5 Search Results for "Wilcox, James R."

Document
DOI: 10.4230/LIPIcs.WABI.2025.12
Extension of Partial Atom-To-Atom Maps: Uniqueness and Algorithms

Authors: Marcos E. González Laffitte, Tieu-Long Phan, and Peter F. Stadler

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

Abstract
Chemical reaction databases typically report the molecular structures of reactant and product compounds, as well as their stoichiometry, but lack information, in particular, on the correspondence of reactant and product atoms. These atom-to-atom maps (AAM), however, are crucial for applications including chemical synthesis planning in organic chemistry and the analysis of isotope labeling experiments in modern metabolomics. AAMs therefore need to be reconstructed computationally. This situation is aggravated, furthermore, by the fact that chemically correct AAMs are, fundamentally, determined by quantum-mechanical phenomena and thus cannot be reliably computed by solving graph-theoretical optimization problems defined by the reactant and product structures. A viable solution for this problem is to shift the focus into first identifying a partial AAM containing the reaction center, i.e., covering the atoms incident with all bonds that change during a reaction. This then leads to the problem of extending the partial map to the full reaction. The AAM of a reaction is faithfully represented by the Imaginary Transition State (ITS) graph, providing a convenient graph-theoretic framework to address the questions of when and how a partial AAM can be extended. We show that an unique extension exists whenever, and only if, these partial AAMs cover the reaction center. In this case their extension can be computed by solving a constrained graph-isomorphism search between specific subgraphs of ITS graphs. We close by benchmarking different tools for this task.
Cite as

Marcos E. González Laffitte, Tieu-Long Phan, and Peter F. Stadler. Extension of Partial Atom-To-Atom Maps: Uniqueness and Algorithms. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 12:1-12:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{gonzalezlaffitte_et_al:LIPIcs.WABI.2025.12,
  author =	{Gonz\'{a}lez Laffitte, Marcos E. and Phan, Tieu-Long and Stadler, Peter F.},
  title =	{{Extension of Partial Atom-To-Atom Maps: Uniqueness and Algorithms}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{12:1--12:26},
  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.2025.12},
  URN =		{urn:nbn:de:0030-drops-239410},
  doi =		{10.4230/LIPIcs.WABI.2025.12},
  annote =	{Keywords: atom-to-atom maps, imaginary transition state (ITS) graphs, condensed graph of the reaction (CGR), chemical reaction mechanisms, molecular graphs, metabolic networks, chemical synthesis planning, constrained graph isomorphism}
}
Document
DOI: 10.4230/LIPIcs.ICDT.2025.11
Semantic Foundations of Equality Saturation

Authors: Dan Suciu, Yisu Remy Wang, and Yihong Zhang

Published in: LIPIcs, Volume 328, 28th International Conference on Database Theory (ICDT 2025)

Abstract
Equality saturation is an emerging technique for program and query optimization developed in the programming language community. It performs term rewriting over an E-graph, a data structure that compactly represents a program space. Despite its popularity, the theory of equality saturation lags behind the practice. In this paper, we define a fixpoint semantics of equality saturation based on tree automata and uncover deep connections between equality saturation and the chase. We characterize the class of chase sequences that correspond to equality saturation. We study the complexities of terminations of equality saturation in three cases: single-instance, all-term-instance, and all-E-graph-instance. Finally, we define a syntactic criterion based on acyclicity that implies equality saturation termination.
Cite as

Dan Suciu, Yisu Remy Wang, and Yihong Zhang. Semantic Foundations of Equality Saturation. In 28th International Conference on Database Theory (ICDT 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 328, pp. 11:1-11:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{suciu_et_al:LIPIcs.ICDT.2025.11,
  author =	{Suciu, Dan and Wang, Yisu Remy and Zhang, Yihong},
  title =	{{Semantic Foundations of Equality Saturation}},
  booktitle =	{28th International Conference on Database Theory (ICDT 2025)},
  pages =	{11:1--11:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-364-5},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{328},
  editor =	{Roy, Sudeepa and Kara, Ahmet},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICDT.2025.11},
  URN =		{urn:nbn:de:0030-drops-229523},
  doi =		{10.4230/LIPIcs.ICDT.2025.11},
  annote =	{Keywords: the chase, equality saturation, term rewriting, tree automata, query optimization}
}
Document
Database Theory in Action
DOI: 10.4230/LIPIcs.ICDT.2025.34
Database Theory in Action: Search-Based Program Optimization

