arXiv subjects

Jehoshua Bruck

Publications and source records attributed to Jehoshua Bruck.

At least 37 records · Page 2Linked to original sources

arXiv2018

Evolution of $k$-mer Frequencies and Entropy in Duplication and Substitution Mutation Systems

Genomic evolution can be viewed as string-editing processes driven by mutations. An understanding of the statistical properties resulting from these mutation processes is of value in a variety of tasks related to biological sequence data, e.g., estimation of model parameters and compression. At the same time, due to the complexity of these processes, designing tractable stochastic models and analyzing them are challenging. In this paper, we study two kinds of systems, each representing a set of mutations. In the first system, tandem duplications and substitution mutations are allowed and in the other, interspersed duplications. We provide stochastic models and, via stochastic approximation, study the evolution of substring frequencies for these two systems separately. Specifically, we show that $k$-mer frequencies converge almost surely and determine the limit set. Furthermore, we present a method for finding upper bounds on entropy for such systems.

cs.IT↗

arXiv2018

The Capacity of Some Pólya String Models

We study random string-duplication systems, which we call Pólya string models. These are motivated by DNA storage in living organisms, and certain random mutation processes that affect their genome. Unlike previous works that study the combinatorial capacity of string-duplication systems, or various string statistics, this work provides exact capacity or bounds on it, for several probabilistic models. In particular, we study the capacity of noisy string-duplication systems, including the tandem-duplication, end-duplication, and interspersed-duplication systems. Interesting connections are drawn between some systems and the signature of random permutations, as well as to the beta distribution common in population genetics.

cs.IT↗

arXiv2018

Two Deletion Correcting Codes from Indicator Vectors

Construction of capacity achieving deletion correcting codes has been a baffling challenge for decades. A recent breakthrough by Brakensiek $et~al$., alongside novel applications in DNA storage, have reignited the interest in this longstanding open problem. In spite of recent advances, the amount of redundancy in existing codes is still orders of magnitude away from being optimal. In this paper, a novel approach for constructing binary two-deletion correcting codes is proposed. By this approach, parity symbols are computed from indicator vectors (i.e., vectors that indicate the positions of certain patterns) of the encoded message, rather than from the message itself. Most interestingly, the parity symbols and the proof of correctness are a direct generalization of their counterparts in the Varshamov-Tenengolts construction. Our techniques require $7\log(n)+o(\log(n)$ redundant bits to encode an~$n$-bit message, which is near-optimal.

cs.IT↗

arXiv2017

Generic Secure Repair for Distributed Storage

This paper studies the problem of repairing secret sharing schemes, i.e., schemes that encode a message into $n$ shares, assigned to $n$ nodes, so that any $n-r$ nodes can decode the message but any colluding $z$ nodes cannot infer any information about the message. In the event of node failures so that shares held by the failed nodes are lost, the system needs to be repaired by reconstructing and reassigning the lost shares to the failed (or replacement) nodes. This can be achieved trivially by a trustworthy third-party that receives the shares of the available nodes, recompute and reassign the lost shares. The interesting question, studied in the paper, is how to repair without a trustworthy third-party. The main issue that arises is repair security: how to maintain the requirement that any colluding $z$ nodes, including the failed nodes, cannot learn any information about the message, during and after the repair process? We solve this secure repair problem from the perspective of secure multi-party computation. Specifically, we design generic repair schemes that can securely repair any (scalar or vector) linear secret sharing schemes. We prove a lower bound on the repair bandwidth of secure repair schemes and show that the proposed secure repair schemes achieve the optimal repair bandwidth up to a small constant factor when $n$ dominates $z$, or when the secret sharing scheme being repaired has optimal rate. We adopt a formal information-theoretic approach in our analysis and bounds. A main idea in our schemes is to allow a more flexible repair model than the straightforward one-round repair model implicitly assumed by existing secure regenerating codes. Particularly, the proposed secure repair schemes are simple and efficient two-round protocols.

cs.IT↗

arXiv2016

Duplication Distance to the Root for Binary Sequences

We study the tandem duplication distance between binary sequences and their roots. In other words, the quantity of interest is the number of tandem duplication operations of the form $\seq x = \seq a \seq b \seq c \to \seq y = \seq a \seq b \seq b \seq c$, where $\seq x$ and $\seq y$ are sequences and $\seq a$, $\seq b$, and $\seq c$ are their substrings, needed to generate a binary sequence of length $n$ starting from a square-free sequence from the set $\{0,1,01,10,010,101\}$. This problem is a restricted case of finding the duplication/deduplication distance between two sequences, defined as the minimum number of duplication and deduplication operations required to transform one sequence to the other. We consider both exact and approximate tandem duplications. For exact duplication, denoting the maximum distance to the root of a sequence of length $n$ by $f(n)$, we prove that $f(n)=Θ(n)$. For the case of approximate duplication, where a $β$-fraction of symbols may be duplicated incorrectly, we show that the maximum distance has a sharp transition from linear in $n$ to logarithmic at $β=1/2$. We also study the duplication distance to the root for sequences with a given root and for special classes of sequences, namely, the de Bruijn sequences, the Thue-Morse sequence, and the Fibbonaci words. The problem is motivated by genomic tandem duplication mutations and the smallest number of tandem duplication events required to generate a given biological sequence.

