Computer Science: Formal Languages and Concurrency

Publications since 2020

Published | Accepted | Submitted

Published:

2024

Jesús A. Jiménez González, A strong Gram classification of non-negative unit forms of Dynkin type A_r, Fundamenta Informaticae, vol. 191, no. 1, pp. 17-66, 2024
Marek Nowicki. 2024. “Benchmarking the TeraSort Algorithm on Ethernet Cluster: Benchmarking Apache Hadoop based implementation”. W HPI Future SOC Lab: Proceedings 2020, red. Christoph Meinel, Andreas Polze, Karsten Beins, Rolf Strotmann, Ulrich Seibold, Kurt Rödszus, Jürgen Müller, Jürgen Sommer, 159:97-108. Technische Berichte Des Hasso-Plattner-Instituts Für Digital Engineering an Der Universität Potsdam. Universitätsverlag Potsdam.
Marek Nowicki. 2024. “Benchmarking the Sort Algorithm on Ethernet Cluster: Benchmarking PCJ – a library for parallel computing in Java”. W HPI Future SOC Lab: Proceedings 2020, red. Christoph Meinel, Andreas Polze, Karsten Beins, Rolf Strotmann, Ulrich Seibold, Kurt Rödszus, Jürgen Müller, Jürgen Sommer, 159:53-63. Technische Berichte Des Hasso-Plattner-Instituts Für Digital Engineering an Der Universität Potsdam. Universitätsverlag Potsdam.
Marek Nowicki. 2024. “Benchmarking Java on Ethernet Cluster: Benchmarking PCJ – a Library for Parallel Computing in Java”. W HPI Future SOC Lab: Proceedings 2019, red. Christoph Meinel, Andreas Polze, Karsten Beins, Rolf Strotmann, Ulrich Seibold, Kurt Rödszus, i Jürgen Müller, 158:263–271. Technische Berichte Des Hasso-Plattner-Instituts Für Digital Engineering an Der Universität Potsdam. Universitätsverlag Potsdam.
Marek Nowicki, Benson K. Muite, i Mehmet Can Boysan. 2024. “Benchmarking FFT on an Ethernet Cluster: Latency, Bandwidth and MPI Benchmarks”. W HPI Future SOC Lab: Proceedings 2019, red. Christoph Meinel, Andreas Polze, Karsten Beins, Rolf Strotmann, Ulrich Seibold, Kurt Rödszus, i Jürgen Müller, 158:93–98. Technische Berichte Des Hasso-Plattner-Instituts Für Digital Engineering an Der Universität Potsdam. Universitätsverlag Potsdam.
Marek Nowicki. 2024. “Scratch : podstawy na przykładzie gry Wąż”. W Informatyka w edukacji : kształcenie informatyczne drogą do cyfrowej transformacji społeczeństwa, red. Anna Beata Kwiatkowska i Maciej Sysło, 284–294.
K. Barylska, A. Gogolińska, “Blood glucose levels regulation in a healthy and in a diabetic person modelled with Petri Nets.”, Petri Net games, examples and quizzes for education, contest and fun (2024)
K. Barylska, A. Gogolińska, “Petri nets in modeling glucose regulating processes in the liver”, International Workshop on Petri Nets and Software Engineering (2024)
Kaniecki Mariusz, Mikulski Łukasz, On categorical approach to reaction systems, Natural Computing, 2024, vol. 23, p.295-307
Artur Męski, Maciej Koutny, Łukasz Mikulski, Wojciech Penczek: Reaction mining for reaction systems. Nat. Comput. 23(2): 323-343 (2024)
Ryszard Janicki, Jetty Kleijn, Maciej Koutny, Łukasz Mikulski: Relational Structures for Interval Order Semantics of Concurrent Systems. Petri Nets 2024: 153-174
Torben Ægidius Mogensen, Łukasz Mikulski: Reversible Computation – 16th International Conference, RC 2024, Toruń, Poland, July 4-5, 2024, Proceedings. Lecture Notes in Computer Science 14680, Springer 2024
Wojciech Jamroga, Yan Kim, Damian Kurpiewski: Scalable Verification of Social Explainable AI by Variable Abstraction. ICAART (1) 2024: 149-158,
https://home.ipipan.waw.pl/w.jamroga/papers/sai+abstraction24uppaal.pdf
Damian Kurpiewski, Mateusz Kamiński, Wojciech Jamroga: STV+FLY: On-the-Fly Model Checking of Strategic Ability in Multi-Agent Systems. ECAI 2024: 4483-4486, https://ebooks.iospress.nl/doi/10.3233/FAIA241035
Mateusz Kamiński, Damian Kurpiewski, Wojciech Jamroga: STV+KH: Towards Practical Verification of Strategic Ability for Knowledge and Information Flow. AAMAS 2024: 2812-2814 STV+KH: Towards Practical Verification of Strategic Ability for Knowledge and Information Flow – Best Demo Award work
Przymus Piotr, Fejzer Mikołaj, Narębski Jakub, Krzysztof Stencel, “How I learned to stop worrying and love ChatGPT” W: 2024 IEEE/ACM 21st International Conference on Mining Software Repositories (MSR), 15-16 April 2024, Lisbon, Portugal (140 pkt).
Hideo Bannai, Juha Kärkkäinen, Dominik Köppl, Marcin Piątkowski “Constructing and Indexing the Bijective and the Extended Burrows-Wheeler Transform”, Information and Computation (2024)

