7 Search Results for "Burns, Matthew"

Document
DOI: 10.4230/LIPIcs.ITCS.2026.65
Characterizing Off-Chain Influence Proof Transaction Fee Mechanisms

Authors: Aadityan Ganesh, Clayton Thomas, and S. Matthew Weinberg

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

Abstract
Roughgarden [Roughgarden, 2020] initiates the study of Transaction Fee Mechanisms (TFMs), and posits that the on-chain game of a "good" TFM should be on-chain simple (OnC-S), i.e., incentive compatible for both the users and the miner. Recent work of Ganesh, Thomas an Weinberg [Ganesh et al., 2024] posit that they should additionally be Off-Chain Influence-Proof (OffC-IP), which means that the miner cannot achieve any additional revenue by separately conducting an off-chain auction to determine on-chain inclusion. They observe that a cryptographic second-price auction satisfies both properties, but leave open the question of whether other mechanisms (such as those not dependent on cryptography) satisfy these properties. In this paper, we characterize OffC-IP TFMs: They are those satisfying a burn identity relating the burn rule to the allocation rule. In particular, we show that auction is OffC-IP if and only if its (induced direct-revelation) allocation rule X̄(⋅) and burn rule B̅(⋅) (both of which take as input users' values v₁, … , v_n) are truthful when viewing (X̄(⋅), B̅(⋅)) as the allocation and pricing rule of a multi-item auction for a single additive buyer with values (φ(v₁),…, φ(v_n)) equal to the users' virtual values. Building on this burn identity, we characterize OffC-IP and OnC-S TFMs that are deterministic and do not use cryptography: They are posted-price mechanisms with specially-tuned burns. As a corollary, we show that such TFMs can only exist with infinite supply and prior-dependence. However, we show that for randomized TFMs, there are additional OnC-S and OffC-IP auctions that do not use cryptography (even when there is {finite} supply, under prior-dependence with a bounded prior distribution). Holistically, our results show that while OffC-IP is a fairly stringent requirement, families of OffC-IP mechanisms can be found for a variety of settings.
Cite as

Aadityan Ganesh, Clayton Thomas, and S. Matthew Weinberg. Characterizing Off-Chain Influence Proof Transaction Fee Mechanisms. In 17th Innovations in Theoretical Computer Science Conference (ITCS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 362, pp. 65:1-65:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{ganesh_et_al:LIPIcs.ITCS.2026.65,
  author =	{Ganesh, Aadityan and Thomas, Clayton and Weinberg, S. Matthew},
  title =	{{Characterizing Off-Chain Influence Proof Transaction Fee Mechanisms}},
  booktitle =	{17th Innovations in Theoretical Computer Science Conference (ITCS 2026)},
  pages =	{65:1--65:23},
  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.2026.65},
  URN =		{urn:nbn:de:0030-drops-253527},
  doi =		{10.4230/LIPIcs.ITCS.2026.65},
  annote =	{Keywords: Transaction Fee Mechanism Design, Off-Chain Influence Proofness, Blockchain, Decentralized Finance, Simple Auctions}
}
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.ECRTS.2025.12
Real-Time System Evaluation Techniques: A Systematic Mapping Study

Authors: Tilmann L. Unte and Sebastian Altmeyer

Published in: LIPIcs, Volume 335, 37th Euromicro Conference on Real-Time Systems (ECRTS 2025)

Abstract
A systematic mapping study assesses a broad selection of research publications with the aim of categorizing them according to a research question. We present the first systematic mapping study on evaluation practices within the field of real-time systems, by analyzing publications from the top three conferences ECRTS, RTAS, and RTSS from 2017 until 2024. Our study provides a comprehensive view on the evaluation practices prevalent in our community, including benchmark software, task set and graph generators, case studies, industrial challenges, and custom solutions. Based on our study, we construct and publish a dataset enabling quantitative analysis of evaluation practices within the real-time systems community. Our analysis indicates shortcomings in current practice: custom case studies are abundant, while industrial challenges have very minor impact. Reproducibility has only been shown for a small subset of evaluations and there is no indication of change. Adoption of new and improved tools and benchmarks is very slow or even non-existent. Evaluation must not be viewed as an obligation when publishing a paper, but as a key element in ensuring practicability, comparability, and reproducibility. Based on our study, we conclude that our community currently falls short on these objectives.
Cite as

Tilmann L. Unte and Sebastian Altmeyer. Real-Time System Evaluation Techniques: A Systematic Mapping Study. In 37th Euromicro Conference on Real-Time Systems (ECRTS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 335, pp. 12:1-12:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{unte_et_al:LIPIcs.ECRTS.2025.12,
  author =	{Unte, Tilmann L. and Altmeyer, Sebastian},
  title =	{{Real-Time System Evaluation Techniques: A Systematic Mapping Study}},
  booktitle =	{37th Euromicro Conference on Real-Time Systems (ECRTS 2025)},
  pages =	{12:1--12:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-377-5},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{335},
  editor =	{Mancuso, Renato},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECRTS.2025.12},
  URN =		{urn:nbn:de:0030-drops-235903},
  doi =		{10.4230/LIPIcs.ECRTS.2025.12},
  annote =	{Keywords: Systematic Mapping Study, Real-Time Systems, Evaluation}
}
Document
DOI: 10.4230/LIPIcs.ECRTS.2025.17
Theoretical Foundations of Utility Accrual for Real-Time Systems

