24 Search Results for "Block, Alexander R."


Document
Detecting Causality in the Presence of Byzantine Processes: The Synchronous Systems Case

Authors: Anshuman Misra and Ajay D. Kshemkalyani

Published in: LIPIcs, Volume 278, 30th International Symposium on Temporal Representation and Reasoning (TIME 2023)


Abstract
Detecting causality or the happens before relation between events in a distributed system is a fundamental building block for distributed applications. It was recently proved that this problem cannot be solved in an asynchronous distributed system in the presence of Byzantine processes, irrespective of whether the communication mechanism is via unicasts, multicasts, or broadcasts. In light of this impossibility result, we turn attention to synchronous systems and examine the possibility of solving the causality detection problem in such systems. In this paper, we prove that causality detection between events can be solved in the presence of Byzantine processes in a synchronous distributed system. The positive result holds for unicast, multicast, as well as broadcast modes of communication. We prove the result by providing an algorithm. Our solution uses the Replicated State Machine (RSM) approach and vector clocks.

Cite as

Anshuman Misra and Ajay D. Kshemkalyani. Detecting Causality in the Presence of Byzantine Processes: The Synchronous Systems Case. In 30th International Symposium on Temporal Representation and Reasoning (TIME 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 278, pp. 11:1-11:14, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)


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@InProceedings{misra_et_al:LIPIcs.TIME.2023.11,
  author =	{Misra, Anshuman and Kshemkalyani, Ajay D.},
  title =	{{Detecting Causality in the Presence of Byzantine Processes: The Synchronous Systems Case}},
  booktitle =	{30th International Symposium on Temporal Representation and Reasoning (TIME 2023)},
  pages =	{11:1--11:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-298-3},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{278},
  editor =	{Artikis, Alexander and Bruse, Florian and Hunsberger, Luke},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.TIME.2023.11},
  URN =		{urn:nbn:de:0030-drops-191017},
  doi =		{10.4230/LIPIcs.TIME.2023.11},
  annote =	{Keywords: Byzantine fault-tolerance, causality, happens before, distributed system, message-passing, synchronous system}
}
Document
Extended Abstract
Answer Set Automata: A Learnable Pattern Specification Framework for Complex Event Recognition (Extended Abstract)

Authors: Nikos Katzouris and Georgios Paliouras

Published in: LIPIcs, Volume 278, 30th International Symposium on Temporal Representation and Reasoning (TIME 2023)


Abstract
Complex Event Recognition (CER) systems detect event occurrences in streaming input using predefined event patterns. Techniques that learn event patterns from data are highly desirable in CER. Since such patterns are typically represented by symbolic automata, we propose a family of such automata where the transition-enabling conditions are defined by Answer Set Programming (ASP) rules, and which, thanks to the strong connections of ASP to symbolic learning, are learnable from data. We present such a learning approach in ASP, capable of jointly learning the structure of an automaton and its transition guards' definitions from building-block predicates, and a scalable, incremental version thereof that progressively revises models learnt from mini-batches using Monte Carlo Tree Search. We evaluate our approach on three CER datasets and empirically demonstrate its efficacy.

Cite as

Nikos Katzouris and Georgios Paliouras. Answer Set Automata: A Learnable Pattern Specification Framework for Complex Event Recognition (Extended Abstract). In 30th International Symposium on Temporal Representation and Reasoning (TIME 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 278, pp. 17:1-17:3, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)


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@InProceedings{katzouris_et_al:LIPIcs.TIME.2023.17,
  author =	{Katzouris, Nikos and Paliouras, Georgios},
  title =	{{Answer Set Automata: A Learnable Pattern Specification Framework for Complex Event Recognition}},
  booktitle =	{30th International Symposium on Temporal Representation and Reasoning (TIME 2023)},
  pages =	{17:1--17:3},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-298-3},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{278},
  editor =	{Artikis, Alexander and Bruse, Florian and Hunsberger, Luke},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.TIME.2023.17},
  URN =		{urn:nbn:de:0030-drops-191071},
  doi =		{10.4230/LIPIcs.TIME.2023.17},
  annote =	{Keywords: Event Pattern Learning, Answer Set Programming}
}
Document
A Graph-Theoretic Formulation of Exploratory Blockmodeling

Authors: Alexander Bille, Niels Grüttemeier, Christian Komusiewicz, and Nils Morawietz

Published in: LIPIcs, Volume 265, 21st International Symposium on Experimental Algorithms (SEA 2023)


Abstract
We present a new simple graph-theoretic formulation of the exploratory blockmodeling problem on undirected and unweighted one-mode networks. Our formulation takes as input the network G and the maximum number t of blocks for the solution model. The task is to find a minimum-size set of edge insertions and deletions that transform the input graph G into a graph G' with at most t neighborhood classes. Herein, a neighborhood class is a maximal set of vertices with the same neighborhood. The neighborhood classes of G' directly give the blocks and block interactions of the computed blockmodel. We analyze the classic and parameterized complexity of the exploratory blockmodeling problem, provide a branch-and-bound algorithm, an ILP formulation and several heuristics. Finally, we compare our exact algorithms to previous ILP-based approaches and show that the new algorithms are faster for t ≥ 4.

