25 Search Results for "Cook, Joshua"

Document
DOI: 10.4230/LIPIcs.SWAT.2026.30
Parallel Algorithms for Group Isomorphism via Code Equivalence

Authors: Michael Levet

Published in: LIPIcs, Volume 370, 20th Scandinavian Symposium on Algorithm Theory (SWAT 2026)

Abstract
In this paper, we exhibit AC³ isomorphism tests for coprime extensions H ⋉ N where H is elementary Abelian and N is Abelian; and groups where Rad(G) = Z(G) is elementary Abelian and G = Soc^{*}(G). The fact that isomorphism testing for these families is in P was established respectively by Qiao, Sarma, and Tang (STACS 2011), and Grochow and Qiao (CCC 2014, SIAM J. Comput. 2017). The polynomial-time isomorphism tests for both of these families crucially leveraged small (size O(log |G|)) instances of Linear Code Equivalence (Babai, SODA 2011). Here, we combine Luks' group-theoretic method for Graph Isomorphism (FOCS 1980, J. Comput. Syst. Sci. 1982) with the fact that G is given by its multiplication table, to implement the corresponding instances of Linear Code Equivalence in AC³. As a byproduct of our work, we show that isomorphism testing of arbitrary central-radical groups is decidable using AC circuits of depth O(log³ n) and size n^{O(log log n)}. This improves upon the previous bound of n^{O(log log n)}-time due to Grochow and Qiao (ibid.).
Cite as

Michael Levet. Parallel Algorithms for Group Isomorphism via Code Equivalence. In 20th Scandinavian Symposium on Algorithm Theory (SWAT 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 370, pp. 30:1-30:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{levet:LIPIcs.SWAT.2026.30,
  author =	{Levet, Michael},
  title =	{{Parallel Algorithms for Group Isomorphism via Code Equivalence}},
  booktitle =	{20th Scandinavian Symposium on Algorithm Theory (SWAT 2026)},
  pages =	{30:1--30:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-421-5},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{370},
  editor =	{Fraigniaud, Pierre},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SWAT.2026.30},
  URN =		{urn:nbn:de:0030-drops-260660},
  doi =		{10.4230/LIPIcs.SWAT.2026.30},
  annote =	{Keywords: Group Isomorphism, Circuit Complexity, Code Equivalence}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2026.42
Time and Space Efficient Deterministic List Decoding

Authors: Joshua Cook and Dana Moshkovitz

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

Abstract
Error correcting codes encode messages by codewords in such a way that even if some of the codeword is corrupted, the message can be decoded. Typical decoding algorithms for error correcting codes either use linear space or quadratic time. A natural question is whether codes can be decoded in near-linear time and sub-linear space simultaneously. A recent result by Cook and Moshkovitz gave efficient decoders that can uniquely decode Reed-Muller and other codes from a constant fraction (less than half) of corruption. In this work, we address the problem of list decoding in near-linear time and sub-linear space. In the list decoding setting, most of the codeword is corrupted, and one wants to output a short list of potential messages that contains the true message. For any constants γ, τ > 0, we give decoders for Reed-Muller codes that can decode from 1-γ fraction of corruptions in time n^{1+τ} and space n^{τ}. Our decoders work by extending the iterative correction technique of Cook and Moshkovitz. However, that technique, which gradually decreases the number of corruptions in the message, was tailored to the unique decoding setting. We first identify an intermediate problem, codewords list recovery, for which we can make iterative correction work. We then show how to reduce general list decoding to the codewords list recovery problem in efficient time and space. The reduction relies on local correction and testing. In the codewords list recovery problem, the input consists of n unordered lists containing exactly the symbols from L codewords, where a small fraction of the lists is corrupted. The goal is to find the L codewords. In addition, we prove that any linear code with time-space efficient encoding or decoding must be local, in the sense that the codewords satisfy a local linear constraint. This rules out codes like Reed-Solomon from having time-space efficient encoding or decoding.
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Joshua Cook and Dana Moshkovitz. Time and Space Efficient Deterministic List Decoding. In 17th Innovations in Theoretical Computer Science Conference (ITCS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 362, pp. 42:1-42:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{cook_et_al:LIPIcs.ITCS.2026.42,
  author =	{Cook, Joshua and Moshkovitz, Dana},
  title =	{{Time and Space Efficient Deterministic List Decoding}},
  booktitle =	{17th Innovations in Theoretical Computer Science Conference (ITCS 2026)},
  pages =	{42:1--42:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-410-9},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{362},
  editor =	{Saraf, Shubhangi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2026.42},
  URN =		{urn:nbn:de:0030-drops-253292},
  doi =		{10.4230/LIPIcs.ITCS.2026.42},
  annote =	{Keywords: Reed-Muller code, local correction, local testing}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2026.60
Total Search Problems in ZPP

