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Document

DOI: 10.4230/LIPIcs.STACS.2026.65

Demystifying Codensity Monads via Duality

Authors: Fabian Lenke, Nico Wittrock, Stefan Milius, and Henning Urbat

Published in: LIPIcs, Volume 364, 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)

Abstract

Codensity monads provide a universal method to generate complex monads from simple functors. Recently, a wide range of important monads in logic, denotational semantics, and probabilistic computation, such as several incarnations of the ultrafilter monad, the Vietoris monad, and the Giry monad, have been presented as codensity monads, using complex arguments. We propose a unifying categorical approach to codensity presentations of monads, based on the idea of relating the presenting functor to a dense functor via a suitable duality between categories. We prove a general presentation result applying to every such situation and demonstrate that most codensity presentations known in the literature emerge from this strikingly simple duality-based setup, drastically alleviating the complexity of their proofs and in many cases completely reducing them to standard duality results. Additionally, we derive a number of novel codensity presentations using our framework, including the first non-trivial codensity presentations for the filter monads on sets and topological spaces, the lower Vietoris monad on topological spaces, and the expectation monad on sets.

Cite as

Fabian Lenke, Nico Wittrock, Stefan Milius, and Henning Urbat. Demystifying Codensity Monads via Duality. In 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 364, pp. 65:1-65:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{lenke_et_al:LIPIcs.STACS.2026.65,
  author =	{Lenke, Fabian and Wittrock, Nico and Milius, Stefan and Urbat, Henning},
  title =	{{Demystifying Codensity Monads via Duality}},
  booktitle =	{43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)},
  pages =	{65:1--65:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-412-3},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{364},
  editor =	{Mahajan, Meena and Manea, Florin and McIver, Annabelle and Thắng, Nguy\~{ê}n Kim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2026.65},
  URN =		{urn:nbn:de:0030-drops-255549},
  doi =		{10.4230/LIPIcs.STACS.2026.65},
  annote =	{Keywords: Codensity, Monad, Duality}
}

Document

DOI: 10.4230/LIPIcs.CSL.2026.28

Resourceful Traces for Commuting Processes

Authors: Matthew Earnshaw, Chad Nester, and Mario Román

Published in: LIPIcs, Volume 363, 34th EACSL Annual Conference on Computer Science Logic (CSL 2026)

Abstract

We show that, when the actions of a Mazurkiewicz trace are considered not merely as atomic but as transformations from a specified type of inputs to a specified type of outputs, we obtain a novel notion of presentation for effectful categories (also known as generalized Freyd categories), a well-known algebraic structure in the semantics of side-effecting computation. Like the usual representation of traces as graphs, our notion of presentation gives rise to a graphical representation of morphisms in effectful categories. We use our presentations to give a construction of the commuting tensor product of free effectful categories, capturing the combination of systems in which the actions of each must commute with one another, while still permitting exchange of resources.

Cite as

Matthew Earnshaw, Chad Nester, and Mario Román. Resourceful Traces for Commuting Processes. In 34th EACSL Annual Conference on Computer Science Logic (CSL 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 363, pp. 28:1-28:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{earnshaw_et_al:LIPIcs.CSL.2026.28,
  author =	{Earnshaw, Matthew and Nester, Chad and Rom\'{a}n, Mario},
  title =	{{Resourceful Traces for Commuting Processes}},
  booktitle =	{34th EACSL Annual Conference on Computer Science Logic (CSL 2026)},
  pages =	{28:1--28:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-411-6},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{363},
  editor =	{Guerrini, Stefano and K\"{o}nig, Barbara},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CSL.2026.28},
  URN =		{urn:nbn:de:0030-drops-254522},
  doi =		{10.4230/LIPIcs.CSL.2026.28},
  annote =	{Keywords: Mazurkiewicz traces, premonoidal categories, monoidal categories, effectful categories}
}

Document

DOI: 10.4230/LIPIcs.CSL.2026.29

Parametric Iteration in Resource Theories

Authors: Alessandro Di Giorgio, Pawel Sobocinski, and Niels Voorneveld

Published in: LIPIcs, Volume 363, 34th EACSL Annual Conference on Computer Science Logic (CSL 2026)