Cite as

Alexander Bille, Niels Grüttemeier, Christian Komusiewicz, and Nils Morawietz. A Graph-Theoretic Formulation of Exploratory Blockmodeling. In 21st International Symposium on Experimental Algorithms (SEA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 265, pp. 14:1-14:20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)


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@InProceedings{bille_et_al:LIPIcs.SEA.2023.14,
  author =	{Bille, Alexander and Gr\"{u}ttemeier, Niels and Komusiewicz, Christian and Morawietz, Nils},
  title =	{{A Graph-Theoretic Formulation of Exploratory Blockmodeling}},
  booktitle =	{21st International Symposium on Experimental Algorithms (SEA 2023)},
  pages =	{14:1--14:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-279-2},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{265},
  editor =	{Georgiadis, Loukas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2023.14},
  URN =		{urn:nbn:de:0030-drops-183648},
  doi =		{10.4230/LIPIcs.SEA.2023.14},
  annote =	{Keywords: Clustering, Exact Algorithms, ILP-Formulation, Branch-and-Bound, Social Networks}
}
Document
On Relaxed Locally Decodable Codes for Hamming and Insertion-Deletion Errors

Authors: Alexander R. Block, Jeremiah Blocki, Kuan Cheng, Elena Grigorescu, Xin Li, Yu Zheng, and Minshen Zhu

Published in: LIPIcs, Volume 264, 38th Computational Complexity Conference (CCC 2023)


Abstract
Locally Decodable Codes (LDCs) are error-correcting codes C:Σⁿ → Σ^m, encoding messages in Σⁿ to codewords in Σ^m, with super-fast decoding algorithms. They are important mathematical objects in many areas of theoretical computer science, yet the best constructions so far have codeword length m that is super-polynomial in n, for codes with constant query complexity and constant alphabet size. In a very surprising result, Ben-Sasson, Goldreich, Harsha, Sudan, and Vadhan (SICOMP 2006) show how to construct a relaxed version of LDCs (RLDCs) with constant query complexity and almost linear codeword length over the binary alphabet, and used them to obtain significantly-improved constructions of Probabilistically Checkable Proofs. In this work, we study RLDCs in the standard Hamming-error setting, and introduce their variants in the insertion and deletion (Insdel) error setting. Standard LDCs for Insdel errors were first studied by Ostrovsky and Paskin-Cherniavsky (Information Theoretic Security, 2015), and are further motivated by recent advances in DNA random access bio-technologies. Our first result is an exponential lower bound on the length of Hamming RLDCs making 2 queries (even adaptively), over the binary alphabet. This answers a question explicitly raised by Gur and Lachish (SICOMP 2021) and is the first exponential lower bound for RLDCs. Combined with the results of Ben-Sasson et al., our result exhibits a "phase-transition"-type behavior on the codeword length for some constant-query complexity. We achieve these lower bounds via a transformation of RLDCs to standard Hamming LDCs, using a careful analysis of restrictions of message bits that fix codeword bits. We further define two variants of RLDCs in the Insdel-error setting, a weak and a strong version. On the one hand, we construct weak Insdel RLDCs with almost linear codeword length and constant query complexity, matching the parameters of the Hamming variants. On the other hand, we prove exponential lower bounds for strong Insdel RLDCs. These results demonstrate that, while these variants are equivalent in the Hamming setting, they are significantly different in the insdel setting. Our results also prove a strict separation between Hamming RLDCs and Insdel RLDCs.

Cite as

Alexander R. Block, Jeremiah Blocki, Kuan Cheng, Elena Grigorescu, Xin Li, Yu Zheng, and Minshen Zhu. On Relaxed Locally Decodable Codes for Hamming and Insertion-Deletion Errors. In 38th Computational Complexity Conference (CCC 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 264, pp. 14:1-14:25, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)


