21 Search Results for "Lutz, Jack H."

Document
DOI: 10.4230/LIPIcs.STACS.2026.75
Effective Versions of Strong Measure Zero

Authors: Matthew Rayman

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

Abstract
Effective versions of strong measure zero sets are developed for various levels of complexity and computability. It is shown that the sets can be equivalently defined using a generalization of supermartingales called odds supermartingales, success rates on supermartingales, predictors, and coverings. We show Borel’s conjecture that a set has strong measure zero if and only if it is countable holds in the time and space bounded setting. At the level of computability this does not hold. We show the computable level contains sequences at arbitrary levels of the hyperarithmetical hierarchy. This is done by proving a correspondence principle yielding a condition for the sets of computable strong measure zero to agree with the classical sets of strong measure zero. An algorithmic version of strong measure zero using lower semicomputability is defined. We show that this notion is equivalent to the set of NCR reals studied by Reimann and Slaman, thereby giving new characterizations of this set. Effective strong packing dimension zero is investigated by requiring success with respect to the limit inferior instead of the limit superior. It is proven that every sequence in the corresponding algorithmic class is decidable. At the level of computability, the sets coincide with a notion of weak countability that we define.
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Matthew Rayman. Effective Versions of Strong Measure Zero. In 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 364, pp. 75:1-75:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{rayman:LIPIcs.STACS.2026.75,
  author =	{Rayman, Matthew},
  title =	{{Effective Versions of Strong Measure Zero}},
  booktitle =	{43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)},
  pages =	{75:1--75:18},
  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.2026.75},
  URN =		{urn:nbn:de:0030-drops-255648},
  doi =		{10.4230/LIPIcs.STACS.2026.75},
  annote =	{Keywords: Strong measure zero, NCR, Effective fractal dimensions, Borel’s Conjecture, Hausdorff dimension, Packing dimension}
}
Document
DOI: 10.4230/LIPIcs.CSL.2026.18
A Modular Framework for Proof-Search via Formalised Modal Completeness in HOL Light

Authors: Antonella Bilotta, Marco Maggesi, and Cosimo Perini Brogi

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

Abstract
We extend the existing HOL Light Library for Modal Systems (HOLMS) to support a modular implementation of modal reasoning within the HOL Light proof assistant. We deeply embed axiomatic calculi and relational semantics for seven normal modal logics (K, T, B, K4, S4, S5, GL) and formalise modal adequacy theorems for these systems. We then leverage those formalisations to implement a mechanism for automated reasoning via proof-search in the associated labelled sequent calculi, which we shallowly embed in HOL Light’s goal-stack mechanism. This way, we equip the general-purpose proof assistant with (semi)decision procedures for these logics that, in case of failure to construct a proof for the input formula, return a certified countermodel within the appropriate class for the logic under consideration. On the methodological side, we propose a precise measure of the modularity of our approach by systematically adopting Christopher Strachey’s distinction between ad hoc and parametric polymorphism throughout the library.
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Antonella Bilotta, Marco Maggesi, and Cosimo Perini Brogi. A Modular Framework for Proof-Search via Formalised Modal Completeness in HOL Light. In 34th EACSL Annual Conference on Computer Science Logic (CSL 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 363, pp. 18:1-18:29, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{bilotta_et_al:LIPIcs.CSL.2026.18,
  author =	{Bilotta, Antonella and Maggesi, Marco and Perini Brogi, Cosimo},
  title =	{{A Modular Framework for Proof-Search via Formalised Modal Completeness in HOL Light}},
  booktitle =	{34th EACSL Annual Conference on Computer Science Logic (CSL 2026)},
  pages =	{18:1--18:29},
  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.2026.18},
  URN =		{urn:nbn:de:0030-drops-254427},
  doi =		{10.4230/LIPIcs.CSL.2026.18},
  annote =	{Keywords: Modal logic, HOL Light, Labelled sequent calculi, Logical verification, Interactive theorem proving, Automated proof-search}
}
Document
Invited Paper
DOI: 10.4230/OASIcs.RW.2024/2025.7
Modern Datalog: Concepts, Methods, Applications (Invited Paper)

