86 Search Results for "El-Mhamdi, El-Mahdi"


Volume

LIPIcs, Volume 201

21st International Workshop on Algorithms in Bioinformatics (WABI 2021)

WABI 2021, August 2-4, 2021, Virtual Conference

Editors: Alessandra Carbone and Mohammed El-Kebir

Document
Visualization and the Humanities: Towards a Shared Research Agenda (Dagstuhl Seminar 23381)

Authors: Johanna Drucker, Mennatallah El-Assady, Uta Hinrichs, Florian Windhager, and Derya Akbaba

Published in: Dagstuhl Reports, Volume 13, Issue 9 (2024)


Abstract
This report documents the program and the outcomes of Dagstuhl Seminar 23381 "Visualization and the Humanities: Towards a Shared Research Agenda". The seminar was motivated by the fact that visualization has become a vital element in (digital) humanist research practices recently, while the value and impact of research at the intersection of visualization and the humanities is still widely debated and frequently contested from both sides. Visualization scholars critique the service-oriented focus on visualization as a tool to facilitate humanist research, which hampers the discovery of complementary and mutually enriching research perspectives for all fields involved. At the same time, humanists warn of visualizations' roots in the quantitative sciences which introduce non-trivial shifts in the topology of knowledge-power, creating epistemic, political, ethical, pedagogical, and cultural tensions. Building on advances in this young and highly interdisciplinary research area, the seminar discussed how to leverage synergies and how to build productively on tensions between methodologies at the intersection of visualization and (digital) humanities fields that span a vast spectrum of research philosophies and methods. The seminar thus brought together researchers and practitioners from the fields of visualization, computer science, the humanities, and design to reflect on existing research methods within visualization and the humanities, to identify tensions and synergies between the different fields, and to develop concrete avenues that address and leverage these.

Cite as

Johanna Drucker, Mennatallah El-Assady, Uta Hinrichs, Florian Windhager, and Derya Akbaba. Visualization and the Humanities: Towards a Shared Research Agenda (Dagstuhl Seminar 23381). In Dagstuhl Reports, Volume 13, Issue 9, pp. 137-165, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@Article{drucker_et_al:DagRep.13.9.137,
  author =	{Drucker, Johanna and El-Assady, Mennatallah and Hinrichs, Uta and Windhager, Florian and Akbaba, Derya},
  title =	{{Visualization and the Humanities: Towards a Shared Research Agenda (Dagstuhl Seminar 23381)}},
  pages =	{137--165},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2024},
  volume =	{13},
  number =	{9},
  editor =	{Drucker, Johanna and El-Assady, Mennatallah and Hinrichs, Uta and Windhager, Florian and Akbaba, Derya},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.13.9.137},
  URN =		{urn:nbn:de:0030-drops-198246},
  doi =		{10.4230/DagRep.13.9.137},
  annote =	{Keywords: Digital humanities, arts, humanities, methodology, research program, visualization}
}
Document
On the Exact Matching Problem in Dense Graphs

Authors: Nicolas El Maalouly, Sebastian Haslebacher, and Lasse Wulf

Published in: LIPIcs, Volume 289, 41st International Symposium on Theoretical Aspects of Computer Science (STACS 2024)


Abstract
In the Exact Matching problem, we are given a graph whose edges are colored red or blue and the task is to decide for a given integer k, if there is a perfect matching with exactly k red edges. Since 1987 it is known that the Exact Matching Problem can be solved in randomized polynomial time. Despite numerous efforts, it is still not known today whether a deterministic polynomial-time algorithm exists as well. In this paper, we make substantial progress by solving the problem for a multitude of different classes of dense graphs. We solve the Exact Matching problem in deterministic polynomial time for complete r-partite graphs, for unit interval graphs, for bipartite unit interval graphs, for graphs of bounded neighborhood diversity, for chain graphs, and for graphs without a complete bipartite t-hole. We solve the problem in quasi-polynomial time for Erdős-Rényi random graphs G(n, 1/2). We also reprove an earlier result for bounded independence number/bipartite independence number. We use two main tools to obtain these results: A local search algorithm as well as a generalization of an earlier result by Karzanov.

