34 Search Results for "Cook, James"

Document
Research
DOI: 10.4230/TGDK.3.2.3
GraphRAG on Technical Documents - Impact of Knowledge Graph Schema

Authors: Henri Scaffidi, Melinda Hodkiewicz, Caitlin Woods, and Nicole Roocke

Published in: TGDK, Volume 3, Issue 2 (2025). Transactions on Graph Data and Knowledge, Volume 3, Issue 2

Abstract
Retrieval Augmented Generation (RAG) is seeing rapid adoption in industry to enable employees to query information captured in proprietary data for their organisation. In this work, we test the impact of domain-relevant knowledge graph schemas on the results of Microsoft’s GraphRAG pipeline. Our approach aims to address the poor quality of GraphRAG responses on technical reports rich in domain-specific terms. The use case involves technical reports about geology, chemistry and mineral processing published by the Minerals Research Institute of Western Australia (MRIWA). Four schemas are considered: a simple five-class minerals domain expert-developed schema, an expanded minerals domain schema, the Microsoft GraphRAG auto-generated schema, and a schema-less GraphRAG. These are compared to a conventional baseline RAG. Performance is evaluated using a scoring approach that accounts for the mix of correct, incorrect, additional, and missing content in RAG responses. The results show that the simple five-class minerals domain schema extracts approximately 10% more entities from the MRIWA reports than the other schema options. Additionally, both the five-class and the expanded eight-class minerals domain schemas produce the most factually correct answers and the fewest hallucinations. We attribute this to the minerals-specific schemas extracting more relevant, domain-specific information during the Indexing stage. As a result, the Query stage’s context window includes more high-value content. This contributes to the observed improvement in answer quality compared to the other pipelines. In contrast, pipelines with fewer domain-related entities in the KG retrieve less valuable information, leaving more room for irrelevant content in the context window. Baseline RAG responses were typically shorter, less complete, and contained more hallucinations compared to our GraphRAG pipelines. We provide a complete set of resources at https://github.com/nlp-tlp/GraphRAG-on-Minerals-Domain/tree/main. These resources include links to the MRIWA reports, a set of questions (from simple to challenging) along with domain-expert curated answers, schemas, and evaluations of the pipelines.
Cite as

Henri Scaffidi, Melinda Hodkiewicz, Caitlin Woods, and Nicole Roocke. GraphRAG on Technical Documents - Impact of Knowledge Graph Schema. In Transactions on Graph Data and Knowledge (TGDK), Volume 3, Issue 2, pp. 3:1-3:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@Article{scaffidi_et_al:TGDK.3.2.3,
  author =	{Scaffidi, Henri and Hodkiewicz, Melinda and Woods, Caitlin and Roocke, Nicole},
  title =	{{GraphRAG on Technical Documents - Impact of Knowledge Graph Schema}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{3:1--3:24},
  ISSN =	{2942-7517},
  year =	{2025},
  volume =	{3},
  number =	{2},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.3.2.3},
  URN =		{urn:nbn:de:0030-drops-248131},
  doi =		{10.4230/TGDK.3.2.3},
  annote =	{Keywords: RAG, minerals, local search, global search, entity extraction, competency questions}
}
Document
DOI: 10.4230/LIPIcs.TQC.2025.11
Quantum Catalytic Space

Authors: Harry Buhrman, Marten Folkertsma, Ian Mertz, Florian Speelman, Sergii Strelchuk, Sathyawageeswar Subramanian, and Quinten Tupker

Published in: LIPIcs, Volume 350, 20th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2025)

Abstract
Space complexity is a key field of study in theoretical computer science. In the quantum setting there are clear motivations to understand the power of space-restricted computation, as qubits are an especially precious and limited resource. Recently, a new branch of space-bounded complexity called catalytic computing has shown that reusing space is a very powerful computational resource, especially for subroutines that incur little to no space overhead. While quantum catalysis in an information theoretic context, and the power of "dirty" qubits for quantum computation, has been studied over the years, these models are generally not suitable for use in quantum space-bounded algorithms, as they either rely on specific catalytic states or destroy the memory being borrowed. We define the notion of catalytic computing in the quantum setting and show a number of initial results about the model. First, we show that quantum catalytic logspace can always be computed quantumly in polynomial time; the classical analogue of this is the largest open question in catalytic computing. This also allows quantum catalytic space to be defined in an equivalent way with respect to circuits instead of Turing machines. We also prove that quantum catalytic logspace can simulate log-depth threshold circuits, a class which is known to contain (and believed to strictly contain) quantum logspace, thus showcasing the power of quantum catalytic space. Finally we show that both unitary quantum catalytic logspace and classical catalytic logspace can be simulated in the one-clean qubit model.
Cite as