Authors: Markus Krötzsch

Published in: OASIcs, Volume 138, Joint Proceedings of the 20th and 21st Reasoning Web Summer Schools (RW 2024 & RW 2025)

Abstract
Pure Datalog is arguably the most fundamental rule language, elegant and simple, but also often too limited to be useful in practice. This has motivated the introduction of many new expressive features, ranging from datatypes and related functions, over aggregates and semi-ring generalisations, to existential quantifiers and complex terms. In spite of their variety, all these approaches remain true to the nature of Datalog as a direct, pattern-based way of computing on structured data. We therefore find that a modern notion of Datalog is emerging, distinctly different from other approaches of logic programming and with its own set of related methods and applications. In this course, we introduce Datalog and its most common extensions, and explain when and how these features can be used together (which is often, but not always, safe to do). We further look at modern Datalog systems and some of their primary use cases. Hands-on work with Datalog and its extensions is done with the free Datalog engine https://knowsys.github.io/nemo-doc/. The course is accessible to all audiences and does not assume specific prior knowledge.
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Markus Krötzsch. Modern Datalog: Concepts, Methods, Applications (Invited Paper). In Joint Proceedings of the 20th and 21st Reasoning Web Summer Schools (RW 2024 & RW 2025). Open Access Series in Informatics (OASIcs), Volume 138, pp. 7:1-7:41, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{krotzsch:OASIcs.RW.2024/2025.7,
  author =	{Kr\"{o}tzsch, Markus},
  title =	{{Modern Datalog: Concepts, Methods, Applications}},
  booktitle =	{Joint Proceedings of the 20th and 21st Reasoning Web Summer Schools (RW 2024 \& RW 2025)},
  pages =	{7:1--7:41},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-405-5},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{138},
  editor =	{Artale, Alessandro and Bienvenu, Meghyn and Garc{\'\i}a, Yazm{\'\i}n Ib\'{a}\~{n}ez and Murlak, Filip},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.RW.2024/2025.7},
  URN =		{urn:nbn:de:0030-drops-250524},
  doi =		{10.4230/OASIcs.RW.2024/2025.7},
  annote =	{Keywords: Datalog, query language, knowlegde representation and reasoning, logic programming, Horn logic, SPARQL, datatypes and aggregation, lecture notes, tutorial}
}
Document
DOI: 10.4230/LIPIcs.DNA.31.3
Reachability in Deletion-Only Chemical Reaction Networks

Authors: Bin Fu, Timothy Gomez, Ryan Knobel, Austin Luchsinger, Aiden Massie, Marco Rodriguez, Adrian Salinas, Robert Schweller, and Tim Wylie

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

Abstract
For general discrete Chemical Reaction Networks (CRNs), the fundamental problem of reachability - the question of whether a target configuration can be produced from a given initial configuration - was recently shown to be Ackermann-complete. However, many open questions remain about which features of the CRN model drive this complexity. We study a restricted class of CRNs with void rules, reactions that only decrease species counts. We further examine this regime in the motivated model of step CRNs, which allow additional species to be introduced in discrete stages. With and without steps, we characterize the complexity of the reachability problem for CRNs with void rules. We show that, without steps, reachability remains polynomial-time solvable for bimolecular systems but becomes NP-complete for larger reactions. Conversely, with just a single step, reachability becomes NP-complete even for bimolecular systems. Our results provide a nearly complete classification of void-rule reachability problems into tractable and intractable cases, with only a single exception.
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Bin Fu, Timothy Gomez, Ryan Knobel, Austin Luchsinger, Aiden Massie, Marco Rodriguez, Adrian Salinas, Robert Schweller, and Tim Wylie. Reachability in Deletion-Only Chemical Reaction Networks. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 3:1-3:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{fu_et_al:LIPIcs.DNA.31.3,
  author =	{Fu, Bin and Gomez, Timothy and Knobel, Ryan and Luchsinger, Austin and Massie, Aiden and Rodriguez, Marco and Salinas, Adrian and Schweller, Robert and Wylie, Tim},
  title =	{{Reachability in Deletion-Only Chemical Reaction Networks}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{3:1--3:21},
  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.31.3},
  URN =		{urn:nbn:de:0030-drops-238521},
  doi =		{10.4230/LIPIcs.DNA.31.3},
  annote =	{Keywords: CRN, Chemical Reaction Network, Reachability, Void Reactions}
}
Document
DOI: 10.4230/LIPIcs.DNA.31.8
An Axiomatic Study of Leveraging Blockers to Self-Assemble Arbitrary Shapes via Temperature Programming

