arXiv subjects

Eitan Yaakobi

Publications and source records attributed to Eitan Yaakobi.

At least 91 records · Page 5Linked to original sources

arXiv2023

Universal Framework for Parametric Constrained Coding

Constrained coding is a fundamental field in coding theory that tackles efficient communication through constrained channels. While channels with fixed constraints have a general optimal solution, there is increasing demand for parametric constraints that are dependent on the message length. Several works have tackled such parametric constraints through iterative algorithms, yet they require complex constructions specific to each constraint to guarantee convergence through monotonic progression. In this paper, we propose a universal framework for tackling any parametric constrained-channel problem through a novel simple iterative algorithm. By reducing an execution of this iterative algorithm to an acyclic graph traversal, we prove a surprising result that guarantees convergence with efficient average time complexity even without requiring any monotonic progression. We demonstrate the effectiveness of this universal framework by applying it to a variety of both local and global channel constraints. We begin by exploring the local constraints involving illegal substrings of variable length, where the universal construction essentially iteratively replaces forbidden windows. We apply this local algorithm to the minimal periodicity, minimal Hamming weight, local almost-balanced Hamming weight and the previously-unsolved minimal palindrome constraints. We then continue by exploring global constraints, and demonstrate the effectiveness of the proposed construction on the repeat-free encoding, reverse-complement encoding, and the open problem of global almost-balanced encoding. For reverse-complement, we also tackle a previously-unsolved version of the constraint that addresses overlapping windows. Overall, the proposed framework generates state-of-the-art constructions with significant ease while also enabling the simultaneous integration of multiple constraints for the first time.

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arXiv2022

Invertible Bloom Lookup Tables with Listing Guarantees

The Invertible Bloom Lookup Table (IBLT) is a probabilistic concise data structure for set representation that supports a listing operation as the recovery of the elements in the represented set. Its applications can be found in network synchronization and traffic monitoring as well as in error-correction codes. IBLT can list its elements with probability affected by the size of the allocated memory and the size of the represented set, such that it can fail with small probability even for relatively small sets. While previous works only studied the failure probability of IBLT, this work initiates the worst case analysis of IBLT that guarantees successful listing for all sets of a certain size. The worst case study is important since the failure of IBLT imposes high overhead. We describe a novel approach that guarantees successful listing when the set satisfies a tunable upper bound on its size. To allow that, we develop multiple constructions that are based on various coding techniques such as stopping sets and the stopping redundancy of error-correcting codes, Steiner systems, and covering arrays as well as new methodologies we develop. We analyze the sizes of IBLTs with listing guarantees obtained by the various methods as well as their mapping memory consumption. Lastly, we study lower bounds on the achievable sizes of IBLT with listing guarantees and verify the results in the paper by simulations.

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arXiv2022

Codes for Constrained Periodicity

Reliability is an inherent challenge for the emerging nonvolatile technology of racetrack memories, and there exists a fundamental relationship between codes designed for racetrack memories and codes with constrained periodicity. Previous works have sought to construct codes that avoid periodicity in windows, yet have either only provided existence proofs or required high redundancy. This paper provides the first constructions for avoiding periodicity that are both efficient (average-linear time) and with low redundancy (near the lower bound). The proposed algorithms are based on iteratively repairing windows which contain periodicity until all the windows are valid. Intuitively, such algorithms should not converge as there is no monotonic progression; yet, we prove convergence with average-linear time complexity by exploiting subtle properties of the encoder. Overall, we both provide constructions that avoid periodicity in all windows, and we also study the cardinality of such constraints.

