4 Search Results for "Han, Jie"


Document
Polynomial-Time Verification and Testing of Implementations of the Snapshot Data Structure

Authors: Gal Amram, Avi Hayoun, Lior Mizrahi, and Gera Weiss

Published in: LIPIcs, Volume 246, 36th International Symposium on Distributed Computing (DISC 2022)


Abstract
We analyze correctness of implementations of the snapshot data structure in terms of linearizability. We show that such implementations can be verified in polynomial time. Additionally, we identify a set of representative executions for testing and show that the correctness of each of these executions can be validated in linear time. These results present a significant speedup considering that verifying linearizability of implementations of concurrent data structures, in general, is EXPSPACE-complete in the number of program-states, and testing linearizability is NP-complete in the length of the tested execution. The crux of our approach is identifying a class of executions, which we call simple, such that a snapshot implementation is linearizable if and only if all of its simple executions are linearizable. We then divide all possible non-linearizable simple executions into three categories and construct a small automaton that recognizes each category. We describe two implementations (one for verification and one for testing) of an automata-based approach that we develop based on this result and an evaluation that demonstrates significant improvements over existing tools. For verification, we show that restricting a state-of-the-art tool to analyzing only simple executions saves resources and allows the analysis of more complex cases. Specifically, restricting attention to simple executions finds bugs in 27 instances, whereas, without this restriction, we were only able to find 14 of the 30 bugs in the instances we examined. We also show that our technique accelerates testing performance significantly. Specifically, our implementation solves the complete set of 900 problems we generated, whereas the state-of-the-art linearizability testing tool solves only 554 problems.

Cite as

Gal Amram, Avi Hayoun, Lior Mizrahi, and Gera Weiss. Polynomial-Time Verification and Testing of Implementations of the Snapshot Data Structure. In 36th International Symposium on Distributed Computing (DISC 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 246, pp. 5:1-5:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)


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@InProceedings{amram_et_al:LIPIcs.DISC.2022.5,
  author =	{Amram, Gal and Hayoun, Avi and Mizrahi, Lior and Weiss, Gera},
  title =	{{Polynomial-Time Verification and Testing of Implementations of the Snapshot Data Structure}},
  booktitle =	{36th International Symposium on Distributed Computing (DISC 2022)},
  pages =	{5:1--5:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-255-6},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{246},
  editor =	{Scheideler, Christian},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DISC.2022.5},
  URN =		{urn:nbn:de:0030-drops-171964},
  doi =		{10.4230/LIPIcs.DISC.2022.5},
  annote =	{Keywords: Snapshot, Linearizability, Verification, Formal Methods}
}
Document
Track A: Algorithms, Complexity and Games
The Decision Problem for Perfect Matchings in Dense Hypergraphs

Authors: Luyining Gan and Jie Han

Published in: LIPIcs, Volume 229, 49th International Colloquium on Automata, Languages, and Programming (ICALP 2022)


Abstract
Given 1 ≤ 𝓁 < k and δ ≥ 0, let PM(k,𝓁,δ) be the decision problem for the existence of perfect matchings in n-vertex k-uniform hypergraphs with minimum 𝓁-degree at least δ binom(n-𝓁,k-𝓁). For k ≥ 3, the decision problem in general k-uniform hypergraphs, equivalently PM(k,𝓁,0), is one of Karp’s 21 NP-complete problems. Moreover, for k ≥ 3, a reduction of Szymańska showed that PM(k, 𝓁, δ) is NP-complete for δ < 1-(1-1/k)^{k-𝓁}. A breakthrough by Keevash, Knox and Mycroft [STOC '13] resolved this problem for 𝓁 = k-1 by showing that PM(k, k-1, δ) is in P for δ > 1/k. Based on their result for 𝓁 = k-1, Keevash, Knox and Mycroft conjectured that PM(k, 𝓁, δ) is in P for every δ > 1-(1-1/k)^{k-𝓁}. In this paper it is shown that this decision problem for perfect matchings can be reduced to the study of the minimum 𝓁-degree condition forcing the existence of fractional perfect matchings. That is, we hopefully solve the "computational complexity" aspect of the problem by reducing it to a well-known extremal problem in hypergraph theory. In particular, together with existing results on fractional perfect matchings, this solves the conjecture of Keevash, Knox and Mycroft for 𝓁 ≥ 0.4k.

