glutamine in a resource allocation model of energy metabolism in cancer and yeast cells. npj Systems Biology and Applications, (10)1Springer Science and Business Media LLC, July 2024. [PUMA: imported topic_lifescience] URL

E. B. L. Mackay, C. J. R. Murphy-Barltrop, and P. Jonathan. The SPAR Model: A New Paradigm for Multivariate Extremes: Application to Joint Distributions of Metocean Variables. Journal of Offshore Mechanics and Arctic Engineering, (147)1ASME International, July 2024. [PUMA: imported topic_mathfoundation] URL

Patrick Ebel, Courtney M Goodridge, Aravinda Ramakrishnan Srinivasan, Mark Colley, Hauke Sandhaus, Philipp Hock, Philipp Wintersberger, Christian Janssen, and Pavlo Bazilinskyy. Changing Lanes Toward Open Science: Openness and Transparency in Automotive User Research. OSF, July 2024. [PUMA: topic_visualcomputing] URL

Gaia Olcese, Paul D Bates, Jeffrey C Neal, Christopher C Sampson, Oliver E J Wing, Niall Quinn, Callum J R Murphy-Barltrop, and Izzy Probyn. Developing a fluvial and pluvial stochastic flood model of Southeast Asia. Water Resour. Res., (60)6American Geophysical Union (AGU), June 2024. [PUMA: topic_mathfoundation]

Joseph DeCorte, Benjamin Brown, and Jens Meiler. Interpretable deep-learning pKa prediction for small molecule drugs via atomic sensitivity analysis. American Chemical Society (ACS), June 2024. [PUMA: imported topic_lifescience] URL

Caleb A. H. Jones, Benjamin P. Brown, Daniel C. Schultz, Julie Engers, Valerie M. Kramlinger, Jens Meiler, and Craig W. Lindsley. Computer-Aided Design and Biological Evaluation of Diazaspirocyclic D4R Antagonists. ACS Chemical Neuroscience, (15)12:2396–2407, American Chemical Society (ACS), June 2024. [PUMA: imported topic_lifescience] URL

Hamid Farzaneh, João Paulo Cardoso De Lima, Ali Nezhadi Khelejani, Asif Ali Khan, Mahta Mayahinia, Mehdi Tahoori, and Jeronimo Castrillon. SHERLOCK: Scheduling Efficient and Reliable Bulk Bitwise Operations in NVMs. Proceedings of the 61th Annual Design Automation Conference (DAC'24), ACM, June 2024. [PUMA: topic_software]

Moritz Ertelt, Rocco Moretti, Jens Meiler, and Clara T. Schoeder. Self-supervised machine learning methods for protein design improve sampling, but not the identification of high-fitness variants. Cold Spring Harbor Laboratory, June 2024. [PUMA: imported topic_lifescience] URL

Hannah Marie Eichholz, Alissa Cornelis, Benjamin Wolf, Hanna Grubitzsch, Philip Friedrich, Ahmad Makky, Bahriye Aktas, Josef Alfons Käs, and Holger Stepan. Anatomy of the fetal membranes: insights from spinning disk confocal microscopy. Arch. Gynecol. Obstet., (309)5:1919--1923, May 2024. [PUMA: Amnion; membranes; Premature Chorion; membrane microscopy; preterm microfractures; Anatomy; Confocal Fluorescence Preterm rupture labor Fetal topic_earthenvironment of]

Abibe Useini, Inken Kaja Schwerin, Georg Künze, and Norbert Sträter. Structural Studies on the Binding Mode of Bisphenols to PPARγ. Biomolecules, (14)6:640, MDPI AG, May 2024. [PUMA: imported topic_lifescience] URL

Shreya Arya, Justin Curry, and Sayan Mukherjee. A Sheaf-Theoretic Construction of Shape Space. Foundations of Computational Mathematics, May 2024. [PUMA: imported topic_mathfoundation]

Sebastian Schmidt, Ines Zelch, Janek Bevendorff, Benno Stein, Matthias Hagen, and Martin Potthast. Detecting Generated Native Ads in Conversational Search. Companion Proceedings of the ACM on Web Conference 2024, (5):722–725, ACM, May 2024. [PUMA: topic_language] URL