cs.IT↗

arXiv2016

Duplication-Correcting Codes for Data Storage in the DNA of Living Organisms

The ability to store data in the DNA of a living organism has applications in a variety of areas including synthetic biology and watermarking of patented genetically-modified organisms. Data stored in this medium is subject to errors arising from various mutations, such as point mutations, indels, and tandem duplication, which need to be corrected to maintain data integrity. In this paper, we provide error-correcting codes for errors caused by tandem duplications, which create a copy of a block of the sequence and insert it in a tandem manner, i.e., next to the original. In particular, we present two families of codes for correcting errors due to tandem-duplications of a fixed length, the first family can correct any number of errors while the second corrects a bounded number of errors. We also study codes for correcting tandem duplications of length up to a given constant $k$, where we are primarily focused on the cases of $k=2,3$. Finally, we provide a full classification of the sets of lengths allowed in tandem duplication that result in a unique root for all sequences.

cs.IT↗

arXiv2016

Communication Efficient Secret Sharing

A secret sharing scheme is a method to store information securely and reliably. Particularly, in a threshold secret sharing scheme, a secret is encoded into $n$ shares, such that any set of at least $t_1$ shares suffice to decode the secret, and any set of at most $t_2 < t_1$ shares reveal no information about the secret. Assuming that each party holds a share and a user wishes to decode the secret by receiving information from a set of parties; the question we study is how to minimize the amount of communication between the user and the parties. We show that the necessary amount of communication, termed "decoding bandwidth", decreases as the number of parties that participate in decoding increases. We prove a tight lower bound on the decoding bandwidth, and construct secret sharing schemes achieving the bound. Particularly, we design a scheme that achieves the optimal decoding bandwidth when $d$ parties participate in decoding, universally for all $t_1 \le d \le n$. The scheme is based on Shamir's secret sharing scheme and preserves its simplicity and efficiency. In addition, we consider secure distributed storage where the proposed communication efficient secret sharing schemes further improve disk access complexity during decoding.

cs.IT↗

arXiv2016

Optimal Rebuilding of Multiple Erasures in MDS Codes

MDS array codes are widely used in storage systems due to their computationally efficient encoding and decoding procedures. An MDS code with $r$ redundancy nodes can correct any $r$ node erasures by accessing all the remaining information in the surviving nodes. However, in practice, $e$ erasures is a more likely failure event, for $1\le e<r$. Hence, a natural question is how much information do we need to access in order to rebuild $e$ storage nodes? We define the rebuilding ratio as the fraction of remaining information accessed during the rebuilding of $e$ erasures. In our previous work we constructed MDS codes, called zigzag codes, that achieve the optimal rebuilding ratio of $1/r$ for the rebuilding of any systematic node when $e=1$, however, all the information needs to be accessed for the rebuilding of the parity node erasure. The (normalized) repair bandwidth is defined as the fraction of information transmitted from the remaining nodes during the rebuilding process. For codes that are not necessarily MDS, Dimakis et al. proposed the regenerating codes framework where any $r$ erasures can be corrected by accessing some of the remaining information, and any $e=1$ erasure can be rebuilt from some subsets of surviving nodes with optimal repair bandwidth. In this work, we study 3 questions on rebuilding of codes: (i) We show a fundamental trade-off between the storage size of the node and the repair bandwidth similar to the regenerating codes framework, and show that zigzag codes achieve the optimal rebuilding ratio of $e/r$ for MDS codes, for any $1\le e\le r$. (ii) We construct systematic codes that achieve optimal rebuilding ratio of $1/r$, for any systematic or parity node erasure. (iii) We present error correction algorithms for zigzag codes, and in particular demonstrate how these codes can be corrected beyond their minimum Hamming distances.

cs.IT↗

arXiv2015

Asymmetric Error Correction and Flash-Memory Rewriting using Polar Codes

We propose efficient coding schemes for two communication settings: 1. asymmetric channels, and 2. channels with an informed encoder. These settings are important in non-volatile memories, as well as optical and broadcast communication. The schemes are based on non-linear polar codes, and they build on and improve recent work on these settings. In asymmetric channels, we tackle the exponential storage requirement of previously known schemes, that resulted from the use of large Boolean functions. We propose an improved scheme, that achieves the capacity of asymmetric channels with polynomial computational complexity and storage requirement. The proposed non-linear scheme is then generalized to the setting of channel coding with an informed encoder, using a multicoding technique. We consider specific instances of the scheme for flash memories, that incorporate error-correction capabilities together with rewriting. Since the considered codes are non-linear, they eliminate the requirement of previously known schemes (called polar write-once-memory codes) for shared randomness between the encoder and the decoder. Finally, we mention that the multicoding scheme is also useful for broadcast communication in Marton's region, improving upon previous schemes for this setting.