Authors: Noah Fleming, Stefan Grosser, Siddhartha Jain, Jiawei Li, Hanlin Ren, Morgan Shirley, and Weiqiang Yuan

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

Abstract
We initiate a systematic study of TFZPP, the class of total NP search problems solvable by polynomial time randomized algorithms. TFZPP contains a variety of important search problems such as Bertrand-Chebyshev (finding a prime between N and 2N), refuter problems for many circuit lower bounds, and Lossy-Code. The Lossy-Code problem has found prominence due to its fundamental connections to derandomization, catalytic computing, and the metamathematics of complexity theory, among other areas. While TFZPP collapses to FP under standard derandomization assumptions in the white-box setting, we are able to separate TFZPP from the major TFNP subclasses in the black-box setting. In fact, we are able to separate it from every uniform TFNP class assuming that NP is not in quasi-polynomial time. To do so, we extend the connection between proof complexity and black-box TFNP to randomized proof systems and randomized reductions. Next, we turn to developing a taxonomy of TFZPP problems. We highlight a problem called Nephew, originating from an infinity axiom in set theory. We show that Nephew is in PWPP∩ TFZPP and conjecture that it is not reducible to Lossy-Code. Intriguingly, except for some artificial examples, most other black-box TFZPP problems that we are aware of reduce to Lossy-Code: - We define a problem called Empty-Child capturing finding a leaf in a rooted (binary) tree, and show that this problem is equivalent to Lossy-Code. We also show that a variant of Empty-Child with "heights" is complete for the intersection of SOPL and Lossy-Code. - We strengthen Lossy-Code with several combinatorial inequalities such as the AM-GM inequality. Somewhat surprisingly, we show the resulting new problems are still reducible to Lossy-Code. A technical highlight of this result is that they are proved by formalizations in bounded arithmetic, specifically in Jeřábek’s theory APC₁ (JSL 2007). - Finally, we show that the Dense-Linear-Ordering problem reduces to Lossy-Code.
Cite as

Noah Fleming, Stefan Grosser, Siddhartha Jain, Jiawei Li, Hanlin Ren, Morgan Shirley, and Weiqiang Yuan. Total Search Problems in ZPP. In 17th Innovations in Theoretical Computer Science Conference (ITCS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 362, pp. 60:1-60:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{fleming_et_al:LIPIcs.ITCS.2026.60,
  author =	{Fleming, Noah and Grosser, Stefan and Jain, Siddhartha and Li, Jiawei and Ren, Hanlin and Shirley, Morgan and Yuan, Weiqiang},
  title =	{{Total Search Problems in ZPP}},
  booktitle =	{17th Innovations in Theoretical Computer Science Conference (ITCS 2026)},
  pages =	{60:1--60:26},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-410-9},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{362},
  editor =	{Saraf, Shubhangi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2026.60},
  URN =		{urn:nbn:de:0030-drops-253473},
  doi =		{10.4230/LIPIcs.ITCS.2026.60},
  annote =	{Keywords: TFNP, lossy code, randomized proof systems, query complexity}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2026.99
AC⁰[p]-Frege Cannot Efficiently Prove That Constant-Depth Algebraic Circuit Lower Bounds Are Hard