Harry Buhrman, Marten Folkertsma, Ian Mertz, Florian Speelman, Sergii Strelchuk, Sathyawageeswar Subramanian, and Quinten Tupker. Quantum Catalytic Space. In 20th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 350, pp. 11:1-11:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{buhrman_et_al:LIPIcs.TQC.2025.11,
  author =	{Buhrman, Harry and Folkertsma, Marten and Mertz, Ian and Speelman, Florian and Strelchuk, Sergii and Subramanian, Sathyawageeswar and Tupker, Quinten},
  title =	{{Quantum Catalytic Space}},
  booktitle =	{20th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2025)},
  pages =	{11:1--11:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-392-8},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{350},
  editor =	{Fefferman, Bill},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.TQC.2025.11},
  URN =		{urn:nbn:de:0030-drops-240606},
  doi =		{10.4230/LIPIcs.TQC.2025.11},
  annote =	{Keywords: quantum computing, quantum complexity, space-bounded algorithms, catalytic computation, one clean qubit}
}
Document
DOI: 10.4230/LIPIcs.WADS.2025.49
On the I/O Complexity of the Cocke-Younger-Kasami Algorithm and of a Family of Related Dynamic Programming Algorithms

Authors: Lorenzo De Stefani and Vedant Gupta

Published in: LIPIcs, Volume 349, 19th International Symposium on Algorithms and Data Structures (WADS 2025)

Abstract
Asymptotically tight lower bounds are derived for the Input/Output (I/O) complexity of a class of dynamic programming algorithms, including matrix chain multiplication, optimal polygon triangulation, and the construction of optimal binary search trees. Assuming no recomputation of intermediate values, we establish an Ω(n³/(√M B)) I/O lower bound, where n denotes the size of the input and M denotes the size of the available fast memory (cache). When recomputation is allowed, we show that the same bound holds for M < cn, where c is a positive constant. In the case where M ≥ 2n, we show an Ω(n/B) I/O lower bound. We also discuss algorithms for which the number of executed I/O operations matches asymptotically each of the presented lower bounds, which are thus asymptotically tight. Additionally, we refine our general method to obtain a lower bound for the I/O complexity of the Cocke-Younger-Kasami algorithm, where the size of the grammar impacts the I/O complexity. An upper bound with asymptotically matching performance in many cases is also provided.
Cite as

Lorenzo De Stefani and Vedant Gupta. On the I/O Complexity of the Cocke-Younger-Kasami Algorithm and of a Family of Related Dynamic Programming Algorithms. In 19th International Symposium on Algorithms and Data Structures (WADS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 349, pp. 49:1-49:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{destefani_et_al:LIPIcs.WADS.2025.49,
  author =	{De Stefani, Lorenzo and Gupta, Vedant},
  title =	{{On the I/O Complexity of the Cocke-Younger-Kasami Algorithm and of a Family of Related Dynamic Programming Algorithms}},
  booktitle =	{19th International Symposium on Algorithms and Data Structures (WADS 2025)},
  pages =	{49:1--49:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-398-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{349},
  editor =	{Morin, Pat and Oh, Eunjin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WADS.2025.49},
  URN =		{urn:nbn:de:0030-drops-242800},
  doi =		{10.4230/LIPIcs.WADS.2025.49},
  annote =	{Keywords: I/O complexity, Dynamic Programming Algorithms, Lower Bounds, Recomputation, Cocke-Younger-Kasami}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2025.6
Catalytic Computing and Register Programs Beyond Log-Depth

Authors: Yaroslav Alekseev, Yuval Filmus, Ian Mertz, Alexander Smal, and Antoine Vinciguerra

