18 Search Results for "Hicks, Michael"

Document
DOI: 10.4230/LIPIcs.FORC.2026.10
Packing Compact Subgraphs with Applications to Districting

Authors: Ho-Lin Chen, Po-Yu Chou, Prathamesh Dharangutte, Jie Gao, Shang-En Huang, and Fang-Yi Yu

Published in: LIPIcs, Volume 368, 7th Symposium on Foundations of Responsible Computing (FORC 2026)

Abstract
Packing disjoint subgraphs in a given graph is a fundamental problem with many applications. Motivated by political districting, we focus on connected subgraphs that are compact (e.g., having constant radius from a single center vertex) and that satisfy additional composition requirements, such as a minimum population/weight threshold or balanced weight types (e.g., political affiliations). We aim to maximize coverage by disjoint districts that meet these requirements. In this work, we present new results that substantially improve the previously known bounds on balanced star districts for planar and minor-free graphs [Prathamesh Dharangutte et al., 2025]. In particular, we improve the approximation factor from O(log n) to O(1) for packing balanced star districts using the exact same algorithm, but with a refined analysis. We also extend the results beyond planar graphs to minor-free graphs and an even broader family of graphs of bounded expansion. Additionally, we obtain an O(1) approximation for packing radius-k districts (with a constant k) in planar and apex-minor-free graphs. In order to get a (1+ε) approximation on the max coverage, we show that this can be achieved if we allow a slight relaxation of the balancedness parameters (by a factor that can be made arbitrarily close to 1), for bounded radius-k districts on planar and apex-minor-free graphs. We show that all of these results can also be obtained if we enforce a minimum weight threshold for each district as the composition requirement, rather than balancedness. We present various results on hardness and hardness of approximation for this variant, by graph and district types.
Cite as

Ho-Lin Chen, Po-Yu Chou, Prathamesh Dharangutte, Jie Gao, Shang-En Huang, and Fang-Yi Yu. Packing Compact Subgraphs with Applications to Districting. In 7th Symposium on Foundations of Responsible Computing (FORC 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 368, pp. 10:1-10:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{chen_et_al:LIPIcs.FORC.2026.10,
  author =	{Chen, Ho-Lin and Chou, Po-Yu and Dharangutte, Prathamesh and Gao, Jie and Huang, Shang-En and Yu, Fang-Yi},
  title =	{{Packing Compact Subgraphs with Applications to Districting}},
  booktitle =	{7th Symposium on Foundations of Responsible Computing (FORC 2026)},
  pages =	{10:1--10:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-419-2},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{368},
  editor =	{Lin, Huijia (Rachel)},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FORC.2026.10},
  URN =		{urn:nbn:de:0030-drops-259820},
  doi =		{10.4230/LIPIcs.FORC.2026.10},
  annote =	{Keywords: Approximation algorithms, algorithmic fairness}
}
Document
DOI: 10.4230/LIPIcs.SoCG.2026.53
Constructing Doppelgängers of Greedy Geometric Spanners in Practice

Authors: Anirban Ghosh

Published in: LIPIcs, Volume 367, 42nd International Symposium on Computational Geometry (SoCG 2026)

Abstract
Greedy geometric spanners are considered to be the gold standard for their near-optimal guarantees in terms of sparsity and total weight. However, their inefficient construction poses significant challenges for large-scale geometric networks, especially for low values of stretch factors (< 2). We present Θ-Greedy, a simple and practical parallel algorithm engineered for constructing doppelgängers of greedy geometric spanners that empirically resemble the greedy spanners in key structural and performance metrics, including average degree, degree, and lightness. Unlike approximate greedy spanners, doppelgängers of greedy spanners are almost indistinguishable from the actual greedy spanners in practice. In our experiments, Θ-Greedy consistently produced greedy spanner doppelgängers across a broad range of synthetic and real-world datasets, offering the first practical alternative to the computationally intensive greedy spanners. Θ-Greedy can construct a 1.1-spanner on a 128K-element uniformly distributed point set in well under 5 minutes. In contrast, Bucketing, the most practical greedy spanner algorithm, takes around 3 hours. For million-sized point sets, Θ-Greedy can run to completion in a few hours, making it much faster than Bucketing, which takes days to finish. In extensive experiments on synthetic and real-world datasets, Θ-Greedy delivered speedups of up to 147x over Bucketing while preserving greedy-like sparsity and weight. For broader uses of the algorithm and reproducibility, we share our engineered C++ code.
Cite as

