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Microarray datasets are highly dimensional, with a small number of collected samples in comparison to thousands of features. This poses a significant challenge that affects the interpretation, applicability and validation of the analytical results. Matrix factorizations have proven to be a useful method for describing data in terms of a small number of meta-features, which reduces noise, while still capturing the essential features of the data. Three novel and mutually relevant methods are presented in this paper: 1) gradient-based matrix factorization with two adaptive learning rates (in accordance with the number of factor matrices) and their automatic updates; 2) nonparametric criterion for the selection of the number of factors; and 3) nonnegative version of the gradient-based matrix factorization which doesn't require any extra computational costs in difference to the existing methods. We demonstrate effectiveness of the proposed methods to the supervised classification of gene expression data.

The work submits new release of the FlowVision software designed for automation of engineering calculations in computational fluid dynamics: FlowVision 3.09.05. The FlowVision software is used for solving different industrial problems. Its popularity is based on the capability to solve complex non-tradition problems involving different physical processes. The paradigm of complete automation of labor-intensive and time-taking processes like grid generation makes FlowVision attractive for many engineers. FlowVision is completely developer-independent software. It includes an advanced graphical interface, the system for specifying a computational project as well as the system for flow visualization on planes, on curvilinear surfaces and in volume by means of different methods: plots, color contours, iso-lines, iso-surfaces, vector fields. Besides that, FlowVision provides tools for calculation of integral characteristics on surfaces and in volumetric regions.

The software is based on the finite-volume approach to approximation of the partial differential equations describing fluid motion and accompanying physical processes. It provides explicit and implicit methods for time integration of these equations. The software includes automated generator of unstructured grid with capability of its local dynamic adaptation. The solver involves two-level parallelism which allows calculations on computers with distributed and shared memory (coexisting in the same hardware). FlowVision incorporates a wide spectrum of physical models: different turbulence models, models for mass transfer accounting for chemical reactions and radioactive decay, several combustion models, a dispersed phase model, an electro-hydrodynamic model, an original VOF model for tracking moving interfaces. It should be noted that turbulence can be simulated within URANS, LES, and ILES approaches. FlowVision simulates fluid motion with velocities corresponding to all possible flow regimes: from incompressible to hypersonic. This is achieved by using an original all-speed velocity-pressure split algorithm for integration of the Navier-Stokes equations.

FlowVision enables solving multi-physic problems with use of different modeling tools. For instance, one can simulate multi-phase flows with use of the VOF method, flows past bodies moving across a stationary grid (within Euler approach), flows in rotary machines with use of the technology of sliding grid. Besides that, the software solves fluid-structure interaction problems using the technology of two-way coupling of FlowVision with finite-element codes. Two examples of solving challenging problems in the FlowVision software are demonstrated in the given article. The first one is splashdown of a spacecraft after deceleration by means of jet engines. This problem is characterized by presence of moving bodies and contact surface between the air and the water in the computational domain. The supersonic jets interact with the air-water interphase. The second problem is simulation of the work of a human heart with artificial and natural valves designed on the basis of tomographic investigations with use of a finite-element model of the heart. This problem is characterized by two-way coupling between the “liquid” computational domain and the finite-element model of the hart muscles.

The problem of online convex optimization naturally occurs in cases when there is an update of statistical information. The mirror descent method is well known for non-smooth optimization problems. Mirror descent is an extension of the subgradient method for solving non-smooth convex optimization problems in the case of a non-Euclidean distance. This paper is devoted to a stochastic variant of recently proposed Mirror Descent methods for convex online optimization problems with convex Lipschitz (generally, non-smooth) functional constraints. This means that we can still use the value of the functional constraint, but instead of (sub)gradient of the objective functional and the functional constraint, we use their stochastic (sub)gradients. More precisely, assume that on a closed subset of $n$-dimensional vector space, $N$ convex Lipschitz non-smooth functionals are given. The problem is to minimize the arithmetic mean of these functionals with a convex Lipschitz constraint. Two methods are proposed, for solving this problem, using stochastic (sub)gradients: adaptive method (does not require knowledge of Lipschitz constant neither for the objective functional, nor for the functional of constraint) and non-adaptivemethod (requires knowledge of Lipschitz constant for the objective functional and the functional of constraint). Note that it is allowed to calculate the stochastic (sub)gradient of each functional only once. In the case of non-negative regret, we find that the number of non-productive steps is $O$($N$), which indicates the optimality of the proposed methods. We consider an arbitrary proximal structure, which is essential for decisionmaking problems. The results of numerical experiments are presented, allowing to compare the work of adaptive and non-adaptive methods for some examples. It is shown that the adaptive method can significantly improve the number of the found solutions.

