18 Search Results for "Wilson, Paul W."


Document
Demand-Aware Small-World Networks on Clustered Demands

Authors: Chen Avin, Robert Elsässer, Aleksander Figiel, Darya Melnyk, and Stefan Schmid

Published in: LIPIcs, Volume 361, 29th International Conference on Principles of Distributed Systems (OPODIS 2025)


Abstract
Small-world networks are attractive for the efficient routing they provide, requiring only a low link density. They have hence also been considered for the design of distributed systems, such as peer-to-peer networks. However, existing small-world network designs are oblivious to the actual traffic they serve. In this paper, we initiate the study of demand-aware small-world networks. In particular, we extend the Kleinberg graph model, by allowing the nodes to choose the distribution of long-range links according to the traffic demand. We present a formal analysis of the weighted route lengths for the important case of clustered demands. We show both in theory and in simulations, using real-world traffic workloads, that demand-aware small-world graphs can significantly outperform their demand-oblivious counterparts.

Cite as

Chen Avin, Robert Elsässer, Aleksander Figiel, Darya Melnyk, and Stefan Schmid. Demand-Aware Small-World Networks on Clustered Demands. In 29th International Conference on Principles of Distributed Systems (OPODIS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 361, pp. 28:1-28:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@InProceedings{avin_et_al:LIPIcs.OPODIS.2025.28,
  author =	{Avin, Chen and Els\"{a}sser, Robert and Figiel, Aleksander and Melnyk, Darya and Schmid, Stefan},
  title =	{{Demand-Aware Small-World Networks on Clustered Demands}},
  booktitle =	{29th International Conference on Principles of Distributed Systems (OPODIS 2025)},
  pages =	{28:1--28:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-409-3},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{361},
  editor =	{Arusoaie, Andrei and Onica, Emanuel and Spear, Michael and Tucci-Piergiovanni, Sara},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.OPODIS.2025.28},
  URN =		{urn:nbn:de:0030-drops-252017},
  doi =		{10.4230/LIPIcs.OPODIS.2025.28},
  annote =	{Keywords: Small-world networks, demand-aware network designs, algorithms and analysis, clustering}
}
Document
Conversational Agents: A Framework for Evaluation (CAFE) (Dagstuhl Perspectives Workshop 24352)

Authors: Christine Bauer, Li Chen, Nicola Ferro, Norbert Fuhr, Avishek Anand, Timo Breuer, Guglielmo Faggioli, Ophir Frieder, Hideo Joho, Jussi Karlgren, Johannes Kiesel, Bart P. Knijnenburg, Aldo Lipani, Lien Michiels, Andrea Papenmeier, Maria Soledad Pera, Mark Sanderson, Scott Sanner, Benno Stein, Johanne R. Trippas, Karin Verspoor, and Martijn C. Willemsen

Published in: Dagstuhl Manifestos, Volume 11, Issue 1 (2025)


Abstract
During the workshop, we deeply discussed what CONversational Information ACcess (CONIAC) is and its unique features, proposing a world model abstracting it, and defined the Conversational Agents Framework for Evaluation (CAFE) for the evaluation of CONIAC systems, consisting of six major components: 1) goals of the system’s stakeholders, 2) user tasks to be studied in the evaluation, 3) aspects of the users carrying out the tasks, 4) evaluation criteria to be considered, 5) evaluation methodology to be applied, and 6) measures for the quantitative criteria chosen.

