13 Search Results for "Francis, Nadime"

Document
Track B: Automata, Logic, Semantics, and Theory of Programming
DOI: 10.4230/LIPIcs.ICALP.2026.160
Gray Codes with Constant Delay and Constant Auxiliary Space

Authors: Antoine Amarilli, Claire David, Nadime Francis, Victor Marsault, Mikaël Monet, and Yann Strozecki

Published in: LIPIcs, Volume 374, 53rd International Colloquium on Automata, Languages, and Programming (ICALP 2026)

Abstract
We give the first two algorithms to enumerate all binary words of {0,1}^𝓁 (like Gray codes) while ensuring that the delay and the auxiliary space is independent from 𝓁, i.e., constant time for each word, and constant memory in addition to the 𝓁 bits storing the current word. Our algorithms are given in two new computational models: tape machines and deque machines. We also study more restricted models, queue machines and stack machines, and show that they cannot enumerate all binary words with constant auxiliary space, even with unrestricted delay. A tape machine is a Turing machine that stores the current binary word on a single working tape of length 𝓁 (which never increases), using no other tape. The machine has a single head and must edit its tape to reach all possible words of {0,1}^𝓁, and output them (in unit time, by entering special output states), with no duplicates. Hence a tape machine uses constant auxiliary space by definition (up to the head position). We construct a tape machine that achieves this task with constant delay between consecutive outputs, so that the machine implements a so-called skew-tolerant quasi-Gray code. We then construct a more involved tape machine that implements a Gray code. A deque machine stores the current binary word on a double-ended queue of length 𝓁, and stores a constant-size internal state. It works as a tape machine, except that it modifies the content of the deque by performing push and pop operations on the endpoints. Hence again a deque machine uses constant auxiliary space by definition. We construct deque machines that enumerate all words of {0,1}^𝓁 with constant-delay. The main technical challenge in this model is to correctly detect when enumeration has finished.
Cite as

Antoine Amarilli, Claire David, Nadime Francis, Victor Marsault, Mikaël Monet, and Yann Strozecki. Gray Codes with Constant Delay and Constant Auxiliary Space. In 53rd International Colloquium on Automata, Languages, and Programming (ICALP 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 374, pp. 160:1-160:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{amarilli_et_al:LIPIcs.ICALP.2026.160,
  author =	{Amarilli, Antoine and David, Claire and Francis, Nadime and Marsault, Victor and Monet, Mika\"{e}l and Strozecki, Yann},
  title =	{{Gray Codes with Constant Delay and Constant Auxiliary Space}},
  booktitle =	{53rd International Colloquium on Automata, Languages, and Programming (ICALP 2026)},
  pages =	{160:1--160:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-428-4},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{374},
  editor =	{Bhattacharya, Sayan and Nanongkai, Danupon and Benedikt, Michael and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2026.160},
  URN =		{urn:nbn:de:0030-drops-265485},
  doi =		{10.4230/LIPIcs.ICALP.2026.160},
  annote =	{Keywords: Gray code, Constant delay, Constant auxiliary space, Enumeration algorithms, Linear bounded automata, Tape machine, Deque machines, Counter implementation}
}
Document
DOI: 10.4230/LIPIcs.ICDT.2026.13
Complexity of Evaluating GQL Queries

Authors: Diego Figueira, Anthony W. Lin, and Liat Peterfreund

Published in: LIPIcs, Volume 365, 29th International Conference on Database Theory (ICDT 2026)

Abstract
GQL has recently emerged as the standard query language over graph databases, particularly, property graphs. Indeed, this is analogous to the role of SQL for relational databases. Unlike SQL, however, fundamental problems regarding GQL are still unsolved, most notably the complexity of query evaluation. In this paper we provide a complete solution to this problem for the core fragment of GQL and for its extension with path restrictors. In particular, we show that the data complexity of these fragments is P^NP[log]-complete in general, and drops to NL-complete when restrictors are disallowed. Using techniques from embedded finite model theory, we show that this is true, even when the queries use data from infinite concrete domains such as real numbers with arithmetic. In proving these results, we establish and exploit tight connections between GQL and query languages over relational databases, especially extensions of relational calculus with transitive closure operators and fragments of second-order logic.
Cite as

