Related papers: Sequence Reconstruction for Limited-Magnitude Erro…
Regenerating codes are efficient methods for distributed storage in storage networks, where node failures are common. They guarantee low cost data reconstruction and repair through accessing only a predefined number of arbitrarily chosen…
We construct maximally recoverable codes (corresponding to partial MDS codes) which are based on linearized Reed-Solomon codes. The new codes have a smaller field size requirement compared with known constructions. For certain asymptotic…
This paper studies the sequence reconstruction problem for a channel inspired by protein identification. We introduce a coloring channel, where a sequence is transmitted through a channel that deletes all symbols not belonging to a fixed…
This paper develops a new method for recovering m-sparse signals that is simultaneously uniform and quick. We present a reconstruction algorithm whose run time, O(m log^2(m) log^2(d)), is sublinear in the length d of the signal. The…
As the global need for large-scale data storage is rising exponentially, existing storage technologies are approaching their theoretical and functional limits in terms of density and energy consumption, making DNA based storage a potential…
The sequence reconstruction problem was proposed by Levenshtein in 2001. In this model, a sequence from a code is transmitted over several channels, and the decoder receives the distinct outputs from each channel. The main problem is to…
This paper deals with gene networks whose dynamics is assumed to be generated by a continuous-time, linear, time invariant, finite dimensional system (LTI) at steady state. In particular, we deal with the problem of network reconstruction…
We consider linear network error correction (LNEC) coding when errors may occur on edges of a communication network of which the topology is known. In this paper, we first revisit and explore the framework of LNEC coding, and then unify two…
Matrix product operators allow efficient descriptions (or realizations) of states on a 1D lattice. We consider the task of learning a realization of minimal dimension from copies of an unknown state, such that the resulting operator is…
Maximum-distance-separable (MDS) codes are a class of erasure codes that are widely adopted to enhance the reliability of distributed storage systems (DSS). In (n, k) MDS coded DSS, the original data are stored into n distributed nodes in…
Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire…
We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…
Levenshtein first introduced the sequence reconstruction problem in $2001$. In the realm of combinatorics, the sequence reconstruction problem is equivalent to determining the value of $N(n,d,t)$, which represents the maximum size of the…
Motivated by mutation processes occurring in in-vivo DNA-storage applications, a channel that mutates stored strings by duplicating substrings as well as substituting symbols is studied. Two models of such a channel are considered: one in…
This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern…
DNA data storage systems encode digital data into DNA strands, enabling dense and durable storage. Efficient data retrieval depends on coverage depth, a key performance metric. We study the random access coverage depth problem and focus on…
Motivated by polymer-based data-storage platforms that use chains of binary synthetic polymers as the recording media and read the content via tandem mass spectrometers, we propose a new family of codes that allows for both unique string…
Motivated by communication channels in which the transmitted sequences are subject to random permutations, as well as by certain DNA storage systems, we study the error control problem in settings where the information is stored/transmitted…
Many application areas rely on models that can be readily simulated but lack a closed-form likelihood, or an accurate approximation under arbitrary parameter values. Existing parameter estimation approaches in this setting are generally…
$\epsilon$-Minimum Storage Regenerating ($\epsilon$-MSR) codes form a special class of Maximum Distance Separable (MDS) codes, providing mechanisms for exact regeneration of a single code block in their codewords by downloading slighly…