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@InProceedings{block_et_al:LIPIcs.CCC.2023.14,
  author =	{Block, Alexander R. and Blocki, Jeremiah and Cheng, Kuan and Grigorescu, Elena and Li, Xin and Zheng, Yu and Zhu, Minshen},
  title =	{{On Relaxed Locally Decodable Codes for Hamming and Insertion-Deletion Errors}},
  booktitle =	{38th Computational Complexity Conference (CCC 2023)},
  pages =	{14:1--14:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-282-2},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{264},
  editor =	{Ta-Shma, Amnon},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CCC.2023.14},
  URN =		{urn:nbn:de:0030-drops-182847},
  doi =		{10.4230/LIPIcs.CCC.2023.14},
  annote =	{Keywords: Relaxed Locally Decodable Codes, Hamming Errors, Insdel Errors, Lower Bounds}
}
Document
A Fast Data Structure for Dynamic Graphs Based on Hash-Indexed Adjacency Blocks

Authors: Alexander van der Grinten, Maria Predari, and Florian Willich

Published in: LIPIcs, Volume 233, 20th International Symposium on Experimental Algorithms (SEA 2022)


Abstract
Several dynamic graph data structures have been proposed in literature. Yet, these data structures either offer limited support for arbitrary graph algorithms or they are designed as part of specific frameworks (e.g., for GPUs or specialized hardware). Such frameworks are difficult to adopt to arbitrary graph computations and lead practitioners to fall back to less sophisticated solutions when dealing with dynamic graphs. In this work, we propose a new "dynamic hashed blocks" (DHB) data structure for sparse dynamic graphs and matrices on general-purpose CPU architectures. DHB combines an efficient block-based memory layout to store incident edges with an additional per-vertex hash index for high degree vertices. This hash index allows us to quickly insert edges without introducing duplicates, while the block-based memory layout retains advantageous cache locality properties of traditional adjacency arrays. Experiments show that DHB outperforms competing dynamic graph structures for edge insertions, updates, deletions, and traversal operations. Compared to static CSR layouts, DHB exhibits only a small overhead in traversal performance. DHB’s interface is similar to general-purpose abstract graph data types and can be easily used as a drop-in replacement for traditional adjacency arrays. To demonstrate that, we modify the well-known NetworKit framework to use DHB instead of its own dynamic graph representation. Experiments show that this modification only slightly penalizes the performance of graph algorithms while considerably boosting update rates.

Cite as

Alexander van der Grinten, Maria Predari, and Florian Willich. A Fast Data Structure for Dynamic Graphs Based on Hash-Indexed Adjacency Blocks. In 20th International Symposium on Experimental Algorithms (SEA 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 233, pp. 11:1-11:18, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2022)


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@InProceedings{vandergrinten_et_al:LIPIcs.SEA.2022.11,
  author =	{van der Grinten, Alexander and Predari, Maria and Willich, Florian},
  title =	{{A Fast Data Structure for Dynamic Graphs Based on Hash-Indexed Adjacency Blocks}},
  booktitle =	{20th International Symposium on Experimental Algorithms (SEA 2022)},
  pages =	{11:1--11:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-251-8},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{233},
  editor =	{Schulz, Christian and U\c{c}ar, Bora},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2022.11},
  URN =		{urn:nbn:de:0030-drops-165453},
  doi =		{10.4230/LIPIcs.SEA.2022.11},
  annote =	{Keywords: dynamic graph data structures, sparse matrix layout, dynamic algorithms, parallel algorithms, graph analysis}
}
Document
P₄-free Partition and Cover Numbers & Applications

Authors: Alexander R. Block, Simina Brânzei, Hemanta K. Maji, Himanshi Mehta, Tamalika Mukherjee, and Hai H. Nguyen

Published in: LIPIcs, Volume 199, 2nd Conference on Information-Theoretic Cryptography (ITC 2021)