Diego Figueira, Anthony W. Lin, and Liat Peterfreund. Complexity of Evaluating GQL Queries. In 29th International Conference on Database Theory (ICDT 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 365, pp. 13:1-13:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{figueira_et_al:LIPIcs.ICDT.2026.13,
  author =	{Figueira, Diego and Lin, Anthony W. and Peterfreund, Liat},
  title =	{{Complexity of Evaluating GQL Queries}},
  booktitle =	{29th International Conference on Database Theory (ICDT 2026)},
  pages =	{13:1--13:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-413-0},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{365},
  editor =	{ten Cate, Balder and Funk, Maurice},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICDT.2026.13},
  URN =		{urn:nbn:de:0030-drops-256278},
  doi =		{10.4230/LIPIcs.ICDT.2026.13},
  annote =	{Keywords: Graph query languages, GQL, complexity, database theory}
}
Document
DOI: 10.4230/LIPIcs.ICDT.2026.18
Output-Sensitive Evaluation of Acyclic Conjunctive Regular Path Queries

Authors: Mahmoud Abo Khamis, Alexandru-Mihai Hurjui, Ahmet Kara, Dan Olteanu, Dan Suciu, and Zilu Tian

Published in: LIPIcs, Volume 365, 29th International Conference on Database Theory (ICDT 2026)

Abstract
Conjunctive Regular Path Queries, or CRPQs for short, are an essential construct in graph query languages. In this paper, we propose the first output-sensitive algorithm for evaluating acyclic CRPQs. It is output-sensitive in the sense that its complexity is a function of the sizes of the input graph and of the query output and not of the output sizes of the regular expressions that appear in the query, as these latter sizes can be larger than the query output size. Our algorithm proceeds in two stages. In the first stage, it contracts the given query into a free-connex acyclic one such that the output of the original query can be obtained from the output of the contracted one. This contraction removes bound variables by composing regular expressions or by promoting bound variables to free ones. The minimum necessary number of promoted bound variables gives the contraction width, which is a novel parameter specific to CRPQs. In the second stage, our algorithm evaluates the free-connex acyclic CRPQ and projects away the columns of the promoted bound variables. It ensures output-sensitivity by computing the calibrated outputs of the regular expressions appearing in the free-connex acyclic CRPQ in time proportional to their sizes. Our algorithm has lower complexity than the state-of-the-art approaches for problem instances where the query output is asymptotically smaller than the output sizes of the regular expressions that appear in the query.
Cite as

Mahmoud Abo Khamis, Alexandru-Mihai Hurjui, Ahmet Kara, Dan Olteanu, Dan Suciu, and Zilu Tian. Output-Sensitive Evaluation of Acyclic Conjunctive Regular Path Queries. In 29th International Conference on Database Theory (ICDT 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 365, pp. 18:1-18:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{abokhamis_et_al:LIPIcs.ICDT.2026.18,
  author =	{Abo Khamis, Mahmoud and Hurjui, Alexandru-Mihai and Kara, Ahmet and Olteanu, Dan and Suciu, Dan and Tian, Zilu},
  title =	{{Output-Sensitive Evaluation of Acyclic Conjunctive Regular Path Queries}},
  booktitle =	{29th International Conference on Database Theory (ICDT 2026)},
  pages =	{18:1--18:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-413-0},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{365},
  editor =	{ten Cate, Balder and Funk, Maurice},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICDT.2026.18},
  URN =		{urn:nbn:de:0030-drops-256321},
  doi =		{10.4230/LIPIcs.ICDT.2026.18},
  annote =	{Keywords: graph databases, regular path queries, output-sensitive algorithms}
}
Document
DOI: 10.4230/LIPIcs.ICDT.2026.22
View-Based Query Determinacy for Walk-Based Semantics

