Проблемы динамического управления. Сборник научных трудов
In this paper, we study the Maximum Happy Vertices and the Maximum Happy Edges problems (MHV and MHE for short). Very recently, the problems attracted a lot of attention and were studied in Agrawal ’17, Aravind et al. ’16, Choudhari and Reddy ’18, Misra and Reddy ’17. Main focus of our work is lower bounds on the computational complexity of these problems. Established lower bounds can be divided into the following groups: NP-hardness of the above guarantee parameterization, kernelization lower bounds (answering questions of Misra and Reddy ’17), exponential lower bounds under the Set Cover Conjecture and the Exponential Time Hypothesis, and inapproximability results. Moreover, we present an O∗(ℓk)O∗(ℓk) randomized algorithm for MHV and an O∗(2k)O∗(2k) algorithm for MHE, where ℓℓ is the number of colors used and k is the number of required happy vertices or edges. These algorithms cannot be improved to subexponential taking proved lower bounds into account.
The current state of information systems of the Pushchino Research Center of the Russian Academy of Sciences to successfully solve the problems of computational biology.
One of the key advances in genome assembly that has led to a significant improvement in contig lengths has been improved algorithms for utilization of paired reads (mate-pairs). While in most assemblers, mate-pair information is used in a post-processing step, the recently proposed Paired de Bruijn Graph (PDBG) approach incorporates the mate-pair information directly in the assembly graph structure. However, the PDBG approach faces difficulties when the variation in the insert sizes is high. To address this problem, we first transform mate-pairs into edge-pair histograms that allow one to better estimate the distance between edges in the assembly graph that represent regions linked by multiple mate-pairs. Further, we combine the ideas of mate-pair transformation and PDBGs to construct new data structures for genome assembly: pathsets and pathset graphs.
Optimization Approaches for Solving String Selection Problems provides an overview of optimization methods for a wide class of genomics-related problems in relation to the string selection problems. This class of problems addresses the recognition of similar characteristics or differences within biological sequences. Specifically, this book considers a large class of problems, ranging from the closest string and substring problems, to the farthest string and substring problems, to the far from most string problem. Each problem includes a detailed description, highlighting both biological and mathematical features and presents state-of-the-art approaches.
A model for organizing cargo transportation between two node stations connected by a railway line which contains a certain number of intermediate stations is considered. The movement of cargo is in one direction. Such a situation may occur, for example, if one of the node stations is located in a region which produce raw material for manufacturing industry located in another region, and there is another node station. The organization of freight traﬃc is performed by means of a number of technologies. These technologies determine the rules for taking on cargo at the initial node station, the rules of interaction between neighboring stations, as well as the rule of distribution of cargo to the ﬁnal node stations. The process of cargo transportation is followed by the set rule of control. For such a model, one must determine possible modes of cargo transportation and describe their properties. This model is described by a ﬁnite-dimensional system of diﬀerential equations with nonlocal linear restrictions. The class of the solution satisfying nonlocal linear restrictions is extremely narrow. It results in the need for the “correct” extension of solutions of a system of diﬀerential equations to a class of quasi-solutions having the distinctive feature of gaps in a countable number of points. It was possible numerically using the Runge–Kutta method of the fourth order to build these quasi-solutions and determine their rate of growth. Let us note that in the technical plan the main complexity consisted in obtaining quasi-solutions satisfying the nonlocal linear restrictions. Furthermore, we investigated the dependence of quasi-solutions and, in particular, sizes of gaps (jumps) of solutions on a number of parameters of the model characterizing a rule of control, technologies for transportation of cargo and intensity of giving of cargo on a node station.