In this work we consider a possibility to use the conception of $(\delta, L)$-model of a function for optimization tasks, whereby solving a primal problem there is a necessity to recover a solution of a dual problem. The conception of $(\delta, L)$-model is based on the conception of $(\delta, L)$-oracle which was proposed by Devolder–Glineur–Nesterov, herewith the authors proposed approximate a function with an upper bound using a convex quadratic function with some additive noise $\delta$. They managed to get convex quadratic upper bounds with noise even for nonsmooth functions. The conception of $(\delta, L)$-model continues this idea by using instead of a convex quadratic function a more complex convex function in an upper bound. Possibility to recover the solution of a dual problem gives great benefits in different problems, for instance, in some cases, it is faster to find a solution in a primal problem than in a dual problem. Note that primal-dual methods are well studied, but usually each class of optimization problems has its own primal-dual method. Our goal is to develop a method which can find solutions in different classes of optimization problems. This is realized through the use of the conception of $(\delta, L)$-model and adaptive structure of our methods. Thereby, we developed primal-dual adaptive gradient method and fast gradient method with $(\delta, L)$-model and proved convergence rates of the methods, moreover, for some classes of optimization problems the rates are optimal. The main idea is the following: we find a dual solution to an approximation of a primal problem using the conception of $(\delta, L)$-model. It is much easier to find a solution to an approximated problem, however, we have to do it in each step of our method, thereby the principle of “divide and conquer” is realized.

The article provides approaches to evolutionary modelling of synthesis of organised systems and analyses methodological problems of evolutionary computations of this kind. Based on the analysis of works on evolutionary cybernetics, evolutionary theory, systems theory and synergetics, we conclude that there are open problems in formalising the synthesis of organised systems and modelling their evolution. The article emphasises that the theoretical basis for the practice of evolutionary modelling is the principles of the modern synthetic theory of evolution. Our software project uses a virtual computing environment for machine synthesis of problem solving algorithms. In the process of modelling, we obtained the results on the basis of which we conclude that there are a number of conditions that fundamentally limit the applicability of genetic programming methods in the tasks of synthesis of functional structures. The main limitations are the need for the fitness function to track the step-by-step approach to the solution of the problem and the inapplicability of this approach to the problems of synthesis of hierarchically organised systems. We note that the results obtained in the practice of evolutionary modelling in general for the whole time of its existence, confirm the conclusion the possibilities of genetic programming are fundamentally limited in solving problems of synthesizing the structure of organized systems. As sources of fundamental difficulties for machine synthesis of system structures the article points out the absence of directions for gradient descent in structural synthesis and the absence of regularity of random appearance of new organised structures. The considered problems are relevant for the theory of biological evolution. The article substantiates the statement about the biological specificity of practically possible ways of synthesis of the structure of organised systems. As a theoretical interpretation of the discussed problem, we propose to consider the system-evolutionary concept of P.K.Anokhin. The process of synthesis of functional structures in this context is an adaptive response of organisms to external conditions based on their ability to integrative synthesis of memory, needs and information about current conditions. The results of actual studies are in favour of this interpretation. We note that the physical basis of biological integrativity may be related to the phenomena of non-locality and non-separability characteristic of quantum systems. The problems considered in this paper are closely related to the problem of creating strong artificial intelligence.

We present the iterative algorithm that solves numerically both Urysohn type Fredholm and Volterra nonlinear one-dimensional nonsingular integral equations of the second kind to a specified, modest user-defined accuracy. The algorithm is based on descending recursive sequence of quadratures. Convergence of numerical scheme is guaranteed by fixed-point theorems. Picard’s method of integrating successive approximations is of great importance for the existence theory of integral equations but surprisingly very little appears on numerical algorithms for its direct implementation in the literature. We show that successive approximations method can be readily employed in numerical solution of integral equations. By that the quadrature algorithm is thoroughly designed. It is based on the explicit form of fifth-order embedded Runge–Kutta rule with adaptive step-size self-control. Since local error estimates may be cheaply obtained, continuous monitoring of the quadrature makes it possible to create very accurate automatic numerical schemes and to reduce considerably the main drawback of Picard iterations namely the extremely large amount of computations with increasing recursion depth. Our algorithm is organized so that as compared to most approaches the nonlinearity of integral equations does not induce any additional computational difficulties, it is very simple to apply and to make a program realization. Our algorithm exhibits some features of universality. First, it should be stressed that the method is as easy to apply to nonlinear as to linear equations of both Fredholm and Volterra kind. Second, the algorithm is equipped by stopping rules by which the calculations may to considerable extent be controlled automatically. A compact C++-code of described algorithm is presented. Our program realization is self-consistent: it demands no preliminary calculations, no external libraries and no additional memory is needed. Numerical examples are provided to show applicability, efficiency, robustness and accuracy of our approach.

