Reduction of dynamical biochemical reaction networks in computational biology

Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as combinatorial explosion are strong obstacles against analyzing the dynamics of large models of this type. Multi-scaleness is another property of these networks, that can be used to get past some of these obstacles. Networks with many well separated time scales, can be reduced to simpler networks, in a way that depends only on the orders of magnitude and not on the exact values of the kinetic parameters. The main idea used for such robust simplifications of networks is the concept of dominance among model elements, allowing hierarchical organization of these elements according to their effects on the network dynamics. This concept finds a natural formulation in tropical geometry. We revisit, in the light of these new ideas, the main approaches to model reduction of reaction networks, such as quasi-steady state and quasi-equilibrium approximations, and provide practical recipes for model reduction of linear and nonlinear networks. We also discuss the application of model reduction to backward pruning machine learning techniques

Topology Control Algorithm considering Antenna Radiation Pattern in Three-Dimensional Wireless Sensor Networks

Topology control is a key issue of wireless sensor network to reduce energy consumption and communication collision. Topology control algorithms in three-dimensional space have been proposed by modifying existing two-dimensional algorithms. These algorithms are based on the theoretical assumption that transmission power is radiated equally to the all directions by using isotropic antenna model. However, isotropic antenna does not exist, which is hypothetical antenna to compare the real antenna performance. In the real network, dipole antenna is applied, and because of the radiation pattern, performance of topology control algorithm is degraded. We proposed local remapping algorithm to solve the problem and applied it to existing topology control algorithms. Simulation results show that our algorithm increases performance of existing algorithms and reduces power consumption

Context guided retrieval

This paper presents a hierarchical case representation that uses a context guided retrieval method The performance of this method is compared to that of a simple flat file representation using standard nearest neighbour retrieval. The data presented in this paper is more extensive than that presented in an earlier paper by the same authors. The estimation of the construction costs of light industrial warehouse buildings is used as the test domain. Each case in the system comprises approximately 400 features. These are structured into a hierarchical case representation that holds more general contextual features at its top and specific building elements at its leaves. A modified nearest neighbour retrieval algorithm is used that is guided by contextual similarity. Problems are decomposed into sub-problems and solutions recomposed into a final solution. The comparative results show that the context guided retrieval method using the hierarchical case representation is significantly more accurate than the simpler flat file representation and standard nearest neighbour retrieval