cs.IT↗

arXiv2015

Capacity and Expressiveness of Genomic Tandem Duplication

The majority of the human genome consists of repeated sequences. An important type of repeated sequences common in the human genome are tandem repeats, where identical copies appear next to each other. For example, in the sequence $AGTC\underline{TGTG}C$, $TGTG$ is a tandem repeat, that may be generated from $AGTCTGC$ by a tandem duplication of length $2$. In this work, we investigate the possibility of generating a large number of sequences from a \textit{seed}, i.e.\ a small initial string, by tandem duplications of bounded length. We study the capacity of such a system, a notion that quantifies the system's generating power. Our results include \textit{exact capacity} values for certain tandem duplication string systems. In addition, motivated by the role of DNA sequences in expressing proteins via RNA and the genetic code, we define the notion of the \textit{expressiveness} of a tandem duplication system as the capability of expressing arbitrary substrings. We then \textit{completely} characterize the expressiveness of tandem duplication systems for general alphabet sizes and duplication lengths. In particular, based on a celebrated result by Axel Thue from 1906, presenting a construction for ternary square-free sequences, we show that for alphabets of size 4 or larger, bounded tandem duplication systems, regardless of the seed and the bound on duplication length, are not fully expressive, i.e. they cannot generate all strings even as substrings of other strings. Note that the alphabet of size 4 is of particular interest as it pertains to the genomic alphabet. Building on this result, we also show that these systems do not have full capacity. In general, our results illustrate that duplication lengths play a more significant role than the seed in generating a large number of sequences for these systems.

cs.IT↗

arXiv2015

Rewriting Flash Memories by Message Passing

This paper constructs WOM codes that combine rewriting and error correction for mitigating the reliability and the endurance problems in flash memory. We consider a rewriting model that is of practical interest to flash applications where only the second write uses WOM codes. Our WOM code construction is based on binary erasure quantization with LDGM codes, where the rewriting uses message passing and has potential to share the efficient hardware implementations with LDPC codes in practice. We show that the coding scheme achieves the capacity of the rewriting model. Extensive simulations show that the rewriting performance of our scheme compares favorably with that of polar WOM code in the rate region where high rewriting success probability is desired. We further augment our coding schemes with error correction capability. By drawing a connection to the conjugate code pairs studied in the context of quantum error correction, we develop a general framework for constructing error-correction WOM codes. Under this framework, we give an explicit construction of WOM codes whose codewords are contained in BCH codes.

cs.IT↗

arXiv2014

Rank-Modulation Rewrite Coding for Flash Memories

The current flash memory technology focuses on the cost minimization of its static storage capacity. However, the resulting approach supports a relatively small number of program-erase cycles. This technology is effective for consumer devices (e.g., smartphones and cameras) where the number of program-erase cycles is small. However, it is not economical for enterprise storage systems that require a large number of lifetime writes. The proposed approach in this paper for alleviating this problem consists of the efficient integration of two key ideas: (i) improving reliability and endurance by representing the information using relative values via the rank modulation scheme and (ii) increasing the overall (lifetime) capacity of the flash device via rewriting codes, namely, performing multiple writes per cell before erasure. This paper presents a new coding scheme that combines rank modulation with rewriting. The key benefits of the new scheme include: (i) the ability to store close to 2 bits per cell on each write with minimal impact on the lifetime of the memory, and (ii) efficient encoding and decoding algorithms that make use of capacity-achieving write-once-memory (WOM) codes that were proposed recently.

cs.IT↗

arXiv2014

Explicit MDS Codes for Optimal Repair Bandwidth

MDS codes are erasure-correcting codes that can correct the maximum number of erasures for a given number of redundancy or parity symbols. If an MDS code has $r$ parities and no more than $r$ erasures occur, then by transmitting all the remaining data in the code, the original information can be recovered. However, it was shown that in order to recover a single symbol erasure, only a fraction of $1/r$ of the information needs to be transmitted. This fraction is called the repair bandwidth (fraction). Explicit code constructions were given in previous works. If we view each symbol in the code as a vector or a column over some field, then the code forms a 2D array and such codes are especially widely used in storage systems. In this paper, we address the following question: given the length of the column $l$, number of parities $r$, can we construct high-rate MDS array codes with optimal repair bandwidth of $1/r$, whose code length is as long as possible? In this paper, we give code constructions such that the code length is $(r+1)\log_r l$.

