39 Search Results for "Martin, Russell"

Document
DOI: 10.4230/OASIcs.ICPEC.2024.5
Kumon-Inspired Approach to Teaching Programming Fundamentals

Authors: Ivone Amorim, Pedro Baltazar Vasconcelos, and João Pedro Pedroso

Published in: OASIcs, Volume 122, 5th International Computer Programming Education Conference (ICPEC 2024)

Abstract
Integration of introductory programming into higher education programs beyond computer science has lead to an increase in the failure and drop out rates of programming courses. In this context, programming instructors have explored new methodologies by introducing dynamic elements in the teaching-learning process, such as automatic code evaluation systems and gamification. Even though these methods have shown to be successful in improving students' engagement, they do not address all the existing problems and new strategies should be explored. In this work, we propose a new approach that combines the strengths of the Kumon method for personalized learning and progressive skill acquisition with the ability of online judge systems to provide automated assessment and immediate feedback. This approach has been used in teaching Programming I to students in several bachelor degrees and led to a 10% increase in exam approval rates compared to the baseline editions in which our Kumon-inspired methodology was not implemented.
Cite as

Ivone Amorim, Pedro Baltazar Vasconcelos, and João Pedro Pedroso. Kumon-Inspired Approach to Teaching Programming Fundamentals. In 5th International Computer Programming Education Conference (ICPEC 2024). Open Access Series in Informatics (OASIcs), Volume 122, pp. 5:1-5:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{amorim_et_al:OASIcs.ICPEC.2024.5,
  author =	{Amorim, Ivone and Vasconcelos, Pedro Baltazar and Pedroso, Jo\~{a}o Pedro},
  title =	{{Kumon-Inspired Approach to Teaching Programming Fundamentals}},
  booktitle =	{5th International Computer Programming Education Conference (ICPEC 2024)},
  pages =	{5:1--5:13},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-347-8},
  ISSN =	{2190-6807},
  year =	{2024},
  volume =	{122},
  editor =	{Santos, Andr\'{e} L. and Pinto-Albuquerque, Maria},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.ICPEC.2024.5},
  URN =		{urn:nbn:de:0030-drops-209749},
  doi =		{10.4230/OASIcs.ICPEC.2024.5},
  annote =	{Keywords: Programming teaching, Programming education, Kumon method, Progressive learning, Online judge system}
}
Document
DOI: 10.4230/LIPIcs.ESA.2024.3
From Donkeys to Kings in Tournaments

Authors: Amir Abboud, Tomer Grossman, Moni Naor, and Tomer Solomon

Published in: LIPIcs, Volume 308, 32nd Annual European Symposium on Algorithms (ESA 2024)

Abstract
A tournament is an orientation of a complete graph. A vertex that can reach every other vertex within two steps is called a king. We study the complexity of finding k kings in a tournament graph. We show that the randomized query complexity of finding k ≤ 3 kings is O(n), and for the deterministic case it takes the same amount of queries (up to a constant) as finding a single king (the best known deterministic algorithm makes O(n^{3/2}) queries). On the other hand, we show that finding k ≥ 4 kings requires Ω(n²) queries, even in the randomized case. We consider the RAM model for k ≥ 4. We show an algorithm that finds k kings in time O(kn²), which is optimal for constant values of k. Alternatively, one can also find k ≥ 4 kings in time n^{ω} (the time for matrix multiplication). We provide evidence that this is optimal for large k by suggesting a fine-grained reduction from a variant of the triangle detection problem.
Cite as

Amir Abboud, Tomer Grossman, Moni Naor, and Tomer Solomon. From Donkeys to Kings in Tournaments. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 3:1-3:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{abboud_et_al:LIPIcs.ESA.2024.3,
  author =	{Abboud, Amir and Grossman, Tomer and Naor, Moni and Solomon, Tomer},
  title =	{{From Donkeys to Kings in Tournaments}},
  booktitle =	{32nd Annual European Symposium on Algorithms (ESA 2024)},
  pages =	{3:1--3:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-338-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{308},
  editor =	{Chan, Timothy and Fischer, Johannes and Iacono, John and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2024.3},
  URN =		{urn:nbn:de:0030-drops-210740},
  doi =		{10.4230/LIPIcs.ESA.2024.3},
  annote =	{Keywords: Tournament Graphs, Kings, Query Complexity, Fine Grained Complexity}
}
Document
DOI: 10.4230/LIPIcs.ESA.2024.51
Better Diameter Algorithms for Bounded VC-Dimension Graphs and Geometric Intersection Graphs

Authors: Lech Duraj, Filip Konieczny, and Krzysztof Potępa

Published in: LIPIcs, Volume 308, 32nd Annual European Symposium on Algorithms (ESA 2024)

