8 Search Results for "Tate, Ross"

Document
DOI: 10.4230/LIPIcs.WABI.2025.11
Mutational Signature Refitting on Sparse Pan-Cancer Data

Authors: Gal Gilad, Teresa M. Przytycka, and Roded Sharan

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

Abstract
Mutational processes shape cancer genomes, leaving characteristic marks that are termed signatures. The level of activity of each such process, or its signature exposure, provides important information on the disease, improving patient stratification and the prediction of drug response. Thus, there is growing interest in developing refitting methods that decipher those exposures. Previous work in this domain was unsupervised in nature, employing algebraic decomposition and probabilistic inference methods. Here we provide a supervised approach to the problem of signature refitting and show its superiority over current methods. Our method, SuRe, leverages a neural network model to capture correlations between signature exposures in real data. We show that SuRe outperforms previous methods on sparse mutation data from tumor type specific data sets, as well as pan-cancer data sets, with an increasing advantage as the data become sparser. We further demonstrate its utility in clinical settings.
Cite as

Gal Gilad, Teresa M. Przytycka, and Roded Sharan. Mutational Signature Refitting on Sparse Pan-Cancer Data. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 11:1-11:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gilad_et_al:LIPIcs.WABI.2025.11,
  author =	{Gilad, Gal and Przytycka, Teresa M. and Sharan, Roded},
  title =	{{Mutational Signature Refitting on Sparse Pan-Cancer Data}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{11:1--11:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.11},
  URN =		{urn:nbn:de:0030-drops-239374},
  doi =		{10.4230/LIPIcs.WABI.2025.11},
  annote =	{Keywords: mutational signatures, signature refitting, cancer genomics, genomic data analysis, somatic mutations}
}
Document
DOI: 10.4230/LIPIcs.GIScience.2025.5
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.FSCD.2025.14
From Partial to Monadic: Combinatory Algebra with Effects

Authors: Liron Cohen, Ariel Grunfeld, Dominik Kirst, and Étienne Miquey

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

Abstract
Partial Combinatory Algebras (PCAs) provide a foundational model of the untyped λ-calculus and serve as the basis for many notions of computability, such as realizability theory. However, PCAs support a very limited notion of computation by only incorporating non-termination as a computational effect. To provide a framework that better internalizes a wide range of computational effects, this paper puts forward the notion of Monadic Combinatory Algebras (MCAs). MCAs generalize the notion of PCAs by structuring the combinatory algebra over an underlying computational effect, embodied by a monad. We show that MCAs can support various side effects through the underlying monad, such as non-determinism, stateful computation and continuations. We further obtain a categorical characterization of MCAs within Freyd Categories, following a similar connection for PCAs. Moreover, we explore the application of MCAs in realizability theory, presenting constructions of effectful realizability triposes and assemblies derived through evidenced frames, thereby generalizing traditional PCA-based realizability semantics. The monadic generalization of the foundational notion of PCAs provides a comprehensive and powerful framework for internally reasoning about effectful computations, paving the path to a more encompassing study of computation and its relationship with realizability models and programming languages.
Cite as

Liron Cohen, Ariel Grunfeld, Dominik Kirst, and Étienne Miquey. From Partial to Monadic: Combinatory Algebra with Effects. In 10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 337, pp. 14:1-14:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{cohen_et_al:LIPIcs.FSCD.2025.14,
  author =	{Cohen, Liron and Grunfeld, Ariel and Kirst, Dominik and Miquey, \'{E}tienne},
  title =	{{From Partial to Monadic: Combinatory Algebra with Effects}},
  booktitle =	{10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025)},
  pages =	{14:1--14:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-374-4},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{337},
  editor =	{Fern\'{a}ndez, Maribel},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSCD.2025.14},
  URN =		{urn:nbn:de:0030-drops-236297},
  doi =		{10.4230/LIPIcs.FSCD.2025.14},
  annote =	{Keywords: Combinatory algebras, Monads, Effects, Realizability, Evidenced frames}
}
Document
Invited Talk
DOI: 10.4230/LIPIcs.FSCD.2025.1
Computation First: Rebuilding Constructivism with Effects (Invited Talk)

Authors: Liron Cohen

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

Abstract
Constructive logic and type theory have traditionally been grounded in pure, effect-free model of computation. This paper argues that such a restriction is not a foundational necessity but a historical artifact, and it advocates for a broader perspective of effectful constructivism, where computational effects, such as state, non-determinism, and exceptions, are directly and internally embedded in the logical and computational foundations. We begin by surveying examples where effects reshape logical principles, and then outline three approaches to effectful constructivism, focusing on realizability models: Monadic Combinatory Algebras, which extend classical partial combinatory algebras with effectful computation; Evidenced Frames, a flexible semantic structure capable of uniformly capturing a wide range of effects; and Effectful Higher-Order Logic (EffHOL), a syntactic approach that directly translates logical propositions into specifications for effectful programs. We further illustrate how concrete type theories can internalize effects, via the family of type theories TT^□_C. Together, these works demonstrate that effectful constructivism is not merely possible but a natural and robust extension of traditional frameworks.
Cite as