2023

Marcos Zambrano, Laura Judith, Przymus, Piotr et al. “A toolbox of machine learning software to support microbiome analysis.” Frontiers in Microbiology 14: 1250806. (140 pkt) https://www.frontiersin.org/articles/10.3389/fmicb.2023.1250806/abstract, (2023, November)
Bała Piotr, Nowicki Marek, Czy jesteśmy gotowi na naukę programowania równoległego w szkole?, W: Informatyka w edukacji : edukacja informatyczna : wyzwania współczesnego świata / Kwiatkowska Anna Beata, Sysło Maciej (red.), 2023, Toruń, Wydawnictwo Adam Marszałek, s.127-136, ISBN 978-83-8180-810-1
Nowicki M., Górski Ł., Bała P.; Performance evaluation of Java/PCJ implementation of parallel algorithms on the cloud (extended version); Concurrency and Computation: Practice and Experience (2023); https://doi.org/10.1002/cpe.6536
Advancing microbiome research with machine learning : key findings from the ML4Microbiome COST action D’Elia Domenica, Truu Jaak, Lahti Leo, P. Przymus [i in.], Frontiers in Microbiology, 2023, vol. 14, s.1-8. DOI:10.3389/fmicb.2023.1257002 (140 pkt)
The Secret Life of CVEs, Przymus Piotr, Fejzer Mikołaj, Narębski Jakub [i in.], W: IEEE/ACM 20th International Conference on Mining Software Repositories MSR 2023, Melbourne, Australia, 15-16 May 2023: proceedings , 2023, Los Alamitos, Institute of Electrical and Electronics Engineers, s.362-366, ISBN 979-8-3503-1184-6. DOI:10.1109/msr59073.2023.00056, konferencja A, (140 pkt)
Krzysztof Kaczmarski, Jakub Narębski, Stanisław Piotrowski, Piotr Przymus, “Fast JSON parser using metaprogramming on GPU”, 2022 IEEE 9th International Conference on Data Science and Advanced Analytics (DSAA), konferencja A, (140 pkt)
Ryszard Janicki, Maciej Koutny, Łukasz Mikulski: Interval Traces with Mutex Relation. Petri Nets 2023: 145-166, B
Wojciech Jamroga, Damian Kurpiewski: Pretty Good Strategies and Where to Find Them. EUMAS 2023: 363-380
Damian Kurpiewski, Wojciech Jamroga, Teofil Sidoruk: Towards Modelling and Verification of Social Explainable AI. ICAART (1) 2023: 396-403
Juha Kärkkäinen, Marcin Piatkowski, Simon J. Puglisi: String inference from longest-common-prefix array. Theor. Comput. Sci. 942: 180-199 (2023)
Wojciech Jamroga, Damian Kurpiewski, Łukasz Mikulski, Teofil Sidoruk: Trust Topologies in Verification of Social Explainable AI, Trends in Logic XXIII: Bridges between Logic, Ethics and Social Sciences (BLESS) (2023)