Authors: Jiaqi Lu, Rahul Santhanam, and Iddo Tzameret

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

Abstract
We study whether lower bounds against constant-depth algebraic circuits computing the Permanent over finite fields (Limaye-Srinivasan-Tavenas [J. ACM, 2025] and Forbes [CCC'24]) are hard to prove in certain proof systems. We focus on a DNF formula that expresses that such lower bounds are hard for constant-depth algebraic proofs. Using an adaptation of the diagonalization framework of Santhanam and Tzameret (SIAM J. Comput., 2025), we show unconditionally that this family of DNF formulas does not admit polynomial-size propositional AC⁰[p]-Frege proofs, infinitely often. This rules out the possibility that the DNF family is easy, and establishes that its status is either that of a hard tautology for AC⁰[p]-Frege or else unprovable (i.e., not a tautology). While it remains open whether the DNFs in question are tautologies, we provide evidence in this direction. In particular, under the plausible assumption that certain (weak) properties of multilinear algebra - specifically, those involving tensor rank - do not admit short constant-depth algebraic proofs, the DNFs are tautologies. We also observe that several weaker variants of the DNF formula are provably tautologies, and we show that the question of whether the DNFs are tautologies connects to conjectures of Razborov (ICALP'96) and Krajíček (J. Symb. Log., 2004). Additionally, our result has the following special features: ii) Existential depth amplification: the DNF formula considered is parameterised by a constant depth d bounding the depth of the algebraic proofs. We show that there exists some fixed depth d such that if there are no small depth-d algebraic proofs of certain circuit lower bounds for the Permanent, then there are no such small algebraic proofs in any constant depth. iii) Necessity: We show that our result is a necessary step towards establishing lower bounds against constant-depth algebraic proofs, and more generally against any sufficiently strong proof system. In particular, showing there are no short proofs for our DNF formulas, obtained by replacing "constant-depth algebraic circuits" with any "reasonable" algebraic circuit class C, is necessary in order to prove any super-polynomial lower bounds against algebraic proofs operating with circuits from C.
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Jiaqi Lu, Rahul Santhanam, and Iddo Tzameret. AC⁰[p]-Frege Cannot Efficiently Prove That Constant-Depth Algebraic Circuit Lower Bounds Are Hard. In 17th Innovations in Theoretical Computer Science Conference (ITCS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 362, pp. 99:1-99:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{lu_et_al:LIPIcs.ITCS.2026.99,
  author =	{Lu, Jiaqi and Santhanam, Rahul and Tzameret, Iddo},
  title =	{{AC⁰\lbrackp\rbrack-Frege Cannot Efficiently Prove That Constant-Depth Algebraic Circuit Lower Bounds Are Hard}},
  booktitle =	{17th Innovations in Theoretical Computer Science Conference (ITCS 2026)},
  pages =	{99:1--99:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-410-9},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{362},
  editor =	{Saraf, Shubhangi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2026.99},
  URN =		{urn:nbn:de:0030-drops-253865},
  doi =		{10.4230/LIPIcs.ITCS.2026.99},
  annote =	{Keywords: Complexity, Lower bounds, Proof complexity, AC⁰\lbrackp\rbrack-Frege, Diagonalisation, Algebraic complexity}
}
Document
DOI: 10.4230/LIPIcs.FSTTCS.2025.3
PDQMA = DQMA = NEXP: QMA with Hidden Variables and Non-Collapsing Measurements

Authors: Scott Aaronson, Sabee Grewal, Vishnu Iyer, Simon C. Marshall, and Ronak Ramachandran

Published in: LIPIcs, Volume 360, 45th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2025)

Abstract
We define and study a variant of QMA (Quantum Merlin Arthur) in which Arthur can make multiple non-collapsing measurements to Merlin’s witness state, in addition to ordinary collapsing measurements. By analogy to the class PDQP defined by Aaronson, Bouland, Fitzsimons, and Lee (2014), we call this class PDQMA. Our main result is that PDQMA = NEXP; this result builds on the PCP theorem and complements the result of Aaronson (2018) that PDQP/qpoly = ALL. While the result has little to do with quantum mechanics, we also show a more "quantum" result: namely, that QMA with the ability to inspect the entire history of a hidden variable is equal to NEXP, under mild assumptions on the hidden-variable theory. We also observe that a quantum computer, augmented with quantum advice and the ability to inspect the history of a hidden variable, can solve any decision problem in polynomial time.
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Scott Aaronson, Sabee Grewal, Vishnu Iyer, Simon C. Marshall, and Ronak Ramachandran. PDQMA = DQMA = NEXP: QMA with Hidden Variables and Non-Collapsing Measurements. In 45th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 360, pp. 3:1-3:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{aaronson_et_al:LIPIcs.FSTTCS.2025.3,
  author =	{Aaronson, Scott and Grewal, Sabee and Iyer, Vishnu and Marshall, Simon C. and Ramachandran, Ronak},
  title =	{{PDQMA = DQMA = NEXP: QMA with Hidden Variables and Non-Collapsing Measurements}},
  booktitle =	{45th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2025)},
  pages =	{3:1--3:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-406-2},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{360},
  editor =	{Aiswarya, C. and Mehta, Ruta and Roy, Subhajit},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSTTCS.2025.3},
  URN =		{urn:nbn:de:0030-drops-250828},
  doi =		{10.4230/LIPIcs.FSTTCS.2025.3},
  annote =	{Keywords: quantum Merlin-Arthur, non-collapsing measurements, hidden-variable theories}
}
Document
DOI: 10.4230/LIPIcs.GD.2025.21
On Geometric Bipartite Graphs with Asymptotically Smallest Zarankiewicz Numbers

Authors: Parinya Chalermsook, Ly Orgo, and Minoo Zarsav

Published in: LIPIcs, Volume 357, 33rd International Symposium on Graph Drawing and Network Visualization (GD 2025)

