Networks for systems biology: conceptual connection of data and function

The purpose of this study is to survey the use of networks and network-based methods in systems biology. This study starts with an introduction to graph theory and basic measures allowing to quantify structural properties of networks. Then, the authors present important network classes and gene networks as well as methods for their analysis. In the last part of this study, the authors review approaches that aim at analysing the functional organisation of gene networks and the use of networks in medicine. In addition to this, the authors advocate networks as a systematic approach to general problems in systems biology, because networks are capable of assuming multiple roles that are very beneficial connecting experimental data with a functional interpretation in biological terms.

HOS-Based Semi-Blind Spatial Equalization for MIMO Rayleigh Fading Channels

In this paper we concentrate on the direct semi-blind spatial equalizer design for MIMO systems with Rayleigh fading channels. Our aim is to develop an algorithm which can outperform the classical training based method with the same training information used, and avoid the problems of low convergence speed and local minima due to pure blind methods. A general semi-blind cost function is first constructed which incorporates both the training information from the known data and some kind of higher order statistics (HOS) from the unknown sequence. Then, based on the developed cost function, we propose two semi-blind iterative and adaptive algorithms to find the desired spatial equalizer. To further improve the performance and convergence speed of the proposed adaptive method, we propose a technique to find the optimal choice of step size. Simulation results demonstrate the performance of the proposed algorithms and comparable schemes.

A mixed cost-function adaptive algorithm for ADSL time-domain equalization

We propose a mixed cost-function adaptive initialization algorithm for the time domain equalizer in a discrete multitone (DMT)-based asymmetric digital subscriber line. Using our approach, a higher convergence rate than that of the commonly used least-mean square algorithm is obtained, whilst attaining bit rates close to the optimum maximum shortening SNR and the upper bound SNR. Furthermore, our proposed method outperforms the minimum mean-squared error design for a range of time domain equalizer (TEQ) filter lengths. The improved performance outweighs the small increase in computational complexity required. A block variant of our proposed algorithm is also presented to overcome the increased latency imposed on the feedback path of the adaptive system.

Improving the ultra-low-power performance of IEEE 802.15.6 by adaptive synchronisation

In ultra-low data rate wireless sensor networks (WSNs) waking up just to listen to a beacon every superframe can be a major waste of energy. This study introduces MedMAC, a medium access protocol for ultra-low data rate WSNs that achieves significant energy efficiency through a novel synchronisation mechanism. The new draft IEEE 802.15.6 standard for body area networks includes a sub-class of applications such as medical implantable devices and long-term micro miniature sensors with ultra-low power requirements. It will be desirable for these devices to have 10 years or more of operation between battery changes, or to have average current requirements matched to energy harvesting technology. Simulation results are presented to show that the MedMAC allows nodes to maintain synchronisation to the network while sleeping through many beacons with a significant increase in energy efficiency during periods of particularly low data transfer. Results from a comparative analysis of MedMAC and IEEE 802.15.6 MAC show that MedMAC has superior efficiency with energy savings of between 25 and 87 for the presented scenarios. © 2011 The Institution of Engineering and Technology.

Adaptive Measurement-Based Policy-Driven QoS Management with Fuzzy-Rule-based Resource Allocation

Fixed and wireless networks are increasingly converging towards common connectivity with IP-based core networks. Providing effective end-to-end resource and QoS management in such complex heterogeneous converged network scenarios requires unified, adaptive and scalable solutions to integrate and co-ordinate diverse QoS mechanisms of different access technologies with IP-based QoS. Policy-Based Network Management (PBNM) is one approach that could be employed to address this challenge. Hence, a policy-based framework for end-to-end QoS management in converged networks, CNQF (Converged Networks QoS Management Framework) has been proposed within our project. In this paper, the CNQF architecture, a Java implementation of its prototype and experimental validation of key elements are discussed. We then present a fuzzy-based CNQF resource management approach and study the performance of our implementation with real traffic flows on an experimental testbed. The results demonstrate the efficacy of our resource-adaptive approach for practical PBNM systems

Local network-based measures to assess the inferability of different regulatory networks

The purpose of this study is to compare the inferability of various synthetic as well as real biological regulatory networks. In order to assess differences we apply local network-based measures. That means, instead of applying global measures, we investigate and assess an inference algorithm locally, on the level of individual edges and subnetworks. We demonstrate the behaviour of our local network-based measures with respect to different regulatory networks by conducting large-scale simulations. As inference algorithm we use exemplarily ARACNE. The results from our exploratory analysis allow us not only to gain new insights into the strength and weakness of an inference algorithm with respect to characteristics of different regulatory networks, but also to obtain information that could be used to design novel problem-specific statistical estimators.

