Related papers: On Algebraic Approaches for DNA Codes with Multipl…
Deep learning is widely used to uncover hidden patterns in large code corpora. To achieve this, constructing a format that captures the relevant characteristics and features of source code is essential. Graph-based representations have…
DNA strands serve as a storage medium for $4$-ary data over the alphabet $\{A,T,G,C\}$. DNA data storage promises formidable information density, long-term durability, and ease of replicability. However, information in this intriguing…
Code-based Distributed Matrix Multiplication (DMM) has been extensively studied in distributed computing for efficiently performing large-scale matrix multiplication using coding theoretic techniques. The communication cost and recovery…
DNA sequence encoding is fundamental to gene function prediction, protein synthesis, and diverse downstream biological tasks. Despite the substantial progress achieved by large-scale DNA sequence pretraining, existing studies have…
Since the completion of the human genome sequencing project in 2001, significant progress has been made in areas such as gene regulation editing and protein structure prediction. However, given the vast amount of genomic data, the segments…
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 DNA sequences alignment method based on inverted index. Now most large scale information retrieval system are all use inverted index as the basic data structure. But its application in DNA sequence alignment is…
Maximum distance separable (in short, MDS), near MDS (in short, NMDS), and self-orthogonal codes play a pivotal role in algebraic coding theory, particularly in applications such as quantum communications and secret sharing scheme.…
A method for encoding information in DNA sequences is described. The method is based on the precision-resolution framework, and is aimed to work in conjunction with a recently suggested terminator-free template independent DNA synthesis…
Graph-structured data is central to many scientific and industrial domains, where the goal is often to optimize objectives defined over graph structures. Given the combinatorial complexity of graph spaces, such optimization problems are…
A covering code is a set of codewords with the property that the union of balls, suitably defined, around these codewords covers an entire space. Generally, the goal is to find the covering code with the minimum size codebook. While most…
We present a computational method to evaluate the end-to-end and the contour length distribution functions of short DNA molecules described by a mesoscopic Hamiltonian. The method generates a large statistical ensemble of possible…
A mathematical algorithm to describe DNA or RNA sequences of $N$ nucleotides by a string of $2N$ integers numbers is presented in the framework of the so called crystal basis model of the genetic code. The description allows to define a not…
Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…
The minimum distance is one of the most important combinatorial characterizations of a code. The maximum likelihood decoding problem is one of the most important algorithmic problems of a code. While these problems are known to be hard for…
Fragment-based shape signature techniques have proven to be powerful tools for computer-aided drug design. They allow scientists to search for target molecules with some similarity to a known active compound. They do not require reference…
Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events…
The analysis of biological sequencing data has been one of the biggest applications of string algorithms. The approaches used in many such applications are based on the analysis of k-mers, which are short fixed-length strings present in a…
Binary self-dual codes with large minimum distances, such as the extended Hamming code and the Golay code, are fascinating objects in the coding theory. They are closely related to sporadic simple groups, lattices and invariant theory. A…
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,…