Authors: Yihong Zhang, Dan Suciu, Yisu Remy Wang, and Max Willsey

Published in: LIPIcs, Volume 328, 28th International Conference on Database Theory (ICDT 2025)

Abstract
Recent work in programming languages developed an approach to term rewritings based on equality saturation (EqSat), which, instead of applying destructively the rewrite rules, maintains all equivalent expressions in a structure called an E-graph. This paper describes two surprising connections between EqSat and databases, going both ways. On one hand equality saturation can be viewed as a query evaluation problem, with great benefits. On the other hand, most sophisticated SQL query optimizers are based on the Volcano/Cascades framework which, we explain, is a variant of EqSat.
Cite as

Yihong Zhang, Dan Suciu, Yisu Remy Wang, and Max Willsey. Database Theory in Action: Search-Based Program Optimization. In 28th International Conference on Database Theory (ICDT 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 328, pp. 34:1-34:6, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{zhang_et_al:LIPIcs.ICDT.2025.34,
  author =	{Zhang, Yihong and Suciu, Dan and Wang, Yisu Remy and Willsey, Max},
  title =	{{Database Theory in Action: Search-Based Program Optimization}},
  booktitle =	{28th International Conference on Database Theory (ICDT 2025)},
  pages =	{34:1--34:6},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-364-5},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{328},
  editor =	{Roy, Sudeepa and Kara, Ahmet},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICDT.2025.34},
  URN =		{urn:nbn:de:0030-drops-229759},
  doi =		{10.4230/LIPIcs.ICDT.2025.34},
  annote =	{Keywords: Query optimization, program optimization, Cascades framework, equality saturation, Datalog}
}
Document
DOI: 10.4230/LIPIcs.ITP.2019.26
Ornaments for Proof Reuse in Coq

Authors: Talia Ringer, Nathaniel Yazdani, John Leo, and Dan Grossman

Published in: LIPIcs, Volume 141, 10th International Conference on Interactive Theorem Proving (ITP 2019)

Abstract
Ornaments express relations between inductive types with the same inductive structure. We implement fully automatic proof reuse for a particular class of ornaments in a Coq plugin, and show how such a tool can give programmers the rewards of using indexed inductive types while automating away many of the costs. The plugin works directly on Coq code; it is the first ornamentation tool for a non-embedded dependently typed language. It is also the first tool to automatically identify ornaments: To lift a function or proof, the user must provide only the source type, the destination type, and the source function or proof. In taking advantage of the mathematical properties of ornaments, our approach produces faster functions and smaller terms than a more general approach to proof reuse in Coq.
Cite as

Talia Ringer, Nathaniel Yazdani, John Leo, and Dan Grossman. Ornaments for Proof Reuse in Coq. In 10th International Conference on Interactive Theorem Proving (ITP 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 141, pp. 26:1-26:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

Copy BibTex To Clipboard

@InProceedings{ringer_et_al:LIPIcs.ITP.2019.26,
  author =	{Ringer, Talia and Yazdani, Nathaniel and Leo, John and Grossman, Dan},
  title =	{{Ornaments for Proof Reuse in Coq}},
  booktitle =	{10th International Conference on Interactive Theorem Proving (ITP 2019)},
  pages =	{26:1--26:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-122-1},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{141},
  editor =	{Harrison, John and O'Leary, John and Tolmach, Andrew},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITP.2019.26},
  URN =		{urn:nbn:de:0030-drops-110816},
  doi =		{10.4230/LIPIcs.ITP.2019.26},
  annote =	{Keywords: ornaments, proof reuse, proof automation}
}
Document
DOI: 10.4230/LIPIcs.SNAPL.2017.19
Programming Language Abstractions for Modularly Verified Distributed Systems

