9 Search Results for "Genet, Thomas"


Document
An Isabelle/HOL Formalization of Semi-Thue and Conditional Semi-Thue Systems

Authors: Dohan Kim

Published in: LIPIcs, Volume 352, 16th International Conference on Interactive Theorem Proving (ITP 2025)


Abstract
We present a formalized framework for semi-Thue and conditional semi-Thue systems for studying monoids and their word problem using the Isabelle/HOL proof assistant. We provide a formalized decision procedure for the word problem of monoids if they are finitely presented by complete semi-Thue systems. In particular, we present a new formalized method for checking confluence using (conditional) critical pairs for certain conditional semi-Thue systems. We propose and formalize an inference system for generating conditional equational theories and Thue congruences using conditional semi-Thue systems. Then we provide a new formalized decision procedure for the word problem of monoids which have finite complete (reductive) conditional presentations.

Cite as

Dohan Kim. An Isabelle/HOL Formalization of Semi-Thue and Conditional Semi-Thue Systems. In 16th International Conference on Interactive Theorem Proving (ITP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 352, pp. 10:1-10:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@InProceedings{kim:LIPIcs.ITP.2025.10,
  author =	{Kim, Dohan},
  title =	{{An Isabelle/HOL Formalization of Semi-Thue and Conditional Semi-Thue Systems}},
  booktitle =	{16th International Conference on Interactive Theorem Proving (ITP 2025)},
  pages =	{10:1--10:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-396-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{352},
  editor =	{Forster, Yannick and Keller, Chantal},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITP.2025.10},
  URN =		{urn:nbn:de:0030-drops-246081},
  doi =		{10.4230/LIPIcs.ITP.2025.10},
  annote =	{Keywords: semi-Thue systems, conditional semi-Thue systems, conditional string rewriting, monoids, word problem}
}
Document
Human Readable Compression of GFA Paths Using Grammar-Based Code

Authors: Peter Heringer and Daniel Doerr

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


Abstract
Pangenome graphs offer a compact and comprehensive representation of genomic diversity, improving tasks such as variant calling, genotyping, and other downstream analyses. Although the underlying graph structures scale sublinearly with the number of haplotypes, the widely used GFA file format suffers from rapidly growing file sizes due to the explicit and repetitive encoding of haplotype paths. In this work, we introduce an extension to the GFA format that enables efficient grammar-based compression of haplotype paths while retaining human readability. In addition, grammar-based encoding provides an efficient in-memory data structure that does not require decompression, but conversely improves the runtime of many computational tasks that involve haplotype comparisons. We present sqz, a method that makes use of the proposed format extension to encode haplotype paths using byte pair encoding, a grammar-based compression scheme. We evaluate sqz on recent human pangenome graphs from Heumos et al. and the Human Pangenome Reference Consortium (HPRC), comparing it to existing compressors bgzip, gbz, and sequitur. sqz scales sublinearly with the number of haplotypes in a pangenome graph and consistently achieves higher compression ratios than sequitur and up to 5 times better compression than bgzip in HPRC graphs and up to 10 times in the graph from Heumos et al.. When combined with bgzip, sqz matches or excels the compression ratio of gbz across all our datasets. These results demonstrate the potential of our proposed extension of the GFA format in reducing haplotype path redundancy and improving storage efficiency for pangenome graphs.

Cite as

Peter Heringer and Daniel Doerr. Human Readable Compression of GFA Paths Using Grammar-Based Code. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 14:1-14:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@InProceedings{heringer_et_al:LIPIcs.WABI.2025.14,
  author =	{Heringer, Peter and Doerr, Daniel},
  title =	{{Human Readable Compression of GFA Paths Using Grammar-Based Code}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{14:1--14:19},
  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.2025.14},
  URN =		{urn:nbn:de:0030-drops-239395},
  doi =		{10.4230/LIPIcs.WABI.2025.14},
  annote =	{Keywords: pangenomics, pangenome graphs, compression, grammar-based code, byte pair encoding}
}
Document
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
Survey
Knowledge Graph Embeddings: Open Challenges and Opportunities

Authors: Russa Biswas, Lucie-Aimée Kaffee, Michael Cochez, Stefania Dumbrava, Theis E. Jendal, Matteo Lissandrini, Vanessa Lopez, Eneldo Loza Mencía, Heiko Paulheim, Harald Sack, Edlira Kalemi Vakaj, and Gerard de Melo

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
While Knowledge Graphs (KGs) have long been used as valuable sources of structured knowledge, in recent years, KG embeddings have become a popular way of deriving numeric vector representations from them, for instance, to support knowledge graph completion and similarity search. This study surveys advances as well as open challenges and opportunities in this area. For instance, the most prominent embedding models focus primarily on structural information. However, there has been notable progress in incorporating further aspects, such as semantics, multi-modal, temporal, and multilingual features. Most embedding techniques are assessed using human-curated benchmark datasets for the task of link prediction, neglecting other important real-world KG applications. Many approaches assume a static knowledge graph and are unable to account for dynamic changes. Additionally, KG embeddings may encode data biases and lack interpretability. Overall, this study provides an overview of promising research avenues to learn improved KG embeddings that can address a more diverse range of use cases.

