Noise Reduction in EEG Signals using Convolutional Autoencoding Techniques

The presence of noise in electroencephalography (EEG) signals can significantly reduce the accuracy of the analysis of the signal. This study assesses to what extent stacked autoencoders designed using one-dimensional convolutional neural network layers can reduce noise in EEG signals. The EEG signals, obtained from 81 people, were processed by a two-layer one-dimensional convolutional autoencoder (CAE), whom performed 3 independent button pressing tasks. The signal-to-noise ratios (SNRs) of the signals before and after processing were calculated and the distributions of the SNRs were compared. The performance of the model was compared to noise reduction performance of Principal Component Analysis, with 95% explained variance, by comparing the Harrell-Davis decile differences between the SNR distributions of both methods and the raw signal SNR distribution for each task. It was found that the CAE outperformed PCA for the full dataset across all three tasks, however the CAE did not outperform PCA for the person specific datasets in any of the three tasks. The results indicate that CAEs can perform better than PCA for noise reduction in EEG signals, but performance of the model may be training size dependent

Efficient Acquisition and Denoising of Full-Range Event-Related Potentials Following Transient Stimulation of the Auditory Pathway

This body of work relates to recent advances in the field of human auditory event-related potentials (ERP), specifically the fast, deconvolution-based ERP acquisition as well as single-response based preprocessing, denoising and subsequent analysis methods. Its goal is the contribution of a cohesive set of methods facilitating the fast, reliable acquisition of the whole electrophysiological response generated by the auditory pathway from the brainstem to the cortex following transient acoustical stimulation. The present manuscript is divided into three sequential areas of investigation : First, the general feasibility of simultaneously acquiring auditory brainstem, middle-latency and late ERP single responses is demonstrated using recordings from 15 normal hearing subjects. Favourable acquisition parameters (i.e., sampling rate, bandpass filter settings and interstimulus intervals) are established, followed by signal analysis of the resulting ERP in terms of their dominant intrinsic scales to determine the properties of an optimal signal representation with maximally reduced sample count by means of nonlinear resampling on a logarithmic timebase. This way, a compression ratio of 16.59 is achieved. Time-scale analysis of the linear-time and logarithmic-time ERP single responses is employed to demonstrate that no important information is lost during compressive resampling, which is additionally supported by a comparative evaluation of the resulting average waveforms - here, all prominent waves remain visible, with their characteristic latencies and amplitudes remaining essentially unaffected by the resampling process. The linear-time and resampled logarithmic-time signal representations are comparatively investigated regarding their susceptibility to the types of physiological and technical noise frequently contaminating ERP recordings. While in principle there already exists a plethora of well-investigated approaches towards the denoising of ERP single-response representations to improve signal quality and/or reduce necessary aquisition times, the substantially altered noise characteristics of the obtained, resampled logarithmic-time single response representations as opposed to their linear-time equivalent necessitates a reevaluation of the available methods on this type of data. Additionally, two novel, efficient denoising