28 Search Results for "Johnson, Rob"

Document
DOI: 10.4230/LIPIcs.ESA.2025.111
Hardness of Median and Center in the Ulam Metric

Authors: Nick Fischer, Elazar Goldenberg, Mursalin Habib, and Karthik C. S.

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

Abstract
The classical rank aggregation problem seeks to combine a set X of n permutations into a single representative "consensus" permutation. In this paper, we investigate two fundamental rank aggregation tasks under the well-studied Ulam metric: computing a median permutation (which minimizes the sum of Ulam distances to X) and computing a center permutation (which minimizes the maximum Ulam distance to X) in two settings. - Continuous Setting: In the continuous setting, the median/center is allowed to be any permutation. It is known that computing a center in the Ulam metric is NP-hard and we add to this by showing that computing a median is NP-hard as well via a simple reduction from the Max-Cut problem. While this result may not be unexpected, it had remained elusive until now and confirms a speculation by Chakraborty, Das, and Krauthgamer [SODA '21]. - Discrete Setting: In the discrete setting, the median/center must be a permutation from the input set. We fully resolve the fine-grained complexity of the discrete median and discrete center problems under the Ulam metric, proving that the naive Õ(n² L)-time algorithm (where L is the length of the permutation) is conditionally optimal. This resolves an open problem raised by Abboud, Bateni, Cohen-Addad, Karthik C. S., and Seddighin [APPROX '23]. Our reductions are inspired by the known fine-grained lower bounds for similarity measures, but we face and overcome several new highly technical challenges.
Cite as

Nick Fischer, Elazar Goldenberg, Mursalin Habib, and Karthik C. S.. Hardness of Median and Center in the Ulam Metric. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 111:1-111:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{fischer_et_al:LIPIcs.ESA.2025.111,
  author =	{Fischer, Nick and Goldenberg, Elazar and Habib, Mursalin and Karthik C. S.},
  title =	{{Hardness of Median and Center in the Ulam Metric}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{111:1--111:17},
  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.2025.111},
  URN =		{urn:nbn:de:0030-drops-245809},
  doi =		{10.4230/LIPIcs.ESA.2025.111},
  annote =	{Keywords: Ulam distance, median, center, rank aggregation, fine-grained complexity}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.82
Buffered Partially-Persistent External-Memory Search Trees

Authors: Gerth Stølting Brodal, Casper Moldrup Rysgaard, and Rolf Svenning

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

Abstract
We present an optimal partially-persistent external-memory search tree with amortized I/O bounds matching those achieved by the non-persistent B^{ε}-tree by Brodal and Fagerberg [SODA 2003]. In a partially-persistent data structure, each update creates a new version. All past versions can be queried, but only the current version can be updated. Operations should be efficient with respect to the size N_v of the accessed version v. For any parameter 0 < ε < 1, our data structure supports insertions and deletions in amortized 𝒪(1/(ε B^{1 - ε}) log_B N_v) I/Os, where B is the external-memory block size. It also supports successor and range reporting queries in amortized 𝒪(1/ε log_B N_v + K/B) I/Os, where K is the number of keys reported. The space usage of the data structure is linear in the total number of updates. We make the standard and minimal assumption that the internal memory has size M ≥ 2B. The previous state-of-the-art external-memory partially-persistent search tree by Arge, Danner and Teh [JEA 2003] supports all operations in worst-case 𝒪(log_B N_v + K/B) I/Os, matching the bounds achieved by the classical B-tree by Bayer and McCreight [Acta Informatica 1972]. Our data structure successfully combines buffering updates with partial persistence. The I/O bounds can also be achieved in the worst-case sense, by slightly modifying our data structure and under the requirement that the memory size M = Ω(B^{1-ε} log₂(max_v N_v)). For updates, where the I/O bound is o(1), we assume that the I/Os are performed evenly spread out among the updates (by performing buffer-overflows incrementally). The worst-case result slightly improves the memory requirement over the previous ephemeral external-memory dictionary by Das, Iacono, and Nekrich (ISAAC 2022), who achieved matching worst-case I/O bounds but required M = Ω(B log_B N), where N is the size of the current dictionary.
Cite as

