DROPS

Document

DOI: 10.4230/LIPIcs.SEA.2026.26

Engineering Algorithms for Dynamic Greedy Set Cover

Authors: Amitai Uzrad

Published in: LIPIcs, Volume 371, 24th International Symposium on Experimental Algorithms (SEA 2026)

Abstract

In the dynamic set cover problem, the input is a dynamic universe of elements and a fixed collection of sets. As elements are inserted or deleted, the goal is to efficiently maintain an approximate minimum set cover. While the past decade has seen significant theoretical breakthroughs for this problem, a notable gap remains between theoretical design and practical performance, as no comprehensive experimental study currently exists to validate these results. In this paper, we bridge this gap by implementing and evaluating four greedy-based dynamic algorithms across a diverse range of real-world instances. We derive our implementations from state-of-the-art frameworks - such as [GKKP(STOC'17); SU(STOC'23); SUZ(FOCS'24)] - which we simplify by identifying and modifying intricate subroutines that optimize asymptotic bounds but hinder practical performance. We evaluate these algorithms based on solution quality (set cover size) and efficiency, which comprises update time - the time required to update the solution following each insertion/deletion - and recourse - the number of changes made to the solution per update. Each algorithm uses a parameter β to balance quality against efficiency; we investigate the influence of this tradeoff parameter on each algorithm and then perform a comparative analysis to evaluate the algorithms against each other. Our results provide the first practical insights into which algorithmic strategies provide the most value in realistic scenarios.

Cite as

Amitai Uzrad. Engineering Algorithms for Dynamic Greedy Set Cover. In 24th International Symposium on Experimental Algorithms (SEA 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 371, pp. 26:1-26:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{uzrad:LIPIcs.SEA.2026.26,
  author =	{Uzrad, Amitai},
  title =	{{Engineering Algorithms for Dynamic Greedy Set Cover}},
  booktitle =	{24th International Symposium on Experimental Algorithms (SEA 2026)},
  pages =	{26:1--26:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-422-2},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{371},
  editor =	{Aum\"{u}ller, Martin and Finocchi, Irene},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2026.26},
  URN =		{urn:nbn:de:0030-drops-260308},
  doi =		{10.4230/LIPIcs.SEA.2026.26},
  annote =	{Keywords: Dynamic graphs, set cover, recourse}
}

Document

DOI: 10.4230/LIPIcs.SoCG.2026.75

Geodesics of Length Less Than πR in a Set of Reach R Are Unique and Continuous with Respect to the Endpoints

Authors: André Lieutier and Mathijs Wintraecken

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

Abstract

Positive reach underpins many results in computational geometry and topology. It is used for triangulation criteria, topological inference, and manifold learning. The geometric properties of these sets have therefore been studied intensely. Here we focus on the shortest paths or minimizing geodesics in these sets. Our main result states that minimizing geodesics of length strictly less than π R in a set of reach R are unique. This in turn implies that such minimizing geodesics are continuous with respect to the endpoints.

Cite as

André Lieutier and Mathijs Wintraecken. Geodesics of Length Less Than πR in a Set of Reach R Are Unique and Continuous with Respect to the Endpoints. In 42nd International Symposium on Computational Geometry (SoCG 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 367, pp. 75:1-75:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{lieutier_et_al:LIPIcs.SoCG.2026.75,
  author =	{Lieutier, Andr\'{e} and Wintraecken, Mathijs},
  title =	{{Geodesics of Length Less Than \piR in a Set of Reach R Are Unique and Continuous with Respect to the Endpoints}},
  booktitle =	{42nd International Symposium on Computational Geometry (SoCG 2026)},
  pages =	{75:1--75:12},
  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.2026.75},
  URN =		{urn:nbn:de:0030-drops-258823},
  doi =		{10.4230/LIPIcs.SoCG.2026.75},
  annote =	{Keywords: Reach, geodesics, metric geometry}
}

Document

DOI: 10.4230/LIPIcs.ICDT.2026.14

Lower Bounds for the Algorithmic Complexity of Learned Indexes

Authors: Luis Alberto Croquevielle, Roman Sokolovskii, and Thomas Heinis

Published in: LIPIcs, Volume 365, 29th International Conference on Database Theory (ICDT 2026)

