Related papers: On Codes for the Noisy Substring Channel
DNA storage systems face significant challenges, including insertion, deletion, and substitution (IDS) errors. Therefore, designing effective synchronization codes, i.e., codes capable of correcting IDS errors, is essential for DNA storage…
DNA is a promising medium for digital information storage for its exceptional density and durability. While prior studies advanced coding theory, workflow design, and simulation tools, challenges such as synthesis costs, sequencing errors,…
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…
We study the theoretical performance of a combined approach to demodulation and decoding of binary continuous-phase modulated signals under repetition-like codes. This technique is motivated by a need to transmit packetized or framed data…
The goal of a denoising algorithm is to reconstruct a signal from its noise-corrupted observations. Perfect reconstruction is seldom possible and performance is measured under a given fidelity criterion. In a recent work, the authors…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
With the emergence of new storage and communication methods, the insertion, deletion, and substitution (IDS) channel has attracted considerable attention. However, many topics on the IDS channel and the associated Levenshtein distance…
Synthetic DNA approaches 227.5 exabytes per gram of storage density with stability over millennial timescales. Realising this capacity requires error-correction codes that recover data from substantial synthesis and sequencing errors.…
Recently deep neural networks have been successfully used for various classification tasks, especially for problems with massive perfectly labeled training data. However, it is often costly to have large-scale credible labels in real-world…
We propose a new coding scheme, called the delayed coding (DC) scheme, for channels with insertion, deletion, and substitution (IDS) errors. The proposed scheme employs delayed encoding and non-iterative detection and decoding strategies to…
After being trained, classifiers must often operate on data that has been corrupted by noise. In this paper, we consider the impact of such noise on the features of binary classifiers. Inspired by tools for classifier robustness, we…
The advent of high-throughput sequencing technologies has revolutionized genome analysis by enabling the rapid and cost-effective sequencing of large genomes. Despite these advancements, the increasing complexity and volume of genomic data…
Shaping codes are used to generate code sequences in which the symbols obey a prescribed probability distribution. They arise naturally in the context of source coding for noiseless channels with unequal symbol costs. Recently, shaping…
We introduce a novel method to analyse complete genomes and recognise some distinctive features by means of an adaptive compression algorithm, which is not DNA-oriented. We study the Information Content as a function of the number of…
Not only is network coding essential to achieve the capacity of a single-session multicast network, it can also help to improve the throughput of wireless networks with multiple unicast sessions when overheard information is available. Most…
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…
Noise in data appears to be inevitable in most real-world machine learning applications and would cause severe overfitting problems. Not only can data features contain noise, but labels are also prone to be noisy due to human input. In this…
Changes in a cell's external or internal conditions are usually reflected in the concentrations of the relevant transcription factors. These proteins in turn modulate the expression levels of the genes under their control and sometimes need…
Motivated by DNA based data storage system, we investigate the errors that occur when synthesizing DNA strands in parallel, where each strand is appended one nucleotide at a time by the machine according to a template supersequence. If…
We study data structures in the presence of adversarial noise. We want to encode a given object in a succinct data structure that enables us to efficiently answer specific queries about the object, even if the data structure has been…