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Hyperdimensional computing (HDC) is an emerging computational paradigm for representing compositional information as high-dimensional vectors and has a promising potential in applications ranging from machine learning to neuromorphic computing. One of the long-standing challenges in HDC is factoring a compositional representation to its constituent factors, also known as the recovery problem. In this article, we take a novel approach to solve the recovery problem and propose the use of random linear codes. These codes are subspaces over the Boolean field and are a well-studied topic in information theory with various applications in digital communication. We begin by showing that hyperdimensional encoding using random linear codes retains favorable properties of the prevalent (ordinary) random codes; hence, HD representations using the two methods have comparable information storage capabilities. We proceed to show that random linear codes offer a rich subcode structure that can be used to form key-value stores, which encapsulate the most used cases of HDC. Most important, we show that under the framework we develop, random linear codes admit simple recovery algorithms to factor (either bundled or bound) compositional representations. The former relies on constructing certain linear equation systems over the Boolean field, the solution to which reduces the search space dramatically and strictly outperforms exhaustive search in many cases. The latter employs the subspace structure of these codes to achieve provably correct factorization. Both methods are strictly faster than the state-of-the-art resonator networks, often by an order of magnitude. We implemented our techniques in Python using a benchmark software library and demonstrated promising experimental results. [ABSTRACT FROM AUTHOR]

Current approach for the detection of cancer is based on identifying genetic mutations typical to tumor cells. This approach is effective only when cancer has already emerged, however, it might be in a stage too advanced for effective treatment. Cancer is caused by the continuous accumulation of mutations; is it possible to measure the time-dependent information of mutation accumulation and predict the emergence of cancer? We hypothesize that the mutation history derived from the tandem repeat regions in blood-derived DNA carries information about the accumulation of the cancer driver mutations in other tissues. To validate our hypothesis, we computed the mutation histories from the tandem repeat regions in blood-derived exomic DNA of 3874 TCGA patients with different cancer types and found a statistically significant signal with specificity ranging from 66% to 93% differentiating Glioblastoma patients from other cancer patients. Our approach and findings offer a new direction for future cancer prediction and early cancer detection based on information derived from blood-derived DNA. [ABSTRACT FROM AUTHOR]

The interest in channel models in which the data is sent as an unordered set of binary strings has increased lately, due to emerging applications in DNA storage, among others. In this paper we analyze the minimal redundancy of binary codes for this channel under substitution errors, and provide several constructions, some of which are shown to be asymptotically optimal up to constants. The surprising result in this paper is that while the information vector is sliced into a set of unordered strings, the amount of redundant bits that are required to correct errors is order-wise equivalent to the amount required in the classical error correcting paradigm. [ABSTRACT FROM AUTHOR]

Gradient coding is a technique for straggler mitigation in distributed learning. In this paper we design novel gradient codes using tools from classical coding theory, namely, cyclic MDS codes, which compare favorably with existing solutions, both in the applicable range of parameters and in the complexity of the involved algorithms. Second, we introduce an approximate variant of the gradient coding problem, in which we settle for approximate gradient computation instead of the exact one. This approach enables graceful degradation, i.e., the $\ell _{2}$ error of the approximate gradient is a decreasing function of the number of stragglers. Our main result is that normalized adjacency matrices of expander graphs yield excellent approximate gradient codes, which enable significantly less computation compared to exact gradient coding, and guarantee faster convergence than trivial solutions under standard assumptions. We experimentally test our approach on Amazon EC2, and show that the generalization error of approximate gradient coding is very close to the full gradient while requiring significantly less computation from the workers. [ABSTRACT FROM AUTHOR]

Private computation is a generalization of private information retrieval, in which a user is able to compute a function on a distributed dataset without revealing the identity of that function to the servers. In this paper, it is shown that Lagrange encoding, a powerful technique for encoding Reed-Solomon codes, enables private computation in many cases of interest. In particular, we present a scheme that enables private computation of polynomials of any degree on Lagrange encoded data, while being robust to Byzantine and straggling servers, and to servers colluding to attempt to deduce the identities of the functions to be evaluated. Moreover, incorporating ideas from the well-known Shamir secret sharing scheme allows the data itself to be concealed from the servers as well. Our results extend private computation to high degree polynomials and to data-privacy, and reveal a tight connection between private computation and coded computation. [ABSTRACT FROM AUTHOR]