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

Abstract
In a seminal work, Buhrman et al. (STOC 2014) defined the class CSPACE(s,c) of problems solvable in space s with an additional catalytic tape of size c, which is a tape whose initial content must be restored at the end of the computation. They showed that uniform TC¹ circuits are computable in catalytic logspace, i.e., CL = CSPACE(O(log{n}), 2^{O(log{n})}), thus giving strong evidence that catalytic space gives L strict additional power. Their study focuses on an arithmetic model called register programs, which has been a focal point in development since then. Understanding CL remains a major open problem, as TC¹ remains the most powerful containment to date. In this work, we study the power of catalytic space and register programs to compute circuits of larger depth. Using register programs, we show that for every ε > 0, SAC² ⊆ CSPACE (O((log²n)/(log log n)), 2^{O(log^{1+ε} n)}) . On the other hand, we know that SAC² ⊆ TC² ⊆ CSPACE(O(log²{n}) , 2^{O(log{n})}). Our result thus shows an O(log log n) factor improvement on the free space needed to compute SAC², at the expense of a nearly-polynomial-sized catalytic tape. We also exhibit non-trivial register programs for matrix powering, which is a further step towards showing NC² ⊆ CL.
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Yaroslav Alekseev, Yuval Filmus, Ian Mertz, Alexander Smal, and Antoine Vinciguerra. Catalytic Computing and Register Programs Beyond Log-Depth. In 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 345, pp. 6:1-6:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{alekseev_et_al:LIPIcs.MFCS.2025.6,
  author =	{Alekseev, Yaroslav and Filmus, Yuval and Mertz, Ian and Smal, Alexander and Vinciguerra, Antoine},
  title =	{{Catalytic Computing and Register Programs Beyond Log-Depth}},
  booktitle =	{50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)},
  pages =	{6:1--6:18},
  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.2025.6},
  URN =		{urn:nbn:de:0030-drops-241136},
  doi =		{10.4230/LIPIcs.MFCS.2025.6},
  annote =	{Keywords: catalytic computing, circuit classes, polynomial method}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2025.17
Sensitivity and Query Complexity Under Uncertainty

Authors: Deepu Benson, Balagopal Komarath, Nikhil Mande, Sai Soumya Nalli, Jayalal Sarma, and Karteek Sreenivasaiah

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

Abstract
In this paper, we study the query complexity of Boolean functions in the presence of uncertainty, motivated by parallel computation with an unlimited number of processors where inputs are allowed to be unknown. We allow each query to produce three results: zero, one, or unknown. The output could also be: zero, one, or unknown, with the constraint that we should output "unknown" only when we cannot determine the answer from the revealed input bits. Such an extension of a Boolean function is called its hazard-free extension. - We prove an analogue of Huang’s celebrated sensitivity theorem [Annals of Mathematics, 2019] in our model of query complexity with uncertainty. - We show that the deterministic query complexity of the hazard-free extension of a Boolean function is at most quadratic in its randomized query complexity and quartic in its quantum query complexity, improving upon the best-known bounds in the Boolean world. - We exhibit an exponential gap between the smallest depth (size) of decision trees computing a Boolean function, and those computing its hazard-free extension. - We present general methods to convert decision trees for Boolean functions to those for their hazard-free counterparts, and show optimality of this construction. We also parameterize this result by the maximum number of unknown values in the input. - We show lower bounds on size complexity of decision trees for hazard-free extensions of Boolean functions in terms of the number of prime implicants and prime implicates of the underlying Boolean function.
Cite as

Deepu Benson, Balagopal Komarath, Nikhil Mande, Sai Soumya Nalli, Jayalal Sarma, and Karteek Sreenivasaiah. Sensitivity and Query Complexity Under Uncertainty. In 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 345, pp. 17:1-17:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{benson_et_al:LIPIcs.MFCS.2025.17,
  author =	{Benson, Deepu and Komarath, Balagopal and Mande, Nikhil and Nalli, Sai Soumya and Sarma, Jayalal and Sreenivasaiah, Karteek},
  title =	{{Sensitivity and Query Complexity Under Uncertainty}},
  booktitle =	{50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)},
  pages =	{17:1--17:17},
  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.2025.17},
  URN =		{urn:nbn:de:0030-drops-241240},
  doi =		{10.4230/LIPIcs.MFCS.2025.17},
  annote =	{Keywords: CREW-PRAM, query complexity, decision trees, sensitivity, hazard-free extensions}
}
Document
DOI: 10.4230/LIPIcs.DNA.31.2
A Coupled Reconfiguration Mechanism That Enables Powerful, Pseudoknot-Robust DNA Strand Displacement Devices with 2-Stranded Inputs

