42 Search Results for "Schwartz, Russell"

Volume

LIPIcs, Volume 88

17th International Workshop on Algorithms in Bioinformatics (WABI 2017)

WABI 2017, August 21-23, 2017, Boston, MA, USA

Editors: Russell Schwartz and Knut Reinert

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.STACS.2026.25
Homomorphism Indistinguishability, Multiplicity Automata Equivalence, and Polynomial Identity Testing

Authors: Marek Černý and Tim Seppelt

Published in: LIPIcs, Volume 364, 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)

Abstract
Two graphs G and H are homomorphism indistinguishable over a graph class ℱ if they admit the same number of homomorphisms from every graph F ∈ ℱ. Many graph isomorphism relaxations such as (quantum) isomorphism and cospectrality can be characterised as homomorphism indistinguishability over specific graph classes. Thereby, the problems HomInd(ℱ) of deciding homomorphism indistinguishability over ℱ subsume diverse graph isomorphism relaxations whose complexities range from logspace to undecidable. Establishing the first general result on the complexity of HomInd(ℱ), Seppelt (MFCS 2024) showed that HomInd(ℱ) is in randomised polynomial time for every graph class ℱ of bounded treewidth that can be defined in counting monadic second-order logic CMSO₂. We show that this algorithm is conditionally optimal, i.e. it cannot be derandomised unless polynomial identity testing is in P. For CMSO₂-definable graph classes ℱ of bounded pathwidth, we improve the previous complexity upper bound for HomInd(ℱ) from P to C_ = L and show that this is tight. Secondarily, we establish a connection between homomorphism indistinguishability and multiplicity automata equivalence which allows us to pinpoint the complexity of the latter problem as C_ = L-complete.
Cite as

Marek Černý and Tim Seppelt. Homomorphism Indistinguishability, Multiplicity Automata Equivalence, and Polynomial Identity Testing. In 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 364, pp. 25:1-25:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{cerny_et_al:LIPIcs.STACS.2026.25,
  author =	{\v{C}ern\'{y}, Marek and Seppelt, Tim},
  title =	{{Homomorphism Indistinguishability, Multiplicity Automata Equivalence, and Polynomial Identity Testing}},
  booktitle =	{43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)},
  pages =	{25:1--25:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-412-3},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{364},
  editor =	{Mahajan, Meena and Manea, Florin and McIver, Annabelle and Thắng, Nguy\~{ê}n Kim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2026.25},
  URN =		{urn:nbn:de:0030-drops-255144},
  doi =		{10.4230/LIPIcs.STACS.2026.25},
  annote =	{Keywords: treewidth, Courcelle’s theorem, logspace, multiplicity automata, polynomial identity testing}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2026.86
The Secretary Problem with Predictions and a Chosen Order

Authors: Helia Karisani, Mohammadreza Daneshvaramoli, Hedyeh Beyhaghi, Mohammad Hajiesmaili, and Cameron Musco

Published in: LIPIcs, Volume 362, 17th Innovations in Theoretical Computer Science Conference (ITCS 2026)

Abstract
We study a learning-augmented variant of the secretary problem, recently introduced by Fujii and Yoshida (2023). In this variant, the decision-maker has access to machine-learned predictions of candidate values in advance. The key challenge is to balance consistency and robustness: when the predictions are accurate, the algorithm should hire a near-best secretary; however, if they are inaccurate, the algorithm should still achieve a bounded competitive ratio. We consider both the standard Random Order Secretary Problem (ROSP), where candidates arrive in a uniform random order, and a more natural model in the learning-augmented setting, where the decision-maker can choose the arrival order based on the predicted candidate values. This model, which we call the Chosen Order Secretary Problem (COSP), can capture scenarios such as an interview schedule that is set by the decision-maker. We propose a novel algorithm that applies to both ROSP and COSP. Building on the approach of Fujii and Yoshida, our method switches from fully trusting predictions to a threshold-based rule when a large deviation of a prediction is observed. Importantly, unlike the algorithm of Fujii and Yoshida, our algorithm uses randomization as part of its decision logic. We show that if ε ∈ [0,1] denotes the maximum multiplicative prediction error, then for ROSP our algorithm achieves competitive ratio max {0.221, (1-ε)/(1+ε)}, improving on a previous bound of max {0.215, (1-ε)/(1+ε)} due to Fujii and Yoshida [Fujii and Yoshida, 2023]. For COSP, our algorithm achieves max {0.262, (1-ε)/(1+ε)}. This surpasses a 0.25 upper bound on the worst-case competitive ratio that applies to the approach of Fujii and Yoshida, and gets closer to the classical secretary benchmark of 1/e ≈ 0.368, which is an upper bound for any algorithm. Our result for COSP highlights the benefit of integrating predictions with arrival-order control in online decision-making.
Cite as