Abstract

Many algorithms are specified with respect to a fixed but unknown parameter. Examples of this are especially common in cryptography, where protocols often feature a security parameter such as the bit length of a secret key. Our aim is to capture this phenomenon in a more abstract setting. We focus on resource theories - general calculi of processes with a string diagrammatic syntax - introducing a general parametric iteration construction. By instantiating this construction within the Markov category of probabilistic Boolean circuits and equipping it with a suitable metric, we are able to capture the notion of negligibility via asymptotic equivalence, in a compositional way. This allows us to use diagrammatic reasoning to prove simple cryptographic theorems - for instance, proving that guessing a randomly generated key has negligible success.

Cite as

Alessandro Di Giorgio, Pawel Sobocinski, and Niels Voorneveld. Parametric Iteration in Resource Theories. In 34th EACSL Annual Conference on Computer Science Logic (CSL 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 363, pp. 29:1-29:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{digiorgio_et_al:LIPIcs.CSL.2026.29,
  author =	{Di Giorgio, Alessandro and Sobocinski, Pawel and Voorneveld, Niels},
  title =	{{Parametric Iteration in Resource Theories}},
  booktitle =	{34th EACSL Annual Conference on Computer Science Logic (CSL 2026)},
  pages =	{29:1--29:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-411-6},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{363},
  editor =	{Guerrini, Stefano and K\"{o}nig, Barbara},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CSL.2026.29},
  URN =		{urn:nbn:de:0030-drops-254541},
  doi =		{10.4230/LIPIcs.CSL.2026.29},
  annote =	{Keywords: Markov categories, Cryptography, String diagrams, Asymptotic equivalence}
}

Document

DOI: 10.4230/LIPIcs.ESA.2025.105

Parameterized Algorithms for Computing Pareto Sets

Authors: Joshua Marc Könen, Heiko Röglin, and Tarek Stuck

Published in: LIPIcs, Volume 351, 33rd Annual European Symposium on Algorithms (ESA 2025)

Abstract

The problem of computing the set of Pareto-optimal solutions has been studied for a variety of multiobjective optimization problems. For many such problems, algorithms are known that compute the Pareto set in (weak) output-polynomial time. These algorithms are often based on dynamic programming and by weak output-polynomial time, we mean that the running time depends polynomially on the size of the Pareto set but also on the sizes of the Pareto sets of the subproblems that occur in the dynamic program. For some problems, like the multiobjective minimum spanning tree problem, such algorithms are not known to exist and for other problems, like multiobjective versions of many NP-hard problems, such algorithms cannot exist, unless 𝒫 = 𝒩𝒫. Dynamic programming over tree decompositions is a common technique in parameterized algorithms. In this paper, we study whether this technique can also be applied to compute Pareto sets of multiobjective optimization problems. We first derive an algorithm to compute the Pareto set for the multicriteria s-t cut problem and show how this result can be applied to a polygon aggregation problem arising in cartography that has recently been introduced by Rottmann et al. (GIScience 2021). We also show how to apply these techniques to also compute the Pareto set of the multiobjective minimum spanning tree problem and for the multiobjective TSP. The running time of our algorithms is O(f(w)⋅poly(n,p_{max})), where f is some function in the treewidth w, n is the input size, and p_{max} is an upper bound on the size of the Pareto sets of the subproblems that occur in the dynamic program. Finally, we present an experimental evaluation of computing Pareto sets on real-world instances of polygon aggregation problems. For this matter we devised a task-specific data structure that allows for efficient storage and modification of large sets of Pareto-optimal solutions. Throughout the implementation process, we incorporated several improved strategies and heuristics that significantly reduced both runtime and memory usage, enabling us to solve instances with treewidth of up to 22 within reasonable amount of time. Moreover, we conducted a preprocessing study to compare different tree decompositions in terms of their estimated overall runtime.