Abstract
We develop a framework for algorithms finding the diameter in graphs of bounded distance Vapnik-Chervonenkis dimension, in (parameterized) subquadratic time complexity. The class of bounded distance VC-dimension graphs is wide, including, e.g. all minor-free graphs. We build on the work of Ducoffe et al. [SODA'20, SIGCOMP'22], improving their technique. With our approach the algorithms become simpler and faster, working in 𝒪{(k ⋅ n^{1-1/d} ⋅ m ⋅ polylog(n))} time complexity for the graph on n vertices and m edges, where k is the diameter and d is the distance VC-dimension of the graph. Furthermore, it allows us to use the improved technique in more general setting. In particular, we use this framework for geometric intersection graphs, i.e. graphs where vertices are identical geometric objects on a plane and the adjacency is defined by intersection. Applying our approach for these graphs, we partially answer a question posed by Bringmann et al. [SoCG'22], finding an 𝒪{(n^{7/4} ⋅ polylog(n))} parameterized diameter algorithm for unit square intersection graph of size n, as well as a more general algorithm for convex polygon intersection graphs.
Cite as

Lech Duraj, Filip Konieczny, and Krzysztof Potępa. Better Diameter Algorithms for Bounded VC-Dimension Graphs and Geometric Intersection Graphs. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 51:1-51:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{duraj_et_al:LIPIcs.ESA.2024.51,
  author =	{Duraj, Lech and Konieczny, Filip and Pot\k{e}pa, Krzysztof},
  title =	{{Better Diameter Algorithms for Bounded VC-Dimension Graphs and Geometric Intersection Graphs}},
  booktitle =	{32nd Annual European Symposium on Algorithms (ESA 2024)},
  pages =	{51:1--51:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-338-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{308},
  editor =	{Chan, Timothy and Fischer, Johannes and Iacono, John and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2024.51},
  URN =		{urn:nbn:de:0030-drops-211229},
  doi =		{10.4230/LIPIcs.ESA.2024.51},
  annote =	{Keywords: Graph Diameter, Geometric Intersection Graphs, Vapnik-Chervonenkis Dimension}
}
Document
DOI: 10.4230/LIPIcs.ESA.2024.102
SubModST: A Fast Generic Solver for Submodular Maximization with Size Constraints

Authors: Henning Martin Woydt, Christian Komusiewicz, and Frank Sommer

Published in: LIPIcs, Volume 308, 32nd Annual European Symposium on Algorithms (ESA 2024)

Abstract
In the Cardinality-Constrained Maximization (Minimization) problem the input is a universe 𝒰, a function f: 2^{{𝒰}} → ℝ, and an integer k, and the task is to find a set S ⊆ 𝒰 with |S| ≤ k that maximizes (minimizes) f(S). Many well-studied problems such as Facility Location, Partial Dominating Set, Group Closeness Centrality and Euclidean k-Medoid Clustering are special cases of Cardinality-Constrained Maximization (Minimization). All the above-mentioned problems have the diminishing return property, that is, the improvement of adding an element e ∈ 𝒰 to a set S is at least as large as adding e to any superset of S. This property is called submodularity for maximization problems and supermodularity for minimization problems. In this work we develop a new exact branch-and-cut algorithm SubModST for the generic Submodular Cardinality-Constrained Maximization and Supermodular Cardinality-Constrained Minimization. We develop several speed-ups for SubModST and we show their effectiveness on six example problems. We show that SubModST outperforms the state-of-the-art solvers developed by Csókás and Vinkó [J. Glob. Optim. '24] and Uematsu et al. [J. Oper. Res. Soc. Japan '20] for Submodular Cardinality-Constrained Maximization by orders of magnitudes.
Cite as

Henning Martin Woydt, Christian Komusiewicz, and Frank Sommer. SubModST: A Fast Generic Solver for Submodular Maximization with Size Constraints. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 102:1-102:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{woydt_et_al:LIPIcs.ESA.2024.102,
  author =	{Woydt, Henning Martin and Komusiewicz, Christian and Sommer, Frank},
  title =	{{SubModST: A Fast Generic Solver for Submodular Maximization with Size Constraints}},
  booktitle =	{32nd Annual European Symposium on Algorithms (ESA 2024)},
  pages =	{102:1--102:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-338-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{308},
  editor =	{Chan, Timothy and Fischer, Johannes and Iacono, John and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2024.102},
  URN =		{urn:nbn:de:0030-drops-211730},
  doi =		{10.4230/LIPIcs.ESA.2024.102},
  annote =	{Keywords: Branch-and-Cut, Lazy Evaluations, Facility Location, Group Closeness Centrality, Partial Dominating Set}
}
Document
DOI: 10.4230/LIPIcs.AFT.2024.30
Profitable Manipulations of Cryptographic Self-Selection Are Statistically Detectable

Authors: Linda Cai, Jingyi Liu, S. Matthew Weinberg, and Chenghan Zhou

Published in: LIPIcs, Volume 316, 6th Conference on Advances in Financial Technologies (AFT 2024)

