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Application of the kinetic type model for study of a spatial spread of COVID-19
Computer Research and Modeling, 2021, v. 13, no. 3, pp. 611-627A simple model based on a kinetic-type equation is proposed to describe the spread of a virus in space through the migration of virus carriers from a certain center. The consideration is carried out on the example of three countries for which such a one-dimensional model is applicable: Russia, Italy and Chile. The geographical location of these countries and their elongation in the direction from the centers of infection (Moscow, Milan and Lombardia in general, as well as Santiago, respectively) makes it possible to use such an approximation. The aim is to determine the dynamic density of the infected in time and space. The model is two-parameter. The first parameter is the value of the average spreading rate associated with the transfer of infected moving by transport vehicles. The second parameter is the frequency of the decrease of the infected as they move through the country, which is associated with the passengers reaching their destination, as well as with quarantine measures. The parameters are determined from the actual known data for the first days of the spatial spread of the epidemic. An analytical solution is being built; simple numerical methods are also used to obtain a series of calculations. The geographical spread of the disease is a factor taken into account in the model, the second important factor is that contact infection in the field is not taken into account. Therefore, the comparison of the calculated values with the actual data in the initial period of infection coincides with the real data, then these data become higher than the model data. Those no less model calculations allow us to make some predictions. In addition to the speed of infection, a similar “speed of recovery” is possible. When such a speed is found for the majority of the country's population, a conclusion is made about the beginning of a global recovery, which coincides with real data.
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Data-driven simulation of a two-phase flow in heterogenous porous media
Computer Research and Modeling, 2021, v. 13, no. 4, pp. 779-792The numerical methods used to simulate the evolution of hydrodynamic systems require the considerable use of computational resources thus limiting the number of possible simulations. The data-driven simulation technique is one promising approach to the development of heuristic models, which may speed up the study of such models. In this approach, machine learning methods are used to tune the weights of an artificial neural network that predicts the state of a physical system at a given point in time based on initial conditions. This article describes an original neural network architecture and a novel multi-stage training procedure which create a heuristic model of a two-phase flow in a heterogeneous porous medium. The neural network-based model predicts the states of the grid cells at an arbitrary timestep (within the known constraints), taking in only the initial conditions: the properties of the heterogeneous permeability of the medium and the location of sources and sinks. The proposed model requires orders of magnitude less processor time in comparison with the classical numerical method, which served as a criterion for evaluating the effectiveness of the trained model. The proposed architecture includes a number of subnets trained in various combinations on several datasets. The techniques of adversarial training and weight transfer are utilized.
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Monitoring the spread of Sosnowskyi’s hogweed using a random forest machine learning algorithm in Google Earth Engine
Computer Research and Modeling, 2022, v. 14, no. 6, pp. 1357-1370Examining the spectral response of plants from data collected using remote sensing has a lot of potential for solving real-world problems in different fields of research. In this study, we have used the spectral property to identify the invasive plant Heracleum sosnowskyi Manden from satellite imagery. H. sosnowskyi is an invasive plant that causes many harms to humans, animals and the ecosystem at large. We have used data collected from the years 2018 to 2020 containing sample geolocation data from the Moscow Region where this plant exists and we have used Sentinel-2 imagery for the spectral analysis towards the aim of detecting it from the satellite imagery. We deployed a Random Forest (RF) machine learning model within the framework of Google Earth Engine (GEE). The algorithm learns from the collected data, which is made up of 12 bands of Sentinel-2, and also includes the digital elevation together with some spectral indices, which are used as features in the algorithm. The approach used is to learn the biophysical parameters of H. sosnowskyi from its reflectances by fitting the RF model directly from the data. Our results demonstrate how the combination of remote sensing and machine learning can assist in locating H. sosnowskyi, which aids in controlling its invasive expansion. Our approach provides a high detection accuracy of the plant, which is 96.93%.
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Substantiation of optimum planting schemes for forest plantations: a computer experiment
Computer Research and Modeling, 2016, v. 8, no. 2, pp. 333-343Views (last year): 2. Citations: 2 (RSCI).The article presents the results of computer simulations aimed to assess the influence of tree spatial locations (planting schemes) on the productivity and the dynamics of soil fertility in forest plantations. The growth of aspen (Populus tremula L.) in plantations with short rotation (30 years) was simulated in the EFIMOD system of models with the soil and climatic data matching forested lands in the Mari El Republic. The outcome reveals that higher biomass rates, increase in soil organic matter stocks, and the minimal loss of soil nitrogen can be obtained when the distance between trees in the row equals 1–4 m and 4–6 м in aisles.
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Technoscape: multi-agent model for evolution of network of cities, joined by production and trade links
Computer Research and Modeling, 2022, v. 14, no. 1, pp. 163-178The paper presents agent-based model for city formation named Technoscape which is both local and nonlocal. Technoscape can, to a certain degree, be also assumed as a model for emergence of global economy. The current version of the model implements very simple way of agents’ behavior and interaction, still the model provides rather interesting spatio-temporal patterns.
