23 Search Results for "Jones, Mitchell"

Document
DOI: 10.4230/LIPIcs.SoCG.2026.65
Near-Optimal Dynamic Steiner Spanners for Constant-Curvature Spaces

Authors: Sándor Kisfaludi-Bak and Geert van Wordragen

Published in: LIPIcs, Volume 367, 42nd International Symposium on Computational Geometry (SoCG 2026)

Abstract
We consider Steiner spanners in Euclidean and non-Euclidean geometries. In the Euclidean setting, a recent line of work initiated by Le and Solomon [FOCS'19] and further improved by Chang et al. [SoCG'24] obtained Steiner (1+ε)-spanners of size O_d(ε^{(1-d)/2} log(1/ε) n), nearly matching the lower bound Ω_d(ε^{(1-d)/2} n) of Bhore and Tóth [SIDMA'22]. We obtain Steiner (1+ε)-spanners of size O_d(ε^{(1-d)/2} log(1/ε)n) not only in d-dimensional Euclidean space, but also in d-dimensional spherical and hyperbolic space. For any fixed dimension d, the obtained edge count is optimal up to an O(log(1/ε)) factor in each of these spaces. Unlike earlier constructions, our Steiner spanners are based on simple quadtrees, and they can be dynamically maintained, leading to efficient data structures for dynamic approximate nearest neighbours and bichromatic closest pair. In the hyperbolic setting, we also show that 2-spanners in the hyperbolic plane must have Ω(nlog n) edges, and we obtain a 2-spanner of size O_d(nlog n) in d-dimensional hyperbolic space, matching our lower bound for any constant d. Finally, we give a Steiner spanner with additive error ε in hyperbolic space with O_d(ε^{(1-d)/2} log(α(n)/ε)n) edges, where α(n) is the inverse Ackermann function. Our techniques generalize to closed orientable surfaces of constant curvature as well as to some other quotient spaces.
Cite as

Sándor Kisfaludi-Bak and Geert van Wordragen. Near-Optimal Dynamic Steiner Spanners for Constant-Curvature Spaces. In 42nd International Symposium on Computational Geometry (SoCG 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 367, pp. 65:1-65:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{kisfaludibak_et_al:LIPIcs.SoCG.2026.65,
  author =	{Kisfaludi-Bak, S\'{a}ndor and van Wordragen, Geert},
  title =	{{Near-Optimal Dynamic Steiner Spanners for Constant-Curvature Spaces}},
  booktitle =	{42nd International Symposium on Computational Geometry (SoCG 2026)},
  pages =	{65:1--65:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-418-5},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{367},
  editor =	{Ahn, Hee-Kap and Hoffmann, Michael and Nayyeri, Amir},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2026.65},
  URN =		{urn:nbn:de:0030-drops-258728},
  doi =		{10.4230/LIPIcs.SoCG.2026.65},
  annote =	{Keywords: hyperbolic geometry, Steiner spanner, dynamic approximate nearest neighbours}
}
Document
DOI: 10.4230/LIPIcs.SoCG.2026.13
Dynamic Light Spanners in Doubling Metrics

Authors: Sujoy Bhore, Jonathan Conroy, and Arnold Filtser

Published in: LIPIcs, Volume 367, 42nd International Symposium on Computational Geometry (SoCG 2026)

Abstract
A t-spanner of a point set X in a metric space (𝒳, δ) is a graph G with vertex set P such that, for any pair of points u,v ∈ X, the distance between u and v in G is at most t times δ(u,v). We study the problem of maintaining a spanner for a dynamic point set X - that is, when X undergoes a sequence of insertions and deletions - in a metric space of constant doubling dimension. For any constant ε > 0, we maintain a (1+ε)-spanner of P whose total weight remains within a constant factor of the weight of the minimum spanning tree of X. Each update (insertion or deletion) can be performed in poly(log Φ) time, where Φ denotes the aspect ratio of X. Prior to our work, no efficient dynamic algorithm for maintaining a light-weight spanner was known even for point sets in low-dimensional Euclidean space.
Cite as

