9 Search Results for "Ward, Rachel"


Document
Research
Mining Inter-Document Argument Structures in Scientific Papers for an Argument Web

Authors: Florian Ruosch, Cristina Sarasua, and Abraham Bernstein

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


Abstract
In Argument Mining, predicting argumentative relations between texts (or spans) remains one of the most challenging aspects, even more so in the cross-document setting. This paper makes three key contributions to advance research in this domain. We first extend an existing dataset, the Sci-Arg corpus, by annotating it with explicit inter-document argumentative relations, thereby allowing arguments to be distributed over several documents forming an Argument Web; these new annotations are published using Semantic Web technologies (RDF, OWL). Second, we explore and evaluate three automated approaches for predicting these inter-document argumentative relations, establishing critical baselines on the new dataset. We find that a simple classifier based on discourse indicators with access to context outperforms neural methods. Third, we conduct a comparative analysis of these approaches for both intra- and inter-document settings, identifying statistically significant differences in results that indicate the necessity of distinguishing between these two scenarios. Our findings highlight significant challenges in this complex domain and open crucial avenues for future research on the Argument Web of Science, particularly for those interested in leveraging Semantic Web technologies and knowledge graphs to understand scholarly discourse. With this, we provide the first stepping stones in the form of a benchmark dataset, three baseline methods, and an initial analysis for a systematic exploration of this field relevant to the Web of Data and Science.

Cite as

Florian Ruosch, Cristina Sarasua, and Abraham Bernstein. Mining Inter-Document Argument Structures in Scientific Papers for an Argument Web. In Transactions on Graph Data and Knowledge (TGDK), Volume 3, Issue 3, pp. 4:1-4:33, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@Article{ruosch_et_al:TGDK.3.3.4,
  author =	{Ruosch, Florian and Sarasua, Cristina and Bernstein, Abraham},
  title =	{{Mining Inter-Document Argument Structures in Scientific Papers for an Argument Web}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{4:1--4:33},
  ISSN =	{2942-7517},
  year =	{2025},
  volume =	{3},
  number =	{3},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.3.3.4},
  URN =		{urn:nbn:de:0030-drops-252159},
  doi =		{10.4230/TGDK.3.3.4},
  annote =	{Keywords: Argument Mining, Large Language Models, Knowledge Graphs, Link Prediction}
}
Document
Cache Timing Leakages in Zero-Knowledge Protocols

Authors: Shibam Mukherjee, Christian Rechberger, and Markus Schofnegger

Published in: LIPIcs, Volume 354, 7th Conference on Advances in Financial Technologies (AFT 2025)


Abstract
The area of modern zero-knowledge proof systems has seen a significant rise in popularity over the last couple of years, with new techniques and optimized constructions emerging on a regular basis. As the field matures, the aspect of implementation attacks becomes more relevant, however side-channel attacks on zero-knowledge proof systems have seen surprisingly little treatment so far. In this paper, we give an overview of potential attack vectors and show that some of the underlying finite field libraries, and implementations of heavily used components like hash functions using them, are vulnerable w.r.t. cache attacks on CPUs. On the positive side, we demonstrate that the computational overhead to protect against these attacks is relatively small.

Cite as

Shibam Mukherjee, Christian Rechberger, and Markus Schofnegger. Cache Timing Leakages in Zero-Knowledge Protocols. In 7th Conference on Advances in Financial Technologies (AFT 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 354, pp. 1:1-1:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@InProceedings{mukherjee_et_al:LIPIcs.AFT.2025.1,
  author =	{Mukherjee, Shibam and Rechberger, Christian and Schofnegger, Markus},
  title =	{{Cache Timing Leakages in Zero-Knowledge Protocols}},
  booktitle =	{7th Conference on Advances in Financial Technologies (AFT 2025)},
  pages =	{1:1--1:26},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-400-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{354},
  editor =	{Avarikioti, Zeta and Christin, Nicolas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.AFT.2025.1},
  URN =		{urn:nbn:de:0030-drops-247201},
  doi =		{10.4230/LIPIcs.AFT.2025.1},
  annote =	{Keywords: zero-knowledge, protocol, cache timing, side-channel, leakage}
}
Document
APPROX
Budget and Profit Approximations for Spanning Tree Interdiction