Cite as

Luyining Gan and Jie Han. The Decision Problem for Perfect Matchings in Dense Hypergraphs. In 49th International Colloquium on Automata, Languages, and Programming (ICALP 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 229, pp. 64:1-64:16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2022)


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@InProceedings{gan_et_al:LIPIcs.ICALP.2022.64,
  author =	{Gan, Luyining and Han, Jie},
  title =	{{The Decision Problem for Perfect Matchings in Dense Hypergraphs}},
  booktitle =	{49th International Colloquium on Automata, Languages, and Programming (ICALP 2022)},
  pages =	{64:1--64:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-235-8},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{229},
  editor =	{Boja\'{n}czyk, Miko{\l}aj and Merelli, Emanuela and Woodruff, David P.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2022.64},
  URN =		{urn:nbn:de:0030-drops-164057},
  doi =		{10.4230/LIPIcs.ICALP.2022.64},
  annote =	{Keywords: Computational Complexity, Perfect Matching, Hypergraph}
}
Document
Short Paper
Representation of Interdependencies Between Urban Networks by a Multi-Layer Graph (Short Paper)

Authors: Laura Pinson, Géraldine Del Mondo, and Pierrick Tranouez

Published in: LIPIcs, Volume 142, 14th International Conference on Spatial Information Theory (COSIT 2019)


Abstract
The RGC4 (Urban resilience and Crisis Management in a Context of Slow Flood to Slow Kinetics) project aims to develop tools to help manage critical technical networks as part of the management process of crisis in a context of slow kinetic flooding in Paris. This project focuses on cascading models to identify a number of inter-dependencies between networks and to define tools capable of coordinating the actions of managers before and during the crisis. This paper revisits the conceptual and methodological bases of networks approach to study the inter-dependencies between networks. Research that studies the return to service of infrastructure networks often angle it from the perspective of operational research. The article proposes a graph theory perspective based on a multi-layer network approach and shows how to characterize the inter-dependencies between networks at three process levels (macro, meso, micro)

Cite as

Laura Pinson, Géraldine Del Mondo, and Pierrick Tranouez. Representation of Interdependencies Between Urban Networks by a Multi-Layer Graph (Short Paper). In 14th International Conference on Spatial Information Theory (COSIT 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 142, pp. 4:1-4:8, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{pinson_et_al:LIPIcs.COSIT.2019.4,
  author =	{Pinson, Laura and Del Mondo, G\'{e}raldine and Tranouez, Pierrick},
  title =	{{Representation of Interdependencies Between Urban Networks by a Multi-Layer Graph}},
  booktitle =	{14th International Conference on Spatial Information Theory (COSIT 2019)},
  pages =	{4:1--4:8},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-115-3},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{142},
  editor =	{Timpf, Sabine and Schlieder, Christoph and Kattenbeck, Markus and Ludwig, Bernd and Stewart, Kathleen},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.COSIT.2019.4},
  URN =		{urn:nbn:de:0030-drops-110962},
  doi =		{10.4230/LIPIcs.COSIT.2019.4},
  annote =	{Keywords: graph theory, multi-layer network, inter-dependencies, urban networks, urban resilience}
}
Document
Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem

Authors: Yutong Qiu, Cong Ma, Han Xie, and Carl Kingsford

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


Abstract
Transcriptomic structural variants (TSVs) - large-scale transcriptome sequence change due to structural variation - are common, especially in cancer. Detecting TSVs is a challenging computational problem. Sample heterogeneity (including differences between alleles in diploid organisms) is a critical confounding factor when identifying TSVs. To improve TSV detection in heterogeneous RNA-seq samples, we introduce the Multiple Compatible Arrangement Problem (MCAP), which seeks k genome rearrangements to maximize the number of reads that are concordant with at least one rearrangement. This directly models the situation of a heterogeneous or diploid sample. We prove that MCAP is NP-hard and provide a 1/4-approximation algorithm for k=1 and a 3/4-approximation algorithm for the diploid case (k=2) assuming an oracle for k=1. Combining these, we obtain a 3/16-approximation algorithm for MCAP when k=2 (without an oracle). We also present an integer linear programming formulation for general k. We characterize the graph structures that require k>1 to satisfy all edges and show such structures are prevalent in cancer samples. We evaluate our algorithms on 381 TCGA samples and 2 cancer cell lines and show improved performance compared to the state-of-the-art TSV-calling tool, SQUID.

Cite as

Yutong Qiu, Cong Ma, Han Xie, and Carl Kingsford. Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 18:1-18:5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


Copy BibTex To Clipboard

@InProceedings{qiu_et_al:LIPIcs.WABI.2019.18,
  author =	{Qiu, Yutong and Ma, Cong and Xie, Han and Kingsford, Carl},
  title =	{{Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem}},
  booktitle =	{19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
  pages =	{18:1--18:5},
  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.2019.18},
  URN =		{urn:nbn:de:0030-drops-110483},
  doi =		{10.4230/LIPIcs.WABI.2019.18},
  annote =	{Keywords: transcriptomic structural variation, integer linear programming, heterogeneity}
}
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