Influence of network topology and data collection on network inference.

We recently developed an approach for testing the accuracy of network inference algorithms by applying them to biologically realistic simulations with known network topology. Here, we seek to determine the degree to which the network topology and data sampling regime influence the ability of our Bayesian network inference algorithm, NETWORKINFERENCE, to recover gene regulatory networks. NETWORKINFERENCE performed well at recovering feedback loops and multiple targets of a regulator with small amounts of data, but required more data to recover multiple regulators of a gene. When collecting the same number of data samples at different intervals from the system, the best recovery was produced by sampling intervals long enough such that sampling covered propagation of regulation through the network but not so long such that intervals missed internal dynamics. These results further elucidate the possibilities and limitations of network inference based on biological data.

Domain decomposition using a 2-level correction scheme

The PHYSICA software was developed to enable multiphysics modelling allowing for interaction between Computational Fluid Dynamics (CFD) and Computational Solid Mechanics (CSM) and Computational Aeroacoustics (CAA). PHYSICA uses the finite volume method with 3-D unstructured meshes to enable the modelling of complex geometries. Many engineering applications involve significant computational time which needs to be reduced by means of a faster solution method or parallel and high performance algorithms. It is well known that multigrid methods serve as a fast iterative scheme for linear and nonlinear diffusion problems. This papers attempts to address two major issues of this iterative solver, including parallelisation of multigrid methods and their applications to time dependent multiscale problems.

Domain decomposition methods for welding problems

This paper, a 2-D non-linear electric arc-welding problem is considered. It is assumed that the moving arc generates an unknown quantity of energy which makes the problem an inverse problem with an unknown source. Robust algorithms to solve such problems e#ciently, and in certain circumstances in real-time, are of great technological and industrial interest. There are other types of inverse problems which involve inverse determination of heat conductivity or material properties [CDJ63][TE98], inverse problems in material cutting [ILPP98], and retrieval of parameters containing discontinuities [IK90]. As in the metal cutting problem, the temperature of a very hot surface is required and it relies on the use of thermocouples. Here, the solution scheme requires temperature measurements lied in the neighbourhood of the weld line in order to retrieve the unknown heat source. The size of this neighbourhood is not considered in this paper, but rather a domain decomposition concept is presented and an examination of the accuracy of the retrieved source are presented. This paper is organised as follows. The inverse problem is formulated and a method for the source retrieval is presented in the second section. The source retrieval method is based on an extension of the 1-D source retrieval method as proposed in [ILP].

A critical examination of node-similarity based graph matching algorithms

In this paper, we shall critically examine a special class of graph matching algorithms that follow the approach of node-similarity measurement. A high-level algorithm framework, namely node-similarity graph matching framework (NSGM framework), is proposed, from which, many existing graph matching algorithms can be subsumed, including the eigen-decomposition method of Umeyama, the polynomial-transformation method of Almohamad, the hubs and authorities method of Kleinberg, and the kronecker product successive projection methods of Wyk, etc. In addition, improved algorithms can be developed from the NSGM framework with respects to the corresponding results in graph theory. As the observation, it is pointed out that, in general, any algorithm which can be subsumed from NSGM framework fails to work well for graphs with non-trivial auto-isomorphism structure.

Application-Specific Instruction Set Processor for SoC implementation of Modern Signal Processing Algorithms

A novel application-specific instruction set processor (ASIP) for use in the construction of modern signal processing systems is presented. This is a flexible device that can be used in the construction of array processor systems for the real-time implementation of functions such as singular-value decomposition (SVD) and QR decomposition (QRD), as well as other important matrix computations. It uses a coordinate rotation digital computer (CORDIC) module to perform arithmetic operations and several approaches are adopted to achieve high performance including pipelining of the micro-rotations, the use of parallel instructions and a dual-bus architecture. In addition, a novel method for scale factor correction is presented which only needs to be applied once at the end of the computation. This also reduces computation time and enhances performance. Methods are described which allow this processor to be used in reduced dimension (i.e., folded) array processor structures that allow tradeoffs between hardware and performance. The net result is a flexible matrix computational processing element (PE) whose functionality can be changed under program control for use in a wider range of scenarios than previous work. Details are presented of the results of a design study, which considers the application of this decomposition PE architecture in a combined SVD/QRD system and demonstrates that a combination of high performance and efficient silicon implementation are achievable. © 2005 IEEE.