Abstract

Learned index structures aim to accelerate queries by training machine learning models to approximate the rank function associated with a database attribute. While effective in practice, their theoretical limitations are not fully understood. We present a framework for proving lower bounds on query time for learned indexes, expressed in terms of their space overhead and parameterized by the model class used for approximation. Our formulation captures a broad family of one-dimensional learned indexes, including most existing designs, as piecewise model-based predictors. We solve the problem of lower bounding query time in two steps: first, we use probabilistic tools to control the effect of sampling when the database attribute is drawn from a probability distribution. Then, we analyze the approximation-theoretic problem of how to optimally represent a cumulative distribution function with approximators from a given model class. Within this framework, we derive lower bounds under a range of modeling and distributional assumptions, paying particular attention to the case of piecewise linear and piecewise constant model classes, which are common in practical implementations. Our analysis shows how tools from approximation theory, such as quantization and Kolmogorov widths, can be leveraged to formalize the space-time trade-offs inherent to learned index structures. The resulting bounds illuminate core limitations of these methods.

Cite as

Luis Alberto Croquevielle, Roman Sokolovskii, and Thomas Heinis. Lower Bounds for the Algorithmic Complexity of Learned Indexes. In 29th International Conference on Database Theory (ICDT 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 365, pp. 14:1-14:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{croquevielle_et_al:LIPIcs.ICDT.2026.14,
  author =	{Croquevielle, Luis Alberto and Sokolovskii, Roman and Heinis, Thomas},
  title =	{{Lower Bounds for the Algorithmic Complexity of Learned Indexes}},
  booktitle =	{29th International Conference on Database Theory (ICDT 2026)},
  pages =	{14:1--14:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-413-0},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{365},
  editor =	{ten Cate, Balder and Funk, Maurice},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICDT.2026.14},
  URN =		{urn:nbn:de:0030-drops-256285},
  doi =		{10.4230/LIPIcs.ICDT.2026.14},
  annote =	{Keywords: Learned Indexes, Stochastic Processes, Approximation Theory}
}

Document

DOI: 10.4230/OASIcs.DX.2025.1

Beyond Static Diagnosis: A Temporal ASP Framework for HVAC Fault Detection

Authors: Roxane Koitz-Hristov, Liliana Marie Prikler, and Franz Wotawa

Published in: OASIcs, Volume 136, 36th International Conference on Principles of Diagnosis and Resilient Systems (DX 2025)

Abstract

Improving sustainability in the building sector requires more efficient operation of energy-intensive systems such as Heating, Ventilation, and Air Conditioning (HVAC). We present a novel diagnostic framework for HVAC systems that integrates Answer Set Programming (ASP) with Functional Event Calculus (FEC). Our approach exploits the declarative nature of ASP for modeling and incorporates FEC to capture temporal system dynamics. We demonstrate the feasibility of our approach through a case study on a real-world heating system, where we model key components and system constraints. Our evaluation on nominal and faulty traces shows that exploiting ASP in combination with FEC can identify plausible diagnoses. Moreover, we explore the difference between static and rolling-window strategies and provide insights into runtime versus soundness on those variants. Our work provides a step toward the practical application of ASP-based temporal reasoning in building diagnostics.

Cite as

Roxane Koitz-Hristov, Liliana Marie Prikler, and Franz Wotawa. Beyond Static Diagnosis: A Temporal ASP Framework for HVAC Fault Detection. In 36th International Conference on Principles of Diagnosis and Resilient Systems (DX 2025). Open Access Series in Informatics (OASIcs), Volume 136, pp. 1:1-1:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{koitzhristov_et_al:OASIcs.DX.2025.1,
  author =	{Koitz-Hristov, Roxane and Prikler, Liliana Marie and Wotawa, Franz},
  title =	{{Beyond Static Diagnosis: A Temporal ASP Framework for HVAC Fault Detection}},
  booktitle =	{36th International Conference on Principles of Diagnosis and Resilient Systems (DX 2025)},
  pages =	{1:1--1:20},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-394-2},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{136},
  editor =	{Quinones-Grueiro, Marcos and Biswas, Gautam and Pill, Ingo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.DX.2025.1},
  URN =		{urn:nbn:de:0030-drops-247901},
  doi =		{10.4230/OASIcs.DX.2025.1},
  annote =	{Keywords: Model-based diagnosis, Answer set programming, HVAC, Modeling for diagnosis, Experimental evaluation}
}

Document

PhD Panel

DOI: 10.4230/OASIcs.DX.2025.16

Unsupervised Multimodal Learning for Fault Diagnosis and Prognosis - Application to Radiotherapy Systems (PhD Panel)

Authors: Kélian Poujade, Louise Travé-Massuyès, Jérémy Pirard, and Laure Vieillevigne