Cite as

Joshua Marc Könen, Heiko Röglin, and Tarek Stuck. Parameterized Algorithms for Computing Pareto Sets. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 105:1-105:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{konen_et_al:LIPIcs.ESA.2025.105,
  author =	{K\"{o}nen, Joshua Marc and R\"{o}glin, Heiko and Stuck, Tarek},
  title =	{{Parameterized Algorithms for Computing Pareto Sets}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{105:1--105:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-395-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{351},
  editor =	{Benoit, Anne and Kaplan, Haim and Wild, Sebastian 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.2025.105},
  URN =		{urn:nbn:de:0030-drops-245749},
  doi =		{10.4230/LIPIcs.ESA.2025.105},
  annote =	{Keywords: parameterized algorithms, treewidth, multicriteria optimization problems, multicriteria MST, multicriteria TSP, polygon aggregation}
}

Document

DOI: 10.4230/LIPIcs.MFCS.2025.61

Quantum Relaxations of CSP and Structure Isomorphism

Authors: Amin Karamlou

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

Abstract

We investigate quantum relaxations of two key decision problems in computer science: the constraint satisfaction problem (CSP) and the structure isomorphism problem. CSP asks whether a homomorphism exists between two relational structures, while structure isomorphism seeks an isomorphism between them. In recent years, it has become increasingly apparent that many special cases of CSP can be reformulated in terms of the existence of perfect classical strategies in non-local games, a key topic of study in quantum information theory. These games have allowed us to study quantum advantage in relation to many important decision problems, such as the k-colouring problem, and the problem of solving binary constraint systems. Abramsky et al. (2017) have shown that all of these games can be seen as special instances of a non-local CSP game. Moreover, they show that perfect quantum strategies in this CSP game can be viewed as Kleisli morphisms of a graded monad on the category of relational structures, which they dub the quantum monad. In this way, the quantum monad provides a categorical characterisation of quantum advantage for the non-local CSP game. In this work we solidify and expand the results of Abramsky et al., answering several of their open questions. Firstly, we compare the definition of quantum graph homomorphisms arising from this work with an earlier definition of the concept due to Mančinska and Roberson and show that there are graphs which exhibit quantum advantage under one definition but not the other. Our second contribution is to extend the results of Abramsky et al. which only hold in the tensor product framework of quantum mechanics to the commuting operator framework. Next, we study a non-local structure isomorphism game, which generalises the well-studied graph isomorphism game. We show how the construction of the quantum monad can be refined to provide categorical semantics for quantum strategies in this game. This results in a category where morphisms coincide with quantum homomorphisms and isomorphisms coincide with quantum isomorphisms.

Cite as

Amin Karamlou. Quantum Relaxations of CSP and Structure Isomorphism. In 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 345, pp. 61:1-61:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{karamlou:LIPIcs.MFCS.2025.61,
  author =	{Karamlou, Amin},
  title =	{{Quantum Relaxations of CSP and Structure Isomorphism}},
  booktitle =	{50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)},
  pages =	{61:1--61:18},
  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.2025.61},
  URN =		{urn:nbn:de:0030-drops-241686},
  doi =		{10.4230/LIPIcs.MFCS.2025.61},
  annote =	{Keywords: CSP, graph isomorphism, quantum information, non-local game, quantum graph homomorphism, monad}
}

Document

DOI: 10.4230/LIPIcs.GIScience.2025.14

Guiding Geospatial Analysis Processes in Dealing with Modifiable Areal Unit Problems

Authors: Guoray Cai and Yue Hao

Published in: LIPIcs, Volume 346, 13th International Conference on Geographic Information Science (GIScience 2025)

Abstract

Geospatial analysis has been widely applied in different domains for critical decision making. However, the results of spatial analysis are often plagued with uncertainties due to measurement errors, choice of data representations, and unintended transformation artifacts. A well known example of such problems is the Modifiable Areal Unit Problem (MAUP) which has well documented effects on the outcome of spatial analysis on area-aggregated data. Existing methods for addressing the effects of MAUP are limited, are technically complex, and are often inaccessible to practitioners. As a result, analysts tend to ignore the effects of MAUP in practice due to lack of expertise, high cognitive loads, and resource limitations. To address these challenges, this paper proposes a machine-guidance approach to augment the analyst’s capacity in mitigating the effect of MAUP. Based on an analysis of practical challenges faced by human analysts, we identified multiple opportunities for the machine to guide the analysts by alerting to the rise of MAUP, assessing the impact of MAUP, choosing mitigation methods, and generating visual guidance messages using GIS functions and tools. For each of the opportunities, we characterize the behavior patterns and the underlying guidance strategies that generate the behavior. We illustrate the behavior of machine guidance using a hotspot analysis scenario in the context of crime policing, where MAUP has strong effects on the patterns of crime hotspots. Finally, we describe the computational framework used to build a prototype guidance system and identify a number of research questions to be addressed. We conclude by discussing how the machine guidance approach could be an answer to some of the toughest problems in geospatial analysis.