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Christine Bauer, Li Chen, Nicola Ferro, Norbert Fuhr, Avishek Anand, Timo Breuer, Guglielmo Faggioli, Ophir Frieder, Hideo Joho, Jussi Karlgren, Johannes Kiesel, Bart P. Knijnenburg, Aldo Lipani, Lien Michiels, Andrea Papenmeier, Maria Soledad Pera, Mark Sanderson, Scott Sanner, Benno Stein, Johanne R. Trippas, Karin Verspoor, and Martijn C. Willemsen. Conversational Agents: A Framework for Evaluation (CAFE) (Dagstuhl Perspectives Workshop 24352). In Dagstuhl Manifestos, Volume 11, Issue 1, pp. 19-67, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@Article{bauer_et_al:DagMan.11.1.19,
  author =	{Bauer, Christine and Chen, Li and Ferro, Nicola and Fuhr, Norbert and Anand, Avishek and Breuer, Timo and Faggioli, Guglielmo and Frieder, Ophir and Joho, Hideo and Karlgren, Jussi and Kiesel, Johannes and Knijnenburg, Bart P. and Lipani, Aldo and Michiels, Lien and Papenmeier, Andrea and Pera, Maria Soledad and Sanderson, Mark and Sanner, Scott and Stein, Benno and Trippas, Johanne R. and Verspoor, Karin and Willemsen, Martijn C.},
  title =	{{Conversational Agents: A Framework for Evaluation (CAFE) (Dagstuhl Perspectives Workshop 24352)}},
  pages =	{19--67},
  journal =	{Dagstuhl Manifestos},
  ISSN =	{2193-2433},
  year =	{2025},
  volume =	{11},
  number =	{1},
  editor =	{Bauer, Christine and Chen, Li and Ferro, Nicola and Fuhr, Norbert and Anand, Avishek and Breuer, Timo and Faggioli, Guglielmo and Frieder, Ophir and Joho, Hideo and Karlgren, Jussi and Kiesel, Johannes and Knijnenburg, Bart P. and Lipani, Aldo and Michiels, Lien and Papenmeier, Andrea and Pera, Maria Soledad and Sanderson, Mark and Sanner, Scott and Stein, Benno and Trippas, Johanne R. and Verspoor, Karin and Willemsen, Martijn C.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagMan.11.1.19},
  URN =		{urn:nbn:de:0030-drops-252722},
  doi =		{10.4230/DagMan.11.1.19},
  annote =	{Keywords: Conversational Agents, Evaluation, Information Access}
}
Document
Fairness and Efficiency in Two-Sided Matching Markets

Authors: Pallavi Jain, Palash Jha, and Shubham Solanki

Published in: LIPIcs, Volume 360, 45th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2025)


Abstract
We propose a new fairness notion, motivated by the practical challenge of allocating teaching assistants (TAs) to courses in a department. Each course requires a certain number of TAs and each TA has preferences over the courses they want to assist. Similarly, each course instructor has preferences over the TAs who applied for their course. We demand fairness and efficiency for both sides separately, giving rise to the following criteria: (i) every course gets the required number of TAs and the average utility of the assigned TAs meets a threshold; (ii) the allocation of courses to TAs is envy-free, where a TA envies another TA if the former prefers the latter’s course and has a higher or equal grade in that course. Note that the definition of envy-freeness here differs from the one in the literature, and we call it merit-based envy-freeness. We show that the problem of finding a merit-based envy-free and efficient matching is NP-hard even for very restricted settings, such as two courses and uniform valuations; constant degree, constant capacity of TAs for every course, valuations in the range {0,1,2,3}, identical valuations from TAs, and even more. To find tractable results, we consider some restricted instances, such as, strict valuation of TAs for courses, the difference between the number of positively valued TAs for a course and the capacity, the number of positively valued TAs/courses, types of valuation functions, and obtained some polynomial-time solvable cases, showing the contrast with intractable results. We further studied the problem in the paradigm of parameterized algorithms and designed some exact and approximation algorithms.

Cite as

Pallavi Jain, Palash Jha, and Shubham Solanki. Fairness and Efficiency in Two-Sided Matching Markets. In 45th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 360, pp. 38:1-38:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@InProceedings{jain_et_al:LIPIcs.FSTTCS.2025.38,
  author =	{Jain, Pallavi and Jha, Palash and Solanki, Shubham},
  title =	{{Fairness and Efficiency in Two-Sided Matching Markets}},
  booktitle =	{45th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2025)},
  pages =	{38:1--38:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-406-2},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{360},
  editor =	{Aiswarya, C. and Mehta, Ruta and Roy, Subhajit},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSTTCS.2025.38},
  URN =		{urn:nbn:de:0030-drops-251186},
  doi =		{10.4230/LIPIcs.FSTTCS.2025.38},
  annote =	{Keywords: Fair Matching, Envy-Freeness, Efficiency}
}
Document
Edge Clique Partition and Cover Beyond Independence