Cite as

Nicolas El Maalouly, Sebastian Haslebacher, and Lasse Wulf. On the Exact Matching Problem in Dense Graphs. In 41st International Symposium on Theoretical Aspects of Computer Science (STACS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 289, pp. 33:1-33:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{elmaalouly_et_al:LIPIcs.STACS.2024.33,
  author =	{El Maalouly, Nicolas and Haslebacher, Sebastian and Wulf, Lasse},
  title =	{{On the Exact Matching Problem in Dense Graphs}},
  booktitle =	{41st International Symposium on Theoretical Aspects of Computer Science (STACS 2024)},
  pages =	{33:1--33:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-311-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{289},
  editor =	{Beyersdorff, Olaf and Kant\'{e}, Mamadou Moustapha and Kupferman, Orna and Lokshtanov, Daniel},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2024.33},
  URN =		{urn:nbn:de:0030-drops-197437},
  doi =		{10.4230/LIPIcs.STACS.2024.33},
  annote =	{Keywords: Exact Matching, Perfect Matching, Red-Blue Matching, Bounded Color Matching, Local Search, Derandomization}
}
Document
Exact Matching: Correct Parity and FPT Parameterized by Independence Number

Authors: Nicolas El Maalouly, Raphael Steiner, and Lasse Wulf

Published in: LIPIcs, Volume 283, 34th International Symposium on Algorithms and Computation (ISAAC 2023)


Abstract
Given an integer k and a graph where every edge is colored either red or blue, the goal of the exact matching problem is to find a perfect matching with the property that exactly k of its edges are red. Soon after Papadimitriou and Yannakakis (JACM 1982) introduced the problem, a randomized polynomial-time algorithm solving the problem was described by Mulmuley et al. (Combinatorica 1987). Despite a lot of effort, it is still not known today whether a deterministic polynomial-time algorithm exists. This makes the exact matching problem an important candidate to test the popular conjecture that the complexity classes P and RP are equal. In a recent article (MFCS 2022), progress was made towards this goal by showing that for bipartite graphs of bounded bipartite independence number, a polynomial time algorithm exists. In terms of parameterized complexity, this algorithm was an XP-algorithm parameterized by the bipartite independence number. In this article, we introduce novel algorithmic techniques that allow us to obtain an FPT-algorithm. If the input is a general graph we show that one can at least compute a perfect matching M which has the correct number of red edges modulo 2, in polynomial time. This is motivated by our last result, in which we prove that an FPT algorithm for general graphs, parameterized by the independence number, reduces to the problem of finding in polynomial time a perfect matching M with at most k red edges and the correct number of red edges modulo 2.

Cite as

Nicolas El Maalouly, Raphael Steiner, and Lasse Wulf. Exact Matching: Correct Parity and FPT Parameterized by Independence Number. In 34th International Symposium on Algorithms and Computation (ISAAC 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 283, pp. 28:1-28:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{elmaalouly_et_al:LIPIcs.ISAAC.2023.28,
  author =	{El Maalouly, Nicolas and Steiner, Raphael and Wulf, Lasse},
  title =	{{Exact Matching: Correct Parity and FPT Parameterized by Independence Number}},
  booktitle =	{34th International Symposium on Algorithms and Computation (ISAAC 2023)},
  pages =	{28:1--28:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-289-1},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{283},
  editor =	{Iwata, Satoru and Kakimura, Naonori},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2023.28},
  URN =		{urn:nbn:de:0030-drops-193302},
  doi =		{10.4230/LIPIcs.ISAAC.2023.28},
  annote =	{Keywords: Perfect Matching, Exact Matching, Independence Number, Parameterized Complexity}
}
Document
A CP Approach for the Liner Shipping Network Design Problem

Authors: Yousra El Ghazi, Djamal Habet, and Cyril Terrioux

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


Abstract
The liner shipping network design problem consists, for a shipowner, in determining, on the one hand, which maritime lines (in the form of rotations serving a set of ports) to open, and, on the other hand, the assignment of ships (container ships) with the adapted sizes for the different lines to carry all the container flows. In this paper, we propose a modeling of this problem using constraint programming. Then, we present a preliminary study of its solving using a state-of-the-art solver, namely the OR-Tools CP-SAT solver.

