Exact Reconstruction From Insertions in Synchronization Codes

DOI10.1109/TIT.2017.2649493zbMATH Open1366.94453arXiv1604.03000OpenAlexW2963712885MaRDI QIDQ5280904FDOQ5280904

Authors: Frederic Sala, Ryan Gabrys, Clayton Schoeny, Lara Dolecek 

Publication date: 27 July 2017

Published in: IEEE Transactions on Information Theory (Search for Journal in Brave)

Abstract: This work studies problems in data reconstruction, an important area with numerous applications. In particular, we examine the reconstruction of binary and non-binary sequences from synchronization (insertion/deletion-correcting) codes. These sequences have been corrupted by a fixed number of symbol insertions (larger than the minimum edit distance of the code), yielding a number of distinct traces to be used for reconstruction. We wish to know the minimum number of traces needed for exact reconstruction. This is a general version of a problem tackled by Levenshtein for uncoded sequences. We introduce an exact formula for the maximum number of common supersequences shared by sequences at a certain edit distance, yielding an upper bound on the number of distinct traces necessary to guarantee exact reconstruction. Without specific knowledge of the codewords, this upper bound is tight. We apply our results to the famous single deletion/insertion-correcting Varshamov-Tenengolts (VT) codes and show that a significant number of VT codeword pairs achieve the worst-case number of outputs needed for exact reconstruction. We also consider extensions to other channels, such as adversarial deletion and insertion/deletion channels and probabilistic channels.

Full work available at URL: https://arxiv.org/abs/1604.03000

Mathematics Subject Classification ID

Shift register sequences and sequences over finite alphabets in information and communication theory (94A55)

Cited In (5)

• Balanced reconstruction codes for single edits
• Reconstruction of permutations distorted by single Kendall \(\tau\)-errors
• New dimension-independent upper bounds on linear insdel codes
• Sequence reconstruction problem for deletion channels: a complete asymptotic solution
• Information-Theoretic Foundations of DNA Data Storage

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