Abstract
Cryptographic Self-Selection is a common primitive underlying leader-selection for Proof-of-Stake blockchain protocols. The concept was first popularized in Algorand [Jing Chen and Silvio Micali, 2019], who also observed that the protocol might be manipulable. [Matheus V. X. Ferreira et al., 2022] provide a concrete manipulation that is strictly profitable for a staker of any size (and also prove upper bounds on the gains from manipulation). Separately, [Maryam Bahrani and S. Matthew Weinberg, 2024; Aviv Yaish et al., 2023] initiate the study of undetectable profitable manipulations of consensus protocols with a focus on the seminal Selfish Mining strategy [Eyal and Sirer, 2014] for Bitcoin’s Proof-of-Work longest-chain protocol. They design a Selfish Mining variant that, for sufficiently large miners, is strictly profitable yet also indistinguishable to an onlooker from routine latency (that is, a sufficiently large profit-maximizing miner could use their strategy to strictly profit over being honest in a way that still appears to the rest of the network as though everyone is honest but experiencing mildly higher latency. This avoids any risk of negatively impacting the value of the underlying cryptocurrency due to attack detection). We investigate the detectability of profitable manipulations of the canonical cryptographic self-selection leader selection protocol introduced in [Jing Chen and Silvio Micali, 2019] and studied in [Matheus V. X. Ferreira et al., 2022], and establish that for any player with α < (3-√5)/2 ≈ 0.38 fraction of the total stake, every strictly profitable manipulation is statistically detectable. Specifically, we consider an onlooker who sees only the random seed of each round (and does not need to see any other broadcasts by any other players). We show that the distribution of the sequence of random seeds when any player is profitably manipulating the protocol is inconsistent with any distribution that could arise by honest stakers being offline or timing out (for a natural stylized model of honest timeouts).
Cite as

Linda Cai, Jingyi Liu, S. Matthew Weinberg, and Chenghan Zhou. Profitable Manipulations of Cryptographic Self-Selection Are Statistically Detectable. In 6th Conference on Advances in Financial Technologies (AFT 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 316, pp. 30:1-30:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{cai_et_al:LIPIcs.AFT.2024.30,
  author =	{Cai, Linda and Liu, Jingyi and Weinberg, S. Matthew and Zhou, Chenghan},
  title =	{{Profitable Manipulations of Cryptographic Self-Selection Are Statistically Detectable}},
  booktitle =	{6th Conference on Advances in Financial Technologies (AFT 2024)},
  pages =	{30:1--30:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-345-4},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{316},
  editor =	{B\"{o}hme, Rainer and Kiffer, Lucianna},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.AFT.2024.30},
  URN =		{urn:nbn:de:0030-drops-209660},
  doi =		{10.4230/LIPIcs.AFT.2024.30},
  annote =	{Keywords: Blockchain, Cryptocurrency, Proof-of-Stake, Strategic Mining, Statistical Detection}
}
Document
RANDOM
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2024.56
Fast and Slow Mixing of the Kawasaki Dynamics on Bounded-Degree Graphs

Authors: Aiya Kuchukova, Marcus Pappik, Will Perkins, and Corrine Yap

Published in: LIPIcs, Volume 317, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2024)

Abstract
We study the worst-case mixing time of the global Kawasaki dynamics for the fixed-magnetization Ising model on the class of graphs of maximum degree Δ. Proving a conjecture of Carlson, Davies, Kolla, and Perkins, we show that below the tree uniqueness threshold, the Kawasaki dynamics mix rapidly for all magnetizations. Disproving a conjecture of Carlson, Davies, Kolla, and Perkins, we show that the regime of fast mixing does not extend throughout the regime of tractability for this model: there is a range of parameters for which there exist efficient sampling algorithms for the fixed-magnetization Ising model on max-degree Δ graphs, but the Kawasaki dynamics can take exponential time to mix. Our techniques involve showing spectral independence in the fixed-magnetization Ising model and proving a sharp threshold for the existence of multiple metastable states in the Ising model with external field on random regular graphs.
Cite as

Aiya Kuchukova, Marcus Pappik, Will Perkins, and Corrine Yap. Fast and Slow Mixing of the Kawasaki Dynamics on Bounded-Degree Graphs. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 317, pp. 56:1-56:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{kuchukova_et_al:LIPIcs.APPROX/RANDOM.2024.56,
  author =	{Kuchukova, Aiya and Pappik, Marcus and Perkins, Will and Yap, Corrine},
  title =	{{Fast and Slow Mixing of the Kawasaki Dynamics on Bounded-Degree Graphs}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2024)},
  pages =	{56:1--56:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-348-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{317},
  editor =	{Kumar, Amit and Ron-Zewi, Noga},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX/RANDOM.2024.56},
  URN =		{urn:nbn:de:0030-drops-210493},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2024.56},
  annote =	{Keywords: ferromagnetic Ising model, fixed-magnetization Ising model, Kawasaki dynamics, Glauber dynamics, mixing time}
}
Document
DOI: 10.4230/LIPIcs.AFT.2024.14
SoK: Zero-Knowledge Range Proofs

