arXiv subjects

Tuvi Etzion

Publications and source records attributed to Tuvi Etzion.

At least 37 records · Page 2Linked to original sources

arXiv2024

Repairing Reed-Solomon Codes with Side Information

We generalize the problem of recovering a lost/erased symbol in a Reed-Solomon code to the scenario in which some side information about the lost symbol is known. The side information is represented as a set $S$ of linearly independent combinations of the sub-symbols of the lost symbol. When $S = \varnothing$, this reduces to the standard problem of repairing a single codeword symbol. When $S$ is a set of sub-symbols of the erased one, this becomes the repair problem with partially lost/erased symbol. We first establish that the minimum repair bandwidth depends on $|S|$ and not the content of $S$ and construct a lower bound on the repair bandwidth of a linear repair scheme with side information $S$. We then consider the well-known subspace-polynomial repair schemes and show that their repair bandwidths can be optimized by choosing the right subspaces. Finally, we demonstrate several parameter regimes where the optimal bandwidths can be achieved for full-length Reed-Solomon codes.

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arXiv2024

On de Bruijn Covering Sequences and Arrays

An $(m,n,R)$-de Bruijn covering array (dBCA) is a doubly periodic $M \times N$ array over an alphabet of size $q$ such that the set of all its $m \times n$ windows form a covering code with radius $R$. An upper bound of the smallest array area of an $(m,n,R)$-dBCA is provided using a probabilistic technique which is similar to the one that was used for an upper bound on the length of a de Bruijn covering sequence. A folding technique to construct a dBCA from a de Bruijn covering sequence or de Bruijn covering sequences code is presented. Several new constructions that yield shorter de Bruijn covering sequences and $(m,n,R)$-dBCAs with smaller areas are also provided. These constructions are mainly based on sequences derived from cyclic codes, self-dual sequences, primitive polynomials, an interleaving technique, folding, and mutual shifts of sequences with the same covering radius. Finally, constructions of de Bruijn covering sequences codes are also discussed.

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arXiv2024

Repairing with Zero Skip Cost

To measure repair latency at helper nodes, we introduce a new metric called skip cost that quantifies the number of contiguous sections accessed on a disk. We provide explicit constructions of zigzag codes and fractional repetition codes that incur zero skip cost

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arXiv2024

Recovery Sets of Subspaces from a Simplex Code

Recovery sets for vectors and subspaces are important in the construction of distributed storage system codes. These concepts are also interesting in their own right. In this paper, we consider the following very basic recovery question: what is the maximum number of possible pairwise disjoint recovery sets for each recovered element? The recovered elements in this work are d-dimensional subspaces of a $k$-dimensional vector space over GF(q). Each server stores one representative for each distinct one-dimensional subspace of the k-dimensional vector space, or equivalently a distinct point of PG(k-1,q). As column vectors, the associated vectors of the stored one-dimensional subspaces form the generator matrix of the $[(q^k -1)/(q-1),k,q^{k-1}]$ simplex code over GF(q). Lower bounds and upper bounds on the maximum number of such recovery sets are provided. It is shown that generally, these bounds are either tight or very close to being tight.

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arXiv2024

Deep DNA Storage: Scalable and Robust DNA Storage via Coding Theory and Deep Learning

DNA-based storage is an emerging technology that enables digital information to be archived in DNA molecules. This method enjoys major advantages over magnetic and optical storage solutions such as exceptional information density, enhanced data durability, and negligible power consumption to maintain data integrity. To access the data, an information retrieval process is employed, where some of the main bottlenecks are the scalability and accuracy, which have a natural tradeoff between the two. Here we show a modular and holistic approach that combines Deep Neural Networks (DNN) trained on simulated data, Tensor-Product (TP) based Error-Correcting Codes (ECC), and a safety margin mechanism into a single coherent pipeline. We demonstrated our solution on 3.1MB of information using two different sequencing technologies. Our work improves upon the current leading solutions by up to x3200 increase in speed, 40% improvement in accuracy, and offers a code rate of 1.6 bits per base in a high noise regime. In a broader sense, our work shows a viable path to commercial DNA storage solutions hindered by current information retrieval processes.