Liron Cohen. Computation First: Rebuilding Constructivism with Effects (Invited Talk). In 10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 337, pp. 1:1-1:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{cohen:LIPIcs.FSCD.2025.1,
  author =	{Cohen, Liron},
  title =	{{Computation First: Rebuilding Constructivism with Effects}},
  booktitle =	{10th International Conference on Formal Structures for Computation and Deduction (FSCD 2025)},
  pages =	{1:1--1:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-374-4},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{337},
  editor =	{Fern\'{a}ndez, Maribel},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSCD.2025.1},
  URN =		{urn:nbn:de:0030-drops-236167},
  doi =		{10.4230/LIPIcs.FSCD.2025.1},
  annote =	{Keywords: Effectful constructivism, realizability, type theory, monadic combinatory algebras, evidenced frame}
}
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)

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@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)

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@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.SNAPL.2019.6
The Dynamic Practice and Static Theory of Gradual Typing

Authors: Michael Greenberg

Published in: LIPIcs, Volume 136, 3rd Summit on Advances in Programming Languages (SNAPL 2019)

Abstract
We can tease apart the research on gradual types into two `lineages': a pragmatic, implementation-oriented dynamic-first lineage and a formal, type-theoretic, static-first lineage. The dynamic-first lineage’s focus is on taming particular idioms - `pre-existing conditions' in untyped programming languages. The static-first lineage’s focus is on interoperation and individual type system features, rather than the collection of features found in any particular language. Both appear in programming languages research under the name "gradual typing", and they are in active conversation with each other. What are these two lineages? What challenges and opportunities await the static-first lineage? What progress has been made so far?
Cite as

Michael Greenberg. The Dynamic Practice and Static Theory of Gradual Typing. In 3rd Summit on Advances in Programming Languages (SNAPL 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 136, pp. 6:1-6:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{greenberg:LIPIcs.SNAPL.2019.6,
  author =	{Greenberg, Michael},
  title =	{{The Dynamic Practice and Static Theory of Gradual Typing}},
  booktitle =	{3rd Summit on Advances in Programming Languages (SNAPL 2019)},
  pages =	{6:1--6:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-113-9},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{136},
  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.2019.6},
  URN =		{urn:nbn:de:0030-drops-105495},
  doi =		{10.4230/LIPIcs.SNAPL.2019.6},
  annote =	{Keywords: dynamic typing, gradual typing, static typing, implementation, theory, challenge problems}
}
Document
Invited Talk
DOI: 10.4230/LIPIcs.ECOOP.2017.3
Retargeting Gradual Typing (Invited Talk)

Authors: Ross Tate

Published in: LIPIcs, Volume 74, 31st European Conference on Object-Oriented Programming (ECOOP 2017)

Abstract
Gradual typing is often motivated by efforts to add types to massive untyped code bases. A major challenge here is the fact that these code bases were not written with types in mind, yet the goal is to add types to them without requiring any significant changes in their implementation. Thus, critical to this application is the notion that gradual typing is being added onto a preexisting system. But gradual typing also has applications in education, prototyping, and scripting. It allows programmers to ignore types while they are learning programmatic reasoning, while they are experimenting with new designs, or while they are interacting with external systems. At the same time, gradual typing allows these programmers to utilize APIs with types that provide navigable documentation, that concisely describe interfaces, and that enable IDEs to provide assistance. In these applications, programmers are working with types even when they are not writing types. By targeting just these applications, we can lift a major burden from gradual typing. Rather than being added to something that already exists, here gradual typing can be integrated into the software-development process, into the core language design, and into the run-time environment, with each component designed to support gradual typing from conception. This retargeting provides significant flexibility, enabling designers to tradeoff various capabilities of gradual typing. For example, a designer might choose to require some minor annotation burden in untyped programs for, say, a hundred-fold improvement in run-time performance. For the past half decade I have been exploring gradual typing behind the scenes in both academia and industry, and I will be presenting my experiences with these design tradeoffs so far.
Cite as

Ross Tate. Retargeting Gradual Typing (Invited Talk). In 31st European Conference on Object-Oriented Programming (ECOOP 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 74, p. 3:1, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{tate:LIPIcs.ECOOP.2017.3,
  author =	{Tate, Ross},
  title =	{{Retargeting Gradual Typing}},
  booktitle =	{31st European Conference on Object-Oriented Programming (ECOOP 2017)},
  pages =	{3:1--3:1},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-035-4},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{74},
  editor =	{M\"{u}ller, Peter},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2017.3},
  URN =		{urn:nbn:de:0030-drops-72802},
  doi =		{10.4230/LIPIcs.ECOOP.2017.3},
  annote =	{Keywords: Design, Efficiency, Gradual Typing, Nominal Types}
}
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