4 Search Results for "Rodríguez, Alfonso"

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
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.14
Algorithms for the Diverse-k-SAT Problem: The Geometry of Satisfying Assignments

Authors: Per Austrin, Ioana O. Bercea, Mayank Goswami, Nutan Limaye, and Adarsh Srinivasan

Published in: LIPIcs, Volume 334, 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)

Abstract
Given a k-CNF formula and an integer s ≥ 2, we study algorithms that obtain s solutions to the formula that are as dispersed as possible. For s = 2, this problem of computing the diameter of a k-CNF formula was initiated by Creszenzi and Rossi, who showed strong hardness results even for k = 2. The current best upper bound [Angelsmark and Thapper '04] goes to 4ⁿ as k → ∞. As our first result, we show that this quadratic blow up is not necessary by utilizing the Fast-Fourier transform (FFT) to give a O^*(2ⁿ) time exact algorithm for computing the diameter of any k-CNF formula. For s > 2, the problem was raised in the SAT community (Nadel '11) and several heuristics have been proposed for it, but no algorithms with theoretical guarantees are known. We give exact algorithms using FFT and clique-finding that run in O^*(2^{(s-1)n}) and O^*(s² |Ω_{𝐅}|^{ω ⌈ s/3 ⌉}) respectively, where |Ω_{𝐅}| is the size of the solutions space of the formula 𝐅 and ω is the matrix multiplication exponent. However, current SAT algorithms for finding one solution run in time O^*(2^{ε_{k}n}) for ε_{k} ≈ 1-Θ(1/k), which is much faster than all above run times. As our main result, we analyze two popular SAT algorithms - PPZ (Paturi, Pudlák, Zane '97) and Schöning’s ('02) algorithms, and show that in time poly(s)O^*(2^{ε_{k}n}), they can be used to approximate diameter as well as the dispersion (s > 2) problem. While we need to modify Schöning’s original algorithm for technical reasons, we show that the PPZ algorithm, without any modification, samples solutions in a geometric sense. We believe this geometric sampling property of PPZ may be of independent interest. Finally, we focus on diverse solutions to NP-complete optimization problems, and give bi-approximations running in time poly(s)O^*(2^{ε n}) with ε < 1 for several problems such as Maximum Independent Set, Minimum Vertex Cover, Minimum Hitting Set, Feedback Vertex Set, Multicut on Trees and Interval Vertex Deletion. For all of these problems, all existing exact methods for finding optimal diverse solutions have a runtime with at least an exponential dependence on the number of solutions s. Our methods show that by relaxing to bi-approximations, this dependence on s can be made polynomial.
Cite as

Per Austrin, Ioana O. Bercea, Mayank Goswami, Nutan Limaye, and Adarsh Srinivasan. Algorithms for the Diverse-k-SAT Problem: The Geometry of Satisfying Assignments. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 14:1-14:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{austrin_et_al:LIPIcs.ICALP.2025.14,
  author =	{Austrin, Per and Bercea, Ioana O. and Goswami, Mayank and Limaye, Nutan and Srinivasan, Adarsh},
  title =	{{Algorithms for the Diverse-k-SAT Problem: The Geometry of Satisfying Assignments}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{14:1--14:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-372-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{334},
  editor =	{Censor-Hillel, Keren and Grandoni, Fabrizio and Ouaknine, Jo\"{e}l and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2025.14},
  URN =		{urn:nbn:de:0030-drops-233916},
  doi =		{10.4230/LIPIcs.ICALP.2025.14},
  annote =	{Keywords: Exponential time algorithms, Satisfiability, k-SAT, PPZ, Sch\"{o}ning, Dispersion, Diversity}
}
Document
Position
DOI: 10.4230/TGDK.1.1.5
Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities

Authors: Jiaoyan Chen, Hang Dong, Janna Hastings, Ernesto Jiménez-Ruiz, Vanessa López, Pierre Monnin, Catia Pesquita, Petr Škoda, and Valentina Tamma

Published in: TGDK, Volume 1, Issue 1 (2023): Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 1, Issue 1

Abstract
The term life sciences refers to the disciplines that study living organisms and life processes, and include chemistry, biology, medicine, and a range of other related disciplines. Research efforts in life sciences are heavily data-driven, as they produce and consume vast amounts of scientific data, much of which is intrinsically relational and graph-structured. The volume of data and the complexity of scientific concepts and relations referred to therein promote the application of advanced knowledge-driven technologies for managing and interpreting data, with the ultimate aim to advance scientific discovery. In this survey and position paper, we discuss recent developments and advances in the use of graph-based technologies in life sciences and set out a vision for how these technologies will impact these fields into the future. We focus on three broad topics: the construction and management of Knowledge Graphs (KGs), the use of KGs and associated technologies in the discovery of new knowledge, and the use of KGs in artificial intelligence applications to support explanations (explainable AI). We select a few exemplary use cases for each topic, discuss the challenges and open research questions within these topics, and conclude with a perspective and outlook that summarizes the overarching challenges and their potential solutions as a guide for future research.
Cite as