Abstract
This paper considers the Zarankiewicz problem in bipartite graphs with low-dimensional geometric representation (i.e., low Ferrers dimension). Let Z(n;k) be the maximum number of edges in a bipartite graph with n nodes and is free of a k-by-k biclique. Note that Z(n;k) ∈ Ω(nk) for all "natural" graph classes. Our first result reveals a separation between bipartite graphs of Ferrers dimension three and four: while we show that Z(n;k) ≤ 9n(k-1) for graphs of Ferrers dimension three, Z(n;k) ∈ Ω(n k ⋅ (log n)/(log log n)) for Ferrers dimension four graphs (Chan & Har-Peled, 2023) (Chazelle, 1990). To complement this, we derive a tight upper bound of 2n(k-1) for chordal bipartite graphs and 54n(k-1) for grid intersection graphs (GIG), a prominent graph class residing in four Ferrers dimensions and capturing planar bipartite graphs as well as bipartite intersection graphs of rectangles. Previously, the best-known bound for GIG was Z(n;k) ∈ O(2^{O(k)} n), implied by the results of Fox & Pach (2006) and Mustafa & Pach (2016). Our results advance and offer new insights into the interplay between Ferrers dimensions and extremal combinatorics.
Cite as

Parinya Chalermsook, Ly Orgo, and Minoo Zarsav. On Geometric Bipartite Graphs with Asymptotically Smallest Zarankiewicz Numbers. In 33rd International Symposium on Graph Drawing and Network Visualization (GD 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 357, pp. 21:1-21:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{chalermsook_et_al:LIPIcs.GD.2025.21,
  author =	{Chalermsook, Parinya and Orgo, Ly and Zarsav, Minoo},
  title =	{{On Geometric Bipartite Graphs with Asymptotically Smallest Zarankiewicz Numbers}},
  booktitle =	{33rd International Symposium on Graph Drawing and Network Visualization (GD 2025)},
  pages =	{21:1--21:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-403-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{357},
  editor =	{Dujmovi\'{c}, Vida and Montecchiani, Fabrizio},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.GD.2025.21},
  URN =		{urn:nbn:de:0030-drops-250074},
  doi =		{10.4230/LIPIcs.GD.2025.21},
  annote =	{Keywords: Bipartite graph classes, extremal graph theory, geometric intersection graphs, Zarankiewicz problem, bicliques}
}
Document
Research
DOI: 10.4230/TGDK.3.2.3
GraphRAG on Technical Documents - Impact of Knowledge Graph Schema

Authors: Henri Scaffidi, Melinda Hodkiewicz, Caitlin Woods, and Nicole Roocke

Published in: TGDK, Volume 3, Issue 2 (2025). Transactions on Graph Data and Knowledge, Volume 3, Issue 2

Abstract
Retrieval Augmented Generation (RAG) is seeing rapid adoption in industry to enable employees to query information captured in proprietary data for their organisation. In this work, we test the impact of domain-relevant knowledge graph schemas on the results of Microsoft’s GraphRAG pipeline. Our approach aims to address the poor quality of GraphRAG responses on technical reports rich in domain-specific terms. The use case involves technical reports about geology, chemistry and mineral processing published by the Minerals Research Institute of Western Australia (MRIWA). Four schemas are considered: a simple five-class minerals domain expert-developed schema, an expanded minerals domain schema, the Microsoft GraphRAG auto-generated schema, and a schema-less GraphRAG. These are compared to a conventional baseline RAG. Performance is evaluated using a scoring approach that accounts for the mix of correct, incorrect, additional, and missing content in RAG responses. The results show that the simple five-class minerals domain schema extracts approximately 10% more entities from the MRIWA reports than the other schema options. Additionally, both the five-class and the expanded eight-class minerals domain schemas produce the most factually correct answers and the fewest hallucinations. We attribute this to the minerals-specific schemas extracting more relevant, domain-specific information during the Indexing stage. As a result, the Query stage’s context window includes more high-value content. This contributes to the observed improvement in answer quality compared to the other pipelines. In contrast, pipelines with fewer domain-related entities in the KG retrieve less valuable information, leaving more room for irrelevant content in the context window. Baseline RAG responses were typically shorter, less complete, and contained more hallucinations compared to our GraphRAG pipelines. We provide a complete set of resources at https://github.com/nlp-tlp/GraphRAG-on-Minerals-Domain/tree/main. These resources include links to the MRIWA reports, a set of questions (from simple to challenging) along with domain-expert curated answers, schemas, and evaluations of the pipelines.
Cite as

Henri Scaffidi, Melinda Hodkiewicz, Caitlin Woods, and Nicole Roocke. GraphRAG on Technical Documents - Impact of Knowledge Graph Schema. In Transactions on Graph Data and Knowledge (TGDK), Volume 3, Issue 2, pp. 3:1-3:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@Article{scaffidi_et_al:TGDK.3.2.3,
  author =	{Scaffidi, Henri and Hodkiewicz, Melinda and Woods, Caitlin and Roocke, Nicole},
  title =	{{GraphRAG on Technical Documents - Impact of Knowledge Graph Schema}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{3:1--3:24},
  ISSN =	{2942-7517},
  year =	{2025},
  volume =	{3},
  number =	{2},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.3.2.3},
  URN =		{urn:nbn:de:0030-drops-248131},
  doi =		{10.4230/TGDK.3.2.3},
  annote =	{Keywords: RAG, minerals, local search, global search, entity extraction, competency questions}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.10
DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs

Authors: Ali Ghaffaari, Alexander Schönhuth, and Tobias Marschall

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

Abstract
Determining the distance between two loci within a genomic region is a recurrent operation in various tasks in computational genomics. A notable example of this task arises in paired-end read mapping as a form of validation of distances between multiple alignments. While straightforward for a single genome, graph-based reference structures render the operation considerably more involved. Given the sheer number of such queries in a typical read mapping experiment, an efficient algorithm for answering distance queries is crucial. In this paper, we introduce DiVerG, a compact data structure as well as a fast and scalable algorithm, for constructing distance indexes for general sequence graphs on multi-core CPU and many-core GPU architectures. DiVerG is based on PairG [Jain et al., 2019], but overcomes the limitations of PairG by exploiting the extensive potential for improvements in terms of scalability and space efficiency. As a consequence, DiVerG can process substantially larger datasets, such as whole human genomes, which are unmanageable by PairG. DiVerG offers faster index construction time and consistently faster query time with gains proportional to the size of the underlying compact data structure. We demonstrate that our method performs favorably on multiple real datasets at various scales. DiVerG achieves superior performance over PairG; e.g. resulting to 2.5-4x speed-up in query time, 44-340x smaller index size, and 3-50x faster construction time for the genome graph of the MHC region, as a particularly variable region of the human genome. The implementation is available at: https://github.com/cartoonist/diverg
Cite as

Ali Ghaffaari, Alexander Schönhuth, and Tobias Marschall. DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 10:1-10:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ghaffaari_et_al:LIPIcs.WABI.2025.10,
  author =	{Ghaffaari, Ali and Sch\"{o}nhuth, Alexander and Marschall, Tobias},
  title =	{{DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{10:1--10:24},
  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.2025.10},
  URN =		{urn:nbn:de:0030-drops-239369},
  doi =		{10.4230/LIPIcs.WABI.2025.10},
  annote =	{Keywords: Sequence graph, distance index, read mapping, sparse matrix}
}
Document
DOI: 10.4230/LIPIcs.SAT.2025.11
Better Extension Variables in DQBF via Independence

Authors: Leroy Chew and Tomáš Peitl

Published in: LIPIcs, Volume 341, 28th International Conference on Theory and Applications of Satisfiability Testing (SAT 2025)

Abstract
We show that extension variables in (D)QBF can be generalised by conditioning on universal assignments. The benefit of this is that the dependency sets of such conditioned extension variables can be made smaller to allow easier refutations. This simple modification instantly solves many challenges in p-simulating the QBF expansion rule, which cannot be p-simulated in proof systems that have strategy extraction [Leroy Chew and Judith Clymo, 2020]. Simulating expansion is even more crucial in DQBF, where other methods are incomplete. In this paper we provide an overview of the strength of this new independent extension rule. We find that a new version of Extended Frege called IndExtFrege + ∀red can p-simulate a multitude of difficult QBF and DQBF techniques, even techniques that are difficult to approach with eFrege + ∀red. We show five p-simulations, that IndExtFrege + ∀red p-simulates QRAT, DQBF-IR-calc, IR(𝒟^rrs)-calc, Fork-Resolution and DQRAT which together underpin most DQBF solving and preprocessing techniques. The p-simulations work despite these systems using complicated rules and our new extension rule being relatively simple. Moreover, unlike recent p-simulations by eFrege + ∀red we can simulate the proof rules line by line, which allows us to mix QBF rules more easily with other inference steps.
Cite as

Leroy Chew and Tomáš Peitl. Better Extension Variables in DQBF via Independence. In 28th International Conference on Theory and Applications of Satisfiability Testing (SAT 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 341, pp. 11:1-11:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{chew_et_al:LIPIcs.SAT.2025.11,
  author =	{Chew, Leroy and Peitl, Tom\'{a}\v{s}},
  title =	{{Better Extension Variables in DQBF via Independence}},
  booktitle =	{28th International Conference on Theory and Applications of Satisfiability Testing (SAT 2025)},
  pages =	{11:1--11:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-381-2},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{341},
  editor =	{Berg, Jeremias and Nordstr\"{o}m, Jakob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAT.2025.11},
  URN =		{urn:nbn:de:0030-drops-237453},
  doi =		{10.4230/LIPIcs.SAT.2025.11},
  annote =	{Keywords: DQBF, QBF, Proof Systems, Dependency Schemes, RAT, Extended Frege, Skolem functions}
}
Document
DOI: 10.4230/LIPIcs.CCC.2025.17
Space-Bounded Quantum Interactive Proof Systems