Sujoy Bhore, Jonathan Conroy, and Arnold Filtser. Dynamic Light Spanners in Doubling Metrics. In 42nd International Symposium on Computational Geometry (SoCG 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 367, pp. 13:1-13:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{bhore_et_al:LIPIcs.SoCG.2026.13,
  author =	{Bhore, Sujoy and Conroy, Jonathan and Filtser, Arnold},
  title =	{{Dynamic Light Spanners in Doubling Metrics}},
  booktitle =	{42nd International Symposium on Computational Geometry (SoCG 2026)},
  pages =	{13:1--13:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-418-5},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{367},
  editor =	{Ahn, Hee-Kap and Hoffmann, Michael and Nayyeri, Amir},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2026.13},
  URN =		{urn:nbn:de:0030-drops-258193},
  doi =		{10.4230/LIPIcs.SoCG.2026.13},
  annote =	{Keywords: Dynamic data structures, spanners, light-weight, Euclidean metrics, doubling metrics}
}
Document
DOI: 10.4230/OASIcs.NINeS.2026.18
TURBO: Utility-Aware Bandwidth Allocation for Cloud-Augmented Autonomous Control

Authors: Peter Schafhalter, Alexander Krentsel, Hongbo Wei, Joseph E. Gonzalez, Sylvia Ratnasamy, Scott Shenker, and Ion Stoica

Published in: OASIcs, Volume 139, 1st New Ideas in Networked Systems (NINeS 2026)

Abstract
Autonomous driving system progress has been driven by improvements in machine learning (ML) models, whose computational demands now exceed what edge devices alone can provide. The cloud offers abundant compute, but the network has long been treated as an unreliable bottleneck rather than a co-equal part of the autonomous vehicle control loop. We argue that this separation is no longer tenable: safety-critical autonomy requires co-design of control, models, and network resource allocation itself. We introduce TURBO, a cloud-augmented control framework that addresses this challenge, formulating bandwidth allocation and control pipeline configuration across both the car and cloud as a joint optimization problem. TURBO maximizes benefit to the car while guaranteeing safety in the face of highly variable network conditions. We implement TURBO and evaluate it in both simulation and real-world deployment, showing it can improve average accuracy by up to 15.6%pt over existing on-vehicle-only pipelines. Our code is made available at www.github.com/NetSys/turbo.
Cite as

Peter Schafhalter, Alexander Krentsel, Hongbo Wei, Joseph E. Gonzalez, Sylvia Ratnasamy, Scott Shenker, and Ion Stoica. TURBO: Utility-Aware Bandwidth Allocation for Cloud-Augmented Autonomous Control. In 1st New Ideas in Networked Systems (NINeS 2026). Open Access Series in Informatics (OASIcs), Volume 139, pp. 18:1-18:34, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{schafhalter_et_al:OASIcs.NINeS.2026.18,
  author =	{Schafhalter, Peter and Krentsel, Alexander and Wei, Hongbo and Gonzalez, Joseph E. and Ratnasamy, Sylvia and Shenker, Scott and Stoica, Ion},
  title =	{{TURBO: Utility-Aware Bandwidth Allocation for Cloud-Augmented Autonomous Control}},
  booktitle =	{1st New Ideas in Networked Systems (NINeS 2026)},
  pages =	{18:1--18:34},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-414-7},
  ISSN =	{2190-6807},
  year =	{2026},
  volume =	{139},
  editor =	{Argyraki, Katerina and Panda, Aurojit},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.NINeS.2026.18},
  URN =		{urn:nbn:de:0030-drops-256039},
  doi =		{10.4230/OASIcs.NINeS.2026.18},
  annote =	{Keywords: autonomous vehicles, bandwidth allocation, cloud computing, edge computing, machine learning}
}
Document
DOI: 10.4230/OASIcs.NINeS.2026.24
SwiftQueue: Optimizing Low-Latency Applications with Swift Packet Queuing

Authors: Siddhant Ray, Xi Jiang, Jack Luo, Nick Feamster, and Junchen Jiang

Published in: OASIcs, Volume 139, 1st New Ideas in Networked Systems (NINeS 2026)