Authors: Hope Amber Johnson and Anne Condon

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

Abstract
DNA strand displacement, a collective name for certain behaviors of short strands of DNA, has been used to build many interesting molecular devices over the past few decades. Among those devices are general implementation schemes for Chemical Reaction Networks, suggesting a place in an abstraction hierarchy for complex molecular programming. However, the possibilities of DNA strand displacement are far from fully explored. On a theoretical level, most DNA strand displacement systems are built out of a few simple motifs, with the space of possible motifs otherwise unexplored. On a practical level, the desire for general, large-scale DNA strand displacement systems is not fulfilled. Those systems that are scalable are not general, and those that are general don't scale up well. We have recently been exploring the space of possibilities for DNA strand displacement systems where all input complexes are made out of at most two strands of DNA. As a test case, we've had an open question of whether such systems can implement general Chemical Reaction Networks, in a way that has a certain set of other desirable properties - reversible, systematic, O(1) toeholds, bimolecular reactions, and correct according to CRN bisimulation - that the state-of-the-art implementations with more than 2-stranded inputs have. Until now we've had a few results that have all but one of those desirable properties, including one based on a novel mechanism we called coupled reconfiguration, but that depended on the physically questionable assumption that pseudoknots cannot occur. We wondered whether the same type of mechanism could be done in a pseudoknot-robust way. In this work we show that in fact, coupled reconfiguration can be done in a pseudoknot-robust way, and this mechanism can implement general Chemical Reaction Networks with all inputs being single strands of DNA. Going further, the same motifs used in this mechanism can implement stacks and surface-based bimolecular reactions. Those have been previously studied as part of polymer extensions of the Chemical Reaction Network model, and on an abstract model level, the resulting extensions are Turing-complete in ways the base Chemical Reaction Network model is not. Our mechanisms are significantly different from previously tested DNA strand displacement systems, which raises questions about their ability to be implemented experimentally, but we have some reasons to believe the challenges are solvable. So we present the pseudoknot-robust coupled reconfiguration mechanism and its use for general Chemical Reaction Network implementations; we present the extensions of the mechanism to stack and surface reactions; and we discuss the possible obstacles and solutions to experimental implementation, as well as the theoretical implications of this mechanism.
Cite as

Hope Amber Johnson and Anne Condon. A Coupled Reconfiguration Mechanism That Enables Powerful, Pseudoknot-Robust DNA Strand Displacement Devices with 2-Stranded Inputs. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 2:1-2:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{johnson_et_al:LIPIcs.DNA.31.2,
  author =	{Johnson, Hope Amber and Condon, Anne},
  title =	{{A Coupled Reconfiguration Mechanism That Enables Powerful, Pseudoknot-Robust DNA Strand Displacement Devices with 2-Stranded Inputs}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{2:1--2:23},
  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.31.2},
  URN =		{urn:nbn:de:0030-drops-238514},
  doi =		{10.4230/LIPIcs.DNA.31.2},
  annote =	{Keywords: Molecular programming, DNA strand displacement, Chemical Reaction Networks}
}
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.
Cite as

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.31.9
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.
Cite as

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.CONCUR.2025.4
Monitorability for the Modal Mu-Calculus over Systems with Data: From Practice to Theory

Authors: Luca Aceto, Antonis Achilleos, Duncan Paul Attard, Léo Exibard, Adrian Francalanza, Anna Ingólfsdóttir, and Karoliina Lehtinen

Published in: LIPIcs, Volume 348, 36th International Conference on Concurrency Theory (CONCUR 2025)