Authors: Rafail Ostrovsky, Yuval Rabani, and Yoav Siman Tov

Published in: LIPIcs, Volume 353, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)


Abstract
We give polynomial time logarithmic approximation guarantees for the budget minimization, as well as for the profit maximization versions of minimum spanning tree interdiction. In this problem, the goal is to remove some edges of an undirected graph with edge weights and edge costs, so as to increase the weight of a minimum spanning tree. In the budget minimization version, the goal is to minimize the total cost of the removed edges, while achieving a desired increase Δ in the weight of the minimum spanning tree. An alternative objective within the same framework is to maximize the profit of interdiction, namely the increase in the weight of the minimum spanning tree, subject to a budget constraint. There are known polynomial time O(1) approximation guarantees for a similar objective (maximizing the total cost of the tree, rather than the increase). However, the guarantee does not seem to apply to the increase in cost. Moreover, the same techniques do not seem to apply to the budget version. Our approximation guarantees are motivated by studying the question of minimizing the cost of increasing the minimum spanning tree by any amount. We show that in contrast to the budget and profit problems, this version of interdiction is polynomial time-solvable, and we give an efficient algorithm for solving it. The solution motivates a graph-theoretic relaxation of the NP-hard interdiction problem. The gain in minimum spanning tree weight, as a function of the set of removed edges, is super-modular. Thus, the budget problem is an instance of minimizing a linear function subject to a super-modular covering constraint. We use the graph-theoretic relaxation to design and analyze a batch greedy-based algorithm.

Cite as

Rafail Ostrovsky, Yuval Rabani, and Yoav Siman Tov. Budget and Profit Approximations for Spanning Tree Interdiction. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 353, pp. 7:1-7:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@InProceedings{ostrovsky_et_al:LIPIcs.APPROX/RANDOM.2025.7,
  author =	{Ostrovsky, Rafail and Rabani, Yuval and Siman Tov, Yoav},
  title =	{{Budget and Profit Approximations for Spanning Tree Interdiction}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)},
  pages =	{7:1--7:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-397-3},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{353},
  editor =	{Ene, Alina and Chattopadhyay, Eshan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX/RANDOM.2025.7},
  URN =		{urn:nbn:de:0030-drops-243733},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2025.7},
  annote =	{Keywords: minimum spanning tree, spanning tree interdiction, combinatorial approximation algorithms, partial cut}
}
Document
Generalized De Bruijn Words, Invertible Necklaces, and the Burrows-Wheeler Transform

Authors: Gabriele Fici and Estéban Gabory

Published in: LIPIcs, Volume 345, 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)


Abstract
We define generalized de Bruijn words as those words having a Burrows-Wheeler transform that is a concatenation of permutations of the alphabet. We show that generalized de Bruijn words are in 1-to-1 correspondence with Hamiltonian cycles in the generalized de Bruijn graphs, introduced in the early '80s in the context of network design. When the size of the alphabet is a prime p, we define invertible necklaces as those whose BWT-matrix is non-singular. We show that invertible necklaces of length n correspond to normal bases of the finite field 𝔽_{pⁿ}, and that they form an Abelian group isomorphic to the Reutenauer group RG_pⁿ. Using known results in abstract algebra, we can make a bridge between generalized de Bruijn words and invertible necklaces. In particular, we highlight a correspondence between binary de Bruijn words of order d+1, binary necklaces of length 2^{d} having an odd number of 1’s, invertible BWT matrices of size 2^{d}× 2^{d}, and normal bases of the finite field 𝔽_{2^{2^{d}}}.