Authors: Jian-Jia Chen, Junjie Shi, Mario Günzel, Georg von der Brüggen, Kuan-Hsun Chen, and Peter Bella

Published in: LIPIcs, Volume 335, 37th Euromicro Conference on Real-Time Systems (ECRTS 2025)

Abstract
Providing guaranteed quantification of properties of soft real-time systems is important in practice to ensure that a system performs correctly most of the time. We study utility accrual for real-time systems, in which the utility of a real-time job is defined as a time utility function with respect to its response time. Essentially, we answer the fundamental questions: Does the utility accrual of a periodic real-time task in the long run converge to a single value? If yes, to which value? We first show that concrete problem instances exist where evaluating the utility accrual by simulating the scheduling algorithm or conducting scheduling experiments in a long run is erroneous. Afterwards, we show how to construct a Markov chain to model the interactions between the scheduling policy, the probabilistic workload of a periodic real-time task, the service provided by the system to serve the task, and the effect on the utility accrual. For such a Markov chain, we also provide the theoretical fundamentals to determine whether the utility accrual converges in the long run and the derivation of the utility accrual if it converges.
Cite as

Jian-Jia Chen, Junjie Shi, Mario Günzel, Georg von der Brüggen, Kuan-Hsun Chen, and Peter Bella. Theoretical Foundations of Utility Accrual for Real-Time Systems. In 37th Euromicro Conference on Real-Time Systems (ECRTS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 335, pp. 17:1-17:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{chen_et_al:LIPIcs.ECRTS.2025.17,
  author =	{Chen, Jian-Jia and Shi, Junjie and G\"{u}nzel, Mario and von der Br\"{u}ggen, Georg and Chen, Kuan-Hsun and Bella, Peter},
  title =	{{Theoretical Foundations of Utility Accrual for Real-Time Systems}},
  booktitle =	{37th Euromicro Conference on Real-Time Systems (ECRTS 2025)},
  pages =	{17:1--17:26},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-377-5},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{335},
  editor =	{Mancuso, Renato},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECRTS.2025.17},
  URN =		{urn:nbn:de:0030-drops-235950},
  doi =		{10.4230/LIPIcs.ECRTS.2025.17},
  annote =	{Keywords: Soft Real-Time Systems, Utility Accrual, Markov Chains, Dismiss Points}
}
Document
Resource Paper
DOI: 10.4230/TGDK.2.2.7
Whelk: An OWL EL+RL Reasoner Enabling New Use Cases

Authors: James P. Balhoff and Christopher J. Mungall

Published in: TGDK, Volume 2, Issue 2 (2024): Special Issue on Resources for Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 2, Issue 2

Abstract
Many tasks in the biosciences rely on reasoning with large OWL terminologies (Tboxes), often combined with even larger databases. In particular, a common task is retrieval queries that utilize relational expressions; for example, “find all genes expressed in the brain or any part of the brain”. Automated reasoning on these ontologies typically relies on scalable reasoners targeting the EL subset of OWL, such as ELK. While the introduction of ELK has been transformative in the incorporation of reasoning into bio-ontology quality control and production pipelines, we have encountered limitations when applying it to use cases involving high throughput query answering or reasoning about datasets describing instances (Aboxes). Whelk is a fast OWL reasoner for combined EL+RL reasoning. As such, it is particularly useful for many biological ontology tasks, particularly those characterized by large Tboxes using the EL subset of OWL, combined with Aboxes targeting the RL subset of OWL. Whelk is implemented in Scala and utilizes immutable functional data structures, which provides advantages when performing incremental or dynamic reasoning tasks. Whelk supports querying complex class expressions at a substantially greater rate than ELK, and can answer queries or perform incremental reasoning tasks in parallel, enabling novel applications of OWL reasoning.
Cite as

James P. Balhoff and Christopher J. Mungall. Whelk: An OWL EL+RL Reasoner Enabling New Use Cases. In Special Issue on Resources for Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 2, Issue 2, pp. 7:1-7:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{balhoff_et_al:TGDK.2.2.7,
  author =	{Balhoff, James P. and Mungall, Christopher J.},
  title =	{{Whelk: An OWL EL+RL Reasoner Enabling New Use Cases}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{7:1--7:17},
  ISSN =	{2942-7517},
  year =	{2024},
  volume =	{2},
  number =	{2},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.2.2.7},
  URN =		{urn:nbn:de:0030-drops-225918},
  doi =		{10.4230/TGDK.2.2.7},
  annote =	{Keywords: Web Ontology Language, OWL, Semantic Web, ontology, reasoner}
}
Document
Position
DOI: 10.4230/TGDK.1.1.2
Large Language Models and Knowledge Graphs: Opportunities and Challenges