Authors: Fedor V. Fomin, Petr A. Golovach, Danil Sagunov, and Kirill Simonov

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


Abstract
Covering and partitioning the edges of a graph into cliques are classical problems at the intersection of combinatorial optimization and graph theory, having been studied through a range of algorithmic and complexity-theoretic lenses. Despite the well-known fixed-parameter tractability of these problems when parameterized by the total number of cliques, such a parameterization often fails to be meaningful for sparse graphs. In many real-world instances, on the other hand, the minimum number of cliques in an edge cover or partition can be very close to the size of a maximum independent set α(G). Motivated by this observation, we investigate above-α parameterizations of the edge clique cover and partition problems. Concretely, we introduce and study Edge Clique Cover Above Independent Set (ECC/α) and Edge Clique Partition Above Independent Set (ECP/α), where the goal is to cover or partition all edges of a graph using at most α(G) + k cliques, and k is the parameter. Our main results reveal a distinct complexity landscape for the two variants. We show that ECP/α is fixed-parameter tractable, whereas ECC/α is NP-complete for all k ≥ 2, yet can be solved in polynomial time for k ∈ {0,1}. These findings highlight intriguing differences between the two problems when viewed through the lens of parameterization above a natural lower bound. Finally, we demonstrate that ECC/α becomes fixed-parameter tractable when parameterized by k + ω(G), where ω(G) is the size of a maximum clique of the graph G. This result is particularly relevant for sparse graphs, in which ω is typically small. For H-minor free graphs, we design a subexponential algorithm of running time f(H)^√k ⋅ n^𝒪(1).

Cite as

Fedor V. Fomin, Petr A. Golovach, Danil Sagunov, and Kirill Simonov. Edge Clique Partition and Cover Beyond Independence. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 43:1-43:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@InProceedings{fomin_et_al:LIPIcs.ESA.2025.43,
  author =	{Fomin, Fedor V. and Golovach, Petr A. and Sagunov, Danil and Simonov, Kirill},
  title =	{{Edge Clique Partition and Cover Beyond Independence}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{43:1--43:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-395-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{351},
  editor =	{Benoit, Anne and Kaplan, Haim and Wild, Sebastian and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2025.43},
  URN =		{urn:nbn:de:0030-drops-245113},
  doi =		{10.4230/LIPIcs.ESA.2025.43},
  annote =	{Keywords: edge clique partition, edge clique cover, independence number, parameterized complexity, above guarantee}
}
Document
On the Complexity of Finding 1-Center Spanning Trees

Authors: Pin-Hsian Lee, Meng-Tsung Tsai, and Hung-Lung Wang

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


Abstract
We consider the problem of finding a spanning tree T of a given undirected graph G such that any other spanning tree can be obtained from T by removing k edges and subsequently adding k edges, where k is minimized over all spanning trees of G. We refer to this minimum k as the treeradius of G. Treeradius is an interesting graph parameter with natural interpretations: (1) It is the smallest radius of a Hamming ball centered at an extreme point of the spanning tree polytope that covers the entire polytope. (2) Any graph with bounded treeradius also has bounded treewidth. Consequently, if a problem admits a fixed-parameter algorithm parameterized by treewidth, it also admits a fixed-parameter algorithm parameterized by treeradius. In this paper, we show that computing the exact treeradius for n-vertex graphs requires 2^Ω(n) time under the Exponential Time Hypothesis (ETH) and does not admit a PTAS, with an inapproximability bound of 1153/1152, unless P = NP. This hardness result is surprising, as treeradius has significantly higher ETH complexity compared to analogous problems on shortest path polytopes and star subgraph polytopes.

Cite as

Pin-Hsian Lee, Meng-Tsung Tsai, and Hung-Lung Wang. On the Complexity of Finding 1-Center Spanning Trees. In 19th International Symposium on Algorithms and Data Structures (WADS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 349, pp. 43:1-43:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@InProceedings{lee_et_al:LIPIcs.WADS.2025.43,
  author =	{Lee, Pin-Hsian and Tsai, Meng-Tsung and Wang, Hung-Lung},
  title =	{{On the Complexity of Finding 1-Center Spanning Trees}},
  booktitle =	{19th International Symposium on Algorithms and Data Structures (WADS 2025)},
  pages =	{43:1--43:19},
  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.2025.43},
  URN =		{urn:nbn:de:0030-drops-242743},
  doi =		{10.4230/LIPIcs.WADS.2025.43},
  annote =	{Keywords: Treeradius, Spanning tree polytope, Shortest s, t-path polytope}
}
Document
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
A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences

