Related papers: Exact Reconstruction from Insertions in Synchroniz…
Trace reconstruction considers the task of recovering an unknown string $x \in \{0,1\}^n$ given a number of independent "traces", i.e., subsequences of $x$ obtained by randomly and independently deleting every symbol of $x$ with some…
This paper studies \emph{linear} and \emph{affine} error-correcting codes for correcting synchronization errors such as insertions and deletions. We call such codes linear/affine insdel codes. Linear codes that can correct even a single…
Erasure coding techniques are used to increase the reliability of distributed storage systems while minimizing storage overhead. Also of interest is minimization of the bandwidth required to repair the system following a node failure. In a…
A single deletion error correcting code (SDECC) is a set of fixed-length sequences consisting of two types of symbols, 0 and 1, such that the original sequence can be recovered for at most one deletion error. The upper bound for the size of…
We introduce synchronization strings as a novel way of efficiently dealing with synchronization errors, i.e., insertions and deletions. Synchronization errors are strictly more general and much harder to deal with than commonly considered…
The problem of reconstructing strings from their substring spectra has a long history and in its most simple incarnation asks for determining under which conditions the spectrum uniquely determines the string. We study the problem of coded…
The {\em insertion-deletion channel} takes as input a binary string $x \in\{0, 1\}^n$, and outputs a string $\widetilde{x}$ where some of the bits have been deleted and others inserted independently at random. In the {\em trace…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
Data synchronization is a fundamental problem with applications in diverse fields such as cloud storage, genomics, and distributed systems. This paper addresses the challenge of synchronizing two files, one of which is a subsequence of the…
A new class of exact-repair regenerating codes is constructed by stitching together shorter erasure correction codes, where the stitching pattern can be viewed as block designs. The proposed codes have the "help-by-transfer" property where…
The minimum distance graph of a code has the codewords as vertices and edges exactly when the Hamming distance between two codewords equals the minimum distance of the code. A constructive proof for reconstructibility of an extended perfect…
Motivated by applications in in-vivo DNA storage, we study codes for correcting duplications. A reverse-complement duplication of length $k$ is the insertion of the reversed and complemented copy of a substring of length $k$ adjacent to its…
We examine an error-correcting coding framework in which each coded symbol is constrained to be a function of a fixed subset of the message symbols. With an eye toward distributed storage applications, we seek to design systematic codes…
In this paper, we investigate binary reconstruction codes capable of correcting one deletion and one substitution. We define the \emph{single-deletion single-substitution ball} function $ \mathcal{B} $ as a mapping from a sequence to the…
Trace reconstruction is the problem of learning an unknown string $x$ from independent traces of $x$, where traces are generated by independently deleting each bit of $x$ with some deletion probability $q$. In this paper, we initiate the…
In this paper, we investigate the problem of designing $(n, N; \mathcal{B})$-reconstruction codes for $N\in \{14,11,9,5\}$, where $\mathcal{B}$ is the single-deletion single-substitution ball function that maps a sequence to the set of all…
The sequence reconstruction problem, introduced by Levenshtein in 2001, considers a communication setting in which a sender transmits a codeword and the receiver observes K independent noisy versions of this codeword. In this work, we study…
The problem of reconstructing a sequence from the set of its length-$k$ substrings has received considerable attention due to its various applications in genomics. We study an uncoded version of this problem where multiple random sources…
Recent experiments have demonstrated the feasibility of storing digital information in macromolecules such as DNA and protein. However, the DNA storage channel is prone to errors such as deletions, insertions, and substitutions. During the…
Mean-based reconstruction is a fundamental, natural approach to worst-case trace reconstruction over channels with synchronization errors. It is known that $\exp(O(n^{1/3}))$ traces are necessary and sufficient for mean-based worst-case…