EXtreme Analytics for MINing Data spaces

Deliverables

Application Cases and Architecture Requirements
Extreme Data Flow Patterns – Report
Data and Workflow Management Toolbox Alpha Status Report
Dissemination & Communication Interim Report
Architecture of AQIS
Continuous Improvements of Architecture, and Release management Process and System
Impact Master Plan

Publications

terazi: AI Fairness Tool for Doubly Imbalanced Data

Author(s): Asli Umay Ozturk; Yigit Sever; Ata Yalcin; Viktoria Pauw; Stephan Hachinger; Ismail Hakki Toroslu; Pinar Karagoz
Published in: Proceedings of the 34th ACM International Conference on Information and Knowledge Management, 2025
Publisher: ACM
DOI: 10.1145/3746252.3761465

Wine in the Cloud, or: Smart Vineyards with a Distributed “Extreme Data Database” and Supercomputing

Author(s): Piyush Harsh,,∗ Stephan Hachinger, Marc Derquennes, Andy Edmonds,Pinar Karagoz, Martin Golasowski, Mohamad Hayek and Jan Martinovič
Published in: ISGC&HEPiX2023, 2023
Publisher: PoS
DOI: 10.22323/1.434.0021

Explaining Veracity Predictions with Evidence Summarization: A Multi-Task Model Approach

Author(s): Recep Firat Cekinel, Pinar Karagoz
Published in: 2024 IEEE International Conference on Big Data (BigData), 2025
Publisher: IEEE
DOI: 10.48550/ARXIV.2402.06443

Multimodal Fact-Checking with Vision Language Models: A Probing Classifier based Solution with Embedding Strategies

Author(s): Karagöz, Pınar; Çekinel, Recep Fırat; Çöltekin, Çağrı
Published in: Proceedings of the 31st International Conference on Computational Linguistics, 2025
Publisher: Association for Computational Linguistics
DOI: 10.48550/ARXIV.2412.05155

Halton Scheduler For Masked Generative Image Transformer

Author(s): Victor Besnier, Mickael Chen, David Hurych, Eduardo Valle, Matthieu Cord
Published in: International Conference on Learning Representations (ICLR), 2025
Publisher: OpenReview
DOI: 10.48550/ARXIV.2503.17076

Three Pillars improving Vision Foundation Model Distillation for Lidar

Author(s): Gilles Puy, Spyros Gidaris, Alexandre Boulch, Oriane Siméoni, Corentin Sautier, Patrick Pérez, Andrei Bursuc, Renaud Marlet
Published in: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), 2024
Publisher: IEEE/CVPR
DOI: 10.48550/ARXIV.2310.17504

Annealed Winner-Takes-All for Motion Forecasting

Author(s): Xu, Yihong; Letzelter, Victor; Chen, Mickaël; Zablocki, Éloi; Cord, Matthieu
Published in: 2025 IEEE International Conference on Robotics and Automation (ICRA), 2025
Publisher: IEEE
DOI: 10.48550/ARXIV.2409.11172

Database-aided Workflows on HPC for Plasma Physics Simulation

Author(s): Viktoria Maike Paula Pauw, Hachinger Stephan, Jan Martinovič, Stephan Hachinger
Published in: Proceedings of International Symposium on Grids & Clouds (ISGC2025) — PoS(ISGC2025), 2025
Publisher: Sissa Medialab
DOI: 10.22323/1.488.0024

Make Satire Boring Again: Reducing Stylistic Bias of Satirical Corpus by Utilizing Generative LLMs

Author(s): Öztürk, Aslı Umay; Çekinel, Recep Fırat; Karagöz, Pınar
Published in: Proceedings of the 18th Workshop on Building and Using Comparable Corpora (BUCC), 2025
Publisher: Association for Computational Linguistics
DOI: 10.48550/ARXIV.2412.09247

Management of Physics Simulations with Databases

Author(s): Viktoria Maike Paula Pauw, David Číž, Vojtěch Mlýnský, Pavel Banáš, Michal Otyepka, Stephan Hachinger, Jan Martinovič
Published in: Proceedings of International Symposium on Grids & Clouds (ISGC) 2024 — PoS(ISGC2024), 2024
Publisher: Sissa Medialab
DOI: 10.22323/1.458.0031

Towards Motion Forecasting with Real-World Perception Inputs: Are End-to-End Approaches Competitive?