Authors: Haonan Wu, Antonio Blanca, and Paul Medvedev

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


Abstract
K-mer-based analysis of genomic data is ubiquitous, but the presence of repetitive k-mers continues to pose problems for the accuracy of many methods. For example, the Mash tool (Ondov et al. 2016) can accurately estimate the substitution rate between two low-repetitive sequences from their k-mer sketches; however, it is inaccurate on repetitive sequences such as the centromere of a human chromosome. Follow-up work by Blanca et al. (2021) has attempted to model how mutations affect k-mer sets based on strong assumptions that the sequence is non-repetitive and that mutations do not create spurious k-mer matches. However, the theoretical foundations for extending an estimator like Mash to work in the presence of repeat sequences have been lacking. In this work, we relax the non-repetitive assumption and propose a novel estimator for the mutation rate. We derive theoretical bounds on our estimator’s bias. Our experiments show that it remains accurate for repetitive genomic sequences, such as the alpha satellite higher order repeats in centromeres. We demonstrate our estimator’s robustness across diverse datasets and various ranges of the substitution rate and k-mer size. Finally, we show how sketching can be used to avoid dealing with large k-mer sets while retaining accuracy. Our software is available at https://github.com/medvedevgroup/Repeat-Aware_Substitution_Rate_Estimator.

Cite as

Haonan Wu, Antonio Blanca, and Paul Medvedev. A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 20:1-20:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@InProceedings{wu_et_al:LIPIcs.WABI.2025.20,
  author =	{Wu, Haonan and Blanca, Antonio and Medvedev, Paul},
  title =	{{A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{20:1--20:20},
  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.2025.20},
  URN =		{urn:nbn:de:0030-drops-239465},
  doi =		{10.4230/LIPIcs.WABI.2025.20},
  annote =	{Keywords: k-mers, sketching, mutation rates}
}
Document
Georeferencing Historical Maps at Scale

Authors: Rere-No-A-Rangi Pope and Marcus Frean

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


Abstract
This paper presents a novel approach to automatically georeferencing historical maps using an algorithm based on salient line intersections. Our algorithm addresses the challenges inherent in linking historical map images to contemporary cadastral data, particularly those due to temporal discrepancies, cartographic distortions, and map image noise. By extracting and comparing angular relationships between cadastral features, termed monads and dyads, we establish a robust method for performing record linkage by identifying corresponding spatial patterns across disparate datasets. We employ a Bayesian framework to quantify the likelihood of dyad matches corrupted by measurement noise. The algorithm’s performance was evaluated by selecting a map image and finding putative angle correspondences from the entirety of Aotearoa New Zealand. Even when restricted to a single dyad match, >99% of candidate regions can be successfully filtered out. We discuss the implications and limitations, and suggest strategies for further enhancing the algorithm’s robustness and efficiency. Our work is motivated by previous work in the areas of critical GIS, critical cartography and spatial justice and seeks to contribute to the areas of Spatial Data Science, Historical GIS and GIScience.

Cite as

Rere-No-A-Rangi Pope and Marcus Frean. Georeferencing Historical Maps at Scale. In 13th International Conference on Geographic Information Science (GIScience 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 346, pp. 11:1-11:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@InProceedings{pope_et_al:LIPIcs.GIScience.2025.11,
  author =	{Pope, Rere-No-A-Rangi and Frean, Marcus},
  title =	{{Georeferencing Historical Maps at Scale}},
  booktitle =	{13th International Conference on Geographic Information Science (GIScience 2025)},
  pages =	{11:1--11:11},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-378-2},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{346},
  editor =	{Sila-Nowicka, Katarzyna and Moore, Antoni and O'Sullivan, David and Adams, Benjamin and Gahegan, Mark},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.GIScience.2025.11},
  URN =		{urn:nbn:de:0030-drops-238400},
  doi =		{10.4230/LIPIcs.GIScience.2025.11},
  annote =	{Keywords: Historical GIS, Georeferencing, Record Linkage, Spatial Data Justice}
}
Document
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
Fast Pseudoalignment Queries on Compressed Colored de Bruijn Graphs

