Related papers: Insertion and Deletion Correction in Polymer-based…
The ability to store data in the DNA of a living organism has applications in a variety of areas including synthetic biology and watermarking of patented genetically-modified organisms. Data stored in this medium is subject to errors…
Synthetic sequence-controlled polymers promise to transform polymer science by combining the chemical versatility of synthetic polymers with the precise sequence-mediated functionality of biological proteins. However, design of these…
Regenerating codes are efficient methods for distributed storage in storage networks, where node failures are common. They guarantee low cost data reconstruction and repair through accessing only a predefined number of arbitrarily chosen…
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…
We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…
DNA Data storage has recently attracted much attention due to its durable preservation and extremely high information density (bits per gram) properties. In this work, we propose a hybrid coding strategy comprising of generalized…
Synthetic polymers are versatile and widely used materials. Similar to small organic molecules, a large chemical space of such materials is hypothetically accessible. Computational property prediction and virtual screening can accelerate…
Reconstruction codes are generalizations of error-correcting codes that can correct errors by a given number of noisy reads. The study of such codes was initiated by Levenshtein in 2001 and developed recently due to applications in modern…
Consider two or more strings $\mathbf{x}^1,\mathbf{x}^2,\ldots,$ that are concatenated to form $\mathbf{x}=\langle \mathbf{x}^1,\mathbf{x}^2,\ldots \rangle$. Suppose that up to $\delta$ deletions occur in each of the concatenated strings.…
Distributed storage systems with replication are well known for storing large amount of data. A large number of replication is done in order to provide reliability. This makes the system expensive. Various methods have been proposed over…
In the \emph{trace reconstruction problem}, an unknown source string $x \in \{0,1\}^n$ is sent through a probabilistic \emph{deletion channel} which independently deletes each bit with probability $\delta$ and concatenates the surviving…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (i.e. rarely accessed), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
We propose coding techniques that limit the length of homopolymers runs, ensure the GC-content constraint, and are capable of correcting a single edit error in strands of nucleotides in DNA-based data storage systems. In particular, for…
In this review paper, we delve into the nascent field of molecular data storage, focusing on system implementations and code constructions. We start by providing an overview of basic concepts in synthetic and computational biology.…
Recent work has demonstrated that using a carefully designed sensing matrix rather than a random one, can improve the performance of compressed sensing. In particular, a well-designed sensing matrix can reduce the coherence between the…
With the surge of the powerful quantum computer, lattice-based cryptography proliferated the latest cryptography hardware implementation due to its resistance against quantum computers. Among the computational blocks of lattice-based…
Large-alphabet strings are common in scenarios such as information retrieval and natural-language processing. The efficient storage and processing of such strings usually introduces several challenges that are not witnessed in…
Modern FFT/NTT analytics, coded computation, and privacy-preserving ML interface routinely move polynomial frames across NICs, storage, and accelerators. However, even rare silent data corruption (SDC) can flip a few ring coefficients and…
A covering code is a set of codewords with the property that the union of balls, suitably defined, around these codewords covers an entire space. Generally, the goal is to find the covering code with the minimum size codebook. While most…
In this paper, we investigate binary reconstruction codes capable of correcting one deletion and one substitution. We define the \emph{single-deletion single-substitution ball} function $ \mathcal{B} $ as a mapping from a sequence to the…