Related papers: On the Sequence Reconstruction Problem for the Sin…
Let $\mathcal{B}(\cdot)$ be an error ball function. A set of $q$-ary sequences of length $n$ is referred to as an \emph{$(n,q,N;\mathcal{B})$-reconstruction code} if each sequence $\boldsymbol{x}$ within this set can be uniquely…
Consider a length-$n$ sequence $\bm{x}$ over a $q$-ary alphabet. The \emph{fixed-length Levenshtein ball} $\mathcal{L}_t(\bm{x})$ of radius $t$ encompasses all length-$n$ $q$-ary sequences that can be derived from $\bm{x}$ by performing $t$…
We study segmented burst-deletion channels motivated by the observation that synchronization errors commonly occur in a bursty manner in real-world settings. In this channel model, transmitted sequences are implicitly divided into…
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…
List decoding of insertions and deletions in the Levenshtein metric is considered. The Levenshtein distance between two sequences is the minimum number of insertions and deletions needed to turn one of the sequences into the other. In this…
The problem of storing large amounts of information safely for a long period of time has become essential. One of the most promising new data storage mediums are the polymer-based data storage systems, like the DNA-storage system. These…
In the trace reconstruction problem an unknown string ${\bf x}=(x_0,\dots,x_{n-1})\in\{0,1,...,m-1\}^n$ is observed through the deletion channel, which deletes each $x_k$ with a certain probability, yielding a contracted string…
Motivated by mutation processes occurring in in-vivo DNA-storage applications, a channel that mutates stored strings by duplicating substrings as well as substituting symbols is studied. Two models of such a channel are considered: one in…
The ''trace reconstruction'' problem asks, given an unknown binary string $x$ and a channel that repeatedly returns ''traces'' of $x$ with each bit randomly deleted with some probability $p$, how many traces are needed to recover $x$? There…
We consider the problem of designing low-redundancy codes in settings where one must correct deletions in conjunction with substitutions or adjacent transpositions; a combination of errors that is usually observed in DNA-based data storage.…
We develop upper bounds on code size for an independent and identically distributed deletion and insertion channels for a given code length and target frame error probability. The bounds are obtained as a variation of a general converse…
With the emergence of new storage and communication methods, the insertion, deletion, and substitution (IDS) channel has attracted considerable attention. However, many topics on the IDS channel and the associated Levenshtein distance…
The reconstruction problem for permutations on $n$ elements from their erroneous patterns which are distorted by transpositions is presented in this paper. It is shown that for any $n \geq 3$ an unknown permutation is uniquely…
We study the problem of reconstructing an unknown point in $\mathbb{R}^d$ from approximate linear queries. This setting arises naturally in applications ranging from low-dimensional remote sensing and signal recovery to high-dimensional…
We study error-correcting codes in the space $\mathcal{S}_{n,q}$ of length-$n$ multisets over a $q$-ary alphabet under the deletion metric, motivated by permutation channels in which ordering is completely lost and errors act only on symbol…
In the trace reconstruction problem, one seeks to reconstruct a binary string $s$ from a collection of traces, each of which is obtained by passing $s$ through a deletion channel. It is known that $\exp(\tilde O(n^{1/5}))$ traces suffice to…
The process of DNA-based data storage (DNA storage for short) can be mathematically modelled as a communication channel, termed DNA storage channel, whose inputs and outputs are sets of unordered sequences. To design error correcting codes…
In the standard trace reconstruction problem, the goal is to \emph{exactly} reconstruct an unknown source string $\mathsf{x} \in \{0,1\}^n$ from independent "traces", which are copies of $\mathsf{x}$ that have been corrupted by a…
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 the trace reconstruction problem our goal is to learn an unknown string $x\in \{0,1\}^n$ given independent traces of $x$. A trace is obtained by independently deleting each bit of $x$ with some probability $\delta$ and concatenating the…