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The 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.

The article presents the numerical modeling and study of the kinetic model of propane pyrolysis. The study of the reaction kinetics is a necessary stage in modeling the dynamics of the gas flow in the reactor.

The kinetic model of propane pyrolysis is a nonlinear system of ordinary differential equations of the first order with parameters, the role of which is played by the reaction rate constants. Math modeling of processes is based on the use of the mass conservation law. To solve an initial (forward) problem, implicit methods for solving stiff ordinary differential equation systems are used. The model contains 60 input kinetic parameters and 17 output parameters corresponding to the reaction substances, of which only 9 are observable. In the process of solving the problem of estimating parameters (inverse problem), there is a question of non-uniqueness of the set of parameters that satisfy the experimental data. Therefore, before solving the inverse problem, the possibility of determining the parameters of the model is analyzed (analysis of identifiability).

To analyze identifiability, we use the orthogonal method, which has proven itself well for analyzing models with a large number of parameters. The algorithm is based on the analysis of the sensitivity matrix by the methods of differential and linear algebra, which shows the degree of dependence of the unknown parameters of the models on the given measurements. The analysis of sensitivity and identifiability showed that the parameters of the model are stably determined from a given set of experimental data. The article presents a list of model parameters from most to least identifiable. Taking into account the analysis of the identifiability of the mathematical model, restrictions were introduced on the search for less identifiable parameters when solving the inverse problem.

The inverse problem of estimating the parameters was solved using a genetic algorithm. The article presents the found optimal values of the kinetic parameters. A comparison of the experimental and calculated dependences of the concentrations of propane, main and by-products of the reaction on temperature for different flow rates of the mixture is presented. The conclusion about the adequacy of the constructed mathematical model is made on the basis of the correspondence of the results obtained to physicochemical laws and experimental data.

In this article we consider min-min type of problems or minimization by two groups of variables. In some way it is similar to classic min-max saddle point problem. Although, saddle point problems are usually more difficult in some way. Min-min problems may occur in case if some groups of variables in convex optimization have different dimensions or if these groups have different domains. Such problem structure gives us an ability to split the main task to subproblems, and allows to tackle it with mixed oracles. However existing articles on this topic cover only zeroth and first order oracles, in our work we consider high-order tensor methods to solve inner problem and fast gradient method to solve outer problem.

We assume, that outer problem is constrained to some convex compact set, and for the inner problem we consider both unconstrained case and being constrained to some convex compact set. By definition, tensor methods use high-order derivatives, so the time per single iteration of the method depends a lot on the dimensionality of the problem it solves. Therefore, we suggest, that the dimension of the inner problem variable is not greater than 1000. Additionally, we need some specific assumptions to be able to use mixed oracles. Firstly, we assume, that the objective is convex in both groups of variables and its gradient by both variables is Lipschitz continuous. Secondly, we assume the inner problem is strongly convex and its gradient is Lipschitz continuous. Also, since we are going to use tensor methods for inner problem, we need it to be p-th order Lipschitz continuous ($p > 1$). Finally, we assume strong convexity of the outer problem to be able to use fast gradient method for strongly convex functions.

We need to emphasize, that we use superfast tensor method to tackle inner subproblem in unconstrained case. And when we solve inner problem on compact set, we use accelerated high-order composite proximal method.

Additionally, in the end of the article we compare the theoretical complexity of obtained methods with regular gradient method, which solves the mentioned problem as regular convex optimization problem and doesn’t take into account its structure (Remarks 1 and 2).

The paper provides a comparative analysis of the results obtained by various approaches to modeling the process of artillery shot. In this connection, the main problem of internal ballistics and its particular case of the Lagrange problem are formulated in averaged parameters, where, within the framework of the assumptions of the thermodynamic approach, the distribution of pressure and gas velocity over the projectile space for a channel of variable cross section is taken into account for the first time. The statement of the Lagrange problem is also presented in the framework of the gas-dynamic approach, taking into account the spatial (one-dimensional and two-dimensional axisymmetric) changes in the characteristics of the ballistic process. The control volume method is used to numerically solve the system of Euler gas-dynamic equations. Gas parameters at the boundaries of control volumes are determined using a selfsimilar solution to the Riemann problem. Based on the Godunov method, a modification of the Osher scheme is proposed, which allows to implement a numerical calculation algorithm with a second order of accuracy in coordinate and time. The solutions obtained in the framework of the thermodynamic and gas-dynamic approaches are compared for various loading parameters. The effect of projectile mass and chamber broadening on the distribution of the ballistic parameters of the shot and the dynamics of the projectile motion was studied. It is shown that the thermodynamic approach, in comparison with the gas-dynamic approach, leads to a systematic overestimation of the estimated muzzle velocity of the projectile in the entire range of parameters studied, while the difference in muzzle velocity can reach 35%. At the same time, the discrepancy between the results obtained in the framework of one-dimensional and two-dimensional gas-dynamic models of the shot in the same range of change in parameters is not more than 1.3%.

