Related papers: Algorithms of self-synchronizing single-deletion-c…
Quantum convolutional code was introduced recently as an alternative way to protect vital quantum information. To complete the analysis of quantum convolutional code, I report a way to decode certain quantum convolutional codes based on the…
Recent work by Smagloy et al. (ISIT 2020) shows that the redundancy of a single-deletion $s$-substitution correcting code is asymptotically at least $(s+1)\log n+o(\log n)$, where $n$ is the length of the codes. They also provide a…
This paper studies two problems that are motivated by the novel recent approach of composite DNA that takes advantage of the DNA synthesis property which generates a huge number of copies for every synthesized strand. Under this paradigm,…
Single individual haplotyping is an NP-hard problem that emerges when attempting to reconstruct an organism's inherited genetic variations using data typically generated by high-throughput DNA sequencing platforms. Genomes of diploid…
Frameshift translation is an important phenomenon that contributes to the appearance of novel Coding DNA Sequences (CDS) and functions in gene evolution, by allowing alternative amino acid translations of genes coding regions. Frameshift…
In a distributed information application an encoder compresses an arbitrary vector while a similar reference vector is available to the decoder as side information. For the Hamming-distance similarity measure, and when guaranteed perfect…
In this paper, we propose a fast decoder algorithm for uniquely decodable (errorless) code sets for overloaded synchronous optical code-division multiple-access (O-CDMA) systems. The proposed decoder is designed in a such a way that the…
The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to…
Tandem duplication in DNA is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain {\em et al.} (2016) proposed the study of codes that…
Non-uniquely decodable codes can be defined as the codes that cannot be uniquely decoded without additional disambiguation information. These are mainly the class of non-prefix-free codes, where a codeword can be a prefix of other(s), and…
This paper studies the complicated interplay of the completion time (as a measure of throughput) and the decoding delay performance in instantly decodable network coded (IDNC) systems over wireless broadcast erasure channels with memory,…
Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…
To address the issue of increased bit error rates during the later stages of linear search in denoising diffusion error correction codes, we propose a novel method that optimizes denoising diffusion error correction codes (ECC) using cosine…
This paper studies \emph{linear} and \emph{affine} error-correcting codes for correcting synchronization errors such as insertions and deletions. We call such codes linear/affine insdel codes. Linear codes that can correct even a single…
Constrained sequence (CS) codes, including fixed-length CS codes and variable-length CS codes, have been widely used in modern wireless communication and data storage systems. Sequences encoded with constrained sequence codes satisfy…
We investigate the possibility of encoding multiple solutions of a problem in a single chromosome. The best solution encoded in an individual will represent (will provide the fitness of) that individual. In order to obtain some benefits the…
We consider the problem of encoding information in a system of N=K+R processors that operate in a decentralized manner, i.e., without a central processor which orchestrates the operation. The system involves K source processors, each…
Network security is a growing issue, with the evolution of computer systems and expansion of attacks. Biological systems have been inspiring scientists and designs for new adaptive solutions, such as genetic algorithms. In this paper, we…
Nanopore sequencing technology remains highly error-prone, making efficient error correction essential in DNA-based data storage. Prior work addressed high error rates using convolutional codes with their decoder coupled with the…
Quantum computers herald the arrival of a new era in which previously intractable computational problems will be solved efficiently. However, quantum technology is held down by decoherence, a phenomenon that is omnipresent in the quantum…