2022

Kamila Barylska, Anna Gogolińska, Acyclic and Cyclic Reversing Computations in Petri Nets, Fundamenta Informaticae, vol. 184, no. 4, pp. 273-296, 2021 (acceptance date: 03.02.2022), doi: https://dl.acm.org/doi/abs/10.3233/FI-2021-2099,
Kamila Barylska, Anna Gogolińska, Łukasz Mikulski, Anna Philippou, Marcin Piątkowski, Kyriaki Psara, Formal translation from reversing Petri nets to coloured Petri nets, RC 2022: Reversible Computation pp 172–186, DOI:10.1007/978-3-031-09005-9_12
A. Mróz, K. Zając, Weyl roots and equivalences of integral quadratic forms, Linear Algebra Appl. 650 (2022), 210–235 doi: https://doi.org/10.1016/j.laa.2022.06.007
Marek Nowicki, w: Informatyka w edukacji : uczniowie i nauczyciele w szkole przyszłości / Kwiatkowska Anna, Sysło Maciej (red.), 2022, Toruń, Wydawnictwo Adam Marszałek, s.414-424, ISBN 978-83-8180-645-9
Ryszard Janicki, Jetty Kleijn, Maciej Koutny, Łukasz Mikulski: Paradigms of Concurrency – Observations, Behaviours, and Systems – a Petri Net View. Studies in Computational Intelligence 1020, Springer 2022, ISBN 978-3-662-64819-3, pp. 1-317
Federica Adobbati, Łukasz Mikulski: Analysing Multi-Agent Systems using 1-safe Petri Nets. PNSE@Petri Nets 2022: 139-155
Łukasz Mikulski, Wojciech Jamroga, Damian Kurpiewski: Towards Assume-Guarantee Verification of Strategic Ability. AAMAS 2022: 1702-1704, A*
Damian Kurpiewski, Wojtek Jamroga, Łukasz Maśko, Łukasz Mikulski, Witold Pazderski, Wojciech Penczek and Teofil Sidoruk: Verification of Multi-Agent Properties in Electronic Voting: A Case Study. AiML 2022: 531-555
Mikołaj Marek Fejzer; Jakub Narebski; Piotr Marian Przymus; Krzysztof Stencel, Tracking Buggy Files: New Efficient Adaptive Bug Localization Algorithm, IEEE Transactions on Software Engineering, https://ieeexplore.ieee.org/document/9372820, (online publication: 2021), Q1
Wojciech Jamroga, Damian Kurpiewski, Vadim Malvone: How to measure usable security: Natural strategies in voting protocols . J. Comput. Secur. 30(3): 381-409 (2022)
Damian Kurpiewski, Łukasz Mikulski, Wojciech Jamroga: STV+AGR: Towards Practical Verification of Strategic Ability Using Assume-Guarantee Reasoning. PRIMA 2022
Łukasz Mikulski, Wojciech Jamroga, Damian Kurpiewski: Assume-Guarantee Verification of Strategic Ability. PRIMA 2022

2021

David de Frutos-Escrig, Maciej Koutny, Lukasz Mikulski: Investigating Reversibility of Steps in Petri Nets. Fundam. Informaticae 183(1-2): 67-96 (2021)
B. Makuracki, A. Mróz, Quadratic algorithm to compute the Dynkin type of a positive definite quasi-Cartan matrix, Mathematics of Computation 90 (2021), 389-412 (doi.org/10.1090/mcom/3559, opubl. online 2020.8.1), Q1.
Marcos-Zambrano, Laura Judith, Piotr Przymus, et al. “Applications of machine learning in human microbiome studies: a review on feature selection, biomarker identification, disease prediction and treatment.” Frontiers in Microbiology 12 (2021): 313, https://www.frontiersin.org/articles/10.3389/fmicb.2021.634511/full .
Moreno-Indias, Isabel, Piotr Przymus, et al. “Statistical and machine learning techniques in human microbiome studies: contemporary challenges and solutions.” Frontiers in Microbiology 12 (2021): 277, https://www.frontiersin.org/articles/10.3389/fmicb.2021.635781/full .
Nowicki M., Górski Ł., Bała P. (2021) Performance Evaluation of Java/PCJ Implementation of Parallel Algorithms on the Cloud. In: Balis B. et al. (eds) Euro-Par 2020: Parallel Processing Workshops. Euro-Par 2020. Lecture Notes in Computer Science, vol 12480. Springer, Cham. https://doi.org/10.1007/978-3-030-71593-9_17, A.
Marek Nowicki; Łukasz Górski; Piotr Bała, PCJ Java Library as a solution to integrate HPC, Big Data and Artificial Intelligence workloads, Journal of Big Data, https://doi.org/10.1186/s40537-021-00454-6 .
Nowicki M., Górski Ł., Bała P.; Performance evaluation of Java/PCJ implementation of parallel algorithms on the cloud (extended version); Concurrency and Computation: Practice and Experience (2021); https://doi.org/10.1002/cpe.6536
Gogolińska, Anna, Wiesław Nowak. “Bipartite Graphs—Petri Nets in Biology Modeling.” Graph-Based Modelling in Science, Technology and Art. Springer, Cham, 2022. 175-200.
B. Makuracki, A. Mróz, Coefficients of non-negative quasi-Cartan matrices, their symmetrizers and Gram matrices, Discrete Appl. Math. 303 (2021), 108-121, doi.org/10.1016/j.dam.2020.05.022, dostępna online .
Ryszard Janicki, Jetty Kleijn, Maciej Koutny, Łukasz Mikulski: Relational Structures for Concurrent Behaviours. Theoretical Computer Science (2021), Vol. 862, S. 174-192, il., 10.1016/j.tcs, on-line .
Mikulski Łukasz, Petre Ion, “Preface : Special issue on reaction systems.”, Theoretical Computer Science, 2021, Vol. 881, S. 1-2, 10.1016/j.tcs.
Eyob Gebrehiwot Gebregeorgis, Justyna Boniecka, Marcin Piątkowski, Iain Robertson, Cyrille B. K. Rathgeber. “SabaTracheid 1.0 : a novel program for quantitative analysis of conifer wood anatomy : a demonstration on African Juniper from the Blue Nile basin.”, Frontiers in Plant Science, 2021, vol. 12, pp. 1-10, Q1.
Hideo Bannai, Juha Kärkkäinen, Dominik Köppl, Marcin Piątkowski “Constructing the bijective and the extended Burrows-Wheeler transform in linear time.”, 32nd Annual Symposium on Combinatorial Pattern Matching CPM 2021, LIPIcs – Leibniz International Proceedings in Informatics, vol. 191
Marek Nowicki, Łukasz Górski, Piotr Bała; Scalable computing in Java with PCJ Library. Improved collective operations; In: Proceedings of International Symposium on Grids and Clouds 2021 — PoS(ISGC2021), vol. 378, 2021, p. 7, https://doi.org/10.22323/1.378.0007

