Related papers: CoHSI V: Identical multiple scale-independent syst…
In the context of quantum information, highly nonlinear regimes, such as those supporting solitons, are marginally investigated. We miss general methods for quantum solitons, although they can act as entanglement generators or as…
Despite the recent progress of automated program verification techniques, fully automated verification of programs manipulating recursive data structures remains a challenge. We introduce solvable tuple patterns (STPs) and conjunctive STPs…
We investigate a densely packed, non-random arrangement of forty-six chromosomes (46,XY) in human nuclei. Here, we model systems-level chromosomal crosstalk by unifying intrinsic parameters (chromosomal length and number of genes) across…
Predicting the structure of a protein from its sequence is a cornerstone task of molecular biology. Established methods in the field, such as homology modeling and fragment assembly, appeared to have reached their limit. However, this year…
Life on earth is distinguished by long-lived correlations in time. The patterns of material organization that characterize living organisms today are contingent on events that occurred billions of years ago. This contingency is a necessary…
Chargaff's second parity rule for short oligonucleotides states that the frequency of any short nucleotide sequence on a strand is approximately equal to the frequency of its reverse complement on the same strand. Recent studies have shown…
A representation of the genetic code as a six-dimensional Boolean hypercube is proposed. It is assumed here that this structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition.…
Until recently, techniques for obtaining lower bounds for kernelization were one of the most sought after tools in the field of parameterized complexity. Now, after a strong influx of techniques, we are in the fortunate situation of having…
This paper is dedicated to lossless data compression with probability estimation using neural networks. First, we propose a probability estimation architecture based on a chain of neural predictors, so that each unit of the chain is defined…
A schema is a naturally defined subset of the space of fixed-length binary strings. The Holland Schema Theorem gives a lower bound on the expected fraction of a population in a schema after one generation of a simple genetic algorithm. This…
Deep learning has made significant progress in protein structure prediction, advancing the development of computational biology. However, despite the high accuracy achieved in predicting single-chain structures, a significant number of…
Sampled-data (SD) systems, which are composed of both discrete- and continuous-time components, are arguably one of the most common classes of cyberphysical systems in practice; most modern controllers are implemented on digital platforms…
Among the unsolved problems in computational biology, protein folding is one of the most interesting challenges. To study this folding, tools like neural networks and genetic algorithms have received a lot of attention, mainly due to the…
Phase separation mechanisms can produce a variety of complicated and intricate microstructures, which often can be difficult to characterize in a quantitative way. In recent years, a number of novel topological metrics for microstructures…
This paper proposes a novel entropy encoding technique for lossless data compression. Representing a message string by its lexicographic index in the permutations of its symbols results in a compressed version matching Shannon entropy of…
The present work is devoted to describe a set of rules explaining the discriminating versus non-discriminating behavior of the di-basic stages and to characterize the role of each base in determining such a behavior. Bases are analyze as…
The first quantum technologies to solve computational problems that are beyond the capabilities of classical computers are likely to be devices that exploit characteristics inherent to a particular physical system, to tackle a bespoke…
A genome-wide association study (GWAS) correlates marker variation with trait variation in a sample of individuals. Each study subject is genotyped at a multitude of SNPs (single nucleotide polymorphisms) spanning the genome. Here we assume…
Many complex systems present an intrinsic bipartite nature and are often described and modeled in terms of networks [1-5]. Examples include movies and actors [1, 2, 4], authors and scientific papers [6-9], email accounts and emails [10],…
The principle of similarity, or homophily, is often used to explain patterns observed in complex networks such as transitivity and the abundance of triangles (3-cycles). However, many phenomena from division of labor to protein-protein…