Authors: Miranda Christ, Foteini Baldimtsi, Konstantinos Kryptos Chalkias, Deepak Maram, Arnab Roy, and Joy Wang

Published in: LIPIcs, Volume 316, 6th Conference on Advances in Financial Technologies (AFT 2024)

Abstract
Zero-knowledge range proofs (ZKRPs) allow a prover to convince a verifier that a secret value lies in a given interval. ZKRPs have numerous applications: from anonymous credentials and auctions, to confidential transactions in cryptocurrencies. At the same time, a plethora of ZKRP constructions exist in the literature, each with its own trade-offs. In this work, we systematize the knowledge around ZKRPs. We create a classification of existing constructions based on the underlying building techniques, and we summarize their properties. We provide comparisons between schemes both in terms of properties as well as efficiency levels, and construct a guideline to assist in the selection of an appropriate ZKRP for different application requirements. Finally, we discuss a number of interesting open research problems.
Cite as

Miranda Christ, Foteini Baldimtsi, Konstantinos Kryptos Chalkias, Deepak Maram, Arnab Roy, and Joy Wang. SoK: Zero-Knowledge Range Proofs. In 6th Conference on Advances in Financial Technologies (AFT 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 316, pp. 14:1-14:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{christ_et_al:LIPIcs.AFT.2024.14,
  author =	{Christ, Miranda and Baldimtsi, Foteini and Chalkias, Konstantinos Kryptos and Maram, Deepak and Roy, Arnab and Wang, Joy},
  title =	{{SoK: Zero-Knowledge Range Proofs}},
  booktitle =	{6th Conference on Advances in Financial Technologies (AFT 2024)},
  pages =	{14:1--14:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-345-4},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{316},
  editor =	{B\"{o}hme, Rainer and Kiffer, Lucianna},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.AFT.2024.14},
  URN =		{urn:nbn:de:0030-drops-209504},
  doi =		{10.4230/LIPIcs.AFT.2024.14},
  annote =	{Keywords: Range proofs, zero knowledge}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2024.20
Taking a Closer Look: An Outlier-Driven Approach to Compilation-Time Optimization

Authors: Florian Huemer, David Leopoldseder, Aleksandar Prokopec, Raphael Mosaner, and Hanspeter Mössenböck

Published in: LIPIcs, Volume 313, 38th European Conference on Object-Oriented Programming (ECOOP 2024)

Abstract
Improving compilation time in optimizing compilers is challenging due to their large number of interconnected components. This includes compiler optimizations, compiler tiers, heuristics, and profiling information. Despite this complexity, research in compilation-time optimization is often guided by analyzing metrics of entire program runs, such as the total compilation time and overall memory footprint. This coarse-grained perspective hides relevant information, such as source program functions for which the compiler allocates a lot of memory or compiler optimizations with a high impact on the total compilation time. This leaves high-level metrics as the only reference point for driving optimization design. Consequently, compilation-time regressions in one program function that are obscured by improvements in other functions stay undetected, while the impacts of compiler changes on untouched parts of the compiler are mainly unknown. Furthermore, developers overlook long-standing compiler defects because their high-level metrics do not change over time. To address these limitations, we propose ICON, a new data-driven approach to compilation-time optimization that breaks up high-level metrics into individual source program functions, compiler optimizations, or even into individual instructions in the compiler source code. Our methodology enables an iterative in-depth compilation-time analysis, focusing on outliers to identify optimization opportunities. We show that outliers, both in terms of time spent in a particular compiler optimization, and in terms of individual compilations that take substantially longer, can reveal potential problems in the compiler implementation. We applied our approach to GraalVM and extracted data for multiple of its language runtimes. We analyzed the resulting data, present the first detailed look into the distribution of compilation time in the GraalVM compiler, a state-of-the-art multi-language compiler, and identified defects that led to regressions in overall compilation time or the compilation time of specific languages. We furthermore designed two optimizations based on the identified outliers that improve compilation time between 2.25% and 9.45%. We believe that our approach can guide compiler developers in finding usually overlooked optimization potential and defects, and focus future research efforts in making compilers more efficient.
Cite as