Anirban Ghosh. Constructing Doppelgängers of Greedy Geometric Spanners in Practice. In 42nd International Symposium on Computational Geometry (SoCG 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 367, pp. 53:1-53:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{ghosh:LIPIcs.SoCG.2026.53,
  author =	{Ghosh, Anirban},
  title =	{{Constructing Doppelg\"{a}ngers of Greedy Geometric Spanners in Practice}},
  booktitle =	{42nd International Symposium on Computational Geometry (SoCG 2026)},
  pages =	{53:1--53:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-418-5},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{367},
  editor =	{Ahn, Hee-Kap and Hoffmann, Michael and Nayyeri, Amir},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2026.53},
  URN =		{urn:nbn:de:0030-drops-258599},
  doi =		{10.4230/LIPIcs.SoCG.2026.53},
  annote =	{Keywords: geometric graph, geometric spanners, greedy spanners, algorithm engineering}
}
Document
DOI: 10.4230/LIPIcs.AFT.2025.21
Pool Formation in Oceanic Games: Shapley Value and Proportional Sharing

Authors: Aggelos Kiayias, Elias Koutsoupias, Evangelos Markakis, and Panagiotis Tsamopoulos

Published in: LIPIcs, Volume 354, 7th Conference on Advances in Financial Technologies (AFT 2025)

Abstract
We study a game-theoretic model for pool formation in Proof of Stake blockchain protocols. In such systems, stakeholders can form pools as a means of obtaining regular rewards from participation in ledger maintenance, with the power of each pool being dependent on its collective stake. The question we are interested in is the design of mechanisms, i.e., "reward sharing schemes," that suitably split rewards among pool members and achieve favorable properties in the resulting pool configuration. With this in mind, we initiate a non-cooperative game-theoretic analysis of the well known Shapley value scheme from cooperative game theory into the context of blockchains. In particular, we focus on the oceanic model of games, proposed by Milnor and Shapley (1978), which is suitable for populations where a small set of large players coexists with a big mass of rather small, negligible players. This provides an appropriate level of abstraction for pool formation processes that occur among the stakeholders of a blockchain. We provide comparisons between the Shapley mechanism and the more standard proportional scheme, in terms of attained decentralization, via a Price of Stability analysis and in terms of susceptibility to Sybil attacks, i.e., the strategic splitting of a players' stake with the intention of participating in multiple pools for increased profit. Interestingly, while the widely deployed proportional scheme appears to have certain advantages, the Shapley value scheme, which rewards higher the most pivotal players, emerges as a competitive alternative, by being able to bypass some of the downsides of proportional sharing in terms of Sybil attack susceptibility, while also not being far from optimal guarantees w.r.t. decentralization. Finally, we also complement our study with some variations of proportional sharing, where the profit is split in proportion to a superadditive or a subadditive function of the stake, showing that our results for the Shapley value scheme are maintained in comparison to these functions as well.
Cite as

Aggelos Kiayias, Elias Koutsoupias, Evangelos Markakis, and Panagiotis Tsamopoulos. Pool Formation in Oceanic Games: Shapley Value and Proportional Sharing. In 7th Conference on Advances in Financial Technologies (AFT 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 354, pp. 21:1-21:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{kiayias_et_al:LIPIcs.AFT.2025.21,
  author =	{Kiayias, Aggelos and Koutsoupias, Elias and Markakis, Evangelos and Tsamopoulos, Panagiotis},
  title =	{{Pool Formation in Oceanic Games: Shapley Value and Proportional Sharing}},
  booktitle =	{7th Conference on Advances in Financial Technologies (AFT 2025)},
  pages =	{21:1--21:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-400-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{354},
  editor =	{Avarikioti, Zeta and Christin, Nicolas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.AFT.2025.21},
  URN =		{urn:nbn:de:0030-drops-247409},
  doi =		{10.4230/LIPIcs.AFT.2025.21},
  annote =	{Keywords: Shapley value, Nash equilibria, Price of Stability, Reward sharing schemes, Proof of Stake blockchains}
}
Document
DOI: 10.4230/LIPIcs.AFT.2025.23
Transaction Fee Market Design for Parallel Execution

Authors: Bahar Acilan, Andrei Constantinescu, Lioba Heimbach, and Roger Wattenhofer

Published in: LIPIcs, Volume 354, 7th Conference on Advances in Financial Technologies (AFT 2025)