Authors: François Le Gall, Yupan Liu, Harumichi Nishimura, and Qisheng Wang

Published in: LIPIcs, Volume 339, 40th Computational Complexity Conference (CCC 2025)

Abstract
We introduce two models of space-bounded quantum interactive proof systems, QIPL and QIP_{U}L. The QIP_{U}L model, a space-bounded variant of quantum interactive proofs (QIP) introduced by Watrous (CC 2003) and Kitaev and Watrous (STOC 2000), restricts verifier actions to unitary circuits. In contrast, QIPL allows logarithmically many pinching intermediate measurements per verifier action, making it the weakest model that encompasses the classical model of Condon and Ladner (JCSS 1995). We characterize the computational power of QIPL and QIP_{U}L. When the message number m is polynomially bounded, QIP_{U}L ⊊ QIPL unless P = NP: - QIPL^HC, a subclass of QIPL defined by a high-concentration condition on yes instances, exactly characterizes NP. - QIP_{U}L is contained in P and contains SAC¹ ∪ BQL, where SAC¹ denotes problems solvable by classical logarithmic-depth, semi-unbounded fan-in circuits. However, this distinction vanishes when m is constant. Our results further indicate that (pinching) intermediate measurements uniquely impact space-bounded quantum interactive proofs, unlike in space-bounded quantum computation, where BQL = BQ_{U}L. We also introduce space-bounded unitary quantum statistical zero-knowledge (QSZK_{U}L), a specific form of QIP_{U}L proof systems with statistical zero-knowledge against any verifier. This class is a space-bounded variant of quantum statistical zero-knowledge (QSZK) defined by Watrous (SICOMP 2009). We prove that QSZK_{U}L = BQL, implying that the statistical zero-knowledge property negates the computational advantage typically gained from the interaction.
Cite as

François Le Gall, Yupan Liu, Harumichi Nishimura, and Qisheng Wang. Space-Bounded Quantum Interactive Proof Systems. In 40th Computational Complexity Conference (CCC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 339, pp. 17:1-17:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{legall_et_al:LIPIcs.CCC.2025.17,
  author =	{Le Gall, Fran\c{c}ois and Liu, Yupan and Nishimura, Harumichi and Wang, Qisheng},
  title =	{{Space-Bounded Quantum Interactive Proof Systems}},
  booktitle =	{40th Computational Complexity Conference (CCC 2025)},
  pages =	{17:1--17:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-379-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{339},
  editor =	{Srinivasan, Srikanth},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CCC.2025.17},
  URN =		{urn:nbn:de:0030-drops-237115},
  doi =		{10.4230/LIPIcs.CCC.2025.17},
  annote =	{Keywords: Intermediate measurements, Quantum interactive proofs, Space-bounded quantum computation}
}
Document
DOI: 10.4230/LIPIcs.CCC.2025.15
Algebraic Pseudorandomness in VNC⁰

Authors: Robert Andrews

Published in: LIPIcs, Volume 339, 40th Computational Complexity Conference (CCC 2025)

Abstract
We study the arithmetic complexity of hitting set generators, which are pseudorandom objects used for derandomization of the polynomial identity testing problem. We give new explicit constructions of hitting set generators whose outputs are computable in VNC⁰, i.e., can be computed by arithmetic formulas of constant size. Unconditionally, we construct a VNC⁰-computable generator that hits arithmetic circuits of constant depth and polynomial size. We also give conditional constructions, under strong but plausible hardness assumptions, of VNC⁰-computable generators that hit arithmetic formulas and arithmetic branching programs of polynomial size, respectively. As a corollary of our constructions, we derive lower bounds for subsystems of the Geometric Ideal Proof System of Grochow and Pitassi. Constructions of such generators are implicit in prior work of Kayal on lower bounds for the degree of annihilating polynomials. Our main contribution is a construction whose correctness relies on circuit complexity lower bounds rather than degree lower bounds.
Cite as

Robert Andrews. Algebraic Pseudorandomness in VNC⁰. In 40th Computational Complexity Conference (CCC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 339, pp. 15:1-15:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{andrews:LIPIcs.CCC.2025.15,
  author =	{Andrews, Robert},
  title =	{{Algebraic Pseudorandomness in VNC⁰}},
  booktitle =	{40th Computational Complexity Conference (CCC 2025)},
  pages =	{15:1--15:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-379-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{339},
  editor =	{Srinivasan, Srikanth},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CCC.2025.15},
  URN =		{urn:nbn:de:0030-drops-237092},
  doi =		{10.4230/LIPIcs.CCC.2025.15},
  annote =	{Keywords: Polynomial identity testing, Algebraic circuits, Ideal Proof System}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.22
New Bounds for the Ideal Proof System in Positive Characteristic

Authors: Amik Raj Behera, Nutan Limaye, Varun Ramanathan, and Srikanth Srinivasan