Published in: OASIcs, Volume 136, 36th International Conference on Principles of Diagnosis and Resilient Systems (DX 2025)

Abstract

Modern complex systems, such as radiotherapy machines, require robust strategies for fault detection, diagnosis, and prognosis to ensure operational continuity and patient safety. While data-driven methods have gained traction, few studies address diagnostic and prognostic tasks using multimodal operational data under unsupervised or semi-supervised learning settings. This gap is particularly critical given the scarcity of labeled failure data in real-world environments. This work aims to design a unified approach for fault detection, diagnosis, and prognosis using multimodal data in the absence of complete labeling. To this end, autoencoders (AEs) are employed due to their suitability for unsupervised and self-supervised learning, flexibility in handling heterogeneous data, and ability to construct latent representations optimized for various downstream tasks. A specific implementation based on a Long Short-Term Memory β-Variational Autoencoder (LSTM-β-VAE) was developed to detect anomalies in machine logs. This framework is applied to TomoTherapy® systems - a highly complex and under-explored use case within the radiotherapy domain. Initial results demonstrate strong anomaly detection performance on both a public benchmark dataset (HDFS) and a proprietary dataset derived from real-world TomoTherapy® machine faults. Beyond methodology, the paper includes a concise literature review of multimodal learning and data-driven diagnosis and prognosis with a focus on AEs. Based on this review, key research directions are identified for the continuation of the thesis, especially the integration of explainable AI as a means to enhance diagnosis capabilities in the absence of labeled faults.

Cite as

Kélian Poujade, Louise Travé-Massuyès, Jérémy Pirard, and Laure Vieillevigne. Unsupervised Multimodal Learning for Fault Diagnosis and Prognosis - Application to Radiotherapy Systems (PhD Panel). In 36th International Conference on Principles of Diagnosis and Resilient Systems (DX 2025). Open Access Series in Informatics (OASIcs), Volume 136, pp. 16:1-16:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{poujade_et_al:OASIcs.DX.2025.16,
  author =	{Poujade, K\'{e}lian and Trav\'{e}-Massuy\`{e}s, Louise and Pirard, J\'{e}r\'{e}my and Vieillevigne, Laure},
  title =	{{Unsupervised Multimodal Learning for Fault Diagnosis and Prognosis - Application to Radiotherapy Systems}},
  booktitle =	{36th International Conference on Principles of Diagnosis and Resilient Systems (DX 2025)},
  pages =	{16:1--16:17},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-394-2},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{136},
  editor =	{Quinones-Grueiro, Marcos and Biswas, Gautam and Pill, Ingo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.DX.2025.16},
  URN =		{urn:nbn:de:0030-drops-248058},
  doi =		{10.4230/OASIcs.DX.2025.16},
  annote =	{Keywords: Artificial Intelligence, Diagnosis, Prognosis, Radiotherapy machines}
}

Document

DX Competition

DOI: 10.4230/OASIcs.DX.2025.15

Data-Driven Fault Detection and Isolation Enhanced with System Structural Relationships (DX Competition)

Authors: Austin Coursey, Abel Diaz-Gonzalez, Marcos Quinones-Grueiro, and Gautam Biswas

Published in: OASIcs, Volume 136, 36th International Conference on Principles of Diagnosis and Resilient Systems (DX 2025)

Abstract

Fault detection and isolation are becoming increasingly important as modern systems become more complex. To encourage the development of new fault detection solutions that can operate with limited noisy data and an incomplete mathematical model, the DX 2025 LiU-ICE competition for diagnosis of the air path of an internal combustion engine was introduced. In this paper, we present our winning solution to this competition. Our fault detection architecture starts with a semi-supervised Transformer Autoencoder trained to reconstruct nominal data. Detected faults are then passed through a rule-based fault persistence filter that aims to suppress false positives. Once a fault is detected, we use four neural networks trained to estimate features determined from structural analysis of a partial system model. The residuals of these networks are fed to a supervised fault classification network that estimates the fault probabilities. With this architecture, we achieved an 87% detection rate with a 0% false alarm rate on the provided competition data. Additionally, our isolation architecture assigned the correct fault 73.8% probabilty on average. On unseen competition data from a new driving cycle, we achieved a 100% detection rate and assigned the correct fault 66.2% probability on average. On the other hand, the Transformer Autoencoder failed to transfer to the new driving conditions, causing many false alarms. We discuss ways future work can reduce this.