Inferring the conservative causal core of gene regulatory networks

Background
Inferring gene regulatory networks from large-scale expression data is an important problem that received much attention in recent years. These networks have the potential to gain insights into causal molecular interactions of biological processes. Hence, from a methodological point of view, reliable estimation methods based on observational data are needed to approach this problem practically.

Results
In this paper, we introduce a novel gene regulatory network inference (GRNI) algorithm, called C3NET. We compare C3NET with four well known methods, ARACNE, CLR, MRNET and RN, conducting in-depth numerical ensemble simulations and demonstrate also for biological expression data from E. coli that C3NET performs consistently better than the best known GRNI methods in the literature. In addition, it has also a low computational complexity. Since C3NET is based on estimates of mutual information values in conjunction with a maximization step, our numerical investigations demonstrate that our inference algorithm exploits causal structural information in the data efficiently.

Conclusions
For systems biology to succeed in the long run, it is of crucial importance to establish methods that extract large-scale gene networks from high-throughput data that reflect the underlying causal interactions among genes or gene products. Our method can contribute to this endeavor by demonstrating that an inference algorithm with a neat design permits not only a more intuitive and possibly biological interpretation of its working mechanism but can also result in superior results.

Rapid design of a single chip adaptive beamformer

This paper presents the design of a single chip adaptive beamformer which contains 5 million transistors and can perform 50 GigaFlops. The core processor of the adaptive beamformer is a QR-array processor implemented on a fully efficient linear systolic architecture. The paper highlights a number of rapid design techniques that have been used to realize the design. These include an architecture synthesis tool for quickly developing the circuit architecture and the utilization of a library of parameterizable silicon intellectual property (IP) cores, to rapidly develop the circuit layouts.

A hybrid mixed cost-function TEQ initialization algorithm for ADSL modems

In this paper, we present a hybrid mixed cost-function adaptive initialization algorithm for the time domain equalizer in a discrete multitone (DMT)-based asymmetric digital subscriber loop. Using our approach, a higher convergence rate than that of the commonly used least-mean square algorithm is obtained, whilst attaining bit rates close to the optimum maximum shortening SNR and the upper bound SNR. Moreover, our proposed method outperforms the minimum mean-squared error design for a range of TEQ filter lengths.

A taxonomy for wavelet neural networks applied to nonlinear modelling

This article presents a novel classification of wavelet neural networks based on the orthogonality/non-orthogonality of neurons and the type of nonlinearity employed. On the basis of this classification different network types are studied and their characteristics illustrated by means of simple one-dimensional nonlinear examples. For multidimensional problems, which are affected by the curse of dimensionality, the idea of spherical wavelet functions is considered. The behaviour of these networks is also studied for modelling of a low-dimension map.

A new Jacobian matrix for optimal learning of single-layer neural networks

This paper investigates the learning of a wide class of single-hidden-layer feedforward neural networks (SLFNs) with two sets of adjustable parameters, i.e., the nonlinear parameters in the hidden nodes and the linear output weights. The main objective is to both speed up the convergence of second-order learning algorithms such as Levenberg-Marquardt (LM), as well as to improve the network performance. This is achieved here by reducing the dimension of the solution space and by introducing a new Jacobian matrix. Unlike conventional supervised learning methods which optimize these two sets of parameters simultaneously, the linear output weights are first converted into dependent parameters, thereby removing the need for their explicit computation. Consequently, the neural network (NN) learning is performed over a solution space of reduced dimension. A new Jacobian matrix is then proposed for use with the popular second-order learning methods in order to achieve a more accurate approximation of the cost function. The efficacy of the proposed method is shown through an analysis of the computational complexity and by presenting simulation results from four different examples.