Published in: LIPIcs, Volume 334, 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)

Abstract
In this work, we prove upper and lower bounds over fields of positive characteristics for several fragments of the Ideal Proof System (IPS), an algebraic proof system introduced by Grochow and Pitassi (J. ACM 2018). Our results extend the works of Forbes, Shpilka, Tzameret, and Wigderson (Theory of Computing 2021) and also of Govindasamy, Hakoniemi, and Tzameret (FOCS 2022). These works primarily focused on proof systems over fields of characteristic 0, and we are able to extend these results to positive characteristic. The question of proving general IPS lower bounds over positive characteristic is motivated by the important question of proving AC⁰[p]-Frege lower bounds. This connection was observed by Grochow and Pitassi (J. ACM 2018). Additional motivation comes from recent developments in algebraic complexity theory due to Forbes (CCC 2024) who showed how to extend previous lower bounds over characteristic 0 to positive characteristic. In our work, we adapt the functional lower bound method of Forbes et al. (Theory of Computing 2021) to prove exponential-size lower bounds for various subsystems of IPS. In order to establish these size lower bounds, we first prove a tight degree lower bound for a variant of Subset Sum over positive characteristic. This forms the core of all our lower bounds. Additionally, we derive upper bounds for the instances presented above. We show that they have efficient constant-depth IPS refutations. This demonstrates that constant-depth IPS refutations are stronger than the proof systems considered above even in positive characteristic. We also show that constant-depth IPS can efficiently refute a general class of instances, namely all symmetric instances, thereby further uncovering the strength of these algebraic proofs in positive characteristic.
Cite as

Amik Raj Behera, Nutan Limaye, Varun Ramanathan, and Srikanth Srinivasan. New Bounds for the Ideal Proof System in Positive Characteristic. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 22:1-22:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{behera_et_al:LIPIcs.ICALP.2025.22,
  author =	{Behera, Amik Raj and Limaye, Nutan and Ramanathan, Varun and Srinivasan, Srikanth},
  title =	{{New Bounds for the Ideal Proof System in Positive Characteristic}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{22:1--22:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-372-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{334},
  editor =	{Censor-Hillel, Keren and Grandoni, Fabrizio and Ouaknine, Jo\"{e}l 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.2025.22},
  URN =		{urn:nbn:de:0030-drops-233992},
  doi =		{10.4230/LIPIcs.ICALP.2025.22},
  annote =	{Keywords: Ideal Proof Systems, Algebraic Complexity, Positive Characteristic}
}
Document
Survey
DOI: 10.4230/TGDK.3.1.3
Uncertainty Management in the Construction of Knowledge Graphs: A Survey

Authors: Lucas Jarnac, Yoan Chabot, and Miguel Couceiro

Published in: TGDK, Volume 3, Issue 1 (2025). Transactions on Graph Data and Knowledge, Volume 3, Issue 1

Abstract
Knowledge Graphs (KGs) are a major asset for companies thanks to their great flexibility in data representation and their numerous applications, e.g., vocabulary sharing, Q&A or recommendation systems. To build a KG, it is a common practice to rely on automatic methods for extracting knowledge from various heterogeneous sources. However, in a noisy and uncertain world, knowledge may not be reliable and conflicts between data sources may occur. Integrating unreliable data would directly impact the use of the KG, therefore such conflicts must be resolved. This could be done manually by selecting the best data to integrate. This first approach is highly accurate, but costly and time-consuming. That is why recent efforts focus on automatic approaches, which represent a challenging task since it requires handling the uncertainty of extracted knowledge throughout its integration into the KG. We survey state-of-the-art approaches in this direction and present constructions of both open and enterprise KGs. We then describe different knowledge extraction methods and discuss downstream tasks after knowledge acquisition, including KG completion using embedding models, knowledge alignment, and knowledge fusion in order to address the problem of knowledge uncertainty in KG construction. We conclude with a discussion on the remaining challenges and perspectives when constructing a KG taking into account uncertainty.
Cite as

Lucas Jarnac, Yoan Chabot, and Miguel Couceiro. Uncertainty Management in the Construction of Knowledge Graphs: A Survey. In Transactions on Graph Data and Knowledge (TGDK), Volume 3, Issue 1, pp. 3:1-3:48, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@Article{jarnac_et_al:TGDK.3.1.3,
  author =	{Jarnac, Lucas and Chabot, Yoan and Couceiro, Miguel},
  title =	{{Uncertainty Management in the Construction of Knowledge Graphs: A Survey}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{3:1--3:48},
  ISSN =	{2942-7517},
  year =	{2025},
  volume =	{3},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.3.1.3},
  URN =		{urn:nbn:de:0030-drops-233733},
  doi =		{10.4230/TGDK.3.1.3},
  annote =	{Keywords: Knowledge reconciliation, Uncertainty, Heterogeneous sources, Knowledge graph construction}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2025.79
Catalytic Communication