Abstract
Given the low throughput of blockchains like Bitcoin and Ethereum, scalability - the ability to process an increasing number of transactions - has become a central focus of blockchain research. One promising approach is the parallelization of transaction execution across multiple threads. However, achieving efficient parallelization requires a redesign of the incentive structure within the fee market. Currently, the fee market does not differentiate between transactions that access multiple high-demand storage keys (i.e., unique identifiers for individual data entries) versus a single low-demand one, as long as they require the same computational effort. Addressing this discrepancy is crucial for enabling more effective parallel execution. In this work, we aim to bridge the gap between the current fee market and the need for parallel execution by exploring alternative fee market designs. To this end, we propose a framework consisting of two key components: a Gas Computation Mechanism (GCM), which quantifies the load a transaction places on the network in terms of parallelization and computation, measured in units of gas, and a Transaction Fee Mechanism (TFM), which assigns a price to each unit of gas. We additionally introduce a set of desirable properties for a GCM, propose several candidate mechanisms, and evaluate them against these criteria. Our analysis highlights two strong candidates: the weighted area GCM, which integrates smoothly with existing TFMs such as EIP‑1559 and satisfies a broad subset of the outlined properties, and the time-proportional makespan GCM, which assigns gas costs based on the context of the entire block’s schedule and, through this dependence on the overall execution outcome, captures the dynamics of parallel execution more accurately.
Cite as

Bahar Acilan, Andrei Constantinescu, Lioba Heimbach, and Roger Wattenhofer. Transaction Fee Market Design for Parallel Execution. In 7th Conference on Advances in Financial Technologies (AFT 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 354, pp. 23:1-23:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{acilan_et_al:LIPIcs.AFT.2025.23,
  author =	{Acilan, Bahar and Constantinescu, Andrei and Heimbach, Lioba and Wattenhofer, Roger},
  title =	{{Transaction Fee Market Design for Parallel Execution}},
  booktitle =	{7th Conference on Advances in Financial Technologies (AFT 2025)},
  pages =	{23:1--23:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-400-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{354},
  editor =	{Avarikioti, Zeta and Christin, Nicolas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.AFT.2025.23},
  URN =		{urn:nbn:de:0030-drops-247426},
  doi =		{10.4230/LIPIcs.AFT.2025.23},
  annote =	{Keywords: blockchain, transaction fee mechanism, parallel execution}
}
Document
DOI: 10.4230/LIPIcs.ITP.2025.5
A Mechanized First-Order Theory of Algebraic Data Types with Pattern Matching

Authors: Joshua M. Cohen

Published in: LIPIcs, Volume 352, 16th International Conference on Interactive Theorem Proving (ITP 2025)

Abstract
Algebraic data types (ADTs) and pattern matching are widely used to write elegant functional programs and to specify program behavior. These constructs are critical to most general-purpose interactive theorem provers (e.g. Lean, Rocq/Coq), first-order SMT-based deductive verifiers (e.g. Dafny, VeriFast), and intermediate verification languages (e.g. Why3). Such features require layers of compilation - in Rocq, pattern matches are compiled to remove nesting, while SMT-based tools further axiomatize ADTs with a first-order specification. However, these critical steps have been omitted from prior formalizations of such toolchains (e.g. MetaRocq). We give the first proved-sound sophisticated pattern matching compiler (based on Maranget’s compilation to decision trees) and first-order axiomatization of ADTs, both based on Why3 implementations. We prove the soundness of exhaustiveness checking, extending pen-and-paper proofs from the literature, and formulate a robustness property with which we find an exhaustiveness-related bug in Why3. We show that many of our proofs could be useful for reasoning about any first-order program verifier supporting ADTs.
Cite as

Joshua M. Cohen. A Mechanized First-Order Theory of Algebraic Data Types with Pattern Matching. In 16th International Conference on Interactive Theorem Proving (ITP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 352, pp. 5:1-5:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{cohen:LIPIcs.ITP.2025.5,
  author =	{Cohen, Joshua M.},
  title =	{{A Mechanized First-Order Theory of Algebraic Data Types with Pattern Matching}},
  booktitle =	{16th International Conference on Interactive Theorem Proving (ITP 2025)},
  pages =	{5:1--5:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-396-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{352},
  editor =	{Forster, Yannick and Keller, Chantal},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITP.2025.5},
  URN =		{urn:nbn:de:0030-drops-246046},
  doi =		{10.4230/LIPIcs.ITP.2025.5},
  annote =	{Keywords: Pattern Matching Compilation, Algebraic Data Types, First-Order Logic}
}
Document
DOI: 10.4230/OASIcs.SpaceCHI.2025.27
Assessing the Use of Mixed Reality as a Valid Tool for Human-Robot Interaction Studies in the Context of Space Exploration

Authors: Enrico Guerra, Sebastian Thomas Büttner, Alper Beşer, and Michael Prilla

Published in: OASIcs, Volume 130, Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025)

Abstract
Mixed Reality (MR) is a technology with strong potential for advancing research in Human-Robot Interaction (HRI) for space exploration. Apart from the efficiency and high flexibility MR can offer, we argue that its benefits for HRI research in space contexts lies particularly in its ability to aid human-in-the-loop development, offer realistic hybrid simulations, and foster broader participation in HRI research in the space exploration context. However, we believe that this is only plausible if MR-based simulations can yield comparable results to fully physical approaches in human-centred studies. In this position paper, we highlight several arguments in favour of MR as a tool for space HRI research, while emphasising the importance of the open question regarding its scientific validity. We believe MR could become a central tool for preparing for future human-robotic space exploration missions and significantly diversify research in this domain.
Cite as

