Related papers: Improved Coding over Sets for DNA-Based Data Stora…
This work is motivated by the problem of error correction in bit-shift channels with the so-called $ (d,k) $ input constraints (where successive $ 1 $'s are required to be separated by at least $ d $ and at most $ k $ zeros, $ 0 \leq d < k…
The main obstacles for the practical deployment of DNA-based data storage platforms are the prohibitively high cost of synthetic DNA and the large number of errors introduced during synthesis. In particular, synthetic DNA products contain…
Encoding digital information into DNA sequences offers an attractive potential solution for storing rapidly growing data under the information age and the rise of artificial intelligence. However, practical implementations of DNA storage…
"Independent and identically distributed" errors do not accurately capture the noisy behavior of real-world data storage and information transmission technologies. Motivated by this, we study channels with input-correlated synchronization…
DNA-based data storage systems face practical challenges due to the high cost of DNA synthesis. A strategy to address the problem entails encoding data via topological modifications of the DNA sugar-phosphate backbone. The DNA Punchcards…
DNA is a promising storage medium, but its stability and occurrence of Indel errors pose a significant challenge. The relative occurrence of Guanine(G) and Cytosine(C) in DNA is crucial for its longevity, and reverse complementary base…
In this paper, we consider the problem of variable packet-error coding, which emerges in network communication scenarios where a source transmits information to a destination through multiple disjoint paths. The objective is to design codes…
Enzymatic DNA labeling is a powerful tool with applications in biochemistry, molecular biology, biotechnology, medical science, and genomic research. This paper contributes to the evolving field of DNA-based data storage by presenting a…
We consider data transmission over a network where each edge is an erasure channel and where the inner nodes transmit a random linear combination of their incoming information. We distinguish two channel models in this setting, the row and…
This paper is concerned with the problem of error-free communication over the i.i.d. duplication channel which acts on a transmitted sequence $ x_1 \cdots x_n $ by inserting a random number of copies of each symbol $ x_i $ next to the…
Quantum error correction requires the use of error syndromes derived from measurements that may be unreliable. Recently, quantum data-syndrome (QDS) codes have been proposed as a possible approach to protect against both data and syndrome…
Deep Neural Networks (DNNs) have revolutionized computer vision. We now have DNNs that achieve top (performance) results in many problems, including object recognition, facial expression analysis, and semantic segmentation, to name but a…
Secure codes are widely-studied combinatorial structures which were introduced for traitor tracing in broadcast encryption. To determine the maximum size of such structures is the main research objective. In this paper, we investigate the…
We provide a general formulation for the code-based test compression problem with fixed-length input blocks and propose a solution approach based on Evolutionary Algorithms. In contrast to existing code-based methods, we allow unspecified…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
Motivation: Next Generation Sequencing technologies revolutionized many fields in biology by enabling the fast and cheap sequencing of large amounts of genomic data. The ever increasing sequencing capacities enabled by current sequencing…
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…
This study explores the self-synchronization problem in DNA coding, specifically addressing single-deletion errors without using delimiters between codewords. We aim to identify the beginning of each codeword without using delimiters,…
A new deep-neural-network (DNN) based error correction encoder architecture for channels with feedback, called Deep Extended Feedback (DEF), is presented in this paper. The encoder in the DEF architecture transmits an information message…
Noisy shuffling channels capture the main characteristics of DNA storage systems where distinct segments of data are received out of order, after being corrupted by substitution errors. For realistic schemes with short-length segments,…