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Anina Gruica

Publications and source records attributed to Anina Gruica.

At least 19 recordsLinked to original sources

The Generalized Random Access Problem for Linear Codes

Random access is a central requirement in DNA-based storage systems: one would like to recover selected information symbols without sequencing the whole encoded object. A recent combinatorial model associates to a generator matrix $G\in F_q^{k\times n}$ the random variable $τ_i(G)$, measuring the number of sampled columns needed to recover the information vector $e_i$. We study the cardinality-based extremal and finite-geometric aspects of simultaneous multi-symbol recovery. For a nonempty set $I\subseteq[k]$, let $τ_I(G)$ denote the number of random column samples needed until all vectors $e_i$, $i\in I$, lie in the span of the observed columns. This variable interpolates between the singleton random access problem and the full-recovery problem underlying coverage depth. For each $m$, we introduce uniform worst-case and average parameters over all requested sets $I$ with $|I|=m$. Using the known subset-counting formula for $E[τ_I(G)]$, we establish general upper and lower bounds for these parameters. In particular, the lower bounds are expressed through order statistics of the singleton recovery variables and specialize to the known singleton bounds when $m=1$. For systematic MDS encoders, we record an equivalent form of the known multi-symbol expectation formula and derive monotonicity and asymptotic consequences. For simplex encoders in arbitrary dimension, we obtain closed formulae in terms of Gaussian binomial coefficients; the full-recovery endpoint agrees with the known coverage-depth formula for simplex codes. Finally, in dimension three we study balanced quasi-arcs and compare their values with the simplex and MDS benchmarks.

cs.IT↗

Linear Code Conversion in the Merge Regime: General Bounds and Reed-Muller Constructions

Erasure codes are a core component of most existing large-scale distributed storage systems, ensuring reliability against node failures. Recent work has shown that adapting code parameters to changing node failure rates can lead to significant storage savings. The default approach is to re-encode the data under a new code, which consumes substantial system resources. Code conversion was introduced to reduce this cost. However, existing work has mainly focused on conversions within specific classes of codes. In this paper, we study scalar linear code conversion in the merge regime for arbitrary linear codes. We derive universal lower bounds on the write and read costs in terms of unchanged and read symbols. The bounds are refined using generalized Hamming weights, which capture support-growth properties of subcodes and can give sharper estimates than minimum-distance-only arguments. We show that the framework recovers known bounds for important special cases and can be strictly stronger when the final code has nontrivial jumps in its generalized Hamming weight hierarchy. We then apply the framework to Reed-Muller codes and construct explicit Reed-Muller convertible codes using the Plotkin decomposition. For a natural Reed-Muller parameter regime, the construction attains the derived write-cost lower bound. For the read cost, the generalized-Hamming-weight analysis is sharp for one initial block, while a gap remains for the other block.

cs.IT↗

Explicit and asymptotically good constructions of Algebraic Geometry codes in the sum-rank metric

Algebraic Geometry (AG) codes (i.e. linear codes from algebraic function fields) in the Hamming metric were proposed by Goppa in 1980 and have been intensively studied ever since. Linearized Algebraic Geometry codes, the analogue of AG codes in the sum-rank metric, were instead introduced more recently [9], using quotients of the ring of Ore polynomials with coefficients in an algebraic function field. In this paper, we further investigate the results in [9], providing explicit, optimal and asymptotic constructions.

cs.IT↗

Serving Every Symbol: All-Symbol PIR and Batch Codes

A $t$-all-symbol PIR code and a $t$-all-symbol batch code of dimension $k$ consist of $n$ servers storing linear combinations of $k$ information symbols with the following recovery property: any symbol stored by a server can be recovered from $t$ pairwise disjoint subsets of servers. In the batch setting, we further require that any multiset of size $t$ of stored symbols can be recovered from~$t$ disjoint subsets of servers. This framework unifies and extends several well-known code families, including one-step majority-logic decodable codes, (functional) PIR codes, and (functional) batch codes. In this paper, we determine the minimum code length for some small values of $k$ and $t$, characterize structural properties of codes attaining this optimum, and derive bounds that show the trade-offs between length, dimension, minimum distance, and $t$. In addition, we study MDS codes and the simplex code, demonstrating how these classical families fit within our framework, and establish new cases of an open conjecture from \cite{YAAKOBI2020} concerning the minimal $t$ for which the simplex code is a $t$-functional batch code.

