Forming the Architecture of a Multi-Layered Model of Physical Data Storage for Complex Telemedicine Systems

The relevance of this research is determined by the need to study the issues of improving data storage technologies for complex telemedicine systems. The objective is to create a multi-layered data storage model for complex telemedicine systems to ensure the most complete use of their capacity and the timely expansion of existing storage. The research is conducted on the basis of an analysis of existing opportunities and problems in the field of data storage technologies. An analysis of the main features of the development of data storage technologies revealed that the existing models have no detailed description of the recording and physical storage of data bits, which is necessary for describing the storage process. Different architectures are reviewed, and their strengths and weaknesses are discussed. Within the framework of a demonstration experiment using the Kohonen neural network apparatus as a tool for solving the problem of placing objects in accordance with the required parameters, it is shown that the proposed storage system resource management model is operable and allows solving the problem of rational use of physical resources. As a result, a multilevel model of data storage is proposed, which combines the levels of storage process organization and technology. The distinguishing feature of this method is the comparison of storage organization levels, data media, and characteristics of physical storage and stored files. Doi: 10.28991/HIJ-2023-04-04-09 Full Text: PD

A Fuzzy Approach to the Synthesis of Cognitive Maps for Modeling Decision Making in Complex Systems

The object of this study is fuzzy cognitive modeling as a means of studying semistructured socio-economic systems. The features of constructing cognitive maps, providing the ability to choose management decisions in complex semistructured socio-economic systems, are described. It is shown that further improvement of technologies necessary for developing decision support systems and their practical use is still relevant. This work aimed to improve the accuracy of cognitive modeling of semistructured systems based on a fuzzy cognitive map of structuring nonformalized situations (MSNS) with the evaluation of root-mean-square error (RMSE) and mean average squared error (MASE) coefficients. In order to achieve the goal, the following main methods were used: systems analysis methods, fuzzy logic and fuzzy sets theory postulates, theory of integral wavelet transform, correlation and autocorrelation analyses. As a result, a new methodology for constructing MSNS was proposed—a map of structuring nonformalized situations that combines the positive properties of previous fuzzy cognitive maps. The solution of modeling problems based on this methodology should increase the reliability and quality of analysis and modeling of semistructured systems and processes under uncertainty. The analysis using open datasets proved that compared to the classical ARIMA, SVR, MLP, and Fuzzy time series models, our proposed model provides better performance in terms of MASE and RMSE metrics, which confirms its advantage. Thus, it is advisable to use our proposed algorithm in the future as a mathematical basis for developing software tools for the analysis and modeling of problems in semistructured systems and processes. Doi: 10.28991/ESJ-2022-06-02-012 Full Text: PD

Development of an Algorithm for Multicriteria Optimization of Deep Learning Neural Networks

Nowadays, machine learning methods are actively used to process big data. A promising direction is neural networks, in which structure optimization occurs on the principles of self-configuration. Genetic algorithms are applied to solve this nontrivial problem. Most multicriteria evolutionary algorithms use a procedure known as non-dominant sorting to rank decisions. However, the efficiency of procedures for adding points and updating rank values in non-dominated sorting (incremental non-dominated sorting) remains low. In this regard, this research improves the performance of these algorithms, including the condition of an asynchronous calculation of the fitness of individuals. The relevance of the research is determined by the fact that although many scholars and specialists have studied the self-tuning of neural networks, they have not yet proposed a comprehensive solution to this problem. In particular, algorithms for efficient non-dominated sorting under conditions of incremental and asynchronous updates when using evolutionary methods of multicriteria optimization have not been fully developed to date. To achieve this goal, a hybrid co-evolutionary algorithm was developed that significantly outperforms all algorithms included in it, including error-back propagation and genetic algorithms that operate separately. The novelty of the obtained results lies in the fact that the developed algorithms have minimal asymptotic complexity. The practical value of the developed algorithms is associated with the fact that they make it possible to solve applied problems of increased complexity in a practically acceptable time. Doi: 10.28991/HIJ-2023-04-01-011 Full Text: PD

Adaptation of the Landau-Migdal Quasiparticle Pattern to Strongly Correlated Fermi Systems