Cite as

Russa Biswas, Lucie-Aimée Kaffee, Michael Cochez, Stefania Dumbrava, Theis E. Jendal, Matteo Lissandrini, Vanessa Lopez, Eneldo Loza Mencía, Heiko Paulheim, Harald Sack, Edlira Kalemi Vakaj, and Gerard de Melo. Knowledge Graph Embeddings: Open Challenges and Opportunities. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 4:1-4:32, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@Article{biswas_et_al:TGDK.1.1.4,
  author =	{Biswas, Russa and Kaffee, Lucie-Aim\'{e}e and Cochez, Michael and Dumbrava, Stefania and Jendal, Theis E. and Lissandrini, Matteo and Lopez, Vanessa and Menc{\'\i}a, Eneldo Loza and Paulheim, Heiko and Sack, Harald and Vakaj, Edlira Kalemi and de Melo, Gerard},
  title =	{{Knowledge Graph Embeddings: Open Challenges and Opportunities}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{4:1--4:32},
  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.1.1.4},
  URN =		{urn:nbn:de:0030-drops-194783},
  doi =		{10.4230/TGDK.1.1.4},
  annote =	{Keywords: Knowledge Graphs, KG embeddings, Link prediction, KG applications}
}
Document
Position
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
Survey
How Does Knowledge Evolve in Open Knowledge Graphs?

Authors: Axel Polleres, Romana Pernisch, Angela Bonifati, Daniele Dell'Aglio, Daniil Dobriy, Stefania Dumbrava, Lorena Etcheverry, Nicolas Ferranti, Katja Hose, Ernesto Jiménez-Ruiz, Matteo Lissandrini, Ansgar Scherp, Riccardo Tommasini, and Johannes Wachs

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
Openly available, collaboratively edited Knowledge Graphs (KGs) are key platforms for the collective management of evolving knowledge. The present work aims t o provide an analysis of the obstacles related to investigating and processing specifically this central aspect of evolution in KGs. To this end, we discuss (i) the dimensions of evolution in KGs, (ii) the observability of evolution in existing, open, collaboratively constructed Knowledge Graphs over time, and (iii) possible metrics to analyse this evolution. We provide an overview of relevant state-of-the-art research, ranging from metrics developed for Knowledge Graphs specifically to potential methods from related fields such as network science. Additionally, we discuss technical approaches - and their current limitations - related to storing, analysing and processing large and evolving KGs in terms of handling typical KG downstream tasks.

Cite as

Axel Polleres, Romana Pernisch, Angela Bonifati, Daniele Dell'Aglio, Daniil Dobriy, Stefania Dumbrava, Lorena Etcheverry, Nicolas Ferranti, Katja Hose, Ernesto Jiménez-Ruiz, Matteo Lissandrini, Ansgar Scherp, Riccardo Tommasini, and Johannes Wachs. How Does Knowledge Evolve in Open Knowledge Graphs?. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 11:1-11:59, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@Article{polleres_et_al:TGDK.1.1.11,
  author =	{Polleres, Axel and Pernisch, Romana and Bonifati, Angela and Dell'Aglio, Daniele and Dobriy, Daniil and Dumbrava, Stefania and Etcheverry, Lorena and Ferranti, Nicolas and Hose, Katja and Jim\'{e}nez-Ruiz, Ernesto and Lissandrini, Matteo and Scherp, Ansgar and Tommasini, Riccardo and Wachs, Johannes},
  title =	{{How Does Knowledge Evolve in Open Knowledge Graphs?}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{11:1--11:59},
  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.1.1.11},
  URN =		{urn:nbn:de:0030-drops-194855},
  doi =		{10.4230/TGDK.1.1.11},
  annote =	{Keywords: KG evolution, temporal KG, versioned KG, dynamic KG}
}
Document
Automata-Based Verification of Relational Properties of Functions over Algebraic Data Structures

Authors: Théo Losekoot, Thomas Genet, and Thomas Jensen

Published in: LIPIcs, Volume 260, 8th International Conference on Formal Structures for Computation and Deduction (FSCD 2023)


Abstract
This paper is concerned with automatically proving properties about the input-output relation of functional programs operating over algebraic data types. Recent results show how to approximate the image of a functional program using a regular tree language. Though expressive, those techniques cannot prove properties relating the input and the output of a function, e.g., proving that the output of a function reversing a list has the same length as the input list. In this paper, we built upon those results and define a procedure to compute or over-approximate such a relation. Instead of representing the image of a function by a regular set of terms, we represent (an approximation of) the input-output relation by a regular set of tuples of terms. Regular languages of tuples of terms are recognized using a tree automaton recognizing convolutions of terms, where a convolution transforms a tuple of terms into a term built on tuples of symbols. Both the program and the properties are transformed into predicates and Constrained Horn clauses (CHCs). Then, using an Implication Counter Example procedure (ICE), we infer a model of the clauses, associating to each predicate a regular relation. In this ICE procedure, checking if a given model satisfies the clauses is undecidable in general. We overcome undecidability by proposing an incomplete but sound inference procedure for such relational regular properties. Though the procedure is incomplete, its implementation performs well on 120 examples. It efficiently proves non-trivial relational properties or finds counter-examples.