Enrico Guerra, Sebastian Thomas Büttner, Alper Beşer, and Michael Prilla. Assessing the Use of Mixed Reality as a Valid Tool for Human-Robot Interaction Studies in the Context of Space Exploration. In Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025). Open Access Series in Informatics (OASIcs), Volume 130, pp. 27:1-27:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{guerra_et_al:OASIcs.SpaceCHI.2025.27,
  author =	{Guerra, Enrico and B\"{u}ttner, Sebastian Thomas and Be\c{s}er, Alper and Prilla, Michael},
  title =	{{Assessing the Use of Mixed Reality as a Valid Tool for Human-Robot Interaction Studies in the Context of Space Exploration}},
  booktitle =	{Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025)},
  pages =	{27:1--27:11},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-384-3},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{130},
  editor =	{Bensch, Leonie and Nilsson, Tommy and Nisser, Martin and Pataranutaporn, Pat and Schmidt, Albrecht and Sumini, Valentina},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.SpaceCHI.2025.27},
  URN =		{urn:nbn:de:0030-drops-240175},
  doi =		{10.4230/OASIcs.SpaceCHI.2025.27},
  annote =	{Keywords: Mixed Reality, Augmented Reality, Human-Robot Interaction, Space Exploration, Validity}
}
Document
Extended Abstract
DOI: 10.4230/OASIcs.Programming.2025.1
Comparing R Bytecode Compilers Written in R, Java, and Rust (Extended Abstract)

Authors: Pierre Donat-Bouillud, Filip Křikava, Jakob Hain, Adam Plodek, and Jan Vitek

Published in: OASIcs, Volume 134, Companion Proceedings of the 9th International Conference on the Art, Science, and Engineering of Programming (Programming 2025)

Abstract
This paper presents a comparative analysis of three implementations of the R bytecode compiler: the official R implementation, a Java-based compiler, and a Rust-based compiler. The R compiler, written in R itself, poses challenges in terms of performance and maintainability. We evaluate designs of the compilers, their trade-offs, and performance characteristics. The Rust version outperforms the Java version, which itself outperforms the R version.
Cite as

Pierre Donat-Bouillud, Filip Křikava, Jakob Hain, Adam Plodek, and Jan Vitek. Comparing R Bytecode Compilers Written in R, Java, and Rust (Extended Abstract). In Companion Proceedings of the 9th International Conference on the Art, Science, and Engineering of Programming (Programming 2025). Open Access Series in Informatics (OASIcs), Volume 134, pp. 1:1-1:6, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{donatbouillud_et_al:OASIcs.Programming.2025.1,
  author =	{Donat-Bouillud, Pierre and K\v{r}ikava, Filip and Hain, Jakob and Plodek, Adam and Vitek, Jan},
  title =	{{Comparing R Bytecode Compilers Written in R, Java, and Rust}},
  booktitle =	{Companion Proceedings of the 9th International Conference on the Art, Science, and Engineering of Programming (Programming 2025)},
  pages =	{1:1--1:6},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-382-9},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{134},
  editor =	{Edwards, Jonathan and Perera, Roly and Petricek, Tomas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Programming.2025.1},
  URN =		{urn:nbn:de:0030-drops-242854},
  doi =		{10.4230/OASIcs.Programming.2025.1},
  annote =	{Keywords: R, bytecode, compiler}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2025.85
Cutoff Theorems for the Equivalence of Parameterized Quantum Circuits

Authors: Neil J. Ross and Scott Wesley

Published in: LIPIcs, Volume 345, 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)

Abstract
Many promising quantum algorithms in economics, medical science, and material science rely on circuits that are parameterized by a large number of angles. To ensure that these algorithms are efficient, these parameterized circuits must be heavily optimized. However, most quantum circuit optimizers are not verified, so this procedure is known to be error-prone. For this reason, there is growing interest in the design of equivalence checking algorithms for parameterized quantum circuits. In this paper, we define a generalized class of parameterized circuits with arbitrary rotations and show that this problem is decidable for cyclotomic gate sets. We propose a cutoff-based procedure which reduces the problem of verifying the equivalence of parameterized quantum circuits to the problem of verifying the equivalence of finitely many parameter-free quantum circuits. Because the number of parameter-free circuits grows exponentially with the number of parameters, we also propose a probabilistic variant of the algorithm for cases when the number of parameters is intractably large. We show that our techniques extend to equivalence modulo global phase, and describe an efficient angle sampling procedure for cyclotomic gate sets.
Cite as