Cite as

Austin Coursey, Abel Diaz-Gonzalez, Marcos Quinones-Grueiro, and Gautam Biswas. Data-Driven Fault Detection and Isolation Enhanced with System Structural Relationships (DX Competition). In 36th International Conference on Principles of Diagnosis and Resilient Systems (DX 2025). Open Access Series in Informatics (OASIcs), Volume 136, pp. 15:1-15:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{coursey_et_al:OASIcs.DX.2025.15,
  author =	{Coursey, Austin and Diaz-Gonzalez, Abel and Quinones-Grueiro, Marcos and Biswas, Gautam},
  title =	{{Data-Driven Fault Detection and Isolation Enhanced with System Structural Relationships}},
  booktitle =	{36th International Conference on Principles of Diagnosis and Resilient Systems (DX 2025)},
  pages =	{15:1--15:17},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-394-2},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{136},
  editor =	{Quinones-Grueiro, Marcos and Biswas, Gautam and Pill, Ingo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.DX.2025.15},
  URN =		{urn:nbn:de:0030-drops-248043},
  doi =		{10.4230/OASIcs.DX.2025.15},
  annote =	{Keywords: fault detection, fault isolation, autoencoder}
}

Document

DOI: 10.4230/LIPIcs.AFT.2025.35

On-Chain Decentralized Learning and Cost-Effective Inference for DeFi Attack Mitigation

Authors: Abdulrahman Alhaidari, Balaji Palanisamy, and Prashant Krishnamurthy

Published in: LIPIcs, Volume 354, 7th Conference on Advances in Financial Technologies (AFT 2025)

Abstract

Billions of dollars are lost every year in DeFi platforms by transactions exploiting business logic or accounting vulnerabilities. Existing defenses focus on static code analysis, public mempool screening, attacker contract detection, or trusted off-chain monitors, none of which prevents exploits submitted through private relays or malicious contracts that execute within the same block. We present the first decentralized, fully on-chain learning framework that: (i) performs gas-prohibitive computation on Layer-2 to reduce cost, (ii) propagates verified model updates to Layer-1, and (iii) enables gas-bounded, low-latency inference inside smart contracts. A novel Proof-of-Improvement (PoIm) protocol governs the training process and verifies each decentralized micro update as a self-verifying training transaction. Updates are accepted by PoIm only if they demonstrably improve at least one core metric (e.g., accuracy, F1-score, precision, or recall) on a public benchmark without degrading any of the other core metrics, while adversarial proposals get financially penalized through an adaptable test set for evolving threats. We develop quantization and loop-unrolling techniques that enable inference for logistic regression, SVM, MLPs, CNNs, and gated RNNs (with support for formally verified decision tree inference) within the Ethereum block gas limit, while remaining bit-exact to their off-chain counterparts, formally proven in Z3. We curate 298 unique real-world exploits (2020 - 2025) with 402 exploit transactions across eight EVM chains, collectively responsible for $3.74 B in losses. We demonstrate that on-chain ML governed by PoIm detects previously unseen attacks with over 97% attack detection accuracy and 82.0% F1. A single inference, such as one made via an external call, typically incurs zero cost. Fully on-chain inference consumes 57,603 gas (≈ $0.18) for linear models, 143,647 gas (≈ $0.49) for CNN(F2, K1), and 506,397 gas (≈ $1.77) for CNN(F8, K4) on L1 (e.g., Ethereum). Our results show that practical and continually evolving DeFi defenses can be embedded directly in protocol logic without trusted guardians, and our solution achieves highly cost-effective protection while filling a critical gap between vulnerability scanners and real-time transaction screening.

Cite as

Abdulrahman Alhaidari, Balaji Palanisamy, and Prashant Krishnamurthy. On-Chain Decentralized Learning and Cost-Effective Inference for DeFi Attack Mitigation. In 7th Conference on Advances in Financial Technologies (AFT 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 354, pp. 35:1-35:27, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{alhaidari_et_al:LIPIcs.AFT.2025.35,
  author =	{Alhaidari, Abdulrahman and Palanisamy, Balaji and Krishnamurthy, Prashant},
  title =	{{On-Chain Decentralized Learning and Cost-Effective Inference for DeFi Attack Mitigation}},
  booktitle =	{7th Conference on Advances in Financial Technologies (AFT 2025)},
  pages =	{35:1--35:27},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-400-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{354},
  editor =	{Avarikioti, Zeta and Christin, Nicolas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.AFT.2025.35},
  URN =		{urn:nbn:de:0030-drops-247548},
  doi =		{10.4230/LIPIcs.AFT.2025.35},
  annote =	{Keywords: DeFi attacks, on-chain machine learning, decentralized learning, real-time defense}
}

