4 Search Results for "Soliman, Sylvain"

Document
DOI: 10.4230/LIPIcs.CP.2025.17
Scalable Counting of Minimal Trap Spaces and Fixed Points in Boolean Networks

Authors: Mohimenul Kabir, Van-Giang Trinh, Samuel Pastva, and Kuldeep S Meel

Published in: LIPIcs, Volume 340, 31st International Conference on Principles and Practice of Constraint Programming (CP 2025)

Abstract
Boolean Networks (BNs) serve as a fundamental modeling framework for capturing complex dynamical systems across various domains, including systems biology, computational logic, and artificial intelligence. A crucial property of BNs is the presence of trap spaces - subspaces of the state space that, once entered, cannot be exited. Minimal trap spaces, in particular, play a significant role in analyzing the long-term behavior of BNs, making their efficient enumeration and counting essential. The fixed points in BNs are a special case of minimal trap spaces. In this work, we formulate several meaningful counting problems related to minimal trap spaces and fixed points in BNs. These problems provide valuable insights both within BN theory (e.g., in probabilistic reasoning and dynamical analysis) and in broader application areas, including systems biology, abstract argumentation, and logic programming. To address these computational challenges, we propose novel methods based on approximate answer set counting, leveraging techniques from answer set programming. Our approach efficiently approximates the number of minimal trap spaces and the number of fixed points without requiring exhaustive enumeration, making it particularly well-suited for large-scale BNs. Our experimental evaluation on an extensive and diverse set of benchmark instances shows that our methods significantly improve the feasibility of counting minimal trap spaces and fixed points, paving the way for new applications in BN analysis and beyond.
Cite as

Mohimenul Kabir, Van-Giang Trinh, Samuel Pastva, and Kuldeep S Meel. Scalable Counting of Minimal Trap Spaces and Fixed Points in Boolean Networks. In 31st International Conference on Principles and Practice of Constraint Programming (CP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 340, pp. 17:1-17:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{kabir_et_al:LIPIcs.CP.2025.17,
  author =	{Kabir, Mohimenul and Trinh, Van-Giang and Pastva, Samuel and Meel, Kuldeep S},
  title =	{{Scalable Counting of Minimal Trap Spaces and Fixed Points in Boolean Networks}},
  booktitle =	{31st International Conference on Principles and Practice of Constraint Programming (CP 2025)},
  pages =	{17:1--17:26},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-380-5},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{340},
  editor =	{de la Banda, Maria Garcia},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CP.2025.17},
  URN =		{urn:nbn:de:0030-drops-238780},
  doi =		{10.4230/LIPIcs.CP.2025.17},
  annote =	{Keywords: Computational systems biology, Boolean network, Fixed point, Trap space, Answer set counting, Projected counting, Abstract argumentation, Logic programming}
}
Document
DOI: 10.4230/LIPIcs.ECRTS.2025.9
DAMA: A Dual Arbitration Mechanism for Mixed-Criticality Applications

Authors: Wafic Lawand and Rodolfo Pellizzoni

Published in: LIPIcs, Volume 335, 37th Euromicro Conference on Real-Time Systems (ECRTS 2025)

Abstract
We discuss hardware resource management in mixed-criticality systems, where requestors may issue latency-critical (LTC) and non-latency-critical (NLTC) requests. LTC requests must adhere to strict latency bounds imposed by safety-critical applications, but timely servicing NLTC requests is necessary to maximize overall system performance in the average case. In this paper, we address this tradeoff for a shared memory resource by proposing DAMA, a dual arbitration mechanism that imposes an upper bound on the cumulative latency of LTC requests without unduly impacting NLTC performance. DAMA comprises a high-performance arbiter, a real-time arbiter, and a mechanism that constantly monitors the cumulative latency of requests suffered by each requestor. DAMA primarily executes in high-performance mode and only switches to real-time mode in the rare instances when its incorporated mechanism detects a violation of a task’s timing guarantee. We demonstrate the effectiveness of our arbitration scheme by adapting a predictable prefetcher that issues NLTC requests and attaching it to the L1 caches of our cores. We show both formally and experimentally that DAMA provides timing guarantees for LTC requests while processing other NLTC requests. We also demonstrate that with a negligible overhead of less than 1.5% on the cumulative latency bound of LTC requests, DAMA can achieve an equivalent average performance to a prefetcher that processes requests under a high-performance arbitration scheme.
Cite as

Wafic Lawand and Rodolfo Pellizzoni. DAMA: A Dual Arbitration Mechanism for Mixed-Criticality Applications. In 37th Euromicro Conference on Real-Time Systems (ECRTS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 335, pp. 9:1-9:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{lawand_et_al:LIPIcs.ECRTS.2025.9,
  author =	{Lawand, Wafic and Pellizzoni, Rodolfo},
  title =	{{DAMA: A Dual Arbitration Mechanism for Mixed-Criticality Applications}},
  booktitle =	{37th Euromicro Conference on Real-Time Systems (ECRTS 2025)},
  pages =	{9:1--9:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-377-5},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{335},
  editor =	{Mancuso, Renato},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECRTS.2025.9},
  URN =		{urn:nbn:de:0030-drops-235875},
  doi =		{10.4230/LIPIcs.ECRTS.2025.9},
  annote =	{Keywords: Real-time Systems, Mixed-criticality Applications, Memory controllers, Prefetchers}
}
Document
DOI: 10.4230/LIPIcs.CP.2023.35
Efficient Enumeration of Fixed Points in Complex Boolean Networks Using Answer Set Programming

