This thesis investigates computational musical tonality estimation from an audio signal. We present a hidden Markov model (HMM) in which relationships between chords and keys are expressed as probabilities of emitting observable chords from a hidden key sequence. The model is tested first using symbolic chord annotations as observations, and gives excellent global key recognition rates on a set of Beatles songs. The initial model is extended for audio input by using an existing chord recognition algorithm, which allows it to be tested on a much larger database. We show that a simple model of the upper partials in the signal improves percentage scores. We also present a variant of the HMM which has a continuous observation probability density, but show that the discrete version gives better performance. Then follows a detailed analysis of the effects on key estimation and computation time of changing the low level signal processing parameters. We find that much of the high frequency information can be omitted without loss of accuracy, and significant computational savings can be made by applying a threshold to the transform kernels. Results show that there is no single ideal set of parameters for all music, but that tuning the parameters can make a difference to accuracy. We discuss methods of evaluating more complex tonal changes than a single global key, and compare a metric that measures similarity to a ground truth to metrics that are rooted in music retrieval. We show that the two measures give different results, and so recommend that the choice of evaluation metric is determined by the intended application. Finally we draw together our conclusions and use them to suggest areas for continuation of this research, in the areas of tonality model development, feature extraction, evaluation methodology, and applications of computational tonality estimation.

Many species use visual features to avoid predation by several methods, such as concealing themselves, deceiving predators and hindering capture. One of the most striking strategies is aposematism, or warning coloration, in which prey use conspicuous visual signals to advertise chemical or physical defences, and thereby deter predators from attacking. My thesis focuses on the form of these warning signals, namely which elements of visual patterns might be most effective in generating predator avoidance, as well as how these different visual features relate to defence levels and ultimately to prey survival in the wild. To address these issues, I studied the warning signals of Lepidoptera and in particular burnet moths (Zygaenidae: Zygaeninae), day-flying moths with distinctive red and black wings and the remarkable ability to both synthesise defensive compounds and sequester them from their host plants. Technological advances and a growing understanding of animal vision mean that animal signals can be studied in an increasingly precise and ecologically-relevant way. Throughout this thesis, I use sophisticated methods to quantify both the defensive chemicals and wing coloration of burnet moths, as perceived by their avian predators. I examine the key features of day-flying defended Lepidoptera, then focus on the potential for quantitative signal honesty in burnet moths. I explore the relationship between defence levels and measures of coloration, both within the six-spot burnet moth, Zygaena filipendulae, and across species in the Zygaenidae, then test the effects of variation in warning signals on predation risk for artificial burnet-like prey in the field. My work highlights some of the complicating factors that should be accounted for in the study of warning coloration, especially when investigating the potential for quantitative signal honesty. I hope my thesis will provide a basis for future research on the defensive strategies of day-flying moths and inspire others to pursue investigations into aposematism in the Zygaenidae.

The safety signal hypothesis suggests that during the absence of stimuli predicting impending shock, the organism is not fearful. The stimuli which predict the absence of shock are therefore called safety signals. The purpose of the present study was to investigate some critical properties of safety signals. Such stimuli in an avoidance or escape situation, according to the opponent process model, are expected to acquire hedonic value opposite to shock. This study examined differences in conditioning variables between safety signals predicting different intensities of shock, and between safety signals present in procedures using predicted shock, and procedures using unpredicted shock. Additionally, the effects of inescapable unpredicted shock with no safety signals present were examined. The general procedure involved exposing pigeons to aversive Pavlovian conditioning and subsequently autoshaping these birds to stimuli which had predicted safety in the aversive situation. Dependent measures included trials to acquisition of the autoshaped response and subsequent rate of keypecking. In the six experimental groups, pigeons were repeatedly and inescapably shocked at either 30 or 90 volts. Each individual 0.5 sec shock was (a) predicted by a specific stimulus or (b) not predicted. Additionally and explicitly unpaired with the shock, a safety signal was presented. For each voltage level, a control group was repeatedly shocked with no stimuli presented at any time. Control groups were included which (a) received no aversive conditioning, (b) were autoshaped to a stimulus which had previously predicted shock, (c) received the aversive conditioning, and (4) were exposed to various stimuli but received no aversive reinforcement. The principal finding was that preexposure to strong shock resulted in delays in response acquisition during subsequent autoshaping. This suggests that the learned helplessness hypothesis obtains with classically conditioned responding. Additionally, the importance of shock-alone control groups in the study of transfer effects is critical. Due to the lack of statistical power, the study was not definitive regarding the nature of safety signals or appetitive-to-appetitive transfers. Statistically significant differences were only found on acquisition measures, and no such differences were found on performance measures.