Gerth Stølting Brodal, Casper Moldrup Rysgaard, and Rolf Svenning. Buffered Partially-Persistent External-Memory Search Trees. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 82:1-82:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{brodal_et_al:LIPIcs.ESA.2025.82,
  author =	{Brodal, Gerth St{\o}lting and Rysgaard, Casper Moldrup and Svenning, Rolf},
  title =	{{Buffered Partially-Persistent External-Memory Search Trees}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{82:1--82:18},
  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.2025.82},
  URN =		{urn:nbn:de:0030-drops-245507},
  doi =		{10.4230/LIPIcs.ESA.2025.82},
  annote =	{Keywords: B-tree, buffered updates, partial persistence, external memory}
}
Document
DOI: 10.4230/OASIcs.SpaceCHI.2025.15
Integrating Human-In-The-Loop AI to Tackle Space Communication Delay Challenges

Authors: Nikos Mavrakis, Effie Lai-Chong Law, and Hubert P. H. Shum

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

Abstract
Deep space missions face significant communication delays that disrupt both operational workflows and psychological support for crew members. Unlike low Earth orbit operations, delays ranging from several minutes to nearly an hour make real-time communication with mission control infeasible, forcing crews to act with greater independence under uncertain conditions. This position paper examines how human-in-the-loop AI, digital twins, and edge AI can be integrated to mitigate these delays while maintaining astronaut autonomy and engagement. We argue that human-in-the-loop AI enables decision-making processes that are responsive to local context while remaining adaptable to changing mission demands. Digital twins offer real-time simulation and predictive modelling capabilities, allowing astronauts to explore options and troubleshoot without waiting for ground input. Edge AI brings computation closer to data sources, enabling low-latency inference onboard spacecraft for time-critical decisions. These ideas are explored through two use cases: using deepfakes to support emotionally resonant communication with loved ones, and applying visual-language models for onboard fault diagnosis and adaptive task replanning. We conclude with reflections on system design challenges under constrained and high-stakes conditions.
Cite as

Nikos Mavrakis, Effie Lai-Chong Law, and Hubert P. H. Shum. Integrating Human-In-The-Loop AI to Tackle Space Communication Delay Challenges. In Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025). Open Access Series in Informatics (OASIcs), Volume 130, pp. 15:1-15:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{mavrakis_et_al:OASIcs.SpaceCHI.2025.15,
  author =	{Mavrakis, Nikos and Law, Effie Lai-Chong and Shum, Hubert P. H.},
  title =	{{Integrating Human-In-The-Loop AI to Tackle Space Communication Delay Challenges}},
  booktitle =	{Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025)},
  pages =	{15:1--15:16},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-384-3},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{130},
  editor =	{Bensch, Leonie and Nilsson, Tommy and Nisser, Martin and Pataranutaporn, Pat and Schmidt, Albrecht and Sumini, Valentina},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.SpaceCHI.2025.15},
  URN =		{urn:nbn:de:0030-drops-240051},
  doi =		{10.4230/OASIcs.SpaceCHI.2025.15},
  annote =	{Keywords: Human-in-the-loop AI, communication delays, human spaceflight}
}
Document
APPROX
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2025.10
Improved Approximation Guarantees for Advertisement Placement

Authors: Waldo Gálvez, Roberto Oliva, and Victor Verdugo

Published in: LIPIcs, Volume 353, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)

Abstract
The advertisement placement problem involves selecting and scheduling ads within a timeline that has capacity constraints to maximize profit. Each task is characterized by its height, width, and profit, and must be fully scheduled across multiple time slots. This problem models practical scenarios such as internet advertising and energy management, and it also generalizes classical combinatorial optimization problems like the knapsack and bin packing problems. We present a simple (2+ε)-approximation algorithm for any ε > 0, which improves upon the state-of-the-art 3+ε factor established by Freund and Naor twenty years ago. Our approach combines rounding techniques with dynamic programming and an efficient extension of list scheduling. Furthermore, we enhance this method with linear programming techniques to provide an almost optimal (1+ε)-approximation algorithm under resource augmentation, which allows for a slight increase in time slot capacities.
Cite as

