arXiv subjects

Eitan Yaakobi

Publications and source records attributed to Eitan Yaakobi.

At least 109 records · Page 6Linked to original sources

arXiv2021

Reconstruction of Strings from their Substrings Spectrum

This paper studies reconstruction of strings based upon their substrings spectrum. Under this paradigm, it is assumed that all substrings of some fixed length are received and the goal is to reconstruct the string. While many existing works assumed that substrings are received error free, we follow in this paper the noisy setup of this problem that was first studied by Gabrys and Milenkovic. The goal of this study is twofold. First we study the setup in which not all substrings in the multispectrum are received, and then we focus on the case where the read substrings are not error free. In each case we provide specific code constructions of strings that their reconstruction is guaranteed even in the presence of failure in either model. We present efficient encoding and decoding maps and analyze the cardinality of the code constructions, while studying the cases where the rates of our codes approach 1.

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arXiv2021

Criss-Cross Insertion and Deletion Correcting Codes

This paper studies the problem of constructing codes correcting deletions in arrays. Under this model, it is assumed that an $n\times n$ array can experience deletions of rows and columns. These deletion errors are referred to as $(t_r,t_c)$-criss-cross deletions if $t_r$ rows and $t_c$ columns are deleted, while a code correcting these deletion patterns is called a $(t_r,t_c)$-criss-cross deletion correction code. The definitions for criss-cross insertions are similar. It is first shown that when $t_r=t_c$ the problems of correcting criss-cross deletions and criss-cross insertions are equivalent. The focus of this paper lies on the case of $(1,1)$-criss-cross deletions. A non-asymptotic upper bound on the cardinality of $(1,1)$-criss-cross deletion correction codes is shown which assures that the redundancy is at least $2n-3+2\log n$ bits. A code construction with an existential encoding and an explicit decoding algorithm is presented. The redundancy of the construction is at most $2n+4 \log n + 7 +2 \log e$. A construction with explicit encoder and decoder is presented. The explicit encoder adds an extra $5\log n + 5$ bits of redundancy to the construction.

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arXiv2021

Correctable Erasure Patterns in Product Topologies

Locality enables storage systems to recover failed nodes from small subsets of surviving nodes. The setting where nodes are partitioned into subsets, each allowing for local recovery, is well understood. In this work we consider a generalization introduced by Gopalan et al., where, viewing the codewords as arrays, constraints are imposed on the columns and rows in addition to some global constraints. Specifically, we present a generic method of adding such global parity-checks and derive new results on the set of correctable erasure patterns. Finally, we relate the set of correctable erasure patterns in the considered topology to those correctable in tensor-product codes.

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arXiv2021

The Zero Cubes Free and Cubes Unique Multidimensional Constraints

This paper studies two families of constraints for two-dimensional and multidimensional arrays. The first family requires that a multidimensional array will not contain a cube of zeros of some fixed size and the second constraint imposes that there will not be two identical cubes of a given size in the array. These constraints are natural extensions of their one-dimensional counterpart that have been rigorously studied recently. For both of these constraint we present conditions of the size of the cube for which the asymptotic rate of the set of valid arrays approaches 1 as well as conditions for the redundancy to be at most a single symbol. For the first family we present an efficient encoding algorithm that uses a single symbol to encode arbitrary information into a valid array and for the second family we present a similar encoder for the two-dimensional case. The results in the paper are also extended to similar constraints where the sub-array is not necessarily a cube, but a box of arbitrary dimensions and only its volume is bounded.

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arXiv2021

The Capacity of Single-Server Weakly-Private Information Retrieval

A private information retrieval (PIR) protocol guarantees that a user can privately retrieve files stored in a database without revealing any information about the identity of the requested file. Existing information-theoretic PIR protocols ensure perfect privacy, i.e., zero information leakage to the servers storing the database, but at the cost of high download. In this work, we present weakly-private information retrieval (WPIR) schemes that trade off perfect privacy to improve the download cost when the database is stored on a single server. We study the tradeoff between the download cost and information leakage in terms of mutual information (MI) and maximal leakage (MaxL) privacy metrics. By relating the WPIR problem to rate-distortion theory, the download-leakage function, which is defined as the minimum required download cost of all single-server WPIR schemes for a given level of information leakage and a fixed file size, is introduced. By characterizing the download-leakage function for the MI and MaxL metrics, the capacity of single-server WPIR is fully described.

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arXiv2020

Lifted Multiplicity Codes

Lifted Reed-Solomon codes and multiplicity codes are two classes of evaluation codes that allow for the design of high-rate codes that can recover every codeword or information symbol from many disjoint sets. Recently, the underlying approaches have been combined to construct lifted bi-variate multiplicity codes, that can further improve on the rate. We continue the study of these codes by providing lower bounds on the rate and distance for lifted multiplicity codes obtained from polynomials in an arbitrary number of variables. Specifically, we investigate a subcode of a lifted multiplicity code formed by the linear span of $m$-variate monomials whose restriction to an arbitrary line in $\mathbb{F}_q^m$ is equivalent to a low-degree uni-variate polynomial. We find the tight asymptotic behavior of the fraction of such monomials when the number of variables $m$ is fixed and the alphabet size $q=2^\ell$ is large. For some parameter regimes, lifted multiplicity codes are then shown to have a better trade-off between redundancy and the number of disjoint recovering sets for every codeword or information symbol than previously known constructions. Additionally, we present a local self-correction algorithm for lifted multiplicity codes.