A Virtual Inspection Technique for Assessing the Dimensional Accuracy of Forged Compressor Blades Using FE Modeling and CMM Inspection

This paper presents research for developing a virtual inspection system that evaluates the dimensional tolerance of forged aerofoil blades formed using the finite element (FE) method. Conventional algorithms adopted by modern coordinate measurement processes have been incorporated with the latest free-form surface evaluation techniques to provide a robust framework for the dimensional inspection of FE aerofoil models. The accuracy of the approach had been verified with a strong correlation obtained between the virtual inspection data and coordinate measurement data from corresponding aerofoil components.

Effect of Selfish Node Behavior on Efficient Topology Design

The problem of topology control is to assign per-node transmission power such that the resulting topology is energy efficient and satisfies certain global properties such as connectivity. The conventional approach to achieve these objectives is based on the fundamental assumption that nodes are socially responsible. We examine the following question: if nodes behave in a selfish manner, how does it impact the overall connectivity and energy consumption in the resulting topologies? We pose the above problem as a noncooperative game and use game-theoretic analysis to address it. We study Nash equilibrium properties of the topology control game and evaluate the efficiency of the induced topology when nodes employ a greedy best response algorithm. We show that even when the nodes have complete information about the network, the steady-state topologies are suboptimal. We propose a modified algorithm based on a better response dynamic and show that this algorithm is guaranteed to converge to energy-efficient and connected topologies. Moreover, the node transmit power levels are more evenly distributed, and the network performance is comparable to that obtained from centralized algorithms.

A heuristic model for the simulation of the deformation of elastic and spongy material for virtual reality applications

This paper presents a practical algorithm for the simulation of interactive deformation in a 3D polygonal mesh model. The algorithm combines the conventional simulation of deformation using a spring-mass-damping model, solved by explicit numerical integration, with a set of heuristics to describe certain features of the transient behaviour, to increase the speed and stability of solution. In particular, this algorithm was designed to be used in the simulation of synthetic environments where it is necessary to model realistically, in real time, the effect on non-rigid surfaces being touched, pushed, pulled or squashed. Such objects can be solid or hollow, and have plastic, elastic or fabric-like properties. The algorithm is presented in an integrated form including collision detection and adaptive refinement so that it may be used in a self-contained way as part of a simulation loop to include human interface devices that capture data and render a realistic stereoscopic image in real time. The algorithm is designed to be used with polygonal mesh models representing complex topology, such as the human anatomy in a virtual-surgery training simulator. The paper evaluates the model behaviour qualitatively and then concludes with some examples of the use of the algorithm.

QR decomposition-based matrix inversion for high performance embedded MIMO receivers

Real-time matrix inversion is a key enabling technology in multiple-input multiple-output (MIMO) communications systems, such as 802.11n. To date, however, no matrix inversion implementation has been devised which supports real-time operation for these standards. In this paper, we overcome this barrier by presenting a novel matrix inversion algorithm which is ideally suited to high performance floating-point implementation. We show how the resulting architecture offers fundamentally higher performance than currently published matrix inversion approaches and we use it to create the first reported architecture capable of supporting real-time 802.11n operation. Specifically, we present a matrix inversion approach based on modified squared Givens rotations (MSGR). This is a new QR decomposition algorithm which overcomes critical limitations in other QR algorithms that prohibits their application to MIMO systems. In addition, we present a novel modification that further reduces the complexity of MSGR by almost 20%. This enables real-time implementation with negligible reduction in the accuracy of the inversion operation, or the BER of a MIMO receiver based on this.