The work is dedicated to investigation of possibility to increase the efficiency of solving external aerodynamic problems. Methodical questions of using locally-adaptive grids and wall functions for numerical simulation of turbulent flows past flying vehicles are studied. Reynolds-averaged Navier–Stokes equations are integrated. The equations are closed by standard $k–\varepsilon$ turbulence model. Subsonic turbulent flow of perfect compressible viscous gas past airfoil RAE 2822 is considered. Calculations are performed in CFD software FlowVision. The efficiency of using the technology of smoothing diffusion fluxes and the Bradshaw formula for turbulent viscosity is analyzed. These techniques are regarded as means of increasing the accuracy of solving aerodynamic problems on locally-adaptive grids. The obtained results show that using the technology of smoothing diffusion fluxes essentially decreases the discrepancy between computed and experimental values of the drag coefficient. In addition, the distribution of the skin friction coefficient over the curvilinear surface of the airfoil becomes more regular. These results indicate that the given technology is an effective way to increase the accuracy of calculations on locally-adaptive grids. The Bradshaw formula for the dynamic coefficient of turbulent viscosity is traditionally used in the SST $k–\omega$ turbulence model. The possibility to implement it in the standard $k–\varepsilon$ turbulence model is investigated in the present article. The calculations show that this formula provides good agreement of integral aerodynamic characteristics and the distribution of the pressure coefficient over the airfoil surface with experimental data. Besides that, it essentially augments the accuracy of simulation of the flow in the boundary layer and in the wake. On the other hand, using the Bradshaw formula in the simulation of the air flow past airfoil RAE 2822 leads to under-prediction of the skin friction coefficient. For this reason, the conclusion is made that practical use of the Bradshaw formula requires its preliminary validation and calibration on reliable experimental data available for the considered flows. The results of the work as a whole show that using the technologies discussed in numerical solution of external aerodynamic problems on locally-adaptive grids together with wall functions provides the computational accuracy acceptable for quick assessment of the aerodynamic characteristics of a flying vehicle. So, one can deduce that the FlowVision software is an effective tool for preliminary design studies, for conceptual design, and for aerodynamic shape optimization.

Recently, saddle point problems have received much attention due to their powerful modeling capability for a lot of problems from diverse domains. Applications of these problems occur in many applied areas, such as robust optimization, distributed optimization, game theory, and many applications in machine learning such as empirical risk minimization and generative adversarial networks training. Therefore, many researchers have actively worked on developing numerical methods for solving saddle point problems in many different settings. This paper is devoted to developing a numerical method for solving saddle point problems in the nonconvex uniformly-concave setting. We study a general class of saddle point problems with composite structure and H\"older-continuous higher-order derivatives. To solve the problem under consideration, we propose an approach in which we reduce the problem to a combination of two auxiliary optimization problems separately for each group of variables, the outer minimization problem w.r.t. primal variables, and the inner maximization problem w.r.t the dual variables. For solving the outer minimization problem, we use the Adaptive Gradient Method, which is applicable for nonconvex problems and also works with an inexact oracle that is generated by approximately solving the inner problem. For solving the inner maximization problem, we use the Restarted Unified Acceleration Framework, which is a framework that unifies the high-order acceleration methods for minimizing a convex function that has H\"older-continuous higher-order derivatives. Separate complexity bounds are provided for the number of calls to the first-order oracles for the outer minimization problem and higher-order oracles for the inner maximization problem. Moreover, the complexity of the whole proposed approach is then estimated.

In this study we discuss methods to solve optimal control problems based on neural network techniques. We study hierarchical dynamical two-level system for surface water quality control. The system consists of a supervisor (government) and a few agents (enterprises). We consider this problem from the point of agents. In this case we solve optimal control problem with constraints. To solve this problem, we use Pontryagin’s maximum principle, with which we obtain optimality conditions. To solve emerging ODEs, we use feedforward neural network. We provide a review of existing techniques to study such problems and a review of neural network’s training methods. To estimate the error of numerical solution, we propose to use defect analysis method, adapted for neural networks. This allows one to get quantitative error estimations of numerical solution. We provide examples of our method’s usage for solving synthetic problem and a surface water quality control model. We compare the results of this examples with known solution (when provided) and the results of shooting method. In all cases the errors, estimated by our method are of the same order as the errors compared with known solution. Moreover, we study surface water quality control problem when no solutions is provided by other methods. This happens because of relatively large time interval and/or the case of several agents. In the latter case we seek Nash equilibrium between agents. Thus, in this study we show the ability of neural networks to solve various problems including optimal control problems and differential games and we show the ability of quantitative estimation of an error. From the numerical results we conclude that the presence of the supervisor is necessary for achieving the sustainable development.

In this paper the problem of automated building of a citation graph from a collection of scientific documents is considered as a sequence of machine learning tasks. The overall data processing technology is described which consists of six stages: preprocessing, metainformation extraction, bibliography lists extraction, splitting bibliography lists into separate bibliography records, standardization of each bibliography record, and record linkage. The goal of this paper is to provide a survey of approaches and algorithms suitable for each stage, motivate the choice of the best combination of algorithms, and adapt some of them for multilingual bibliographies processing. For some of the tasks new algorithms and heuristics are proposed and evaluated on the mixed English and Russian documents corpora.