Cite as

Guoray Cai and Yue Hao. Guiding Geospatial Analysis Processes in Dealing with Modifiable Areal Unit Problems. In 13th International Conference on Geographic Information Science (GIScience 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 346, pp. 14:1-14:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{cai_et_al:LIPIcs.GIScience.2025.14,
  author =	{Cai, Guoray and Hao, Yue},
  title =	{{Guiding Geospatial Analysis Processes in Dealing with Modifiable Areal Unit Problems}},
  booktitle =	{13th International Conference on Geographic Information Science (GIScience 2025)},
  pages =	{14:1--14:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-378-2},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{346},
  editor =	{Sila-Nowicka, Katarzyna and Moore, Antoni and O'Sullivan, David and Adams, Benjamin and Gahegan, Mark},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.GIScience.2025.14},
  URN =		{urn:nbn:de:0030-drops-238433},
  doi =		{10.4230/LIPIcs.GIScience.2025.14},
  annote =	{Keywords: Machine Guidance, Geo-Spatial Analysis, Modifiable Areal Unit Problem (MAUP)}
}

Document

DOI: 10.4230/LIPIcs.WABI.2025.10

DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs

Authors: Ali Ghaffaari, Alexander Schönhuth, and Tobias Marschall

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

Abstract

Determining the distance between two loci within a genomic region is a recurrent operation in various tasks in computational genomics. A notable example of this task arises in paired-end read mapping as a form of validation of distances between multiple alignments. While straightforward for a single genome, graph-based reference structures render the operation considerably more involved. Given the sheer number of such queries in a typical read mapping experiment, an efficient algorithm for answering distance queries is crucial. In this paper, we introduce DiVerG, a compact data structure as well as a fast and scalable algorithm, for constructing distance indexes for general sequence graphs on multi-core CPU and many-core GPU architectures. DiVerG is based on PairG [Jain et al., 2019], but overcomes the limitations of PairG by exploiting the extensive potential for improvements in terms of scalability and space efficiency. As a consequence, DiVerG can process substantially larger datasets, such as whole human genomes, which are unmanageable by PairG. DiVerG offers faster index construction time and consistently faster query time with gains proportional to the size of the underlying compact data structure. We demonstrate that our method performs favorably on multiple real datasets at various scales. DiVerG achieves superior performance over PairG; e.g. resulting to 2.5-4x speed-up in query time, 44-340x smaller index size, and 3-50x faster construction time for the genome graph of the MHC region, as a particularly variable region of the human genome. The implementation is available at: https://github.com/cartoonist/diverg

Cite as

Ali Ghaffaari, Alexander Schönhuth, and Tobias Marschall. DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 10:1-10:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ghaffaari_et_al:LIPIcs.WABI.2025.10,
  author =	{Ghaffaari, Ali and Sch\"{o}nhuth, Alexander and Marschall, Tobias},
  title =	{{DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{10:1--10:24},
  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.2025.10},
  URN =		{urn:nbn:de:0030-drops-239369},
  doi =		{10.4230/LIPIcs.WABI.2025.10},
  annote =	{Keywords: Sequence graph, distance index, read mapping, sparse matrix}
}