Cite as

Yousra El Ghazi, Djamal Habet, and Cyril Terrioux. A CP Approach for the Liner Shipping Network Design Problem. In 29th International Conference on Principles and Practice of Constraint Programming (CP 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 280, pp. 16:1-16:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{elghazi_et_al:LIPIcs.CP.2023.16,
  author =	{El Ghazi, Yousra and Habet, Djamal and Terrioux, Cyril},
  title =	{{A CP Approach for the Liner Shipping Network Design Problem}},
  booktitle =	{29th International Conference on Principles and Practice of Constraint Programming (CP 2023)},
  pages =	{16:1--16:21},
  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-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.CP.2023.16},
  URN =		{urn:nbn:de:0030-drops-190532},
  doi =		{10.4230/LIPIcs.CP.2023.16},
  annote =	{Keywords: Constraint optimization problem, modeling, solving, industrial application}
}
Document
Learning a Generic Value-Selection Heuristic Inside a Constraint Programming Solver

Authors: Tom Marty, Tristan François, Pierre Tessier, Louis Gautier, Louis-Martin Rousseau, and Quentin Cappart

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


Abstract
Constraint programming is known for being an efficient approach to solving combinatorial problems. Important design choices in a solver are the branching heuristics, designed to lead the search to the best solutions in a minimum amount of time. However, developing these heuristics is a time-consuming process that requires problem-specific expertise. This observation has motivated many efforts to use machine learning to automatically learn efficient heuristics without expert intervention. Although several generic variable-selection heuristics are available in the literature, the options for value-selection heuristics are more scarce. We propose to tackle this issue by introducing a generic learning procedure that can be used to obtain a value-selection heuristic inside a constraint programming solver. This has been achieved thanks to the combination of a deep Q-learning algorithm, a tailored reward signal, and a heterogeneous graph neural network. Experiments on graph coloring, maximum independent set, and maximum cut problems show that this framework competes with the well-known impact-based and activity-based search heuristics and can find solutions close to optimality without requiring a large number of backtracks.

Cite as

Tom Marty, Tristan François, Pierre Tessier, Louis Gautier, Louis-Martin Rousseau, and Quentin Cappart. Learning a Generic Value-Selection Heuristic Inside a Constraint Programming Solver. In 29th International Conference on Principles and Practice of Constraint Programming (CP 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 280, pp. 25:1-25:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{marty_et_al:LIPIcs.CP.2023.25,
  author =	{Marty, Tom and Fran\c{c}ois, Tristan and Tessier, Pierre and Gautier, Louis and Rousseau, Louis-Martin and Cappart, Quentin},
  title =	{{Learning a Generic Value-Selection Heuristic Inside a Constraint Programming Solver}},
  booktitle =	{29th International Conference on Principles and Practice of Constraint Programming (CP 2023)},
  pages =	{25:1--25:19},
  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.2023.25},
  URN =		{urn:nbn:de:0030-drops-190625},
  doi =		{10.4230/LIPIcs.CP.2023.25},
  annote =	{Keywords: Branching heuristic, Deep reinforcement learning}
}
Document
Integrated Rigorous Analysis in Cyber-Physical Systems Engineering (Dagstuhl Seminar 23041)

Authors: Erika Abraham, Stefan Hallerstede, John Hatcliff, Danielle Stewart, and Noah Abou El Wafa

Published in: Dagstuhl Reports, Volume 13, Issue 1 (2023)


Abstract
This report documents the program and the outcomes of the Dagstuhl Seminar 23041 "Integrated Rigorous Analysis in Cyber-Physical Systems (CPS) Engineering". This seminar brought together academic and industry representations from a variety of domains with backgrounds in different techniques to develop a roadmap for addressing the current challenges in the area of CPS engineering. An overarching theme was the potential use of integrated models and associated methodologies that support cross-technique information/results sharing and smooth workflow hand-offs between individual tools and methods.