Franz Baader, and Filippo De Bortoli. The abstract expressive power of first-order and description logics with concrete domains. Proceedings of the 39th ACM/SIGAPP Symposium on Applied Computing, ACM, New York, NY, USA, April 2024. [PUMA: topic_knowledge]

Palina Pliushcheuskaya, Sandeep Kesh, Emma Kaufmann, Sophie Wucherpfennig, Frank Schwede, Georg Künze, and Vasilica Nache. Similar Binding Modes of cGMP Analogues Limit Selectivity in Modulating Retinal CNG Channels via the Cyclic Nucleotide-Binding Domain. ACS Chemical Neuroscience, (15)8:1652–1668, American Chemical Society (ACS), April 2024. [PUMA: imported topic_lifescience] URL

Hamid Farzaneh, Joao Paulo Cardoso De Lima, Mengyuan Li, Asif Ali Khan, Xiaobo Sharon Hu, and Jeronimo Castrillon. C4CAM: A compiler for CAM-based in-memory accelerators. Proceedings of the 29th ACM International Conference on Architectural Support for Programming Languages and Operating Systems, Volume 3, ACM, New York, NY, USA, April 2024. [PUMA: topic_software]

Robert Haase, Christian Tischer, Jean-Karim Heriche, and Nico Scherf. Benchmarking Large Language Models for Bio-Image Analysis Code Generation. Cold Spring Harbor Laboratory, April 2024. [PUMA: imported topic_neuroinspired unit_transfer] URL

Michael Rade, Nora Grieb, Ronald Weiss, Jaren Sia, Luise Fischer, Patrick Born, Andreas Boldt, Stephan Fricke, Paul Franz, Jonathan Scolnick, Lakshmi Venkatraman, Stacy Xu, Christina Kloetzer, Simone Heyn, Anne Sophie Kubasch, Ronny Baber, Song Yau Wang, Enrica Bach, Sandra Hoffmann, Jule Ussmann, Birthe Schetschorke, Saskia Hell, Sebastian Schwind, Klaus H. Metzeler, Marco Herling, Madlen Jentzsch, Georg-Nikolaus Franke, Ulrich Sack, Ulrike Köhl, Uwe Platzbecker, Kristin Reiche, Vladan Vucinic, and Maximilian Merz. Single-cell multiomic dissection of response and resistance to chimeric antigen receptor T cells against BCMA in relapsed multiple myeloma. Nature Cancer, April 2024. [PUMA: topic_lifescience] URL

Matti Wiegmann, Jan Heinrich Reimer, Maximilian Ernst, Martin Potthast, Matthias Hagen, and Benno Stein. A Mastodon Corpus to Evaluate Federated Microblog Search. In Sheikh Farzana, Maik Fröbe, Michael Granitzer, Gijs Hendriksen, Djoerd Hiemstra, Martin Potthast, and Saber Zerhoudi (Eds.), Proceedings of the First International Workshop on Open Web Search (WOWS 2024), (3689):37--49, CEUR Workshop Proceedings, March 2024. [PUMA: topic_language topic_lifescience] URL

Jan-Niklas Eckardt, Waldemar Hahn, Christoph Röllig, Sebastian Stasik, Uwe Platzbecker, Carsten Müller-Tidow, Hubert Serve, Claudia D. Baldus, Christoph Schliemann, Kerstin Schäfer-Eckart, Maher Hanoun, Martin Kaufmann, Andreas Burchert, Christian Thiede, Johannes Schetelig, Martin Sedlmayr, Martin Bornhäuser, Markus Wolfien, and Jan Moritz Middeke. Mimicking clinical trials with synthetic acute myeloid leukemia patients using generative artificial intelligence. npj Digital Medicine, (7)1:76, March 2024. [PUMA: topic_lifescience] URL

Henry Kirveslahti, and Sayan Mukherjee. Representing fields without correspondences: the lifted Euler characteristic transform. J. Appl. Comput. Topol., (8)1:1--34, Springer Science and Business Media LLC, March 2024. [PUMA: transform corresponcence topic_mathfoundation Euler characteristic]