Waldo Gálvez, Roberto Oliva, and Victor Verdugo. Improved Approximation Guarantees for Advertisement Placement. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 353, pp. 10:1-10:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{galvez_et_al:LIPIcs.APPROX/RANDOM.2025.10,
  author =	{G\'{a}lvez, Waldo and Oliva, Roberto and Verdugo, Victor},
  title =	{{Improved Approximation Guarantees for Advertisement Placement}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)},
  pages =	{10:1--10:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-397-3},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{353},
  editor =	{Ene, Alina and Chattopadhyay, Eshan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX/RANDOM.2025.10},
  URN =		{urn:nbn:de:0030-drops-243762},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2025.10},
  annote =	{Keywords: Advertisement Placement, Two-dimensional Packing, Geometric Knapsack, Resource Allocation}
}
Document
DOI: 10.4230/LIPIcs.WADS.2025.47
B-Treaps Revised: Write Efficient Randomized Block Search Trees with High Load

Authors: Roodabeh Safavi and Martin P. Seybold

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

Abstract
Uniquely represented (UR) data structures represent each logical state with a unique storage state. We study the problem of maintaining a dynamic set of n keys from a totally ordered universe in this context. UR structures are also called "strongly history independent" structures in the literature. We introduce a two-layer data structure called (α,ε)-Randomized Block Search Tree (RBST) that is uniquely represented and suitable for external memory (EM). Though RBSTs naturally generalize the well-known binary Treaps, several new ideas are needed to analyze the expected search, update, and storage efficiency in terms of block-reads, block-writes, and blocks stored. We prove that searches have O(ε^{-1} + log_α n) block-reads, that dynamic updates perform O(ε^{-1} + log_α(n)/α) block-writes and O(ε^{-2}+(1+(ε^{-1}+log n)/α)log_α n) block-reads, and that (α, ε)-RBSTs have an asymptotic load-factor of at least (1-ε) for every ε ∈ (0,1/2]. Thus (α, ε)-RBSTs improve on the known, uniquely represented B-Treap [Golovin; ICALP'09]. Compared with non-UR structures, the RBST is also, to the best of our knowledge, the first external memory structure that is storage-efficient and has a non-amortized, write-efficient update bound.
Cite as

Roodabeh Safavi and Martin P. Seybold. B-Treaps Revised: Write Efficient Randomized Block Search Trees with High Load. In 19th International Symposium on Algorithms and Data Structures (WADS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 349, pp. 47:1-47:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{safavi_et_al:LIPIcs.WADS.2025.47,
  author =	{Safavi, Roodabeh and Seybold, Martin P.},
  title =	{{B-Treaps Revised: Write Efficient Randomized Block Search Trees with High Load}},
  booktitle =	{19th International Symposium on Algorithms and Data Structures (WADS 2025)},
  pages =	{47:1--47:23},
  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.2025.47},
  URN =		{urn:nbn:de:0030-drops-242786},
  doi =		{10.4230/LIPIcs.WADS.2025.47},
  annote =	{Keywords: Unique Representation, Randomization, Top-Down Analysis, Block Search Tree, Write-Efficiency, Storage-Efficiency}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2025.20
Kernelization in Almost Linear Time for Clustering into Bounded Vertex Cover Components

Authors: Sriram Bhyravarapu, Pritesh Kumar, Madhumita Kundu, Shivesh K. Roy, Sahiba, and Saket Saurabh

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

Abstract
Motivated by the growing interest in graph clustering and the framework proposed during the Dagstuhl Seminar 23331, we consider a natural specialization of this general approach (as also suggested during the seminar). The seminar introduced a broad perspective on clustering, where the goal is to partition a graph into connected components (or "clusters") that satisfy simple structural integrity constraints - not necessarily limited to cliques. In our work, we focus on the case where each cluster is required to have bounded vertex cover number. Specifically, a connected component C satisfies this condition if there exists a set S ⊆ V(C) with |S| ≤ d such that C - S is an independent set. We study this within the framework of the {Vertex Deletion to d-Vertex Cover Components} ({Vertex Deletion to d-VCC}) problem: given a graph G and an integer k, the task is to determine whether there exists a vertex set S ⊆ V(G) of size at most k such that every connected component of G - S has vertex cover number at most d. We also examine the edge-deletion variant, {Edge Deletion to d-Vertex Cover Components} ({Edge Deletion to d-VCC}), where the goal is to delete at most k edges so that each connected component of the resulting graph has vertex cover number at most d. We obtain following results. 1) {Vertex Deletion to d-VCC} admits a kernel with {𝒪}(d⁶k³) vertices and {𝒪}(d⁹k⁴) edges. 2) {Edge Deletion to d-VCC}, admits a kernel with {𝒪}(d⁴k) vertices and {𝒪}(d⁵k) edges. Both of our kernelization algorithms run in time 𝒪(1.253^d ⋅ (kd)^{𝒪(1)} ⋅ n log n). It is important to note that, unless the Exponential Time Hypothesis (ETH) fails, the dependence on d cannot be improved to 2^{o(d)}, as the case k = 0 reduces to solving the classical Vertex Cover problem, which is known to require 2^{Ω(d)} time under ETH. A key ingredient in our kernelization algorithms is a structural result about the hereditary graph class 𝒢_d, consisting of graphs in which every connected component has vertex cover number at most d. We show that 𝒢_d admits a finite obstruction set (with respect to the induced subgraph relation) of size 2^{𝒪(d²)}, where each obstruction graph has at most 3d + 2 vertices. This combinatorial result may be of independent interest.
Cite as