cs.IT↗

Convertible Codes for Data and Device Heterogeneity

Distributed storage systems must handle both data heterogeneity, arising from non-uniform access demands, and device heterogeneity, caused by time-varying node reliability. In this paper, we study convertible codes, which enable the transformation of one code into another with minimum cost in the merge regime, addressing the latter. We derive general lower bounds on the read and write costs of linear code conversion, applicable to arbitrary linear codes. We then focus on Reed-Muller codes, which efficiently handle data heterogeneity, addressing the former issue, and construct explicit conversion procedures that, for the first time, combine both forms of heterogeneity for distributed data storage.

cs.IT↗

The Geometry of Codes for Random Access in DNA Storage

Effective and reliable data retrieval is critical for the feasibility of DNA storage, and the development of random access efficiency plays a key role in its practicality and reliability. In this paper, we study the Random Access Problem, which asks to compute the expected number of samples one needs in order to recover an information strand. Unlike previous work, we took a geometric approach to the problem, aiming to understand which geometric structures lead to codes that perform well in terms of reducing the random access expectation (Balanced Quasi-Arcs). As a consequence, two main results are obtained. The first is a construction for $k=3$ that outperforms previous constructions aiming to reduce the random access expectation. The second, exploiting a result from~\cite{gruica2024reducing}, is the proof of a conjecture from~\cite{bar2023cover} for rate $1/2$ codes in any dimension.

cs.IT↗

A Combinatorial Perspective on Random Access Efficiency for DNA Storage

We investigate the fundamental limits of the recently proposed random access coverage depth problem for DNA data storage. Under this paradigm, it is assumed that the user information consists of $k$ information strands, which are encoded into $n$ strands via a generator matrix $G$. During the sequencing process, the strands are read uniformly at random, as each strand is available in a large number of copies. In this context, the random access coverage depth problem refers to the expected number of reads (i.e., sequenced strands) required to decode a specific information strand requested by the user. This problem heavily depends on the generator matrix $G$, and besides computing the expectation for different choices of $G$, the goal is to construct matrices that minimize the maximum expectation over all possible requested information strands, denoted by $T_{\max}(G)$. In this paper, we introduce new techniques to investigate the random access coverage depth problem, capturing its combinatorial nature and identifying the structural properties of generator matrices that are advantageous. We establish two general formulas to determine $T_{\max}(G)$ for arbitrary generator matrices. The first formula depends on the linear dependencies between columns of $G$, whereas the second formula takes into account recovery sets and their intersection structure. We also introduce the concept of recovery balanced codes and provide three sufficient conditions for a code to be recovery balanced. These conditions can be used to compute $T_{\max}(G)$ for various families of codes, such as MDS, simplex, Hamming, and binary Reed-Muller codes. Additionally, we study the performance of modified systematic MDS and simplex matrices, showing that the best results for $T_{\max}(G)$ are achieved with a specific combination of encoded strands and replication of the information strands.

cs.IT↗

Reed-Solomon Codes Against Insertions and Deletions: Full-Length and Rate-$1/2$ Codes