Authors: James R. Wilcox, Ilya Sergey, and Zachary Tatlock

Published in: LIPIcs, Volume 71, 2nd Summit on Advances in Programming Languages (SNAPL 2017)

Abstract
Distributed systems are rarely developed as monolithic programs. Instead, like any software, these systems may consist of multiple program components, which are then compiled separately and linked together. Modern systems also incorporate various services interacting with each other and with client applications. However, state-of-the-art verification tools focus predominantly on verifying standalone, closed-world protocols or systems, thus failing to account for the compositional nature of distributed systems. For example, standalone verification has the drawback that when protocols and their optimized implementations evolve, one must re-verify the entire system from scratch, instead of leveraging compositionality to contain the reverification effort. In this paper, we focus on the challenge of modular verification of distributed systems with respect to high-level protocol invariants as well as for low-level implementation safety properties. We argue that the missing link between the two is a programming paradigm that would allow one to reason about both high-level distributed protocols and low-level implementation primitives in a single verification-friendly framework. Such a link would make it possible to reap the benefits from both the vast body of research in distributed computing, focused on modular protocol decomposition and consistency properties, as well as from the recent advances in program verification, enabling construction of provably correct systems implementations. To showcase the modular verification challenges, we present some typical scenarios of decomposition between a distributed protocol and its implementations. We then describe our ongoing research agenda, in which we are attempting to address the outlined problems by providing a typing discipline and a set of domain-specific primitives for specifying, implementing and verifying distributed systems. Our approach, mechanized within a proof assistant, provides the means of decomposition necessary for modular proofs about distributed protocols and systems.
Cite as

James R. Wilcox, Ilya Sergey, and Zachary Tatlock. Programming Language Abstractions for Modularly Verified Distributed Systems. In 2nd Summit on Advances in Programming Languages (SNAPL 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 71, pp. 19:1-19:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

Copy BibTex To Clipboard

@InProceedings{wilcox_et_al:LIPIcs.SNAPL.2017.19,
  author =	{Wilcox, James R. and Sergey, Ilya and Tatlock, Zachary},
  title =	{{Programming Language Abstractions for Modularly Verified Distributed Systems}},
  booktitle =	{2nd Summit on Advances in Programming Languages (SNAPL 2017)},
  pages =	{19:1--19:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-032-3},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{71},
  editor =	{Lerner, Benjamin S. and Bod{\'\i}k, Rastislav and Krishnamurthi, Shriram},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SNAPL.2017.19},
  URN =		{urn:nbn:de:0030-drops-71266},
  doi =		{10.4230/LIPIcs.SNAPL.2017.19},
  annote =	{Keywords: Distributed systems, program verification, distributed protocols, domain-specific languages, type systems, dependent types, program logics.}
}
  • Refine by Type
  • 5 Document/PDF
  • 3 Document/HTML

  • Refine by Publication Year
  • 3 2025
  • 1 2019
  • 1 2017

  • Refine by Author
  • 2 Suciu, Dan
  • 2 Wang, Yisu Remy
  • 2 Zhang, Yihong
  • 1 González Laffitte, Marcos E.
  • 1 Grossman, Dan
  • Show More...

  • Refine by Series/Journal
  • 5 LIPIcs

  • Refine by Classification
  • 2 Theory of computation → Equational logic and rewriting
  • 1 Software and its engineering → Formal software verification
  • 1 Theory of computation → Database query processing and optimization (theory)
  • 1 Theory of computation → Discrete optimization
  • 1 Theory of computation → Graph algorithms analysis
  • Show More...

  • Refine by Keyword
  • 2 equality saturation
  • 1 Cascades framework
  • 1 Datalog
  • 1 Distributed systems
  • 1 Query optimization
  • Show More...

Any Issues?
X

Feedback on the Current Page

CAPTCHA

Thanks for your feedback!

Feedback submitted to Dagstuhl Publishing

Could not send message

Please try again later or send an E-mail
© 2023-2026 Schloss Dagstuhl – LZI GmbH Schloss Dagstuhl – LZI GmbH About DROPS Imprint Privacy Contact