Neil J. Ross and Scott Wesley. Cutoff Theorems for the Equivalence of Parameterized Quantum Circuits. In 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 345, pp. 85:1-85:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ross_et_al:LIPIcs.MFCS.2025.85,
  author =	{Ross, Neil J. and Wesley, Scott},
  title =	{{Cutoff Theorems for the Equivalence of Parameterized Quantum Circuits}},
  booktitle =	{50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)},
  pages =	{85:1--85:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-388-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{345},
  editor =	{Gawrychowski, Pawe{\l} and Mazowiecki, Filip and Skrzypczak, Micha{\l}},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2025.85},
  URN =		{urn:nbn:de:0030-drops-241921},
  doi =		{10.4230/LIPIcs.MFCS.2025.85},
  annote =	{Keywords: Quantum Circuits, Parameterized Equivalence Checking}
}
Document
DOI: 10.4230/LIPIcs.DNA.31.1
Algorithmic Hardness of the Partition Function for Nucleic Acid Strands

Authors: Gwendal Ducloz, Ahmed Shalaby, and Damien Woods

Published in: LIPIcs, Volume 347, 31st International Conference on DNA Computing and Molecular Programming (DNA 31) (2025)

Abstract
To understand and engineer biological and artificial nucleic acid systems, algorithms are employed for prediction of secondary structures at thermodynamic equilibrium. Dynamic programming algorithms are used to compute the most favoured, or Minimum Free Energy (MFE), structure, and the Partition Function (PF) - a tool for assigning a probability to any structure. However, in some situations, such as when there are large numbers of strands, or pseudoknotted systems, NP-hardness results show that such algorithms are unlikely, but only for MFE. Curiously, algorithmic hardness results were not shown for PF, leaving two open questions on the complexity of PF for multiple strands and single strands with pseudoknots. The challenge is that while the MFE problem cares only about one, or a few structures, PF is a summation over the entire secondary structure space, giving theorists the vibe that computing PF should not only be as hard as MFE, but should be even harder. We answer both questions. First, we show that computing PF is #P-hard for systems with an unbounded number of strands, answering a question of Condon Hajiaghayi, and Thachuk [DNA27]. Second, for even a single strand, but allowing pseudoknots, we find that PF is #P-hard. Our proof relies on a novel magnification trick that leads to a tightly-woven set of reductions between five key thermodynamic problems: MFE, PF, their decision versions, and #SSEL that counts structures of a given energy. Our reductions show these five problems are fundamentally related for any energy model amenable to magnification. That general classification clarifies the mathematical landscape of nucleic acid energy models and yields several open questions.
Cite as

Gwendal Ducloz, Ahmed Shalaby, and Damien Woods. Algorithmic Hardness of the Partition Function for Nucleic Acid Strands. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 1:1-1:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ducloz_et_al:LIPIcs.DNA.31.1,
  author =	{Ducloz, Gwendal and Shalaby, Ahmed and Woods, Damien},
  title =	{{Algorithmic Hardness of the Partition Function for Nucleic Acid Strands}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{1:1--1:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-399-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{347},
  editor =	{Schaeffer, Josie and Zhang, Fei},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.1},
  URN =		{urn:nbn:de:0030-drops-238504},
  doi =		{10.4230/LIPIcs.DNA.31.1},
  annote =	{Keywords: Partition function, minimum free energy, nucleic acid, DNA, RNA, secondary structure, computational complexity, #P-hardness}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.9
Dolphyin: A Combinatorial Algorithm for Identifying 1-Dollo Phylogenies in Cancer

Authors: Daniel W. Feng and Mohammed El-Kebir

Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)