Sriram Bhyravarapu, Pritesh Kumar, Madhumita Kundu, Shivesh K. Roy, Sahiba, and Saket Saurabh. Kernelization in Almost Linear Time for Clustering into Bounded Vertex Cover Components. In 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 345, pp. 20:1-20:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bhyravarapu_et_al:LIPIcs.MFCS.2025.20,
  author =	{Bhyravarapu, Sriram and Kumar, Pritesh and Kundu, Madhumita and Roy, Shivesh K. and Sahiba and Saurabh, Saket},
  title =	{{Kernelization in Almost Linear Time for Clustering into Bounded Vertex Cover Components}},
  booktitle =	{50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)},
  pages =	{20:1--20:18},
  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.2025.20},
  URN =		{urn:nbn:de:0030-drops-241276},
  doi =		{10.4230/LIPIcs.MFCS.2025.20},
  annote =	{Keywords: Parameterized complexity, Polynomial Kernels, Vertex Cover, Finite Forbidden Characterization}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2025.73
Counting Locally Optimal Tours in the TSP

Authors: Bodo Manthey and Jesse van Rhijn

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

Abstract
We show that the problem of counting 2-optimal tours in instances of the Travelling Salesperson Problem (TSP) on complete graphs is #P-complete. In addition, we show that the expected number of 2-optimal tours in random instances of the TSP on complete graphs is O(1.2098ⁿ √{n!}). Based on numerical experiments, we conjecture that the true bound is at most O(√{n!}), which is approximately the square root of the total number of tours.
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Bodo Manthey and Jesse van Rhijn. Counting Locally Optimal Tours in the TSP. In 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 345, pp. 73:1-73:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{manthey_et_al:LIPIcs.MFCS.2025.73,
  author =	{Manthey, Bodo and van Rhijn, Jesse},
  title =	{{Counting Locally Optimal Tours in the TSP}},
  booktitle =	{50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)},
  pages =	{73:1--73:17},
  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.2025.73},
  URN =		{urn:nbn:de:0030-drops-241807},
  doi =		{10.4230/LIPIcs.MFCS.2025.73},
  annote =	{Keywords: Travelling salesman problem, probabilistic analysis, local search, heuristics, 2-opt}
}
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.2025.11
Mutational Signature Refitting on Sparse Pan-Cancer Data

Authors: Gal Gilad, Teresa M. Przytycka, and Roded Sharan

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

Abstract
Mutational processes shape cancer genomes, leaving characteristic marks that are termed signatures. The level of activity of each such process, or its signature exposure, provides important information on the disease, improving patient stratification and the prediction of drug response. Thus, there is growing interest in developing refitting methods that decipher those exposures. Previous work in this domain was unsupervised in nature, employing algebraic decomposition and probabilistic inference methods. Here we provide a supervised approach to the problem of signature refitting and show its superiority over current methods. Our method, SuRe, leverages a neural network model to capture correlations between signature exposures in real data. We show that SuRe outperforms previous methods on sparse mutation data from tumor type specific data sets, as well as pan-cancer data sets, with an increasing advantage as the data become sparser. We further demonstrate its utility in clinical settings.
Cite as