Helia Karisani, Mohammadreza Daneshvaramoli, Hedyeh Beyhaghi, Mohammad Hajiesmaili, and Cameron Musco. The Secretary Problem with Predictions and a Chosen Order. In 17th Innovations in Theoretical Computer Science Conference (ITCS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 362, pp. 86:1-86:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{karisani_et_al:LIPIcs.ITCS.2026.86,
  author =	{Karisani, Helia and Daneshvaramoli, Mohammadreza and Beyhaghi, Hedyeh and Hajiesmaili, Mohammad and Musco, Cameron},
  title =	{{The Secretary Problem with Predictions and a Chosen Order}},
  booktitle =	{17th Innovations in Theoretical Computer Science Conference (ITCS 2026)},
  pages =	{86:1--86:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-410-9},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{362},
  editor =	{Saraf, Shubhangi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2026.86},
  URN =		{urn:nbn:de:0030-drops-253734},
  doi =		{10.4230/LIPIcs.ITCS.2026.86},
  annote =	{Keywords: Secretary problem, learning-augmented algorithms, online algorithms}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2026.104
Dimension-Free Correlated Sampling for the Hypersimplex

Authors: Joseph (Seffi) Naor, Nitya Raju, Abhishek Shetty, Aravind Srinivasan, Renata Valieva, and David Wajc

Published in: LIPIcs, Volume 362, 17th Innovations in Theoretical Computer Science Conference (ITCS 2026)

Abstract
Sampling from multiple distributions so as to maximize overlap has been studied by statisticians since the 1950s. Since the 2000s, such correlated sampling from the probability simplex has been a powerful building block in disparate areas of theoretical computer science. We study a generalization of this problem to sampling sets from given vectors in the hypersimplex, i.e., outputting sets of size (at most) k ∈ [n], while maximizing the overlap of the sampled sets. Specifically, the expected difference between two output sets should be at most α times their input vectors' 𝓁₁ distance. A value of α = O(log n) is known to be achievable, due to Chen et al. (ICALP'17). We improve this factor to O(log k), independent of the ambient dimension n. Our algorithm satisfies other desirable properties, including (up to a log^* n factor) input-sparsity sampling time, logarithmic parallel depth and dynamic update time, as well as preservation of submodular objectives. Anticipating broader use of correlated sampling algorithms for the hypersimplex, we present applications of our algorithm to online paging, offline approximation of metric multi-labeling, and swift multi-scenario submodular welfare approximating reallocation.
Cite as

Joseph (Seffi) Naor, Nitya Raju, Abhishek Shetty, Aravind Srinivasan, Renata Valieva, and David Wajc. Dimension-Free Correlated Sampling for the Hypersimplex. In 17th Innovations in Theoretical Computer Science Conference (ITCS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 362, pp. 104:1-104:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{naor_et_al:LIPIcs.ITCS.2026.104,
  author =	{Naor, Joseph (Seffi) and Raju, Nitya and Shetty, Abhishek and Srinivasan, Aravind and Valieva, Renata and Wajc, David},
  title =	{{Dimension-Free Correlated Sampling for the Hypersimplex}},
  booktitle =	{17th Innovations in Theoretical Computer Science Conference (ITCS 2026)},
  pages =	{104:1--104:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-410-9},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{362},
  editor =	{Saraf, Shubhangi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2026.104},
  URN =		{urn:nbn:de:0030-drops-253918},
  doi =		{10.4230/LIPIcs.ITCS.2026.104},
  annote =	{Keywords: Correlated Rounding, Dependent Rounding}
}
Document
DOI: 10.4230/DagMan.11.1.19
Conversational Agents: A Framework for Evaluation (CAFE) (Dagstuhl Perspectives Workshop 24352)