Abstract
Several recent cancer phylogeny inference methods have used the k-Dollo evolutionary model for single-nucleotide variants. Specifically, in this problem one is given an m × n binary matrix B and seeks a rooted tree T with m leaves that correspond to the m rows of B, and each node of T is labeled by a binary state for each of the n characters subject to the restriction that each character is gained at most once (0-to-1 transition) and subsequently lost at most k times (1-to-0 transitions). The 1-Dollo variant, also known as the persistent perfect phylogeny where one is restricted to at most k = 1 losses per character, has been studied extensively, but its hardness remains an open question. Here, we prove that the 1-Dollo Linear Phylogeny (1DLP) problem, where we additionally require the resulting 1-Dollo phylogeny T to be linear, is equivalent to verifying whether the input matrix B adheres to the Consecutive Ones Property (C1P), which can be solved in polynomial time. Due to the equivalence, several known NP-hardness results for relevant variants of C1P carry over to 1DLP, including the minimization of false negatives (0-to-1 modifications to the input matrix B) or the allowance of 2 gains and 2 losses. We furthermore show how we can recursively decompose any, not necessarily linear, 1-Dollo phylogeny T into several 1-Dollo linear phylogenies, connected by matching branching points. We extend this characterization to matrices B that admit 1-Dollo phylogenies, giving necessary and sufficient conditions for the existence of a novel decomposition of B into several submatrices and corresponding branching points. This decomposition forms the basis of Dolphyin, a new exponential-time algorithm for inferring 1-Dollo phylogenies that efficiently leverages the determination of linear 1-Dollo phylogenies as a subroutine. Dolphyin can also be applied to input matrices B with false negatives. We demonstrate that Dolphyin is runtime-competitive with a previous integer linear programming based algorithm SPhyR on simulated datasets. We additionally analyze simulated datasets with false negative errors and find that in the median case, Dolphyin infers 1-Dollo phylogenies with inferred error rates at or below the ground truth rate. Finally, we apply Dolphyin to 99 acute myeloid leukemia single-cell sequencing datasets, finding that the majority of the cancers can be explained by 1-Dollo phylogenies with false negative error rates in line with the used sequencing technology. Availability. Dolphyin is available at: https://github.com/elkebir-group/Dolphyin.
Cite as

Daniel W. Feng and Mohammed El-Kebir. Dolphyin: A Combinatorial Algorithm for Identifying 1-Dollo Phylogenies in Cancer. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 9:1-9:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{feng_et_al:LIPIcs.WABI.2025.9,
  author =	{Feng, Daniel W. and El-Kebir, Mohammed},
  title =	{{Dolphyin: A Combinatorial Algorithm for Identifying 1-Dollo Phylogenies in Cancer}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{9:1--9:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.9},
  URN =		{urn:nbn:de:0030-drops-239356},
  doi =		{10.4230/LIPIcs.WABI.2025.9},
  annote =	{Keywords: Intra-tumor heterogeneity, persistent perfect phylogeny, consecutive ones property, combinatorics}
}
Document
DOI: 10.4230/LIPIcs.FSCD.2025.5
The Cost of Skeletal Call-By-Need, Smoothly

Authors: Beniamino Accattoli, Francesco Magliocca, Loïc Peyrot, and Claudio Sacerdoti Coen

Published in: LIPIcs, Volume 337, 10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025)

Abstract
Skeletal call-by-need is an optimization of call-by-need evaluation also known as "fully lazy sharing": when the duplication of a value has to take place, it is first split into "skeleton", which is then duplicated, and "flesh" which is instead kept shared. Here, we provide two cost analyses of skeletal call-by-need. Firstly, we provide a family of terms showing that skeletal call-by-need can be asymptotically exponentially faster than call-by-need in both time and space; it is the first such evidence, to our knowledge. Secondly, we prove that skeletal call-by-need can be implemented efficiently, that is, with bi-linear overhead. This result is obtained by providing a new smooth presentation of ideas by Shivers and Wand for the reconstruction of skeletons, which is then smoothly plugged into the study of an abstract machine following the distillation technique by Accattoli et al.
Cite as

Beniamino Accattoli, Francesco Magliocca, Loïc Peyrot, and Claudio Sacerdoti Coen. The Cost of Skeletal Call-By-Need, Smoothly. In 10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 337, pp. 5:1-5:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{accattoli_et_al:LIPIcs.FSCD.2025.5,
  author =	{Accattoli, Beniamino and Magliocca, Francesco and Peyrot, Lo\"{i}c and Sacerdoti Coen, Claudio},
  title =	{{The Cost of Skeletal Call-By-Need, Smoothly}},
  booktitle =	{10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025)},
  pages =	{5:1--5:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-374-4},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{337},
  editor =	{Fern\'{a}ndez, Maribel},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSCD.2025.5},
  URN =		{urn:nbn:de:0030-drops-236206},
  doi =		{10.4230/LIPIcs.FSCD.2025.5},
  annote =	{Keywords: \lambda-calculus, abstract machines, call-by-need, cost models}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.130
An Efficient Algorithm to Compute the Minimum Free Energy of Interacting Nucleic Acid Strands