Abstract
Runtime verification consists in checking whether a system satisfies a given specification by observing the execution trace it produces. In the regular setting, the modal μ-calculus provides a versatile formalism for expressing specifications of the control flow of the system. This paper focuses on the data flow and studies an extension of that logic that allows it to express data-dependent properties, identifying fragments that can be verified at runtime and with what correctness guarantees. The logic studied here is closely related with register automata with guessing. That correspondence yields a monitor synthesis algorithm, and a strict hierarchy among the various fragments of the logic, in contrast to the regular setting. We then exhibit a fragment of the logic that can express all monitorable formulae in the logic without greatest fixed-points but not in the full logic, and show this is the best we can get.
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Luca Aceto, Antonis Achilleos, Duncan Paul Attard, Léo Exibard, Adrian Francalanza, Anna Ingólfsdóttir, and Karoliina Lehtinen. Monitorability for the Modal Mu-Calculus over Systems with Data: From Practice to Theory. In 36th International Conference on Concurrency Theory (CONCUR 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 348, pp. 4:1-4:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{aceto_et_al:LIPIcs.CONCUR.2025.4,
  author =	{Aceto, Luca and Achilleos, Antonis and Attard, Duncan Paul and Exibard, L\'{e}o and Francalanza, Adrian and Ing\'{o}lfsd\'{o}ttir, Anna and Lehtinen, Karoliina},
  title =	{{Monitorability for the Modal Mu-Calculus over Systems with Data: From Practice to Theory}},
  booktitle =	{36th International Conference on Concurrency Theory (CONCUR 2025)},
  pages =	{4:1--4:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-389-8},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{348},
  editor =	{Bouyer, Patricia and van de Pol, Jaco},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CONCUR.2025.4},
  URN =		{urn:nbn:de:0030-drops-239546},
  doi =		{10.4230/LIPIcs.CONCUR.2025.4},
  annote =	{Keywords: Runtime verification, monitorability, \muHML with data, register automata}
}
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.
Cite as

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
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.CP.2025.19
Analyzing Self-Stabilization of Synchronous Unison via Propositional Satisfiability

Authors: Asma Khoualdia, Sami Cherif, Stéphane Devismes, and Léo Robert

Published in: LIPIcs, Volume 340, 31st International Conference on Principles and Practice of Constraint Programming (CP 2025)

Abstract
Synchronous unison is a classical clock synchronization problem in distributed computing, and especially in self-stabilization. This paper explores the self-stabilization of a synchronous unison algorithm proposed by Arora et al. using a propositional satisfiability-based approach. We give a logical formulation of the algorithm. This formulation includes the uniqueness of clock values at each node, the updates of clocks based on the minimum clock value in the neighborhood, and the detection of convergence or divergence. To optimize the models, additional constraints are introduced to reduce redundant cases of initial configurations to be analyzed. Our approach not only verifies the algorithm’s behaviour but also offers insights into enhancing its robustness and applicability to broader distributed systems.
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Asma Khoualdia, Sami Cherif, Stéphane Devismes, and Léo Robert. Analyzing Self-Stabilization of Synchronous Unison via Propositional Satisfiability. In 31st International Conference on Principles and Practice of Constraint Programming (CP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 340, pp. 19:1-19:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{khoualdia_et_al:LIPIcs.CP.2025.19,
  author =	{Khoualdia, Asma and Cherif, Sami and Devismes, St\'{e}phane and Robert, L\'{e}o},
  title =	{{Analyzing Self-Stabilization of Synchronous Unison via Propositional Satisfiability}},
  booktitle =	{31st International Conference on Principles and Practice of Constraint Programming (CP 2025)},
  pages =	{19:1--19:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-380-5},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{340},
  editor =	{de la Banda, Maria Garcia},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CP.2025.19},
  URN =		{urn:nbn:de:0030-drops-238806},
  doi =		{10.4230/LIPIcs.CP.2025.19},
  annote =	{Keywords: Self-stabilization, Synchronous Unison, Satisfiability}
}
Document
DOI: 10.4230/LIPIcs.CP.2025.21
Practically Feasible Proof Logging for Pseudo-Boolean Optimization

Authors: Wietze Koops, Daniel Le Berre, Magnus O. Myreen, Jakob Nordström, Andy Oertel, Yong Kiam Tan, and Marc Vinyals

Published in: LIPIcs, Volume 340, 31st International Conference on Principles and Practice of Constraint Programming (CP 2025)