Authors: Nadime Francis

Published in: LIPIcs, Volume 365, 29th International Conference on Database Theory (ICDT 2026)

Abstract
The view-based query determinacy problem asks, given a view 𝒱 and a query Q whether the information contained in 𝒱 always suffices to answer the query Q. It is a notoriously hard problem that is known to be undecidable even in very restricted settings. Here, we study it in the context of graph databases and regular path queries and views evaluated under several "walk-based semantics", that is, semantics in which queries and views return the matched walks in full as opposed to the classical "endpoint semantics". Our main finding is that view-based query determinacy is decidable for regular path queries under both trail and shortest walk semantics.
Cite as

Nadime Francis. View-Based Query Determinacy for Walk-Based Semantics. In 29th International Conference on Database Theory (ICDT 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 365, pp. 22:1-22:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{francis:LIPIcs.ICDT.2026.22,
  author =	{Francis, Nadime},
  title =	{{View-Based Query Determinacy for Walk-Based Semantics}},
  booktitle =	{29th International Conference on Database Theory (ICDT 2026)},
  pages =	{22:1--22:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-413-0},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{365},
  editor =	{ten Cate, Balder and Funk, Maurice},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICDT.2026.22},
  URN =		{urn:nbn:de:0030-drops-256362},
  doi =		{10.4230/LIPIcs.ICDT.2026.22},
  annote =	{Keywords: graph databases, regular path queries, trail semantics, shortest walk semantics, view-based query determinacy}
}
Document
Database Theory in Action
DOI: 10.4230/LIPIcs.ICDT.2026.26
Database Theory in Action: From Inexpressibility to Efficiency in GQL’s Order-Constrained Paths

Authors: Hadar Rotschield and Liat Peterfreund

Published in: LIPIcs, Volume 365, 29th International Conference on Database Theory (ICDT 2026)

Abstract
Pattern matching of core GQL, the new ISO standard for querying property graphs, cannot check whether edge values are increasing along a path, as established in recent work. We present a constructive translation that overcomes this limitation by compiling the increasing-edges condition into the input graph. Remarkably, the benefit of this construction goes beyond restoring expressiveness. In our proof-of-concept implementation in Neo4j’s Cypher, where such path constraints are expressible but costly, our compiled version runs faster and avoids timeouts. This illustrates how a theoretically motivated translation can not only close an expressiveness gap but also bring practical performance gains.
Cite as

Hadar Rotschield and Liat Peterfreund. Database Theory in Action: From Inexpressibility to Efficiency in GQL’s Order-Constrained Paths. In 29th International Conference on Database Theory (ICDT 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 365, pp. 26:1-26:5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{rotschield_et_al:LIPIcs.ICDT.2026.26,
  author =	{Rotschield, Hadar and Peterfreund, Liat},
  title =	{{Database Theory in Action: From Inexpressibility to Efficiency in GQL’s Order-Constrained Paths}},
  booktitle =	{29th International Conference on Database Theory (ICDT 2026)},
  pages =	{26:1--26:5},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-413-0},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{365},
  editor =	{ten Cate, Balder and Funk, Maurice},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICDT.2026.26},
  URN =		{urn:nbn:de:0030-drops-256408},
  doi =		{10.4230/LIPIcs.ICDT.2026.26},
  annote =	{Keywords: Property graphs, ISO GQL, Graph Query Languages, Pattern Matching}
}
Document
DOI: 10.4230/OASIcs.Manzini.14
BWT Indexes for Optimal Joins in Graph Databases

Authors: Diego Arroyuelo and Gonzalo Navarro

Published in: OASIcs, Volume 131, The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday (2025)