Florian Huemer, David Leopoldseder, Aleksandar Prokopec, Raphael Mosaner, and Hanspeter Mössenböck. Taking a Closer Look: An Outlier-Driven Approach to Compilation-Time Optimization. In 38th European Conference on Object-Oriented Programming (ECOOP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 313, pp. 20:1-20:28, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{huemer_et_al:LIPIcs.ECOOP.2024.20,
  author =	{Huemer, Florian and Leopoldseder, David and Prokopec, Aleksandar and Mosaner, Raphael and M\"{o}ssenb\"{o}ck, Hanspeter},
  title =	{{Taking a Closer Look: An Outlier-Driven Approach to Compilation-Time Optimization}},
  booktitle =	{38th European Conference on Object-Oriented Programming (ECOOP 2024)},
  pages =	{20:1--20:28},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-341-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{313},
  editor =	{Aldrich, Jonathan and Salvaneschi, Guido},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2024.20},
  URN =		{urn:nbn:de:0030-drops-208693},
  doi =		{10.4230/LIPIcs.ECOOP.2024.20},
  annote =	{Keywords: Compilation time, outliers, dynamic languages, virtual machines, GraalVM, ICON}
}
Document
DOI: 10.4230/LIPIcs.DNA.30.2
Domain-Based Nucleic-Acid Minimum Free Energy: Algorithmic Hardness and Parameterized Bounds

Authors: Erik D. Demaine, Timothy Gomez, Elise Grizzell, Markus Hecher, Jayson Lynch, Robert Schweller, Ahmed Shalaby, and Damien Woods

Published in: LIPIcs, Volume 314, 30th International Conference on DNA Computing and Molecular Programming (DNA 30) (2024)

Abstract
Molecular programmers and nanostructure engineers use domain-level design to abstract away messy DNA/RNA sequence, chemical and geometric details. Such domain-level abstractions are enforced by sequence design principles and provide a key principle that allows scaling up of complex multistranded DNA/RNA programs and structures. Determining the most favoured secondary structure, or Minimum Free Energy (MFE), of a set of strands, is typically studied at the sequence level but has seen limited domain-level work. We analyse the computational complexity of MFE for multistranded systems in a simple setting were we allow only 1 or 2 domains per strand. On the one hand, with 2-domain strands, we find that the MFE decision problem is NP-complete, even without pseudoknots, and requires exponential time algorithms assuming SAT does. On the other hand, in the simplest case of 1-domain strands there are efficient MFE algorithms for various binding modes. However, even in this single-domain case, MFE is P-hard for promiscuous binding, where one domain may bind to multiple as experimentally used by Nikitin [Nat Chem., 2023], which in turn implies that strands consisting of a single domain efficiently implement arbitrary Boolean circuits.
Cite as

Erik D. Demaine, Timothy Gomez, Elise Grizzell, Markus Hecher, Jayson Lynch, Robert Schweller, Ahmed Shalaby, and Damien Woods. Domain-Based Nucleic-Acid Minimum Free Energy: Algorithmic Hardness and Parameterized Bounds. In 30th International Conference on DNA Computing and Molecular Programming (DNA 30). Leibniz International Proceedings in Informatics (LIPIcs), Volume 314, pp. 2:1-2:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{demaine_et_al:LIPIcs.DNA.30.2,
  author =	{Demaine, Erik D. and Gomez, Timothy and Grizzell, Elise and Hecher, Markus and Lynch, Jayson and Schweller, Robert and Shalaby, Ahmed and Woods, Damien},
  title =	{{Domain-Based Nucleic-Acid Minimum Free Energy: Algorithmic Hardness and Parameterized Bounds}},
  booktitle =	{30th International Conference on DNA Computing and Molecular Programming (DNA 30)},
  pages =	{2:1--2:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-344-7},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{314},
  editor =	{Seki, Shinnosuke and Stewart, Jaimie Marie},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.30.2},
  URN =		{urn:nbn:de:0030-drops-209304},
  doi =		{10.4230/LIPIcs.DNA.30.2},
  annote =	{Keywords: Domain-based DNA designs, minimum free energy, efficient algorithms, NP-hard, P-hard, NC, fixed-parameter tractable}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.14
A Unifying Taxonomy of Pattern Matching in Degenerate Strings and Founder Graphs

Authors: Rocco Ascone, Giulia Bernardini, Alessio Conte, Massimo Equi, Esteban Gabory, Roberto Grossi, and Nadia Pisanti

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
Elastic Degenerate (ED) strings and Elastic Founder (EF) graphs are two versions of acyclic components of pangenomes. Both ED strings and EF graphs (which we collectively name variable strings) extend the well-known notion of indeterminate string. Recent work has extensively investigated algorithmic tasks over these structures, and over several other variable strings notions that they generalise. Among such tasks, the basic operation of matching a pattern into a text, which can serve as a toolkit for many pangenomic data analyses using these data structures, deserves special attention. In this paper we: (1) highlight a clear taxonomy within both ED strings and EF graphs ranging through variable strings of all types, from the linear string up to the most general one; (2) investigate the problem PvarT(X,Y) of matching a solid or variable pattern of type X into a variable text of type Y; (3) using as a reference the quadratic conditional lower bounds that are known for PvarT(solid,ED) and PvarT(solid,EF), for all possible types of variable strings X and Y we either prove the quadratic conditional lower bound for PvarT(X,Y), or provide non-trivial, often sub-quadratic, upper bounds, also exploiting the above-mentioned taxonomy.
Cite as