Cite as

Erika Abraham, Stefan Hallerstede, John Hatcliff, Danielle Stewart, and Noah Abou El Wafa. Integrated Rigorous Analysis in Cyber-Physical Systems Engineering (Dagstuhl Seminar 23041). In Dagstuhl Reports, Volume 13, Issue 1, pp. 155-183, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@Article{abraham_et_al:DagRep.13.1.155,
  author =	{Abraham, Erika and Hallerstede, Stefan and Hatcliff, John and Stewart, Danielle and Wafa, Noah Abou El},
  title =	{{Integrated Rigorous Analysis in Cyber-Physical Systems Engineering (Dagstuhl Seminar 23041)}},
  pages =	{155--183},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2023},
  volume =	{13},
  number =	{1},
  editor =	{Abraham, Erika and Hallerstede, Stefan and Hatcliff, John and Stewart, Danielle and Wafa, Noah Abou El},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagRep.13.1.155},
  URN =		{urn:nbn:de:0030-drops-191209},
  doi =		{10.4230/DagRep.13.1.155},
  annote =	{Keywords: cyber-physical systems, formal methods, rigorous modelling and analysis, systems engineering}
}
Document
APPROX
An Approximation Algorithm for the Exact Matching Problem in Bipartite Graphs

Authors: Anita Dürr, Nicolas El Maalouly, and Lasse Wulf

Published in: LIPIcs, Volume 275, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2023)


Abstract
In 1982 Papadimitriou and Yannakakis introduced the Exact Matching problem, in which given a red and blue edge-colored graph G and an integer k one has to decide whether there exists a perfect matching in G with exactly k red edges. Even though a randomized polynomial-time algorithm for this problem was quickly found a few years later, it is still unknown today whether a deterministic polynomial-time algorithm exists. This makes the Exact Matching problem an important candidate to test the RP=P hypothesis. In this paper we focus on approximating Exact Matching. While there exists a simple algorithm that computes in deterministic polynomial-time an almost perfect matching with exactly k red edges, not a lot of work focuses on computing perfect matchings with almost k red edges. In fact such an algorithm for bipartite graphs running in deterministic polynomial-time was published only recently (STACS'23). It outputs a perfect matching with k' red edges with the guarantee that 0.5k ≤ k' ≤ 1.5k. In the present paper we aim at approximating the number of red edges without exceeding the limit of k red edges. We construct a deterministic polynomial-time algorithm, which on bipartite graphs computes a perfect matching with k' red edges such that k/3 ≤ k' ≤ k.

Cite as

Anita Dürr, Nicolas El Maalouly, and Lasse Wulf. An Approximation Algorithm for the Exact Matching Problem in Bipartite Graphs. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 275, pp. 18:1-18:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{durr_et_al:LIPIcs.APPROX/RANDOM.2023.18,
  author =	{D\"{u}rr, Anita and El Maalouly, Nicolas and Wulf, Lasse},
  title =	{{An Approximation Algorithm for the Exact Matching Problem in Bipartite Graphs}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2023)},
  pages =	{18:1--18:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-296-9},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{275},
  editor =	{Megow, Nicole and Smith, Adam},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX/RANDOM.2023.18},
  URN =		{urn:nbn:de:0030-drops-188436},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2023.18},
  annote =	{Keywords: Perfect Matching, Exact Matching, Red-Blue Matching, Approximation Algorithms, Bounded Color Matching}
}
Document
Inferring Temporally Consistent Migration Histories

Authors: Mrinmoy Saha Roddur, Sagi Snir, and Mohammed El-Kebir

Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)