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

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

Abstract
During the workshop, we deeply discussed what CONversational Information ACcess (CONIAC) is and its unique features, proposing a world model abstracting it, and defined the Conversational Agents Framework for Evaluation (CAFE) for the evaluation of CONIAC systems, consisting of six major components: 1) goals of the system’s stakeholders, 2) user tasks to be studied in the evaluation, 3) aspects of the users carrying out the tasks, 4) evaluation criteria to be considered, 5) evaluation methodology to be applied, and 6) measures for the quantitative criteria chosen.
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Christine Bauer, Li Chen, Nicola Ferro, Norbert Fuhr, Avishek Anand, Timo Breuer, Guglielmo Faggioli, Ophir Frieder, Hideo Joho, Jussi Karlgren, Johannes Kiesel, Bart P. Knijnenburg, Aldo Lipani, Lien Michiels, Andrea Papenmeier, Maria Soledad Pera, Mark Sanderson, Scott Sanner, Benno Stein, Johanne R. Trippas, Karin Verspoor, and Martijn C. Willemsen. Conversational Agents: A Framework for Evaluation (CAFE) (Dagstuhl Perspectives Workshop 24352). In Dagstuhl Manifestos, Volume 11, Issue 1, pp. 19-67, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@Article{bauer_et_al:DagMan.11.1.19,
  author =	{Bauer, Christine and Chen, Li and Ferro, Nicola and Fuhr, Norbert and Anand, Avishek and Breuer, Timo and Faggioli, Guglielmo and Frieder, Ophir and Joho, Hideo and Karlgren, Jussi and Kiesel, Johannes and Knijnenburg, Bart P. and Lipani, Aldo and Michiels, Lien and Papenmeier, Andrea and Pera, Maria Soledad and Sanderson, Mark and Sanner, Scott and Stein, Benno and Trippas, Johanne R. and Verspoor, Karin and Willemsen, Martijn C.},
  title =	{{Conversational Agents: A Framework for Evaluation (CAFE) (Dagstuhl Perspectives Workshop 24352)}},
  pages =	{19--67},
  journal =	{Dagstuhl Manifestos},
  ISSN =	{2193-2433},
  year =	{2025},
  volume =	{11},
  number =	{1},
  editor =	{Bauer, Christine and Chen, Li and Ferro, Nicola and Fuhr, Norbert and Anand, Avishek and Breuer, Timo and Faggioli, Guglielmo and Frieder, Ophir and Joho, Hideo and Karlgren, Jussi and Kiesel, Johannes and Knijnenburg, Bart P. and Lipani, Aldo and Michiels, Lien and Papenmeier, Andrea and Pera, Maria Soledad and Sanderson, Mark and Sanner, Scott and Stein, Benno and Trippas, Johanne R. and Verspoor, Karin and Willemsen, Martijn C.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagMan.11.1.19},
  URN =		{urn:nbn:de:0030-drops-252722},
  doi =		{10.4230/DagMan.11.1.19},
  annote =	{Keywords: Conversational Agents, Evaluation, Information Access}
}
Document
DOI: 10.4230/OASIcs.SpaceCHI.2025.30
A Research Framework to Develop a Real-Time Synchrony Index to Monitor Team Cohesion and Performance in Long-Duration Space Exploration

Authors: Federico Nemmi, Emma Chabani, Laure Boyer, Charlie Madier, and Daniel Lewkowicz

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

Abstract
As humanity prepares for long-distance space exploration, optimizing group performance, the ability of a group to achieve its goals efficiently, is critical. Astronaut crews will endure isolation, confinement, and operational stress, making group synchrony - the alignment of behaviors, emotions, and physiological states - a key factor in mission success. Synchrony influences team cohesion, performance, and resilience, necessitating effective crew management strategies. This paper proposes a framework for a real-time, unobtrusive index of group synchrony to support astronauts and mission control. Research indicates that team cohesion fluctuates in isolated environments, with reduced communication and interpersonal conflicts emerging over time. A system tracking synchrony could mitigate these issues, providing proactive support and improving remote management. Additionally, it could serve as a cognitive and physiological feedback tool for astronauts and a decision-making aid for mission control, enhancing well-being and efficiency. Our approach integrates behavioral and physiological synchrony measures to assess team cohesion and performance. We propose a multi-modal synchrony index combining movement coordination, communication patterns, and physiological signals such as heart rate, electrodermal activity, and EEG. This index will be validated across different tasks to ensure applicability across diverse mission scenarios. By developing a robust synchrony index, we address a fundamental challenge in space missions: sustaining team effectiveness under extreme conditions. Beyond space exploration, our findings could benefit high-risk, high-isolation teams in submarine crews, polar expeditions, and remote research groups. Our collaboration with the Centre National d'Etudes Spatiales, the Institut de Médecine et de Physiologie Spatiales, and the Toulouse University Hospital marks the first step, with experimental data collection starting this year. Ultimately, this research fosters more adaptive, responsive, and resilient teams for future space missions.
Cite as