Abstract
P₄-free graphs- also known as cographs, complement-reducible graphs, or hereditary Dacey graphs-have been well studied in graph theory. Motivated by computer science and information theory applications, our work encodes (flat) joint probability distributions and Boolean functions as bipartite graphs and studies bipartite P₄-free graphs. For these applications, the graph properties of edge partitioning and covering a bipartite graph using the minimum number of these graphs are particularly relevant. Previously, such graph properties have appeared in leakage-resilient cryptography and (variants of) coloring problems. Interestingly, our covering problem is closely related to the well-studied problem of product (a.k.a., Prague) dimension of loopless undirected graphs, which allows us to employ algebraic lower-bounding techniques for the product/Prague dimension. We prove that computing these numbers is NP-complete, even for bipartite graphs. We establish a connection to the (unsolved) Zarankiewicz problem to show that there are bipartite graphs with size-N partite sets such that these numbers are at least ε⋅N^{1-2ε}, for ε ∈ {1/3,1/4,1/5,...}. Finally, we accurately estimate these numbers for bipartite graphs encoding well-studied Boolean functions from circuit complexity, such as set intersection, set disjointness, and inequality. For applications in information theory and communication & cryptographic complexity, we consider a system where a setup samples from a (flat) joint distribution and gives the participants, Alice and Bob, their portion from this joint sample. Alice and Bob’s objective is to non-interactively establish a shared key and extract the left-over entropy from their portion of the samples as independent private randomness. A genie, who observes the joint sample, provides appropriate assistance to help Alice and Bob with their objective. Lower bounds to the minimum size of the genie’s assistance translate into communication and cryptographic lower bounds. We show that (the log₂ of) the P₄-free partition number of a graph encoding the joint distribution that the setup uses is equivalent to the size of the genie’s assistance. Consequently, the joint distributions corresponding to the bipartite graphs constructed above with high P₄-free partition numbers correspond to joint distributions requiring more assistance from the genie. As a representative application in non-deterministic communication complexity, we study the communication complexity of nondeterministic protocols augmented by access to the equality oracle at the output. We show that (the log₂ of) the P₄-free cover number of the bipartite graph encoding a Boolean function f is equivalent to the minimum size of the nondeterministic input required by the parties (referred to as the communication complexity of f in this model). Consequently, the functions corresponding to the bipartite graphs with high P₄-free cover numbers have high communication complexity. Furthermore, there are functions with communication complexity close to the naïve protocol where the nondeterministic input reveals a party’s input. Finally, the access to the equality oracle reduces the communication complexity of computing set disjointness by a constant factor in contrast to the model where parties do not have access to the equality oracle. To compute the inequality function, we show an exponential reduction in the communication complexity, and this bound is optimal. On the other hand, access to the equality oracle is (nearly) useless for computing set intersection.

Cite as

Alexander R. Block, Simina Brânzei, Hemanta K. Maji, Himanshi Mehta, Tamalika Mukherjee, and Hai H. Nguyen. P₄-free Partition and Cover Numbers & Applications. In 2nd Conference on Information-Theoretic Cryptography (ITC 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 199, pp. 16:1-16:25, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2021)


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@InProceedings{block_et_al:LIPIcs.ITC.2021.16,
  author =	{Block, Alexander R. and Br\^{a}nzei, Simina and Maji, Hemanta K. and Mehta, Himanshi and Mukherjee, Tamalika and Nguyen, Hai H.},
  title =	{{P₄-free Partition and Cover Numbers \& Applications}},
  booktitle =	{2nd Conference on Information-Theoretic Cryptography (ITC 2021)},
  pages =	{16:1--16:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-197-9},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{199},
  editor =	{Tessaro, Stefano},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITC.2021.16},
  URN =		{urn:nbn:de:0030-drops-143357},
  doi =		{10.4230/LIPIcs.ITC.2021.16},
  annote =	{Keywords: Secure keys, Secure private randomness, Gray-Wyner system, Cryptographic complexity, Nondeterministic communication complexity, Leakage-resilience, Combinatorial optimization, Product dimension, Zarankiewicz problem, Algebraic lower-bounding techniques, P₄-free partition number, P₄-free cover number}
}
Document
Invited Talk
Byzantine Agreement and SMR with Sub-Quadratic Message Complexity (Invited Talk)

Authors: Idit Keidar

Published in: LIPIcs, Volume 184, 24th International Conference on Principles of Distributed Systems (OPODIS 2020)


Abstract
Byzantine Agreement (BA) has been studied for four decades by now, but until recently, has been considered at a fairly small scale. In recent years, however, we begin to see practical use-cases of BA in large-scale systems, which motivates a push for reduced communication complexity. Dolev and Reischuk’s well-known lower bound stipulates that any deterministic algorithm requires Ω(n²) communication in the worst-case, and until fairly recently, almost all randomized algorithms have had at least quadratic complexity as well. This talk will present two new algorithms breaking this barrier. The first part of the talk will consider a fully asynchronous setting, focusing on randomized BA whose safety and liveness guarantees hold with high probability. It will present the first asynchronous Byzantine Agreement algorithm with sub-quadratic communication complexity. This algorithm exploits VRF-based committee sampling, which it adapts for the asynchronous model. The second part of the talk will consider the eventually synchronous model, where BA and State Machine Replication (SMR) can be solved with deterministic safety and liveness guarantees. In this context, randomization is used in order to reduce the expected communication complexity. The talk will present an algorithm for round synchronization, which is a building block for BA and SMR and constitutes the main performance bottleneck therein. It will present an algorithm that, for the first time, achieves round synchronization with expected linear message complexity and expected constant latency. Existing protocols can use this round synchronization algorithm to solve Byzantine SMR with the same asymptotic performance. The first part of the talk is based on joint work with Shir Cohen and Alexander Spiegelman, and the second part of the talk is based on joint work with Oded Naor.

