Related papers: Incorporating indel channels into average-case ana…
We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…
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…
Nanopore sequencers are emerging as promising new platforms for high-throughput sequencing. As with other technologies, sequencer errors pose a major challenge for their effective use. In this paper, we present a novel information theoretic…
In the (deletion-channel) trace reconstruction problem, there is an unknown $n$-bit source string $x$. An algorithm is given access to independent traces of $x$, where a trace is formed by deleting each bit of~$x$ independently with…
We consider the following model for sampling pairs of strings: $s_1$ is a uniformly random bitstring of length $n$, and $s_2$ is the bitstring arrived at by applying substitutions, insertions, and deletions to each bit of $s_1$ with some…
Insertion-deletion codes (insdel codes for short) are used for correcting synchronization errors in communications, and in other many interesting fields such as DNA storage, date analysis, race-track memory error correction and language…
This paper considers a binary channel with deletions and insertions, where each input bit is transformed in one of the following ways: it is deleted with probability d, or an extra bit is added after it with probability i, or it is…
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…
This work continues the study of linear error correcting codes against adversarial insertion deletion errors (insdel errors). Previously, the work of Cheng, Guruswami, Haeupler, and Li \cite{CGHL21} showed the existence of asymptotically…
We introduce the following natural generalization of trace reconstruction, parameterized by a deletion probability $\delta \in (0,1)$ and length $n$: There is a length $n$ string of probabilities, $S=p_1,\ldots,p_n,$ and each "trace" is…
In this paper, we consider the Levenshtein's sequence reconstruction problem in the case where the transmitted codeword is chosen from $\{0,1\}^n$ and the channel can delete up to $t$ symbols from the transmitted codeword. We determine the…
The sequence reconstruction problem for insertion/deletion channels has attracted significant attention owing to their applications recently in some emerging data storage systems, such as racetrack memories, DNA-based data storage. Our goal…
The deletion channel takes as input a bit string $\mathbf{x} \in \{0,1\}^n$, and deletes each bit independently with probability $q$, yielding a shorter string. The trace reconstruction problem is to recover an unknown string $\mathbf{x}$…
Although the expenses associated with DNA sequencing have been rapidly decreasing, the current cost of sequencing information stands at roughly $120/GB, which is dramatically more expensive than reading from existing archival storage…
The well-known trace reconstruction problem is the problem of inferring an unknown source string $x \in \{0,1\}^n$ from independent "traces", i.e. copies of $x$ that have been corrupted by a $\delta$-deletion channel which independently…
We consider an \emph{approximate} version of the trace reconstruction problem, where the goal is to recover an unknown string $s\in\{0,1\}^n$ from $m$ traces (each trace is generated independently by passing $s$ through a probabilistic…
Randomised algorithms often employ methods that can fail and that are retried with independent randomness until they succeed. Randomised data structures therefore often store indices of successful attempts, called seeds. If $n$ such seeds…
Several recent works have considered the \emph{trace reconstruction problem}, in which an unknown source string $x\in\{0,1\}^n$ is transmitted through a probabilistic channel which may randomly delete coordinates or insert random bits,…
We study realizable continual linear regression under random task orderings, a common setting for developing continual learning theory. In this setup, the worst-case expected loss after $k$ learning iterations admits a lower bound of…
This paper tackles two problems that fall under the study of coding for insertions and deletions. These problems are motivated by several applications, among them is reconstructing strands in DNA-based storage systems. Under this paradigm,…