Document

DOI: 10.4230/LIPIcs.WABI.2025.14

Human Readable Compression of GFA Paths Using Grammar-Based Code

Authors: Peter Heringer and Daniel Doerr

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

Abstract

Pangenome graphs offer a compact and comprehensive representation of genomic diversity, improving tasks such as variant calling, genotyping, and other downstream analyses. Although the underlying graph structures scale sublinearly with the number of haplotypes, the widely used GFA file format suffers from rapidly growing file sizes due to the explicit and repetitive encoding of haplotype paths. In this work, we introduce an extension to the GFA format that enables efficient grammar-based compression of haplotype paths while retaining human readability. In addition, grammar-based encoding provides an efficient in-memory data structure that does not require decompression, but conversely improves the runtime of many computational tasks that involve haplotype comparisons. We present sqz, a method that makes use of the proposed format extension to encode haplotype paths using byte pair encoding, a grammar-based compression scheme. We evaluate sqz on recent human pangenome graphs from Heumos et al. and the Human Pangenome Reference Consortium (HPRC), comparing it to existing compressors bgzip, gbz, and sequitur. sqz scales sublinearly with the number of haplotypes in a pangenome graph and consistently achieves higher compression ratios than sequitur and up to 5 times better compression than bgzip in HPRC graphs and up to 10 times in the graph from Heumos et al.. When combined with bgzip, sqz matches or excels the compression ratio of gbz across all our datasets. These results demonstrate the potential of our proposed extension of the GFA format in reducing haplotype path redundancy and improving storage efficiency for pangenome graphs.

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Peter Heringer and Daniel Doerr. Human Readable Compression of GFA Paths Using Grammar-Based Code. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 14:1-14:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{heringer_et_al:LIPIcs.WABI.2025.14,
  author =	{Heringer, Peter and Doerr, Daniel},
  title =	{{Human Readable Compression of GFA Paths Using Grammar-Based Code}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{14:1--14:19},
  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.2025.14},
  URN =		{urn:nbn:de:0030-drops-239395},
  doi =		{10.4230/LIPIcs.WABI.2025.14},
  annote =	{Keywords: pangenomics, pangenome graphs, compression, grammar-based code, byte pair encoding}
}

Document

Invited Talk

DOI: 10.4230/LIPIcs.CALCO.2025.1

Effectful Mealy Machines: Coalgebraic and Causal Traces (Invited Talk)

Authors: Filippo Bonchi, Elena Di Lavore, and Mario Román

Published in: LIPIcs, Volume 342, 11th Conference on Algebra and Coalgebra in Computer Science (CALCO 2025)

Abstract

We introduce effectful Mealy machines - a general notion of Mealy machine with global effects - and give them semantics in terms of both bisimilarity and traces. Bisimilarity of effectful Mealy machines is characterized syntactically, via free uniform feedback. Their traces are given a novel semantic coinductive universe in terms of effectful streams. We prove that this framework generalizes standard causal processes and captures existing flavours of Mealy machine, bisimilarity, and trace. This is an extended abstract for the manuscript Effectful Mealy Machines: Bisimulation and Trace that will appear in the proceedings of LiCS 2025 [Bonchi et al., 2025]; an extended version with proofs is also available (arxiv.org/abs/2410.10627) [Bonchi et al., 2025]. We additionally characterise causal processes as lax-natural transformations.

Cite as

Filippo Bonchi, Elena Di Lavore, and Mario Román. Effectful Mealy Machines: Coalgebraic and Causal Traces (Invited Talk). In 11th Conference on Algebra and Coalgebra in Computer Science (CALCO 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 342, pp. 1:1-1:7, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bonchi_et_al:LIPIcs.CALCO.2025.1,
  author =	{Bonchi, Filippo and Di Lavore, Elena and Rom\'{a}n, Mario},
  title =	{{Effectful Mealy Machines: Coalgebraic and Causal Traces}},
  booktitle =	{11th Conference on Algebra and Coalgebra in Computer Science (CALCO 2025)},
  pages =	{1:1--1:7},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-383-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{342},
  editor =	{C\^{i}rstea, Corina and Knapp, Alexander},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CALCO.2025.1},
  URN =		{urn:nbn:de:0030-drops-235596},
  doi =		{10.4230/LIPIcs.CALCO.2025.1},
  annote =	{Keywords: Mealy machines, coinduction, copy-discard categories, premonoidal categories}
}

Document

DOI: 10.4230/LIPIcs.SEA.2025.20

SimdMinimizers: Computing Random Minimizers, fast

Authors: Ragnar Groot Koerkamp and Igor Martayan

Published in: LIPIcs, Volume 338, 23rd International Symposium on Experimental Algorithms (SEA 2025)