Document

APPROX

DOI: 10.4230/LIPIcs.APPROX/RANDOM.2025.8

Multipass Linear Sketches for Geometric LP-Type Problems

Authors: N. Efe Çekirge, William Gay, and David P. Woodruff

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

Abstract

LP-type problems such as the Minimum Enclosing Ball (MEB), Linear Support Vector Machine (SVM), Linear Programming (LP), and Semidefinite Programming (SDP) are fundamental combinatorial optimization problems, with many important applications in machine learning applications such as classification, bioinformatics, and noisy learning. We study LP-type problems in several streaming and distributed big data models, giving ε-approximation linear sketching algorithms with a focus on the high accuracy regime with low dimensionality d, that is, when d < (1/ε)^0.999. Our main result is an O(ds) pass algorithm with O(s(√d/ε)^{3d/s}) ⋅ poly(d, log (1/ε)) space complexity in words, for any parameter s ∈ [1, d log (1/ε)], to solve ε-approximate LP-type problems of O(d) combinatorial and VC dimension. Notably, by taking s = d log (1/ε), we achieve space complexity polynomial in d and polylogarithmic in 1/ε, presenting exponential improvements in 1/ε over current algorithms. We complement our results by showing lower bounds of (1/ε)^Ω(d) for any 1-pass algorithm solving the (1 + ε)-approximation MEB and linear SVM problems, further motivating our multi-pass approach.

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N. Efe Çekirge, William Gay, and David P. Woodruff. Multipass Linear Sketches for Geometric LP-Type Problems. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 353, pp. 8:1-8:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{cekirge_et_al:LIPIcs.APPROX/RANDOM.2025.8,
  author =	{\c{C}ekirge, N. Efe and Gay, William and Woodruff, David P.},
  title =	{{Multipass Linear Sketches for Geometric LP-Type Problems}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)},
  pages =	{8:1--8:25},
  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.2025.8},
  URN =		{urn:nbn:de:0030-drops-243741},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2025.8},
  annote =	{Keywords: Streaming, sketching, LP-type problems}
}

Document

DOI: 10.4230/LIPIcs.DNA.31.4

Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems

Authors: Inhoo Lee, Salvador Buse, and Erik Winfree

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

Abstract

Many molecular systems are best understood in terms of prototypical species and reactions. The central dogma and related biochemistry are rife with examples: gene i is transcribed into RNA i, which is translated into protein i; kinase n phosphorylates substrate m; protein p dimerizes with protein q. Engineered nucleic acid systems also often have this form: oligonucleotide i hybridizes to complementary oligonucleotide j; signal strand n displaces the output of seesaw gate m; hairpin p triggers the opening of target q. When there are many variants of a small number of prototypes, it can be conceptually cleaner and computationally more efficient to represent the full system in terms of indexed species (e.g. for dimerization, M_p, D_pq) and indexed reactions (M_p + M_q → D_pq). Here, we formalize the Indexed Chemical Reaction Network (ICRN) model and describe a Python software package designed to simulate such systems in the well-mixed and reaction-diffusion settings, using a differentiable programming framework originally developed for large-scale neural network models, taking advantage of GPU acceleration when available. Notably, this framework makes it straightforward to train the models’ initial conditions and rate constants to optimize a target behavior, such as matching experimental data, performing a computation, or exhibiting spatial pattern formation. The natural map of indexed chemical reaction networks onto neural network formalisms provides a tangible yet general perspective for translating concepts and techniques from the theory and practice of neural computation into the design of biomolecular systems.

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Inhoo Lee, Salvador Buse, and Erik Winfree. Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 4:1-4:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{lee_et_al:LIPIcs.DNA.31.4,
  author =	{Lee, Inhoo and Buse, Salvador and Winfree, Erik},
  title =	{{Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{4:1--4:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-399-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{347},
  editor =	{Schaeffer, Josie and Zhang, Fei},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.4},
  URN =		{urn:nbn:de:0030-drops-238534},
  doi =		{10.4230/LIPIcs.DNA.31.4},
  annote =	{Keywords: Differentiable Programming, Chemical Reaction Networks, Reaction-Diffusion Systems}
}