Authors: Matthew J. Patitz and Trent A. Rogers

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

Abstract
In this paper we present a theoretical design for tile-based self-assembling systems where individual tile sets that are universal for various tasks (e.g. building shapes or encoding arbitrary data for algorithmic systems) can be provided their input solely using sequences of variations in temperatures. Although there is prior theoretical work in so-called "temperature programming," the results presented here are based upon recent experimental work with "blocked tiles" that provides plausible evidence for their practical implementation. We develop and present an abstract mathematical model, the BlockTAM, for such systems that is based upon the experimental work, and provide constructions within it for universal number encoding systems and a universal shape building construction. These results mirror previous results in temperature programming, covering the two ends of the spectrum that seek to balance the scale factors of assemblies with the number of temperature phases required, while leveraging the features of the BlockTAM that we hope provide a pathway for future experimental implementations.
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Matthew J. Patitz and Trent A. Rogers. An Axiomatic Study of Leveraging Blockers to Self-Assemble Arbitrary Shapes via Temperature Programming. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 8:1-8:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{patitz_et_al:LIPIcs.DNA.31.8,
  author =	{Patitz, Matthew J. and Rogers, Trent A.},
  title =	{{An Axiomatic Study of Leveraging Blockers to Self-Assemble Arbitrary Shapes via Temperature Programming}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{8:1--8:20},
  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.31.8},
  URN =		{urn:nbn:de:0030-drops-238574},
  doi =		{10.4230/LIPIcs.DNA.31.8},
  annote =	{Keywords: DNA tiles, self-assembly, temperature programming}
}
Document
DOI: 10.4230/LIPIcs.DNA.31.9
Synchronous Versus Asynchronous Tile-Based Self-Assembly

Authors: Florent Becker, Phillip Drake, Matthew J. Patitz, and Trent A. Rogers

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

Abstract
In this paper we study the relationship between mathematical models of tile-based self-assembly which differ in terms of the synchronicity of tile additions. In the standard abstract Tile Assembly Model (aTAM), each step of assembly consists of a single tile being added to an assembly. At any given time, each location on the perimeter of an assembly to which a tile can legally bind is called a frontier location, and for each step of assembly one frontier location is randomly selected and a tile is added. In the Synchronous Tile Assembly Model (syncTAM), at each step of assembly every frontier location simultaneously receives a tile. Our results show that while directed, non-cooperative syncTAM systems are capable of universal computation (while directed, non-cooperative aTAM systems are known not to be), and they are capable of building shapes that can't be built within the aTAM, the non-cooperative aTAM is also capable of building shapes that can't be built within the syncTAM even cooperatively. We show a variety of results that demonstrate the similarities and differences between these two models.
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Florent Becker, Phillip Drake, Matthew J. Patitz, and Trent A. Rogers. Synchronous Versus Asynchronous Tile-Based Self-Assembly. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 9:1-9:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{becker_et_al:LIPIcs.DNA.31.9,
  author =	{Becker, Florent and Drake, Phillip and Patitz, Matthew J. and Rogers, Trent A.},
  title =	{{Synchronous Versus Asynchronous Tile-Based Self-Assembly}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{9:1--9:21},
  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.31.9},
  URN =		{urn:nbn:de:0030-drops-238580},
  doi =		{10.4230/LIPIcs.DNA.31.9},
  annote =	{Keywords: self-assembly, noncooperative self-assembly, models of computation, tile assembly systems}
}
Document
DOI: 10.4230/LIPIcs.FSCD.2025.8
The Unification Type of an Equational Theory May Depend on the Instantiation Preorder

