Related papers: Properties and constructions of constrained codes …
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (rarely accessed data), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
This paper presents a novel deep learning based data-driven optimization method. A novel generative adversarial network (GAN) based data-driven distributionally robust chance constrained programming framework is proposed. GAN is applied to…
The study of constant-weight codes in $\ell_1$-metric was motivated by the duplication-correcting problem for data storage in live DNA. It is interesting to determine the maximum size of a code given the length $n$, weight $w$, minimum…
Constraint-based pattern discovery is at the core of numerous data mining tasks. Patterns are extracted with respect to a given set of constraints (frequency, closedness, size, etc). In the context of sequential pattern mining, a large…
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…
In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete…
Reference-guided DNA sequencing and alignment is an important process in computational molecular biology. The amount of DNA data grows very fast, and many new genomes are waiting to be sequenced while millions of private genomes need to be…
In most constraint programming systems, a limited number of search engines is offered while the programming of user-customized search algorithms requires low-level efforts, which complicates the deployment of such algorithms. To alleviate…
This work aims at investigating the impact of DNA geometry, compaction and calculation chain on DNA break and chromosome aberration predictions for high charge and energy (HZE) ions, using the Monte Carlo codes Geant4-DNA, RITRACKS and…
Data compression plays an important role to deal with high volumes of DNA sequences in the field of Bioinformatics. Again data compression techniques directly affect the alignment of DNA sequences. So the time needed to decompress a…
This paper presents and analyzes a novel concatenated coding scheme for enabling error resilience in two distributed storage settings: one being storage using existing regenerating codes and the second being storage using locally repairable…
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…
The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations result from mechanical perturbations in cells. These different topologies have…
The modeling of genomic sequences presents unique challenges due to their length and structural complexity. Traditional sequence models struggle to capture long-range dependencies and biological features inherent in DNA. In this work, we…
This work provides an algebraic framework for source coding with decoder side information and its dual problem, channel coding with encoder side information, showing that nested concatenated codes can achieve the corresponding…
The fall of prices of the high-throughput genome sequencing changes the landscape of modern genomics. A number of large scale projects aimed at sequencing many human genomes are in progress. Genome sequencing also becomes an important aid…
The structures of cyclic DNA codes of odd length over the finite rings R=Z_{4}+wZ_{4}, w^{2}=2 and S=Z_{4}+wZ_{4}+vZ_{4}+wvZ_{4},w^{2}=2,v^{2}=v,wv=vw are studied. The links between the elements of the rings R, S and 16 and 256 codons are…
Based on the theoretical neuroscience, G. Cotardo and A. Ravagnavi in \cite{CR} introduced a kind of asymmetric binary codes called combinatorial neural codes (CN codes for short), with a "matched metric" $\delta_{r}$ called asymmetric…
Motivated by empirical observations of algebraic duplicated sequence length distributions in a broad range of natural genomes, we analytically formulate and solve a class of simple discrete duplication/substitution models that generate…
Relative compression, where a set of similar strings are compressed with respect to a reference string, is a very effective method of compressing DNA datasets containing multiple similar sequences. Relative compression is fast to perform…