A spatial gas-dynamic formulation of the backpressure problem is given, which describes the change in pressure in front of an accelerating projectile as it moves along the barrel channel. It is shown that accounting the projectile’s front, considered in the two-dimensional axisymmetric formulation of the problem, leads to a significant difference in the pressure fields behind the front of the shock wave, compared with the solution in the framework of the onedimensional formulation of the problem, where the projectile’s front is not possible to account. It is concluded that this can significantly affect the results of modeling ballistics of a shot at high shooting velocities.

The article is devoted to studying the application of convex optimization methods to solve the Cauchy problem for the Helmholtz equation, which is ill-posed since the equation belongs to the elliptic type. The Cauchy problem is formulated as an inverse problem and is reduced to a convex optimization problem in a Hilbert space. The functional to be optimized and its gradient are calculated using the solution of boundary value problems, which, in turn, are well-posed and can be approximately solved by standard numerical methods, such as finite-difference schemes and Fourier series expansions. The convergence of the applied fast gradient method and the quality of the solution obtained in this way are experimentally investigated. The experiment shows that the accelerated gradient method — the Similar Triangle Method — converges faster than the non-accelerated method. Theorems on the computational complexity of the resulting algorithms are formulated and proved. It is found that Fourier’s series expansions are better than finite-difference schemes in terms of the speed of calculations and improve the quality of the solution obtained. An attempt was made to use restarts of the Similar Triangle Method after halving the residual of the functional. In this case, the convergence does not improve, which confirms the absence of strong convexity. The experiments show that the inaccuracy of the calculations is more adequately described by the additive concept of the noise in the first-order oracle. This factor limits the achievable quality of the solution, but the error does not accumulate. According to the results obtained, the use of accelerated gradient optimization methods can be the way to solve inverse problems effectively.

The article is devoted to first-order adaptive methods for optimization problems with relatively strongly convex functionals. The concept of relatively strong convexity significantly extends the classical concept of convexity by replacing the Euclidean norm in the definition by the distance in a more general sense (more precisely, by Bregman’s divergence). An important feature of the considered classes of problems is the reduced requirements concerting the level of smoothness of objective functionals. More precisely, we consider relatively smooth and relatively Lipschitz-continuous objective functionals, which allows us to apply the proposed techniques for solving many applied problems, such as the intersection of the ellipsoids problem (IEP), the Support Vector Machine (SVM) for a binary classification problem, etc. If the objective functional is convex, the condition of relatively strong convexity can be satisfied using the problem regularization. In this work, we propose adaptive gradient-type methods for optimization problems with relatively strongly convex and relatively Lipschitzcontinuous functionals for the first time. Further, we propose universal methods for relatively strongly convex optimization problems. This technique is based on introducing an artificial inaccuracy into the optimization model, so the proposed methods can be applied both to the case of relatively smooth and relatively Lipschitz-continuous functionals. Additionally, we demonstrate the optimality of the proposed universal gradient-type methods up to the multiplication by a constant for both classes of relatively strongly convex problems. Also, we show how to apply the technique of restarts of the mirror descent algorithm to solve relatively Lipschitz-continuous optimization problems. Moreover, we prove the optimal estimate of the rate of convergence of such a technique. Also, we present the results of numerical experiments to compare the performance of the proposed methods.

Distributed saddle point problems (SPPs) have numerous applications in optimization, matrix games and machine learning. For example, the training of generated adversarial networks is represented as a min-max optimization problem, and training regularized linear models can be reformulated as an SPP as well. This paper studies distributed nonsmooth SPPs with Lipschitz-continuous objective functions. The objective function is represented as a sum of several components that are distributed between groups of computational nodes. The nodes, or agents, exchange information through some communication network that may be centralized or decentralized. A centralized network has a universal information aggregator (a server, or master node) that directly communicates to each of the agents and therefore can coordinate the optimization process. In a decentralized network, all the nodes are equal, the server node is not present, and each agent only communicates to its immediate neighbors.

We assume that each of the nodes locally holds its objective and can compute its value at given points, i. e. has access to zero-order oracle. Zero-order information is used when the gradient of the function is costly, not possible to compute or when the function is not differentiable. For example, in reinforcement learning one needs to generate a trajectory to evaluate the current policy. This policy evaluation process can be interpreted as the computation of the function value. We propose an approach that uses a smoothing technique, i. e., applies a first-order method to the smoothed version of the initial function. It can be shown that the stochastic gradient of the smoothed function can be viewed as a random two-point gradient approximation of the initial function. Smoothing approaches have been studied for distributed zero-order minimization, and our paper generalizes the smoothing technique on SPPs.