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arXiv2022

Equivalence of Insertion/Deletion Correcting Codes for $d$-dimensional Arrays

We consider the problem of correcting insertion and deletion errors in the $d$-dimensional space. This problem is well understood for vectors (one-dimensional space) and was recently studied for arrays (two-dimensional space). For vectors and arrays, the problem is motivated by several practical applications such as DNA-based storage and racetrack memories. From a theoretical perspective, it is interesting to know whether the same properties of insertion/deletion correcting codes generalize to the $d$-dimensional space. In this work, we show that the equivalence between insertion and deletion correcting codes generalizes to the $d$-dimensional space. As a particular result, we show the following missing equivalence for arrays: a code that can correct $t_\mathrm{r}$ and $t_\mathrm{c}$ row/column deletions can correct any combination of $t_\mathrm{r}^{\mathrm{ins}}+t_\mathrm{r}^{\mathrm{del}}=t_\mathrm{r}$ and $t_\mathrm{c}^{\mathrm{ins}}+t_\mathrm{c}^{\mathrm{del}}=t_\mathrm{c}$ row/column insertions and deletions. The fundamental limit on the redundancy and a construction of insertion/deletion correcting codes in the $d$-dimensional space remain open for future work.

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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

The Input and Output Entropies of the $k$-Deletion/Insertion Channel

The channel output entropy of a transmitted word is the entropy of the possible channel outputs and similarly, the input entropy of a received word is the entropy of all possible transmitted words. The goal of this work is to study these entropy values for the k-deletion, k-insertion channel, where exactly k symbols are deleted, and inserted in the transmitted word, respectively. If all possible words are transmitted with the same probability then studying the input and output entropies is equivalent. For both the 1-insertion and 1-deletion channels, it is proved that among all words with a fixed number of runs, the input entropy is minimized for words with a skewed distribution of their run lengths and it is maximized for words with a balanced distribution of their run lengths. Among our results, we establish a conjecture by Atashpendar et al. which claims that for the binary 1-deletion, the input entropy is maximized for the alternating words. This conjecture is also verified for the 2-deletion channel, where it is proved that constant words with a single run minimize the input entropy.

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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

Reconstruction from Substrings with Partial Overlap

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 works considered two extreme cases in which \emph{all} substrings of some fixed length are read or substrings are read with no overlap, this work considers the setup in which consecutive substrings are read with some given minimum overlap. First, upper bounds are provided on the attainable rates of codes that guarantee unique reconstruction. Then, we present efficient constructions of asymptotically optimal codes that meet the upper bound.

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arXiv2022

Insertion and Deletion Correction in Polymer-based Data Storage

Synthetic polymer-based storage seems to be a particularly promising candidate that could help to cope with the ever-increasing demand for archival storage requirements. It involves designing molecules of distinct masses to represent the respective bits $\{0,1\}$, followed by the synthesis of a polymer of molecular units that reflects the order of bits in the information string. Reading out the stored data requires the use of a tandem mass spectrometer, that fragments the polymer into shorter substrings and provides their corresponding masses, from which the \emph{composition}, i.e. the number of $1$s and $0$s in the concerned substring can be inferred. Prior works have dealt with the problem of unique string reconstruction from the set of all possible compositions, called \emph{composition multiset}. This was accomplished either by determining which string lengths always allow unique reconstruction, or by formulating coding constraints to facilitate the same for all string lengths. Additionally, error-correcting schemes to deal with substitution errors caused by imprecise fragmentation during the readout process, have also been suggested. This work builds on this research by generalizing previously considered error models, mainly confined to substitution of compositions. To this end, we define new error models that consider insertions of spurious compositions and deletions of existing ones, thereby corrupting the composition multiset. We analyze if the reconstruction codebook proposed by Pattabiraman \emph{et al.} is indeed robust to such errors, and if not, propose new coding constraints to remedy this.

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arXiv2021

Multiple Criss-Cross Insertion and Deletion Correcting Codes

This paper investigates the problem of correcting multiple criss-cross insertions and deletions in arrays. More precisely, we study the unique recovery of $n \times n$ arrays affected by $t$-criss-cross deletions defined as any combination of $t_r$ row and $t_c$ column deletions such that $t_r + t_c = t$ for a given $t$. We show an equivalence between correcting $t$-criss-cross deletions and $t$-criss-cross insertions and show that a code correcting $t$-criss-cross insertions/deletions has redundancy at least $tn + t \log n - \log(t!)$. Then, we present an existential construction of $t$-criss-cross insertion/deletion correcting code with redundancy bounded from above by $tn + \mathcal{O}(t^2 \log^2 n)$. The main ingredients of the presented code construction are systematic binary $t$-deletion correcting codes and Gabidulin codes. The first ingredient helps locating the indices of the inserted/deleted rows and columns, thus transforming the insertion/deletion-correction problem into a row/column erasure-correction problem which is then solved using the second ingredient.