Federico Nemmi, Emma Chabani, Laure Boyer, Charlie Madier, and Daniel Lewkowicz. A Research Framework to Develop a Real-Time Synchrony Index to Monitor Team Cohesion and Performance in Long-Duration Space Exploration. In Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025). Open Access Series in Informatics (OASIcs), Volume 130, pp. 30:1-30:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{nemmi_et_al:OASIcs.SpaceCHI.2025.30,
  author =	{Nemmi, Federico and Chabani, Emma and Boyer, Laure and Madier, Charlie and Lewkowicz, Daniel},
  title =	{{A Research Framework to Develop a Real-Time Synchrony Index to Monitor Team Cohesion and Performance in Long-Duration Space Exploration}},
  booktitle =	{Advancing Human-Computer Interaction for Space Exploration (SpaceCHI 2025)},
  pages =	{30:1--30:16},
  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.2025.30},
  URN =		{urn:nbn:de:0030-drops-240200},
  doi =		{10.4230/OASIcs.SpaceCHI.2025.30},
  annote =	{Keywords: Performance, Synchronie, Crew monitoring, Cohesion}
}
Document
RANDOM
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2025.56
Efficient Polynomial Identity Testing over Nonassociative Algebras

Authors: Partha Mukhopadhyay, C. Ramya, and Pratik Shastri

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

Abstract
We design the first efficient polynomial identity testing algorithms over the nonassociative polynomial algebra. In particular, multiplication among the formal variables is commutative but it is not associative. This complements the strong lower bound results obtained over this algebra by Hrubeš, Yehudayoff, and Wigderson [Pavel Hrubes et al., 2010] and Fijalkow, Lagarde, Ohlmann, and Serre [Fijalkow et al., 2021] from the identity testing perspective. Our main results are the following: - We construct nonassociative algebras (both commutative and noncommutative) which have no low degree identities. As a result, we obtain the first Amitsur-Levitzki type theorems [A. S. Amitsur and J. Levitzki, 1950] over nonassociative polynomial algebras. As a direct consequence, we obtain randomized polynomial-time black-box PIT algorithms for nonassociative polynomials which allow evaluation over such algebras. - On the derandomization side, we give a deterministic polynomial-time identity testing algorithm for nonassociative polynomials given by arithmetic circuits in the white-box setting. Previously, such an algorithm was known with the additional restriction of noncommutativity [Vikraman Arvind et al., 2017]. - In the black-box setting, we construct a hitting set of quasipolynomial-size for nonassociative polynomials computed by arithmetic circuits of small depth. Understanding the black-box complexity of identity testing, even in the randomized setting, was open prior to our work.
Cite as

Partha Mukhopadhyay, C. Ramya, and Pratik Shastri. Efficient Polynomial Identity Testing over Nonassociative Algebras. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 353, pp. 56:1-56:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{mukhopadhyay_et_al:LIPIcs.APPROX/RANDOM.2025.56,
  author =	{Mukhopadhyay, Partha and C. Ramya and Shastri, Pratik},
  title =	{{Efficient Polynomial Identity Testing over Nonassociative Algebras}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)},
  pages =	{56:1--56:22},
  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.2025.56},
  URN =		{urn:nbn:de:0030-drops-244224},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2025.56},
  annote =	{Keywords: Polynomial identity testing, nonassociative algebra, arithmetic circuits, black-box algorithms, white-box algorithms}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.4
Haplotype-Aware Long-Read Error Correction

Authors: Parvesh Barak, Daniel Gibney, and Chirag Jain

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

Abstract
Error correction of long reads is an important initial step in genome assembly workflows. For organisms with ploidy greater than one, it is important to preserve haplotype-specific variation during read correction. This challenge has driven the development of several haplotype-aware correction methods. However, existing methods are based on either ad-hoc heuristics or deep learning approaches. In this paper, we introduce a rigorous formulation for this problem. Our approach builds on the minimum error correction framework used in reference-based haplotype phasing. We prove that the proposed formulation for error correction of reads in de novo context, i.e., without using a reference genome, is NP-hard. To make our exact algorithm scale to large datasets, we introduce practical heuristics. Experiments using PacBio HiFi sequencing datasets from human and plant genomes show that our approach achieves accuracy comparable to state-of-the-art methods. The software is freely available at https://github.com/at-cg/HALE.
Cite as

