An extended Kalman filtering approach to modeling nonlinear dynamic gene regulatory networks via short gene expression time series

Copyright [2009] IEEE. This material is posted here with permission of the IEEE. Such permission of the IEEE does not in any way imply IEEE endorsement of any of Brunel University's products or services. Internal or personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution must be obtained from the IEEE by writing to [email protected]. By choosing to view this document, you agree to all provisions of the copyright laws protecting it.In this paper, the extended Kalman filter (EKF) algorithm is applied to model the gene regulatory network from gene time series data. The gene regulatory network is considered as a nonlinear dynamic stochastic model that consists of the gene measurement equation and the gene regulation equation. After specifying the model structure, we apply the EKF algorithm for identifying both the model parameters and the actual value of gene expression levels. It is shown that the EKF algorithm is an online estimation algorithm that can identify a large number of parameters (including parameters of nonlinear functions) through iterative procedure by using a small number of observations. Four real-world gene expression data sets are employed to demonstrate the effectiveness of the EKF algorithm, and the obtained models are evaluated from the viewpoint of bioinformatics

Synchronization of coupled neutral-type neural networks with jumping-mode-dependent discrete and unbounded distributed delays

This is the post-print version of the Article. The official published version can be accessed from the links below - Copyright @ 2013 IEEE.In this paper, the synchronization problem is studied for an array of N identical delayed neutral-type neural networks with Markovian jumping parameters. The coupled networks involve both the mode-dependent discrete-time delays and the mode-dependent unbounded distributed time delays. All the network parameters including the coupling matrix are also dependent on the Markovian jumping mode. By introducing novel Lyapunov-Krasovskii functionals and using some analytical techniques, sufficient conditions are derived to guarantee that the coupled networks are asymptotically synchronized in mean square. The derived sufficient conditions are closely related with the discrete-time delays, the distributed time delays, the mode transition probability, and the coupling structure of the networks. The obtained criteria are given in terms of matrix inequalities that can be efficiently solved by employing the semidefinite program method. Numerical simulations are presented to further demonstrate the effectiveness of the proposed approach.This work was supported in part by the Royal Society of the U.K., the National Natural Science Foundation of China under Grants 61074129, 61174136 and 61134009, and the Natural Science Foundation of Jiangsu Province of China under Grants BK2010313 and BK2011598

Secure thermal infrared communications using engineered blackbody radiation

The thermal (emitted) infrared frequency bands, from 20–40 THz and 60–100 THz, are best known for applications in thermography. This underused and unregulated part of the spectral range offers opportunities for the development of secure communications. The ‘THz Torch' concept was recently presented by the authors. This technology fundamentally exploits engineered blackbody radiation, by partitioning thermally-generated spectral noise power into pre-defined frequency channels; the energy in each channel is then independently pulsed modulated and multiplexing schemes are introduced to create a robust form of short-range secure communications in the far/mid infrared. To date, octave bandwidth (25–50 THz) single-channel links have been demonstrated with 380 bps speeds. Multi-channel ‘THz Torch' frequency division multiplexing (FDM) and frequency-hopping spread-spectrum (FHSS) schemes have been proposed, but only a slow 40 bps FDM scheme has been demonstrated experimentally. Here, we report a much faster 1,280 bps FDM implementation. In addition, an experimental proof-of-concept FHSS scheme is demonstrated for the first time, having a 320 bps data rate. With both 4-channel multiplexing schemes, measured bit error rates (BERs) of < 10(−6) are achieved over a distance of 2.5 cm. Our approach represents a new paradigm in the way niche secure communications can be established over short links

Robust synchronization of an array of coupled stochastic discrete-time delayed neural networks