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arXiv2021

Multi-Server Weakly-Private Information Retrieval

Private information retrieval (PIR) protocols ensure that a user can download a file from a database without revealing any information on the identity of the requested file to the servers storing the database. 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 perfect privacy requirement. We refer to such protocols as weakly-private information retrieval (WPIR) protocols. In particular, for the case of multiple noncolluding replicated servers, we study how the download rate, the upload cost, and the access complexity can be improved when relaxing the full privacy constraint. To quantify the information leakage on the requested file's identity we consider mutual information (MI), worst-case information leakage, and maximal leakage (MaxL). We present two WPIR schemes, denoted by Scheme A and Scheme B, based on two recent PIR protocols and show that the download rate of the former can be optimized by solving a convex optimization problem. We also show that Scheme A achieves an improved download rate compared to the recently proposed scheme by Samy et al. under the so-called $ε$-privacy metric. Additionally, a family of schemes based on partitioning is presented. Moreover, we provide an information-theoretic converse bound for the maximum possible download rate for the MI and MaxL privacy metrics under a practical restriction on the alphabet size of queries and answers. For two servers and two files, the bound is tight under the MaxL metric, which settles the WPIR capacity in this particular case. Finally, we compare the performance of the proposed schemes and their gap to the converse bound.

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arXiv2021

Almost Optimal Construction of Functional Batch Codes Using Hadamard Codes

A \textit{functional $k$-batch} code of dimension $s$ consists of $n$ servers storing linear combinations of $s$ linearly independent information bits. Any multiset request of size $k$ of linear combinations (or requests) of the information bits can be recovered by $k$ disjoint subsets of the servers. The goal under this paradigm is to find the minimum number of servers for given values of $s$ and $k$. A recent conjecture states that for any $k=2^{s-1}$ requests the optimal solution requires $2^s-1$ servers. This conjecture is verified for $s\leq 5$ but previous work could only show that codes with $n=2^s-1$ servers can support a solution for $k=2^{s-2} + 2^{s-4} + \left\lfloor \frac{ 2^{s/2}}{\sqrt{24}} \right\rfloor$ requests. This paper reduces this gap and shows the existence of codes for $k=\lfloor \frac{5}{6}2^{s-1} \rfloor - s$ requests with the same number of servers. Another construction in the paper provides a code with $n=2^{s+1}-2$ servers and $k=2^{s}$ requests, which is an optimal result.These constructions are mainly based on Hadamard codes and equivalently provide constructions for \textit{parallel Random I/O (RIO)} codes.

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arXiv2021

Lifted Reed-Solomon Codes and Lifted Multiplicity Codes

Lifted Reed-Solomon and multiplicity codes are classes of codes, constructed from specific sets of $m$-variate polynomials. These codes 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 for the bi-variate case to construct lifted multiplicity codes, a generalization of lifted codes that can offer further rate improvements. We continue the study of these codes by first establishing new lower bounds on the rate of lifted Reed-Solomon codes for any number of variables $m$, which improve upon the known bounds for any $m\ge 4$. Next, we use these results to provide lower bounds on the rate and distance of lifted multiplicity codes obtained from polynomials in an arbitrary number of variables, which improve upon the known results for any $m\ge 3$. 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 univariate 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. Using these results, we give a new explicit construction of batch codes utilizing lifted Reed-Solomon codes. For some parameter regimes, these codes have a better trade-off between parameters than previously known batch codes. Further, we show that lifted multiplicity codes have a better trade-off between redundancy and the number of disjoint recovering sets for every codeword or information symbol than previously known constructions, thereby providing the best known PIR codes for some parameter regimes. Additionally, we present a new local self-correction algorithm for lifted multiplicity codes.