Authors: Franz Baader and Oliver Fernández Gil

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

Abstract
The unification type of an equational theory is defined using a preorder on substitutions, called the instantiation preorder, whose scope is either restricted to the variables occurring in the unification problem, or unrestricted such that all variables are considered. It has been known for more than three decades that the unification type of an equational theory may vary, depending on which instantiation preorder is used. More precisely, it was shown in 1991 that the theory ACUI of an associative, commutative, and idempotent binary function symbol with a unit is unitary w.r.t. the restricted instantiation preorder, but not unitary w.r.t. the unrestricted one. In 2016 this result was strengthened by showing that the unrestricted type of this theory also cannot be finitary. Here, we considerably improve on this result by proving that ACUI is infinitary w.r.t. the unrestricted instantiation preorder, thus precluding type zero. We also show that, w.r.t. this preorder, the unification type of ACU (where idempotency is removed from the axioms) and of AC (where additionally the unit is removed) is infinitary, though it is respectively unitary and finitary in the restricted case. In the other direction, we prove (using the example of unification in the description logic EL) that the unification type may actually improve from type zero to infinitary when switching from the restricted instantiation preorder to the unrestricted one. In addition, we establish some general results on the relationship between the two instantiation preorders.
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Franz Baader and Oliver Fernández Gil. The Unification Type of an Equational Theory May Depend on the Instantiation Preorder. In 10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 337, pp. 8:1-8:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{baader_et_al:LIPIcs.FSCD.2025.8,
  author =	{Baader, Franz and Fern\'{a}ndez Gil, Oliver},
  title =	{{The Unification Type of an Equational Theory May Depend on the Instantiation Preorder}},
  booktitle =	{10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025)},
  pages =	{8:1--8:24},
  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.2025.8},
  URN =		{urn:nbn:de:0030-drops-236230},
  doi =		{10.4230/LIPIcs.FSCD.2025.8},
  annote =	{Keywords: Unification type, Instantiation preorder, Equational theories, Modal and Description Logics}
}
Document
DOI: 10.4230/LIPIcs.SoCG.2025.20
Polynomial-Time Algorithms for Contiguous Art Gallery and Related Problems

Authors: Ahmad Biniaz, Anil Maheshwari, Magnus Christian Ring Merrild, Joseph S. B. Mitchell, Saeed Odak, Valentin Polishchuk, Eliot W. Robson, Casper Moldrup Rysgaard, Jens Kristian Refsgaard Schou, Thomas Shermer, Jack Spalding-Jamieson, Rolf Svenning, and Da Wei Zheng

Published in: LIPIcs, Volume 332, 41st International Symposium on Computational Geometry (SoCG 2025)