Masoud Taghikhah, Nishant Kumar, Sinisa Segvić, Abouzar Eslami, and Stefan Gumhold. Quantile-based maximum likelihood training for outlier detection. Proc. Conf. AAAI Artif. Intell., (38)19:21610--21618, Association for the Advancement of Artificial Intelligence (AAAI), March 2024. [PUMA: detection maximum outlier Quantile-based training likelihood topic_visualcomputing]

Yannis Dimopoulos, Wolfgang Dvorak, Matthias König, Anna Rapberger, Markus Ulbricht, and Stefan Woltran. Redefining ABA+ semantics via abstract set-to-set attacks. Proc. Conf. AAAI Artif. Intell., (38)9:10493--10500, Association for the Advancement of Artificial Intelligence (AAAI), March 2024. [PUMA: topic_knowledge]

Gijs Hendriksen, Michael Dinzinger, Sheikh Mastura Farzana, Noor Afshan Fathima, Maik Fröbe, Sebastian Schmidt, Saber Zerhoudi, Michael Granitzer, Matthias Hagen, Djoerd Hiemstra, Martin Potthast, and Benno Stein. The Open Web Index: Crawling and Indexing the Web for Public Use. Advances in Information Retrieval. 46th European Conference on IR Research (ECIR 2024), Springer, Berlin Heidelberg New York, March 2024. [PUMA: topic_language]

Shahbaz Syed, Khalid Al Khatib, and Martin Potthast. TL;DR Progress: Multi-faceted Literature Exploration in Text Summarization. In Nikolaos Aletras, and Orphee De Clercq (Eds.), Proceedings of the 18th Conference of the European Chapter of the Association for Computational Linguistics: System Demonstrations, 195--206, Association for Computational Linguistics, St. Julians, Malta, March 2024. [PUMA: imported topic_language] URL

Michael Niemier, Zephan Enciso, Mohammad Mehdi Sharifi, X. Sharon Hu, Ian O'Connor, Alexander Graening, Ravit Sharma, Puneet Gupta, Jeronimo Castrillon, João Paulo C. de Lima, Asif Ali Khan, Hamid Farzaneh, Nashrah Afroze, Asif Islam Khan, and Julien Ryckaert. Smoothing Disruption Across the Stack: Tales of Memory, Heterogeneity, and Compilers. Proceedings of the 2024 Design, Automation and Test in Europe Conference (DATE), 1--10, IEEE, March 2024. [PUMA: topic_software] URL

Moritz Ertelt, Vikram Khipple Mulligan, Jack B. Maguire, Sergey Lyskov, Rocco Moretti, Torben Schiffner, Jens Meiler, and Clara T. Schoeder. Combining machine learning with structure-based protein design to predict and engineer post-translational modifications of proteins. In Joanna Slusky (Eds.), PLOS Computational Biology, (20)3:e1011939, Public Library of Science (PLoS), March 2024. [PUMA: imported topic_lifescience] URL

Grover E. C. Guzman, Peter F. Stadler, and Andre Fujita. Cavity approach for the approximation of spectral density of graphs with heterogeneous structures. Phys. Rev. E, (109)3:034303, American Physical Society, March 2024. [PUMA: imported topic_mathfoundation] URL

Michael Rade, Markus Kreuz, Angelika Borkowetz, Ulrich Sommer, Conny Blumert, Susanne Füssel, Catharina Bertram, Dennis Löffler, Dominik J. Otto, Livia A. Wöller, Carolin Schimmelpfennig, Ulrike Köhl, Ann-Cathrin Gottschling, Pia Hönscheid, Gustavo B. Baretton, Manfred Wirth, Christian Thomas, Friedemann Horn, and Kristin Reiche. A reliable transcriptomic risk-score applicable to formalin-fixed paraffin-embedded biopsies improves outcome prediction in localized prostate cancer. Molecular Medicine, (30)1:19, February 2024. [PUMA: topic_lifescience] URL