Rocco Ascone, Giulia Bernardini, Alessio Conte, Massimo Equi, Esteban Gabory, Roberto Grossi, and Nadia Pisanti. A Unifying Taxonomy of Pattern Matching in Degenerate Strings and Founder Graphs. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 14:1-14:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{ascone_et_al:LIPIcs.WABI.2024.14,
  author =	{Ascone, Rocco and Bernardini, Giulia and Conte, Alessio and Equi, Massimo and Gabory, Esteban and Grossi, Roberto and Pisanti, Nadia},
  title =	{{A Unifying Taxonomy of Pattern Matching in Degenerate Strings and Founder Graphs}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{14:1--14:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.14},
  URN =		{urn:nbn:de:0030-drops-206586},
  doi =		{10.4230/LIPIcs.WABI.2024.14},
  annote =	{Keywords: Pangenomics, pattern matching, degenerate string, founder graph, fine-grained complexity}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.17
A*PA2: Up to 19× Faster Exact Global Alignment

Authors: Ragnar Groot Koerkamp

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
Motivation. Pairwise alignment is at the core of computational biology. Most commonly used exact methods are either based on O(ns) band doubling or O(n+s²) diagonal transition, where n is the sequence length and s the number of errors. However, as the length of sequences has grown, these exact methods are often replaced by approximate methods based on e.g. seed-and-extend and heuristics to bound the computed region. We would like to develop an exact method that matches the performance of these approximate methods. Recently, Astarix introduced the A* shortest path algorithm with the seed heuristic for exact sequence-to-graph alignment. A*PA adapted and improved this for pairwise sequence alignment and achieves near-linear runtime when divergence (error rate) is low, at the cost of being very slow when divergence is high. Methods. We introduce A*PA2, an exact global pairwise aligner with respect to edit distance. The goal of A*PA2 is to unify the near-linear runtime of A*PA on similar sequences with the efficiency of dynamic programming (DP) based methods. Like Edlib, A*PA2 uses Ukkonen’s band doubling in combination with Myers' bitpacking. A*PA2 1) uses large block sizes inspired by Block Aligner, 2) extends this with SIMD (single instruction, multiple data), 3) introduces a new profile for efficient computations, 4) introduces a new optimistic technique for traceback based on diagonal transition, 5) avoids recomputation of states where possible, and 6) applies the heuristics developed in A*PA and improves them using pre-pruning. Results. With the first 4 engineering optimizations, A*PA2-simple has complexity O(ns) and is 6× to 8× faster than Edlib for sequences ≥ 10 kbp. A*PA2-full also includes the heuristic and is often near-linear in practice for sequences with small divergence. The average runtime of A*PA2 is 19× faster than the exact aligners BiWFA and Edlib on >500 kbp long ONT (Oxford Nanopore Technologies) reads of a human genome having 6% divergence on average. On shorter ONT reads of 11% average divergence the speedup is 5.6× (avg. length 11 kbp) and 0.81× (avg. length 800 bp). On all tested datasets, A*PA2 is competitive with or faster than approximate methods.
Cite as

Ragnar Groot Koerkamp. A*PA2: Up to 19× Faster Exact Global Alignment. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 17:1-17:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{grootkoerkamp:LIPIcs.WABI.2024.17,
  author =	{Groot Koerkamp, Ragnar},
  title =	{{A*PA2: Up to 19× Faster Exact Global Alignment}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{17:1--17:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.17},
  URN =		{urn:nbn:de:0030-drops-206610},
  doi =		{10.4230/LIPIcs.WABI.2024.17},
  annote =	{Keywords: Edit distance, Pairwise alignment, A*, Shortest path, Dynamic programming}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.11
The mod-minimizer: A Simple and Efficient Sampling Algorithm for Long k-mers

