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In computer science, we can theoretically neatly separate transmission and processing of information, hardware and software, and programs and their inputs. This is much more intricate in biology, Nevertheless, I argue that Shannon's concept…
The present paper is devoted to foundations of p-adic modelling in genomics. Considering nucleotides, codons, DNA and RNA sequences, amino acids, and proteins as information systems, we have formulated the corresponding p-adic formalisms…
The choice of sentence encoder architecture reflects assumptions about how a sentence's meaning is composed from its constituent words. We examine the contribution of these architectures by holding them randomly initialised and fixed,…
At this point in time there is a need for a new representation of different information, to identify and organize descending its characteristics. Today, science is a powerful tool for the description of reality - the numbers. Why the most…
Proteins are biological polymers that underlie all cellular functions. The first high-resolution protein structures were determined by x-ray crystallography in the 1960s. Since then, there has been continued interest in understanding and…
The structure of the genetic code is discussed in formal terms. A rectangular table of the code ("the code matrix"), whose properties reveal its arithmetical content tagged with the information symbols in several notations. New parameters…
The yearly global production of data is growing exponentially, outpacing the capacity of existing storage media, such as tape and disk, and surpassing our ability to store it. DNA storage - the representation of arbitrary information as…
Living organisms are not just random collections of organic molecules. There is continuous information processing going on in the apparent bouncing around of molecules of life. Optimisation criteria in this information processing can be…
The remarkable structural diversity of modern proteins reflects millions of years of evolution, during which sequence space has expanded while many structural features remain conserved. This conservation is evident not only among homologous…
Traditionally, cognition has been considered a uniquely human capability involving perception, memory, learning, reasoning, and problem-solving. However, recent research shows that cognition is a fundamental ability shared by all living…
Engineered systems typically separate mechanical function from information processing, whereas biological systems can exploit physical structure as a medium for information processing and computation. Motivated by this contrast, recent work…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of…
Data mining is a recognized predictive tool in a variety of areas ranging from bioinformatics and drug design to crystal structure prediction. In the present study, an electronic structure implementation has been combined with structural…
Due to their efficient encoding and decoding algorithms cyclic codes, a subclass of linear codes, have applications in consumer electronics, data storage systems, and communication systems. In this paper, Dickson polynomials of the first…
Block-encodings are ubiquitous in quantum computing as a way to represent data within a unitary operator. While several unstructured methods are applicable to arbitrary data, these techniques are burdened by hidden costs and poor accuracy.…
An iterative decoding algorithm for convolutional codes is presented. It successively processes $N$ consecutive blocks of the received word in order to decode the first block. A bound is presented showing which error configurations can be…
Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…
In nature the three-dimensional structure of a protein is encoded in the corresponding gene. In this paper we describe a new method for encoding the three-dimensional structure of a protein into a binary sequence. The feature of the method…
Locating the boundaries of consecutive blocks of quantum information is a fundamental building block for advanced quantum computation and quantum communication systems. We develop a coding theoretic method for properly locating boundaries…
Convolutional codes are constructed, designed and analysed using row and/or block structures of unit algebraic schemes. Infinite series of such codes and of codes with specific properties are derived. Properties are shown algebraically and…