In a Private Information Retrieval (PIR) protocol, a user can download a file from a database without revealing the identity of the file to each individual server. A PIR protocol is called $t$ -private if the identity of the file remains concealed even if $t$ of the servers collude. Graph based replication is a simple technique, which is prevalent in both theory and practice, for achieving robustness in storage systems. In this technique each file is replicated on two or more storage servers, giving rise to a (hyper-)graph structure. In this paper we study private information retrieval protocols in graph based replication systems. The main interest of this work is understanding the collusion structures which emerge in the underlying graph. Our main contribution is a 2-replication scheme which guarantees perfect privacy from acyclic sets in the graph, and guarantees partial-privacy in the presence of cycles. Furthermore, by providing an upper bound, it is shown that the PIR rate of this scheme is at most a factor of two from its optimal value for regular graphs. Lastly, we extend our results to larger replication factors and to graph-based coding, a generalization of graph based replication that induces smaller storage overhead and larger PIR rate in many cases. [ABSTRACT FROM AUTHOR]

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 closer to optimal than previous constructions. Moreover, the encoding and decoding algorithms have ${O}({n})$ time complexity. [ABSTRACT FROM AUTHOR]

In this paper, we introduce a new channel model termed as the $q$ -ary multi-bit channel. This channel models a memory device, where $q$ -ary symbols ($q=2^{s}$) are stored in the form of current/voltage levels. The symbols are read in a measurement process, which provides a symbol bit in each measurement step, starting from the most significant bit. An error event occurs when not all the symbol bits are known. To deal with such error events, we use GF($q$) low-density parity-check (LDPC) codes and analyze their decoding performance. We start with iterative-decoding threshold analysis and derive optimal edge-label distributions for maximizing the decoding threshold. We later move to a finite-length iterative-decoding analysis and propose an edge-labeling algorithm for the improved decoding performance. We then provide a finite-length maximum-likelihood decoding analysis for both the standard non-binary random ensemble and LDPC ensembles. Finally, we demonstrate by simulations that the proposed edge-labeling algorithm improves the finite-length decoding performance by orders of magnitude. [ABSTRACT FROM AUTHOR]

Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to maintain reliability in reading and writing, new coding schemes must be developed. In a reading technique called shotgun sequencing, a long DNA string is read in a sliding window fashion, and a profile vector is produced. It was recently suggested by Kiah et al. that such a vector can represent the permutation which is induced by its entries, and hence a rank-modulation scheme arises. Although this interpretation suggests high error tolerance, it is unclear which permutations are feasible and how to produce a DNA string whose profile vector induces a given permutation. In this paper, by observing some necessary conditions, an upper bound for the number of feasible permutations is given. Furthermore, a technique for deciding the feasibility of a permutation is devised. By using insights from this technique, an algorithm for producing a considerable number of feasible permutations is given, which applies to any alphabet size and any window length. [ABSTRACT FROM AUTHOR]

The study of regenerating codes has advanced tremendously in recent years. However, most known constructions require large field size and, hence, may be hard to implement in practice. By restructuring a code construction by Rashmi et al., we obtain two explicit families regenerating codes. These codes approach the cut-set bound as the reconstruction degree increases and may be realized over any given finite field if the file size is large enough. Essentially, these codes constitute a constructive proof that the cut-set bound does not imply a field size restriction, unlike some known bounds for ordinary linear codes. The first construction attains the cut-set bound at the MBR point asymptotically for all parameters, whereas the second one attains the cut-set bound at the MSR point asymptotically for low-rate parameters. Even though these codes require a large file size, this restriction is trivially satisfied in most conceivable distributed storage scenarios, that are the prominent motivation for regenerating codes. [ABSTRACT FROM AUTHOR]

A subspace of a finite extension field is called a Sidon space if the product of any two of its elements is unique up to a scalar multiplier from the base field. Sidon spaces were recently introduced by Bachoc et al. as a means to characterize multiplicative properties of subspaces, and yet no explicit constructions were given. In this paper, several constructions of Sidon spaces are provided. In particular, in some of the constructions the relation between $k$ , the dimension of the Sidon space, and $n$ , the dimension of the ambient extension field, is optimal. These constructions are shown to provide cyclic subspace codes, which are useful tools in network coding schemes. To the best of our knowledge, this constitutes the first set of constructions of non-trivial cyclic subspace codes in which the relation between $k$ and $n$ is polynomial, and in particular, linear. As a result, a conjecture by Trautmann et al. regarding the existence of non-trivial cyclic subspace codes is resolved for most parameters, and multi-orbit cyclic subspace codes are attained, whose cardinality is within a constant factor (close to 1/2) from the sphere-packing bound for subspace codes. [ABSTRACT FROM AUTHOR]