Abstract
Low Latency, Low Loss, and Scalable Throughput (L4S), as an emerging router-queue management technique, has seen steady deployment in the industry. An L4S-enabled router assigns each packet to the queue based on the packet header marking. Currently, L4S employs per-flow queue selection, i.e., all packets of a flow are marked the same way and thus use the same queues, even though each packet is marked separately. However, this may hurt tail latency and latency-sensitive applications because transient congestion and queue buildups may only affect a fraction of packets in a flow. We present SwiftQueue, a new L4S queue-selection strategy in which a sender uses a novel per-packet latency predictor to pinpoint which packets likely have latency spikes or drops. The insight is that many packet-level latency variations result from complex interactions among recent packets at shared router queues. Yet, these intricate packet-level latency patterns are hard to learn efficiently by traditional models. Instead, SwiftQueue uses a custom Transformer, which is well-studied for its expressiveness on sequential patterns, to predict the next packet’s latency based on the latencies of recently received ACKs. Based on the predicted latency of each outgoing packet, SwiftQueue’s sender dynamically marks the L4S packet header to assign packets to potentially different queues, even within the same flow. Using real network traces, we show that SwiftQueue is 45-65% more accurate in predicting latency and its variations than state-of-art methods. Based on its latency prediction, SwiftQueue reduces the tail latency for L4S-enabled flows by 36-45%, compared with the existing L4S queue-selection method.
Cite as

Siddhant Ray, Xi Jiang, Jack Luo, Nick Feamster, and Junchen Jiang. SwiftQueue: Optimizing Low-Latency Applications with Swift Packet Queuing. In 1st New Ideas in Networked Systems (NINeS 2026). Open Access Series in Informatics (OASIcs), Volume 139, pp. 24:1-24:29, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{ray_et_al:OASIcs.NINeS.2026.24,
  author =	{Ray, Siddhant and Jiang, Xi and Luo, Jack and Feamster, Nick and Jiang, Junchen},
  title =	{{SwiftQueue: Optimizing Low-Latency Applications with Swift Packet Queuing}},
  booktitle =	{1st New Ideas in Networked Systems (NINeS 2026)},
  pages =	{24:1--24:29},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-414-7},
  ISSN =	{2190-6807},
  year =	{2026},
  volume =	{139},
  editor =	{Argyraki, Katerina and Panda, Aurojit},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.NINeS.2026.24},
  URN =		{urn:nbn:de:0030-drops-256093},
  doi =		{10.4230/OASIcs.NINeS.2026.24},
  annote =	{Keywords: Latency prediction, L4S Queue Management}
}
Document
DOI: 10.4230/LIPIcs.CSL.2026.47
Useful Call-by-Value: A Semantic Interpretation via Quantitative Types

Authors: Pablo Barenbaum, Delia Kesner, and Mariana Milicich

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

Abstract
Useful evaluation is an optimised evaluation mechanism for functional programming languages. It relies on representing terms with sharing and imposing a restricted notion of useful substitutions, that intuitively disallows copying subterms that do not contribute to the progress of the computation. In particular, useful call-by-value evaluation optimises the standard call-by-value strategy by preserving its original semantics. This preservation result has been shown by means of syntactical rewriting techniques, difficult to adapt to alternative variants of the calculi at play. In this work, we present the first semantic model of useful call-by-value evaluation through the non-idempotent intersection type system 𝒰. Our first contribution is a characterisation of termination for useful call-by-value evaluation via system 𝒰. That is, a term is typable in system 𝒰 if and only if it terminates in the useful call-by-value strategy. As a second contribution, we show that system 𝒰 provides a quantitative interpretation for useful call-by-value evaluation, offering exact step-count information for program evaluation. Our third contribution is that termination in call-by-value and useful call-by-value are equivalent. This ensures in particular that call-by-value, which is (potentially) erasing, and useful call-by-value, which is non-erasing, are observationally equivalent. Even though the specification of the operational semantics of useful evaluation is highly complex, system 𝒰 is notably simple. As far as we know, system 𝒰 is one of the scarce quantitative type systems capturing exactly the substitution step-count for variables and abstractions in an open call-by-value strategy.
Cite as