Cite as

Gabriele Fici and Estéban Gabory. Generalized De Bruijn Words, Invertible Necklaces, and the Burrows-Wheeler Transform. In 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 345, pp. 48:1-48:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@InProceedings{fici_et_al:LIPIcs.MFCS.2025.48,
  author =	{Fici, Gabriele and Gabory, Est\'{e}ban},
  title =	{{Generalized De Bruijn Words, Invertible Necklaces, and the Burrows-Wheeler Transform}},
  booktitle =	{50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)},
  pages =	{48:1--48:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-388-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{345},
  editor =	{Gawrychowski, Pawe{\l} and Mazowiecki, Filip and Skrzypczak, Micha{\l}},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2025.48},
  URN =		{urn:nbn:de:0030-drops-241555},
  doi =		{10.4230/LIPIcs.MFCS.2025.48},
  annote =	{Keywords: Burrows-Wheeler Transform, Generalized de Bruijn Word, Generalized de Bruijn Graph, Circulant Matrix, Invertible Necklace, Sandpile Group, Reutenauer Group}
}
Document
Mutational Signature Refitting on Sparse Pan-Cancer Data

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

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


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

Cite as

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


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

Authors: Haonan Wu, Antonio Blanca, and Paul Medvedev

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


Abstract
K-mer-based analysis of genomic data is ubiquitous, but the presence of repetitive k-mers continues to pose problems for the accuracy of many methods. For example, the Mash tool (Ondov et al. 2016) can accurately estimate the substitution rate between two low-repetitive sequences from their k-mer sketches; however, it is inaccurate on repetitive sequences such as the centromere of a human chromosome. Follow-up work by Blanca et al. (2021) has attempted to model how mutations affect k-mer sets based on strong assumptions that the sequence is non-repetitive and that mutations do not create spurious k-mer matches. However, the theoretical foundations for extending an estimator like Mash to work in the presence of repeat sequences have been lacking. In this work, we relax the non-repetitive assumption and propose a novel estimator for the mutation rate. We derive theoretical bounds on our estimator’s bias. Our experiments show that it remains accurate for repetitive genomic sequences, such as the alpha satellite higher order repeats in centromeres. We demonstrate our estimator’s robustness across diverse datasets and various ranges of the substitution rate and k-mer size. Finally, we show how sketching can be used to avoid dealing with large k-mer sets while retaining accuracy. Our software is available at https://github.com/medvedevgroup/Repeat-Aware_Substitution_Rate_Estimator.

Cite as

Haonan Wu, Antonio Blanca, and Paul Medvedev. A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 20:1-20:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)


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@InProceedings{wu_et_al:LIPIcs.WABI.2025.20,
  author =	{Wu, Haonan and Blanca, Antonio and Medvedev, Paul},
  title =	{{A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{20:1--20:20},
  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.2025.20},
  URN =		{urn:nbn:de:0030-drops-239465},
  doi =		{10.4230/LIPIcs.WABI.2025.20},
  annote =	{Keywords: k-mers, sketching, mutation rates}
}
Document
Arbitrary-Length Analogs to de Bruijn Sequences

Authors: Abhinav Nellore and Rachel Ward

Published in: LIPIcs, Volume 223, 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)


Abstract
Let α̃ be a length-L cyclic sequence of characters from a size-K alphabet 𝒜 such that for every positive integer m ≤ L, the number of occurrences of any length-m string on 𝒜 as a substring of α̃ is ⌊ L / K^m ⌋ or ⌈ L / K^m ⌉. When L = K^N for any positive integer N, α̃ is a de Bruijn sequence of order N, and when L ≠ K^N, α̃ shares many properties with de Bruijn sequences. We describe an algorithm that outputs some α̃ for any combination of K ≥ 2 and L ≥ 1 in O(L) time using O(L log K) space. This algorithm extends Lempel’s recursive construction of a binary de Bruijn sequence. An implementation written in Python is available at https://github.com/nelloreward/pkl.

Cite as

Abhinav Nellore and Rachel Ward. Arbitrary-Length Analogs to de Bruijn Sequences. In 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 223, pp. 9:1-9:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)


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@InProceedings{nellore_et_al:LIPIcs.CPM.2022.9,
  author =	{Nellore, Abhinav and Ward, Rachel},
  title =	{{Arbitrary-Length Analogs to de Bruijn Sequences}},
  booktitle =	{33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)},
  pages =	{9:1--9:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-234-1},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{223},
  editor =	{Bannai, Hideo and Holub, Jan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2022.9},
  URN =		{urn:nbn:de:0030-drops-161361},
  doi =		{10.4230/LIPIcs.CPM.2022.9},
  annote =	{Keywords: de Bruijn sequence, de Bruijn word, Lempel’s D-morphism, Lempel’s homomorphism}
}
Document
An Invertible Transform for Efficient String Matching in Labeled Digraphs