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arXiv2024

The Capacity of the Weighted Read Channel

One of the primary sequencing methods gaining prominence in DNA storage is nanopore sequencing, attributed to various factors. In this work, we consider a simplified model of the sequencer, characterized as a channel. This channel takes a sequence and processes it using a sliding window of length $\ell$, shifting the window by $δ$ characters each time. The output of this channel, which we refer to as the read vector, is a vector containing the sums of the entries in each of the windows. The capacity of the channel is defined as the maximal information rate of the channel. Previous works have already revealed capacity values for certain parameters $\ell$ and $δ$. In this work, we show that when $δ< \ell < 2δ$, the capacity value is given by $\frac{1}δ\log_2 \frac{1}{2}(\ell+1+ \sqrt{(\ell+1)^2 - 4(\ell - δ)(\ell-δ+1)})$. Additionally, we construct an upper bound when $2δ< \ell$. Finally, we extend the model to the two-dimensional case and present several results on its capacity.

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arXiv2023

Permutations that separate close elements, and rectangle packings in the torus

Let $n$, $s$ and $k$ be positive integers. For distinct $i,j\in\mathbb{Z}_n$, define $||i,j||_n$ to be the distance between $i$ and $j$ when the elements of $\mathbb{Z}_n$ are written in a circle. So \[ ||i,j||_n=\min\{(i-j)\bmod n,(j-i)\bmod n\}. \] A permutation $π:\mathbb{Z}_n\rightarrow\mathbb {Z}_n$ is \emph{$(s,k)$-clash-free} if $||π(i),π(j)||_n\geq k$ whenever $||i,j||_n<s$. So an $(s,k)$-clash-free permutation moves every pair of close elements (at distance less than $s$) to a pair of elements at large distance (at distance at least $k$). The notion of an $(s,k)$-clash-free permutation can be reformulated in terms of certain packings of $s\times k$ rectangles on an $n\times n$ torus. For integers $n$ and $k$ with $1\leq k<n$, let $σ(n,k)$ be the largest value of $s$ such that an $(s,k)$-clash-free permutation of $\mathbb{Z}_n$ exists. Strengthening a recent paper of Blackburn, which proved a conjecture of Mammoliti and Simpson, we determine the value of $σ(n,k)$ in all cases.

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arXiv2023

Coding for IBLTs with Listing Guarantees

The Invertible Bloom Lookup Table (IBLT) is a probabilistic data structure for set representation, with applications in network and traffic monitoring. It is known for its ability to list its elements, an operation that succeeds with high probability for sufficiently large table. However, listing can fail even for relatively small sets. This paper extends recent work on the worst-case analysis of IBLT, which guarantees successful listing for all sets of a certain size, by introducing more general IBLT schemes. These schemes allow for greater freedom in the implementation of the insert, delete, and listing operations and demonstrate that the IBLT memory can be reduced while still maintaining successful listing guarantees. The paper also explores the time-memory trade-off of these schemes, some of which are based on linear codes and $B_h$-sequences over finite fields.

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arXiv2022

On the Size of Balls and Anticodes of Small Diameter under the Fixed-Length Levenshtein Metric

The rapid development of DNA storage has brought the deletion and insertion channel to the front line of research. When the number of deletions is equal to the number of insertions, the Fixed Length Levenshtein (FLL) metric is the right measure for the distance between two words of the same length. Similar to any other metric, the size of a ball is one of the most fundamental parameters. In this work, we consider the minimum, maximum, and average size of a ball with radius one, in the FLL metric. The related minimum and the maximum size of a maximal anticode with diameter one are also considered.

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arXiv2022

Covering Sequences for $\ell$-Tuples

de Bruijn sequences of order $\ell$, i.e., sequences that contain each $\ell$-tuple as a window exactly once, have found many diverse applications in information theory and most recently in DNA storage. This family of binary sequences has rate of $1/2$. To overcome this low rate, we study $\ell$-tuples covering sequences, which impose that each $\ell$-tuple appears at least once as a window in the sequence. The cardinality of this family of sequences is analyzed while assuming that $\ell$ is a function of the sequence length $n$. Lower and upper bounds on the asymptotic rate of this family are given. Moreover, we study an upper bound for $\ell$ such that the redundancy of the set of $\ell$-tuples covering sequences is at most a single symbol. Lastly, we present efficient encoding and decoding schemes for $\ell$-tuples covering sequences that meet this bound.