The performance of Reed--Solomon codes (RS codes, for short) in the presence of insertion and deletion errors has attracted growing attention in recent literature. In this work, we further study this intriguing mathematical problem, focusing on two regimes. First, we study the question of how well full-length RS codes perform against insertions and deletions. For 2-dimensional RS codes, we provide a complete characterization of codes that cannot correct even a single insertion or deletion. Furthermore, we prove that for sufficiently large field size~$q$, nearly all full-length $2$-dimensional RS codes can correct up to $(1 - δ)q$ insertion and deletion errors for any $0 < δ< 1$. Extending beyond the 2-dimensional case, we show that for any $k \ge 2$, there exists a full-length $k$-dimensional RS code capable of correcting $q / (10k)$ insertion and deletion errors, provided $q$ is large enough. Second, we focus on rate $1/2$ RS codes that can correct a single insertion or deletion error. We present a polynomial-time algorithm that constructs such codes over fields of size $q = Θ(k^4)$. This result matches the existential bound given in \cite{con2023reed}.

cs.IT↗

Making it to First: The Random Access Problem in DNA Storage

In this paper, we study the Random Access Problem in DNA storage, which addresses the challenge of retrieving a specific information strand from a DNA-based storage system. In this framework, the data is represented by $k$ information strands which represent the data and are encoded into $n$ strands using a linear code. Then, each sequencing read returns one encoded strand which is chosen uniformly at random. The goal under this paradigm is to design codes that minimize the expected number of reads required to recover an arbitrary information strand. We fully solve the case when $k=2$, showing that the best possible code attains a random access expectation of $1+\frac{2}{\sqrt{2}+1}\approx 0.914\cdot 2$ for $q$ large enough. Moreover, we generalize a construction from~\cite{GMZ24}, specifically to $k=3$, for any value of $k$. Our construction uses $B_{k-1}$ sequences over $\mathbb{Z}_{q-1}$, that always exist over large finite fields. We show that for every $k\geq 4$, this generalized construction outperforms all previous constructions in terms of reducing the random access expectation.

cs.IT↗

Achieving DNA Labeling Capacity with Minimum Labels through Extremal de Bruijn Subgraphs

DNA labeling is a tool in molecular biology and biotechnology to visualize, detect, and study DNA at the molecular level. In this process, a DNA molecule is labeled by a set of specific patterns, referred to as labels, and is then imaged. The resulting image is modeled as an $(\ell+1)$-ary sequence, where $\ell$ is the number of labels, in which any non-zero symbol indicates the appearance of the corresponding label in the DNA molecule. The labeling capacity refers to the maximum information rate that can be achieved by the labeling process for any given set of labels. The main goal of this paper is to study the minimum number of labels of the same length required to achieve the maximum labeling capacity of 2 for DNA sequences or $\log_2q$ for an arbitrary alphabet of size $q$. The solution to this problem requires the study of path unique subgraphs of the de Bruijn graph with the largest number of edges. We provide upper and lower bounds on this value. We draw new connections to existing literature that let us prove an asymptotic result as the label length tends to infinity.

cs.IT↗

Rank-Metric Codes and Their Parameters

We present the theory of linear rank-metric codes from the point of view of their fundamental parameters. These are: the minimum rank distance, the rank distribution, the maximum rank, the covering radius, and the field size. The focus of this chapter is on the interplay among these parameters and on their significance for the code's (combinatorial) structure. The results covered in this chapter span from the theory of optimal codes and anticodes to very recent developments on the asymptotic density of MRD codes.

cs.IT↗

The Diagonals of a Ferrers Diagram

We propose and develop a theory of Ferrers diagrams and their $q$-rook polynomials solely based on their diagonals. We show that the cardinalities of the diagonals of a Ferrers diagram are equivalent information to their rook numbers, $q$-rook polynomials, and the rank distribution of matrices supported on the diagram. Our approach is based on the concept of \textit{canonical form} of a Ferrers diagrams, and on two simple diagram operations as the main proof tools. In the second part of the paper we develop the same theory for symmetric Ferrers diagrams, considering symmetric and alternating matrices supported on them. As an application of our results, we establish some combinatorial identities linking symmetric and alternating matrices, which do not appear to have an obvious bijective proof, and which generalize some curious results in enumerative combinatorics.