Parvesh Barak, Daniel Gibney, and Chirag Jain. Haplotype-Aware Long-Read Error Correction. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 4:1-4:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{barak_et_al:LIPIcs.WABI.2025.4,
  author =	{Barak, Parvesh and Gibney, Daniel and Jain, Chirag},
  title =	{{Haplotype-Aware Long-Read Error Correction}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{4:1--4:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.4},
  URN =		{urn:nbn:de:0030-drops-239300},
  doi =		{10.4230/LIPIcs.WABI.2025.4},
  annote =	{Keywords: Genome assembly, phasing, clustering, overlap graph, consensus}
}
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.CCC.2025.15
Algebraic Pseudorandomness in VNC⁰

Authors: Robert Andrews

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

Abstract
We study the arithmetic complexity of hitting set generators, which are pseudorandom objects used for derandomization of the polynomial identity testing problem. We give new explicit constructions of hitting set generators whose outputs are computable in VNC⁰, i.e., can be computed by arithmetic formulas of constant size. Unconditionally, we construct a VNC⁰-computable generator that hits arithmetic circuits of constant depth and polynomial size. We also give conditional constructions, under strong but plausible hardness assumptions, of VNC⁰-computable generators that hit arithmetic formulas and arithmetic branching programs of polynomial size, respectively. As a corollary of our constructions, we derive lower bounds for subsystems of the Geometric Ideal Proof System of Grochow and Pitassi. Constructions of such generators are implicit in prior work of Kayal on lower bounds for the degree of annihilating polynomials. Our main contribution is a construction whose correctness relies on circuit complexity lower bounds rather than degree lower bounds.
Cite as

Robert Andrews. Algebraic Pseudorandomness in VNC⁰. In 40th Computational Complexity Conference (CCC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 339, pp. 15:1-15:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{andrews:LIPIcs.CCC.2025.15,
  author =	{Andrews, Robert},
  title =	{{Algebraic Pseudorandomness in VNC⁰}},
  booktitle =	{40th Computational Complexity Conference (CCC 2025)},
  pages =	{15:1--15:15},
  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.2025.15},
  URN =		{urn:nbn:de:0030-drops-237092},
  doi =		{10.4230/LIPIcs.CCC.2025.15},
  annote =	{Keywords: Polynomial identity testing, Algebraic circuits, Ideal Proof System}
}
Document
DOI: 10.4230/LITES.10.1.1
GDBMiner: Mining Precise Input Grammars on (Almost) Any System

Authors: Max Eisele, Johannes Hägele, Christopher Huth, and Andreas Zeller

Published in: LITES, Volume 10, Issue 1 (2025). Leibniz Transactions on Embedded Systems, Volume 10, Issue 1

Abstract
If one knows the input language of the system to be tested, one can generate inputs in a very efficient manner. Grammar-based fuzzers, for instance, produce inputs that are syntactically valid by construction. They are thus much more likely to be accepted by the program under test and to reach code beyond the input parser. Grammar-based fuzzers, however, need a grammar in the first place. Grammar miners are set to extract such grammars from programs. However, current grammar mining tools place huge demands on the source code they are applied on, or are too imprecise, both preventing adoption in industrial practice. We present GDBMiner, a tool to mine input grammars for binaries and executables in any (compiled) programming language, on any operating system, using any processor architecture, even without source code. GDBMiner leverages the GNU debugger (GDB) to step through the program and determine which code locations access which input bytes, generalizing bytes accessed by the same location into grammar elements. GDBMiner is slow, but versatile - and precise: In our evaluation, GDBMiner produces grammars as precise as the (more demanding) Cmimid tool, while producing more precise grammars than the (less demanding) Arvada black-box approach. GDBMiner can be applied on any recursive descent parser that can be debugged via GDB and is available as open source.
Cite as