Pablo Barenbaum, Delia Kesner, and Mariana Milicich. Useful Call-by-Value: A Semantic Interpretation via Quantitative Types. In 34th EACSL Annual Conference on Computer Science Logic (CSL 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 363, pp. 47:1-47:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{barenbaum_et_al:LIPIcs.CSL.2026.47,
  author =	{Barenbaum, Pablo and Kesner, Delia and Milicich, Mariana},
  title =	{{Useful Call-by-Value: A Semantic Interpretation via Quantitative Types}},
  booktitle =	{34th EACSL Annual Conference on Computer Science Logic (CSL 2026)},
  pages =	{47:1--47:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-411-6},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{363},
  editor =	{Guerrini, Stefano and K\"{o}nig, Barbara},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CSL.2026.47},
  URN =		{urn:nbn:de:0030-drops-254721},
  doi =		{10.4230/LIPIcs.CSL.2026.47},
  annote =	{Keywords: Lambda calculus, Evaluation strategies, Call-by-Value, Useful Evaluation, Intersection types, Quantitative models}
}
Document
APPROX
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2025.25
Covering a Few Submodular Constraints and Applications

Authors: Tanvi Bajpai, Chandra Chekuri, and Pooja Kulkarni

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

Abstract
We consider the problem of covering multiple submodular constraints. Given a finite ground set N, a cost function c: N → ℝ_+, r monotone submodular functions f_1,f_2,…,f_r over N and requirements b_1,b_2,…,b_r the goal is to find a minimum cost subset S ⊆ N such that f_i(S) ≥ b_i for 1 ≤ i ≤ r. When r = 1 this is the well-known Submodular Set Cover problem. Previous work [Chekuri et al., 2022] considered the setting when r is large and developed bi-criteria approximation algorithms, and approximation algorithms for the important special case when each f_i is a weighted coverage function. These are fairly general models and capture several concrete and interesting problems as special cases. The approximation ratios for these problem are at least Ω(log r) which is unavoidable when r is part of the input. In this paper, motivated by some recent applications, we consider the problem when r is a fixed constant and obtain two main results. When the f_i are weighted coverage functions from a deletion-closed set system we obtain a (1+ε)(e/(e-1))(1+β)-approximation where β is the approximation ratio for the underlying set cover instances via the natural LP. Second, for covering multiple submodular constraints we obtain a randomized bi-criteria approximation algorithm that for any given integer α ≥ 1 outputs a set S such that f_i(S) ≥ (1-1/e^α-ε)b_i for each i ∈ [r] and 𝔼[c(S)] ≤ (1+ε)α ⋅ OPT. These results show that one can obtain nearly as good an approximation for any fixed r as what one would achieve for r = 1. We also demonstrate applications of our results to implicit covering problems such as fair facility location.
Cite as

Tanvi Bajpai, Chandra Chekuri, and Pooja Kulkarni. Covering a Few Submodular Constraints and Applications. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 353, pp. 25:1-25:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bajpai_et_al:LIPIcs.APPROX/RANDOM.2025.25,
  author =	{Bajpai, Tanvi and Chekuri, Chandra and Kulkarni, Pooja},
  title =	{{Covering a Few Submodular Constraints and Applications}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)},
  pages =	{25:1--25:22},
  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.2025.25},
  URN =		{urn:nbn:de:0030-drops-243917},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2025.25},
  annote =	{Keywords: covering, linear programming, rounding, fairness}
}
Document
DOI: 10.4230/LIPIcs.WADS.2025.32
Fantastic Flips and Where to Find Them: A General Framework for Parameterized Local Search on Partitioning Problems

Authors: Niels Grüttemeier, Nils Morawietz, and Frank Sommer

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

Abstract
Parameterized local search combines classic local search heuristics with the paradigm of parameterized algorithmics. While most local search algorithms aim to improve given solutions by performing one single operation on a given solution, the parameterized approach aims to improve a solution by performing k simultaneous operations. Herein, k is a parameter called search radius for which the value can be chosen by a user. One major goal in the field of parameterized local search is to outline the trade-off between the size of k and the running time of the local search step. In this work, we introduce an abstract framework that generalizes natural parameterized local search approaches for a large class of partitioning problems: Given n items that are partitioned into b bins and a target function that evaluates the quality of the current partition, one asks whether it is possible to improve the solution by removing up to k items from their current bins and reassigning them to other bins. Among others, our framework applies for the local search versions of problems like Cluster Editing, Vector Bin Packing, and Nash Social Welfare. Motivated by a real-world application of the problem Vector Bin Packing, we introduce a parameter called number of types τ ≤ n and show that all problems fitting in our framework can be solved in τ^k ⋅ 2^𝒪(k) ⋅ |I|^𝒪(1) time, where |I| denotes the total input size. In case of Cluster Editing, the parameter τ generalizes the well-known parameter neighborhood diversity of the input graph. We complement these algorithms by showing that for all considered problems, an algorithm significantly improving over our algorithm with running time τ^k ⋅ 2^𝒪(k) ⋅ |I|^𝒪(1) would contradict the Exponential Time Hypothesis. Additionally, we show that even on very restricted instances, all considered problems are W[1]-hard when parameterized by the search radius k alone. In case of the local search version of Vector Bin Packing, we provide an even stronger W[1]-hardness result.
Cite as