Jiaoyan Chen, Hang Dong, Janna Hastings, Ernesto Jiménez-Ruiz, Vanessa López, Pierre Monnin, Catia Pesquita, Petr Škoda, and Valentina Tamma. Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 5:1-5:33, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{chen_et_al:TGDK.1.1.5,
  author =	{Chen, Jiaoyan and Dong, Hang and Hastings, Janna and Jim\'{e}nez-Ruiz, Ernesto and L\'{o}pez, Vanessa and Monnin, Pierre and Pesquita, Catia and \v{S}koda, Petr and Tamma, Valentina},
  title =	{{Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{5:1--5:33},
  year =	{2023},
  volume =	{1},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.1.1.5},
  URN =		{urn:nbn:de:0030-drops-194791},
  doi =		{10.4230/TGDK.1.1.5},
  annote =	{Keywords: Knowledge graphs, Life science, Knowledge discovery, Explainable AI}
}
Document
Invited Talk
DOI: 10.4230/OASIcs.PARMA-DITAM.2022.2
Just-In-Time Composition of Reconfigurable Overlays (Invited Talk)

Authors: Rafael Zamacola, Andrés Otero, Alfonso Rodríguez, and Eduardo de la Torre

Published in: OASIcs, Volume 100, 13th Workshop on Parallel Programming and Run-Time Management Techniques for Many-Core Architectures and 11th Workshop on Design Tools and Architectures for Multicore Embedded Computing Platforms (PARMA-DITAM 2022)

Abstract
This paper describes a framework supporting the automatic composition of reconfigurable overlays laid on top of an FPGA to offload computing-intensive sections of a given application, from an embedded processor to a loosely coupled reconfigurable accelerator. Overlays provide an abstraction layer acting as an intermediate fabric between users' applications and the FPGA fabric. Among the existing flavors, the overlay template proposed in this work is based on a coarse-grain reconfigurable architecture featuring word-level operators, reducing long place-and-route times associated with FPGA designs. The proposed overlays are composed at run-time using a tile-based approach, in which pre-synthesized processing elements are stitched together following a 2D grid pattern and using dynamic and partial reconfiguration. The proposed reconfigurable architecture is accompanied by an automated toolchain that, relying on an LLVM intermediate representation, automatically converts the source code to a data-flow graph that is afterward mapped onto the overlay. A mapping example is provided in this paper to show the possibilities enabled by the framework, including loop mapping and loop unrolling support, features originally described in this work.
Cite as

Rafael Zamacola, Andrés Otero, Alfonso Rodríguez, and Eduardo de la Torre. Just-In-Time Composition of Reconfigurable Overlays (Invited Talk). In 13th Workshop on Parallel Programming and Run-Time Management Techniques for Many-Core Architectures and 11th Workshop on Design Tools and Architectures for Multicore Embedded Computing Platforms (PARMA-DITAM 2022). Open Access Series in Informatics (OASIcs), Volume 100, pp. 2:1-2:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{zamacola_et_al:OASIcs.PARMA-DITAM.2022.2,
  author =	{Zamacola, Rafael and Otero, Andr\'{e}s and Rodr{\'\i}guez, Alfonso and de la Torre, Eduardo},
  title =	{{Just-In-Time Composition of Reconfigurable Overlays}},
  booktitle =	{13th Workshop on Parallel Programming and Run-Time Management Techniques for Many-Core Architectures and 11th Workshop on Design Tools and Architectures for Multicore Embedded Computing Platforms (PARMA-DITAM 2022)},
  pages =	{2:1--2:13},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-231-0},
  ISSN =	{2190-6807},
  year =	{2022},
  volume =	{100},
  editor =	{Palumbo, Francesca and Bispo, Jo\~{a}o and Cherubin, Stefano},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.PARMA-DITAM.2022.2},
  URN =		{urn:nbn:de:0030-drops-161186},
  doi =		{10.4230/OASIcs.PARMA-DITAM.2022.2},
  annote =	{Keywords: FPGA, Dynamic Partial Reconfiguration, Overlay, LLVM, Compilation}
}
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