Computational methods in cancer gene networking

In the past few years, many high-throughput techniques have been developed and applied to biological studies. These techniques such as “next generation” genome sequencing, chip-on-chip, microarray and so on can be used to measure gene expression and gene regulatory elements in a genome-wide scale. Moreover, as these technologies become more affordable and accessible, they have become a driving force in modern biology. As a result, huge amount biological data have been produced, with the expectation of increasing number of such datasets to be generated in the future. High-throughput data are more comprehensive and unbiased, but ‘real signals’ or biological insights, molecular mechanisms and biological principles are buried in the flood of data. In current biological studies, the bottleneck is no longer a lack of data, but the lack of ingenuity and computational means to extract biological insights and principles by integrating knowledge and high-throughput data. 

Here I am reviewing the concepts and principles of network biology and the computational methods which can be applied to cancer research. Furthermore, I am providing a practical guide for computational analysis of cancer gene networks

Statistics of Extreme Gravitational Lensing Events. I.The Zero Shear Case

For a given source and lens pair, there is a thin on-axis tube-like volume behind the lens in which the radiation flux from the source is greatly increased due to gravitational lensing. Any objects (such as dust grains) which pass through such a thin tube will experience strong bursts of radiation, i.e., Extreme Gravitational Lensing Events (EGLE). We study the physics and statistics of EGLE for the case in which finite source size is more important than shear. One of the several possible significant astrophysical effects is investigated with an illustrative calculation.Comment: revised and final published version including a new section on the destruction of dust grains in globular clusters as an exampl

Robust Multi-Criteria Optimal Fuzzy Control of Discrete-Time Nonlinear Systems

This paper presents a novel fuzzy control design of discrete-time nonlinear systems with multiple performance criteria. The purpose behind this work is to improve the traditional fuzzy controller performance to satisfy several performance criteria simultaneously to secure quadratic optimality with an inherent stability property together with a dissipativity type of disturbance reduction. The Takagi–Sugeno-type fuzzy model is used in our control system design. By solving a linear matrix inequality at each time step, the optimal control solution can be found to satisfy mixed performance criteria. The effectiveness of the proposed technique is demonstrated by simulation of the control of the inverted pendulum system on a cart

Robust Multi-Criteria Optimal Fuzzy Control of Continuous-Time Nonlinear Systems

This paper presents a novel fuzzy control design of continuous-time nonlinear systems with multiple performance criteria. The purpose behind this work is to improve the traditional fuzzy controller performance to satisfy several performance criteria simultaneously to secure quadratic optimality with inherent stability property together with dissipativity type of disturbance reduction. The Takagi– Sugeno fuzzy model is used in our control system design. By solving the linear matrix inequality at each time step, the control solution can be found to satisfy the mixed performance criteria. The effectiveness of the proposed technique is demonstrated by simulation of the control of the inverted pendulum system

Second-Order Fault Tolerant Extended Kalman Filter for Discrete Time Nonlinear Systems

As missing sensor data may severely degrade the overall system performance and stability, reliable state estimation is of great importance in modern data-intensive control, computing, and power systems applications. Aiming at providing a more robust and resilient state estimation technique, this paper presents a novel second-order fault-tolerant extended Kalman filter estimation framework for discrete-time stochastic nonlinear systems under sensor failures, bounded observer-gain perturbation, extraneous noise, and external disturbances condition. The failure mechanism of multiple sensors is assumed to be independent of each other with various malfunction rates. The proposed approach is a locally unbiased, minimum estimation error covariance based nonlinear observer designed for dynamic state estimation under these conditions. It has been successfully applied to a benchmark target-trajectory tracking application. Computer simulation studies have demonstrated that the proposed second-order fault-tolerant extended Kalman filter provides more accurate estimation results, in comparison with traditional first- and second-order extended Kalman filter. Experimental results have demonstrated that the proposed second-order fault-tolerant extended Kalman filter can serve as a powerful alternative to the existing nonlinear estimation approaches

Smart Power Grid Synchronization With Fault Tolerant Nonlinear Estimation

Effective real-time state estimation is essential for smart grid synchronization, as electricity demand continues to grow, and renewable energy resources increase their penetration into the grid. In order to provide a more reliable state estimation technique to address the problem of bad data in the PMU-based power synchronization, this paper presents a novel nonlinear estimation framework to dynamically track frequency, voltage magnitudes and phase angles. Instead of directly analyzing in abc coordinate frame, symmetrical component transformation is employed to separate the positive, negative, and zero sequence networks. Then, Clarke\u27s transformation is used to transform the sequence networks into the αβ stationary coordinate frame, which leads to system model formulation. A novel fault tolerant extended Kalman filter based real-time estimation framework is proposed for smart grid synchronization with noisy bad data measurements. Computer simulation studies have demonstrated that the proposed fault tolerant extended Kalman filter (FTEKF) provides more accurate voltage synchronization results than the extended Kalman filter (EKF). The proposed approach has been implemented with dSPACE DS1103 and National Instruments CompactRIO hardware platforms. Computer simulation and hardware instrumentation results have shown the potential applications of FTEKF in smart grid synchronization