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arXiv2020

Array Codes for Functional PIR and Batch Codes

A functional PIR array code is a coding scheme which encodes some $s$ information bits into a $t\times m$ array such that every linear combination of the $s$ information bits has $k$ mutually disjoint recovering sets. Every recovering set consists of some of the array's columns while it is allowed to read at most $\ell$ encoded bits from every column in order to receive the requested linear combination of the information bits. Functional batch array codes impose a stronger property where every multiset request of $k$ linear combinations has $k$ mutually disjoint recovering sets. Locality functional array codes demand that the size of every recovering set is restrained to be at most $r$. Given the values of $s, k, t, \ell,r$, the goal of this paper is to study the optimal value of the number of columns $m$ such that these codes exist. Several lower bounds are presented as well as explicit constructions for several of these parameters.

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arXiv2020

Coding for Sequence Reconstruction for Single Edits

The sequence reconstruction problem, introduced by Levenshtein in 2001, considers a communication scenario where the sender transmits a codeword from some codebook and the receiver obtains multiple noisy reads of the codeword. The common setup assumes the codebook to be the entire space and the problem is to determine the minimum number of distinct reads that is required to reconstruct the transmitted codeword. Motivated by modern storage devices, we study a variant of the problem where the number of noisy reads $N$ is fixed. Specifically, we design reconstruction codes that reconstruct a codeword from $N$ distinct noisy reads. We focus on channels that introduce single edit error (i.e. a single substitution, insertion, or deletion) and their variants, and design reconstruction codes for all values of $N$. In particular, for the case of a single edit, we show that as the number of noisy reads increases, the number of redundant bits required can be gracefully reduced from $\log n+O(1)$ to $\log \log n+O(1)$, and then to $O(1)$, where $n$ denotes the length of a codeword. We also show that the redundancy of certain reconstruction codes is within one bit of optimality.

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arXiv2020

Covering Codes using Insertions or Deletions

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 prior work on covering codes has focused on the Hamming metric, we consider the problem of designing covering codes defined in terms of either insertions or deletions. First, we provide new sphere-covering lower bounds on the minimum possible size of such codes. Then, we provide new existential upper bounds on the size of optimal covering codes for a single insertion or a single deletion that are tight up to a constant factor. Finally, we derive improved upper bounds for covering codes using $R\geq 2$ insertions or deletions. We prove that codes exist with density that is only a factor $O(R \log R)$ larger than the lower bounds for all fixed~$R$. In particular, our upper bounds have an optimal dependence on the word length, and we achieve asymptotic density matching the best known bounds for Hamming distance covering codes.

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arXiv2020

Single-Deletion Single-Substitution Correcting Codes

Correcting insertions/deletions as well as substitution errors simultaneously plays an important role in DNA-based storage systems as well as in classical communications. This paper deals with the fundamental task of constructing codes that can correct a single insertion or deletion along with a single substitution. A non-asymptotic upper bound on the size of single-deletion single-substitution correcting codes is derived, showing that the redundancy of such a code of length $n$ has to be at least $2 \log n$. The bound is presented both for binary and non-binary codes while an extension to single deletion and multiple substitutions is presented for binary codes. An explicit construction of single-deletion single-substitution correcting codes with at most $6 \log n + 8$ redundancy bits is derived. Note that the best known construction for this problem has to use 3-deletion correcting codes whose best known redundancy is roughly $24 \log n$.

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arXiv2020

Partial MDS Codes with Local Regeneration

Partial MDS (PMDS) and sector-disk (SD) codes are classes of erasure codes that combine locality with strong erasure correction capabilities. We construct PMDS and SD codes where each local code is a bandwidth-optimal regenerating MDS code. The constructions require significantly smaller field size than the only other construction known in literature.

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arXiv2020

Optimal Reconstruction Codes for Deletion Channels

The sequence reconstruction problem, introduced by Levenshtein in 2001, considers a communication scenario where the sender transmits a codeword from some codebook and the receiver obtains multiple noisy reads of the codeword. Motivated by modern storage devices, we introduced a variant of the problem where the number of noisy reads $N$ is fixed (Kiah et al. 2020). Of significance, for the single-deletion channel, using $\log_2\log_2 n +O(1)$ redundant bits, we designed a reconstruction code of length $n$ that reconstructs codewords from two distinct noisy reads. In this work, we show that $\log_2\log_2 n -O(1)$ redundant bits are necessary for such reconstruction codes, thereby, demonstrating the optimality of our previous construction. Furthermore, we show that these reconstruction codes can be used in $t$-deletion channels (with $t\ge 2$) to uniquely reconstruct codewords from $n^{t-1}+O\left(n^{t-2}\right)$ distinct noisy reads.