Cite as

Théo Losekoot, Thomas Genet, and Thomas Jensen. Automata-Based Verification of Relational Properties of Functions over Algebraic Data Structures. In 8th International Conference on Formal Structures for Computation and Deduction (FSCD 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 260, pp. 7:1-7:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


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@InProceedings{losekoot_et_al:LIPIcs.FSCD.2023.7,
  author =	{Losekoot, Th\'{e}o and Genet, Thomas and Jensen, Thomas},
  title =	{{Automata-Based Verification of Relational Properties of Functions over Algebraic Data Structures}},
  booktitle =	{8th International Conference on Formal Structures for Computation and Deduction (FSCD 2023)},
  pages =	{7:1--7:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-277-8},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{260},
  editor =	{Gaboardi, Marco and van Raamsdonk, Femke},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSCD.2023.7},
  URN =		{urn:nbn:de:0030-drops-179915},
  doi =		{10.4230/LIPIcs.FSCD.2023.7},
  annote =	{Keywords: Formal verification, Tree automata, Constrained Horn Clauses, Model inference, Relational properties, Algebraic datatypes}
}
Document
Completeness of Tree Automata Completion

Authors: Thomas Genet

Published in: LIPIcs, Volume 108, 3rd International Conference on Formal Structures for Computation and Deduction (FSCD 2018)


Abstract
We consider rewriting of a regular language with a left-linear term rewriting system. We show a completeness theorem on equational tree automata completion stating that, if there exists a regular over-approximation of the set of reachable terms, then equational completion can compute it (or safely under-approximate it). A nice corollary of this theorem is that, if the set of reachable terms is regular, then equational completion can also compute it. This was known to be true for some term rewriting system classes preserving regularity, but was still an open question in the general case. The proof is not constructive because it depends on the regularity of the set of reachable terms, which is undecidable. To carry out those proofs we generalize and improve two results of completion: the Termination and the Upper-Bound theorems. Those theoretical results provide an algorithmic way to safely explore regular approximations with completion. This has been implemented in Timbuk and used to verify safety properties, automatically and efficiently, on first-order and higher-order functional programs.

Cite as

Thomas Genet. Completeness of Tree Automata Completion. In 3rd International Conference on Formal Structures for Computation and Deduction (FSCD 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 108, pp. 16:1-16:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)


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@InProceedings{genet:LIPIcs.FSCD.2018.16,
  author =	{Genet, Thomas},
  title =	{{Completeness of Tree Automata Completion}},
  booktitle =	{3rd International Conference on Formal Structures for Computation and Deduction (FSCD 2018)},
  pages =	{16:1--16:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-077-4},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{108},
  editor =	{Kirchner, H\'{e}l\`{e}ne},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSCD.2018.16},
  URN =		{urn:nbn:de:0030-drops-91868},
  doi =		{10.4230/LIPIcs.FSCD.2018.16},
  annote =	{Keywords: term rewriting systems, regularity preservation, over-approximation, completeness, tree automata, tree automata completion}
}
Document
Reachability Analysis of Innermost Rewriting

Authors: Thomas Genet and Yann Salmon

Published in: LIPIcs, Volume 36, 26th International Conference on Rewriting Techniques and Applications (RTA 2015)


Abstract
We consider the problem of inferring a grammar describing the output of a functional program given a grammar describing its input. Solutions to this problem are helpful for detecting bugs or proving safety properties of functional programs and, several rewriting tools exist for solving this problem. However, known grammar inference techniques are not able to take evaluation strategies of the program into account. This yields very imprecise results when the evaluation strategy matters. In this work, we adapt the Tree Automata Completion algorithm to approximate accurately the set of terms reachable by rewriting under the innermost strategy. We prove that the proposed technique is sound and precise w.r.t. innermost rewriting. The proposed algorithm has been implemented in the Timbuk reachability tool. Experiments show that it noticeably improves the accuracy of static analysis for functional programs using the call-by-value evaluation strategy.

Cite as

Thomas Genet and Yann Salmon. Reachability Analysis of Innermost Rewriting. In 26th International Conference on Rewriting Techniques and Applications (RTA 2015). Leibniz International Proceedings in Informatics (LIPIcs), Volume 36, pp. 177-193, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2015)


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@InProceedings{genet_et_al:LIPIcs.RTA.2015.177,
  author =	{Genet, Thomas and Salmon, Yann},
  title =	{{Reachability Analysis of Innermost Rewriting}},
  booktitle =	{26th International Conference on Rewriting Techniques and Applications (RTA 2015)},
  pages =	{177--193},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-85-9},
  ISSN =	{1868-8969},
  year =	{2015},
  volume =	{36},
  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.RTA.2015.177},
  URN =		{urn:nbn:de:0030-drops-51968},
  doi =		{10.4230/LIPIcs.RTA.2015.177},
  annote =	{Keywords: term rewriting systems, strategy, innermost strategy, tree automata, functiona l program, static analysis}
}
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