Related papers: New constructions of DNA codes under multiple cons…
A genetic algorithm is suitable for exploring large search spaces as it finds an approximate solution. Because of this advantage, genetic algorithm is effective in exploring vast and unknown space such as molecular search space. Though the…
Binary codes are widely used to represent the data due to their small storage and efficient computation. However, there exists an ambiguity problem that lots of binary codes share the same Hamming distance to a query. To alleviate the…
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…
Deep neural network-based architectures give promising results in various domains including pattern recognition. Finding the optimal combination of the hyper-parameters of such a large-sized architecture is tedious and requires a large…
This paper concerns non-overlapping codes, block codes motivated by synchronisation and DNA-based storage applications. Most existing constructions of these codes do not account for the restrictions posed by the physical properties of…
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…
The paper describes an algorithm to compute a consensus sequence from a set of DNA sequences of approximatively identical length generated by 3rd sequencing generation technologies. Its purpose targets DNA storage and is guided by specific…
A quest to determine the complete sequence of a human DNA from telomere to telomere started three decades ago and was finally completed in 2021. This accomplishment was a result of a tremendous effort of numerous experts who engineered…
Gravitational-wave detection strategies are based on a signal analysis technique known as matched filtering. Despite the success of matched filtering, due to its computational cost, there has been recent interest in developing deep…
We initiate the study of DNA-based distributed storage systems, where information is encoded across multiple DNA data storage containers to achieve robustness against container failures. In this setting, data are distributed over $M$…
Questions in computational molecular biology generate various discrete optimization problems, such as DNA sequence alignment and RNA secondary structure prediction. However, the optimal solutions are fundamentally dependent on the…
DNA emerges as a promising medium for the exponential growth of digital data due to its density and durability. This study extends recent research by addressing the \emph{coverage depth problem} in practical scenarios, exploring optimal…
Specific binding of proteins to DNA is one of the most common ways in which gene expression is controlled. Although general rules for the DNA-protein recognition can be derived, the ambiguous and complex nature of this mechanism precludes a…
In this present work, we generalize the study of construction of DNA codes over the rings $\mathcal{R}_\theta=\mathbb{Z}_4+w\mathbb{Z}_4$, $w^2 = \theta $ for $\theta \in \mathbb{Z}_4+w\mathbb{Z}_4$. Rigorous study along with…
We propose generative neural network methods to generate DNA sequences and tune them to have desired properties. We present three approaches: creating synthetic DNA sequences using a generative adversarial network; a DNA-based variant of…
Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these…
Group testing algorithms are very useful tools for DNA library screening. Building on recent work by Levenshtein (2003) and Tonchev (2008), we construct in this paper new infinite classes of combinatorial structures, the existence of which…
Recently, due to the genomic sequence analysis in several types of cancer, the genomic data based on {\em copy number profiles} ({\em CNP} for short) are getting more and more popular. A CNP is a vector where each component is a…
The identification of low-energy conformers for a given molecule is a fundamental problem in computational chemistry and cheminformatics. We assess here a conformer search that employs a genetic algorithm for sampling the low-energy segment…
Neural Architecture Search (NAS), aiming at automatically designing neural architectures by machines, has been considered a key step toward automatic machine learning. One notable NAS branch is the weight-sharing NAS, which significantly…