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Encoding temporal information from the recent past as spatially distributed activations is essential in order for the entire recent past to be simultaneously accessible. Any biological or synthetic agent that relies on the past to…
This paper reports about an approach to the classification of proteins' primary structures taking advantage of the Self Organizing Maps algorithm and of a numerical coding of the aminoacids based upon their physico-chemical properties.…
The paper represents three supplements to the source paper, q-bio/0610044 [q-bio.OT], with three new series of harmonic structures of the genetic code, determined by Gauss arithmetical algorithm; by Table of Minimal Adding, as in…
The arithmetic of natural numbers has a natural and simple encoding within sets, and the simplest set whose structure is not that of any natural number extends this set-theoretic representation to positive and negative integers. The…
Encrypted computing is an emerging technology based on a processor that `works encrypted', taking encrypted inputs to encrypted outputs while data remains in encrypted form throughout. It aims to secure user data against possible insider…
Although Transformers-based architectures excel at processing textual information, their naive adaptation for tabular data often involves flattening the table structure. This simplification can lead to the loss of essential…
We present an extension of sparse PCA, or sparse dictionary learning, where the sparsity patterns of all dictionary elements are structured and constrained to belong to a prespecified set of shapes. This \emph{structured sparse PCA} is…
The systematics of indices of physico-chemical properties of codons and amino acids across the genetic code are examined. Using a simple numerical labelling scheme for nucleic acid bases, data can be fitted as low-order polynomials of the 6…
The vast existing wireless infrastructure features a variety of systems and standards. It is of significant practical value to introduce new features and devices without changing the physical layer/hardware infrastructure, but upgrade it…
In quantum information processing it may be possible to have efficient computation and secure communication beyond the limitations of classical systems. In a fundamental point of view, however, evolution of quantum systems by the laws of…
The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…
How to represent the genetic code? Despite the fact that it is extensively known, the DNA mapping into proteins remains as one of the relevant discoveries of genetics. However, modern genomic signal processing usually requires converting…
In electronics, information has been traditionally stored, processed and communicated using an electron's charge. This paradigm is increasingly turning out to be energy-inefficient, because movement of charge within an…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Despite the wide variety of input types in machine learning, this diversity is often not fully reflected in their representations or model architectures, leading to inefficiencies throughout a model's lifecycle. This paper introduces an…
Quantum information can be processed using large ensembles of ultracold and trapped neutral atoms, building naturally on the techniques developed for high-precision spectroscopy and metrology. This article reviews some of the most important…
Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from…
First-principles calculations show that monatomic strings of carbon have high cohesive energy and axial strength, and exhibit stability even at high temperatures. Due to their flexibility and reactivity, carbon chains are suitable for…
The structural design process for buildings is time-consuming and laborious. To automate this process, structural engineers combine optimization methods with simulation tools to find an optimal design with minimal building mass subject to…
One of the primary goals of information theory is to provide limits on the amount of information it is possible to send through various types of communication channels, and to understand the encoding methods that will allow one to achieve…