Related papers: Error Exponents for DNA Storage Codes with a Varia…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
Decoding sequences that stem from multiple transmissions of a codeword over an insertion, deletion, and substitution channel is a critical component of efficient deoxyribonucleic acid (DNA) data storage systems. In this paper, we consider a…
This paper presents and analyzes a novel concatenated coding scheme for enabling error resilience in two distributed storage settings: one being storage using existing regenerating codes and the second being storage using locally repairable…
We consider a broadcast channel with a degraded message set, in which a single transmitter sends a common message to two receivers and a private message to one of the receivers only. The main goal of this work is to find new lower bounds to…
We study the amount of reliable information that can be stored in a DNA-based storage system composed of short DNA molecules. In this regime, Shomorony and Heckel (2022) put forward a conjecture on the scaling of the number of information…
We describe a strategy for constructing codes for DNA-based information storage by serial composition of weighted finite-state transducers. The resulting state machines can integrate correction of substitution errors; synchronization by…
We examine regular and irregular repeat-accumulate (RA) codes with repetition degrees which are all even. For these codes and with a particular choice of an interleaver, we give an upper bound on the decoding error probability of a…
As a possible implementation of data storage using DNA, multiple strands of DNA are stored in a liquid container so that, in the future, they can be read by an array of DNA readers in parallel. These readers will sample the strands with…
In this paper, we propose a novel iterative encoding algorithm for DNA storage to satisfy both the GC balance and run-length constraints using a greedy algorithm. DNA strands with run-length more than three and the GC balance ratio far from…
Error and erasure exponents for the broadcast channel with degraded message sets are analyzed. The focus of our error probability analysis is on the main receiver where, nominally, both messages are to be decoded. A two-step decoding…
This work studies the deviations of the error exponent of the constant composition code ensemble around its expectation, known as the error exponent of the typical random code (TRC). In particular, it is shown that the probability of…
Owing to its immense storage density and durability, DNA has emerged as a promising storage medium. However, due to technological constraints, data can only be written onto many short DNA molecules called data blocks that are stored in an…
Motivated by applications in DNA storage, we study a setting in which strings are affected by tandem-duplication errors. In particular, we look at two settings: disjoint tandem-duplication errors, and equal-length tandem-duplication errors.…
A recent study by one of the authors has demonstrated the importance of profile vectors in DNA-based data storage. We provide exact values and lower bounds on the number of profile vectors for finite values of alphabet size $q$, read length…
Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…
Convolutional codes are error-correcting linear codes that utilize shift registers to encode. These codes have an arbitrary block size and they can incorporate both past and current information bits. DNA codes represent DNA sequences and…
We derive various error exponents in the bee identification problem under two different decoding rules. Under na\"ive decoding, which decodes each bee independently of the others, we analyze a general discrete memoryless channel and a…
Algorithms based on multiple decoding attempts of Reed-Solomon (RS) codes have recently attracted new attention. Choosing decoding candidates based on rate-distortion (R-D) theory, as proposed previously by the authors, currently provides…
As DNA data storage moves closer to practical deployment, minimizing sequencing coverage depth is essential to reduce both operational costs and retrieval latency. This paper addresses the recently studied Random Access Problem, which…
We initiate the study of DNA-based distributed storage systems, where information is encoded across multiple DNA data storage containers to achieve robustness against container failures. In this setting, data are distributed over $M$…