Non-smooth optimization often arises in many applied problems. The issues of developing efficient computational procedures for such problems in high-dimensional spaces are very topical. First-order methods (subgradient methods) are well applicable here, but in fairly general situations they lead to low speed guarantees for large-scale problems. One of the approaches to this type of problem can be to identify a subclass of non-smooth problems that allow relatively optimistic results on the rate of convergence. For example, one of the options for additional assumptions can be the condition of a sharp minimum, proposed in the late 1960s by B. T. Polyak. In the case of the availability of information about the minimal value of the function for Lipschitz-continuous problems with a sharp minimum, it turned out to be possible to propose a subgradient method with a Polyak step-size, which guarantees a linear rate of convergence in the argument. This approach made it possible to cover a number of important applied problems (for example, the problem of projecting onto a convex compact set). However, both the condition of the availability of the minimal value of the function and the condition of a sharp minimum itself look rather restrictive. In this regard, in this paper, we propose a generalized condition for a sharp minimum, somewhat similar to the inexact oracle proposed recently by Devolder – Glineur – Nesterov. The proposed approach makes it possible to extend the class of applicability of subgradient methods with the Polyak step-size, to the situation of inexact information about the value of the minimum, as well as the unknown Lipschitz constant of the objective function. Moreover, the use of local analogs of the global characteristics of the objective function makes it possible to apply the results of this type to wider classes of problems. We show the possibility of applying the proposed approach to strongly convex nonsmooth problems, also, we make an experimental comparison with the known optimal subgradient method for such a class of problems. Moreover, there were obtained some results connected to the applicability of the proposed technique to some types of problems with convexity relaxations: the recently proposed notion of weak $\beta$-quasi-convexity and ordinary quasiconvexity. Also in the paper, we study a generalization of the described technique to the situation with the assumption that the $\delta$-subgradient of the objective function is available instead of the usual subgradient. For one of the considered methods, conditions are found under which, in practice, it is possible to escape the projection of the considered iterative sequence onto the feasible set of the problem.

The possibility of numerical 3D simulation of thrombi formation is considered.

The developed up to now detailed mathematical models describing formation of thrombi and clots include a great number of equations. Being implemented in a CFD code, the detailed mathematical models require essential computer resources for simulation of the thrombi growth in a blood flow. A reasonable alternative way is using reduced mathematical models. Two models based on the reduced mathematical model for the thrombin generation are described in the given paper.

The first model describes growth of a thrombus in a great vessel (artery). The artery flows are essentially unsteady. They are characterized by pulse waves. The blood velocity here is high compared to that in the vein tree. The reduced model for the thrombin generation and the thrombus growth in an artery is relatively simple. The processes accompanying the thrombin generation in arteries are well described by the zero-order approximation.

A vein flow is characterized lower velocity value, lower gradients, and lower shear stresses. In order to simulate the thrombin generation in veins, a more complex system of equations has to be solved. The model must allow for all the non-linear terms in the right-hand sides of the equations.

The simulation is carried out in the industrial software FlowVision.

The performed numerical investigations have shown the suitability of the reduced models for simulation of thrombin generation and thrombus growth. The calculations demonstrate formation of the recirculation zone behind a thrombus. The concentration of thrombin and the mass fraction of activated platelets are maximum here. Formation of such a zone causes slow growth of the thrombus downstream. At the upwind part of the thrombus, the concentration of activated platelets is low, and the upstream thrombus growth is negligible.

When the blood flow variation during a hart cycle is taken into account, the thrombus growth proceeds substantially slower compared to the results obtained under the assumption of constant (averaged over a hard cycle) conditions. Thrombin and activated platelets produced during diastole are quickly carried away by the blood flow during systole. Account of non-Newtonian rheology of blood noticeably affects the results.

The probabilistic topic model of a text document collection finds two matrices: a matrix of conditional probabilities of topics in documents and a matrix of conditional probabilities of words in topics. Each document is represented by a multiset of words also called the “bag of words”, thus assuming that the order of words is not important for revealing the latent topics of the document. Under this assumption, the problem is reduced to a low-rank non-negative matrix factorization governed by likelihood maximization. In general, this problem is ill-posed having an infinite set of solutions. In order to regularize the solution, a weighted sum of optimization criteria is added to the log-likelihood. When modeling large text collections, storing the first matrix seems to be impractical, since its size is proportional to the number of documents in the collection. At the same time, the topical vector representation (embedding) of documents is necessary for solving many text analysis tasks, such as information retrieval, clustering, classification, and summarization of texts. In practice, the topical embedding is calculated for a document “on-the-fly”, which may require dozens of iterations over all the words of the document. In this paper, we propose a way to calculate a topical embedding quickly, by one pass over document words. For this, an additional constraint is introduced into the model in the form of an equation, which calculates the first matrix from the second one in linear time. Although formally this constraint is not an optimization criterion, in fact it plays the role of a regularizer and can be used in combination with other regularizers within the additive regularization framework ARTM. Experiments on three text collections have shown that the proposed method improves the model in terms of sparseness, difference, logLift and coherence measures of topic quality. The open source libraries BigARTM and TopicNet were used for the experiments.