Author(s): Xu, Yihong; Chambon, Loïck; Zablocki, Éloi; Chen, Mickaël; Alahi, Alexandre; Cord, Matthieu; Pérez, Patrick
Published in: 2024 IEEE International Conference on Robotics and Automation (ICRA), 2024
Publisher: IEEE
DOI: 10.48550/ARXIV.2306.09281

POP-3D: Open-Vocabulary 3D Occupancy Prediction from Images (pre-print version)

Author(s): Antonín Vobecký, Oriane Siméoni, David Hurych, Spyros Gidaris, Andrei Bursuc, Patrick Perez, Josef Sivic
Published in: NeurIPS 2023, 2024
Publisher: NeurIPS

ShowHowTo: Generating Scene-Conditioned Step-by-Step Visual Instructions

Author(s): Tomás Soucek; Prajwal Gatti; Michael Wray; Ivan Laptev; Dima Damen; Josef Sivic
Published in: 2025 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), 2025
Publisher: IEEE
DOI: 10.48550/ARXIV.2412.01987

Cross-Lingual Learning vs. Low-Resource Fine-Tuning: A Case Study with Fact-Checking in Turkish

Author(s): Firat Cekinel, Pinar Karagoz, Cagri Coltekin
Published in: Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024), 2024
Publisher: ELRA and ICCL

OccFeat: Self-supervised Occupancy Feature Prediction for Pretraining BEV Segmentation Networks

Author(s): Sophia Sirko-Galouchenko, Alexandre Boulch, Spyros Gidaris, Andrei Bursuc, Antonin Vobecky, Patrick Pérez, Renaud Marlet
Published in: 2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW), 2024
Publisher: IEEE
DOI: 10.1109/CVPRW63382.2024.00452

GenHowTo: Learning to Generate Actions and State Transformations from Instructional Videos

Author(s): Tomás Soucek; Dima Damen; Michael Wray; Ivan Laptev; Josef Sivic
Published in: 2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), 2024
Publisher: IEEE
DOI: 10.48550/ARXIV.2312.07322

IndexAI: AI Based Index Selection for NoSQL Databases (pre-print version)

Author(s): Mohammad Mahdi Khosravi, Pinar Karagoz, and Ismail Hakki Toroslu
Published in: 2023 IEEE International Conference on Big Data, 2024
Publisher: IEEE
DOI: 10.1109/BigData59044.2023.10386521

Poster: ADAMS4SIMS - Database Curation for MD Simulations

Author(s): Číž, D., Furmánek, R., Pauw, V., Martinovič, J., Otyepka, M., Banáš, P., Mlýnský, V.
Published in: HPCSE 2024, 2024
Publisher: Zenodo
DOI: 10.5281/ZENODO.12704253

Poster: Integrated Database of Force-Field Parameters, Experimental Measurements, and Molecular Dynamics Simulations as a Tool for Force Field Development

Author(s): Pavel Banas, Mlynsky Vojtech, David Ciz, Radek Furmanek, Nestor Pilat, Anna Spackova, Viktoria Pauw, Stephan Hachinger, Jiri Sponer, Jan Martinovic, Michal Otyepka
Published in: CECAM Workshop “RNA Modelling Across Scales” 2025, 2025
Publisher: Zenodo
DOI: 10.5281/ZENODO.19916756

Poster: A universal molecular force field format for transparent and accessible parameters for MD simulations of biomolecular systems

Author(s): Banáš, P., Mlýnský, V., Číž, D., Furmánek, R., Pilát, N., Špačková, A., Pauw, V., Hachinger, S., Šponer, J., Martinovič, J., Otyepka, M.
Published in: CECAM Workshop “RNA Modelling Across Scales”, 2025
Publisher: Zenodo
DOI: 10.5281/ZENODO.19923305