algorithms based on transform coefficient manipulation in the sinogram domain and on an analytic, discrete wavelet filterbank are proposed and subjected to a comparative performance evaluation together with two established denoising methods. To facilitate a thorough comparison, the real-world ERP dataset obtained in the first part of this work is employed alongside synthetic data generated using a phenomenological ERP model evaluated at different signal-to-noise ratios (SNR), with individual gains in multiple outcome metrics being used to objectively assess algorithm performances. Results suggest the proposed denoising algorithms to substantially outperform the state-of-the-art methods in terms of the employed outcome metrics as well as their respective processing times. Furthermore, an efficient stimulus sequence optimization method for use with deconvolution-based ERP acquisition methods is introduced, which achieves consistent noise attenuation within a broad designated frequency range. A novel stimulus presentation paradigm for the fast, interleaved acquisition of auditory brainstem, middle-latency and late responses featuring alternating periods of optimized, high-rate deconvolution sequences and subsequent low-rate stimulation is proposed and investigated in 20 normal hearing subjects. Deconvolved sequence responses containing early and middle-latency ERP components are fused with subsequent late responses using a time-frequency resolved weighted averaging method based on cross-trial regularity, yielding a uniform SNR of the full-range auditory ERP across investigated timescales. Obtained average ERP waveforms exhibit morphologies consistent with both literature values and the reference recordings obtained in the first part of this manuscript, with all prominent waves being visible in the grand average waveforms. The novel stimulation approach cuts acquisition time by a factor of 3.4 while at the same time yielding a substantial gain in the SNR of obtained ERP data. Results suggest the proposed interleaved stimulus presentation and associated postprocessing methodology to be suitable for the fast, reliable extraction of full-range neural correlates of auditory processing in future studies.Diese Arbeit steht im Zusammenhang mit aktuellen Entwicklungen auf dem Gebiet der ereigniskorrelierten Potentiale (EKP) des humanen auditorischen Systems, insbesondere der schnellen, entfaltungsbasierten EKP-Aufzeichnung sowie einzelantwortbasierten Vorverarbeitungs-, Entrauschungs- und nachgelagerten Analysemethoden. Ziel ist die Bereitstellung eines vollständigen Methodensatzes, der eine schnelle, zuverlässige Erfassung der gesamten elektrophysiologischen Aktivität entlang der Hörbahn vom Hirnstamm bis zum Cortex ermöglicht, die als Folge transienter akustischer Stimulation auftritt. Das vorliegende Manuskript gliedert sich in drei aufeinander aufbauende Untersuchungsbereiche : Zunächst wird die generelle Machbarkeit der gleichzeitigen Aufzeichnung von Einzelantworten der auditorischen Hirnstammpotentiale zusammen mit mittelspäten und späten EKP anhand von Referenzmessungen an 15 normalhörenden Probanden demonstriert. Es werden hierzu geeignete Erfassungsparameter (Abtastrate, Bandpassfiltereinstellungen und Interstimulusintervalle) ermittelt, gefolgt von einer Signalanalyse der resultierenden EKP im Hinblick auf deren dominante intrinsische Skalen, um auf dieser Grundlage die Eigenschaften einer optimalen Signaldarstellung mit maximal reduzierter Anzahl an Abtastpunkten zu bestimmen, die durch nichtlineare Neuabtastung auf eine logarithmische Zeitbasis realisiert wird. Hierbei wird ein Kompressionsverhältnis von 16.59 erzielt. Zeit-Skalen-Analysen der uniform und logarithmisch abgetasteten EKP-Einzelantworten zeigen, dass bei der