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arXiv2021

Endurance-Limited Memories: Capacity and Codes

\emph{Resistive memories}, such as \emph{phase change memories} and \emph{resistive random access memories} have attracted significant attention in recent years due to their better scalability, speed, rewritability, and yet non-volatility. However, their \emph{limited endurance} is still a major drawback that has to be improved before they can be widely adapted in large-scale systems. In this work, in order to reduce the wear out of the cells, we propose a new coding scheme, called \emph{endurance-limited memories} (\emph{ELM}) codes, that increases the endurance of these memories by limiting the number of cell programming operations. Namely, an \emph{$\ell$-change $t$-write ELM code} is a coding scheme that allows to write $t$ messages into some $n$ binary cells while guaranteeing that each cell is programmed at most $\ell$ times. In case $\ell=1$, these codes coincide with the well-studied \emph{write-once memory} (\emph{WOM}) codes. We study some models of these codes which depend upon whether the encoder knows on each write the number of times each cell was programmed, knows only the memory state, or even does not know anything. For the decoder, we consider these similar three cases. We fully characterize the capacity regions and the maximum sum-rates of three models where the encoder knows on each write the number of times each cell was programmed. In particular, it is shown that in these models the maximum sum-rate is $\log \sum_{i=0}^{\ell} {t \choose i}$. We also study and expose the capacity regions of the models where the decoder is informed with the number of times each cell was programmed. Finally we present the most practical model where the encoder read the memory before encoding new data and the decoder has no information about the previous states of the memory.

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arXiv2021

Multi-strand Reconstruction from Substrings

The problem of string reconstruction based on its substrings spectrum has received significant attention recently due to its applicability to DNA data storage and sequencing. In contrast to previous works, we consider in this paper a setup of this problem where multiple strings are reconstructed together. Given a multiset $S$ of strings, all their substrings of some fixed length $\ell$, defined as the $\ell$-profile of $S$, are received and the goal is to reconstruct all strings in $S$. A multi-strand $\ell$-reconstruction code is a set of multisets such that every element $S$ can be reconstructed from its $\ell$-profile. Given the number of strings~$k$ and their length~$n$, we first find a lower bound on the value of $\ell$ necessary for existence of multi-strand $\ell$-reconstruction codes with non-vanishing asymptotic rate. We then present two constructions of such codes and show that their rates approach~$1$ for values of $\ell$ that asymptotically behave like the lower bound.

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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

Repeat-Free Codes

In this paper we consider the problem of encoding data into \textit{repeat-free} sequences in which sequences are imposed to contain any $k$-tuple at most once (for predefined $k$). First, the capacity of the repeat-free constraint are calculated. Then, an efficient algorithm, which uses two bits of redundancy, is presented to encode length-$n$ sequences for $k=2+2\log (n)$. This algorithm is then improved to support any value of $k$ of the form $k=a\log (n)$, for $1<a$, while its redundancy is $o(n)$. We also calculate the capacity of repeat-free sequences when combined with local constraints which are given by a constrained system, and the capacity of multi-dimensional repeat-free codes.

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arXiv2021

Partial MDS Codes with Regeneration

Partial MDS (PMDS) and sector-disk (SD) codes are classes of erasure correcting codes that combine locality with strong erasure correction capabilities. We construct PMDS and SD codes with local regeneration where each local code is a bandwidth-optimal regenerating MDS code. In the event of a node failure, these codes reduce both, the number of servers that have to be contacted as well as the amount of network traffic required for the repair process. The constructions require significantly smaller field size than the only other construction known in literature. Further, we present a construction of PMDS codes with global regeneration which allow to efficiently repair patterns of node failures that exceed the local erasure correction capability of the code and thereby invoke repair across different local groups.

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