Poster: Integrated Database of Force-Field Parameters, Experimental Measurements and Molecular Dynamics Simulations as a Tool for Force Field Development

Author(s): Banáš, P., Mlýnský, V., Číž, D., Furmánek, R., Pilát, N., Špačková, A., Pauw, V., Hachinger, S., Šponer, J., Martinovič, J., Otyepka, M.
Published in: EuChemS CompChem 2025 “Shaping the Future of Chemistry”, 2025
Publisher: Zenodo
DOI: 10.5281/ZENODO.17174936

Poster: Optimised DBMS Deployments and DBMS Benchmarks for Extreme Data Workflows

Author(s): Gurbanov, H., Brunati, R., Karagoz, P., Toroslu, I. H., Hayek, M., Golasowski, M., Hachinger, S., Martinovič, J.
Published in: HPCSE 2024, 2024
Publisher: Zenodo
DOI: 10.5281/ZENODO.19923504

Poster: Tuning and tweaking of the state-of-the-art amber OL3 RNA force field

Author(s): Mlýnský, V., Kührová, P., Krepl, M., Stadlbauer, P., Otyepka, M., Bussi, G., Banáš, P., Šponer, J.
Published in: EuChemS CompChem 2023, 2023
Publisher: Zenodo
DOI: 10.5281/ZENODO.19923213

Poster: POP3D: Open-Vocabulary 3D Occupancy Prediction from Images

Author(s): A. Vobecky, O. Siméoni, D. Hurych, S. Gidaris, A. Bursuc, P. Pérez, J. Šivic
Published in: NeurIPS 2023, 2024
Publisher: Zenodo
DOI: 10.5281/ZENODO.12704479

Regularizing Self-supervised 3D Scene Flows with Surface Awareness and Cyclic Consistency

Author(s): Patrik Vacek, David Hurych, Karel Zimmermann, Tomáš Svoboda
Published in: 2024
Publisher: ArXiv
DOI: 10.48550/ARXIV.2312.08879

Poster: Tapping Data Spaces in HPC: Enabling, Exploring and Benchmarking Database & Object Store Usage

Author(s): Mohamad Hayek, Stephan Hachinger, Huseyn Gurbanov, Viktoria Pauw, Martin Golasowski, Jan Martinovič, Pinar Karagoz, Ismail Hakki Toroslu
Published in: SCA/HPC Asia 2026, 2026
Publisher: Zenodo
DOI: 10.5281/ZENODO.19912565

Poster: EXA4MIND AI Inference Service Solution

Author(s): Adam Matus, Jan Martinovic, Jakub Konvicka, Tomas Martinovic, Firat Cekinel, Görkem Özer, Pinar Karagoz, Ismail Toroslu
Published in: SCA/HPC Asia 2026, 2026
Publisher: Zenodo
DOI: 10.5281/ZENODO.19912708

Poster: How to Make Data Pipeline Scalable: A Case Study for Healthcare Data Analytics

Author(s): Atakan Gelecek, Pinar Karagoz Ismail Hakki Toroslu, Stephan Hachinger, Jan Martinovic
Published in: SCA/HPC Asia 2026, 2026
Publisher: Zenodo
DOI: 10.5281/ZENODO.19912338

DocSpider: a dataset of cross-domain natural language querying for MongoDB

Author(s): Arif Görkem Özer; Recep Firat Cekinel; Ismail Hakki Toroslu; Pinar Karagoz
Published in: Natural Language Processing, 2025, ISSN 2977-0424
Publisher: Cambridge University Press
DOI: 10.1017/NLP.2024.63