Abstract
Not only do many biological populations undergo evolution, but population members may also migrate from one location to another. For example, tumor cells may migrate from the primary tumor and seed a new metastasis, and pathogens may migrate from one host to another. One may represent a population’s migration history by labeling the vertices of a given phylogeny T with locations such that an edge incident to vertices with distinct locations represents a migration. Additionally, in some biological populations, taxa from distinct lineages may comigrate from one location to another in a single event, a phenomenon known as a comigration. Here, we show that a previous problem statement for inferring migration histories that are parsimonious in terms of migrations and comigrations may lead to temporally inconsistent solutions. To remedy this deficiency, we introduce precise definitions of temporal consistency of comigrations in a phylogeny, leading to three successive problems. First, we formulate the Temporally Consistent Comigrations (TCC) problem to check if a set of comigrations is temporally consistent and provide a linear time algorithm for solving this problem. Second, we formulate the Parsimonious Consistent Comigration (PCC) problem, which aims to find comigrations given a location labeling of a phylogeny. We show that PCC is NP-hard. Third, we formulate the Parsimonious Consistent Comigration History (PCCH) problem, which infers the migration history given a phylogeny and locations of its extant vertices only. We show that PCCH is NP-hard as well. On the positive side, we propose integer linear programming models to solve the PCC and PCCH problems. We apply our approach to real and simulated data.

Cite as

Mrinmoy Saha Roddur, Sagi Snir, and Mohammed El-Kebir. Inferring Temporally Consistent Migration Histories. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 9:1-9:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{roddur_et_al:LIPIcs.WABI.2023.9,
  author =	{Roddur, Mrinmoy Saha and Snir, Sagi and El-Kebir, Mohammed},
  title =	{{Inferring Temporally Consistent Migration Histories}},
  booktitle =	{23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
  pages =	{9:1--9:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-294-5},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{273},
  editor =	{Belazzougui, Djamal and Ouangraoua, A\"{i}da},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.9},
  URN =		{urn:nbn:de:0030-drops-186357},
  doi =		{10.4230/LIPIcs.WABI.2023.9},
  annote =	{Keywords: Metastasis, Migration, Integer Linear Programming, Maximum parsimony}
}
Document
Balancing Minimum Free Energy and Codon Adaptation Index for Pareto Optimal RNA Design

Authors: Xinyu Gu, Yuanyuan Qi, and Mohammed El-Kebir

Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)


Abstract
The problem of designing an RNA sequence v that encodes for a given target protein w plays an important role in messenger RNA (mRNA) vaccine design. Due to codon degeneracy, there exist exponentially many RNA sequences for a single target protein. These candidate RNA sequences may adopt different secondary structure conformations with varying minimum free energy (MFE), affecting their thermodynamic stability and consequently mRNA half-life. In addition, species-specific codon usage bias, as measured by the codon adaptation index (CAI), also plays an essential role in translation efficiency. While previous works have focused on optimizing either MFE or CAI, more recent works have shown the merits of optimizing both objectives. Importantly, there is a trade-off between MFE and CAI, i.e. optimizing one objective is at the expense of the other. Here, we formulate the Pareto Optimal RNA Design problem, seeking the set of Pareto optimal solutions for which no other solution exists that is better in terms of both MFE and CAI. We introduce DERNA (DEsign RNA), which uses the weighted sum method to enumerate the Pareto front by optimizing convex combinations of both objectives. DERNA uses dynamic programming to solve each convex combination in O(|w|³) time and O(|w|²) space. Compared to a previous approach that only optimizes MFE, we show on a benchmark dataset that DERNA obtains solutions with identical MFE but superior CAI. Additionally, we show that DERNA matches the performance in terms of solution quality of LinearDesign, a recent approach that similarly seeks to balance MFE and CAI. Finally, we demonstrate our method’s potential for mRNA vaccine design using SARS-CoV-2 spike as the target protein.