Copyright [2008] IEEE. This material is posted here with permission of the IEEE. Such permission of the IEEE does not in any way imply IEEE endorsement of any of Brunel University's products or services. Internal or personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution must be obtained from the IEEE by writing to [email protected]. By choosing to view this document, you agree to all provisions of the copyright laws protecting it.This paper is concerned with the robust synchronization problem for an array of coupled stochastic discrete-time neural networks with time-varying delay. The individual neural network is subject to parameter uncertainty, stochastic disturbance, and time-varying delay, where the norm-bounded parameter uncertainties exist in both the state and weight matrices, the stochastic disturbance is in the form of a scalar Wiener process, and the time delay enters into the activation function. For the array of coupled neural networks, the constant coupling and delayed coupling are simultaneously considered. We aim to establish easy-to-verify conditions under which the addressed neural networks are synchronized. By using the Kronecker product as an effective tool, a linear matrix inequality (LMI) approach is developed to derive several sufficient criteria ensuring the coupled delayed neural networks to be globally, robustly, exponentially synchronized in the mean square. The LMI-based conditions obtained are dependent not only on the lower bound but also on the upper bound of the time-varying delay, and can be solved efficiently via the Matlab LMI Toolbox. Two numerical examples are given to demonstrate the usefulness of the proposed synchronization scheme

Solving job shop scheduling problem using genetic algorithm with penalty function

This paper presents a genetic algorithm with a penalty function for the job shop scheduling problem. In the context of proposed algorithm, a clonal selection based hyper mutation and a life span extended strategy is designed. During the search process, an adaptive penalty function is designed so that the algorithm can search in both feasible and infeasible regions of the solution space. Simulated experiments were conducted on 23 benchmark instances taken from the OR-library. The results show the effectiveness of the proposed algorithm

Brokerage and balance: Creating an effective organizational interface for product modularization in multinational R&amp;D

Despite numerous studies on modularity, the modularization processes have received less attention. In the global context, product modularity can be leveraged to satisfy heterogeneous market requirements across countries with low costs. Through a longitudinal case study of HomeTech, we examined how multinational R&D created an effective organizational interface to facilitate recombination of its organizational units, and thus product modularization. We found that three elements of an organizational interface were established through a process composed of three phases in HomeTech R&D: regional concentration, establishing a module pool, and creating architecture leader posts. We also found that the three elements exerted the balancing effect and the brokerage effect so that the organizational interface was effective in facilitating recombination of organizational units. We contribute to the literature through showing how organizational modularity can affect product modularity within a firm. We also reveal the critical role of architecture leaders in product modularization. Finally, we enrich the organizational interface concept by highlighting the combination of elements.N

Bidirectional optimization of the melting spinning process

This is the author's accepted manuscript (under the provisional title "Bi-directional optimization of the melting spinning process with an immune-enhanced neural network"). The final published article is available from the link below. Copyright 2014 @ IEEE.A bidirectional optimizing approach for the melting spinning process based on an immune-enhanced neural network is proposed. The proposed bidirectional model can not only reveal the internal nonlinear relationship between the process configuration and the quality indices of the fibers as final product, but also provide a tool for engineers to develop new fiber products with expected quality specifications. A neural network is taken as the basis for the bidirectional model, and an immune component is introduced to enlarge the searching scope of the solution field so that the neural network has a larger possibility to find the appropriate and reasonable solution, and the error of prediction can therefore be eliminated. The proposed intelligent model can also help to determine what kind of process configuration should be made in order to produce satisfactory fiber products. To make the proposed model practical to the manufacturing, a software platform is developed. Simulation results show that the proposed model can eliminate the approximation error raised by the neural network-based optimizing model, which is due to the extension of focusing scope by the artificial immune mechanism. Meanwhile, the proposed model with the corresponding software can conduct optimization in two directions, namely, the process optimization and category development, and the corresponding results outperform those with an ordinary neural network-based intelligent model. It is also proved that the proposed model has the potential to act as a valuable tool from which the engineers and decision makers of the spinning process could benefit.National Nature Science Foundation of China, Ministry of Education of China, the Shanghai Committee of Science and Technology), and the Fundamental Research Funds for the Central Universities