Cite as

Idit Keidar. Byzantine Agreement and SMR with Sub-Quadratic Message Complexity (Invited Talk). In 24th International Conference on Principles of Distributed Systems (OPODIS 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 184, p. 2:1, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2021)


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@InProceedings{keidar:LIPIcs.OPODIS.2020.2,
  author =	{Keidar, Idit},
  title =	{{Byzantine Agreement and SMR with Sub-Quadratic Message Complexity}},
  booktitle =	{24th International Conference on Principles of Distributed Systems (OPODIS 2020)},
  pages =	{2:1--2:1},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-176-4},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{184},
  editor =	{Bramas, Quentin and Oshman, Rotem and Romano, Paolo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.OPODIS.2020.2},
  URN =		{urn:nbn:de:0030-drops-134874},
  doi =		{10.4230/LIPIcs.OPODIS.2020.2},
  annote =	{Keywords: Distributed Computing, Byzantine Agreement}
}
Document
ACE: Abstract Consensus Encapsulation for Liveness Boosting of State Machine Replication

Authors: Alexander Spiegelman, Arik Rinberg, and Dahlia Malkhi

Published in: LIPIcs, Volume 184, 24th International Conference on Principles of Distributed Systems (OPODIS 2020)


Abstract
With the emergence of attack-prone cross-organization systems, providing asynchronous state machine replication (SMR) solutions is no longer a theoretical concern. This paper presents ACE, a framework for the design of such fault tolerant systems. Leveraging a known paradigm for randomized consensus solutions, ACE wraps existing practical solutions and real-life systems, boosting their liveness under adversarial conditions and, at the same time, promoting load balancing and fairness. Boosting is achieved without modifying the overall design or the engineering of these solutions. ACE is aimed at boosting the prevailing approach for practical fault tolerance. This approach, often named partial synchrony, is based on a leader-based paradigm: a good leader makes progress and a bad leader does no harm. The partial synchrony approach focuses on safety and forgoes liveness under targeted and dynamic attacks. Specifically, an attacker might block specific leaders, e.g., through a denial of service, to prevent progress. ACE provides boosting by running waves of parallel leaders and selecting a winning leader only retroactively, achieving boosting at a linear communication cost increase. ACE is agnostic to the fault model, inheriting it s failure model from the wrapped solution assumptions. As our evaluation shows, an asynchronous Byzantine fault tolerance (BFT) replication system built with ACE around an existing partially synchronous BFT protocol demonstrates reasonable slow-down compared with the base BFT protocol during faultless synchronous scenarios, yet exhibits significant speedup while the system is under attack.

Cite as

Alexander Spiegelman, Arik Rinberg, and Dahlia Malkhi. ACE: Abstract Consensus Encapsulation for Liveness Boosting of State Machine Replication. In 24th International Conference on Principles of Distributed Systems (OPODIS 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 184, pp. 9:1-9:18, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2021)


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@InProceedings{spiegelman_et_al:LIPIcs.OPODIS.2020.9,
  author =	{Spiegelman, Alexander and Rinberg, Arik and Malkhi, Dahlia},
  title =	{{ACE: Abstract Consensus Encapsulation for Liveness Boosting of State Machine Replication}},
  booktitle =	{24th International Conference on Principles of Distributed Systems (OPODIS 2020)},
  pages =	{9:1--9:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-176-4},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{184},
  editor =	{Bramas, Quentin and Oshman, Rotem and Romano, Paolo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.OPODIS.2020.9},
  URN =		{urn:nbn:de:0030-drops-134948},
  doi =		{10.4230/LIPIcs.OPODIS.2020.9},
  annote =	{Keywords: Framework, Asynchronous, Consensus boosting, State Machine Replication}
}
Document
Locally Decodable/Correctable Codes for Insertions and Deletions

Authors: Alexander R. Block, Jeremiah Blocki, Elena Grigorescu, Shubhang Kulkarni, and Minshen Zhu

Published in: LIPIcs, Volume 182, 40th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2020)


Abstract
Recent efforts in coding theory have focused on building codes for insertions and deletions, called insdel codes, with optimal trade-offs between their redundancy and their error-correction capabilities, as well as efficient encoding and decoding algorithms. In many applications, polynomial running time may still be prohibitively expensive, which has motivated the study of codes with super-efficient decoding algorithms. These have led to the well-studied notions of Locally Decodable Codes (LDCs) and Locally Correctable Codes (LCCs). Inspired by these notions, Ostrovsky and Paskin-Cherniavsky (Information Theoretic Security, 2015) generalized Hamming LDCs to insertions and deletions. To the best of our knowledge, these are the only known results that study the analogues of Hamming LDCs in channels performing insertions and deletions. Here we continue the study of insdel codes that admit local algorithms. Specifically, we reprove the results of Ostrovsky and Paskin-Cherniavsky for insdel LDCs using a different set of techniques. We also observe that the techniques extend to constructions of LCCs. Specifically, we obtain insdel LDCs and LCCs from their Hamming LDCs and LCCs analogues, respectively. The rate and error-correction capability blow up only by a constant factor, while the query complexity blows up by a poly log factor in the block length. Since insdel locally decodable/correctble codes are scarcely studied in the literature, we believe our results and techniques may lead to further research. In particular, we conjecture that constant-query insdel LDCs/LCCs do not exist.