Abstract
Graph databases represent data as a labeled directed graph, where the labels refer to properties that connect the entities represented by their source and target vertices. Queries feature, most prominently, sets of edges where source, target, and/or label can be variables; each instantiation of the variables where all the edges occur in the graph is a solution to the query. Worst-case-optimal algorithms to solve those queries have been devised, but they pose significant space requirements. This overhead has hindered the adoption of worst-case-optimal algorithms in real systems. We show that a representation of the graph based on the extended BWT (eBWT), where each edge is seen as an independent string of length 3 (source, label, target) supports worst-case-optimal algorithms while using almost no extra space on top of the raw data. We then show how the idea is generalized to the relational model, where the strings can be longer than 3 and several eBWTs are needed to obtain worst-case optimality. The aim to minimize the amount of space in that case leads to consider novel eBWT variants, where columns other than the last can be chosen. Finally, we show how the same graph representation can be used to solve other typical queries, like finding graph paths that match regular expressions.
Cite as

Diego Arroyuelo and Gonzalo Navarro. BWT Indexes for Optimal Joins in Graph Databases. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 14:1-14:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{arroyuelo_et_al:OASIcs.Manzini.14,
  author =	{Arroyuelo, Diego and Navarro, Gonzalo},
  title =	{{BWT Indexes for Optimal Joins in Graph Databases}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{14:1--14:19},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-390-4},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{131},
  editor =	{Ferragina, Paolo and Gagie, Travis and Navarro, Gonzalo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Manzini.14},
  URN =		{urn:nbn:de:0030-drops-239222},
  doi =		{10.4230/OASIcs.Manzini.14},
  annote =	{Keywords: Graph databases, Ring index, extended BWT, compact data structures}
}
Document
Database Theory in Action
DOI: 10.4230/LIPIcs.ICDT.2025.36
Database Theory in Action: Cypher, GQL, and Regular Path Queries

Authors: Amélie Gheerbrant, Leonid Libkin, Liat Peterfreund, and Alexandra Rogova

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

Abstract
Cypher has so far been the most commonly used query language for property graphs, and served as the foundation of the recently standardized graph query language GQL. In designing the features of GQL, the standards committee addressed the perceived limitations of Cypher. One such limitation is the inability of Cypher, as originally designed, to express all regular path queries (RPQs). Despite this claim having been stated many times as a folklore result, we could not find any proof of it. In this note we formalize the core of Cypher’s pattern matching and formally prove that indeed it falls short of all RPQs, justifying the inclusion of new pattern matching features in GQL.
Cite as

Amélie Gheerbrant, Leonid Libkin, Liat Peterfreund, and Alexandra Rogova. Database Theory in Action: Cypher, GQL, and Regular Path Queries. In 28th International Conference on Database Theory (ICDT 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 328, pp. 36:1-36:5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gheerbrant_et_al:LIPIcs.ICDT.2025.36,
  author =	{Gheerbrant, Am\'{e}lie and Libkin, Leonid and Peterfreund, Liat and Rogova, Alexandra},
  title =	{{Database Theory in Action: Cypher, GQL, and Regular Path Queries}},
  booktitle =	{28th International Conference on Database Theory (ICDT 2025)},
  pages =	{36:1--36:5},
  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.2025.36},
  URN =		{urn:nbn:de:0030-drops-229771},
  doi =		{10.4230/LIPIcs.ICDT.2025.36},
  annote =	{Keywords: Regular path queries, Cypher, GQL, inexpressibility}
}
Document
DOI: 10.4230/LIPIcs.ICDT.2025.31
On Deciding the Data Complexity of Answering Linear Monadic Datalog Queries with LTL Operators

Authors: Alessandro Artale, Anton Gnatenko, Vladislav Ryzhikov, and Michael Zakharyaschev

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

Abstract
Our concern is the data complexity of answering linear monadic datalog queries whose atoms in the rule bodies can be prefixed by operators of linear temporal logic LTL. We first observe that, for data complexity, answering any connected query with operators ○/○- (at the next/previous moment) is either in AC⁰, or in ACC⁰\AC⁰, or NC¹-complete, or L-hard and in NL. Then we show that the problem of deciding L-hardness of answering such queries is PSpace-complete, while checking membership in the classes AC⁰ and ACC⁰ as well as NC¹-completeness can be done in ExpSpace. Finally, we prove that membership in AC⁰ or in ACC⁰, NC¹-completeness, and L-hardness are undecidable for queries with operators ◇/◇- (sometime in the future/past) provided that NC¹ ≠ NL and L ≠ NL.
Cite as

