Related papers: Correcting Contextual Deletions in DNA Nanopore Re…
The DNA storage channel is considered, in which a codeword is comprised of $M$ unordered DNA molecules. At reading time, $N$ molecules are sampled with replacement, and then each molecule is sequenced. A coded-index concatenated-coding…
This work studies problems in data reconstruction, an important area with numerous applications. In particular, we examine the reconstruction of binary and non-binary sequences from synchronization (insertion/deletion-correcting) codes.…
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…
We propose a deterministic method to design irregular Low-Density Parity-Check (LDPC) codes for binary erasure channels (BEC). Compared to the existing methods, which are based on the application of asymptomatic analysis tools such as…
In this paper, we investigate the redundancy of universal coding schemes on smooth parametric sources in the finite-length regime. We derive an upper bound on the probability of the event that a sequence of length $n$, chosen using…
In the emerging field of DNA storage, data is encoded as DNA sequences and stored. The data is read out again by sequencing the stored DNA. Nanopore sequencing is a new sequencing technology that has many advantages over other methods; in…
The persistent storage of big data requires advanced error correction schemes. The classical approach is to use error correcting codes (ECCs). This work studies an alternative approach, which uses the redundancy inherent in data itself for…
Low-depth random circuit codes possess many desirable properties for quantum error correction but have so far only been analyzed in the code capacity setting where it is assumed that encoding gates and syndrome measurements are noiseless.…
Constructing Reed-Solomon (RS) codes that can correct insertion and deletion (ins-del) errors has been the focus of several recent studies. However, efficient decoding algorithms for such codes have received less attention and remain a…
Reconstruction codes are generalizations of error-correcting codes that can correct errors by a given number of noisy reads. The study of such codes was initiated by Levenshtein in 2001 and developed recently due to applications in modern…
We utilize machine learning models which are based on recurrent neural networks to optimize dynamical decoupling (DD) sequences. DD is a relatively simple technique for suppressing the errors in quantum memory for certain noise models. In…
Rescaling a vector $\vec{\delta} \in \mathbb{R}^n$ to a desired length is a common operation in many areas such as data science and machine learning. When the rescaled perturbation $\eta \vec{\delta}$ is added to a starting point $\vec{x}…
Motivated by applications in DNA-based storage, we introduce the new problem of code design in the Damerau metric. The Damerau metric is a generalization of the Levenshtein distance which, in addition to deletions, insertions and…
We study the application of polar codes in deletion channels by analyzing the cascade of a binary erasure channel (BEC) and a deletion channel. We show how polar codes can be used effectively on a BEC with a single deletion, and propose a…
Finding deletion-correcting codes of maximum size has been an open problem for over 70 years, even for a single deletion. In this paper, we propose a novel approach for constructing deletion-correcting codes. A code is a set of sequences…
Recently, codes for correcting a burst of errors have attracted significant attention. One of the most important reasons is that bursts of errors occur in certain emerging techniques, such as DNA storage. In this paper, we investigate a…
Assuming iterative decoding for binary erasure channels (BECs), a novel tree-based technique for upper bounding the bit error rates (BERs) of arbitrary, finite low-density parity-check (LDPC) codes is provided and the resulting bound can be…
We consider deletion correcting codes over a q-ary alphabet. It is well known that any code capable of correcting s deletions can also correct any combination of s total insertions and deletions. To obtain asymptotic upper bounds on code…
Although the expenses associated with DNA sequencing have been rapidly decreasing, the current cost of sequencing information stands at roughly $120/GB, which is dramatically more expensive than reading from existing archival storage…
Motivated by applications in in-vivo DNA storage, we study codes for correcting duplications. A reverse-complement duplication of length $k$ is the insertion of the reversed and complemented copy of a substring of length $k$ adjacent to its…