Cite as

Alexander R. Block, Jeremiah Blocki, Elena Grigorescu, Shubhang Kulkarni, and Minshen Zhu. Locally Decodable/Correctable Codes for Insertions and Deletions. In 40th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 182, pp. 16:1-16:17, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2020)


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@InProceedings{block_et_al:LIPIcs.FSTTCS.2020.16,
  author =	{Block, Alexander R. and Blocki, Jeremiah and Grigorescu, Elena and Kulkarni, Shubhang and Zhu, Minshen},
  title =	{{Locally Decodable/Correctable Codes for Insertions and Deletions}},
  booktitle =	{40th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2020)},
  pages =	{16:1--16:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-174-0},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{182},
  editor =	{Saxena, Nitin and Simon, Sunil},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSTTCS.2020.16},
  URN =		{urn:nbn:de:0030-drops-132577},
  doi =		{10.4230/LIPIcs.FSTTCS.2020.16},
  annote =	{Keywords: Locally decodable/correctable codes, insert-delete channel}
}
Document
Read Mapping on Genome Variation Graphs

Authors: Kavya Vaddadi, Rajgopal Srinivasan, and Naveen Sivadasan

Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)


Abstract
Genome variation graphs are natural candidates to represent a pangenome collection. In such graphs, common subsequences are encoded as vertices and the genomic variations are captured by introducing additional labeled vertices and directed edges. Unlike a linear reference, a reference graph allows a rich representation of the genomic diversities and avoids reference bias. We address the fundamental problem of mapping reads to genome variation graphs. We give a novel mapping algorithm V-MAP for efficient identification of small subgraph of the genome graph for optimal gapped alignment of the read. V-MAP creates space efficient index using locality sensitive minimizer signatures computed using a novel graph winnowing and graph embedding onto metric space for fast and accurate mapping. Experiments involving graph constructed from the 1000 Genomes data and using both real and simulated reads show that V-MAP is fast, memory efficient and can map short reads, as well as PacBio/Nanopore long reads with high accuracy. V-MAP performance was significantly better than the state-of-the-art, especially for long reads.

Cite as

Kavya Vaddadi, Rajgopal Srinivasan, and Naveen Sivadasan. Read Mapping on Genome Variation Graphs. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 7:1-7:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{vaddadi_et_al:LIPIcs.WABI.2019.7,
  author =	{Vaddadi, Kavya and Srinivasan, Rajgopal and Sivadasan, Naveen},
  title =	{{Read Mapping on Genome Variation Graphs}},
  booktitle =	{19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
  pages =	{7:1--7:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-123-8},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{143},
  editor =	{Huber, Katharina T. and Gusfield, Dan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2019.7},
  URN =		{urn:nbn:de:0030-drops-110375},
  doi =		{10.4230/LIPIcs.WABI.2019.7},
  annote =	{Keywords: read mapping, pangenome, genome variation graphs, locality sensitive hashing}
}
Document
Finding All Maximal Perfect Haplotype Blocks in Linear Time

Authors: Jarno Alanko, Hideo Bannai, Bastien Cazaux, Pierre Peterlongo, and Jens Stoye

Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)


Abstract
Recent large-scale community sequencing efforts allow at an unprecedented level of detail the identification of genomic regions that show signatures of natural selection. Traditional methods for identifying such regions from individuals' haplotype data, however, require excessive computing times and therefore are not applicable to current datasets. In 2019, Cunha et al. (Proceedings of BSB 2019) suggested the maximal perfect haplotype block as a very simple combinatorial pattern, forming the basis of a new method to perform rapid genome-wide selection scans. The algorithm they presented for identifying these blocks, however, had a worst-case running time quadratic in the genome length. It was posed as an open problem whether an optimal, linear-time algorithm exists. In this paper we give two algorithms that achieve this time bound, one conceptually very simple one using suffix trees and a second one using the positional Burrows-Wheeler Transform, that is very efficient also in practice.

