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Trace reconstruction with exp(O(n1/3)) samples

Published: 19 June 2017 Publication History

Abstract

In the trace reconstruction problem, an unknown bit string x ∈ {0,1}n is observed through the deletion channel, which deletes each bit of x with some constant probability q, yielding a contracted string x. How many independent copies of x are needed to reconstruct x with high probability? Prior to this work, the best upper bound, due to Holenstein, Mitzenmacher, Panigrahy, and Wieder (2008), was exp(O(n1/2)). We improve this bound to exp(O(n1/3)) using statistics of individual bits in the output and show that this bound is sharp in the restricted model where this is the only information used. Our method, that uses elementary complex analysis, can also handle insertions. Similar results were obtained independently and simultaneously by Anindya De, Ryan O'Donnell and Rocco Servedio.

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MP4 File (d4_sb_t3.mp4)

References

[1]
Tugkan Batu, Sampath Kannan, Sanjeev Khanna, and Andrew McGregor. 2004. Reconstructing strings from random traces. In Proceedings of the Fifteenth Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). Society for Industrial and Applied Mathematics, 910–918. P. Borwein and T. Erdélyi. 1997. Littlewood-type problems on subarcs of the unit circle. Indiana Univ. Math. J. 46, 4 (1997), 1323–1346.
[2]
Littlewood-type problems on {0, 1}. Proc. London Math. Soc. (3) 79, 1 (1999), 22–46.
[3]
Optimal mean-based algorithms for trace reconstruction. In STOC’17—Proceedings of the 2017 ACM Symposium on Theory of Computing. ACM, New York. Wassily Hoeffding. 1963. Probability inequalities for sums of bounded random variables. J. Amer. Statist. Assoc. 58 (1963), 13–30. Thomas Holenstein, Michael Mitzenmacher, Rina Panigrahy, and Udi Wieder. 2008.

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    cover image ACM Conferences
    STOC 2017: Proceedings of the 49th Annual ACM SIGACT Symposium on Theory of Computing
    June 2017
    1268 pages
    ISBN:9781450345286
    DOI:10.1145/3055399
    Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than the author(s) must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected].

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    Publication History

    Published: 19 June 2017

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    Author Tags

    1. Deletion channel
    2. Generating function
    3. Littlewood polynomial
    4. Reconstruction
    5. Sample complexity

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    STOC '17: Symposium on Theory of Computing
    June 19 - 23, 2017
    Montreal, Canada

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    Overall Acceptance Rate 1,469 of 4,586 submissions, 32%

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    Cited By

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    • (2025)Scalable and robust DNA-based storage via coding theory and deep learningNature Machine Intelligence10.1038/s42256-025-01003-zOnline publication date: 21-Feb-2025
    • (2024)Substring Density Estimation From TracesIEEE Transactions on Information Theory10.1109/TIT.2024.341837770:8(5782-5798)Online publication date: 1-Aug-2024
    • (2024)DNA-Based Data Storage Systems: A Review of Implementations and Code ConstructionsIEEE Transactions on Communications10.1109/TCOMM.2024.336774872:7(3803-3828)Online publication date: Jul-2024
    • (2024)Graph Reconstruction from Noisy Random Subgraphs2024 IEEE International Symposium on Information Theory (ISIT)10.1109/ISIT57864.2024.10619491(3462-3467)Online publication date: 7-Jul-2024
    • (2024)On $k$-Mer-Based and Maximum Likelihood Estimation Algorithms for Trace Reconstruction2024 IEEE International Symposium on Information Theory (ISIT)10.1109/ISIT57864.2024.10619392(879-884)Online publication date: 7-Jul-2024
    • (2024)An Instance-Based Approach to the Trace Reconstruction Problem2024 58th Annual Conference on Information Sciences and Systems (CISS)10.1109/CISS59072.2024.10480213(1-6)Online publication date: 13-Mar-2024
    • (2024)Reconstruction algorithms for DNA-storage systemsScientific Reports10.1038/s41598-024-51730-314:1Online publication date: 23-Jan-2024
    • (2023)Optimal Codes Detecting Deletions in Concatenated Binary Strings Applied to Trace ReconstructionIEEE Transactions on Information Theory10.1109/TIT.2023.326928969:9(5687-5700)Online publication date: Sep-2023
    • (2023)Substring Density Estimation from Traces2023 IEEE International Symposium on Information Theory (ISIT)10.1109/ISIT54713.2023.10206758(803-808)Online publication date: 25-Jun-2023
    • (2022)Polynomial-time trace reconstruction in the smoothed complexity modelACM Transactions on Algorithms10.1145/3560819Online publication date: 31-Aug-2022
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