Authors: Ragnar Groot Koerkamp and Giulio Ermanno Pibiri

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
Motivation. Given a string S, a minimizer scheme is an algorithm defined by a triple (k,w,𝒪) that samples a subset of k-mers (k-long substrings) from a string S. Specifically, it samples the smallest k-mer according to the order 𝒪 from each window of w consecutive k-mers in S. Because consecutive windows can sample the same k-mer, the set of the sampled k-mers is typically much smaller than S. More generally, we consider substring sampling algorithms that respect a window guarantee: at least one k-mer must be sampled from every window of w consecutive k-mers. As a sampled k-mer is uniquely identified by its absolute position in S, we can define the density of a sampling algorithm as the fraction of distinct sampled positions. Good methods have low density which, by respecting the window guarantee, is lower bounded by 1/w. It is however difficult to design a sequence-agnostic algorithm with provably optimal density. In practice, the order 𝒪 is usually implemented using a pseudo-random hash function to obtain the so-called random minimizer. This scheme is simple to implement, very fast to compute even in streaming fashion, and easy to analyze. However, its density is almost a factor of 2 away from the lower bound for large windows. Methods. In this work we introduce mod-sampling, a two-step sampling algorithm to obtain new minimizer schemes. Given a (small) parameter t, the mod-sampling algorithm finds the position p of the smallest t-mer in a window. It then samples the k-mer at position pod w. The lr-minimizer uses t = k-w and the mod-minimizer uses t≡ k (mod w). Results. These new schemes have provably lower density than random minimizers and other schemes when k is large compared to w, while being as fast to compute. Importantly, the mod-minimizer achieves optimal density when k → ∞. Although the mod-minimizer is not the first method to achieve optimal density for large k, its proof of optimality is simpler than previous work. We provide pseudocode for a number of other methods and compare to them. In practice, the mod-minimizer has considerably lower density than the random minimizer and other state-of-the-art methods, like closed syncmers and miniception, when k > w. We plugged the mod-minimizer into SSHash, a k-mer dictionary based on minimizers. For default parameters (w,k) = (11,21), space usage decreases by 15% when indexing the whole human genome (GRCh38), while maintaining its fast query time.
Cite as

Ragnar Groot Koerkamp and Giulio Ermanno Pibiri. The mod-minimizer: A Simple and Efficient Sampling Algorithm for Long k-mers. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 11:1-11:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{grootkoerkamp_et_al:LIPIcs.WABI.2024.11,
  author =	{Groot Koerkamp, Ragnar and Pibiri, Giulio Ermanno},
  title =	{{The mod-minimizer: A Simple and Efficient Sampling Algorithm for Long k-mers}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{11:1--11:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.11},
  URN =		{urn:nbn:de:0030-drops-206552},
  doi =		{10.4230/LIPIcs.WABI.2024.11},
  annote =	{Keywords: Minimizers, Randomized algorithms, Sketching, Hashing}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2024.29
Equitable Connected Partition and Structural Parameters Revisited: N-Fold Beats Lenstra

Authors: Václav Blažej, Dušan Knop, Jan Pokorný, and Šimon Schierreich

Published in: LIPIcs, Volume 306, 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)

Abstract
In the Equitable Connected Partition (ECP for short) problem, we are given a graph G = (V,E) together with an integer p ∈ ℕ, and our goal is to find a partition of V into p parts such that each part induces a connected sub-graph of G and the size of each two parts differs by at most 1. On the one hand, the problem is known to be NP-hard in general and W[1]-hard with respect to the path-width, the feedback-vertex set, and the number of parts p combined. On the other hand, fixed-parameter algorithms are known for parameters the vertex-integrity and the max leaf number. In this work, we systematically study ECP with respect to various structural restrictions of the underlying graph and provide a clear dichotomy of its parameterised complexity. Specifically, we show that the problem is in FPT when parameterized by the modular-width and the distance to clique. Next, we prove W[1]-hardness with respect to the distance to cluster, the 4-path vertex cover number, the distance to disjoint paths, and the feedback-edge set, and NP-hardness for constant shrub-depth graphs. Our hardness results are complemented by matching algorithmic upper-bounds: we give an XP algorithm for parameterisation by the tree-width and the distance to cluster. We also give an improved FPT algorithm for parameterisation by the vertex integrity and the first explicit FPT algorithm for the 3-path vertex cover number. The main ingredient of these algorithms is a formulation of ECP as N-fold IP, which clearly indicates that such formulations may, in certain scenarios, significantly outperform existing algorithms based on the famous algorithm of Lenstra.
Cite as

Václav Blažej, Dušan Knop, Jan Pokorný, and Šimon Schierreich. Equitable Connected Partition and Structural Parameters Revisited: N-Fold Beats Lenstra. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 29:1-29:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{blazej_et_al:LIPIcs.MFCS.2024.29,
  author =	{Bla\v{z}ej, V\'{a}clav and Knop, Du\v{s}an and Pokorn\'{y}, Jan and Schierreich, \v{S}imon},
  title =	{{Equitable Connected Partition and Structural Parameters Revisited: N-Fold Beats Lenstra}},
  booktitle =	{49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)},
  pages =	{29:1--29:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-335-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{306},
  editor =	{Kr\'{a}lovi\v{c}, Rastislav and Ku\v{c}era, Anton{\'\i}n},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2024.29},
  URN =		{urn:nbn:de:0030-drops-205857},
  doi =		{10.4230/LIPIcs.MFCS.2024.29},
  annote =	{Keywords: Equitable Connected Partition, structural parameters, fixed-parameter tractability, N-fold integer programming, tree-width, shrub-depth, modular-width}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2024.60
On the Complexity of Community-Aware Network Sparsification