Authors: Jeff Z. Pan, Simon Razniewski, Jan-Christoph Kalo, Sneha Singhania, Jiaoyan Chen, Stefan Dietze, Hajira Jabeen, Janna Omeliyanenko, Wen Zhang, Matteo Lissandrini, Russa Biswas, Gerard de Melo, Angela Bonifati, Edlira Vakaj, Mauro Dragoni, and Damien Graux

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
Large Language Models (LLMs) have taken Knowledge Representation - and the world - by storm. This inflection point marks a shift from explicit knowledge representation to a renewed focus on the hybrid representation of both explicit knowledge and parametric knowledge. In this position paper, we will discuss some of the common debate points within the community on LLMs (parametric knowledge) and Knowledge Graphs (explicit knowledge) and speculate on opportunities and visions that the renewed focus brings, as well as related research topics and challenges.
Cite as

Jeff Z. Pan, Simon Razniewski, Jan-Christoph Kalo, Sneha Singhania, Jiaoyan Chen, Stefan Dietze, Hajira Jabeen, Janna Omeliyanenko, Wen Zhang, Matteo Lissandrini, Russa Biswas, Gerard de Melo, Angela Bonifati, Edlira Vakaj, Mauro Dragoni, and Damien Graux. Large Language Models and Knowledge Graphs: Opportunities and Challenges. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 2:1-2:38, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{pan_et_al:TGDK.1.1.2,
  author =	{Pan, Jeff Z. and Razniewski, Simon and Kalo, Jan-Christoph and Singhania, Sneha and Chen, Jiaoyan and Dietze, Stefan and Jabeen, Hajira and Omeliyanenko, Janna and Zhang, Wen and Lissandrini, Matteo and Biswas, Russa and de Melo, Gerard and Bonifati, Angela and Vakaj, Edlira and Dragoni, Mauro and Graux, Damien},
  title =	{{Large Language Models and Knowledge Graphs: Opportunities and Challenges}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{2:1--2:38},
  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.1.1.2},
  URN =		{urn:nbn:de:0030-drops-194766},
  doi =		{10.4230/TGDK.1.1.2},
  annote =	{Keywords: Large Language Models, Pre-trained Language Models, Knowledge Graphs, Ontology, Retrieval Augmented Language Models}
}
Document
DOI: 10.4230/LIPIcs.SAT.2023.25
Combining Cubic Dynamical Solvers with Make/Break Heuristics to Solve SAT

Authors: Anshujit Sharma, Matthew Burns, and Michael C. Huang

Published in: LIPIcs, Volume 271, 26th International Conference on Theory and Applications of Satisfiability Testing (SAT 2023)

Abstract
Dynamical solvers for combinatorial optimization are usually based on 2superscript{nd} degree polynomial interactions, such as the Ising model. These exhibit high success for problems that map naturally to their formulation. However, SAT requires higher degree of interactions. As such, these quadratic dynamical solvers (QDS) have shown poor solution quality due to excessive auxiliary variables and the resulting increase in search-space complexity. Thus recently, a series of cubic dynamical solver (CDS) models have been proposed for SAT and other problems. We show that such problem-agnostic CDS models still perform poorly on moderate to large problems, thus motivating the need to utilize SAT-specific heuristics. With this insight, our contributions can be summarized into three points. First, we demonstrate that existing make-only heuristics perform poorly on scale-free, industrial-like problems when integrated into CDS. This motivates us to utilize break counts as well. Second, we derive a relationship between make/break and the CDS formulation to efficiently recover break counts. Finally, we utilize this relationship to propose a new make/break heuristic and combine it with a state-of-the-art CDS which is projected to solve SAT problems several orders of magnitude faster than existing software solvers.
Cite as

Anshujit Sharma, Matthew Burns, and Michael C. Huang. Combining Cubic Dynamical Solvers with Make/Break Heuristics to Solve SAT. In 26th International Conference on Theory and Applications of Satisfiability Testing (SAT 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 271, pp. 25:1-25:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{sharma_et_al:LIPIcs.SAT.2023.25,
  author =	{Sharma, Anshujit and Burns, Matthew and Huang, Michael C.},
  title =	{{Combining Cubic Dynamical Solvers with Make/Break Heuristics to Solve SAT}},
  booktitle =	{26th International Conference on Theory and Applications of Satisfiability Testing (SAT 2023)},
  pages =	{25:1--25:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-286-0},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{271},
  editor =	{Mahajan, Meena and Slivovsky, Friedrich},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAT.2023.25},
  URN =		{urn:nbn:de:0030-drops-184871},
  doi =		{10.4230/LIPIcs.SAT.2023.25},
  annote =	{Keywords: Satisfiability, Ising machines, Stochastic Heuristics, Natural Computation}
}
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