Gal Gilad, Teresa M. Przytycka, and Roded Sharan. Mutational Signature Refitting on Sparse Pan-Cancer Data. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 11:1-11:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gilad_et_al:LIPIcs.WABI.2025.11,
  author =	{Gilad, Gal and Przytycka, Teresa M. and Sharan, Roded},
  title =	{{Mutational Signature Refitting on Sparse Pan-Cancer Data}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{11:1--11:23},
  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.2025.11},
  URN =		{urn:nbn:de:0030-drops-239374},
  doi =		{10.4230/LIPIcs.WABI.2025.11},
  annote =	{Keywords: mutational signatures, signature refitting, cancer genomics, genomic data analysis, somatic mutations}
}
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.SAT.2025.32
Efficient Certified Reasoning for Binarized Neural Networks

Authors: Jiong Yang, Yong Kiam Tan, Mate Soos, Magnus O. Myreen, and Kuldeep S. Meel

Published in: LIPIcs, Volume 341, 28th International Conference on Theory and Applications of Satisfiability Testing (SAT 2025)

Abstract
Neural networks have emerged as essential components in safety-critical applications - these use cases demand complex, yet trustworthy computations. Binarized Neural Networks (BNNs) are a type of neural network where each neuron is constrained to a Boolean value; they are particularly well-suited for safety-critical tasks because they retain much of the computational capacities of full-scale (floating-point or quantized) deep neural networks, but remain compatible with satisfiability solvers for qualitative verification and with model counters for quantitative reasoning. However, existing methods for BNN analysis suffer from either limited scalability or susceptibility to soundness errors, which hinders their applicability in real-world scenarios. In this work, we present a scalable and trustworthy approach for both qualitative and quantitative verification of BNNs. Our approach introduces a native representation of BNN constraints in a custom-designed solver for qualitative reasoning, and in an approximate model counter for quantitative reasoning. We further develop specialized proof generation and checking pipelines with native support for BNN constraint reasoning, ensuring trustworthiness for all of our verification results. Empirical evaluations on a BNN robustness verification benchmark suite demonstrate that our certified solving approach achieves a 9× speedup over prior certified CNF and PB-based approaches, and our certified counting approach achieves a 218× speedup over the existing CNF-based baseline. In terms of coverage, our pipeline produces fully certified results for 99% and 86% of the qualitative and quantitative reasoning queries on BNNs, respectively. This is in sharp contrast to the best existing baselines which can fully certify only 62% and 4% of the queries, respectively.
Cite as

Jiong Yang, Yong Kiam Tan, Mate Soos, Magnus O. Myreen, and Kuldeep S. Meel. Efficient Certified Reasoning for Binarized Neural Networks. In 28th International Conference on Theory and Applications of Satisfiability Testing (SAT 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 341, pp. 32:1-32:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{yang_et_al:LIPIcs.SAT.2025.32,
  author =	{Yang, Jiong and Tan, Yong Kiam and Soos, Mate and Myreen, Magnus O. and Meel, Kuldeep S.},
  title =	{{Efficient Certified Reasoning for Binarized Neural Networks}},
  booktitle =	{28th International Conference on Theory and Applications of Satisfiability Testing (SAT 2025)},
  pages =	{32:1--32:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-381-2},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{341},
  editor =	{Berg, Jeremias and Nordstr\"{o}m, Jakob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAT.2025.32},
  URN =		{urn:nbn:de:0030-drops-237665},
  doi =		{10.4230/LIPIcs.SAT.2025.32},
  annote =	{Keywords: Neural network verification, proof certification, SAT solving, approximate model counting}
}
Document
DOI: 10.4230/LIPIcs.SAT.2025.29
Reencoding Unique Literal Clauses

Authors: Aeacus Sheng, Joseph E. Reeves, and Marijn J. H. Heule

Published in: LIPIcs, Volume 341, 28th International Conference on Theory and Applications of Satisfiability Testing (SAT 2025)

Abstract
We present a lightweight reencoding technique that augments propositional formulas containing implicit or explicit exactly-one constraints with auxiliary variables derived from the order encoding. Our approach is based on the observation that many formulas contain clauses where each literal appears only in that clause, and that these unique literal clauses can be replaced by the corresponding sequential counter encoding of exactly-one constraints, which introduces the same variables as the order encoding. We implemented the reencoding in the state-of-the-art SAT solver CaDiCaL with support for proof logging and solution reconstruction. Experiments on SAT Competition benchmarks demonstrate that our technique enables solving dozens of additional formulas. We found that shuffling a formula before reencoding harms performance. To mitigate this issue, we introduce a method that sorts literals within clauses based on the formula structure before applying our reencoding. The same technique also predicts whether reencoding is likely to yield improvements.
Cite as