Locality and non-locality mean here the spatial features of the way the agents interact with each other and with geographical space upon which the evolution takes place. Technoscape agent is some conventional artisan, family, or а producing and trading firm, while there is no difference between production and trade. Agents are located upon and move through bounded two-dimensional space divided into square cells. The model demonstrates processes of agents’ concentration in a small set of cells, which is interpreted as «city» formation. Agents are immortal, they don’t mutate and evolve, though this is interesting perspective for the evolution of the model itself.
Technoscape provides some distinctively new type of self-organization. Partially, this type of selforganization resembles the behavior of segregation model by Thomas Shelling, still that model has evolution rules substantially different from Technoscape. In Shelling model there exist avalanches still simple equilibria exist if no new agents are added to the game board, while in Technoscape no such equilibria exist. At best, we can observe quasi-equilibrium, slowly changing global states.
One non-trivial phenomenon Technoscape exhibits, which also contrasts to Shelling segregation model, is the ability of agents to concentrate in local cells (interpreted as cities) even explicitly and totally ignoring local interactions, using non-local interactions only.
At the same time, while the agents tend to concentrate in large one-cell cities, large scale of such cities does not guarantee them from decay: there always exists a process of «enticement» of agents and their flow to new cities.
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Impact of the non-market advantage on equilibrium in A Hotelling model
Computer Research and Modeling, 2016, v. 8, no. 3, pp. 573-581The principle of minimal differentiation, based on the Hotelling model, is well known in the economy. It is applicable to horizontal differentiated goods of almost any nature. The Hotelling approach to modeling competition of oligopolies corresponds to a modern description of monopolistic competition with increasing returns to scale and imperfect competition. We develop a modification of the Hotelling model that endows a firm with a non-market advantage, which is introduced alike the valence advantage known in problems of political economy. The nonmarket (valence) advantage can be interpreted as advertisement (brand awareness of firms). Problem statement. Consider two firms competing with prices and location. Homogeneous consumers vary with its location on a segment. They minimize their costs, which additively includes the price of the product and the distance from them to the product. The utility function is linear with respect to the price and quadratic with respect to the distance. It is also expected that one of the firms (for certainty, firm № 1) has a market advantage d. The consumers are assumed to take into account the sum of the distance to the product and the market advantage of firm 1. Thus, the strategy of the firms and the consumers depend on two parameters: the unit t of the transport costs and the non-market advantage d. I explore characteristics of the equilibrium in the model as a function of the non-market advantage for different fixed t. The aim of the research is to assess the impact of the non-market advantage on the equlibrium. We prove that the Nash equilibrium exists and it is unique under additive consumers' preferences de-pending on the square of the distance between consumers and firms. This equilibrium is ‘richer’ than that in the original Hotelling model. In particular, non-market advantage can be excessive and inefficient to use.
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Biomathematical system of the nucleic acids description
Computer Research and Modeling, 2020, v. 12, no. 2, pp. 417-434The article is devoted to the application of various methods of mathematical analysis, search for patterns and studying the composition of nucleotides in DNA sequences at the genomic level. New methods of mathematical biology that made it possible to detect and visualize the hidden ordering of genetic nucleotide sequences located in the chromosomes of cells of living organisms described. The research was based on the work on algebraic biology of the doctor of physical and mathematical sciences S. V. Petukhov, who first introduced and justified new algebras and hypercomplex numerical systems describing genetic phenomena. This paper describes a new phase in the development of matrix methods in genetics for studying the properties of nucleotide sequences (and their physicochemical parameters), built on the principles of finite geometry. The aim of the study is to demonstrate the capabilities of new algorithms and discuss the discovered properties of genetic DNA and RNA molecules. The study includes three stages: parameterization, scaling, and visualization. Parametrization is the determination of the parameters taken into account, which are based on the structural and physicochemical properties of nucleotides as elementary components of the genome. Scaling plays the role of “focusing” and allows you to explore genetic structures at various scales. Visualization includes the selection of the axes of the coordinate system and the method of visual display. The algorithms presented in this work are put forward as a new toolkit for the development of research software for the analysis of long nucleotide sequences with the ability to display genomes in parametric spaces of various dimensions. One of the significant results of the study is that new criteria were obtained for the classification of the genomes of various living organisms to identify interspecific relationships. The new concept allows visually and numerically assessing the variability of the physicochemical parameters of nucleotide sequences. This concept also allows one to substantiate the relationship between the parameters of DNA and RNA molecules with fractal geometric mosaics, reveals the ordering and symmetry of polynucleotides, as well as their noise immunity. The results obtained justified the introduction of new terms: “genometry” as a methodology of computational strategies and “genometrica” as specific parameters of a particular genome or nucleotide sequence. In connection with the results obtained, biosemiotics and hierarchical levels of organization of living matter are raised.