Cite as

Xinyu Gu, Yuanyuan Qi, and Mohammed El-Kebir. Balancing Minimum Free Energy and Codon Adaptation Index for Pareto Optimal RNA Design. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 21:1-21:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{gu_et_al:LIPIcs.WABI.2023.21,
  author =	{Gu, Xinyu and Qi, Yuanyuan and El-Kebir, Mohammed},
  title =	{{Balancing Minimum Free Energy and Codon Adaptation Index for Pareto Optimal RNA Design}},
  booktitle =	{23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
  pages =	{21:1--21:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-294-5},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{273},
  editor =	{Belazzougui, Djamal and Ouangraoua, A\"{i}da},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.21},
  URN =		{urn:nbn:de:0030-drops-186479},
  doi =		{10.4230/LIPIcs.WABI.2023.21},
  annote =	{Keywords: Multi-objective optimization, dynamic programming, RNA sequence design, reverse translation, mRNA vaccine design}
}
Document
Consistency of Automated Market Makers

Authors: Vincent Danos and Weijia Wang

Published in: OASIcs, Volume 110, 4th International Conference on Blockchain Economics, Security and Protocols (Tokenomics 2022)


Abstract
Decentralised Finance has popularised Automated Market Makers (AMMs), but surprisingly little research has been done on their consistency. Can a single attacker extract risk-free revenue from an AMM, regardless of price or other users' behaviour? In this paper, we investigate the consistency of a large class of AMMs, including the most widely used ones, and show that consistency holds.

Cite as

Vincent Danos and Weijia Wang. Consistency of Automated Market Makers. In 4th International Conference on Blockchain Economics, Security and Protocols (Tokenomics 2022). Open Access Series in Informatics (OASIcs), Volume 110, pp. 4:1-4:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{danos_et_al:OASIcs.Tokenomics.2022.4,
  author =	{Danos, Vincent and Wang, Weijia},
  title =	{{Consistency of Automated Market Makers}},
  booktitle =	{4th International Conference on Blockchain Economics, Security and Protocols (Tokenomics 2022)},
  pages =	{4:1--4:12},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-274-7},
  ISSN =	{2190-6807},
  year =	{2023},
  volume =	{110},
  editor =	{Amoussou-Guenou, Yackolley and Kiayias, Aggelos and Verdier, Marianne},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/OASIcs.Tokenomics.2022.4},
  URN =		{urn:nbn:de:0030-drops-184217},
  doi =		{10.4230/OASIcs.Tokenomics.2022.4},
  annote =	{Keywords: Automated Market Makers, Decentralised Finance}
}
Document
Exact and Approximate Range Mode Query Data Structures in Practice

Authors: Meng He and Zhen Liu

Published in: LIPIcs, Volume 265, 21st International Symposium on Experimental Algorithms (SEA 2023)


Abstract
We conduct an experimental study on the range mode problem. In the exact version of the problem, we preprocess an array A, such that given a query range [a, b], the most frequent element in A[a, b] can be found efficiently. For this problem, our most important finding is that the strategy of using succinct data structures to encode more precomputed information not only helped Chan et al. (Linear-space data structures for range mode query in arrays, Theory of Computing Systems, 2013) improve previous results in theory but also helps us achieve the best time/space tradeoff in practice; we even go a step further to replace more components in their solution with succinct data structures and improve the performance further. In the approximate version of this problem, a (1+ε)-approximate range mode query looks for an element whose occurrences in A[a,b] is at least F_{a,b}/(1+ε), where F_{a,b} is the frequency of the mode in A[a,b]. We implement all previous solutions to this problems and find that, even when ε = 1/2, the average approximation ratio of these solutions is close to 1 in practice, and they provide much faster query time than the best exact solution. These solutions achieve different useful time-space tradeoffs, and among them, El-Zein et al. (On Approximate Range Mode and Range Selection, 30th International Symposium on Algorithms and Computation, 2019) provide us with one solution whose space usage is only 35.6% to 93.8% of the cost of storing the input array of 32-bit integers (in most cases, the space cost is closer to the lower end, and the average space cost is 20.2 bits per symbol among all datasets). Its non-succinct version also stands out with query support at least several times faster than other O(n/ε)-word structures while using only slightly more space in practice.