Aeacus Sheng, Joseph E. Reeves, and Marijn J. H. Heule. Reencoding Unique Literal Clauses. In 28th International Conference on Theory and Applications of Satisfiability Testing (SAT 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 341, pp. 29:1-29:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{sheng_et_al:LIPIcs.SAT.2025.29,
  author =	{Sheng, Aeacus and Reeves, Joseph E. and Heule, Marijn J. H.},
  title =	{{Reencoding Unique Literal Clauses}},
  booktitle =	{28th International Conference on Theory and Applications of Satisfiability Testing (SAT 2025)},
  pages =	{29:1--29:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-381-2},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{341},
  editor =	{Berg, Jeremias and Nordstr\"{o}m, Jakob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAT.2025.29},
  URN =		{urn:nbn:de:0030-drops-237635},
  doi =		{10.4230/LIPIcs.SAT.2025.29},
  annote =	{Keywords: Satisfiability solving, auxiliary variables, graph coloring}
}
Document
DOI: 10.4230/LIPIcs.SEA.2025.21
PtrHash: Minimal Perfect Hashing at RAM Throughput

Authors: Ragnar Groot Koerkamp

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

Abstract
Motivation. Given a set K of n keys, a minimal perfect hash function (MPHF) is a collision-free bijective map H_mphf from K to {0, … , n-1}. These functions have uses in databases, search engines, and are used in bioinformatics indexing tools such as Pufferfish (using BBHash), and Piscem (PTHash). PTHash is also used in SSHash, a data structure on k-mers that supports membership queries. PTHash only takes around 5% of the total space of SSHash, and thus, trading slightly more space for faster queries is beneficial. Thus, this work presents a (minimal) perfect hash function that first prioritizes query throughput, while also allowing efficient construction for 10⁹ or more elements using 2.4 bits of memory per key. Contributions. Both PTHash and PHOBIC first map all n keys to n/λ < n buckets. Then, each bucket stores a pilot that controls the final hash value of the keys mapping to it. PtrHash builds on this by using 1) fixed-width (uncompressed) 8-bit pilots, 2) a construction algorithm similar to Cuckoo hashing to find suitable pilot values. Further, it partitions the keys, so that keys in each part map to their own set of slots. PtrHash 3) uses the same number of buckets and slots for each part, with 4) a single remap table to map intermediate positions ≥ n to < n, 5) encoded using per-cacheline Elias-Fano coding. Lastly, 6) PtrHash supports streaming queries, where we use prefetching to answer a stream of multiple queries more efficiently than one-by-one processing. Results. With default parameters, PtrHash takes 2.4 bits per key. On 300 million string keys, PtrHash is as fast or faster to build than other MPHFs at a similar size, and at least 2.1× faster to query. When streaming multiple queries, this improves to 3.3× speedup over the fastest alternative, while also being significantly faster to construct. When using 10⁹ integer keys instead, query times are as low as 12 ns/key when iterating in a for loop, or even down to 8 ns/key when using the streaming approach, just short of the 7.4 ns inverse throughput of random memory accesses.
Cite as

Ragnar Groot Koerkamp. PtrHash: Minimal Perfect Hashing at RAM Throughput. In 23rd International Symposium on Experimental Algorithms (SEA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 338, pp. 21:1-21:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{grootkoerkamp:LIPIcs.SEA.2025.21,
  author =	{Groot Koerkamp, Ragnar},
  title =	{{PtrHash: Minimal Perfect Hashing at RAM Throughput}},
  booktitle =	{23rd International Symposium on Experimental Algorithms (SEA 2025)},
  pages =	{21:1--21:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-375-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{338},
  editor =	{Mutzel, Petra and Prezza, Nicola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2025.21},
  URN =		{urn:nbn:de:0030-drops-232597},
  doi =		{10.4230/LIPIcs.SEA.2025.21},
  annote =	{Keywords: Minimal perfect hashing, Compressed Data Structures}
}
Document
DOI: 10.4230/LIPIcs.SEA.2025.25
Blocked Bloom Filters with Choices