2020

Bogdan Aman, Gabriel Ciobanu, Robert Glück, Robin Kaarsgaard, Jarkko Kari, Martin Kutrib, Ivan Lanese, Claudio Antares Mezzina, Łukasz Mikulski, Rajagopal Nagarajan, Iain C. C. Phillips, G. Michele Pinna, Luca Prigioniero, Irek Ulidowski, Germán Vidal: Foundations of Reversible Computation. Selected Results of the COST Action IC1405 2020: 1-40
Evgeny Erofeev, Kamila Barylska, Łukasz Mikulski, Marcin Piątkowski: Generating all minimal petri net unsolvable binary words. Discret. Appl. Math. 274: 35-53 (2020)
Jetty Kleijn, Maciej Koutny, Łukasz Mikulski: Reaction Systems and Enabling Equivalence. Fundam. Inform. 171(1-4): 261-277 (2020)
Janicki Ryszard, Mikulski Łukasz, Algebraic structure of step traces and interval traces, Fundamenta Informaticae, Vol. 175, S. 253-280 (2020)
Kaniecki Mariusz, Kosakowska Justyna, Combinatorial algorithms for binary operations on LR-tableaux with entries equal to 1 with applications to nilpotent linear operators, Fundam. Inform., Vol. 174 no. 2 (2020), S. 121-136, tab., ISSN: 0169-2968 ; eISSN: 1875-8681, DOI: 10.3233/FI-2020-1935
Kaniecki Mariusz, Kosakowska Justyna, Applications of Littlewood-Richardson tableaux to computing generic extension of semisimple invariant subspaces of nilpotent linear operators, Linear Algebra Appl., Vol. 588 (2020), S. 134-159, ISSN: 0024-3795 ; eISSN: 1873-1856, DOI: 10.1016/j.laa.2019.11.019
Łukasz Mikulski, Ion Petre: Preface. Journal of Membrane Computing 2(3): 147-148 (2020)
Nowicki Marek: Comparison of sort algorithms in Hadoop and PCJ. Journal of Big Data, 7, Article number: 101 (2020), doi: https://doi.org/10.1186/s40537-020-00376-9

Accepted:

Marek Nowicki, Running Java/PCJ application using YARN on Ethernet Cluster – Benchmarking PCJ — a library for parallel computing in Java, HPI Future SOC Lab – Proceedings 2021
Marek Nowicki, Running Java/APGAS application on Ethernet Cluster, HPI Future SOC Lab – Proceedings 2021
Marek Nowicki, Running Monte Carlo Pi approximation using Java/APGAS on Ethernet Cluster, HPI Future SOC Lab – Proceedings 2022
Jesús A. Jiménez González, Andrzej Mróz, Bidirected graphs, integral quadratic forms and some Diophantine equations, Discrete Mathematics (2024), 37pp.
Andrzej Mróz, Katarzyna Zając, Weak Dynkin type and the universality of non-negative Coxeter-regular integral quadratic forms, Documenta Mathematica (2024), 19pp.

