Related papers: Iterative DNA Coding Scheme With GC Balance and Ru…
Given a set of strings, the shortest common superstring problem is to find the shortest possible string that contains all the input strings. The problem is NP-hard, but a lot of work has gone into designing approximation algorithms for…
We empirically analyze a simple heuristic for large sparse set cover problems. It uses the weighted greedy algorithm as a basic building block. By multiplicative updates of the weights attached to the elements, the greedy solution is…
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…
DNA has been considered a promising medium for storing digital information. As an essential step in the DNA-based data storage workflow, coding algorithms are responsible to implement functions including bit-to-base transcoding, error…
Compact Genetic Algorithms (cGAs) are condensed variants of classical Genetic Algorithms (GAs) that use a probability vector representation of the population instead of the complete population. cGAs have been shown to significantly reduce…
Because of its high data density and longevity, DNA is emerging as a promising candidate for satisfying increasing data storage needs. Compared to conventional storage media, however, data stored in DNA is subject to a wider range of errors…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (i.e. rarely accessed), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
In this work, we propose a fully differentiable iterative decoder for quantum low-density parity-check (LDPC) codes. The proposed algorithm is composed of classical belief propagation (BP) decoding stages and intermediate graph neural…
Several modern applications involve huge graphs and require fast answers to reachability queries. In more than two decades since first proposals, several approaches have been presented adopting on-line searches, hop labelling or transitive…
Numerous practical medical problems often involve data that possess a combination of both sparse and non-sparse structures. Traditional penalized regularizations techniques, primarily designed for promoting sparsity, are inadequate to…
The DNA storage channel is considered, in which the $M$ Deoxyribonucleic acid (DNA) molecules comprising each codeword are stored without order, sampled $N$ times with replacement, and then sequenced over a discrete memoryless channel. For…
\textit{Drosophila melanogaster} has been established as a model organism for investigating the fundamental principles of developmental gene interactions. The gene expression patterns of \textit{Drosophila melanogaster} can be documented as…
DNA codes have garnered significant interest due to their utilization in digital media storage, cryptography, and DNA computing. In this paper, we first extend the results of constructing reversible group codes \cite{Cengellenmis} and…
Motivated by DNA data storage, we study the expected number of coded symbols drawn from a linear code until a desired information symbol can be decoded - the random access expectation. We focus on generator matrices with a type of symmetry,…
Greedy algorithms for minimizing L0-norm of sparse decomposition have profound application impact on many signal processing problems. In the sparse coding setup, given the observations $\mathrm{y}$ and the redundant dictionary…
This paper considers the problem of reconstructing sparse or compressible signals from one-bit quantized measurements. We study a new method that uses a log-sum penalty function, also referred to as the Gaussian entropy, for sparse signal…
Due to its longevity and enormous information density, DNA is an attractive medium for archival storage. In this work, we study the fundamental limits and trade-offs of DNA-based storage systems by introducing a new channel model, which we…
A common approach to quantifying DNA involves repeated cycles of DNA amplification. This approach, employed by the polymerase chain reaction (PCR), produces outputs that are corrupted by amplification noise, making it challenging to…
To increase the information capacity of DNA storage, composite DNA letters were introduced. We propose a novel channel model for composite DNA in which composite sequences are decomposed into ordered standard non-composite sequences. The…
To make DNA a suitable medium for archival data storage, it is essential to consider the decay process of the strands observed in DNA storage systems. This paper studies the decay process as a probabilistic noisy torn paper channel (TPC),…