Cite as

Jarno Alanko, Hideo Bannai, Bastien Cazaux, Pierre Peterlongo, and Jens Stoye. Finding All Maximal Perfect Haplotype Blocks in Linear Time. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 8:1-8:9, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{alanko_et_al:LIPIcs.WABI.2019.8,
  author =	{Alanko, Jarno and Bannai, Hideo and Cazaux, Bastien and Peterlongo, Pierre and Stoye, Jens},
  title =	{{Finding All Maximal Perfect Haplotype Blocks in Linear Time}},
  booktitle =	{19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
  pages =	{8:1--8:9},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-123-8},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{143},
  editor =	{Huber, Katharina T. and Gusfield, Dan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2019.8},
  URN =		{urn:nbn:de:0030-drops-110388},
  doi =		{10.4230/LIPIcs.WABI.2019.8},
  annote =	{Keywords: Population genomics, selection coefficient, haplotype block, positional Burrows-Wheeler Transform}
}
Document
Synteny Paths for Assembly Graphs Comparison

Authors: Evgeny Polevikov and Mikhail Kolmogorov

Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)


Abstract
Despite the recent developments of long-read sequencing technologies, it is still difficult to produce complete assemblies of eukaryotic genomes in an automated fashion. Genome assembly software typically output assembled fragments (contigs) along with assembly graphs, that encode all possible layouts of these contigs. Graph representation of the assembled genome can be useful for gene discovery, haplotyping, structural variations analysis and other applications. To facilitate the development of new graph-based approaches, it is important to develop algorithms for comparison and evaluation of assembly graphs produced by different software. In this work, we introduce synteny paths: maximal paths of homologous sequence between the compared assembly graphs. We describe Asgan - an algorithm for efficient synteny paths decomposition, and use it to evaluate assembly graphs of various bacterial assemblies produced by different approaches. We then apply Asgan to discover structural variations between the assemblies of 15 Drosophila genomes, and show that synteny paths are robust to contig fragmentation. The Asgan tool is freely available at: https://github.com/epolevikov/Asgan.

Cite as

Evgeny Polevikov and Mikhail Kolmogorov. Synteny Paths for Assembly Graphs Comparison. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 24:1-24:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{polevikov_et_al:LIPIcs.WABI.2019.24,
  author =	{Polevikov, Evgeny and Kolmogorov, Mikhail},
  title =	{{Synteny Paths for Assembly Graphs Comparison}},
  booktitle =	{19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
  pages =	{24:1--24:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-123-8},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{143},
  editor =	{Huber, Katharina T. and Gusfield, Dan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2019.24},
  URN =		{urn:nbn:de:0030-drops-110545},
  doi =		{10.4230/LIPIcs.WABI.2019.24},
  annote =	{Keywords: Assembly graphs, Genome assembly, Synteny blocks, Comparative Genomics}
}
Document
On the Symmetries of and Equivalence Test for Design Polynomials

Authors: Nikhil Gupta and Chandan Saha

Published in: LIPIcs, Volume 138, 44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019)


Abstract
In a Nisan-Wigderson design polynomial (in short, a design polynomial), every pair of monomials share a few common variables. A useful example of such a polynomial, introduced in [Neeraj Kayal et al., 2014], is the following: NW_{d,k}({x}) = sum_{h in F_d[z], deg(h) <= k}{ prod_{i=0}^{d-1}{x_{i, h(i)}}}, where d is a prime, F_d is the finite field with d elements, and k << d. The degree of the gcd of every pair of monomials in NW_{d,k} is at most k. For concreteness, we fix k = ceil[sqrt{d}]. The family of polynomials NW := {NW_{d,k} : d is a prime} and close variants of it have been used as hard explicit polynomial families in several recent arithmetic circuit lower bound proofs. But, unlike the permanent, very little is known about the various structural and algorithmic/complexity aspects of NW beyond the fact that NW in VNP. Is NW_{d,k} characterized by its symmetries? Is it circuit-testable, i.e., given a circuit C can we check efficiently if C computes NW_{d,k}? What is the complexity of equivalence test for NW, i.e., given black-box access to a f in F[{x}], can we check efficiently if there exists an invertible linear transformation A such that f = NW_{d,k}(A * {x})? Characterization of polynomials by their symmetries plays a central role in the geometric complexity theory program. Here, we answer the first two questions and partially answer the third. We show that NW_{d,k} is characterized by its group of symmetries over C, but not over R. We also show that NW_{d,k} is characterized by circuit identities which implies that NW_{d,k} is circuit-testable in randomized polynomial time. As another application of this characterization, we obtain the "flip theorem" for NW. We give an efficient equivalence test for NW in the case where the transformation A is a block-diagonal permutation-scaling matrix. The design of this algorithm is facilitated by an almost complete understanding of the group of symmetries of NW_{d,k}: We show that if A is in the group of symmetries of NW_{d,k} then A = D * P, where D and P are diagonal and permutation matrices respectively. This is proved by completely characterizing the Lie algebra of NW_{d,k}, and using an interplay between the Hessian of NW_{d,k} and the evaluation dimension.