Abstract

Motivation. Because of the rapidly-growing amount of sequencing data, computing sketches of large textual datasets has become an essential preprocessing task. These sketches are typically much smaller than the input sequences, but preserve sufficient information for downstream analysis. Minimizers are an especially popular sketching technique and used in a wide variety of applications. They sample at least one out of every w consecutive k-mers. As DNA sequencers are getting more accurate, some applications can afford to use a larger w and hence sparser and smaller sketches. And as sketches get smaller, their analysis becomes faster, so the time spent sketching the full-sized input becomes more of a bottleneck. Methods. Our library simd-minimizers implements a random minimizer algorithm using SIMD instructions. It supports both AVX2 and NEON architectures. Its main novelty is two-fold. First, it splits the input into 8 chunks that are streamed over in parallel through all steps of the algorithm. This is enabled by using the completely deterministic two-stacks sliding window minimum algorithm, which seems not to have been used before for finding minimizers. Results. Our library is up to 6.8× faster than a scalar implementation of the rescan method when w = 5 is small, and 3.4× faster for larger w = 19. Computing canonical minimizers is less than 50% slower than computing forward minimizers, and over 15× faster than the existing implementation in the minimizer-iter crate. Our library finds all (canonical) minimizers of a 3.2 Gbp human genome in 5.2 (resp. 6.7) seconds.

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Ragnar Groot Koerkamp and Igor Martayan. SimdMinimizers: Computing Random Minimizers, fast. In 23rd International Symposium on Experimental Algorithms (SEA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 338, pp. 20:1-20:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{grootkoerkamp_et_al:LIPIcs.SEA.2025.20,
  author =	{Groot Koerkamp, Ragnar and Martayan, Igor},
  title =	{{SimdMinimizers: Computing Random Minimizers, fast}},
  booktitle =	{23rd International Symposium on Experimental Algorithms (SEA 2025)},
  pages =	{20:1--20:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-375-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{338},
  editor =	{Mutzel, Petra and Prezza, Nicola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2025.20},
  URN =		{urn:nbn:de:0030-drops-232581},
  doi =		{10.4230/LIPIcs.SEA.2025.20},
  annote =	{Keywords: Minimizers, Randomized algorithms, Sketching, Hashing}
}

Document

DOI: 10.4230/LIPIcs.ECOOP.2025.18

Practical Type-Based Taint Checking and Inference

Authors: Nima Karimipour, Kanak Das, Manu Sridharan, and Behnaz Hassanshahi

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

Abstract

Many important security properties can be formulated in terms of flows of tainted data, and improved taint analysis tools to prevent such flows are of critical need. Most existing taint analyses use whole-program static analysis, leading to scalability challenges. Type-based checking is a promising alternative, as it enables modular and incremental checking for fast performance. However, type-based approaches have not been widely adopted in practice, due to challenges with false positives and annotating existing codebases. In this paper, we present a new approach to type-based checking of taint properties that addresses these challenges, based on two key techniques. First, we present a new type-based tainting checker with significantly reduced false positives, via more practical handling of third-party libraries and other language constructs. Second, we present a novel technique to automatically infer tainting type qualifiers for existing code. Our technique supports inference of generic type argument annotations, crucial for tainting properties. We implemented our techniques in a tool TaintTyper and evaluated it on real-world benchmarks. TaintTyper exceeds the recall of a state-of-the-art whole-program taint analyzer, with comparable precision, and 2.93X-22.9X faster checking time. Further, TaintTyper infers annotations comparable to those written by hand, suitable for insertion into source code. TaintTyper is a promising new approach to efficient and practical taint checking.