Authors: Ahmed Shalaby and Damien Woods

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

Abstract
The information-encoding molecules RNA and DNA bind via base pairing to form an exponentially large set of secondary structures. Practitioners need algorithms to predict the most favoured structures, called minimum free energy (MFE) structures, or to compute a partition function that allows assigning a probability to any structure. MFE prediction is NP-hard in the presence pseudoknots - base pairings that violate a restricted planarity condition. However, for single-stranded unpseudoknotted structures, there are polynomial time dynamic programming algorithms. For multiple strands, the problem is significantly more complicated: Codon, Hajiaghayi and Thachuk [DNA27, 2021] proved it NP-hard for N bases and 𝒪(N) strands. Dirks, Bois, Schaeffer, Winfree and Pierce [SIAM Review, 2007] gave a polynomial time partition function algorithm for multiple (𝒪(1)) strands, now widely-used, however their technique did not generalise to MFE which they left open. We give an 𝒪(N⁴) time algorithm for unpseudoknotted multiple (𝒪(1)) strand MFE prediction, answering the open problem from Dirks et al. The challenge lies in considering the rotational symmetry of secondary structures, a global feature not immediately amenable to local subproblem decomposition used in dynamic programming. Our proof has two main technical contributions: First, a characterisation of symmetric secondary structures implying only quadratically many need to be considered when computing the rotational symmetry penalty. Second, that bound is leveraged by a backtracking algorithm to efficiently find the MFE in an exponential space of contenders.
Cite as

Ahmed Shalaby and Damien Woods. An Efficient Algorithm to Compute the Minimum Free Energy of Interacting Nucleic Acid Strands. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 130:1-130:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{shalaby_et_al:LIPIcs.ICALP.2025.130,
  author =	{Shalaby, Ahmed and Woods, Damien},
  title =	{{An Efficient Algorithm to Compute the Minimum Free Energy of Interacting Nucleic Acid Strands}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{130:1--130:20},
  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.2025.130},
  URN =		{urn:nbn:de:0030-drops-235071},
  doi =		{10.4230/LIPIcs.ICALP.2025.130},
  annote =	{Keywords: Minimum free energy, MFE, partition function, nucleic acid, DNA, RNA, secondary structure, computational complexity, algorithm analysis and design, dynamic programming}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2025.13
FuzzFlesh: Randomised Testing of Decompilers via Control Flow Graph-Based Program Generation

Authors: Amber Gorzynski and Alastair F. Donaldson

Published in: LIPIcs, Volume 333, 39th European Conference on Object-Oriented Programming (ECOOP 2025)

Abstract
Decompilation is the process of translating compiled code into high-level code. Control flow recovery is a challenging part of the process. "Misdecompilations" can occur, whereby the decompiled code does not accurately represent the semantics of the compiled code, despite it being syntactically valid. This is problematic because it can mislead users who are trying to reason about the program. We present CFG-based program generation: a novel approach to randomised testing that aims to improve the control flow recovery of decompilers. CFG-based program generation involves randomly generating control flow graphs (CFGs) and paths through each graph. Inspired by prior work in the domain of GPU computing, (CFG, path) pairs are "fleshed" into test programs. Each program is decompiled and recompiled. The test oracle verifies whether the actual runtime path through the graph matches the expected path. Any difference in the execution paths after recompilation indicates a possible misdecompilation. A key benefit of this approach is that it is largely independent of the source and target languages in question because it is focused on control flow. The approach is therefore applicable to numerous decompilation settings. The trade-off resulting from the focus on control flow is that misdecompilation bugs that do not relate to control flow (e.g. bugs that involve specific arithmetic operations) are out of scope. We have implemented this approach in FuzzFlesh, an open-source randomised testing tool. FuzzFlesh can be easily configured to target a variety of low-level languages and decompiler toolchains because most of the CFG and path generation process is language-independent. At present, FuzzFlesh supports testing decompilation of Java bytecode, .NET assembly and x86 machine code. In addition to program generation, FuzzFlesh also includes an automated test-case reducer that operates on the CFG rather than the low-level program, which means that it can be applied to any of the target languages. We present a large experimental campaign applying FuzzFlesh to a variety of decompilers, leading to the discovery of 12 previously-unknown bugs across two language formats, six of which have been fixed. We present experiments comparing our generic FuzzFlesh tool to two state-of-the-art decompiler testing tools targeted at specific languages. As expected, the coverage our generic FuzzFlesh tool achieves on a given decompiler is lower than the coverage achieved by a tool specifically designed for the input format of that decompiler. However, due to its focus on control flow, FuzzFlesh is able to cover sections of control flow recovery code that the targeted tools cannot reach, and identify control flow related bugs that the targeted tools miss.
Cite as

Amber Gorzynski and Alastair F. Donaldson. FuzzFlesh: Randomised Testing of Decompilers via Control Flow Graph-Based Program Generation. In 39th European Conference on Object-Oriented Programming (ECOOP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 333, pp. 13:1-13:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gorzynski_et_al:LIPIcs.ECOOP.2025.13,
  author =	{Gorzynski, Amber and Donaldson, Alastair F.},
  title =	{{FuzzFlesh: Randomised Testing of Decompilers via Control Flow Graph-Based Program Generation}},
  booktitle =	{39th European Conference on Object-Oriented Programming (ECOOP 2025)},
  pages =	{13:1--13:26},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-373-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{333},
  editor =	{Aldrich, Jonathan and Silva, Alexandra},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2025.13},
  URN =		{urn:nbn:de:0030-drops-233062},
  doi =		{10.4230/LIPIcs.ECOOP.2025.13},
  annote =	{Keywords: Decompiler, Reverse Engineering, Control Flow, Software Testing, Fuzzing}
}
Document
Pearl/Brave New Idea
DOI: 10.4230/LIPIcs.ECOOP.2025.41
Shouting at Memory: Where Did My Write Go? (Pearl/Brave New Idea)