Niels Grüttemeier, Nils Morawietz, and Frank Sommer. Fantastic Flips and Where to Find Them: A General Framework for Parameterized Local Search on Partitioning Problems. In 19th International Symposium on Algorithms and Data Structures (WADS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 349, pp. 32:1-32:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gruttemeier_et_al:LIPIcs.WADS.2025.32,
  author =	{Gr\"{u}ttemeier, Niels and Morawietz, Nils and Sommer, Frank},
  title =	{{Fantastic Flips and Where to Find Them: A General Framework for Parameterized Local Search on Partitioning Problems}},
  booktitle =	{19th International Symposium on Algorithms and Data Structures (WADS 2025)},
  pages =	{32:1--32:20},
  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.2025.32},
  URN =		{urn:nbn:de:0030-drops-242631},
  doi =		{10.4230/LIPIcs.WADS.2025.32},
  annote =	{Keywords: Flip-Neighborhood, Cluster Editing, Vector Bin Packing, Vertex Cover, NP-hard problem, Max c-Cut}
}
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.GIScience.2025.12
Large Multi-Modal Model Cartographic Map Comprehension for Textual Locality Georeferencing

Authors: Kalana Wijegunarathna, Kristin Stock, and Christopher B. Jones

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

Abstract
Millions of biological sample records collected in the last few centuries archived in natural history collections are un-georeferenced. Georeferencing complex locality descriptions associated with these collection samples is a highly labour-intensive task collection agencies struggle with. None of the existing automated methods exploit maps that are an essential tool for georeferencing complex relations. We present preliminary experiments and results of a novel method that exploits multi-modal capabilities of recent Large Multi-Modal Models (LMM). This method enables the model to visually contextualize spatial relations it reads in the locality description. We use a grid-based approach to adapt these auto-regressive models for this task in a zero-shot setting. Our experiments conducted on a small manually annotated dataset show impressive results for our approach (∼1 km Average distance error) compared to uni-modal georeferencing with Large Language Models and existing georeferencing tools. The paper also discusses the findings of the experiments in light of an LMM’s ability to comprehend fine-grained maps. Motivated by these results, a practical framework is proposed to integrate this method into a georeferencing workflow.
Cite as

Kalana Wijegunarathna, Kristin Stock, and Christopher B. Jones. Large Multi-Modal Model Cartographic Map Comprehension for Textual Locality Georeferencing. In 13th International Conference on Geographic Information Science (GIScience 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 346, pp. 12:1-12:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{wijegunarathna_et_al:LIPIcs.GIScience.2025.12,
  author =	{Wijegunarathna, Kalana and Stock, Kristin and Jones, Christopher B.},
  title =	{{Large Multi-Modal Model Cartographic Map Comprehension for Textual Locality Georeferencing}},
  booktitle =	{13th International Conference on Geographic Information Science (GIScience 2025)},
  pages =	{12:1--12:19},
  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.2025.12},
  URN =		{urn:nbn:de:0030-drops-238412},
  doi =		{10.4230/LIPIcs.GIScience.2025.12},
  annote =	{Keywords: Large Multi-Modal Models, Large Language Models, LLM, Georeferencing, Natural History collections}
}
Document
DOI: 10.4230/LIPIcs.FSCD.2025.5
The Cost of Skeletal Call-By-Need, Smoothly

Authors: Beniamino Accattoli, Francesco Magliocca, Loïc Peyrot, and Claudio Sacerdoti Coen