Alessandro Artale, Anton Gnatenko, Vladislav Ryzhikov, and Michael Zakharyaschev. On Deciding the Data Complexity of Answering Linear Monadic Datalog Queries with LTL Operators. In 28th International Conference on Database Theory (ICDT 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 328, pp. 31:1-31:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{artale_et_al:LIPIcs.ICDT.2025.31,
  author =	{Artale, Alessandro and Gnatenko, Anton and Ryzhikov, Vladislav and Zakharyaschev, Michael},
  title =	{{On Deciding the Data Complexity of Answering Linear Monadic Datalog Queries with LTL Operators}},
  booktitle =	{28th International Conference on Database Theory (ICDT 2025)},
  pages =	{31:1--31:19},
  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.2025.31},
  URN =		{urn:nbn:de:0030-drops-229723},
  doi =		{10.4230/LIPIcs.ICDT.2025.31},
  annote =	{Keywords: Linear monadic datalog, linear temporal logic, data complexity}
}
Document
DOI: 10.4230/LIPIcs.ICDT.2025.20
A Formal Language Perspective on Factorized Representations

Authors: Benny Kimelfeld, Wim Martens, and Matthias Niewerth

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

Abstract
Factorized representations (FRs) are a well-known tool to succinctly represent results of join queries and have been originally defined using the named database perspective. We define FRs in the unnamed database perspective and use them to establish several new connections. First, unnamed FRs can be exponentially more succinct than named FRs, but this difference can be alleviated by imposing a disjointness condition on columns. Conversely, named FRs can also be exponentially more succinct than unnamed FRs. Second, unnamed FRs are the same as (i.e., isomorphic to) context-free grammars for languages in which each word has the same length. This tight connection allows us to transfer a wide range of results on context-free grammars to database factorization; of which we offer a selection in the paper. Third, when we generalize unnamed FRs to arbitrary sets of tuples, they become a generalization of path multiset representations, a formalism that was recently introduced to succinctly represent sets of paths in the context of graph database query evaluation.
Cite as

Benny Kimelfeld, Wim Martens, and Matthias Niewerth. A Formal Language Perspective on Factorized Representations. In 28th International Conference on Database Theory (ICDT 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 328, pp. 20:1-20:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{kimelfeld_et_al:LIPIcs.ICDT.2025.20,
  author =	{Kimelfeld, Benny and Martens, Wim and Niewerth, Matthias},
  title =	{{A Formal Language Perspective on Factorized Representations}},
  booktitle =	{28th International Conference on Database Theory (ICDT 2025)},
  pages =	{20:1--20:20},
  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.2025.20},
  URN =		{urn:nbn:de:0030-drops-229614},
  doi =		{10.4230/LIPIcs.ICDT.2025.20},
  annote =	{Keywords: Databases, relational databases, graph databases, factorized databases, regular path queries, compact representations}
}
Document
Position
DOI: 10.4230/TGDK.1.1.5
Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities

Authors: Jiaoyan Chen, Hang Dong, Janna Hastings, Ernesto Jiménez-Ruiz, Vanessa López, Pierre Monnin, Catia Pesquita, Petr Škoda, and Valentina Tamma

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 term life sciences refers to the disciplines that study living organisms and life processes, and include chemistry, biology, medicine, and a range of other related disciplines. Research efforts in life sciences are heavily data-driven, as they produce and consume vast amounts of scientific data, much of which is intrinsically relational and graph-structured. The volume of data and the complexity of scientific concepts and relations referred to therein promote the application of advanced knowledge-driven technologies for managing and interpreting data, with the ultimate aim to advance scientific discovery. In this survey and position paper, we discuss recent developments and advances in the use of graph-based technologies in life sciences and set out a vision for how these technologies will impact these fields into the future. We focus on three broad topics: the construction and management of Knowledge Graphs (KGs), the use of KGs and associated technologies in the discovery of new knowledge, and the use of KGs in artificial intelligence applications to support explanations (explainable AI). We select a few exemplary use cases for each topic, discuss the challenges and open research questions within these topics, and conclude with a perspective and outlook that summarizes the overarching challenges and their potential solutions as a guide for future research.
Cite as

