2 Search Results for "Masina, Gabriele"

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.SAT.2023.15
On CNF Conversion for Disjoint SAT Enumeration

Authors: Gabriele Masina, Giuseppe Spallitta, and Roberto Sebastiani

Published in: LIPIcs, Volume 271, 26th International Conference on Theory and Applications of Satisfiability Testing (SAT 2023)

Abstract
Modern SAT solvers are designed to handle problems expressed in Conjunctive Normal Form (CNF) so that non-CNF problems must be CNF-ized upfront, typically by using variants of either Tseitin or Plaisted and Greenbaum transformations. When passing from solving to enumeration, however, the capability of producing partial satisfying assignments that are as small as possible becomes crucial, which raises the question of whether such CNF encodings are also effective for enumeration. In this paper, we investigate both theoretically and empirically the effectiveness of CNF conversions for disjoint SAT enumeration. On the negative side, we show that: (i) Tseitin transformation prevents the solver from producing short partial assignments, thus seriously affecting the effectiveness of enumeration; (ii) Plaisted and Greenbaum transformation overcomes this problem only in part. On the positive side, we show that combining Plaisted and Greenbaum transformation with NNF preprocessing upfront - which is typically not used in solving - can fully overcome the problem and can drastically reduce both the number of partial assignments and the execution time.
Cite as

Gabriele Masina, Giuseppe Spallitta, and Roberto Sebastiani. On CNF Conversion for Disjoint SAT Enumeration. In 26th International Conference on Theory and Applications of Satisfiability Testing (SAT 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 271, pp. 15:1-15:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

Copy BibTex To Clipboard

@InProceedings{masina_et_al:LIPIcs.SAT.2023.15,
  author =	{Masina, Gabriele and Spallitta, Giuseppe and Sebastiani, Roberto},
  title =	{{On CNF Conversion for Disjoint SAT Enumeration}},
  booktitle =	{26th International Conference on Theory and Applications of Satisfiability Testing (SAT 2023)},
  pages =	{15:1--15:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-286-0},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{271},
  editor =	{Mahajan, Meena and Slivovsky, Friedrich},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAT.2023.15},
  URN =		{urn:nbn:de:0030-drops-184775},
  doi =		{10.4230/LIPIcs.SAT.2023.15},
  annote =	{Keywords: CNF conversion, AllSAT, AllSMT}
}
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