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arXiv2020

Coding over Sets for DNA Storage

In this paper we study error-correcting codes for the storage of data in synthetic deoxyribonucleic acid (DNA). We investigate a storage model where a data set is represented by an unordered set of $M$ sequences, each of length $L$. Errors within that model are a loss of whole sequences and point errors inside the sequences, such as insertions, deletions and substitutions. We derive Gilbert-Varshamov lower bounds and sphere packing upper bounds on achievable cardinalities of error-correcting codes within this storage model. We further propose explicit code constructions than can correct errors in such a storage system that can be encoded and decoded efficiently. Comparing the sizes of these codes to the upper bounds, we show that many of the constructions are close to optimal.

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arXiv2020

The Error Probability of Maximum-Likelihood Decoding over Two Deletion Channels

This paper studies the problem of reconstructing a word given several of its noisy copies. This setup is motivated by several applications, among them is reconstructing strands in DNA-based storage systems. Under this paradigm, a word is transmitted over some fixed number of identical independent channels and the goal of the decoder is to output the transmitted word or some close approximation. The main focus of this paper is the case of two deletion channels and studying the error probability of the maximum-likelihood (ML) decoder under this setup. First, it is discussed how the ML decoder operates. Then, we observe that the dominant error patterns are deletions in the same run or errors resulting from alternating sequences. Based on these observations, it is derived that the error probability of the ML decoder is roughly $\frac{3q-1}{q-1}p^2$, when the transmitted word is any $q$-ary sequence and $p$ is the channel's deletion probability. We also study the cases when the transmitted word belongs to the Varshamov Tenengolts (VT) code or the shifted VT code. Lastly, the insertion channel is studied as well. These theoretical results are verified by corresponding simulations.

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arXiv2020

PIR Codes with Short Block Length

In this work private information retrieval (PIR) codes are studied. In a $k$-PIR code, $s$ information bits are encoded in such a way that every information bit has $k$ mutually disjoint recovery sets. The main problem under this paradigm is to minimize the number of encoded bits given the values of $s$ and $k$, where this value is denoted by $P(s,k)$. The main focus of this work is to analyze $P(s,k)$ for a large range of parameters of $s$ and $k$. In particular, we improve upon several of the existing results on this value.

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arXiv2019

Private Proximity Retrieval Codes

A \emph{private proximity retrieval} (\emph{PPR}) scheme is a protocol which allows a user to retrieve the identities of all records in a database that are within some distance $r$ from the user's record $x$. The user's \emph{privacy} at each server is given by the fraction of the record $x$ that is kept private. In this paper, this research is initiated and protocols that offer trade-offs between privacy and computational complexity and storage are studied. In particular, we assume that each server stores a copy of the database and study the required minimum number of servers by our protocol which provides a given privacy level. Each server gets a query in the protocol and the set of queries forms a code. We study the family of codes generated by the set of queries and in particular the minimum number of codewords in such a code which is the minimum number of servers required for the protocol. These codes are closely related to a family of codes known as \emph{covering designs}. We introduce several lower bounds on the sizes of such codes as well as several constructions. This work focuses on the case when the records are binary vectors together with the Hamming distance. Other metrics such as the Johnson metric are also investigated.

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arXiv2019

Weakly-Private Information Retrieval

Private information retrieval (PIR) protocols make it possible to retrieve a file from a database without disclosing any information about the identity of the file being retrieved. These protocols have been rigorously explored from an information-theoretic perspective in recent years. While existing protocols strictly impose that no information is leaked on the file's identity, this work initiates the study of the tradeoffs that can be achieved by relaxing the requirement of perfect privacy. In case the user is willing to leak some information on the identity of the retrieved file, we study how the PIR rate, as well as the upload cost and access complexity, can be improved. For the particular case of replicated servers, we propose two weakly-private information retrieval schemes based on two recent PIR protocols and a family of schemes based on partitioning. Lastly, we compare the performance of the proposed schemes.

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arXiv2019

Clustering-Correcting Codes

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 form of unordered sequences, also called strands, and every strand is synthesized thousands to millions of times, where some of these copies are read back during sequencing. Due to the unordered structure of the strands, an important task in the decoding process is to place them in their correct order. This is usually accomplished by allocating a part of the strand for an index. However, in the presence of errors in the index field, important information on the order of the strands may be lost. Clustering-correcting codes ensure that if the distance between the index fields of two strands is small, then there will be a large distance between their data fields. It is shown how this property enables to place the strands together in their correct clusters even in the presence of errors. We present lower and upper bounds on the size of clustering-correcting codes and an explicit construction of these codes which uses only a single bit of redundancy.

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