Jiaoyan Chen, Hang Dong, Janna Hastings, Ernesto Jiménez-Ruiz, Vanessa López, Pierre Monnin, Catia Pesquita, Petr Škoda, and Valentina Tamma. Knowledge Graphs for the Life Sciences: Recent Developments, 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. 5:1-5:33, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{chen_et_al:TGDK.1.1.5,
  author =	{Chen, Jiaoyan and Dong, Hang and Hastings, Janna and Jim\'{e}nez-Ruiz, Ernesto and L\'{o}pez, Vanessa and Monnin, Pierre and Pesquita, Catia and \v{S}koda, Petr and Tamma, Valentina},
  title =	{{Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{5:1--5:33},
  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.1.1.5},
  URN =		{urn:nbn:de:0030-drops-194791},
  doi =		{10.4230/TGDK.1.1.5},
  annote =	{Keywords: Knowledge graphs, Life science, Knowledge discovery, Explainable AI}
}
Document
Invited Talk
DOI: 10.4230/LIPIcs.ICDT.2023.1
A Researcher’s Digest of GQL (Invited Talk)

Authors: Nadime Francis, Amélie Gheerbrant, Paolo Guagliardo, Leonid Libkin, Victor Marsault, Wim Martens, Filip Murlak, Liat Peterfreund, Alexandra Rogova, and Domagoj Vrgoč

Published in: LIPIcs, Volume 255, 26th International Conference on Database Theory (ICDT 2023)

Abstract
GQL (Graph Query Language) is being developed as a new ISO standard for graph query languages to play the same role for graph databases as SQL plays for relational. In parallel, an extension of SQL for querying property graphs, SQL/PGQ, is added to the SQL standard; it shares the graph pattern matching functionality with GQL. Both standards (not yet published) are hard-to-understand specifications of hundreds of pages. The goal of this paper is to present a digest of the language that is easy for the research community to understand, and thus to initiate research on these future standards for querying graphs. The paper concentrates on pattern matching features shared by GQL and SQL/PGQ, as well as querying facilities of GQL.
Cite as

Nadime Francis, Amélie Gheerbrant, Paolo Guagliardo, Leonid Libkin, Victor Marsault, Wim Martens, Filip Murlak, Liat Peterfreund, Alexandra Rogova, and Domagoj Vrgoč. A Researcher’s Digest of GQL (Invited Talk). In 26th International Conference on Database Theory (ICDT 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 255, pp. 1:1-1:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

Copy BibTex To Clipboard

@InProceedings{francis_et_al:LIPIcs.ICDT.2023.1,
  author =	{Francis, Nadime and Gheerbrant, Am\'{e}lie and Guagliardo, Paolo and Libkin, Leonid and Marsault, Victor and Martens, Wim and Murlak, Filip and Peterfreund, Liat and Rogova, Alexandra and Vrgo\v{c}, Domagoj},
  title =	{{A Researcher’s Digest of GQL}},
  booktitle =	{26th International Conference on Database Theory (ICDT 2023)},
  pages =	{1:1--1:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-270-9},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{255},
  editor =	{Geerts, Floris and Vandevoort, Brecht},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICDT.2023.1},
  URN =		{urn:nbn:de:0030-drops-177434},
  doi =		{10.4230/LIPIcs.ICDT.2023.1},
  annote =	{Keywords: GQL, Property Graph, Query Language, Graph Database, Pattern matching, Multi-Graph}
}
Document
DOI: 10.4230/LIPIcs.ICDT.2015.44
Asymptotic Determinacy of Path Queries using Union-of-Paths Views