Submitted:

Marek Nowicki, Running PLM-APGAS applications on Ethernet Cluster, HPI Future SOC Lab – Proceedings 2022
M. Kaniecki, Box moves and the degeneration partial order in the category of semisimple invariant subspaces of nilpotent linear operators (2023)
M. Kaniecki, J. Kosakowska, Two partial orders on Standard Young Tableaux with applications to invariant subspaces of nilpotent linear operators (2023)
Kamila Barylska, Anna Gogolińska, Łukasz Mikulski, Anna Philippou, Marcin Piątkowski, Kyriaki Psara, Formal Translation from Reversing Petri Nets to Coloured Petri Nets, Fundamenta Informaticae, (2023)
Artur Męski, Maciej Koutny, Łukasz Mikulski, Ion Petre, Wojciech Penczek: Model Checking for Distributed Reaction Systems with rsCTLK (2023)
Marek Nowicki, Piotr Bała, “PCJ: an Open-Source Java library for a multinode parallel computing in the PGAS (Partitioned Global Address Space) paradigm”, SoftwareX (2023)
P. Bała, Ł. Górski, M. Nowicki, “Teaching parallel programming at a computational engineering master’s degree course at the University of Warsaw” (2024)
Marek Nowicki, Magdalena Mroczek, Dhananjay Mukhedkar, Piotr Bała, Ville Nikolai Pimeno, and Laila Sara Arroyo Mühr, HPV-KITE: Sequence analysis software for rapid HPV genotype detection, Briefings in Bioinformatics (2024)
“Analysis and Synthesis of Some Subclasses of Petri Nets”, Raymond Devillers, Kamila Barylska, Petri Nets and Other Models of Concurrency (ToPNoC) – special issue based on Advanced Course on Petri Nets 2023 (2024)
Maciej Koutny, Łukasz Mikulski, Marta Pietkiewicz-Koutny: From Behaviour to Nets via Regions, Petri Nets and Other Models of Concurrency (ToPNoC) – special issue based on Advanced Course on Petri Nets 2023 (2024)
Ryszard Janicki, Jetty Kleijn, Maciej Koutny, Łukasz Mikulski: Analysis of Concurrent Systems, Petri Nets and Other Models of Concurrency (ToPNoC) – special issue based on Advanced Course on Petri Nets 2023 (2024)
Maciej Koutny, Łukasz Mikulski: Quasi-stratified Semantics of Concurrency (2024)
Piotr Przymus, Thomas Durieux, “Wolves in Developers’ Clothing: Analyzing the Software Engineering Practice in the XZ Utils Supply Chain Attack”, submitted to the conference: 2025 IEEE/ACM 22nd International Conference on Mining Software Repositories (MSR) (2024)
Piotr Przymus, Krzysztof Rykaczewski, Adrián Martín-Segura, Jaak Truu, Enrique Carrillo De Santa Pau, Mikhail Kolev, Irina Naskinova, Aleksandra Gruca, Alexia Sampri Marcus Frohme and Alina Nechyporenko, “Deep Learning in Microbiome Analysis: A Comprehensive Review of Neural Network Models”, submitted to journal: Frontiers in Microbiology (2024)
Piotr Przymus, Mikołaj Fejzer, Jakub Narębski, Radosław Woźniak, Łukasz Halada, Aleksander Kazecki, Mykhailo Molchanov and Krzysztof Stencel, “HaPy-Bug — Human Annotated Python Bug Resolution Dataset”, submitted to the conference: 2025 IEEE/ACM 22nd International Conference on Mining Software Repositories (MSR) (2024)
Przymus Piotr, Fejzer Mikołaj, Narębski Jakub, Krzysztof Stencel, “PatchScope – A Modular Tool for Annotating and Analyzing Contributions”, submitted to the conference: 2025 IEEE/ACM 22nd International Conference on Mining Software Repositories (MSR) (2024)
Jesús A. Jiménez González, Andrzej Mróz, A graph theoretic model for the derived categories of gentle algebras and their homological bilinear forms, preprint (2024), web3.arxiv.org/abs/2407.04817