Abstract
We introduce the contiguous art gallery problem which is to guard the boundary of a simple polygon with a minimum number of guards such that each guard covers exactly one contiguous portion of the boundary. Art gallery problems are often NP-hard. In particular, it is NP-hard to minimize the number of guards to see the boundary of a simple polygon, without the contiguity constraint. This paper is a merge of three concurrent works [Ahmad Biniaz et al., 2024; Magnus Christian Ring Merrild et al., 2024; Eliot W. Robson et al., 2024] each showing that (surprisingly) the contiguous art gallery problem is solvable in polynomial time. The common idea of all three approaches is developing a greedy function that maps a point on the boundary to the furthest point on the boundary so that the contiguous interval along the boundary between them could be guarded by one guard. Repeatedly applying this function immediately leads to an OPT+1 approximation. By studying this greedy algorithm, we present three different approaches that achieve an optimal solution. The first and second approach apply this greedy algorithm from different points on the boundary that could be found in advance or on the fly while traversing along the boundary (respectively). The third approach represents this function as a piecewise linear rational function, which can be reduced to an abstract arc cover problem involving infinite families of arcs. We identify other problems that can be represented by similar functions, and solve them via the third approach. From the combinatorial point of view, we show that any n-vertex polygon can be guarded by at most ⌊(n-2)/2⌋ guards. This bound is tight because there are polygons that require this many guards.
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Ahmad Biniaz, Anil Maheshwari, Magnus Christian Ring Merrild, Joseph S. B. Mitchell, Saeed Odak, Valentin Polishchuk, Eliot W. Robson, Casper Moldrup Rysgaard, Jens Kristian Refsgaard Schou, Thomas Shermer, Jack Spalding-Jamieson, Rolf Svenning, and Da Wei Zheng. Polynomial-Time Algorithms for Contiguous Art Gallery and Related Problems. In 41st International Symposium on Computational Geometry (SoCG 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 332, pp. 20:1-20:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{biniaz_et_al:LIPIcs.SoCG.2025.20,
  author =	{Biniaz, Ahmad and Maheshwari, Anil and Merrild, Magnus Christian Ring and Mitchell, Joseph S. B. and Odak, Saeed and Polishchuk, Valentin and Robson, Eliot W. and Rysgaard, Casper Moldrup and Schou, Jens Kristian Refsgaard and Shermer, Thomas and Spalding-Jamieson, Jack and Svenning, Rolf and Zheng, Da Wei},
  title =	{{Polynomial-Time Algorithms for Contiguous Art Gallery and Related Problems}},
  booktitle =	{41st International Symposium on Computational Geometry (SoCG 2025)},
  pages =	{20:1--20:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-370-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{332},
  editor =	{Aichholzer, Oswin and Wang, Haitao},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2025.20},
  URN =		{urn:nbn:de:0030-drops-231720},
  doi =		{10.4230/LIPIcs.SoCG.2025.20},
  annote =	{Keywords: Art Gallery Problem, Computational Geometry, Combinatorics, Discrete Algorithms}
}
Document
Brief Announcement
DOI: 10.4230/LIPIcs.SAND.2025.24
Brief Announcement: Intrinsic Universality in Seeded Active Tile Self-Assembly

Authors: Tim Gomez, Elise Grizzell, Asher Haun, Ryan Knobel, Tom Peters, Robert Schweller, and Tim Wylie

Published in: LIPIcs, Volume 330, 4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025)

Abstract
The Tile Automata (TA) model describes self-assembly systems in which monomers can build structures and transition with an adjacent monomer to change their states. This paper shows that seeded TA is a non-committal intrinsically universal model of self-assembly. We present a single universal Tile Automata system containing approximately 4600 states that can simulate (a) the output assemblies created by any other Tile Automata system Γ, (b) the dynamics involved in building Γ’s assemblies, and (c) Γ’s internal state transitions. It does so in a non-committal way: it preserves the full non-deterministic dynamics of a tile’s potential attachment or transition by selecting its state in a single step, considering all possible outcomes until the moment of selection. The system uses supertiles, each encoding the complete system being simulated. The universal system builds supertiles from its seed, each representing a single tile in Γ, transferring the information to simulate Γ to each new tile. Supertiles may also asynchronously transition states according to the rules of Γ. This result also implies IU for pairwise asynchronous Cellular Automata.
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Tim Gomez, Elise Grizzell, Asher Haun, Ryan Knobel, Tom Peters, Robert Schweller, and Tim Wylie. Brief Announcement: Intrinsic Universality in Seeded Active Tile Self-Assembly. In 4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 330, pp. 24:1-24:6, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gomez_et_al:LIPIcs.SAND.2025.24,
  author =	{Gomez, Tim and Grizzell, Elise and Haun, Asher and Knobel, Ryan and Peters, Tom and Schweller, Robert and Wylie, Tim},
  title =	{{Brief Announcement: Intrinsic Universality in Seeded Active Tile Self-Assembly}},
  booktitle =	{4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025)},
  pages =	{24:1--24:6},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-368-3},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{330},
  editor =	{Meeks, Kitty and Scheideler, Christian},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2025.24},
  URN =		{urn:nbn:de:0030-drops-230772},
  doi =		{10.4230/LIPIcs.SAND.2025.24},
  annote =	{Keywords: Intrinsic Universality, Tile Automata, Cellular Automata, Self-assembly}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2024.72
Algorithmic Dimensions via Learning Functions