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.GIScience.2025.5

Analysis of Points of Interests Recommended for Leisure Walk Descriptions

Authors: Ehsan Hamzei, Thi Minh Hoai Bui, Martin Tomko, and Stephan Winter

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

Abstract

Leisure walking is a physical activity where locomotion through a natural or even urban environment is the goal in itself, e.g., in pursuit of health and wellbeing. In contrast to destination-oriented walks that are focused on navigation efficiency (i.e., shortest or simplest walk from source to destination), leisure walks emphasize experiencing the environment, engaging in activities, and discovering places that may be off route, or intermediate destinations en-route, summarily called points of interest (POIs). POIs are key for recommending leisure walks, yet a detailed analysis of POIs in the context of leisure walking is missing in the literature. This study extracts and annotates POIs of leisure walking recommendations available in WalkingMaps.com.au, creating an annotated dataset to address this research gap and provide a first analysis of leisure walking descriptions. We classify POIs using the verbal description provided in the dataset, match them with data available in OpenStreetMap (OSM), and compare the POIs with nearby alternatives in OSM. Our analysis reveals thematic and spatial patterns in POI selection, offering a machine learning approach to model POI choices for leisure walks. We further evaluate the availability of rich data in OSM for future automated leisure walking recommendation. This study contributes to automated systems for recommending leisure walks, tailoring suggestions based on available information in the spatial open data, and presents an annotated dataset to facilitate future research in this field.

Cite as

Ehsan Hamzei, Thi Minh Hoai Bui, Martin Tomko, and Stephan Winter. Analysis of Points of Interests Recommended for Leisure Walk Descriptions. In 13th International Conference on Geographic Information Science (GIScience 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 346, pp. 5:1-5:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{hamzei_et_al:LIPIcs.GIScience.2025.5,
  author =	{Hamzei, Ehsan and Bui, Thi Minh Hoai and Tomko, Martin and Winter, Stephan},
  title =	{{Analysis of Points of Interests Recommended for Leisure Walk Descriptions}},
  booktitle =	{13th International Conference on Geographic Information Science (GIScience 2025)},
  pages =	{5:1--5:16},
  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.2025.5},
  URN =		{urn:nbn:de:0030-drops-238341},
  doi =		{10.4230/LIPIcs.GIScience.2025.5},
  annote =	{Keywords: leisure walks, points of interest, places, platial information}
}

Document

DOI: 10.4230/LIPIcs.CCC.2025.1

List Decoding Quotient Reed-Muller Codes

Authors: Omri Gotlib, Tali Kaufman, and Shachar Lovett

Published in: LIPIcs, Volume 339, 40th Computational Complexity Conference (CCC 2025)

Abstract

Reed-Muller codes consist of evaluations of n-variate polynomials over a finite field 𝔽 with degree at most d. Much like every linear code, Reed-Muller codes can be characterized by constraints, where a codeword is valid if and only if it satisfies all degree-d constraints. For a subset X̃ ⊆ 𝔽ⁿ, we introduce the notion of X̃-quotient Reed-Muller code. A function F:X̃ → 𝔽 is a valid codeword in the quotient code if it satisfies all the constraints of degree-d polynomials lying in X̃. This gives rise to a novel phenomenon: a quotient codeword may have many extensions to original codewords. This weakens the connection between original codewords and quotient codewords which introduces a richer range of behaviors along with substantial new challenges. Our goal is to answer the following question: what properties of X̃ will imply that the quotient code inherits its distance and list-decoding radius from the original code? We address this question using techniques developed by Bhowmick and Lovett [Abhishek Bhowmick and Shachar Lovett, 2014], identifying key properties of 𝔽ⁿ used in their proof and extending them to general subsets X̃ ⊆ 𝔽ⁿ. By introducing a new tool, we overcome the novel challenge in analyzing the quotient code that arises from the weak connection between original and quotient codewords. This enables us to apply known results from additive combinatorics and algebraic geometry [David Kazhdan and Tamar Ziegler, 2018; David Kazhdan and Tamar Ziegler, 2019; Amichai Lampert and Tamar Ziegler, 2021] to show that when X̃ is a high rank variety, X̃-quotient Reed-Muller codes inherit the distance and list-decoding parameters from the original Reed-Muller codes.