Authors: Nadime Francis

Published in: LIPIcs, Volume 31, 18th International Conference on Database Theory (ICDT 2015)

Abstract
We consider the view determinacy problem over graph databases for queries defined as (possibly infinite) unions of path queries. These queries select pairs of nodes in a graph that are connected through a path whose length falls in a given set. A view specification is a set of such queries. We say that a view specification V determines a query Q if, for all databases D, the answers to V on D contain enough information to answer Q. Our main result states that, given a view V, there exists an explicit bound that depends on V such that we can decide the determinacy problem for all queries that ask for a path longer than this bound, and provide first-order rewritings for the queries that are determined. We call this notion asymptotic determinacy. As a corollary, we can also compute the set of almost all path queries that are determined by V.
Cite as

Nadime Francis. Asymptotic Determinacy of Path Queries using Union-of-Paths Views. In 18th International Conference on Database Theory (ICDT 2015). Leibniz International Proceedings in Informatics (LIPIcs), Volume 31, pp. 44-59, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2015)

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@InProceedings{francis:LIPIcs.ICDT.2015.44,
  author =	{Francis, Nadime},
  title =	{{Asymptotic Determinacy of Path Queries using Union-of-Paths Views}},
  booktitle =	{18th International Conference on Database Theory (ICDT 2015)},
  pages =	{44--59},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-79-8},
  ISSN =	{1868-8969},
  year =	{2015},
  volume =	{31},
  editor =	{Arenas, Marcelo and Ugarte, Mart{\'\i}n},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICDT.2015.44},
  URN =		{urn:nbn:de:0030-drops-49760},
  doi =		{10.4230/LIPIcs.ICDT.2015.44},
  annote =	{Keywords: Graph databases, Views, Determinacy, Rewriting, Path queries}
}
Document
DOI: 10.4230/LIPIcs.FSTTCS.2014.279
Consistency of Injective Tree Patterns

Authors: Claire David, Nadime Francis, and Filip Murlak

Published in: LIPIcs, Volume 29, 34th International Conference on Foundation of Software Technology and Theoretical Computer Science (FSTTCS 2014)

Abstract
Testing if an incomplete description of an XML document is consistent, that is, if it describes a real document conforming to the imposed schema, amounts to deciding if a given tree pattern can be matched injectively into a tree accepted by a fixed automaton. This problem can be solved in polynomial time for patterns that use the child relation and the sibling order, but do not use the descendant relation. For general patterns the problem is in NP, but no lower bound has been known so far. We show that the problem is NP-complete already for patterns using only child and descendant relations. The source of hardness turns out to be the interplay between these relations: for patterns using only descendant we give a polynomial algorithm. We also show that the algorithm can be adapted to patterns using descendant and following-sibling, but combining descendant and next-sibling leads to intractability.
Cite as

Claire David, Nadime Francis, and Filip Murlak. Consistency of Injective Tree Patterns. In 34th International Conference on Foundation of Software Technology and Theoretical Computer Science (FSTTCS 2014). Leibniz International Proceedings in Informatics (LIPIcs), Volume 29, pp. 279-290, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2014)

Copy BibTex To Clipboard

@InProceedings{david_et_al:LIPIcs.FSTTCS.2014.279,
  author =	{David, Claire and Francis, Nadime and Murlak, Filip},
  title =	{{Consistency of Injective Tree Patterns}},
  booktitle =	{34th International Conference on Foundation of Software Technology and Theoretical Computer Science (FSTTCS 2014)},
  pages =	{279--290},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-77-4},
  ISSN =	{1868-8969},
  year =	{2014},
  volume =	{29},
  editor =	{Raman, Venkatesh and Suresh, S. P.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSTTCS.2014.279},
  URN =		{urn:nbn:de:0030-drops-48496},
  doi =		{10.4230/LIPIcs.FSTTCS.2014.279},
  annote =	{Keywords: XML, incomplete information, injective tree patterns, consistency}
}
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