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

Abstract
Skeletal call-by-need is an optimization of call-by-need evaluation also known as "fully lazy sharing": when the duplication of a value has to take place, it is first split into "skeleton", which is then duplicated, and "flesh" which is instead kept shared. Here, we provide two cost analyses of skeletal call-by-need. Firstly, we provide a family of terms showing that skeletal call-by-need can be asymptotically exponentially faster than call-by-need in both time and space; it is the first such evidence, to our knowledge. Secondly, we prove that skeletal call-by-need can be implemented efficiently, that is, with bi-linear overhead. This result is obtained by providing a new smooth presentation of ideas by Shivers and Wand for the reconstruction of skeletons, which is then smoothly plugged into the study of an abstract machine following the distillation technique by Accattoli et al.
Cite as

Beniamino Accattoli, Francesco Magliocca, Loïc Peyrot, and Claudio Sacerdoti Coen. The Cost of Skeletal Call-By-Need, Smoothly. In 10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 337, pp. 5:1-5:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{accattoli_et_al:LIPIcs.FSCD.2025.5,
  author =	{Accattoli, Beniamino and Magliocca, Francesco and Peyrot, Lo\"{i}c and Sacerdoti Coen, Claudio},
  title =	{{The Cost of Skeletal Call-By-Need, Smoothly}},
  booktitle =	{10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025)},
  pages =	{5:1--5:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-374-4},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{337},
  editor =	{Fern\'{a}ndez, Maribel},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSCD.2025.5},
  URN =		{urn:nbn:de:0030-drops-236206},
  doi =		{10.4230/LIPIcs.FSCD.2025.5},
  annote =	{Keywords: \lambda-calculus, abstract machines, call-by-need, cost models}
}
Document
Invited Talk
DOI: 10.4230/LIPIcs.FSCD.2025.3
Unsolvable Terms in Filter Models (Invited Talk)

Authors: Mariangiola Dezani-Ciancaglini, Paola Giannini, and Furio Honsell

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

Abstract
Intersection type theories (itt’s) and filter models, i.e. λ-calculus models generated by itt’s, are reviewed in full generality. In this framework, which subsumes most λ-calculus models in the literature based on Scott-continuous functions, we discuss the interpretation of unsolvable terms. We give a necessary, but not sufficient, condition on an itt for the interpretation of some unsolvable term to be non-trivial in the filter model it generates. This result is obtained building on a type theoretic characterisation of the fine structure of unsolvables.
Cite as

Mariangiola Dezani-Ciancaglini, Paola Giannini, and Furio Honsell. Unsolvable Terms in Filter Models (Invited Talk). In 10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 337, pp. 3:1-3:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{dezaniciancaglini_et_al:LIPIcs.FSCD.2025.3,
  author =	{Dezani-Ciancaglini, Mariangiola and Giannini, Paola and Honsell, Furio},
  title =	{{Unsolvable Terms in Filter Models}},
  booktitle =	{10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025)},
  pages =	{3:1--3:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-374-4},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{337},
  editor =	{Fern\'{a}ndez, Maribel},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSCD.2025.3},
  URN =		{urn:nbn:de:0030-drops-236181},
  doi =		{10.4230/LIPIcs.FSCD.2025.3},
  annote =	{Keywords: \lambda-calculus, Intersection Types, Unsolvable Terms, Filter Models}
}
Document
DOI: 10.4230/LIPIcs.FSCD.2025.20
An Innermost DP Framework for Constrained Higher-Order Rewriting

Authors: Carsten Fuhs, Liye Guo, and Cynthia Kop

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

Abstract
Logically constrained simply-typed term rewriting systems (LCSTRSs) are a higher-order formalism for program analysis with support for primitive data types. The termination problem of LCSTRSs has been studied so far in the setting of full rewriting. This paper modifies the higher-order constrained dependency pair framework to prove innermost termination, which corresponds to the termination of programs under call by value. We also show that the notion of universal computability with respect to innermost rewriting can be effectively handled in the modified, innermost framework, which lays the foundation for open-world termination analysis of programs under call by value via LCSTRSs.
Cite as