The rapidly growing volume of electrophysiological signals has been generated for clinical research in neurological disorders. European Data Format (EDF) is a standard format for storing electrophysiological signals. However, the bottleneck of existing signal analysis tools for handling large-scale datasets is the sequential way of loading large EDF files before performing an analysis. To overcome this, we develop Hadoop-EDF, a distributed signal processing tool to load EDF data in a parallel manner using Hadoop MapReduce. Hadoop-EDF uses a robust data partition algorithm making EDF data parallel processable. We evaluate Hadoop-EDF’s scalability and performance by leveraging two datasets from the National Sleep Research Resource and running experiments on Amazon Web Service clusters. The performance of Hadoop-EDF on a 20-node cluster improves 27 times and 47 times than sequential processing of 200 small-size files and 200 large-size files, respectively. The results demonstrate that Hadoop-EDF is more suitable and effective in processing large EDF files.

Research has shown noncontingent reinforcement (NCR) to be an effective intervention in reducing inappropriate behavior (i.e., problem behavior) when implemented prior to its occurrence in both clinical and applied settings. Some research suggests problem behavior of teenagers and adults with disabilities may be reduced at greater rates when NCR is implemented in combination with signals (e.g., visual timers). Additional research is warranted to investigate if the positive effects of NCR can be enhanced using signals when working with young children with autism. This study evaluated the effects of NCR when implemented with and without a visual timer on the problem behavior of three preschoolers with autism attending a special education day treatment program. All interventions were implemented by classroom staff during typical learning activities. Overall results were inconsistent in determining if NCR with signals may be an effective intervention for reducing problem behavior of preschoolers with autism. However, results suggest NCR with signals may contribute to a reduction in problem behavior for some preschoolers with autism. Additional research will be needed to verify these tentative conclusions.

This thesis reports original work on digital compensation for frequency dependent transfer characteristics and errors in digital PAM/CPFSK (Pulse Amplitude Modulation/Continuous Phase Frequency Shift Keying) quadrature modulators.A particularly flexible and cost effective approach to the implementation of the base-band section of a radio transmitter is to synthesise base-band signals digitally using a DSP (Digital Signal Processor). This approach is limited, however, by the transfer characteristics and errors in the implementation of practical analogue sub-systems. These practical limitations result in undesirable in-band frequency-dependent shaping of the transmitted signals. In the case of FM (Frequency Modulation) signals, this leads to the generation of unwanted side-lobes in the transmitted RF signal spectrum that interfere with signals in adjacent frequency channels. This results in the transmitted signal failing to meet transmission standards requirements.The digital compensation techniques developed and presented in this thesis allow the reduction of undesirable in-band frequency-dependent signal shaping. It is shown that this enables strict requirements on the spectral emissions from the FM transmitter to be met using a flexible and cost effective DSP based modulator system.The contributions of the thesis are in three primary areas:(i) The development of a structure for frequency dependent digital compensation.(ii) The formulation and solution of an optimisation problem that allows the free parameters within the structure to be determined such that effective reduction of unwanted in-band frequency-dependent signal shaping is achieved.(iii) The development of techniques that allow the digital compensation procedure to be successfully implemented on a practical DSP platform.The new digital compensation structure that is proposed uses two digital FIR (Finite ++ / Impulse Response) filters in the digital base-band section of the quadrature modulator: one in the in-phase (I) channel and one in the quadrature (Q) channel. The tap-weights of the FIR filters are determined by solving two optimisation problems: one for each channel. The optimisation problems are formulated using a new approach that ensures that the degrees of freedom in the optimisation i.e., the FIR filter tap-weights, are used effectively to meet the objective of reducing in-band frequency-dependent signal shaping in analogue sub-systems further down the transmission path.A characterisation of the solutions to the optimisation problems enables the identification of techniques that need to be adopted to successfully implement the proposed digital compensation on a practical DSP-based system.The digital compensation technique is demonstrated by implementing and testing the technique on a DSP platform. The results of experimental studies are presented which clearly demonstrate that the digital compensation technique leads to substantial reductions in adjacent channel interference.