Authors: Alessio Campanelli, Giulio Ermanno Pibiri, and Rob Patro

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


Abstract
Motivation. Indexes for the colored de Bruijn graph (c-dBG) play a crucial role in computational biology by facilitating complex tasks such as read mapping and assembly. These indexes map k-mers (substrings of length k) appearing in a large collection of reference strings to the set of identifiers of the strings where they appear. These sets, colloquially referred to as color sets, tend to occupy large quantities of memory, especially for large pangenomes. Our previous work thus focused on leveraging the repetitiveness of the color sets to improve the space effectiveness of the resulting index. As a matter of fact, repetition-aware indexes can be up to one order of magnitude smaller on large pangenomes compared to indexes that do not exploit such repetitiveness. Such improved space effectiveness, on the other hand, imposes an overhead at query time when performing tasks such as pseudoalignment that require the collection and processing of multiple related color sets. Methods. In this paper, we show how to avoid this overhead. We devise novel query algorithms tailored for the specific repetition-aware representations adopted by the Fulgor index, a state-of-the-art c-dBG index, to significantly improve its pseudoalignment efficiency and without consuming additional space. Results. Our results indicate that with increasing redundancy in the pangenomes, the compression factor provided by the Fulgor index increases, while the relative query time actually reduces. For example, while the space of the Fulgor index improves by 2.5× with repetition-aware compression and its query time improves by 1.6× on a collection of 5,000 Salmonella Enterica genomes, these factors become (6.1×,2.8×) and (11.2×,3.2×) for 50,000 and 150,000 genomes respectively. For an even larger collection of 300,000 genomes, we obtained an index that is 22.3× smaller and 2.2× faster.

Cite as

Alessio Campanelli, Giulio Ermanno Pibiri, and Rob Patro. Fast Pseudoalignment Queries on Compressed Colored de Bruijn Graphs. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 6:1-6:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@InProceedings{campanelli_et_al:LIPIcs.WABI.2025.6,
  author =	{Campanelli, Alessio and Pibiri, Giulio Ermanno and Patro, Rob},
  title =	{{Fast Pseudoalignment Queries on Compressed Colored de Bruijn Graphs}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{6:1--6:21},
  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.2025.6},
  URN =		{urn:nbn:de:0030-drops-239327},
  doi =		{10.4230/LIPIcs.WABI.2025.6},
  annote =	{Keywords: Colored de Bruijn graphs, Pseudoalignment, Repetition-aware compression}
}
Document
Modeling and Explaining an Industrial Workforce Allocation and Scheduling Problem

Authors: Ignace Bleukx, Ryma Boumazouza, Tias Guns, Nadine Laage, and Guillaume Poveda

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


Abstract
We present an industrial case on workforce allocation and scheduling in the aircraft manufacturing industry, where available teams need to be assigned to logistical operations. This application presents several challenges such as the scale of the problem, the need for fair workload distribution, and the need for methods for mitigating unforeseen disruptions due to technical malfunctions or incompatible weather conditions. We compare different Constraint Programming (CP) models for the allocation and scheduling problems, with extra focus on modeling the workload balancing component. Additionally, we investigate different techniques for explaining infeasibility of a disrupted schedule, such as conflict computation using Minimal Unsatisfiable Subsets (MUSes) and feasibility restoration using Minimal Correction Subsets (MCSes) or constraint relaxations. Our experimental results show that by using appropriate modeling techniques, the problem can be solved in reasonable time, thereby producing fair schedules. Additionally, we show how invalidated schedules can be explained and restored efficiently to help human operators in solving disruptions to the schedule.

Cite as

Ignace Bleukx, Ryma Boumazouza, Tias Guns, Nadine Laage, and Guillaume Poveda. Modeling and Explaining an Industrial Workforce Allocation and Scheduling Problem. In 31st International Conference on Principles and Practice of Constraint Programming (CP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 340, pp. 6:1-6:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@InProceedings{bleukx_et_al:LIPIcs.CP.2025.6,
  author =	{Bleukx, Ignace and Boumazouza, Ryma and Guns, Tias and Laage, Nadine and Poveda, Guillaume},
  title =	{{Modeling and Explaining an Industrial Workforce Allocation and Scheduling Problem}},
  booktitle =	{31st International Conference on Principles and Practice of Constraint Programming (CP 2025)},
  pages =	{6:1--6:24},
  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.2025.6},
  URN =		{urn:nbn:de:0030-drops-238670},
  doi =		{10.4230/LIPIcs.CP.2025.6},
  annote =	{Keywords: modeling, scheduling, fairness, explanations, feasibility restoration}
}
Document
Experience Paper
WebGlitch: A Randomised Testing Tool for the WebGPU API (Experience Paper)