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Omri Gotlib, Tali Kaufman, and Shachar Lovett. List Decoding Quotient Reed-Muller Codes. In 40th Computational Complexity Conference (CCC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 339, pp. 1:1-1:44, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gotlib_et_al:LIPIcs.CCC.2025.1,
  author =	{Gotlib, Omri and Kaufman, Tali and Lovett, Shachar},
  title =	{{List Decoding Quotient Reed-Muller Codes}},
  booktitle =	{40th Computational Complexity Conference (CCC 2025)},
  pages =	{1:1--1:44},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-379-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{339},
  editor =	{Srinivasan, Srikanth},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CCC.2025.1},
  URN =		{urn:nbn:de:0030-drops-236957},
  doi =		{10.4230/LIPIcs.CCC.2025.1},
  annote =	{Keywords: Reed-Muller Codes, Quotient Code, Quotient Reed-Muller Code, List Decoding, High Rank Variety, High-Order Fourier Analysis, Error-Correcting Codes}
}

Document

DOI: 10.4230/LIPIcs.CCC.2025.34

Witness Encryption and NP-Hardness of Learning

Authors: Halley Goldberg and Valentine Kabanets

Published in: LIPIcs, Volume 339, 40th Computational Complexity Conference (CCC 2025)

Abstract

We study connections between two fundamental questions from computer science theory. (1) Is witness encryption possible for NP [Sanjam Garg et al., 2013]? That is, given an instance x of an NP-complete language L, can one encrypt a secret message with security contingent on the ability to provide a witness for x ∈ L? (2) Is computational learning (in the sense of [Leslie G. Valiant, 1984; Michael J. Kearns et al., 1994]) hard for NP? That is, is there a polynomial-time reduction from instances of L to instances of learning? Our main contribution is that certain formulations of NP-hardness of learning characterize the existence of witness encryption for NP. More specifically, we show: - witness encryption for a language L ∈ NP is equivalent to a half-Levin reduction from L to the Computational Gap Learning problem (denoted CGL [Benny Applebaum et al., 2008]), where a half-Levin reduction is the same as a Levin reduction but only required to preserve witnesses in one direction, and CGL formalizes agnostic learning as a decision problem. We show versions of the statement above for witness encryption secure against non-uniform and uniform adversaries. We also show that witness encryption for NP with ciphertexts of logarithmic length, along with a circuit lower bound for E, are together equivalent to NP-hardness of a generalized promise version of MCSP. We complement the above with a number of unconditional NP-hardness results for agnostic PAC learning. Extending a result of [Shuichi Hirahara, 2022] to the standard setting of boolean circuits, we show NP-hardness of "semi-proper" learning. Namely: - for some polynomial s, it is NP-hard to agnostically learn circuits of size s(n) by circuits of size s(n)⋅ n^{1/(log log n)^O(1)}. Looking beyond the computational model of standard boolean circuits enables us to prove NP-hardness of improper learning (ie. without a restriction on the size of hypothesis returned by the learner). We obtain such results for: - learning circuits with oracle access to a given randomly sampled string, and - learning RAM programs. In particular, we show that a variant of MINLT [Ker-I Ko, 1991] for RAM programs is NP-hard with parameters corresponding to the setting of improper learning. We view these results as partial progress toward the ultimate goal of showing NP-hardness of learning boolean circuits in an improper setting. Lastly, we give some consequences of NP-hardness of learning for private- and public-key cryptography. Improving a main result of [Benny Applebaum et al., 2008], we show that if improper agnostic PAC learning is NP-hard under a randomized non-adaptive reduction (with some restrictions), then NP ⊈ BPP implies the existence of i.o. one-way functions. In contrast, if CGL is NP-hard under a half-Levin reduction, then NP ⊈ BPP implies the existence of i.o. public-key encryption.

Cite as

Halley Goldberg and Valentine Kabanets. Witness Encryption and NP-Hardness of Learning. In 40th Computational Complexity Conference (CCC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 339, pp. 34:1-34:43, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{goldberg_et_al:LIPIcs.CCC.2025.34,
  author =	{Goldberg, Halley and Kabanets, Valentine},
  title =	{{Witness Encryption and NP-Hardness of Learning}},
  booktitle =	{40th Computational Complexity Conference (CCC 2025)},
  pages =	{34:1--34:43},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-379-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{339},
  editor =	{Srinivasan, Srikanth},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CCC.2025.34},
  URN =		{urn:nbn:de:0030-drops-237281},
  doi =		{10.4230/LIPIcs.CCC.2025.34},
  annote =	{Keywords: agnostic PAC learning, witness encryption, NP-hardness}
}

Document

DOI: 10.4230/LIPIcs.SEA.2025.5

A Comparative Study of Compressed, Learned, and Traditional Indexing Methods for Integer Data

Authors: Lorenzo Bellomo, Giuseppe Cianci, Luca de Rosa, Paolo Ferragina, and Mattia Odorisio