Cite as

Meng He and Zhen Liu. Exact and Approximate Range Mode Query Data Structures in Practice. In 21st International Symposium on Experimental Algorithms (SEA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 265, pp. 19:1-19:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{he_et_al:LIPIcs.SEA.2023.19,
  author =	{He, Meng and Liu, Zhen},
  title =	{{Exact and Approximate Range Mode Query Data Structures in Practice}},
  booktitle =	{21st International Symposium on Experimental Algorithms (SEA 2023)},
  pages =	{19:1--19:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-279-2},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{265},
  editor =	{Georgiadis, Loukas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2023.19},
  URN =		{urn:nbn:de:0030-drops-183693},
  doi =		{10.4230/LIPIcs.SEA.2023.19},
  annote =	{Keywords: range mode query, exact range mode query, approximate range mode query}
}
Document
When Should You Wait Before Updating? - Toward a Robustness Refinement

Authors: Swan Dubois, Laurent Feuilloley, Franck Petit, and Mikaël Rabie

Published in: LIPIcs, Volume 257, 2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023)


Abstract
Consider a dynamic network and a given distributed problem. At any point in time, there might exist several solutions that are equally good with respect to the problem specification, but that are different from an algorithmic perspective, because some could be easier to update than others when the network changes. In other words, one would prefer to have a solution that is more robust to topological changes in the network; and in this direction the best scenario would be that the solution remains correct despite the dynamic of the network. In [Arnaud Casteigts et al., 2020], the authors introduced a very strong robustness criterion: they required that for any removal of edges that maintain the network connected, the solution remains valid. They focus on the maximal independent set problem, and their approach consists in characterizing the graphs in which there exists a robust solution (the existential problem), or even stronger, where any solution is robust (the universal problem). As the robustness criteria is very demanding, few graphs have a robust solution, and even fewer are such that all of their solutions are robust. In this paper, we ask the following question: Can we have robustness for a larger class of networks, if we bound the number k of edge removals allowed? To answer this question, we consider three classic problems: maximal independent set, minimal dominating set and maximal matching. For the universal problem, the answers for the three cases are surprisingly different. For minimal dominating set, the class does not depend on the number of edges removed. For maximal matching, removing only one edge defines a robust class related to perfect matchings, but for all other bounds k, the class is the same as for an arbitrary number of edge removals. Finally, for maximal independent set, there is a strict hierarchy of classes: the class for the bound k is strictly larger than the class for bound k+1. For the robustness notion of [Arnaud Casteigts et al., 2020], no characterization of the class for the existential problem is known, only a polynomial-time recognition algorithm. We show that the situation is even worse for bounded k: even for k = 1, it is NP-hard to decide whether a graph has a robust maximal independent set.

Cite as

Swan Dubois, Laurent Feuilloley, Franck Petit, and Mikaël Rabie. When Should You Wait Before Updating? - Toward a Robustness Refinement. In 2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 257, pp. 7:1-7:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{dubois_et_al:LIPIcs.SAND.2023.7,
  author =	{Dubois, Swan and Feuilloley, Laurent and Petit, Franck and Rabie, Mika\"{e}l},
  title =	{{When Should You Wait Before Updating? - Toward a Robustness Refinement}},
  booktitle =	{2nd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2023)},
  pages =	{7:1--7:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-275-4},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{257},
  editor =	{Doty, David and Spirakis, Paul},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2023.7},
  URN =		{urn:nbn:de:0030-drops-179435},
  doi =		{10.4230/LIPIcs.SAND.2023.7},
  annote =	{Keywords: Robustness, dynamic network, temporal graphs, edge removal, connectivity, footprint, packing/covering problems, maximal independent set, maximal matching, minimum dominating set, perfect matching, NP-hardness}
}
Document
Spoofax at Oracle: Domain-Specific Language Engineering for Large-Scale Graph Analytics

Authors: Houda Boukham, Guido Wachsmuth, Toine Hartman, Hamza Boucherit, Oskar van Rest, Hassan Chafi, Sungpack Hong, Martijn Dwars, Arnaud Delamare, and Dalila Chiadmi

Published in: OASIcs, Volume 109, Eelco Visser Commemorative Symposium (EVCS 2023)


Abstract
For the last decade, teams at Oracle relied on the Spoofax language workbench to develop a family of domain-specific languages for graph analytics in research projects and in product development. In this paper, we analyze the requirements for integrating language processors into large-scale graph analytics toolkits and for the development of these language processors as part of a larger product development process. We discuss how Spoofax helps to meet these requirements and point out the need for future improvements.