Max Eisele, Johannes Hägele, Christopher Huth, and Andreas Zeller. GDBMiner: Mining Precise Input Grammars on (Almost) Any System. In LITES, Volume 10, Issue 1 (2025). Leibniz Transactions on Embedded Systems, Volume 10, Issue 1, pp. 1:1-1:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@Article{eisele_et_al:LITES.10.1.1,
  author =	{Eisele, Max and H\"{a}gele, Johannes and Huth, Christopher and Zeller, Andreas},
  title =	{{GDBMiner: Mining Precise Input Grammars on (Almost) Any System}},
  journal =	{Leibniz Transactions on Embedded Systems},
  pages =	{1:1--1:26},
  ISSN =	{2199-2002},
  year =	{2025},
  volume =	{10},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LITES.10.1.1},
  URN =		{urn:nbn:de:0030-drops-230134},
  doi =		{10.4230/LITES.10.1.1},
  annote =	{Keywords: program analysis, testing, input grammar, fuzzing, grammar mining}
}
Document
Vision
DOI: 10.4230/TGDK.1.1.8
Machine Learning and Knowledge Graphs: Existing Gaps and Future Research Challenges

Authors: Claudia d'Amato, Louis Mahon, Pierre Monnin, and Giorgos Stamou

Published in: TGDK, Volume 1, Issue 1 (2023): Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 1, Issue 1

Abstract
The graph model is nowadays largely adopted to model a wide range of knowledge and data, spanning from social networks to knowledge graphs (KGs), representing a successful paradigm of how symbolic and transparent AI can scale on the World Wide Web. However, due to their unprecedented volume, they are generally tackled by Machine Learning (ML) and mostly numeric based methods such as graph embedding models (KGE) and deep neural networks (DNNs). The latter methods have been proved lately very efficient, leading the current AI spring. In this vision paper, we introduce some of the main existing methods for combining KGs and ML, divided into two categories: those using ML to improve KGs, and those using KGs to improve results on ML tasks. From this introduction, we highlight research gaps and perspectives that we deem promising and currently under-explored for the involved research communities, spanning from KG support for LLM prompting, integration of KG semantics in ML models to symbol-based methods, interpretability of ML models, and the need for improved benchmark datasets. In our opinion, such perspectives are stepping stones in an ultimate view of KGs as central assets for neuro-symbolic and explainable AI.
Cite as

Claudia d'Amato, Louis Mahon, Pierre Monnin, and Giorgos Stamou. Machine Learning and Knowledge Graphs: Existing Gaps and Future Research Challenges. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 8:1-8:35, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{damato_et_al:TGDK.1.1.8,
  author =	{d'Amato, Claudia and Mahon, Louis and Monnin, Pierre and Stamou, Giorgos},
  title =	{{Machine Learning and Knowledge Graphs: Existing Gaps and Future Research Challenges}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{8:1--8:35},
  year =	{2023},
  volume =	{1},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.1.1.8},
  URN =		{urn:nbn:de:0030-drops-194824},
  doi =		{10.4230/TGDK.1.1.8},
  annote =	{Keywords: Graph-based Learning, Knowledge Graph Embeddings, Large Language Models, Explainable AI, Knowledge Graph Completion \& Curation}
}
Document
Complete Volume
DOI: 10.4230/LIPIcs.WABI.2017
LIPIcs, Volume 88, WABI'17, Complete Volume

Authors: Russell Schwartz and Knut Reinert

Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)

Abstract
LIPIcs, Volume 88, WABI'17, Complete Volume
Cite as

17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@Proceedings{schwartz_et_al:LIPIcs.WABI.2017,
  title =	{{LIPIcs, Volume 88, WABI'17, Complete Volume}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017},
  URN =		{urn:nbn:de:0030-drops-78120},
  doi =		{10.4230/LIPIcs.WABI.2017},
  annote =	{Keywords: Nonnumerical Algorithms and Problems, Pattern Matching, Algorithms, Life and Medical Sciences}
}
Document
Front Matter
DOI: 10.4230/LIPIcs.WABI.2017.0
Front Matter, Table of Contents, Preface, List of Authors

Authors: Russell Schwartz and Knut Reinert

Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)

Abstract
Front Matter, Table of Contents, Preface, List of Authors
Cite as

17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 0:i-0:xiv, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{schwartz_et_al:LIPIcs.WABI.2017.0,
  author =	{Schwartz, Russell and Reinert, Knut},
  title =	{{Front Matter, Table of Contents, Preface, List of Authors}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{0:i--0:xiv},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.0},
  URN =		{urn:nbn:de:0030-drops-76348},
  doi =		{10.4230/LIPIcs.WABI.2017.0},
  annote =	{Keywords: Front Matter, Table of Contents, Preface, List of Authors}
}
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