arXiv subjects

Avital Boruchovsky

Publications and source records attributed to Avital Boruchovsky.

6 recordsLinked to original sources

arXiv2026

Serving Every Symbol: All-Symbol PIR and Batch Codes

A $t$-all-symbol PIR code and a $t$-all-symbol batch code of dimension $k$ consist of $n$ servers storing linear combinations of $k$ information symbols with the following recovery property: any symbol stored by a server can be recovered from $t$ pairwise disjoint subsets of servers. In the batch setting, we further require that any multiset of size $t$ of stored symbols can be recovered from~$t$ disjoint subsets of servers. This framework unifies and extends several well-known code families, including one-step majority-logic decodable codes, (functional) PIR codes, and (functional) batch codes. In this paper, we determine the minimum code length for some small values of $k$ and $t$, characterize structural properties of codes attaining this optimum, and derive bounds that show the trade-offs between length, dimension, minimum distance, and $t$. In addition, we study MDS codes and the simplex code, demonstrating how these classical families fit within our framework, and establish new cases of an open conjecture from \cite{YAAKOBI2020} concerning the minimal $t$ for which the simplex code is a $t$-functional batch code.

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arXiv2025

Making it to First: The Random Access Problem in DNA Storage

In this paper, we study the Random Access Problem in DNA storage, which addresses the challenge of retrieving a specific information strand from a DNA-based storage system. In this framework, the data is represented by $k$ information strands which represent the data and are encoded into $n$ strands using a linear code. Then, each sequencing read returns one encoded strand which is chosen uniformly at random. The goal under this paradigm is to design codes that minimize the expected number of reads required to recover an arbitrary information strand. We fully solve the case when $k=2$, showing that the best possible code attains a random access expectation of $1+\frac{2}{\sqrt{2}+1}\approx 0.914\cdot 2$ for $q$ large enough. Moreover, we generalize a construction from~\cite{GMZ24}, specifically to $k=3$, for any value of $k$. Our construction uses $B_{k-1}$ sequences over $\mathbb{Z}_{q-1}$, that always exist over large finite fields. We show that for every $k\geq 4$, this generalized construction outperforms all previous constructions in terms of reducing the random access expectation.

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arXiv2024

On Nearly Perfect Covering Codes

Nearly perfect packing codes are those codes that meet the Johnson upper bound on the size of error-correcting codes. This bound is an improvement to the sphere-packing bound. A related bound for covering codes is known as the van Wee bound. Codes that meet this bound will be called nearly perfect covering codes. In this paper, such codes with covering radius one will be considered. It will be proved that these codes can be partitioned into three families depending on the smallest distance between neighboring codewords. Some of the codes contained in these families will be completely characterized. Other properties of these codes will be considered too. Construction for codes for each such family will be presented, the weight distribution and the distance distribution of codes from these families are characterized. Finally, extended nearly perfect covering code will be considered and unexpected equivalence classes of codes of the three types will be defined based on the extended codes.

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arXiv2024

DNA-Correcting Codes: End-to-end Correction in DNA Storage Systems

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 that the output of the storage system is unique for any valid set of input strands. To this end, we introduce a novel distance metric to capture the unique behavior of the DNA storage system and provide necessary and sufficient conditions for DNA-correcting codes. The paper also includes several bounds and constructions of DNA-correcting codes.

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arXiv2024

Permutation Recovery Problem against Deletion Errors for DNA Data Storage

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 unordered way. To handle the unordered nature of DNA data storage systems, a unique address is typically prepended to each data block to form a DNA strand. However, DNA storage systems are prone to errors and generate multiple noisy copies of each strand called DNA reads. Thus, we study the permutation recovery problem against deletions errors for DNA data storage. The permutation recovery problem for DNA data storage requires one to reconstruct the addresses or in other words to uniquely identify the noisy reads. By successfully reconstructing the addresses, one can essentially determine the correct order of the data blocks, effectively solving the clustering problem. We first show that we can almost surely identify all the noisy reads under certain mild assumptions. We then propose a permutation recovery procedure and analyze its complexity.

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arXiv2023

Data-Driven Bee Identification for DNA Strands

We study a data-driven approach to the bee identification problem for DNA strands. The bee-identification problem, introduced by Tandon et al. (2019), requires one to identify $M$ bees, each tagged by a unique barcode, via a set of $M$ noisy measurements. Later, Chrisnata et al. (2022) extended the model to case where one observes $N$ noisy measurements of each bee, and applied the model to address the unordered nature of DNA storage systems. In such systems, a unique address is typically prepended to each DNA data block to form a DNA strand, but the address may possibly be corrupted. While clustering is usually used to identify the address of a DNA strand, this requires $\mathcal{M}^2$ data comparisons (when $\mathcal{M}$ is the number of reads). In contrast, the approach of Chrisnata et al. (2022) avoids data comparisons completely. In this work, we study an intermediate, data-driven approach to this identification task. For the binary erasure channel, we first show that we can almost surely correctly identify all DNA strands under certain mild assumptions. Then we propose a data-driven pruning procedure and demonstrate that on average the procedure uses only a fraction of $\mathcal{M}^2$ data comparisons. Specifically, for $\mathcal{M}= 2^n$ and erasure probability $p$, the expected number of data comparisons performed by the procedure is $κ\mathcal{M}^2$, where $\left(\frac{1+2p-p^2}{2}\right)^n \leq κ\leq \left(\frac{1+p}{2}\right)^n $.

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