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Nima Karimipour, Kanak Das, Manu Sridharan, and Behnaz Hassanshahi. Practical Type-Based Taint Checking and Inference. In 39th European Conference on Object-Oriented Programming (ECOOP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 333, pp. 18:1-18:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{karimipour_et_al:LIPIcs.ECOOP.2025.18,
  author =	{Karimipour, Nima and Das, Kanak and Sridharan, Manu and Hassanshahi, Behnaz},
  title =	{{Practical Type-Based Taint Checking and Inference}},
  booktitle =	{39th European Conference on Object-Oriented Programming (ECOOP 2025)},
  pages =	{18:1--18:25},
  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.2025.18},
  URN =		{urn:nbn:de:0030-drops-233119},
  doi =		{10.4230/LIPIcs.ECOOP.2025.18},
  annote =	{Keywords: Static analysis, Taint Analysis, Pluggable type systems, Security, Inference}
}

Document

DOI: 10.4230/OASIcs.FMBC.2025.10

Program Logics for Ledgers

Authors: Orestis Melkonian, Wouter Swierstra, and James Chapman

Published in: OASIcs, Volume 129, 6th International Workshop on Formal Methods for Blockchains (FMBC 2025)

Abstract

Distributed ledgers nowadays manage substantial monetary funds in the form of cryptocurrencies such as Bitcoin, Ethereum, and Cardano. For such ledgers to be safe, operations that add new entries must be cryptographically sound - but it is less clear how to reason effectively about such ever-growing linear data structures. This paper demonstrates how distributed ledgers may be viewed as computer programs, that, when executed, transfer funds between various parties. As a result, familiar program logics, such as Hoare logic, are applied in a novel setting. Borrowing ideas from concurrent separation logic, this enables modular reasoning principles over arbitrary fragments of any ledger. All of our results have been mechanised in the Agda proof assistant.

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Orestis Melkonian, Wouter Swierstra, and James Chapman. Program Logics for Ledgers. In 6th International Workshop on Formal Methods for Blockchains (FMBC 2025). Open Access Series in Informatics (OASIcs), Volume 129, pp. 10:1-10:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{melkonian_et_al:OASIcs.FMBC.2025.10,
  author =	{Melkonian, Orestis and Swierstra, Wouter and Chapman, James},
  title =	{{Program Logics for Ledgers}},
  booktitle =	{6th International Workshop on Formal Methods for Blockchains (FMBC 2025)},
  pages =	{10:1--10:22},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-371-3},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{129},
  editor =	{Marmsoler, Diego and Xu, Meng},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.FMBC.2025.10},
  URN =		{urn:nbn:de:0030-drops-230370},
  doi =		{10.4230/OASIcs.FMBC.2025.10},
  annote =	{Keywords: blockchain, distributed ledgers, UTxO separation logic, program semantics, formal verification, Agda}
}

Document

DOI: 10.4230/LIPIcs.ITCS.2025.76

A Quantum Unique Games Conjecture

Authors: Hamoon Mousavi and Taro Spirig

Published in: LIPIcs, Volume 325, 16th Innovations in Theoretical Computer Science Conference (ITCS 2025)

Abstract

After the NP-hardness of computational problems such as 3SAT and MaxCut was established, a natural next step was to explore whether these problems remain hard to approximate. While the quantum nonlocal games extensions of some of these problems are known to be hard - indeed undecidable - their inapproximability remains largely unresolved. In this work, we introduce definitions for the quantum extensions of Label-Cover and Unique-Label-Cover. We show that these problems play a similarly crucial role in studying the inapproximability of quantum constraint satisfaction problems as they do in the classical setting.

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Hamoon Mousavi and Taro Spirig. A Quantum Unique Games Conjecture. In 16th Innovations in Theoretical Computer Science Conference (ITCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 325, pp. 76:1-76:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{mousavi_et_al:LIPIcs.ITCS.2025.76,
  author =	{Mousavi, Hamoon and Spirig, Taro},
  title =	{{A Quantum Unique Games Conjecture}},
  booktitle =	{16th Innovations in Theoretical Computer Science Conference (ITCS 2025)},
  pages =	{76:1--76:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-361-4},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{325},
  editor =	{Meka, Raghu},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2025.76},
  URN =		{urn:nbn:de:0030-drops-227047},
  doi =		{10.4230/LIPIcs.ITCS.2025.76},
  annote =	{Keywords: hardness of approximation, quantum computing, noncommutative constraint satisfaction problems, Fourier analysis}
}

Document

DOI: 10.4230/LIPIcs.CSL.2025.44

Classical Linear Logic in Perfect Banach Lattices

Authors: Pedro H. Azevedo de Amorim, Leon Witzman, and Dexter Kozen

Published in: LIPIcs, Volume 326, 33rd EACSL Annual Conference on Computer Science Logic (CSL 2025)