kompressiven Neuabtastung keine relevante Information verloren geht, was durch eine vergleichende Auswertung der resultierenden, gemittelten Wellenformen zusätzlich gestützt wird - alle prominenten Wellen bleiben sichtbar und sind hinsichtlich ihrer charakteristischen Latenzen und Amplituden von der Neuabtastung weitgehend unbeeinflusst. Die uniforme und logarithmische Signalrepräsentation werden hinsichtlich ihrer Anfälligkeit für die üblicherweise bei der EKP-Aufzeichnung auftretenden physiologischen und technischen Störquellen vergleichend untersucht. Obwohl bereits eine Fülle von gut etablierten Ansätzen für die Entrauschung von EKP-Einzelantwortdarstellungen zur Verbesserung der Signalqualität und/oder zur Reduktion der benötigten Erfassungszeiten existiert, erfordern die wesentlich veränderten Störeigenschaften der vorliegenden, logarithmisch abgetasteten Einzelantwortdarstellungen im Gegensatz zu ihrem uniformen Äquivalent eine Neubewertung der verfügbaren Methoden für diese Art von Daten. Darüber hinaus werden zwei neuartige, effiziente Entrauschungsalgorithmen geboten, die auf der Koeffizientenmanipulation einer Sinogramm-Repräsentation bzw. einer analytischen, diskreten Wavelet-Zerlegung der Einzelantworten basieren und gemeinsam mit zwei etablierten Entrauschungsmethoden einer vergleichenden Leistungsbewertung unterzogen werden. Um einen umfassenden Vergleich zu ermöglichen, werden der im ersten Teil dieser Arbeit erhaltene EKP-Messdatensatz sowie synthetischen Daten eingesetzt, die mithilfe eines phänomenologischen EKP-Modells bei verschiedenen Signal-Rausch-Abständen (SRA) erzeugt wurden, wobei die individuellen Anstiege in mehreren Zielmetriken zur objektiven Bewertung der Performanz herangezogen werden. Die erhaltenen Ergebnisse deuten darauf hin, dass die vorgeschlagenen Entrauschungsalgorithmen die etablierten Methoden sowohl in den eingesetzten Zielmetriken als auch mit Blick auf die Laufzeiten deutlich übertreffen. Weiterhin wird ein effizientes Reizsequenzoptimierungsverfahren für den Einsatz mit entfaltungsbasierten EKP-Aufzeichnungsmethoden vorgestellt, das eine konsistente Rauschunterdrückung innerhalb eines breiten Frequenzbands erreicht. Ein neuartiges Stimulus-Präsentationsparadigma für die schnelle, verschachtelte Erfassung auditorischer Hirnstammpotentiale, mittlelspäter und später Antworten durch alternierende Darbietung von optimierten, dichter Stimulussequenzen und nachgelagerter, langsamer Einzelstimulation wird eingeführt und in 20 normalhörenden Probanden evaluiert. Entfaltete Sequenzantworten, die frühe und mittlere EKP enthalten, werden mit den nachfolgenden späten Antworten fusioniert, wobei eine Zeit-Frequenz-aufgelöste, gewichtete Mittelung unter Berücksichtigung von Regularität über Einzelantworten hinweg zum Einsatz kommt. Diese erreicht einheitliche SRA der resultierenden EKP-Signale über alle untersuchten Zeitskalen hinweg. Die erhaltenen, gemittelten EKP-Wellenformen weisen Morphologien auf, die sowohl mit einschlägigen Literaturwerten als auch mit den im ersten Teil dieses Manuskripts erhaltenen Referenzaufnahmen konsistent sind, wobei alle markanten Wellen deutlich in den Gesamtmittelwerten sichtbar sind. Das neuartige Stimulationsparadigma verkürzt die Erfassungszeit um den Faktor 3.4 und vergrößert gleichzeitig den erreichten SRA erheblich. Die Ergebnisse deuten darauf hin, dass die vorgeschlagene verschachtelte Stimuluspräsentation und die nachgelagerte EKP-Verarbeitungsmethodik zur schnellen, zuverlässigen Extraktion neuronaler Korrelate der gesamten auditorischen Verarbeitung im Rahmen zukünftiger Studien geeignet sind.Bundesministerium für Bildung und Forschung | Bimodal Fusion - Eine neurotechnologische Optimierungsarchitektur für integrierte bimodale Hörsysteme | 2016-201