Destabilization of Structured RNAs by OPC and TIP4PD Water Models

Author(s): Miroslav Krepl, Vojtěch Mlýnský, Agnesa Rusnáková, Pavel Banáš, Michal Otyepka, Jiří Šponer
Published in: Journal of Chemical Theory and Computation, Issue 22, 2026, ISSN 1549-9618
Publisher: American Chemical Society (ACS)
DOI: 10.1021/ACS.JCTC.5C01678

The Kink-Turn 7 Motif: An Additional Test for RNA Force Field Performance

Author(s): Toon Lemmens, Vojtěch Mlýnský, Jiří Šponer, Martin Pykal, Pavel Banáš, Michal Otyepka, Miroslav Krepl
Published in: Journal of Chemical Theory and Computation, Issue 21, 2025, ISSN 1549-9618
Publisher: American Chemical Society (ACS)
DOI: 10.1021/ACS.JCTC.5C00776

Unsupervised Semantic Segmentation of Urban Scenes via Cross-Modal Distillation

Author(s): Antonín Vobecký; David Hurych; Oriane Siméoni; Spyros Gidaris; Andrei Bursuc; Patrick Pérez; Josef Sivic
Published in: International Journal of Computer Vision, 2025, ISSN 1573-1405
Publisher: Springer Nature
DOI: 10.1007/S11263-024-02320-3

MOCA: Self-supervised Representation Learning by Predicting Masked Online Codebook Assignments

Author(s): Spyros Gidaris, Andrei Bursuc, Oriane Simeoni, Antonin Vobecky, Nikos Komodakis, Matthieu Cord, Patrick Pérez
Published in: Transactions on Machine Learning Research, Issue 2, 2024, ISSN 2835-8856
Publisher: JMLR
DOI: 10.48550/arXiv.2307.09361

Let It Flow: Simultaneous Optimization of 3D Flow and Object Clustering

Author(s): Patrik Vacek, David Hurych, Karel Zimmermann, Tomáš Svoboda
Published in: IEEE Transactions on Intelligent Vehicles, Issue 10, 2026, ISSN 2379-8904
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/TIV.2024.3443316

Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations

Author(s): Vojtěch Mlýnský, Petra Kührová, Petr Stadlbauer, Miroslav Krepl, Michal Otyepka, Pavel Banáš*, and Jiří Šponer*
Published in: (JCTC) Journal of Chemical Theory and Computation, Issue Volume 19, Issue 22, 2023, ISSN 1549-9626
Publisher: ACS Publications
DOI: 10.1021/acs.jctc.3c00990

Computer Folding of Parallel <scp>DNA</scp> G‐Quadruplex: Hitchhiker's Guide to the Conformational Space

Author(s): Michal Janeček, Petra Kührová, Vojtěch Mlýnský, Petr Stadlbauer, Michal Otyepka, Giovanni Bussi, Jiří Šponer, Pavel Banáš
Published in: Journal of Computational Chemistry, Issue 46, 2025, ISSN 0192-8651
Publisher: Wiley
DOI: 10.1002/JCC.27535

Can We Ever Develop an Ideal RNA Force Field? Lessons Learned from Simulations of the UUCG RNA Tetraloop and Other Systems

Author(s): Vojtěch Mlýnský, Petra Kührová, Martin Pykal, Miroslav Krepl, Petr Stadlbauer, Michal Otyepka, Pavel Banáš, Jiří Šponer
Published in: Journal of Chemical Theory and Computation, Issue 21, 2025, ISSN 1549-9618
Publisher: American Chemical Society (ACS)
DOI: 10.1021/ACS.JCTC.4C01357

Data management for distributed computational workflows: An iRODS-based setup and its performance

Author(s): Mohamad Hayek, Martin Golasowski, Stephan Hachinger, Rubén J. García-Hernández, Johannes Munke, Gabriel Lindner, Kateřina Slaninová, Philipp Tunka, Vít Vondrák, Dieter Kranzlmüller, Jan Martinovič
Published in: PLOS One, Issue 21, 2026, ISSN 1932-6203
Publisher: Public Library of Science (PLoS)
DOI: 10.1371/JOURNAL.PONE.0340757

Deliverables

Publications

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