Abstract
Certifying solvers have long been standard for decision problems in Boolean satisfiability (SAT), allowing for proof logging and checking with very limited overhead, but developing similar tools for combinatorial optimization has remained a challenge. A recent promising approach covering a wide range of solving paradigms is pseudo-Boolean proof logging, but this has mostly consisted of proof-of-concept works far from delivering the performance required for real-world deployment. In this work, we present an efficient toolchain based on VeriPB and CakePB for formally verified pseudo-Boolean optimization. We implement proof logging for the full range of techniques in the state-of-the-art solvers RoundingSat and Sat4j, including core-guided search and linear programming integration with Farkas certificates and cut generation. Our experimental evaluation shows that proof logging and checking performance in this much more expressive paradigm is now quite close to the level of SAT solving, and hence is clearly practically feasible.
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Wietze Koops, Daniel Le Berre, Magnus O. Myreen, Jakob Nordström, Andy Oertel, Yong Kiam Tan, and Marc Vinyals. Practically Feasible Proof Logging for Pseudo-Boolean Optimization. In 31st International Conference on Principles and Practice of Constraint Programming (CP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 340, pp. 21:1-21:27, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{koops_et_al:LIPIcs.CP.2025.21,
  author =	{Koops, Wietze and Le Berre, Daniel and Myreen, Magnus O. and Nordstr\"{o}m, Jakob and Oertel, Andy and Tan, Yong Kiam and Vinyals, Marc},
  title =	{{Practically Feasible Proof Logging for Pseudo-Boolean Optimization}},
  booktitle =	{31st International Conference on Principles and Practice of Constraint Programming (CP 2025)},
  pages =	{21:1--21:27},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-380-5},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{340},
  editor =	{de la Banda, Maria Garcia},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CP.2025.21},
  URN =		{urn:nbn:de:0030-drops-238825},
  doi =		{10.4230/LIPIcs.CP.2025.21},
  annote =	{Keywords: proof logging, certifying algorithms, combinatorial optimization, certification, pseudo-Boolean solving, 0-1 integer linear programming}
}
Document
DOI: 10.4230/LIPIcs.CP.2025.26
Parallel MIP Solving with Dynamic Task Decomposition

Authors: Peng Lin, Shaowei Cai, Mengchuan Zou, and Shengqi Chen

Published in: LIPIcs, Volume 340, 31st International Conference on Principles and Practice of Constraint Programming (CP 2025)

Abstract
Mixed Integer Programming (MIP) is a foundational model in operations research. Although significant progress has been made in enhancing sequential MIP solvers through sophisticated techniques and heuristics, remarkable developments in computing resources have made parallel solving a promising direction for performance improvement. In this work, we propose a novel parallel MIP solving framework that employs dynamic task decomposition in a divide-and-conquer paradigm. Our framework incorporates a hardness estimate heuristic to identify challenging solving tasks and a reward decaying mechanism to reinforce the task decomposition decision. We apply our framework to two state-of-the-art open-source MIP solvers, SCIP and HiGHS, yielding efficient parallel solvers. Extensive experiments on the full MIPLIB benchmark, using up to 128 cores, demonstrate that our framework yields substantial performance improvements over modern divide-and-conquer parallel solvers. Moreover, our parallel solvers have established new best known solutions for 16 open MIPLIB instances.
Cite as

Peng Lin, Shaowei Cai, Mengchuan Zou, and Shengqi Chen. Parallel MIP Solving with Dynamic Task Decomposition. In 31st International Conference on Principles and Practice of Constraint Programming (CP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 340, pp. 26:1-26:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{lin_et_al:LIPIcs.CP.2025.26,
  author =	{Lin, Peng and Cai, Shaowei and Zou, Mengchuan and Chen, Shengqi},
  title =	{{Parallel MIP Solving with Dynamic Task Decomposition}},
  booktitle =	{31st International Conference on Principles and Practice of Constraint Programming (CP 2025)},
  pages =	{26:1--26:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-380-5},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{340},
  editor =	{de la Banda, Maria Garcia},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CP.2025.26},
  URN =		{urn:nbn:de:0030-drops-238871},
  doi =		{10.4230/LIPIcs.CP.2025.26},
  annote =	{Keywords: Mixed Integer Programming, Parallel Computing, Complete Search, Task Decomposition}
}
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