Evolving noisy oscillatory dynamics in genetic regulatory networks

We introduce a genetic programming (GP) approach for evolving genetic networks that demonstrate desired dynamics when simulated as a discrete stochastic process. Our representation of genetic networks is based on a biochemical reaction model including key elements such as transcription, translation and post-translational modifications. The stochastic, reaction-based GP system is similar but not identical with algorithmic chemistries. We evolved genetic networks with noisy oscillatory dynamics. The results show the practicality of evolving particular dynamics in gene regulatory networks when modelled with intrinsic noise.

Evolving genetic regulatory networks using an artificial genome

Boolean models of genetic regulatory networks (GRNs) have been shown to exhibit many of the characteristic dynamics of real GRNs, with gene expression patterns settling to point attractors or limit cycles, or displaying chaotic behaviour, depending upon the connectivity of the network and the relative proportions of excitatory and inhibitory interactions. This range of behaviours is only apparent, however, when the nodes of the GRN are updated synchronously, a biologically implausible state of affairs. In this paper we demonstrate that evolution can produce GRNs with interesting dynamics under an asynchronous update scheme. We use an Artificial Genome to generate networks which exhibit limit cycle dynamics when updated synchronously, but collapse to a point attractor when updated asynchronously. Using a hill climbing algorithm the networks are then evolved using a fitness function which rewards patterns of gene expression which revisit as many previously seen states as possible. The final networks exhibit “fuzzy limit cycle” dynamics when updated asynchronously.

Performance analysis of multi-radio AODV in hybrid wireless mesh networks

Wireless Mesh Networks (WMNs), based on commodity hardware, present a promising technology for a wide range of applications due to their self-configuring and self-healing capabilities, as well as their low equipment and deployment costs. One of the key challenges that WMN technology faces is the limited capacity and scalability due to co-channel interference, which is typical for multi-hop wireless networks. A simple and relatively low-cost approach to address this problem is the use of multiple wireless network interfaces (radios) per node. Operating the radios on distinct orthogonal channels permits effective use of the frequency spectrum, thereby, reducing interference and contention. In this paper, we evaluate the performance of the multi-radio Ad-hoc On-demand Distance Vector (AODV) routing protocol with a specific focus on hybrid WMNs. Our simulation results show that under high mobility and traffic load conditions, multi-radio AODV offers superior performance as compared to its single-radio counterpart. We believe that multi-radio AODV is a promising candidate for WMNs, which need to service a large number of mobile clients with low latency and high bandwidth requirements.

Theoretical foundations of neural networks

Neural networks have often been motivated by superficial analogy with biological nervous systems. Recently, however, it has become widely recognised that the effective application of neural networks requires instead a deeper understanding of the theoretical foundations of these models. Insight into neural networks comes from a number of fields including statistical pattern recognition, computational learning theory, statistics, information geometry and statistical mechanics. As an illustration of the importance of understanding the theoretical basis for neural network models, we consider their application to the solution of multi-valued inverse problems. We show how a naive application of the standard least-squares approach can lead to very poor results, and how an appreciation of the underlying statistical goals of the modelling process allows the development of a more general and more powerful formalism which can tackle the problem of multi-modality.

Distributed control of computer communication systems

Flow control in Computer Communication systems is generally a multi-layered structure, consisting of several mechanisms operating independently at different levels. Evaluation of the performance of networks in which different flow control mechanisms act simultaneously is an important area of research, and is examined in depth in this thesis. This thesis presents the modelling of a finite resource computer communication network equipped with three levels of flow control, based on closed queueing network theory. The flow control mechanisms considered are: end-to-end control of virtual circuits, network access control of external messages at the entry nodes and the hop level control between nodes. The model is solved by a heuristic technique, based on an equivalent reduced network and the heuristic extensions to the mean value analysis algorithm. The method has significant computational advantages, and overcomes the limitations of the exact methods. It can be used to solve large network models with finite buffers and many virtual circuits. The model and its heuristic solution are validated by simulation. The interaction between the three levels of flow control are investigated. A queueing model is developed for the admission delay on virtual circuits with end-to-end control, in which messages arrive from independent Poisson sources. The selection of optimum window limit is considered. Several advanced network access schemes are postulated to improve the network performance as well as that of selected traffic streams, and numerical results are presented. A model for the dynamic control of input traffic is developed. Based on Markov decision theory, an optimal control policy is formulated. Numerical results are given and throughput-delay performance is shown to be better with dynamic control than with static control.

Individual differences in human-computer interaction

This thesis initially presents an 'assay' of the literature pertaining to individual differences in human-computer interaction. A series of experiments is then reported, designed to investigate the association between a variety of individual characteristics and various computer task and interface factors. Predictor variables included age, computer expertise, and psychometric tests of spatial visualisation, spatial memory, logical reasoning, associative memory, and verbal ability. These were studied in relation to a variety of computer-based tacks, including: (1) word processing and its component elements; (ii) the location of target words within passages of text; (iii) the navigation of networks and menus; (iv) command generation using menus and command line interfaces; (v) the search and selection of icons and text labels; (vi) information retrieval. A measure of self-report workload was also included in several of these experiments. The main experimental findings included: (i) an interaction between spatial ability and the manipulation of semantic but not spatial interface content; (ii) verbal ability being only predictive of certain task components of word processing; (iii) age differences in word processing and information retrieval speed but not accuracy; (iv) evidence of compensatory strategies being employed by older subjects; (v) evidence of performance strategy differences which disadvantaged high spatial subjects in conditions of low spatial information content; (vi) interactive effects of associative memory, expertise and command strategy; (vii) an association between logical reasoning and word processing but not information retrieval; (viii) an interaction between expertise and cognitive demand; and (ix) a stronger association between cognitive ability and novice performance than expert performance.