Authors: Jack H. Lutz and Andrei N. Migunov

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

Abstract
We characterize the algorithmic dimensions (i.e., the lower and upper asymptotic densities of information) of infinite binary sequences in terms of the inability of learning functions having an algorithmic constraint to detect patterns in them. Our pattern detection criterion is a quantitative extension of the criterion that Zaffora Blando used to characterize the algorithmically random (i.e., Martin-Löf random) sequences. Our proof uses Lutz’s and Mayordomo’s respective characterizations of algorithmic dimension in terms of gales and Kolmogorov complexity.
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Jack H. Lutz and Andrei N. Migunov. Algorithmic Dimensions via Learning Functions. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 72:1-72:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{lutz_et_al:LIPIcs.MFCS.2024.72,
  author =	{Lutz, Jack H. and Migunov, Andrei N.},
  title =	{{Algorithmic Dimensions via Learning Functions}},
  booktitle =	{49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)},
  pages =	{72:1--72:13},
  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.2024.72},
  URN =		{urn:nbn:de:0030-drops-206282},
  doi =		{10.4230/LIPIcs.MFCS.2024.72},
  annote =	{Keywords: algorithmic dimensions, learning functions, randomness}
}
Document
Survey
DOI: 10.4230/TGDK.2.1.4
Logics for Conceptual Data Modelling: A Review

Authors: Pablo R. Fillottrani and C. Maria Keet

Published in: TGDK, Volume 2, Issue 1 (2024): Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge, Volume 2, Issue 1

Abstract
Information modelling for databases and object-oriented information systems avails of conceptual data modelling languages such as EER and UML Class Diagrams. Many attempts exist to add logical rigour to them, for various reasons and with disparate strengths. In this paper we aim to provide a structured overview of the many efforts. We focus on aims, approaches to the formalisation, including key dimensions of choice points, popular logics used, and the main relevant reasoning services. We close with current challenges and research directions.
Cite as

Pablo R. Fillottrani and C. Maria Keet. Logics for Conceptual Data Modelling: A Review. In Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge (TGDK), Volume 2, Issue 1, pp. 4:1-4:30, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{fillottrani_et_al:TGDK.2.1.4,
  author =	{Fillottrani, Pablo R. and Keet, C. Maria},
  title =	{{Logics for Conceptual Data Modelling: A Review}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{4:1--4:30},
  ISSN =	{2942-7517},
  year =	{2024},
  volume =	{2},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.2.1.4},
  URN =		{urn:nbn:de:0030-drops-198616},
  doi =		{10.4230/TGDK.2.1.4},
  annote =	{Keywords: Conceptual Data Modelling, EER, UML, Description Logics, OWL}
}
Document
Position
DOI: 10.4230/TGDK.1.1.5
Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities

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

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

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

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

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@Article{chen_et_al:TGDK.1.1.5,
  author =	{Chen, Jiaoyan and Dong, Hang and Hastings, Janna and Jim\'{e}nez-Ruiz, Ernesto and L\'{o}pez, Vanessa and Monnin, Pierre and Pesquita, Catia and \v{S}koda, Petr and Tamma, Valentina},
  title =	{{Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{5:1--5:33},
  year =	{2023},
  volume =	{1},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.1.1.5},
  URN =		{urn:nbn:de:0030-drops-194791},
  doi =		{10.4230/TGDK.1.1.5},
  annote =	{Keywords: Knowledge graphs, Life science, Knowledge discovery, Explainable AI}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2023.65
A Weyl Criterion for Finite-State Dimension and Applications

Authors: Jack H. Lutz, Satyadev Nandakumar, and Subin Pulari

Published in: LIPIcs, Volume 272, 48th International Symposium on Mathematical Foundations of Computer Science (MFCS 2023)

Abstract
Finite-state dimension, introduced early in this century as a finite-state version of classical Hausdorff dimension, is a quantitative measure of the lower asymptotic density of information in an infinite sequence over a finite alphabet, as perceived by finite automata. Finite-state dimension is a robust concept that now has equivalent formulations in terms of finite-state gambling, lossless finite-state data compression, finite-state prediction, entropy rates, and automatic Kolmogorov complexity. The 1972 Schnorr-Stimm dichotomy theorem gave the first automata-theoretic characterization of normal sequences, which had been studied in analytic number theory since Borel defined them in 1909. This theorem implies, in present-day terminology, that a sequence (or a real number having this sequence as its base-b expansion) is normal if and only if it has finite-state dimension 1. One of the most powerful classical tools for investigating normal numbers is the 1916 Weyl’s criterion, which characterizes normality in terms of exponential sums. Such sums are well studied objects with many connections to other aspects of analytic number theory, and this has made use of Weyl’s criterion especially fruitful. This raises the question whether Weyl’s criterion can be generalized from finite-state dimension 1 to arbitrary finite-state dimensions, thereby making it a quantitative tool for studying data compression, prediction, etc. i.e., Can we characterize all compression ratios using exponential sums?. This paper does exactly this. We extend Weyl’s criterion from a characterization of sequences with finite-state dimension 1 to a criterion that characterizes every finite-state dimension. This turns out not to be a routine generalization of the original Weyl criterion. Even though exponential sums may diverge for non-normal numbers, finite-state dimension can be characterized in terms of the dimensions of the subsequence limits of the exponential sums. In case the exponential sums are convergent, they converge to the Fourier coefficients of a probability measure whose dimension is precisely the finite-state dimension of the sequence. This new and surprising connection helps us bring Fourier analytic techniques to bear in proofs in finite-state dimension, yielding a new perspective. We demonstrate the utility of our criterion by substantially improving known results about preservation of finite-state dimension under arithmetic. We strictly generalize the results by Aistleitner and Doty, Lutz and Nandakumar for finite-state dimensions under arithmetic operations. We use the method of exponential sums and our Weyl criterion to obtain the following new result: If y is a number having finite-state strong dimension 0, then dim_FS(x+qy) = dim_FS(x) and Dim_FS(x+qy) = Dim_FS(x) for any x ∈ ℝ and q ∈ ℚ. This generalization uses recent estimates obtained in the work of Hochman [Hochman, 2014] regarding the entropy of convolutions of probability measures.
Cite as

Jack H. Lutz, Satyadev Nandakumar, and Subin Pulari. A Weyl Criterion for Finite-State Dimension and Applications. In 48th International Symposium on Mathematical Foundations of Computer Science (MFCS 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 272, pp. 65:1-65:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{lutz_et_al:LIPIcs.MFCS.2023.65,
  author =	{Lutz, Jack H. and Nandakumar, Satyadev and Pulari, Subin},
  title =	{{A Weyl Criterion for Finite-State Dimension and Applications}},
  booktitle =	{48th International Symposium on Mathematical Foundations of Computer Science (MFCS 2023)},
  pages =	{65:1--65:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-292-1},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{272},
  editor =	{Leroux, J\'{e}r\^{o}me and Lombardy, Sylvain and Peleg, David},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2023.65},
  URN =		{urn:nbn:de:0030-drops-185997},
  doi =		{10.4230/LIPIcs.MFCS.2023.65},
  annote =	{Keywords: Finite-state dimension, Finite-state compression, Weyl’s criterion, Exponential sums, Normal numbers}
}
Document
DOI: 10.4230/LIPIcs.STACS.2022.48
Extending the Reach of the Point-To-Set Principle

Authors: Jack H. Lutz, Neil Lutz, and Elvira Mayordomo

Published in: LIPIcs, Volume 219, 39th International Symposium on Theoretical Aspects of Computer Science (STACS 2022)