Authors: Matthew K. L. Wong and Alastair F. Donaldson

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


Abstract
We report on our experience designing a new technique and tool for fuzzing implementations of WebGPU, a W3C standard JavaScript API for in-browser GPU computing. We also report on our experience using our WebGlitch tool to test industrial-strength implementations of WebGPU, leading to the discovery of numerous bugs. WebGPU enables programmatic access to a device’s graphics processing unit (GPU) for in-browser GPU computing, and is being implemented by Google, Mozilla and Apple for inclusion in all of the major web browsers. Guaranteeing the security and reliability of WebGPU is crucial to avoid wide-reaching browser security vulnerabilities and to facilitate portability by ensuring uniform behaviour across different platforms. To that end - inspired by randomised compiler testing techniques - our approach to fuzzing creates random, valid-by-construction programs by continuously selecting a WebGPU API function, then recursively generating all requirements necessary for that API call to be valid based on careful modelling of the API specification. This is implemented as a new open source tool, WebGlitch, which we designed in consultation with engineers at Google who work on the Chrome WebGPU implementation. WebGlitch identifies bugs through sanitiser-boosted crash oracles, differential testing, and by identifying cases where valid-by-construction API calls lead to runtime errors. We present an evaluation showing that WebGlitch can find bugs missed by an existing WebGPU fuzzer, wg-fuzz, and across the broader WebGPU ecosystem: to date, WebGlitch has found 24 previously-unknown bugs (15 fixed so far in response to our reports). Among these, 17 bugs affected WebGPU implementations from Google, Mozilla, and the Deno project. WebGlitch found an additional 4 bugs in the shader compilers used by the graphics APIs that WebGPU interfaces with. The remaining 3 bugs affect the widely-used JavaScript runtimes Node.js and Deno. Fuzzing with WebGlitch also led us to identify an ambiguity in the specification of the WebGPU shading language, for which we proposed an amendment that was accepted by W3C and which has been adopted in the latest version of the specification. Analysing the line coverage of a WebGPU implementation by WebGlitch-generated programs revealed that WebGlitch covers code missed by wg-fuzz and the official conformance test suite. Our hope is that this report on the design of WebGlitch and its deployment in practice will be useful for practitioners and researchers interested in using API fuzzing to improve the reliability of industrial codebases.

Cite as

Matthew K. L. Wong and Alastair F. Donaldson. WebGlitch: A Randomised Testing Tool for the WebGPU API (Experience Paper). In 39th European Conference on Object-Oriented Programming (ECOOP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 333, pp. 39:1-39:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@InProceedings{wong_et_al:LIPIcs.ECOOP.2025.39,
  author =	{Wong, Matthew K. L. and Donaldson, Alastair F.},
  title =	{{WebGlitch: A Randomised Testing Tool for the WebGPU API}},
  booktitle =	{39th European Conference on Object-Oriented Programming (ECOOP 2025)},
  pages =	{39:1--39:26},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-373-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{333},
  editor =	{Aldrich, Jonathan and Silva, Alexandra},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2025.39},
  URN =		{urn:nbn:de:0030-drops-233313},
  doi =		{10.4230/LIPIcs.ECOOP.2025.39},
  annote =	{Keywords: Fuzzing, WebGPU, WGSL, API, shaders}
}
Document
FL-RMQ: A Learned Approach to Range Minimum Queries

Authors: Paolo Ferragina and Filippo Lari

Published in: LIPIcs, Volume 331, 36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025)