Authors: Emanuel Herrendorf, Christian Komusiewicz, Nils Morawietz, and Frank Sommer

Published in: LIPIcs, Volume 306, 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)

Abstract
In the NP-hard Π-Network Sparsification problem, we are given an edge-weighted graph G, a collection 𝒞 of c subsets of V(G), called communities, and two numbers 𝓁 and b, and the question is whether there exists a spanning subgraph G' of G with at most 𝓁 edges of total weight at most b such that G'[C] fulfills Π for each community C ∈ 𝒞. We study the fine-grained and parameterized complexity of two special cases of this problem: Connectivity NWS where Π is the connectivity property and Stars NWS, where Π is the property of having a spanning star. First, we provide a tight 2^Ω(n²+c)-time running time lower bound based on the ETH for both problems, where n is the number of vertices in G even if all communities have size at most 4, G is a clique, and every edge has unit weight. For the connectivity property, the unit weight case with G being a clique is the well-studied problem of computing a hypergraph support with a minimum number of edges. We then study the complexity of both problems parameterized by the feedback edge number t of the solution graph G'. For Stars NWS, we present an XP-algorithm for t answering an open question by Korach and Stern [Discret. Appl. Math. '08] who asked for the existence of polynomial-time algorithms for t = 0. In contrast, we show for Connectivity NWS that known polynomial-time algorithms for t = 0 [Korach and Stern, Math. Program. '03; Klemz et al., SWAT '14] cannot be extended to larger values of t by showing NP-hardness for t = 1.
Cite as

Emanuel Herrendorf, Christian Komusiewicz, Nils Morawietz, and Frank Sommer. On the Complexity of Community-Aware Network Sparsification. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 60:1-60:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{herrendorf_et_al:LIPIcs.MFCS.2024.60,
  author =	{Herrendorf, Emanuel and Komusiewicz, Christian and Morawietz, Nils and Sommer, Frank},
  title =	{{On the Complexity of Community-Aware Network Sparsification}},
  booktitle =	{49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)},
  pages =	{60:1--60:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-335-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{306},
  editor =	{Kr\'{a}lovi\v{c}, Rastislav and Ku\v{c}era, Anton{\'\i}n},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2024.60},
  URN =		{urn:nbn:de:0030-drops-206169},
  doi =		{10.4230/LIPIcs.MFCS.2024.60},
  annote =	{Keywords: parameterized complexity, hypergraph support, above guarantee parameterization, exponential-time-hypothesis}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2024.78
C_{2k+1}-Coloring of Bounded-Diameter Graphs

Authors: Marta Piecyk

Published in: LIPIcs, Volume 306, 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)

Abstract
For a fixed graph H, in the graph homomorphism problem, denoted by Hom(H), we are given a graph G and we have to determine whether there exists an edge-preserving mapping φ: V(G) → V(H). Note that Hom(C₃), where C₃ is the cycle of length 3, is equivalent to 3-Coloring. The question of whether 3-Coloring is polynomial-time solvable on diameter-2 graphs is a well-known open problem. In this paper we study the Hom(C_{2k+1}) problem on bounded-diameter graphs for k ≥ 2, so we consider all other odd cycles than C₃. We prove that for k ≥ 2, the Hom(C_{2k+1}) problem is polynomial-time solvable on diameter-(k+1) graphs - note that such a result for k = 1 would be precisely a polynomial-time algorithm for 3-Coloring of diameter-2 graphs. Furthermore, we give subexponential-time algorithms for diameter-(k+2) and -(k+3) graphs. We complement these results with a lower bound for diameter-(2k+2) graphs - in this class of graphs the Hom(C_{2k+1}) problem is NP-hard and cannot be solved in subexponential-time, unless the ETH fails. Finally, we consider another direction of generalizing 3-Coloring on diameter-2 graphs. We consider other target graphs H than odd cycles but we restrict ourselves to diameter 2. We show that if H is triangle-free, then Hom(H) is polynomial-time solvable on diameter-2 graphs.
Cite as

Marta Piecyk. C_{2k+1}-Coloring of Bounded-Diameter Graphs. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 78:1-78:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{piecyk:LIPIcs.MFCS.2024.78,
  author =	{Piecyk, Marta},
  title =	{{C\underline\{2k+1\}-Coloring of Bounded-Diameter Graphs}},
  booktitle =	{49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)},
  pages =	{78:1--78:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-335-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{306},
  editor =	{Kr\'{a}lovi\v{c}, Rastislav and Ku\v{c}era, Anton{\'\i}n},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2024.78},
  URN =		{urn:nbn:de:0030-drops-206348},
  doi =		{10.4230/LIPIcs.MFCS.2024.78},
  annote =	{Keywords: graph homomorphism, odd cycles, diameter}
}
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