Abstract
The point-to-set principle of J. Lutz and N. Lutz (2018) has recently enabled the theory of computing to be used to answer open questions about fractal geometry in Euclidean spaces ℝⁿ. These are classical questions, meaning that their statements do not involve computation or related aspects of logic. In this paper we extend the reach of the point-to-set principle from Euclidean spaces to arbitrary separable metric spaces X. We first extend two fractal dimensions - computability-theoretic versions of classical Hausdorff and packing dimensions that assign dimensions dim(x) and Dim(x) to individual points x ∈ X - to arbitrary separable metric spaces and to arbitrary gauge families. Our first two main results then extend the point-to-set principle to arbitrary separable metric spaces and to a large class of gauge families. We demonstrate the power of our extended point-to-set principle by using it to prove new theorems about classical fractal dimensions in hyperspaces. (For a concrete computational example, the stages E₀, E₁, E₂, … used to construct a self-similar fractal E in the plane are elements of the hyperspace of the plane, and they converge to E in the hyperspace.) Our third main result, proven via our extended point-to-set principle, states that, under a wide variety of gauge families, the classical packing dimension agrees with the classical upper Minkowski dimension on all hyperspaces of compact sets. We use this theorem to give, for all sets E that are analytic, i.e., Σ¹₁, a tight bound on the packing dimension of the hyperspace of E in terms of the packing dimension of E itself.
Cite as

Jack H. Lutz, Neil Lutz, and Elvira Mayordomo. Extending the Reach of the Point-To-Set Principle. In 39th International Symposium on Theoretical Aspects of Computer Science (STACS 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 219, pp. 48:1-48:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{lutz_et_al:LIPIcs.STACS.2022.48,
  author =	{Lutz, Jack H. and Lutz, Neil and Mayordomo, Elvira},
  title =	{{Extending the Reach of the Point-To-Set Principle}},
  booktitle =	{39th International Symposium on Theoretical Aspects of Computer Science (STACS 2022)},
  pages =	{48:1--48:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-222-8},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{219},
  editor =	{Berenbrink, Petra and Monmege, Benjamin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2022.48},
  URN =		{urn:nbn:de:0030-drops-158585},
  doi =		{10.4230/LIPIcs.STACS.2022.48},
  annote =	{Keywords: algorithmic dimensions, geometric measure theory, hyperspace, point-to-set principle}
}
Document
DOI: 10.4230/LIPIcs.DNA.2020.5
Population-Induced Phase Transitions and the Verification of Chemical Reaction Networks

Authors: James I. Lathrop, Jack H. Lutz, Robyn R. Lutz, Hugh D. Potter, and Matthew R. Riley

Published in: LIPIcs, Volume 174, 26th International Conference on DNA Computing and Molecular Programming (DNA 26) (2020)

Abstract
We show that very simple molecular systems, modeled as chemical reaction networks, can have behaviors that exhibit dramatic phase transitions at certain population thresholds. Moreover, the magnitudes of these thresholds can thwart attempts to use simulation, model checking, or approximation by differential equations to formally verify the behaviors of such systems at realistic populations. We show how formal theorem provers can successfully verify some such systems at populations where other verification methods fail.
Cite as

James I. Lathrop, Jack H. Lutz, Robyn R. Lutz, Hugh D. Potter, and Matthew R. Riley. Population-Induced Phase Transitions and the Verification of Chemical Reaction Networks. In 26th International Conference on DNA Computing and Molecular Programming (DNA 26). Leibniz International Proceedings in Informatics (LIPIcs), Volume 174, pp. 5:1-5:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{lathrop_et_al:LIPIcs.DNA.2020.5,
  author =	{Lathrop, James I. and Lutz, Jack H. and Lutz, Robyn R. and Potter, Hugh D. and Riley, Matthew R.},
  title =	{{Population-Induced Phase Transitions and the Verification of Chemical Reaction Networks}},
  booktitle =	{26th International Conference on DNA Computing and Molecular Programming (DNA 26)},
  pages =	{5:1--5:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-163-4},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{174},
  editor =	{Geary, Cody and Patitz, Matthew J.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.2020.5},
  URN =		{urn:nbn:de:0030-drops-129583},
  doi =		{10.4230/LIPIcs.DNA.2020.5},
  annote =	{Keywords: chemical reaction networks, molecular programming, phase transitions, population protocols, verification}
}
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