Authors: Abhinav Nellore, Austin Nguyen, and Reid F. Thompson

Published in: LIPIcs, Volume 191, 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021)


Abstract
Let G = (V, E) be a digraph where each vertex is unlabeled, each edge is labeled by a character in some alphabet Ω, and any two edges with both the same head and the same tail have different labels. The powerset construction gives a transform of G into a weakly connected digraph G' = (V', E') that enables solving the decision problem of whether there is a walk in G matching an arbitrarily long query string q in time linear in |q| and independent of |E| and |V|. We show G is uniquely determined by G' when for every v_𝓁 ∈ V, there is some distinct string s_𝓁 on Ω such that v_𝓁 is the origin of a closed walk in G matching s_𝓁, and no other walk in G matches s_𝓁 unless it starts and ends at v_𝓁. We then exploit this invertibility condition to strategically alter any G so its transform G' enables retrieval of all t terminal vertices of walks in the unaltered G matching q in O(|q| + t log |V|) time. We conclude by proposing two defining properties of a class of transforms that includes the Burrows-Wheeler transform and the transform presented here.

Cite as

Abhinav Nellore, Austin Nguyen, and Reid F. Thompson. An Invertible Transform for Efficient String Matching in Labeled Digraphs. In 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 191, pp. 20:1-20:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)


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@InProceedings{nellore_et_al:LIPIcs.CPM.2021.20,
  author =	{Nellore, Abhinav and Nguyen, Austin and Thompson, Reid F.},
  title =	{{An Invertible Transform for Efficient String Matching in Labeled Digraphs}},
  booktitle =	{32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021)},
  pages =	{20:1--20:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-186-3},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{191},
  editor =	{Gawrychowski, Pawe{\l} and Starikovskaya, Tatiana},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2021.20},
  URN =		{urn:nbn:de:0030-drops-139717},
  doi =		{10.4230/LIPIcs.CPM.2021.20},
  annote =	{Keywords: pattern matching, string matching, Burrows-Wheeler transform, labeled graphs}
}
Document
Fast Cross-Polytope Locality-Sensitive Hashing

Authors: Christopher Kennedy and Rachel Ward

Published in: LIPIcs, Volume 67, 8th Innovations in Theoretical Computer Science Conference (ITCS 2017)


Abstract
We provide a variant of cross-polytope locality sensitive hashing with respect to angular distance which is provably optimal in asymptotic sensitivity and enjoys \mathcal{O}(d \ln d ) hash computation time. Building on a recent result in (Andoni, Indyk, Laarhoven, Razenshteyn '15), we show that optimal asymptotic sensitivity for cross-polytope LSH is retained even when the dense Gaussian matrix is replaced by a fast Johnson-Lindenstrauss transform followed by discrete pseudo-rotation, reducing the hash computation time from \mathcal{O}(d^2) to \mathcal{O}(d \ln d ). Moreover, our scheme achieves the optimal rate of convergence for sensitivity. By incorporating a low-randomness Johnson-Lindenstrauss transform, our scheme can be modified to require only \mathcal{O}(\ln^9(d)) random bits.

Cite as

Christopher Kennedy and Rachel Ward. Fast Cross-Polytope Locality-Sensitive Hashing. In 8th Innovations in Theoretical Computer Science Conference (ITCS 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 67, pp. 53:1-53:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)


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@InProceedings{kennedy_et_al:LIPIcs.ITCS.2017.53,
  author =	{Kennedy, Christopher and Ward, Rachel},
  title =	{{Fast Cross-Polytope Locality-Sensitive Hashing}},
  booktitle =	{8th Innovations in Theoretical Computer Science Conference (ITCS 2017)},
  pages =	{53:1--53:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-029-3},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{67},
  editor =	{Papadimitriou, Christos H.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2017.53},
  URN =		{urn:nbn:de:0030-drops-81936},
  doi =		{10.4230/LIPIcs.ITCS.2017.53},
  annote =	{Keywords: Locality-sensitive hashing, Dimension reduction, Johnson-Lindenstrauss lemma}
}
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