Authors: Van-Giang Trinh, Belaid Benhamou, and Sylvain Soliman

Published in: LIPIcs, Volume 280, 29th International Conference on Principles and Practice of Constraint Programming (CP 2023)

Abstract
Boolean Networks (BNs) are an efficient modeling formalism with applications in various research fields such as mathematics, computer science, and more recently systems biology. One crucial problem in the BN research is to enumerate all fixed points, which has been proven crucial in the analysis and control of biological systems. Indeed, in that field, BNs originated from the pioneering work of R. Thomas on gene regulation and from the start were characterized by their asymptotic behavior: complex attractors and fixed points. The former being notably more difficult to compute exactly, and specific to certain biological systems, the computation of stable states (fixed points) has been the standard way to analyze those BNs for years. However, with the increase in model size and complexity of Boolean update functions, the existing methods for this problem show their limitations. To our knowledge, the most efficient state-of-the-art methods for the fixed point enumeration problem rely on Answer Set Programming (ASP). Motivated by these facts, in this work we propose two new efficient ASP-based methods to solve this problem. We evaluate them on both real-world and pseudo-random models, showing that they vastly outperform four state-of-the-art methods as well as can handle very large and complex models.
Cite as

Van-Giang Trinh, Belaid Benhamou, and Sylvain Soliman. Efficient Enumeration of Fixed Points in Complex Boolean Networks Using Answer Set Programming. In 29th International Conference on Principles and Practice of Constraint Programming (CP 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 280, pp. 35:1-35:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{trinh_et_al:LIPIcs.CP.2023.35,
  author =	{Trinh, Van-Giang and Benhamou, Belaid and Soliman, Sylvain},
  title =	{{Efficient Enumeration of Fixed Points in Complex Boolean Networks Using Answer Set Programming}},
  booktitle =	{29th International Conference on Principles and Practice of Constraint Programming (CP 2023)},
  pages =	{35:1--35:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-300-3},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{280},
  editor =	{Yap, Roland H. C.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CP.2023.35},
  URN =		{urn:nbn:de:0030-drops-190720},
  doi =		{10.4230/LIPIcs.CP.2023.35},
  annote =	{Keywords: Computational systems biology, Boolean network, Fixed point, Answer set programming}
}
Document
DOI: 10.4230/DagSemProc.09091.3
Analyzing various models of Circadian Clock and Cell Cycle coupling

Authors: Attila Csikász-Nagy, Adrien Faure, Roberto Larcher, Paola Lecca, Ivan Mura, Ferenc Jordan, Alida Palmisano, Alessandro Romanel, Sean Sedwards, Heike Siebert, Sylvain Soliman, Denis Thieffry, Judit Zámborszky, Tommaso Mazza, and Paolo Ballarini

Published in: Dagstuhl Seminar Proceedings, Volume 9091, Formal Methods in Molecular Biology (2009)

Abstract
The daily rhythm can influence the proliferation rate of many cell types. In the mammalian system the transcription of the cell cycle regulatory protein Wee1 is controlled by the circadian clock. Zamborszky et al. (2007) present a computational model coupling the cell cycle and circadian rhythm, showing that this coupling can lead to multimodal cell cycle time distributions. Biological data points to additional couplings, including a link back from the cell cycle to the circadian clock. Proper modelling of this coupling requires a more detailed description of both parts of the model. Hence, we aim at further extending and analysing earlier models using a combination of modelling techniques and computer software, including CoSBI lab, BIOCHAM, and GINsim.
Cite as

Attila Csikász-Nagy, Adrien Faure, Roberto Larcher, Paola Lecca, Ivan Mura, Ferenc Jordan, Alida Palmisano, Alessandro Romanel, Sean Sedwards, Heike Siebert, Sylvain Soliman, Denis Thieffry, Judit Zámborszky, Tommaso Mazza, and Paolo Ballarini. Analyzing various models of Circadian Clock and Cell Cycle coupling. In Formal Methods in Molecular Biology. Dagstuhl Seminar Proceedings, Volume 9091, pp. 1-6, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{csikasznagy_et_al:DagSemProc.09091.3,
  author =	{Csik\'{a}sz-Nagy, Attila and Faure, Adrien and Larcher, Roberto and Lecca, Paola and Mura, Ivan and Jordan, Ferenc and Palmisano, Alida and Romanel, Alessandro and Sedwards, Sean and Siebert, Heike and Soliman, Sylvain and Thieffry, Denis and Z\'{a}mborszky, Judit and Mazza, Tommaso and Ballarini, Paolo},
  title =	{{Analyzing various models of Circadian Clock and Cell Cycle coupling}},
  booktitle =	{Formal Methods in Molecular Biology},
  pages =	{1--6},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{9091},
  editor =	{Rainer Breitling and David Roger Gilbert and Monika Heiner and Corrado Priami},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09091.3},
  URN =		{urn:nbn:de:0030-drops-19944},
  doi =		{10.4230/DagSemProc.09091.3},
  annote =	{Keywords: Cell cycle, circadian clock, computational modelling}
}
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