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Cytokines as indicators of the state of the organism in infectious diseases. Experimental data analysis
Computer Research and Modeling, 2020, v. 12, no. 6, pp. 1409-1426When person`s diseases is result of bacterial infection, various characteristics of the organism are used for observation the course of the disease. Currently, one of these indicators is dynamics of cytokine concentrations are produced, mainly by cells of the immune system. There are many types of these low molecular weight proteins in human body and many species of animals. The study of cytokines is important for the interpretation of functional disorders of the body's immune system, assessment of the severity, monitoring the effectiveness of therapy, predicting of the course and outcome of treatment. Cytokine response of the body indicating characteristics of course of disease. For research regularities of such indication, experiments were conducted on laboratory mice. Experimental data are analyzed on the development of pneumonia and treatment with several drugs for bacterial infection of mice. As drugs used immunomodulatory drugs “Roncoleukin”, “Leikinferon” and “Tinrostim”. The data are presented by two types cytokines` concentration in lung tissue and animal blood. Multy-sided statistical ana non statistical analysis of the data allowed us to find common patterns of changes in the “cytokine profile” of the body and to link them with the properties of therapeutic preparations. The studies cytokine “Interleukin-10” (IL-10) and “Interferon Gamma” (IFN$\gamma$) in infected mice deviate from the normal level of infact animals indicating the development of the disease. Changes in cytokine concentrations in groups of treated mice are compared with those in a group of healthy (not infected) mice and a group of infected untreated mice. The comparison is made for groups of individuals, since the concentrations of cytokines are individual and differ significantly in different individuals. Under these conditions, only groups of individuals can indicate the regularities of the processes of the course of the disease. These groups of mice were being observed for two weeks. The dynamics of cytokine concentrations indicates characteristics of the disease course and efficiency of used therapeutic drugs. The effect of a medicinal product on organisms is monitored by the location of these groups of individuals in the space of cytokine concentrations. The Hausdorff distance between the sets of vectors of cytokine concentrations of individuals is used in this space. This is based on the Euclidean distance between the elements of these sets. It was found that the drug “Roncoleukin” and “Leukinferon” have a generally similar and different from the drug “Tinrostim” effect on the course of the disease.
Keywords: data processing, experiment, cytokine, immune system, pneumonia, statistics, approximation, Hausdorff distance. -
The development of an intelligent system for recognizing the volume and weight characteristics of cargo
Computer Research and Modeling, 2021, v. 13, no. 2, pp. 437-450Industrial imaging or “machine vision” is currently a key technology in many industries as it can be used to optimize various processes. The purpose of this work is to create a software and hardware complex for measuring the overall and weight characteristics of cargo based on an intelligent system using neural network identification methods that allow one to overcome the technological limitations of similar complexes implemented on ultrasonic and infrared measuring sensors. The complex to be developed will measure cargo without restrictions on the volume and weight characteristics of cargo to be tariffed and sorted within the framework of the warehouse complexes. The system will include an intelligent computer program that determines the volume and weight characteristics of cargo using the machine vision technology and an experimental sample of the stand for measuring the volume and weight of cargo.
We analyzed the solutions to similar problems. We noted that the disadvantages of the studied methods are very high requirements for the location of the camera, as well as the need for manual operations when calculating the dimensions, which cannot be automated without significant modifications. In the course of the work, we investigated various methods of object recognition in images to carry out subject filtering by the presence of cargo and measure its overall dimensions. We obtained satisfactory results when using cameras that combine both an optical method of image capture and infrared sensors. As a result of the work, we developed a computer program allowing one to capture a continuous stream from Intel RealSense video cameras with subsequent extraction of a three-dimensional object from the designated area and to calculate the overall dimensions of the object. At this stage, we analyzed computer vision techniques; developed an algorithm to implement the task of automatic measurement of goods using special cameras and the software allowing one to obtain the overall dimensions of objects in automatic mode.
Upon completion of the work, this development can be used as a ready-made solution for transport companies, logistics centers, warehouses of large industrial and commercial enterprises.
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Detection of promoter and non-promoter E.coli sequences by analysis of their electrostatic profiles
Computer Research and Modeling, 2015, v. 7, no. 2, pp. 347-359Views (last year): 3.The article is devoted to the idea of using physical properties of DNA instead of sequence along for the aspect of accurate search and annotation of various prokaryotic genomic regions. Particulary, the possibility to use electrostatic potential distribution around DNA sequence as a classifier for identification of a few functional DNA regions was demonstrated. A number of classification models was built providing discrimination of promoters and non-promoter regions (random sequences, coding regions and promoter-like sequences) with accuracy value about 83–85%. The most valueable regions for the discrimination were determined and expected to play a certain role in the process of DNA-recognition by RNA-polymerase.
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