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arXiv2022

Bounds on the Size of Permutation Codes with the Kendall $τ$-Metric

The rank modulation scheme has been proposed for efficient writing and storing data in non-volatile memory storage. Error-correction in the rank modulation scheme is done by considering permutation codes. In this paper we consider codes in the set of all permutations on $n$ elements, $S_n$, using the Kendall $τ$-metric. The main goal of this paper is to derive new bounds on the size of such codes. For this purpose we also consider perfect codes, diameter perfect codes, and the size of optimal anticodes in the Kendall $τ$-metric, structures which have their own considerable interest. We prove that there are no perfect single-error-correcting codes in $S_n$, where $n>4$ is a prime or $4\leq n\leq 10$. We present lower bounds on the size of optimal anticodes with odd diameter. As a consequence we obtain a new upper bound on the size of codes in $S_n$ with even minimum Kendall $τ$-distance. We present larger single-error-correcting codes than the known ones in $S_5$ and $S_7$.

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arXiv2021

Non-Binary Diameter Perfect Constant-Weight Codes

Diameter perfect codes form a natural generalization for perfect codes. They are based on the code-anticode bound which generalizes the sphere-packing bound. The code-anticode bound was proved by Delsarte for distance-regular graphs and it holds for some other metrics too. In this paper we prove the bound for non-binary constant-weight codes with the Hamming metric and characterize the diameter perfect codes and the maximum size anticodes for these codes. We distinguish between six families of non-binary diameter constant-weight codes and four families of maximum size non-binary constant-weight anticodes. Each one of these families of diameter perfect codes raises some different questions. We consider some of these questions and leave lot of ground for further research. Finally, as a consequence, some t-intersecting families related to the well-known Erdös-Ko-Rado theorem, are constructed.

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arXiv2021

On Levenshtein Balls with Radius One

The rapid development of DNA storage has brought the deletion and insertion channel, once again, to the front line of research. When the number of deletions is equal to the number of insertions, the Fixed Length Levenshtein (FLL) metric is the right measure for the distance between two words of the same length. The size of a ball is one of the most fundamental parameters in any metric. The size of the ball with radius one in the FLL metric depends on the number of runs and the length of the alternating segments of the given word. In this work, we find the minimum, maximum, and average size of a ball with radius one, in the FLL metric. The related minimum and maximum sizes of a maximal anticode with diameter one are also calculated.

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arXiv2021

Block-avoiding point sequencings

Let $n$ and $\ell$ be positive integers. Recent papers by Kreher, Stinson and Veitch have explored variants of the problem of ordering the points in a triple system (such as a Steiner triple system, directed triple system or Mendelsohn triple system) on $n$ points so that no block occurs in a segment of $\ell$ consecutive entries (thus the ordering is locally block-avoiding). We describe a greedy algorithm which shows that such an ordering exists, provided that $n$ is sufficiently large when compared to $\ell$. This algorithm leads to improved bounds on the number of points in cases where this was known, but also extends the results to a significantly more general setting (which includes, for example, orderings that avoid the blocks of a design). Similar results for a cyclic variant of this situation are also established. We construct Steiner triple systems and quadruple systems where $\ell$ can be large, showing that a bound of Stinson and Veitch is reasonable. Moreover, we generalise the Stinson--Veitch bound to a wider class of block designs and to the cyclic case. The results of Kreher, Stinson and Veitch were originally inspired by results of Alspach, Kreher and Pastine, who (motivated by zero-sum avoiding sequences in abelian groups) were interested in orderings of points in a partial Steiner triple system where no segment is a union of disjoint blocks. Alspach~\emph{et al.}\ show that, when the system contains at most $k$ pairwise disjoint blocks, an ordering exists when the number of points is more than $15k-5$. By making use of a greedy approach, the paper improves this bound to $9k+O(k^{2/3})$.