The purpose of this thesis was to investigate mechanisms contolling the growth of corneal epithelial cells, particularly the intracellular signals involved with stratification compared with cellular migration and maturation. Buttons of epithelium were cultured in different culture media. The explants were monitored microscopically for their growth patterns and finally fixed and examined for cytokeratin, vimentin and actin. Different growth patterns were observed in the different media, indicating that different signalling patterns must be operating in these cells depending upon the media in which they were grown. To investigate the intracellular pathways controlling the different growth patterns, the protein phosphorylation of different cultures was investigated. The two proteins, p57 and p30, are strongly suggested to be associated with stratification of the epithelial cells. The possible involvement of the common serine kinase, PKC, in controlling the growth pattern of corneal epithelial cells were also investigated. The results suggested that an intracellular pathway involving PKC promotes the maturation and spread of the cells but is not involved in their stratification. These experiments taken together indicate that the different aspects of corneal epithelia cell growth are tightly controlled and may occur quite independently. Specific protein expression appears to be important for stratification, and phosphorylation of proteins by PKC appears to be involved with the maturation of epithelial cells from basal cells. It also indicates that the mature cells are capable of producing the extracellular matrix protein fibronectin which appears to have an important role in causing the spread as distinct from the stratification of the corneal epithelial cells. / Doctor of Philosophy (Ph.D.)

Problems in the demodulation of one, two, and three-dimensional signals are investigated. In one-dimensional linear systems the analytic signal and the Hilbert transform are central to the understanding of both modulation and demodulation. However, it is shown that an efficient nonlinear algorithm exists which is not explicable purely in terms of an approximation to the Hilbert transform. The algorithm is applied to the problem of finding the envelope peak of a white light interferogram. The accuracy of peak location is then shown to compare favourably with conventional, but less efficient, techniques. In two dimensions (2-D) the intensity of a wavefield yields to a phase demodulation technique equivalent to direct phase retrieval. The special symmetry of a Helmholtz wavefield allows a unique inversion of an autocorrelation. More generally, a 2-D (non-Helmholtz) fringe pattern can be demodulated by an isotropic 2-D extension of the Hilbert transform that uses a spiral phase signum function. The range of validity of the new transform is established using the asymptotic method of stationary phase. Simulations of the algorithm confirm that deviations from the ideal occur where the fringe pattern curvature is larger than the fringe frequency. A new self-calibrating algorithm for arbitrary sequences of phase-shifted interferograms is developed using the aforementioned spiral phase transform. The algorithm is shown to work even with discontinuous fringe patterns, which are known to seriously hamper other methods. Initial simulations of the algorithm indicate an accuracy of 5 milliradians is achievable. Previously undocumented connections between the demodulation techniques are uncovered and discussed.

The question of how honesty is maintained in animal communication is a perplexing one, especially in the context of aggressive communication, in which the interests of signalers and receivers are opposed. Relevant information for receivers in aggressive interactions includes the fighting ability of the signaler and its likelihood of attack. Signalers may, however, benefit from manipulation of signals to exaggerate this information. To address questions of signal honesty, this dissertation investigates the use of a performance signal in the song of swamp sparrows (Melospiza georgiana). Performance signals are ones that are physically demanding to perform and that therefore reveal the signaler’s physical ability. The particular measure of vocal performance examined here is vocal deviation, which refers to the ability of birds to produce trilled songs approaching a performance boundary defined by the tradeoff between song trill rate (the rate at which elements of a song are repeated) and frequency bandwidth (the range of frequencies encompassed in a song). Three questions regarding the adaptive significance of vocal performance were investigated in the swamp sparrow 1) whether vocal performance is used as a signal in male-male communication, 2) whether vocal performance should be classified as an index signal of male quality, and 3) whether vocal deviation serves as a signal of aggressive intent. Results from four studies indicate that vocal performance plays a role in male-male signaling. Signalers appear to use vocal performance as a signal and receivers attend to differences in vocal performance. Evidence also indicates that vocal performance can be classified as an index signal, because males are constrained in their ability to produce high performance song and high vocal performance is correlated with aspects of male quality, such as age and size. Finally, this dissertation does not support classification of vocal performance as a signal of aggressive intent, because vocal performance fails to predict aggressive escalation.

Airborne lidar bathymetry (ALB) is a method used to survey and map coastal and littoral zones. Along with extracting seafloor depth and reflectance in the surveyed area, a fundamental requirement of these surveys is to detect underwater targets, hazards, or obstructions. The ability to detect underwater targets depends on a target's dimensions and reflectance, the depth and turbidity of the water, system and survey configuration, data processing capabilities, and algorithmic sophistication. Understanding the effects of each of these factors on the performance of underwater target detection is essential in determining the target detection capabilities of a proposed ALB system. After detailing the development of a simulation environment to model received ALB system waveforms, this work explores the theoretical target detection capabilities of an ALB system.