Authors: Vasileios Klimis

Published in: LIPIcs, Volume 333, 39th European Conference on Object-Oriented Programming (ECOOP 2025)

Abstract
Non-Volatile Memory (NVM) promises persistent data, but verifying that promise on real hardware is challenging due to opaque caching and internal buffers like Intel’s WPQ, which obscure the true state of writes. Traditional validation methods often fall short. This paper introduces a novel perspective: leveraging the subtle timing variations of memory accesses as a direct probe into write persistence. We present a software technique, inspired by echolocation, that uses high-resolution timers to measure memory load latencies. These timings act as distinct signatures ("echoes") revealing whether a write’s data resides in volatile caches or has reached the NVM persistence domain. This offers a non-invasive method to track write progression towards durability. To reliably interpret these potentially noisy timing signatures and systematically explore complex persistence behaviours, we integrate this echolocation probe into an active model learning framework. This synergy enables the automated inference of a system’s actual persistency semantics directly from black-box hardware observations. The approach is hardware-agnostic, adaptive, and scalable. Preliminary experiments on Intel x86 - a platform where persistence validation is notably challenged by the opaque Write Pending Queue (WPQ) - demonstrate the feasibility of our technique. We observed distinct latency clusters differentiating volatile cache accesses from those reaching the persistence domain. This combined approach offers a promising path towards robust and automated validation of NVM persistency across diverse architectures.
Cite as

Vasileios Klimis. Shouting at Memory: Where Did My Write Go? (Pearl/Brave New Idea). In 39th European Conference on Object-Oriented Programming (ECOOP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 333, pp. 41:1-41:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{klimis:LIPIcs.ECOOP.2025.41,
  author =	{Klimis, Vasileios},
  title =	{{Shouting at Memory: Where Did My Write Go?}},
  booktitle =	{39th European Conference on Object-Oriented Programming (ECOOP 2025)},
  pages =	{41:1--41:26},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-373-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{333},
  editor =	{Aldrich, Jonathan and Silva, Alexandra},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2025.41},
  URN =		{urn:nbn:de:0030-drops-233339},
  doi =		{10.4230/LIPIcs.ECOOP.2025.41},
  annote =	{Keywords: Persistency Memory Semantics, Fuzz Testing, Model Learning}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2025.20
Incremental Computing by Differential Execution

Authors: Prashant Kumar, André Pacak, and Sebastian Erdweg

Published in: LIPIcs, Volume 333, 39th European Conference on Object-Oriented Programming (ECOOP 2025)

Abstract
Incremental computing offers the potential for significant performance gains by efficiently updating computations in response to changing data. However, traditional approaches are either problem-specific or use an inefficient all-or-nothing strategy of rerunning affected computations entirely. This paper presents differential semantics, a novel approach that directly embeds the propagation of changes into the semantics of a general-purpose programming language. Given a precise description of input changes, differential semantics rules define how these changes are tracked and propagated through core language constructs like assignments, conditionals, and loops to produce corresponding output changes. We formalize differential semantics and verify key properties, including correctness, using the Rocq proof assistant. We also develop and formally prove a set of optimizations, particularly for loop handling, that enable asymptotic performance improvements. An implementation of the semantics as a differential interpreter achieves order-of-magnitude speedups over recomputation on the Bellman-Ford shortest path algorithm.
Cite as

Prashant Kumar, André Pacak, and Sebastian Erdweg. Incremental Computing by Differential Execution. In 39th European Conference on Object-Oriented Programming (ECOOP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 333, pp. 20:1-20:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{kumar_et_al:LIPIcs.ECOOP.2025.20,
  author =	{Kumar, Prashant and Pacak, Andr\'{e} and Erdweg, Sebastian},
  title =	{{Incremental Computing by Differential Execution}},
  booktitle =	{39th European Conference on Object-Oriented Programming (ECOOP 2025)},
  pages =	{20:1--20:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-373-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{333},
  editor =	{Aldrich, Jonathan and Silva, Alexandra},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2025.20},
  URN =		{urn:nbn:de:0030-drops-233137},
  doi =		{10.4230/LIPIcs.ECOOP.2025.20},
  annote =	{Keywords: Incremental computing, differential semantics, programming language design, formal verification, big-step semantics}
}
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