Authors: Johanna Elena Schmitz, Jens Zentgraf, and Sven Rahmann

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

Abstract
Probabilistic filters are approximate set membership data structures that represent a set of keys in small space, and answer set membership queries without false negative answers, but with a certain allowed false positive probability. Such filters are widely used in database systems, networks, storage systems and in biological sequence analysis because of their fast query times and low space requirements. Starting with Bloom filters in the 1970s, many filter data structures have been developed, each with its own advantages and disadvantages, e.g., Blocked Bloom filters, Cuckoo filters, XOR filters, Ribbon filters, and more. We introduce Blocked Bloom filters with choices that work similarly to Blocked Bloom filters, except that for each key there are two (or more) alternative choices of blocks where the key’s information may be stored. When inserting a key, we select the block using a cost function which takes into account the current load and the additional number of bits to be set in the candidate blocks. The result is a filter that partially inherits the advantages of a Blocked Bloom filter, such as the ability to insert keys rapidly online or the ability to slightly overload the filter with only a small penalty to the false positive rate. At the same time, it avoids the major disadvantage of a Blocked Bloom filter, namely the larger space consumption. Our new data structure uses less space at the same false positive rate, or has a lower false positive rate at the same space consumption as a Blocked Bloom filter. We discuss the methodology, cost functions for block selection, engineered implementation, a detailed performance evaluation and use cases in bioinformatics of Blocked Bloom filters with choices, showing that they can be of practical value. The implementation of the evaluated filters and the workflows used are provided via Gitlab at https://gitlab.com/rahmannlab/blowchoc-filters.
Cite as

Johanna Elena Schmitz, Jens Zentgraf, and Sven Rahmann. Blocked Bloom Filters with Choices. In 23rd International Symposium on Experimental Algorithms (SEA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 338, pp. 25:1-25:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{schmitz_et_al:LIPIcs.SEA.2025.25,
  author =	{Schmitz, Johanna Elena and Zentgraf, Jens and Rahmann, Sven},
  title =	{{Blocked Bloom Filters with Choices}},
  booktitle =	{23rd International Symposium on Experimental Algorithms (SEA 2025)},
  pages =	{25:1--25:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-375-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{338},
  editor =	{Mutzel, Petra and Prezza, Nicola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2025.25},
  URN =		{urn:nbn:de:0030-drops-232631},
  doi =		{10.4230/LIPIcs.SEA.2025.25},
  annote =	{Keywords: Probabilistic filter, Bloom filter, power of two choices}
}
Document
DOI: 10.4230/LIPIcs.SEA.2025.23
Elias-Fano Compression for Space-Efficient Rank and Select Structures

Authors: Lannie Dalton Hough and Abhinav Bhatele

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

Abstract
Bit vectors are an important component in many data structures. Such data structures are used in a variety of applications and domains including databases, search engines, and computational biology. Many use cases depend on being able to perform rank and/or select queries on the bit vector. No existing rank and select structure enabling these queries is most efficient both for space and for time; there is a tradeoff between the two. In practice, the smallest rank and select data structures, cs-poppy and pasta-flat, impose a space overhead of 3.51%, or 3.125% if only rank needs to be supported. In this paper, we present a new data structure, orzo, which reduces the overhead of the rank component by a further 26.5%. We preserve desirable cache-centric design decisions made in prior work, which allows us to minimize the performance penalty of creating a smaller data structure.
Cite as

Lannie Dalton Hough and Abhinav Bhatele. Elias-Fano Compression for Space-Efficient Rank and Select Structures. In 23rd International Symposium on Experimental Algorithms (SEA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 338, pp. 23:1-23:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{hough_et_al:LIPIcs.SEA.2025.23,
  author =	{Hough, Lannie Dalton and Bhatele, Abhinav},
  title =	{{Elias-Fano Compression for Space-Efficient Rank and Select Structures}},
  booktitle =	{23rd International Symposium on Experimental Algorithms (SEA 2025)},
  pages =	{23:1--23:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-375-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{338},
  editor =	{Mutzel, Petra and Prezza, Nicola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2025.23},
  URN =		{urn:nbn:de:0030-drops-232617},
  doi =		{10.4230/LIPIcs.SEA.2025.23},
  annote =	{Keywords: rank and select, cache-aware, succinct data structures, bit vector}
}
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