Related papers: The DNA Coverage Depth Problem: Duality, Weight Di…

In [1], the authors proposed a new model of DNA storage system that integrates all three steps of retrieval and introduced the concept of DNA-correcting codes, which guarantees that the output of the storage system can be decoded to the…

We describe properties and constructions of constraint-based codes for DNA-based data storage which account for the maximum repetition length and AT/GC balance. We present algorithms for computing the number of sequences with maximum…

Due to its high data density and longevity, DNA is considered a promising medium for satisfying ever-increasing data storage needs. However, the diversity of errors that occur in DNA sequences makes efficient error-correction a challenging…

Due to their sequential nature, traditional DNA synthesis methods are expensive in terms of time and resources. They also fabricate multiple copies of the same strand, introducing redundancy. This redundancy can be leveraged to enhance the…

Because of its high data density and longevity, DNA is emerging as a promising candidate for satisfying increasing data storage needs. Compared to conventional storage media, however, data stored in DNA is subject to a wider range of errors…

We consider error-correcting coding for deoxyribonucleic acid (DNA)-based storage using nanopore sequencing. We model the DNA storage channel as a sampling noise channel where the input data is chunked into $M$ short DNA strands, which are…

Data compression is a well-studied (and well-solved) problem in the setup of long coding blocks. But important emerging applications need to compress data to memory words of small fixed widths. This new setup is the subject of this paper.…

Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in arXiv:1203.6233, is what read length and coverage depth…

We present a finite blocklength performance bound for a DNA storage channel with insertions, deletions, and substitutions. The considered bound -- the dependency testing (DT) bound, introduced by Polyanskiy et al. in 2010 -- provides an…

A main puzzle of deep neural networks (DNNs) revolves around the apparent absence of "overfitting", defined in this paper as follows: the expected error does not get worse when increasing the number of neurons or of iterations of gradient…

We study the problem of coded information retrieval for block-structured data, motivated by DNA-based storage systems where a database is partitioned into multiple files that must each be recoverable as an atomic unit. We initiate and…

We study a weighted generalization of the fractional cut-covering problem, which we relate to the maximum cut problem via antiblocker and gauge duality. This relationship allows us to introduce a semidefinite programming (SDP) relaxation…

This paper introduces a new solution to DNA storage that integrates all three steps of retrieval, namely clustering, reconstruction, and error correction. DNA-correcting codes are presented as a unique solution to the problem of ensuring…

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…

The optimizations of both memory depth and kernel functions are critical for wideband digital pre-distortion (DPD). However, the memory depth is usually determined via exhaustive search over a wide range for the sake of linearization…

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…

Motivated by DNA data storage, we study the expected number of coded symbols drawn from a linear code until a desired information symbol can be decoded - the random access expectation. We focus on generator matrices with a type of symmetry,…

DNA-based storage offers unprecedented density and durability, but its scalability is fundamentally limited by the efficiency of parallel strand synthesis. Existing methods either allow unconstrained nucleotide additions to individual…

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…

DNA is an attractive candidate for data storage. Its millennial durability and nanometer scale offer exceptional data density and longevity. Its relevance to medical applications also drives advances in DNA-related biotechnology. To protect…