Carsten Fuhs, Liye Guo, and Cynthia Kop. An Innermost DP Framework for Constrained Higher-Order Rewriting. In 10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 337, pp. 20:1-20:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{fuhs_et_al:LIPIcs.FSCD.2025.20,
  author =	{Fuhs, Carsten and Guo, Liye and Kop, Cynthia},
  title =	{{An Innermost DP Framework for Constrained Higher-Order Rewriting}},
  booktitle =	{10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025)},
  pages =	{20:1--20:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-374-4},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{337},
  editor =	{Fern\'{a}ndez, Maribel},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSCD.2025.20},
  URN =		{urn:nbn:de:0030-drops-236359},
  doi =		{10.4230/LIPIcs.FSCD.2025.20},
  annote =	{Keywords: Higher-order term rewriting, constrained rewriting, innermost termination, call by value, open-world analysis, dependency pairs}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.61
How to Compute the Volume in Low Dimension?

Authors: Arjan Cornelissen, Simon Apers, and Sander Gribling

Published in: LIPIcs, Volume 334, 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)

Abstract
Estimating the volume of a convex body is a canonical problem in theoretical computer science. Its study has led to major advances in randomized algorithms, Markov chain theory, and computational geometry. In particular, determining the query complexity of volume estimation to a membership oracle has been a longstanding open question. Most of the previous work focuses on the high-dimensional limit. In this work, we tightly characterize the deterministic, randomized and quantum query complexity of this problem in the high-precision limit, i.e., when the dimension is constant.
Cite as

Arjan Cornelissen, Simon Apers, and Sander Gribling. How to Compute the Volume in Low Dimension?. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 61:1-61:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{cornelissen_et_al:LIPIcs.ICALP.2025.61,
  author =	{Cornelissen, Arjan and Apers, Simon and Gribling, Sander},
  title =	{{How to Compute the Volume in Low Dimension?}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{61:1--61:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-372-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{334},
  editor =	{Censor-Hillel, Keren and Grandoni, Fabrizio and Ouaknine, Jo\"{e}l and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2025.61},
  URN =		{urn:nbn:de:0030-drops-234381},
  doi =		{10.4230/LIPIcs.ICALP.2025.61},
  annote =	{Keywords: Query complexity, computational geometry, quantum computing, volume estimation, high-precision limit}
}
Document
DOI: 10.4230/LIPIcs.SoCG.2025.42
Range Counting Oracles for Geometric Problems

Authors: Anne Driemel, Morteza Monemizadeh, Eunjin Oh, Frank Staals, and David P. Woodruff

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

Abstract
In this paper, we study estimators for geometric optimization problems in the sublinear geometric model. In this model, we have oracle access to a point set with size n in a discrete space [Δ]^d, where queries can be made to an oracle that responds to orthogonal range counting requests. The query complexity of an optimization problem is measured by the number of oracle queries required to compute an estimator for the problem. We investigate two problems in this framework, the Euclidean Minimum Spanning Tree (MST) and Earth Mover Distance (EMD). For EMD, we show the existence of an estimator that approximates the cost of EMD with O(log Δ)-relative error and O(nΔ/(s^{1+1/d}))-additive error using O(s polylog Δ) range counting queries for any parameter s with 1 ≤ s ≤ n. Moreover, we prove that this bound is tight. For MST, we demonstrate that the weight of MST can be estimated within a factor of (1 ± ε) using Õ(√n) range counting queries.
Cite as

Anne Driemel, Morteza Monemizadeh, Eunjin Oh, Frank Staals, and David P. Woodruff. Range Counting Oracles for Geometric Problems. In 41st International Symposium on Computational Geometry (SoCG 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 332, pp. 42:1-42:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{driemel_et_al:LIPIcs.SoCG.2025.42,
  author =	{Driemel, Anne and Monemizadeh, Morteza and Oh, Eunjin and Staals, Frank and Woodruff, David P.},
  title =	{{Range Counting Oracles for Geometric Problems}},
  booktitle =	{41st International Symposium on Computational Geometry (SoCG 2025)},
  pages =	{42:1--42:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-370-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{332},
  editor =	{Aichholzer, Oswin and Wang, Haitao},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2025.42},
  URN =		{urn:nbn:de:0030-drops-231941},
  doi =		{10.4230/LIPIcs.SoCG.2025.42},
  annote =	{Keywords: Range counting oracles, minimum spanning trees, Earth Mover’s Distance}
}
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