Related papers: Channels with Input-Correlated Synchronization Err…
Channels with synchronization errors, such as deletion and insertion errors, are crucial in DNA storage, data reconstruction, and other applications. These errors introduce memory to the channel, complicating its capacity analysis. This…
Particularly motivated by DNA storage channels, we consider channels with synchronization errors modeled as insertions and deletions, along with substitutions. We focus on the case where the synchronization error process has memory and…
Synchronization channels, such as the well-known deletion channel, are surprisingly harder to analyze than memoryless channels, and they are a source of many fundamental problems in information theory and theoretical computer science. One…
In this paper, we study achievable rates of concatenated coding schemes over a deoxyribonucleic acid (DNA) storage channel. Our channel model incorporates the main features of DNA-based data storage. First, information is stored on many,…
We consider error-correcting coding for DNA-based storage. We model the DNA storage channel as a multi-draw IDS channel where the input data is chunked into $M$ short DNA strands, which are copied a random number of times, and the channel…
This paper is concerned with the problem of error-free communication over the i.i.d. duplication channel which acts on a transmitted sequence $ x_1 \cdots x_n $ by inserting a random number of copies of each symbol $ x_i $ next to the…
We present many new results related to reliable (interactive) communication over insertion-deletion channels. Synchronization errors, such as insertions and deletions, strictly generalize the usual symbol corruption errors and are much…
We propose a new channel model for channels with synchronization errors. Using this model, we give simple, non-trivial and, in some cases, tight lower bounds on the capacity for certain synchronization error channels.
In this paper, we consider the outer channel for DNA-based data storage. When transmitting over the outer channel, each DNA string is treated as a unit/symbol that would be either correctly received, or erased, or corrupted by uniformly…
DNA storage has emerged as a promising solution for large-scale and long-term data preservation. Among various error types, insertions are the most frequent errors occurring in DNA sequences, where the inserted symbol is often identical or…
Channels with synchronization errors, exhibiting deletion and insertion errors, find practical applications in DNA storage, data reconstruction, and various other domains. Presence of insertions and deletions render the channel with memory,…
Owing to its longevity and enormous information density, DNA, the molecule encoding biological information, has emerged as a promising archival storage medium. However, due to technological constraints, data can only be written onto many…
Due to the redundant nature of DNA synthesis and sequencing technologies, a basic model for a DNA storage system is a multi-draw "shuffling-sampling" channel. In this model, a random number of noisy copies of each sequence is observed at…
In most studies of the channel capacity of quantum channels, it is assumed that the errors in each use of the channel are independent. However, recent work has begun to investigate the effects of memory or correlations in the error. This…
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…
We study the amount of reliable information that can be stored in a DNA-based storage system with noisy sequencing, where each codeword is composed of short DNA molecules. We analyze a concatenated coding scheme, where the outer code is…
We consider a new formulation of a class of synchronization error channels and derive analytical bounds and numerical estimates for the capacity of these channels. For the binary channel with only deletions, we obtain an expression for the…
We develop several lower bounds on the capacity of binary input symmetric output channels with synchronization errors which also suffer from other types of impairments such as substitutions, erasures, additive white Gaussian noise (AWGN)…
We consider binary input deletion/substitution channels, which model certain types of synchronization errors encountered in practice. Specifically, we focus on the regime of small deletion and substitution probabilities, and by extending an…
We consider the problem of coding for the substring channel, in which information strings are observed only through their (multisets of) substrings. Due to existing DNA sequencing techniques and applications in DNA-based storage systems,…