Cite as

Nikhil Gupta and Chandan Saha. On the Symmetries of and Equivalence Test for Design Polynomials. In 44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 138, pp. 53:1-53:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{gupta_et_al:LIPIcs.MFCS.2019.53,
  author =	{Gupta, Nikhil and Saha, Chandan},
  title =	{{On the Symmetries of and Equivalence Test for Design Polynomials}},
  booktitle =	{44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019)},
  pages =	{53:1--53:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-117-7},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{138},
  editor =	{Rossmanith, Peter and Heggernes, Pinar and Katoen, Joost-Pieter},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2019.53},
  URN =		{urn:nbn:de:0030-drops-109979},
  doi =		{10.4230/LIPIcs.MFCS.2019.53},
  annote =	{Keywords: Nisan-Wigderson design polynomial, characterization by symmetries, Lie algebra, group of symmetries, circuit testability, flip theorem, equivalence test}
}
Document
The Perfect Matching Reconfiguration Problem

Authors: Marthe Bonamy, Nicolas Bousquet, Marc Heinrich, Takehiro Ito, Yusuke Kobayashi, Arnaud Mary, Moritz Mühlenthaler, and Kunihiro Wasa

Published in: LIPIcs, Volume 138, 44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019)


Abstract
We study the perfect matching reconfiguration problem: Given two perfect matchings of a graph, is there a sequence of flip operations that transforms one into the other? Here, a flip operation exchanges the edges in an alternating cycle of length four. We are interested in the complexity of this decision problem from the viewpoint of graph classes. We first prove that the problem is PSPACE-complete even for split graphs and for bipartite graphs of bounded bandwidth with maximum degree five. We then investigate polynomial-time solvable cases. Specifically, we prove that the problem is solvable in polynomial time for strongly orderable graphs (that include interval graphs and strongly chordal graphs), for outerplanar graphs, and for cographs (also known as P_4-free graphs). Furthermore, for each yes-instance from these graph classes, we show that a linear number of flip operations is sufficient and we can exhibit a corresponding sequence of flip operations in polynomial time.

Cite as

Marthe Bonamy, Nicolas Bousquet, Marc Heinrich, Takehiro Ito, Yusuke Kobayashi, Arnaud Mary, Moritz Mühlenthaler, and Kunihiro Wasa. The Perfect Matching Reconfiguration Problem. In 44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 138, pp. 80:1-80:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{bonamy_et_al:LIPIcs.MFCS.2019.80,
  author =	{Bonamy, Marthe and Bousquet, Nicolas and Heinrich, Marc and Ito, Takehiro and Kobayashi, Yusuke and Mary, Arnaud and M\"{u}hlenthaler, Moritz and Wasa, Kunihiro},
  title =	{{The Perfect Matching Reconfiguration Problem}},
  booktitle =	{44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019)},
  pages =	{80:1--80:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-117-7},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{138},
  editor =	{Rossmanith, Peter and Heggernes, Pinar and Katoen, Joost-Pieter},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2019.80},
  URN =		{urn:nbn:de:0030-drops-110248},
  doi =		{10.4230/LIPIcs.MFCS.2019.80},
  annote =	{Keywords: Combinatorial Reconfiguration, Graph Algorithms, Perfect Matching}
}
Document
On the Qubit Routing Problem

Authors: Alexander Cowtan, Silas Dilkes, Ross Duncan, Alexandre Krajenbrink, Will Simmons, and Seyon Sivarajah

Published in: LIPIcs, Volume 135, 14th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2019)


Abstract
We introduce a new architecture-agnostic methodology for mapping abstract quantum circuits to realistic quantum computing devices with restricted qubit connectivity, as implemented by Cambridge Quantum Computing’s t|ket> compiler. We present empirical results showing the effectiveness of this method in terms of reducing two-qubit gate depth and two-qubit gate count, compared to other implementations.

Cite as

Alexander Cowtan, Silas Dilkes, Ross Duncan, Alexandre Krajenbrink, Will Simmons, and Seyon Sivarajah. On the Qubit Routing Problem. In 14th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 135, pp. 5:1-5:32, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{cowtan_et_al:LIPIcs.TQC.2019.5,
  author =	{Cowtan, Alexander and Dilkes, Silas and Duncan, Ross and Krajenbrink, Alexandre and Simmons, Will and Sivarajah, Seyon},
  title =	{{On the Qubit Routing Problem}},
  booktitle =	{14th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2019)},
  pages =	{5:1--5:32},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-112-2},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{135},
  editor =	{van Dam, Wim and Man\v{c}inska, Laura},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.TQC.2019.5},
  URN =		{urn:nbn:de:0030-drops-103972},
  doi =		{10.4230/LIPIcs.TQC.2019.5},
  annote =	{Keywords: Quantum Computing, Qubit routing, Compilation}
}
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