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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. 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 (Cai et al., 2021). 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 the construction. Furthermore, we show that these reconstruction codes can be used in $t$ -deletion channels (with $t \geqslant 2$) to uniquely reconstruct codewords from ${n^{t-1}}/{(t-1)!}+O\left ({n^{t-2}}\right)$ distinct noisy reads. For the two-deletion channel, using higher order VT syndromes and certain runlength constraints, we designed the class of higher order constrained shifted VT code with $2\log _{2} n +o(\log _{2}(n))$ redundancy bits that can reconstruct any codeword from any $N \geqslant 5$ of its length- $(n-2)$ subsequences. [ABSTRACT FROM AUTHOR]

A 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 $s \leqslant 5$ 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 extended Simplex codes and equivalently provide constructions for parallel Random I/O (RIO) codes. [ABSTRACT FROM AUTHOR]

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 ${t_{\mathrm {r}}}$ row and ${t_{\mathrm {c}}}$ column deletions such that ${t_{\mathrm {r}}}+ {t_{\mathrm {c}}}= {t}$ 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 ${t} n + {t}\log n - \log ({t}!)$. Then, we present an existential construction of a ${t}$ -criss-cross insertion/deletion correcting code with redundancy bounded from above by ${t} n + \mathcal {O}({t}^{2} \log ^{2} n)$. 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. [ABSTRACT FROM AUTHOR]

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 the 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 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, their data fields have large distance. 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 symbol of redundancy. The results are first presented for the Hamming metric and are then extended for the edit distance. [ABSTRACT FROM AUTHOR]

Resistive memories, such as phase change memories and resistive random access memories have attracted significant attention in recent years due to their better scalability, speed, rewritability, and yet non-volatility. However, their 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 endurance-limited memories (ELM) codes, that increases the endurance of these memories by limiting the number of cell programming operations. Namely, an $\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 write-once memory (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 $\log \sum _{i=0}^{\ell } {\binom{t }{ i}}$. 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. [ABSTRACT FROM AUTHOR]

In this paper, we study a model that mimics the programming operation of memory cells. This model was first introduced by Lastras-Montano et al. for continuous-alphabet channels, and later by Bunte and Lapidoth for discrete memoryless channels (DMC). Under this paradigm we assume that cells are programmed sequentially and individually. The programming process is modeled as transmission over a channel, such that it is possible to read the cell state in order to determine its programming success, and in case of programming failure, to reprogram the cell again. Reprogramming a cell can reduce the bit error rate, however this comes with the price of increasing the overall programming time and thereby affecting the writing speed of the memory. An iterative programming scheme is an algorithm which specifies the number of attempts to program each cell. Given the programming channel and constraints on the average and maximum number of attempts to program a cell, we study programming schemes which maximize the number of bits that can be reliably stored in the memory. We extend the results by Bunte and Lapidoth and study this problem when the programming channel is either discrete-input memoryless symmetric channel (including the BSC,BEC, BI-AWGN) or the $Z$ channel. For the BSC and the BEC our analysis is also extended for the case where the error probabilities on consecutive writes are not necessarily the same. Lastly, we also study a related model which is motivated by the synthesis process of DNA molecules. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 perfect 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 $\epsilon $ -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. [ABSTRACT FROM AUTHOR]

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 a 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 symbols required can be gracefully reduced from $\log _{q} n+O(1)$ to $\log _{q} \log _{q} n+O(1)$ , and then to $O(1)$ , where $n$ denotes the length of a codeword. We also show that these reconstruction codes are asymptotically optimal. Finally, via computer simulations, we demonstrate that in certain cases, reconstruction codes can achieve similar performance as classical error-correcting codes with less redundant symbols. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 the window property of de Bruijn sequences, on its shorter subsequences, are defined. These sequences can be also defined and viewed as constrained sequences. Hence, they will be called locally-constrained de Bruijn sequences and a set of such sequences will be called a locally-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 locally-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 to previously known codes. [ABSTRACT FROM AUTHOR]

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 $({t_{\mathrm {r}}}, {t_{\mathrm {c}}})$ -criss-cross deletions if ${t_{\mathrm {r}}}$ rows and ${t_{\mathrm {c}}}$ columns are deleted, while a code correcting these deletion patterns is called a $({t_{\mathrm {r}}}, {t_{\mathrm {c}}})$ -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. [ABSTRACT FROM AUTHOR]

The sequence reconstruction problem corresponds to the model in which a sequence from some code is transmitted over several noisy channels that produce distinct outputs. Then, the channels’ outputs, received by the decoder, are used to recover the transmitted sequence, and the main problem under this paradigm is to calculate the minimum number of channels that enables unique reconstruction of the transmitted word. This problem is equivalent to finding the size of the largest intersection of channels’ outputs sets received after transmitting distinct codewords. Motivated by the error behavior observed in DNA storage systems, the present work extends the study of the reconstruction model to the case in which a binary word is transmitted over channels prone to substitutions, insertions, and deletions. Furthermore, we also study the size of the error balls generated by either one deletion and at most a fixed number of substitutions or one insertion and at most one substitution in a binary word. For the case of only substitutions, we present a decoder of optimal complexity, which improves upon a recent construction of such a decoder. Lastly, a simplification of that decoder is studied in case there are more channels than the minimum required number. [ABSTRACT FROM AUTHOR]

A private proximity retrieval (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 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, 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 receives a query in the protocol and the set of queries forms a code. The main focus in the paper is dedicated to studying the family of codes generated by the set of queries. These codes will be shown to satisfy a specific covering property and will be called private proximity retrieval intersection covering codes. In particular, since the query every server receives is a codeword, the goal is to minimize the number of codewords in such a code which is the minimum number of servers required by the protocol. These codes are closely related to a family of codes known as 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. [ABSTRACT FROM AUTHOR]