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Natural Language Processing (NLP) has transformed various fields beyond linguistics by applying techniques originally developed for human language to the analysis of biological sequences. This review explores the application of NLP methods…
A new set of DNA base-nucleic acid codes and their hypercomplex number representation have been introduced for taking the probability of each nucleotide into full account. A new scoring system has been proposed to suit the hypercomplex…
Background/ Objectives: Resolving the origin of the genetic code is fundamental to understanding how life began its journey out of the chemical world. Since its deciphering some 60 years ago, there is still no general theory of the…
Spread codes and orbit codes are special families of constant dimension subspace codes. These codes have been well-studied for their error correction capability and transmission rate, but the question of how to encode messages has not been…
In this work we present a system based on a Deep Learning approach, by using a Convolutional Neural Network, capable of classifying protein chains of amino acids based on the protein description contained in the Protein Data Bank. Each…
Digital information can be encoded in the building-block sequence of macro-molecules, such as RNA and single-stranded DNA. Methods of "writing" and "reading" macromolecular strands are currently available, but they are slow and expensive.…
In this paper, we study achievable rates of concatenated coding schemes over a deoxyribonucleic acid (DNA) storage channel. Our channel model incorporates the main features of DNA-based data storage. First, information is stored on many,…
Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Organic molecules and quantum circuits/protocols can…
We study permutations over the set of $\ell$-grams, that are feasible in the sense that there is a sequence whose $\ell$-gram frequency has the same ranking as the permutation. Codes, which are sets of feasible permutations, protect…
We wish to suggest an algorithm for biological search including DNA search. Our argument supposes that biological search be performed by quantum search.If we assume this, we can naturally answer the following long lasting puzzles such that…
In this paper it has been developed an algorithm for cryptography, using the Mellin's transform. Cryptography is very important to protect data to ensure that two people, using an insecure channel, may communicate in a secure way. In the…
We investigate the possibility of encoding multiple solutions of a problem in a single chromosome. The best solution encoded in an individual will represent (will provide the fitness of) that individual. In order to obtain some benefits the…
Constrained sequence codes have been widely used in modern communication and data storage systems. Sequences encoded with constrained sequence codes satisfy constraints imposed by the physical channel, hence enabling efficient and reliable…
This paper introduces a new concept. We intend to give life to a software agent. A software agent is a computer program that acts on a user's behalf. We put a DNA inside the agent. DNA is a simple text, a whole roadmap of a network of…
DNA language models are increasingly used to represent genomic sequence, yet their effectiveness depends critically on how raw nucleotides are converted into model inputs. Unlike natural language, DNA offers no canonical boundaries, making…
Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…
Encryption and Decryption is the process of sending a message in a ciphered way that appears meaningless and could be deciphered using a key for security purposes to avoid data breaches. This paper expands on the previous work on…
Generative models have achieved impressive results in many domains including image and text generation. In the natural sciences, generative models have led to rapid progress in automated drug discovery. Many of the current methods focus on…
Text-based representations of chemicals and proteins can be thought of as unstructured languages codified by humans to describe domain-specific knowledge. Advances in natural language processing (NLP) methodologies in the processing of…
DNA data storage is rapidly emerging as a promising solution for long-term data archiving, largely due to its exceptional durability. However, the synthesis of DNA strands remains a significant bottleneck in terms of cost and speed. To…