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

Abstract

The rapid evolution of learned data structures has revolutionized database indexing, particularly for sorted integer datasets. While learned indexes excel in static scenarios due to their low memory footprint, reduced storage requirements, and fast lookup times, benchmarks like SOSD and TLI have largely overlooked compressed indexes and SIMD-based implementations of traditional indexes. This paper addresses this gap by introducing a comprehensive benchmarking framework that (i) evaluates traditional, learned, and compressed indexes across 12 datasets (real and synthetic) of varying types and sizes; (ii) integrates state-of-the-art SIMD-enhanced B-Tree variants; and (iii) measures critical performance metrics such as memory usage, construction time, and lookup efficiency. Our findings reveal that while learned indexes minimize memory usage, a feature useful when internal memory constraints are mandatory, SIMD-enhanced B-Trees consistently achieve superior lookup times with comparable extra space. On the other hand, compressed indexes like LA-vector and EliasFano provide very effective compression of the indexed data with slower access speeds (2x-3x). Another contribution of this paper is a publicly available benchmarking framework (composed of code and datasets) that makes our experiments reproducible and extensible to other indexes and datasets.

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Lorenzo Bellomo, Giuseppe Cianci, Luca de Rosa, Paolo Ferragina, and Mattia Odorisio. A Comparative Study of Compressed, Learned, and Traditional Indexing Methods for Integer Data. In 23rd International Symposium on Experimental Algorithms (SEA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 338, pp. 5:1-5:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bellomo_et_al:LIPIcs.SEA.2025.5,
  author =	{Bellomo, Lorenzo and Cianci, Giuseppe and de Rosa, Luca and Ferragina, Paolo and Odorisio, Mattia},
  title =	{{A Comparative Study of Compressed, Learned, and Traditional Indexing Methods for Integer Data}},
  booktitle =	{23rd International Symposium on Experimental Algorithms (SEA 2025)},
  pages =	{5:1--5:23},
  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.2025.5},
  URN =		{urn:nbn:de:0030-drops-232439},
  doi =		{10.4230/LIPIcs.SEA.2025.5},
  annote =	{Keywords: indexing data structures, compression, algorithm engineering, benchmark}
}

Document

DOI: 10.4230/LIPIcs.SEA.2025.7

Continuous Map Matching to Paths Under Travel Time Constraints

Authors: Yannick Bosch and Sabine Storandt

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

Abstract

In this paper, we study the problem of map matching with travel time constraints. Given a sequence of k spatio-temporal measurements and an embedded path graph with travel time costs, the goal is to snap each measurement to a close-by location in the graph, such that consecutive locations can be reached from one another along the path within the timestamp difference of the respective measurements. This problem arises in public transit data processing as well as in map matching of movement trajectories to general graphs. We show that the classical approach for this problem, which relies on selecting a finite set of candidate locations in the graph for each measurement, cannot guarantee to find a consistent solution. We propose a new algorithm that can deal with an infinite set of candidate locations per measurement. We prove that our algorithm always detects a consistent map matching path (if one exists). Despite the enlarged candidate set, we also demonstrate that our algorithm has superior running time in theory and practice. For a path graph with n nodes, we show that our algorithm runs in 𝒪(k² n log {nk}) and under mild assumptions in 𝒪(k n ^λ + n log³ n) for λ ≈ 0.695. This is a significant improvement over the baseline, which runs in 𝒪(k n²) and which might not even identify a correct solution. The performance of our algorithm hinges on an efficient segment-circle intersection data structure. We describe how to design and implement such a data structure for our application. In the experimental evaluation, we demonstrate the usefulness of our novel algorithm on a diverse set of generated measurements as well as GTFS data.

Cite as

Yannick Bosch and Sabine Storandt. Continuous Map Matching to Paths Under Travel Time Constraints. In 23rd International Symposium on Experimental Algorithms (SEA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 338, pp. 7:1-7:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bosch_et_al:LIPIcs.SEA.2025.7,
  author =	{Bosch, Yannick and Storandt, Sabine},
  title =	{{Continuous Map Matching to Paths Under Travel Time Constraints}},
  booktitle =	{23rd International Symposium on Experimental Algorithms (SEA 2025)},
  pages =	{7:1--7:17},
  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.2025.7},
  URN =		{urn:nbn:de:0030-drops-232457},
  doi =		{10.4230/LIPIcs.SEA.2025.7},
  annote =	{Keywords: Map matching, Travel time, Segment-circle intersection data structure}
}

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