Abstract
We address the problem of designing and implementing a data structure for the Range Minimum Query problem. We show a surprising connection between this classical problem and the geometry of a properly defined set of points in the Cartesian plane. Building on this insight, we hinge upon a well-known result in Computational Geometry to introduce the first RMQ solution that exploits (i.e., learns) the distribution of such 2D-points via proper error-bounded linear approximations. Because of these features, we name the resulting data structure: Fully-Learned RMQ, shortly FL-RMQ. We prove theoretical bounds for its space usage and query time, covering both worst-case scenarios and average-case performance for uniformly distributed inputs. These bounds compare favorably with the ones achievable by the best-known indexing solutions (i.e., the ones that allow access to the indexed array), especially when the input data follow some geometric regularities that we characterize in the paper, thus providing principled evidence of FL-RMQ being a novel data-aware solution to the RMQ problem. We corroborate our theoretical findings with a wide set of experiments showing that FL-RMQ offers more robust space-time trade-offs than the other known practical indexing solutions on both artificial and real-world datasets. We believe that our novel approach to the RMQ problem is noteworthy not only for its interesting space-time trade-offs, but also because it is flexible enough to be applied easily to the encoding variant of RMQ (i.e., the one that does not allow access to the indexed array), and moreover, because it paves the way to research opportunities on possibly other problems.

Cite as

Paolo Ferragina and Filippo Lari. FL-RMQ: A Learned Approach to Range Minimum Queries. In 36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 331, pp. 7:1-7:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@InProceedings{ferragina_et_al:LIPIcs.CPM.2025.7,
  author =	{Ferragina, Paolo and Lari, Filippo},
  title =	{{FL-RMQ: A Learned Approach to Range Minimum Queries}},
  booktitle =	{36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025)},
  pages =	{7:1--7:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-369-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{331},
  editor =	{Bonizzoni, Paola and M\"{a}kinen, Veli},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2025.7},
  URN =		{urn:nbn:de:0030-drops-231014},
  doi =		{10.4230/LIPIcs.CPM.2025.7},
  annote =	{Keywords: Range-Minimum query, Learned data structures, Compact data structures, Experimental results}
}
Document
Vision
Trust, Accountability, and Autonomy in Knowledge Graph-Based AI for Self-Determination

Authors: Luis-Daniel Ibáñez, John Domingue, Sabrina Kirrane, Oshani Seneviratne, Aisling Third, and Maria-Esther Vidal

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
Knowledge Graphs (KGs) have emerged as fundamental platforms for powering intelligent decision-making and a wide range of Artificial Intelligence (AI) services across major corporations such as Google, Walmart, and AirBnb. KGs complement Machine Learning (ML) algorithms by providing data context and semantics, thereby enabling further inference and question-answering capabilities. The integration of KGs with neuronal learning (e.g., Large Language Models (LLMs)) is currently a topic of active research, commonly named neuro-symbolic AI. Despite the numerous benefits that can be accomplished with KG-based AI, its growing ubiquity within online services may result in the loss of self-determination for citizens as a fundamental societal issue. The more we rely on these technologies, which are often centralised, the less citizens will be able to determine their own destinies. To counter this threat, AI regulation, such as the European Union (EU) AI Act, is being proposed in certain regions. The regulation sets what technologists need to do, leading to questions concerning How the output of AI systems can be trusted? What is needed to ensure that the data fuelling and the inner workings of these artefacts are transparent? How can AI be made accountable for its decision-making? This paper conceptualises the foundational topics and research pillars to support KG-based AI for self-determination. Drawing upon this conceptual framework, challenges and opportunities for citizen self-determination are illustrated and analysed in a real-world scenario. As a result, we propose a research agenda aimed at accomplishing the recommended objectives.

Cite as

Luis-Daniel Ibáñez, John Domingue, Sabrina Kirrane, Oshani Seneviratne, Aisling Third, and Maria-Esther Vidal. Trust, Accountability, and Autonomy in Knowledge Graph-Based AI for Self-Determination. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 9:1-9:32, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@Article{ibanez_et_al:TGDK.1.1.9,
  author =	{Ib\'{a}\~{n}ez, Luis-Daniel and Domingue, John and Kirrane, Sabrina and Seneviratne, Oshani and Third, Aisling and Vidal, Maria-Esther},
  title =	{{Trust, Accountability, and Autonomy in Knowledge Graph-Based AI for Self-Determination}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{9:1--9:32},
  ISSN =	{2942-7517},
  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.1.1.9},
  URN =		{urn:nbn:de:0030-drops-194839},
  doi =		{10.4230/TGDK.1.1.9},
  annote =	{Keywords: Trust, Accountability, Autonomy, AI, Knowledge Graphs}
}
Document
Position
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}
}
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