cs.IT↗

arXiv2014

Systematic Codes for Rank Modulation

The goal of this paper is to construct systematic error-correcting codes for permutations and multi-permutations in the Kendall's $τ$-metric. These codes are important in new applications such as rank modulation for flash memories. The construction is based on error-correcting codes for multi-permutations and a partition of the set of permutations into error-correcting codes. For a given large enough number of information symbols $k$, and for any integer $t$, we present a construction for ${(k+r,k)}$ systematic $t$-error-correcting codes, for permutations from $S_{k+r}$, with less redundancy symbols than the number of redundancy symbols in the codes of the known constructions. In particular, for a given $t$ and for sufficiently large $k$ we can obtain $r=t+1$. The same construction is also applied to obtain related systematic error-correcting codes for multi-permutations.

cs.IT↗

arXiv2014

The Capacity of String-Replication Systems

It is known that the majority of the human genome consists of repeated sequences. Furthermore, it is believed that a significant part of the rest of the genome also originated from repeated sequences and has mutated to its current form. In this paper, we investigate the possibility of constructing an exponentially large number of sequences from a short initial sequence and simple replication rules, including those resembling genomic replication processes. In other words, our goal is to find out the capacity, or the expressive power, of these string-replication systems. Our results include exact capacities, and bounds on the capacities, of four fundamental string-replication systems.

cs.IT↗

arXiv2014

Rate-Distortion for Ranking with Incomplete Information

We study the rate-distortion relationship in the set of permutations endowed with the Kendall Tau metric and the Chebyshev metric. Our study is motivated by the application of permutation rate-distortion to the average-case and worst-case analysis of algorithms for ranking with incomplete information and approximate sorting algorithms. For the Kendall Tau metric we provide bounds for small, medium, and large distortion regimes, while for the Chebyshev metric we present bounds that are valid for all distortions and are especially accurate for small distortions. In addition, for the Chebyshev metric, we provide a construction for covering codes.

cs.IT↗

arXiv2013

Systematic Error-Correcting Codes for Rank Modulation

The rank-modulation scheme has been recently proposed for efficiently storing data in nonvolatile memories. Error-correcting codes are essential for rank modulation, however, existing results have been limited. In this work we explore a new approach, \emph{systematic error-correcting codes for rank modulation}. Systematic codes have the benefits of enabling efficient information retrieval and potentially supporting more efficient encoding and decoding procedures. We study systematic codes for rank modulation under Kendall's $τ$-metric as well as under the $\ell_\infty$-metric. In Kendall's $τ$-metric we present $[k+2,k,3]$-systematic codes for correcting one error, which have optimal rates, unless systematic perfect codes exist. We also study the design of multi-error-correcting codes, and provide two explicit constructions, one resulting in $[n+1,k+1,2t+2]$ systematic codes with redundancy at most $2t+1$. We use non-constructive arguments to show the existence of $[n,k,n-k]$-systematic codes for general parameters. Furthermore, we prove that for rank modulation, systematic codes achieve the same capacity as general error-correcting codes. Finally, in the $\ell_\infty$-metric we construct two $[n,k,d]$ systematic multi-error-correcting codes, the first for the case of $d=O(1)$, and the second for $d=Θ(n)$. In the latter case, the codes have the same asymptotic rate as the best codes currently known in this metric.

cs.IT↗

arXiv2013

Access vs. Bandwidth in Codes for Storage

Maximum distance separable (MDS) codes are widely used in storage systems to protect against disk (node) failures. A node is said to have capacity $l$ over some field $\mathbb{F}$, if it can store that amount of symbols of the field. An $(n,k,l)$ MDS code uses $n$ nodes of capacity $l$ to store $k$ information nodes. The MDS property guarantees the resiliency to any $n-k$ node failures. An \emph{optimal bandwidth} (resp. \emph{optimal access}) MDS code communicates (resp. accesses) the minimum amount of data during the repair process of a single failed node. It was shown that this amount equals a fraction of $1/(n-k)$ of data stored in each node. In previous optimal bandwidth constructions, $l$ scaled polynomially with $k$ in codes with asymptotic rate $<1$. Moreover, in constructions with a constant number of parities, i.e. rate approaches 1, $l$ is scaled exponentially w.r.t. $k$. In this paper, we focus on the later case of constant number of parities $n-k=r$, and ask the following question: Given the capacity of a node $l$ what is the largest number of information disks $k$ in an optimal bandwidth (resp. access) $(k+r,k,l)$ MDS code. We give an upper bound for the general case, and two tight bounds in the special cases of two important families of codes. Moreover, the bounds show that in some cases optimal-bandwidth code has larger $k$ than optimal-access code, and therefore these two measures are not equivalent.

cs.IT↗