Related papers: Coding for Polymer-Based Data Storage
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…
We consider the problem of binary string reconstruction from the multiset of its substring compositions, i.e., referred to as the substring composition multiset, first introduced and studied by Acharya et al. We introduce a new algorithm…
A general class of polynomial remainder codes is considered. Such codes are very flexible in rate and length and include Reed-Solomon codes as a special case. As an extension of previous work, two joint error-and-erasure decoding approaches…
This dissertation considers new constructions and decoding approaches for error-correcting codes based on non-conventional polynomials, with the objective of providing new coding solutions to the applications mentioned above. With skew…
In the trace reconstruction problem, one seeks to reconstruct a binary string $s$ from a collection of traces, each of which is obtained by passing $s$ through a deletion channel. It is known that $\exp(\tilde O(n^{1/5}))$ traces suffice to…
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.…
Peer-to-peer distributed storage systems provide reliable access to data through redundancy spread over nodes across the Internet. A key goal is to minimize the amount of bandwidth used to maintain that redundancy. Storing a file using an…
Constrained coding plays a key role in optimizing performance and mitigating errors in applications such as storage and communication, where specific constraints on codewords are required. While non-parametric constraints have been…
We present a novel technique for encoding and decoding constant weight binary codes that uses a geometric interpretation of the codebook. Our technique is based on embedding the codebook in a Euclidean space of dimension equal to the weight…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
A new class of exact-repair regenerating codes is constructed by combining two layers of erasure correction codes together with combinatorial block designs, e.g., Steiner systems, balanced incomplete block designs and t-designs. The…
The demand for innovative synthetic polymers with improved properties is high, but their structural complexity and vast design space hinder rapid discovery. Machine learning-guided molecular design is a promising approach to accelerate…
DNA has emerged as a promising alternative for long-term data storage due to its high capacity, durability, and low-energy potential. However, storing data in DNA presents several challenges. First, it requires complex and costly…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
Data storage in DNA is developing as a possible solution for archival digital data. Recently, to further increase the potential capacity of DNA-based data storage systems, the combinatorial composite DNA synthesis method was suggested. This…
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…
Based on unique decoding of the polynomial residue code with non-pairwise coprime moduli, a polynomial with degree less than that of the least common multiple (lcm) of all the moduli can be accurately reconstructed when the number of…
Reconstructing continuous signals from a small number of discrete samples is a fundamental problem across science and engineering. In practice, we are often interested in signals with 'simple' Fourier structure, such as bandlimited,…
A new family of codes, called clustering-correcting codes, is presented in this paper. This family of codes is motivated by the special structure of data that is stored in DNA-based storage systems. The data stored in these systems has the…