A quasiparticle pattern advanced in Landau's first article on Fermi liquid theory is adapted to elucidate the properties of a class of strongly correlated Fermi systems characterized by a Lifshitz phase diagram featuring a quantum critical point (QCP) where the density of states diverges. The necessary condition for stability of the Landau Fermi Liquid state is shown to break down in such systems, triggering a cascade of topological phase transitions that lead, without symmetry violation, to states with multi-connected Fermi surfaces. The end point of this evolution is found to be an exceptional state whose spectrum of single-particle excitations exhibits a completely flat portion at zero temperature. Analysis of the evolution of the temperature dependence of the single-particle spectrum yields results that provide a natural explanation of classical behavior of this class of Fermi systems in the QCP region.Comment: 26 pages, 14 figures. Dedicated to 100th anniversary of A.B.Migdal birthda

Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor

Mutational signature analysis is commonly performed in cancer genomic studies. Here, we present SigProfilerExtractor, an automated tool for de novo extraction of mutational signatures, and benchmark it against another 13 bioinformatics tools by using 34 scenarios encompassing 2,500 simulated signatures found in 60,000 synthetic genomes and 20,000 synthetic exomes. For simulations with 5% noise, reflecting high-quality datasets, SigProfilerExtractor outperforms other approaches by elucidating between 20% and 50% more true-positive signatures while yielding 5-fold less false-positive signatures. Applying SigProfilerExtractor to 4,643 whole-genome- and 19,184 whole-exome-sequenced cancers reveals four novel signatures. Two of the signatures are confirmed in independent cohorts, and one of these signatures is associated with tobacco smoking. In summary, this report provides a reference tool for analysis of mutational signatures, a comprehensive benchmarking of bioinformatics tools for extracting signatures, and several novel mutational signatures, including one putatively attributed to direct tobacco smoking mutagenesis in bladder tissues

Structural matters in HTSC; the origin and form of stripe organization and checker boarding

The paper deals with the controversial charge and spin self-organization phenomena in the HTSC cuprates, of which neutron, X-ray, STM and ARPES experiments give complementary, sometimes apparently contradictory glimpses. The examination has been set in the context of the boson-fermion, negative-U understanding of HTSC advocated over many years by the author. Stripe models are developed which are 2q in nature and diagonal in form. For such a geometry to be compatible with the data rests upon both the spin and charge arrays being face-centred. Various special doping concentrations are closely looked at, in particular p = 0.1836 or 9/49, which is associated with the maximization of the superconducting condensation energy and the termination of the pseudogap regime. The stripe models are dictated by real space organization of the holes, whereas the dispersionless checkerboarding is interpreted in terms of correlation driven collapse of normal Fermi surface behaviour and response functions. The incommensurate spin diffraction below the resonance energy is seen as in no way expressing spin-wave physics or Fermi surface nesting, but is driven by charge and strain (Jahn-Teller) considerations, and it stands virtually without dispersion. The apparent dispersion comes from the downward dispersion of the resonance peak, and the growth of a further incoherent commensurate peak ensuing from the falling level of charge stripe organization under excitation.Comment: 49 pages with 8 figure

The repertoire of mutational signatures in human cancer.

Somatic mutations in cancer genomes are caused by multiple mutational processes, each of which generates a characteristic mutational signature1. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium2 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we characterized mutational signatures using 84,729,690 somatic mutations from 4,645 whole-genome and 19,184 exome sequences that encompass most types of cancer. We identified 49 single-base-substitution, 11 doublet-base-substitution, 4 clustered-base-substitution and 17 small insertion-and-deletion signatures. The substantial size of our dataset, compared with previous analyses3-15, enabled the discovery of new signatures, the separation of overlapping signatures and the decomposition of signatures into components that may represent associated-but distinct-DNA damage, repair and/or replication mechanisms. By estimating the contribution of each signature to the mutational catalogues of individual cancer genomes, we revealed associations of signatures to exogenous or endogenous exposures, as well as to defective DNA-maintenance processes. However, many signatures are of unknown cause. This analysis provides a systematic perspective on the repertoire of mutational processes that contribute to the development of human cancer

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in selected cancer types have suggested that chromothripsis may be more common than initially inferred from low-resolution copy-number data. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we analyze patterns of chromothripsis across 2,658 tumors from 38 cancer types using whole-genome sequencing data. We find that chromothripsis events are pervasive across cancers, with a frequency of more than 50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy-number states, a considerable fraction of events involve multiple chromosomes and additional structural alterations. In addition to non-homologous end joining, we detect signatures of replication-associated processes and templated insertions. Chromothripsis contributes to oncogene amplification and to inactivation of genes such as mismatch-repair-related genes. These findings show that chromothripsis is a major process that drives genome evolution in human cancer

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts