Decoding non-invasive brain activity with novel deep-learning approaches

This thesis delves into the world of non-invasive electrophysiological brain signals like electroencephalography (EEG) and magnetoencephalography (MEG), focusing on modelling and decoding such data. The research aims to investigate what happens in the brain when we perceive visual stimuli or engage in covert speech (inner speech) and enhance the decoding performance of such stimuli. The findings have significant implications for the development of brain-computer interfaces (BCIs), leading to assistive communication technologies for paralysed individuals. The thesis is divided into two main sections, methodological and experimental work. A central concern in both sections is the large variability present in electrophysiological recordings, whether it be within-subject or between-subject variability, and to a certain extent between-dataset variability. In the methodological sections, we explore the potential of deep learning for brain decoding. The research acknowledges the urgent need for more sophisticated models and larger datasets to improve the decoding and modelling of EEG and MEG signals. We present advancements in decoding visual stimuli using linear models at the individual subject level. We then explore how deep learning techniques can be employed for group decoding, introducing new methods to deal with between-subject variability. Finally, we also explores novel forecasting models of MEG data based on convolutional and Transformer-based architectures. In particular, Transformer-based models demonstrate superior capabilities in generating signals that closely match real brain data, thereby enhancing the accuracy and reliability of modelling the brain’s electrophysiology. In the experimental section, we present a unique dataset containing high-trial inner speech EEG, MEG, and preliminary optically pumped magnetometer (OPM) data. We highlight the limitations of current BCI systems used for communication, which are either invasive or extremely slow. While inner speech decoding from non-invasive brain signals has great promise, it has been a challenging goal in the field with limited decoding approaches, indicating a significant gap that needs to be addressed. Our aim is to investigate different types of inner speech and push decoding performance by collecting a high number of trials and sessions from a few participants. However, the decoding results are found to be mostly negative, underscoring the difficulty of decoding inner speech. In conclusion, this thesis provides valuable insight into the challenges and potential solutions in the field of electrophysiology, particularly in the decoding of visual stimuli and inner speech. The findings could pave the way for future research and advancements in the field, ultimately improving communication capabilities for paralysed individuals

Vibration-based damage localisation: Impulse response identification and model updating methods

Structural health monitoring has gained more and more interest over the recent decades. As the technology has matured and monitoring systems are employed commercially, the development of more powerful and precise methods is the logical next step in this field. Especially vibration sensor networks with few measurement points combined with utilisation of ambient vibration sources are attractive for practical applications, as this approach promises to be cost-effective while requiring minimal modification to the monitored structures. Since efficient methods for damage detection have already been developed for such sensor networks, the research focus shifts towards extracting more information from the measurement data, in particular to the localisation and quantification of damage. Two main concepts have produced promising results for damage localisation. The first approach involves a mechanical model of the structure, which is used in a model updating scheme to find the damaged areas of the structure. Second, there is a purely data-driven approach, which relies on residuals of vibration estimations to find regions where damage is probable. While much research has been conducted following these two concepts, different approaches are rarely directly compared using the same data sets. Therefore, this thesis presents advanced methods for vibration-based damage localisation using model updating as well as a data-driven method and provides a direct comparison using the same vibration measurement data. The model updating approach presented in this thesis relies on multiobjective optimisation. Hence, the applied numerical optimisation algorithms are presented first. On this basis, the model updating parameterisation and objective function formulation is developed. The data-driven approach employs residuals from vibration estimations obtained using multiple-input finite impulse response filters. Both approaches are then verified using a simulated cantilever beam considering multiple damage scenarios. Finally, experimentally obtained data from an outdoor girder mast structure is used to validate the approaches. In summary, this thesis provides an assessment of model updating and residual-based damage localisation by means of verification and validation cases. It is found that the residual-based method exhibits numerical performance sufficient for real-time applications while providing a high sensitivity towards damage. However, the localisation accuracy is found to be superior using the model updating method

Improving Range Estimation of a 3D FLASH LADAR via Blind Deconvolution

The purpose of this research effort is to improve and characterize range estimation in a three-dimensional FLASH LAser Detection And Ranging (3D FLASH LADAR) by investigating spatial dimension blurring effects. The myriad of emerging applications for 3D FLASH LADAR both as primary and supplemental sensor necessitate superior performance including accurate range estimates. Along with range information, this sensor also provides an imaging or laser vision capability. Consequently, accurate range estimates would also greatly aid in image quality of a target or remote scene under interrogation. Unlike previous efforts, this research accounts for pixel coupling by defining the range image mathematical model as a convolution between the system spatial impulse response and the object (target or remote scene) at a particular range slice. Using this model, improved range estimation is possible by object restoration from the data observations. Object estimation is principally performed by deriving a blind deconvolution Generalized Expectation Maximization (GEM) algorithm with the range determined from the estimated object by a normalized correlation method. Theoretical derivations and simulation results are verified with experimental data of a bar target taken from a 3D FLASH LADAR system in a laboratory environment. Additionally, among other factors, range separation estimation variance is a function of two LADAR design parameters (range sampling interval and transmitted pulse-width), which can be optimized using the expected range resolution between two point sources. Using both CRB theory and an unbiased estimator, an investigation is accomplished that finds the optimal pulse-width for several range sampling scenarios using a range resolution metric

Phase-Distortion-Robust Voice-Source Analysis

This work concerns itself with the analysis of voiced speech signals, in particular the analysis of the glottal source signal. Following the source-filter theory of speech, the glottal signal is produced by the vibratory behaviour of the vocal folds and is modulated by the resonances of the vocal tract and radiation characteristic of the lips to form the speech signal. As it is thought that the glottal source signal contributes much of the non-linguistic and prosodical information to speech, it is useful to develop techniques which can estimate and parameterise this signal accurately. Because of vocal tract modulation, estimating the glottal source waveform from the speech signal is a blind deconvolution problem which necessarily makes assumptions about the characteristics of both the glottal source and vocal tract. A common assumption is that the glottal signal and/or vocal tract can be approximated by a parametric model. Other assumptions include the causality of the speech signal: the vocal tract is assumed to be a minimum phase system while the glottal source is assumed to exhibit mixed phase characteristics. However, as the literature review within this thesis will show, the error criteria utilised to determine the parameters are not robust to the conditions under which the speech signal is recorded, and are particularly degraded in the common scenario where low frequency phase distortion is introduced. Those that are robust to this type of distortion are not well suited to the analysis of real-world signals. This research proposes a voice-source estimation and parameterisation technique, called the Power-spectrum-based determination of the Rd parameter (PowRd) method. Illustrated by theory and demonstrated by experiment, the new technique is robust to the time placement of the analysis frame and phase issues that are generally encountered during recording. The method assumes that the derivative glottal flow signal is approximated by the transformed Liljencrants-Fant model and that the vocal tract can be represented by an all-pole filter. Unlike many existing glottal source estimation methods, the PowRd method employs a new error criterion to optimise the parameters which is also suitable to determine the optimal vocal-tract filter order. In addition to the issue of glottal source parameterisation, nonlinear phase recording conditions can also adversely affect the results of other speech processing tasks such as the estimation of the instant of glottal closure. In this thesis, a new glottal closing instant estimation algorithm is proposed which incorporates elements from the state-of-the-art techniques and is specifically designed for operation upon speech recorded under nonlinear phase conditions. The new method, called the Fundamental RESidual Search or FRESS algorithm, is shown to estimate the glottal closing instant of voiced speech with superior precision and comparable accuracy as other existing methods over a large database of real speech signals under real and simulated recording conditions. An application of the proposed glottal source parameterisation method and glottal closing instant detection algorithm is a system which can analyse and re-synthesise voiced speech signals. This thesis describes perceptual experiments which show that, iunder linear and nonlinear recording conditions, the system produces synthetic speech which is generally preferred to speech synthesised based upon a state-of-the-art timedomain- based parameterisation technique. In sum, this work represents a movement towards flexible and robust voice-source analysis, with potential for a wide range of applications including speech analysis, modification and synthesis

Translational pipelines for closed-loop neuromodulation

Closed-loop neuromodulation systems have shown significant potential for addressing unmet needs in the treatment of disorders of the central nervous system, yet progress towards clinical adoption has been slow. Advanced technological developments often stall in the preclinical stage by failing to account for the constraints of implantable medical devices, and due to the lack of research platforms with a translational focus. This thesis presents the development of three clinically relevant research systems focusing on refinements of deep brain stimulation therapies. First, we introduce a system for synchronising implanted and external stimulation devices, allowing for research into multi-site stimulation paradigms, cross-region neural plasticity, and questions of phase coupling. The proposed design aims to sidestep the limited communication capabilities of existing commercial implant systems in providing a stimulation state readout without reliance on telemetry, creating a cross-platform research tool. Next, we present work on the Picostim-DyNeuMo adaptive neuromodulation platform, focusing on expanding device capabilities from activity and circadian adaptation to bioelectric marker--based responsive stimulation. Here, we introduce a computationally optimised implementation of a popular band power--estimation algorithm suitable for deployment in the DyNeuMo system. The new algorithmic capability was externally validated to establish neural state classification performance in two widely-researched use cases: Parkinsonian beta bursts and seizures. For in vivo validation, a pilot experiment is presented demonstrating responsive neurostimulation to cortical alpha-band activity in a non-human primate model for the modulation of attention state. Finally, we turn our focus to the validation of a recently developed method to provide computationally efficient real-time phase estimation. Following theoretical analysis, the method is integrated into the commonly used Intan electrophysiological recording platform, creating a novel closed-loop optogenetics research platform. The performance of the research system is characterised through a pilot experiment, targeting the modulation of cortical theta-band activity in a transgenic mouse model

Blind image deconvolution: nonstationary Bayesian approaches to restoring blurred photos

High quality digital images have become pervasive in modern scientific and everyday life — in areas from photography to astronomy, CCTV, microscopy, and medical imaging. However there are always limits to the quality of these images due to uncertainty and imprecision in the measurement systems. Modern signal processing methods offer the promise of overcoming some of these problems by postprocessing these blurred and noisy images. In this thesis, novel methods using nonstationary statistical models are developed for the removal of blurs from out of focus and other types of degraded photographic images. The work tackles the fundamental problem blind image deconvolution (BID); its goal is to restore a sharp image from a blurred observation when the blur itself is completely unknown. This is a “doubly illposed” problem — extreme lack of information must be countered by strong prior constraints about sensible types of solution. In this work, the hierarchical Bayesian methodology is used as a robust and versatile framework to impart the required prior knowledge. The thesis is arranged in two parts. In the first part, the BID problem is reviewed, along with techniques and models for its solution. Observation models are developed, with an emphasis on photographic restoration, concluding with a discussion of how these are reduced to the common linear spatially-invariant (LSI) convolutional model. Classical methods for the solution of illposed problems are summarised to provide a foundation for the main theoretical ideas that will be used under the Bayesian framework. This is followed by an indepth review and discussion of the various prior image and blur models appearing in the literature, and then their applications to solving the problem with both Bayesian and nonBayesian techniques. The second part covers novel restoration methods, making use of the theory presented in Part I. Firstly, two new nonstationary image models are presented. The first models local variance in the image, and the second extends this with locally adaptive noncausal autoregressive (AR) texture estimation and local mean components. These models allow for recovery of image details including edges and texture, whilst preserving smooth regions. Most existing methods do not model the boundary conditions correctly for deblurring of natural photographs, and a Chapter is devoted to exploring Bayesian solutions to this topic. Due to the complexity of the models used and the problem itself, there are many challenges which must be overcome for tractable inference. Using the new models, three different inference strategies are investigated: firstly using the Bayesian maximum marginalised a posteriori (MMAP) method with deterministic optimisation; proceeding with the stochastic methods of variational Bayesian (VB) distribution approximation, and simulation of the posterior distribution using the Gibbs sampler. Of these, we find the Gibbs sampler to be the most effective way to deal with a variety of different types of unknown blurs. Along the way, details are given of the numerical strategies developed to give accurate results and to accelerate performance. Finally, the thesis demonstrates state of the art results in blind restoration of synthetic and real degraded images, such as recovering details in out of focus photographs

Virtual metrology for plasma etch processes.

Plasma processes can present dicult control challenges due to time-varying dynamics and a lack of relevant and/or regular measurements. Virtual metrology (VM) is the use of mathematical models with accessible measurements from an operating process to estimate variables of interest. This thesis addresses the challenge of virtual metrology for plasma processes, with a particular focus on semiconductor plasma etch. Introductory material covering the essentials of plasma physics, plasma etching, plasma measurement techniques, and black-box modelling techniques is rst presented for readers not familiar with these subjects. A comprehensive literature review is then completed to detail the state of the art in modelling and VM research for plasma etch processes. To demonstrate the versatility of VM, a temperature monitoring system utilising a state-space model and Luenberger observer is designed for the variable specic impulse magnetoplasma rocket (VASIMR) engine, a plasma-based space propulsion system. The temperature monitoring system uses optical emission spectroscopy (OES) measurements from the VASIMR engine plasma to correct temperature estimates in the presence of modelling error and inaccurate initial conditions. Temperature estimates within 2% of the real values are achieved using this scheme. An extensive examination of the implementation of a wafer-to-wafer VM scheme to estimate plasma etch rate for an industrial plasma etch process is presented. The VM models estimate etch rate using measurements from the processing tool and a plasma impedance monitor (PIM). A selection of modelling techniques are considered for VM modelling, and Gaussian process regression (GPR) is applied for the rst time for VM of plasma etch rate. Models with global and local scope are compared, and modelling schemes that attempt to cater for the etch process dynamics are proposed. GPR-based windowed models produce the most accurate estimates, achieving mean absolute percentage errors (MAPEs) of approximately 1:15%. The consistency of the results presented suggests that this level of accuracy represents the best accuracy achievable for the plasma etch system at the current frequency of metrology. Finally, a real-time VM and model predictive control (MPC) scheme for control of plasma electron density in an industrial etch chamber is designed and tested. The VM scheme uses PIM measurements to estimate electron density in real time. A predictive functional control (PFC) scheme is implemented to cater for a time delay in the VM system. The controller achieves time constants of less than one second, no overshoot, and excellent disturbance rejection properties. The PFC scheme is further expanded by adapting the internal model in the controller in real time in response to changes in the process operating point

Virtual metrology for plasma etch processes.

Plasma processes can present dicult control challenges due to time-varying dynamics and a lack of relevant and/or regular measurements. Virtual metrology (VM) is the use of mathematical models with accessible measurements from an operating process to estimate variables of interest. This thesis addresses the challenge of virtual metrology for plasma processes, with a particular focus on semiconductor plasma etch. Introductory material covering the essentials of plasma physics, plasma etching, plasma measurement techniques, and black-box modelling techniques is rst presented for readers not familiar with these subjects. A comprehensive literature review is then completed to detail the state of the art in modelling and VM research for plasma etch processes. To demonstrate the versatility of VM, a temperature monitoring system utilising a state-space model and Luenberger observer is designed for the variable specic impulse magnetoplasma rocket (VASIMR) engine, a plasma-based space propulsion system. The temperature monitoring system uses optical emission spectroscopy (OES) measurements from the VASIMR engine plasma to correct temperature estimates in the presence of modelling error and inaccurate initial conditions. Temperature estimates within 2% of the real values are achieved using this scheme. An extensive examination of the implementation of a wafer-to-wafer VM scheme to estimate plasma etch rate for an industrial plasma etch process is presented. The VM models estimate etch rate using measurements from the processing tool and a plasma impedance monitor (PIM). A selection of modelling techniques are considered for VM modelling, and Gaussian process regression (GPR) is applied for the rst time for VM of plasma etch rate. Models with global and local scope are compared, and modelling schemes that attempt to cater for the etch process dynamics are proposed. GPR-based windowed models produce the most accurate estimates, achieving mean absolute percentage errors (MAPEs) of approximately 1:15%. The consistency of the results presented suggests that this level of accuracy represents the best accuracy achievable for the plasma etch system at the current frequency of metrology. Finally, a real-time VM and model predictive control (MPC) scheme for control of plasma electron density in an industrial etch chamber is designed and tested. The VM scheme uses PIM measurements to estimate electron density in real time. A predictive functional control (PFC) scheme is implemented to cater for a time delay in the VM system. The controller achieves time constants of less than one second, no overshoot, and excellent disturbance rejection properties. The PFC scheme is further expanded by adapting the internal model in the controller in real time in response to changes in the process operating point