Authors: Edward Pyne, Nathan S. Sheffield, and William Wang

Published in: LIPIcs, Volume 325, 16th Innovations in Theoretical Computer Science Conference (ITCS 2025)

Abstract
The study of space-bounded computation has drawn extensively from ideas and results in the field of communication complexity. Catalytic Computation (Buhrman, Cleve, Koucký, Loff and Speelman, STOC 2013) studies the power of bounded space augmented with a pre-filled hard drive that can be used non-destructively during the computation. Presently, many structural questions in this model remain open. Towards a better understanding of catalytic space, we define a model of catalytic communication complexity and prove new upper and lower bounds. In our model, Alice and Bob share a blackboard with a tiny number of free bits, and a larger section with an arbitrary initial configuration. They must jointly compute a function of their inputs, communicating only via the blackboard, and must always reset the blackboard to its initial configuration. We prove several upper and lower bounds: 1) We characterize the simplest nontrivial model, that of one bit of free space and three rounds, in terms of 𝔽₂ rank. In particular, we give natural problems that are solvable with a minimal-sized blackboard that require near-maximal (randomized) communication complexity, and vice versa. 2) We show that allowing constantly many free bits, as opposed to one, allows an exponential improvement on the size of the blackboard for natural problems. To do so, we connect the problem to existence questions in extremal graph theory. 3) We give tight connections between our model and standard notions of non-uniform catalytic computation. Using this connection, we show that with an arbitrary constant number of rounds and bits of free space, one can compute all functions in TC⁰. We view this model as a step toward understanding the value of filled space in computation.
Cite as

Edward Pyne, Nathan S. Sheffield, and William Wang. Catalytic Communication. In 16th Innovations in Theoretical Computer Science Conference (ITCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 325, pp. 79:1-79:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{pyne_et_al:LIPIcs.ITCS.2025.79,
  author =	{Pyne, Edward and Sheffield, Nathan S. and Wang, William},
  title =	{{Catalytic Communication}},
  booktitle =	{16th Innovations in Theoretical Computer Science Conference (ITCS 2025)},
  pages =	{79:1--79:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-361-4},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{325},
  editor =	{Meka, Raghu},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2025.79},
  URN =		{urn:nbn:de:0030-drops-227076},
  doi =		{10.4230/LIPIcs.ITCS.2025.79},
  annote =	{Keywords: Catalytic computation, Branching programs, Communication complexity}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2025.34
Directed Hypercube Routing, a Generalized Lehman-Ron Theorem, and Monotonicity Testing

Authors: Deeparnab Chakrabarty and C. Seshadhri

Published in: LIPIcs, Volume 325, 16th Innovations in Theoretical Computer Science Conference (ITCS 2025)

Abstract
Motivated by applications to monotonicity testing, Lehman and Ron (JCTA, 2001) proved the existence of a collection of vertex disjoint paths between comparable sub-level sets in the directed hypercube. The main technical contribution of this paper is a new proof method that yields a generalization of their theorem: we prove the existence of two edge-disjoint collections of vertex disjoint paths. Our main conceptual contributions are conjectures on directed hypercube flows with simultaneous vertex and edge capacities of which our generalized Lehman-Ron theorem is a special case. We show that these conjectures imply directed isoperimetric theorems, and in particular, the robust directed Talagrand inequality due to Khot, Minzer, and Safra (SIAM J. on Comp, 2018). These isoperimetric inequalities, that relate the directed surface area (of a set in the hypercube) to its distance to monotonicity, have been crucial in obtaining the best monotonicity testers for Boolean functions. We believe our conjectures pave the way towards combinatorial proofs of these directed isoperimetry theorems.
Cite as

Deeparnab Chakrabarty and C. Seshadhri. Directed Hypercube Routing, a Generalized Lehman-Ron Theorem, and Monotonicity Testing. In 16th Innovations in Theoretical Computer Science Conference (ITCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 325, pp. 34:1-34:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{chakrabarty_et_al:LIPIcs.ITCS.2025.34,
  author =	{Chakrabarty, Deeparnab and Seshadhri, C.},
  title =	{{Directed Hypercube Routing, a Generalized Lehman-Ron Theorem, and Monotonicity Testing}},
  booktitle =	{16th Innovations in Theoretical Computer Science Conference (ITCS 2025)},
  pages =	{34:1--34:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-361-4},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{325},
  editor =	{Meka, Raghu},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2025.34},
  URN =		{urn:nbn:de:0030-drops-226623},
  doi =		{10.4230/LIPIcs.ITCS.2025.34},
  annote =	{Keywords: Monotonicity testing, isoperimetric inequalities, hypercube routing}
}
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