Abstract

In recent years, researchers have proposed various models of linear logic with strong connections to measure theory, with probabilistic coherence spaces (PCoh) being one of the most prominent. One of the main limitations of the PCoh model is that it cannot interpret continuous measures. To overcome this obstacle, Ehrhard has extended PCoh to a category of positive cones and linear Scott-continuous functions and shown that it is a model of intuitionistic linear logic. In this work we show that the category PBanLat₁ of perfect Banach lattices and positive linear functions of norm at most 1 can serve the same purpose, with some added benefits. We show that PBanLat₁ is a model of classical linear logic (without exponential) and that PCoh embeds fully and faithfully in PBanLat₁ while preserving the monoidal and *-autonomous structures. Finally, we show how PBanLat₁ can be used to give semantics to a higher-order probabilistic programming language.

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Pedro H. Azevedo de Amorim, Leon Witzman, and Dexter Kozen. Classical Linear Logic in Perfect Banach Lattices. In 33rd EACSL Annual Conference on Computer Science Logic (CSL 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 326, pp. 44:1-44:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{azevedodeamorim_et_al:LIPIcs.CSL.2025.44,
  author =	{Azevedo de Amorim, Pedro H. and Witzman, Leon and Kozen, Dexter},
  title =	{{Classical Linear Logic in Perfect Banach Lattices}},
  booktitle =	{33rd EACSL Annual Conference on Computer Science Logic (CSL 2025)},
  pages =	{44:1--44:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-362-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{326},
  editor =	{Endrullis, J\"{o}rg and Schmitz, Sylvain},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CSL.2025.44},
  URN =		{urn:nbn:de:0030-drops-228013},
  doi =		{10.4230/LIPIcs.CSL.2025.44},
  annote =	{Keywords: Probabilistic Semantics, Linear Logic, Categorical Semantics}
}

Document

DOI: 10.4230/LIPIcs.CALCO.2023.9

String Diagram Rewriting Modulo Commutative (Co)Monoid Structure

Authors: Aleksandar Milosavljević, Robin Piedeleu, and Fabio Zanasi

Published in: LIPIcs, Volume 270, 10th Conference on Algebra and Coalgebra in Computer Science (CALCO 2023)

Abstract

String diagrams constitute an intuitive and expressive graphical syntax that has found application in a very diverse range of fields including concurrency theory, quantum computing, control theory, machine learning, linguistics, and digital circuits. Rewriting theory for string diagrams relies on a combinatorial interpretation as double-pushout rewriting of certain hypergraphs. As previously studied, there is a "tension" in this interpretation: in order to make it sound and complete, we either need to add structure on string diagrams (in particular, Frobenius algebra structure) or pose restrictions on double-pushout rewriting (resulting in "convex" rewriting). From the string diagram viewpoint, imposing a full Frobenius structure may not always be natural or desirable in applications, which motivates our study of a weaker requirement: commutative monoid structure. In this work we characterise string diagram rewriting modulo commutative monoid equations, via a sound and complete interpretation in a suitable notion of double-pushout rewriting of hypergraphs.

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Aleksandar Milosavljević, Robin Piedeleu, and Fabio Zanasi. String Diagram Rewriting Modulo Commutative (Co)Monoid Structure. In 10th Conference on Algebra and Coalgebra in Computer Science (CALCO 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 270, pp. 9:1-9:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{milosavljevic_et_al:LIPIcs.CALCO.2023.9,
  author =	{Milosavljevi\'{c}, Aleksandar and Piedeleu, Robin and Zanasi, Fabio},
  title =	{{String Diagram Rewriting Modulo Commutative (Co)Monoid Structure}},
  booktitle =	{10th Conference on Algebra and Coalgebra in Computer Science (CALCO 2023)},
  pages =	{9:1--9:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-287-7},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{270},
  editor =	{Baldan, Paolo and de Paiva, Valeria},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CALCO.2023.9},
  URN =		{urn:nbn:de:0030-drops-188067},
  doi =		{10.4230/LIPIcs.CALCO.2023.9},
  annote =	{Keywords: String diagrams, Double-pushout rewriting, Commutative monoid}
}

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