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arXiv2020

Explicit Baranyai Partitions for Quadruples, Part I: Quadrupling Constructions

It is well known that, whenever $k$ divides $n$, the complete $k$-uniform hypergraph on $n$ vertices can be partitioned into disjoint perfect matchings. Equivalently, the set of $k$-subsets of an $n$-set can be partitioned into parallel classes so that each parallel class is a partition of the $n$-set. This result is known as Baranyai's theorem, which guarantees the existence of \emph{Baranyai partitions}. Unfortunately, the proof of Baranyai's theorem uses network flow arguments, making this result non-explicit. In particular, there is no known method to produce Baranyai partitions in time and space that scale linearly with the number of hyperedges in the hypergraph. It is desirable for certain applications to have an explicit construction that generates Baranyai partitions in linear time. Such an efficient construction is known for $k=2$ and $k=3$. In this paper, we present an explicit recursive quadrupling construction for $k=4$ and $n=4t$, where $t \equiv 0,3,4,6,8,9 ~(\text{mod}~12)$. In a follow-up paper (Part II), the other values of~$t$, namely $t \equiv 1,2,5,7,10,11 ~(\text{mod}~12)$, will be considered.

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arXiv2020

Large Sets with Multiplicity

Large sets of combinatorial designs has always been a fascinating topic in design theory. These designs form a partition of the whole space into combinatorial designs with the same parameters. In particular, a large set of block designs, whose blocks are of size $k$ taken from an $n$-set, is a partition of all the $k$-subsets of the $n$-set into disjoint copies of block designs, defined on the $n$-set, and with the same parameters. The current most intriguing question in this direction is whether large sets of Steiner quadruple systems exist and to provide explicit constructions for those parameters for which they exist. In view of its difficulty no one ever presented an explicit construction even for one nontrivial order. Hence, we seek for related generalizations. As generalizations, to the existence question of large sets, we consider two related questions. The first one to provide constructions for sets on Steiner systems in which each block (quadruple or a $k$-subset) is contained in exactly $μ$ systems. The second question is to provide constructions for large set of H-designs (mainly for quadruples, but also for larger block size). We prove the existence of such systems for many parameters using orthogonal arrays, perpendicular arrays, ordered designs, sets of permutations, and one-factorizations of the complete graph.

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arXiv2020

Constrained de Bruijn Codes: Properties, Enumeration, Constructions, and Applications

The de Bruijn graph, its sequences, and their various generalizations, have found many applications in information theory, including many new ones in the last decade. In this paper, motivated by a coding problem for emerging memory technologies, a set of sequences which generalize sequences in the de Bruijn graph are defined. These sequences can be also defined and viewed as constrained sequences. Hence, they will be called constrained de Bruijn sequences and a set of such sequences will be called a constrained de Bruijn code. Several properties and alternative definitions for such codes are examined and they are analyzed as generalized sequences in the de Bruijn graph (and its generalization) and as constrained sequences. Various enumeration techniques are used to compute the total number of sequences for any given set of parameters. A construction method of such codes from the theory of shift-register sequences is proposed. Finally, we show how these constrained de Bruijn sequences and codes can be applied in constructions of codes for correcting synchronization errors in the $\ell$-symbol read channel and in the racetrack memory channel. For this purpose, these codes are superior in their size on previously known codes.

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arXiv2020

Subspace Packings -- Constructions and Bounds

The Grassmannian $\mathcal{G}_q(n,k)$ is the set of all $k$-dimensional subspaces of the vector space $\mathbb{F}_q^n$. Kötter and Kschischang showed that codes in Grassmannian space can be used for error-correction in random network coding. On the other hand, these codes are $q$-analogs of codes in the Johnson scheme, i.e., constant dimension codes. These codes of the Grassmannian $\mathcal{G}_q(n,k)$ also form a family of $q$-analogs of block designs and they are called subspace designs. In this paper, we examine one of the last families of $q$-analogs of block designs which was not considered before. This family, called subspace packings, is the $q$-analog of packings, and was considered recently for network coding solution for a family of multicast networks called the generalized combination networks. A subspace packing $t$-$(n,k,λ)_q$ is a set $\mathcal{S}$ of $k$-subspaces from $\mathcal{G}_q(n,k)$ such that each $t$-subspace of $\mathcal{G}_q(n,t)$ is contained in at most $λ$ elements of $\mathcal{S}$. The goal of this work is to consider the largest size of such subspace packings. We derive a sequence of lower and upper bounds on the maximum size of such packings, analyse these bounds, and identify the important problems for further research in this area.

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