Cite as

Houda Boukham, Guido Wachsmuth, Toine Hartman, Hamza Boucherit, Oskar van Rest, Hassan Chafi, Sungpack Hong, Martijn Dwars, Arnaud Delamare, and Dalila Chiadmi. Spoofax at Oracle: Domain-Specific Language Engineering for Large-Scale Graph Analytics. In Eelco Visser Commemorative Symposium (EVCS 2023). Open Access Series in Informatics (OASIcs), Volume 109, pp. 5:1-5:8, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{boukham_et_al:OASIcs.EVCS.2023.5,
  author =	{Boukham, Houda and Wachsmuth, Guido and Hartman, Toine and Boucherit, Hamza and van Rest, Oskar and Chafi, Hassan and Hong, Sungpack and Dwars, Martijn and Delamare, Arnaud and Chiadmi, Dalila},
  title =	{{Spoofax at Oracle: Domain-Specific Language Engineering for Large-Scale Graph Analytics}},
  booktitle =	{Eelco Visser Commemorative Symposium (EVCS 2023)},
  pages =	{5:1--5:8},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-267-9},
  ISSN =	{2190-6807},
  year =	{2023},
  volume =	{109},
  editor =	{L\"{a}mmel, Ralf and Mosses, Peter D. and Steimann, Friedrich},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/OASIcs.EVCS.2023.5},
  URN =		{urn:nbn:de:0030-drops-177756},
  doi =		{10.4230/OASIcs.EVCS.2023.5},
  annote =	{Keywords: language workbench, domain-specific language}
}
Document
Consistent Query Answering for Primary Keys and Conjunctive Queries with Counting

Authors: Aziz Amezian El Khalfioui and Jef Wijsen

Published in: LIPIcs, Volume 255, 26th International Conference on Database Theory (ICDT 2023)


Abstract
The problem of consistent query answering for primary keys and self-join-free conjunctive queries has been intensively studied in recent years and is by now well understood. In this paper, we study an extension of this problem with counting. The queries we consider count how many times each value occurs in a designated (possibly composite) column of an answer to a full conjunctive query. In a setting of database repairs, we adopt the semantics of [Arenas et al., ICDT 2001] which computes tight lower and upper bounds on these counts, where the bounds are taken over all repairs. Ariel Fuxman defined in his PhD thesis a syntactic class of queries, called Cforest, for which this computation can be done by executing two first-order queries (one for lower bounds, and one for upper bounds) followed by simple counting steps. We use the term "parsimonious counting" for this computation. A natural question is whether Cforest contains all self-join-free conjunctive queries that admit parsimonious counting. We answer this question negatively. We define a new syntactic class of queries, called Cparsimony, and prove that it contains all (and only) self-join-free conjunctive queries that admit parsimonious counting.

Cite as

Aziz Amezian El Khalfioui and Jef Wijsen. Consistent Query Answering for Primary Keys and Conjunctive Queries with Counting. In 26th International Conference on Database Theory (ICDT 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 255, pp. 23:1-23:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{amezianelkhalfioui_et_al:LIPIcs.ICDT.2023.23,
  author =	{Amezian El Khalfioui, Aziz and Wijsen, Jef},
  title =	{{Consistent Query Answering for Primary Keys and Conjunctive Queries with Counting}},
  booktitle =	{26th International Conference on Database Theory (ICDT 2023)},
  pages =	{23:1--23:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-270-9},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{255},
  editor =	{Geerts, Floris and Vandevoort, Brecht},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ICDT.2023.23},
  URN =		{urn:nbn:de:0030-drops-177659},
  doi =		{10.4230/LIPIcs.ICDT.2023.23},
  annote =	{Keywords: Consistent query answering, primary key, conjunctive query, aggregation, counting}
}
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