The problem of storing permutations in a distributed manner arises in several common scenarios, such as efficient updates of a large, encrypted, or compressed data set. This problem may be addressed in either a combinatorial or a coding approach. The former approach boils down to presenting large sets of permutations with locality, that is, any symbol of the permutation can be computed from a small set of other symbols. In the latter approach, a permutation may be coded in order to achieve locality. Both approaches must present low query complexity to allow the user to find an element efficiently. We discuss both approaches, and give a particular focus to the combinatorial one. In the combinatorial approach, we provide upper and lower bounds for the maximal size of a set of permutations with locality, and provide several simple constructions which attain the upper bound. In cases where the upper bound is not attained, we provide alternative constructions using a variety of tools, such as Reed-Solomon codes, permutation polynomials, and multi-permutations. In addition, several low-rate constructions of particular interest are discussed. In the coding approach we discuss an alternative representation of permutations, present a paradigm for supporting arbitrary powers of the stored permutation, and conclude with a proof of concept that permutations may be stored more efficiently than ordinary strings over the same alphabet. [ABSTRACT FROM AUTHOR]

A novel technique for construction of minimum storage regenerating (MSR) codes is presented. Based on this technique, three explicit constructions of MSR codes are given. The first two constructions provide access-optimal MSR codes, with two and three parities, respectively, which attain the sub-packetization bound for access-optimal codes. The third construction provides longer MSR codes with three parities (i.e., codes with larger number of systematic nodes). This improvement is achieved at the expense of the access-optimality and the field size. In addition to a minimum storage in a node, all three constructions allow the entire data to be recovered from a minimal number of storage nodes. That is, given storage \ell in each node, the entire stored data can be recovered from any 2\log _{2} \ell for two parity nodes, and either 3\log _{3}\ell or 4\log 3\ell for three parities. Second, in the first two constructions, a helper node accesses the minimum number of its symbols for repair of a failed node (access-optimality). The goal of this paper is to provide a construction of such optimal codes over the smallest possible finite fields. The generator matrix of these codes is based on perfect matchings of complete graphs and hypergraphs, and on a rational canonical form of matrices. For two parities, the field size is reduced by a factor of two for access-optimal codes compared to previous constructions. For three parities, in the first construction a field size of at least 6\log 3 \ell +1 (or 3\log 3 \ell +1 for fields with characteristic 2) is sufficient, and in the second construction the field size is larger, yet linear in \log 3\ell . Both constructions with three parities provide a significant improvement over previous works due to either decreased field size or lower subpacketization. [ABSTRACT FROM PUBLISHER]

Gabidulin codes can be seen as the rank-metric equivalent of Reed–Solomon codes. It was recently proved, using subspace polynomials, that Gabidulin codes cannot be list decoded beyond the so-called Johnson radius. In another result, cyclic subspace codes were constructed by inspecting the connection between subspaces and their subspace polynomials. In this paper, these subspace codes are used to prove two bounds on the list size in decoding certain Gabidulin codes. The first bound is an existential one, showing that exponentially sized lists exist for codes with specific parameters. The second bound presents exponentially sized lists explicitly for a different set of parameters. Both bounds rule out the possibility of efficiently list decoding several families of Gabidulin codes for any radius beyond half the minimum distance. Such a result was known so far only for non-linear rank-metric codes, and not for Gabidulin codes. Using a standard operation called lifting, identical results also follow for an important class of constant dimension subspace codes. [ABSTRACT FROM AUTHOR]

Subspace codes have received an increasing interest recently due to their application in error correction for random network coding. In particular, cyclic subspace codes are possible candidates for large codes with efficient encoding and decoding algorithms. In this paper, we consider such cyclic codes and provide constructions of optimal codes for which their codewords do not have full orbits. We further introduce a new way to represent subspace codes by a class of polynomials called subspace polynomials. We present some constructions of such codes, which are cyclic and analyze their parameters. [ABSTRACT FROM AUTHOR]

Linear codes over finite extension fields have widespread applications in theory and practice. In some scenarios, the decoder has a sequential access to the codeword symbols, giving rise to a hierarchical erasure structure. In this paper we develop a mathematical framework for hierarchical erasures over extension fields, provide several bounds and constructions, and discuss potential applications in distributed storage and flash memories. Our results show intimate connection to Universally Decodable Matrices, as well as to Reed-Solomon and Gabidulin codes. [ABSTRACT FROM AUTHOR]