math.CO↗

Generalised Evasive Subspaces

We introduce and explore a new concept of evasive subspace with respect to a collection of subspaces sharing a common dimension, most notably partial spreads. We show that this concept generalises known notions of subspace scatteredness and evasiveness. We establish various upper bounds for the dimension of an evasive subspace with respect to arbitrary partial spreads, obtaining improvements for the Desarguesian ones. We also establish existence results for evasive spaces in a non-constructive way, using a graph theory approach. The upper and lower bounds we derive have a precise interpretation as bounds for the critical exponent of certain combinatorial geometries. Finally, we investigate connections between the notion of evasive space we introduce and the theory of rank-metric codes, obtaining new results on the covering radius and on the existence of minimal vector rank-metric codes.

math.CO↗

LRCs: Duality, LP Bounds, and Field Size

We develop a duality theory of locally recoverable codes (LRCs) and apply it to establish a series of new bounds on their parameters. We introduce and study a refined notion of weight distribution that captures the code's locality. Using a duality result analogous to a MacWilliams identity, we then derive an LP-type bound that improves on the best known bounds in several instances. Using a dual distance bound and the theory of generalized weights, we obtain non-existence results for optimal LRCs over small fields. In particular, we show that an optimal LRC must have both minimum distance and block length relatively small compared to the field size.

cs.IT↗

Densities of Codes of Various Linearity Degrees in Translation-Invariant Metric Spaces

We investigate the asymptotic density of error-correcting codes with good distance properties and prescribed linearity degree, including sublinear and nonlinear codes. We focus on the general setting of finite translation-invariant metric spaces, and then specialize our results to the Hamming metric, to the rank metric, and to the sum-rank metric. Our results show that the asymptotic density of codes heavily depends on the imposed linearity degree and the chosen metric.

cs.IT↗

Duality and LP Bounds for Codes with Locality

We initiate the study of the duality theory of locally recoverable codes, with a focus on the applications. We characterize the locality of a code in terms of the dual code, and introduce a class of invariants that refine the classical weight distribution. In this context, we establish a duality theorem analogous to (but very different from) a MacWilliams identity. As an application of our results, we obtain two new bounds for the parameters of a locally recoverable code, including an LP bound that improves on the best available bounds in several instances.

cs.IT↗

Rook Theory of the Etzion-Silberstein Conjecture

In 2009, Etzion and Siberstein proposed a conjecture on the largest dimension of a linear space of matrices over a finite field in which all nonzero matrices are supported on a Ferrers diagram and have rank bounded below by a given integer. Although several cases of the conjecture have been established in the past decade, proving or disproving it remains to date a wide open problem. In this paper, we take a new look at the Etzion-Siberstein Conjecture, investigating its connection with rook theory. Our results show that the combinatorics behind this open problem is closely linked to the theory of $q$-rook polynomials associated with Ferrers diagrams, as defined by Garsia and Remmel. In passing, we give a closed formula for the trailing degree of the $q$-rook polynomial associated with a Ferrers diagram in terms of the cardinalities of its diagonals. The combinatorial approach taken in this paper allows us to establish some new instances of the Etzion-Silberstein Conjecture using a non-constructive argument. We also solve the asymptotic version of the conjecture over large finite fields, answering a current open question.

math.CO↗

Convolutional codes over finite chain rings, MDP codes and their characterization

In this paper, we develop the theory of convolutional codes over finite commutative chain rings. In particular, we focus on maximum distance profile (MDP) convolutional codes and we provide a characterization of these codes, generalizing the one known for fields. Moreover, we relate (reverse) MDP convolutional codes over a finite chain ring with (reverse) MDP convolutional codes over its residue field. Finally, we provide a construction of (reverse) MDP convolutional codes over finite chain rings generalizing the notion of (reverse) superregular matrices.

cs.IT↗