Validation of membrane protein topology models by oxidative labeling and mass spectrometry

Computer-assisted topology predictions are widely used to build low-resolution structural models of integral membrane proteins (IMPs). Experimental validation of these models by traditional methods is labor intensive and requires modifications that might alter the IMP native conformation. This work employs oxidative labeling coupled with mass spectrometry (MS) as a validation tool for computer-generated topology models. ·OH exposure introduces oxidative modifications in solvent-accessible regions, whereas buried segments (e.g., transmembrane helices) are non-oxidizable. The Escherichia coli protein WaaL (O-antigen ligase) is predicted to have 12 transmembrane helices and a large extramembrane domain (Pérez et al., Mol. Microbiol. 2008, 70, 1424). Tryptic digestion and LC-MS/MS were used to map the oxidative labeling behavior of WaaL. Met and Cys exhibit high intrinsic reactivities with ·OH, making them sensitive probes for solvent accessibility assays. Overall, the oxidation pattern of these residues is consistent with the originally proposed WaaL topology. One residue (M151), however, undergoes partial oxidation despite being predicted to reside within a transmembrane helix. Using an improved computer algorithm, a slightly modified topology model was generated that places M151 closer to the membrane interface. On the basis of the labeling data, it is concluded that the refined model more accurately reflects the actual topology of WaaL. We propose that the combination of oxidative labeling and MS represents a useful strategy for assessing the accuracy of IMP topology predictions, supplementing data obtained in traditional biochemical assays. In the future, it might be possible to incorporate oxidative labeling data directly as constraints in topology prediction algorithms.

Algorithms for Self-Healing Networks

Many modern networks are \emph{reconfigurable}, in the sense that the topology of the network can be changed by the nodes in the network. For example, peer-to-peer, wireless and ad-hoc networks are reconfigurable. More generally, many social networks, such as a company's organizational chart; infrastructure networks, such as an airline's transportation network; and biological networks, such as the human brain, are also reconfigurable. Modern reconfigurable networks have a complexity unprecedented in the history of engineering, resembling more a dynamic and evolving living animal rather than a structure of steel designed from a blueprint. Unfortunately, our mathematical and algorithmic tools have not yet developed enough to handle this complexity and fully exploit the flexibility of these networks. We believe that it is no longer possible to build networks that are scalable and never have node failures. Instead, these networks should be able to admit small, and maybe, periodic failures and still recover like skin heals from a cut. This process, where the network can recover itself by maintaining key invariants in response to attack by a powerful adversary is what we call \emph{self-healing}. Here, we present several fast and provably good distributed algorithms for self-healing in reconfigurable dynamic networks. Each of these algorithms have different properties, a different set of gaurantees and limitations. We also discuss future directions and theoretical questions we would like to answer. %in the final dissertation that this document is proposed to lead to.

Hierarchical demand response using dantzig-wolfe decomposition

Demand Side Management (DSM) programmes are designed to shift electrical loads from peak times. Demand Response (DR) algorithms automate this process for controllable loads. DR can be implemented explicitly in terms of Peak to Average Ratio Reduction (PARR), in which case the maximum peak load is minimised over a prediction horizon by manipulating the amount of energy given to controllable loads at different times. A hierarchical predictive PARR algorithm is presented here based on Dantzig-Wolfe decomposition. © 2013 IEEE.

Hierarchical Demand Response for Peak Reduction using Dantzig‐Wolfe Decomposition

Demand Response (DR) algorithms manipulate the energy consumption schedules of controllable loads so as to satisfy grid objectives. Implementation of DR algorithms using a centralised agent can be problematic for scalability reasons, and there are issues related to the privacy of data and robustness to communication failures. Thus it is desirable to use a scalable decentralised algorithm for the implementation of DR. In this paper, a hierarchical DR scheme is proposed for Peak Minimisation (PM) based on Dantzig-Wolfe Decomposition (DWD). In addition, a Time Weighted Maximisation option is included in the cost function which improves the Quality of Service for devices seeking to receive their desired energy sooner rather than later. The paper also demonstrates how the DWD algorithm can be implemented more efficiently through the calculation of the upper and lower cost bounds after each DWD iteration.

Novel Application of Genetic Sequencing algorithms to optimisation of hardware resource sharing for DSP

Field programmable gate array (FPGA) technology is a powerful platform for implementing computationally complex, digital signal processing (DSP) systems. Applications that are multi-modal, however, are designed for worse case conditions. In this paper, genetic sequencing techniques are applied to give a more sophisticated decomposition of the algorithmic variations, thus allowing an unified hardware architecture which gives a 10-25% area saving and 15% power saving for a digital radar receiver.