Application of Higher-Order Statistics and Subspace-Based Techniques to the Analysis and Diagnosis of Electrocardiogram Signals

The first and main contribution of this research work is the higher-order statistics (HOS)-based non-linear analysis and subsequent diagnosis of abnormal electrocardiogram (ECG) signals, particularly myocardial ischaemia. In the time domain; the second-, third-, and the fourth-order cumulants have been used in the analysis. In the frequency domain; up to the tenth-order polyspectra have been exploited. This HOS-based analysis of normal and ischaemic electrocardiogram signals has led to the identification of certain key discriminant features for the two physiological states of the heart. These features are then fed to different backpropagation-based multiple layer perceptrons for classification. The second contribution is a proposed new methodology to discriminate patients with angina pectoris or with old myocardial infarction (MI) during the first 60 seconds of stress test (or in some cases using rest ECG). It is based on the pseudo-spectral Multiple Signal Classification (MUSIC) and has the potential of being highly sensitive diagnostic signal processing tool. The third contribution is the development of a novel higher-order statistics, high-resolution estimator for quadratically coupled frequencies based on subspace spectral estimation. Extensive studies of cumulants, bispectra and bicoherence-squared of normal and ischaemic ECG signals collected from MIT and ST-T European databases has enabled us to see key discriminant features in both the third- and fourth-order cumulant domains. In the frequency domain, the polyspectral study has been extended to the lOth-order poly spectra. By calculating one-dimensional polyspectrum slices using an algorithm developed by Zhou and Giannakis (1995) a considerable reduction in the CPU time has been achieved. Furthermore, Zhou’s algorithm has been further extended to estimate the polycoherency slices which are used to characterise non-linearities in normal and ischaemic ECG signals. An important finding in this thesis is the decrease of the order of non-linearity representing the electrocardiogram signals of ischaemic patients. This thesis also includes the results of a pilot study involving eighteen healthy subjects (MIT database) and confirmed that the ECG signal is non-Gaussian, cyclostationary and quasi periodic. Combined spectral and bispectral analysis of the signal revealed that there are unique harmonic characteristics for the P-wave, QRS complex and T-wave and other frequencies due to harmonic interactions. In this work three linear and one non-linear adaptive filtering/predictions techniques have been applied to noisy ECG signals and their respective performances appraised. It is shown that the Kalman filter gives the best mean-square error MSE error but its comparatively long execution time and problems arising from ill-conditioning of the state-error covariance matrix render it of limited use in ECG applications. It is also shown that the LMS-based quadratic and cubic Volterra filters are the most superior for the ECG signal prediction. For ECG classifications; three multi-layer perceptrons employing back-propagation and modified back-propagation algorithms, and using two sets from the higher-order most discriminant features as their inputs, have yielded fairly high classification rates

Advanced robust non-invasive foetal heart detection techniques during active labour using one pair of transabdominal electrodes

The thesis proposes and evaluates three state-of-the-art signal processing techniques to detect fetal heartbeats within each maternal cardiac cycle, during labour contractions, using only a pair of transabdominal electrodes. The first and second techniques are, namely, the structured third- order cumulant-slice-template matching and the bispectral-contours-template matching for fetal QRS identification, respectively. The third technique is based on the modified and appropriately weighted spectral multiple signal classification (MUSIC) with incorporated covariance matrix for uterine contraction noise-like interfering signals also contaminated with noise. Essentially, two modifications to the standard MUSIC have been developed in order to enhance the performance of the spectral estimator in our applied work. The first modification involves the introduction of an optimised weighting function to the segmented ECG covariance matrix, and is chiefly aimed at enhancing the fetal QRS major spectral peak which occurs at around 30 Hz against the mother QRS major spectral peak usually occurring around 17 Hz and all other noise contributions. Additional optional pseudo-bispectral enhancement to sharpen the maternal and fetal spectral peaks, in particular when the mother and fetal R-waves are temporally coincident, have been achieved. The second modification to the spectral MUSIC is the removal of the unjustified assumption that only white Gaussian noise is present and the incorporation of the actual measured labour uterine contraction covariance matrix in reconfigured subspace analysis. This inevitably leads to the generalised eigenvectors - eigenvalues decomposition modern signal processing. This is now coined the modified, interference incorporated pseudo-spectral MUSIC. The above mentioned first and second techniques are higher-order statistics-based (HOS) and hybrid involving both signal processing and NN classifiers. The third technique is second-order statistics-based (SOS). In all techniques, the removal of signal non-linearity with the aid of non-linear Volterra synthesisers plays a crucial part in the fetal detection integrity. Accurately assessed fetal heart classification rates as high as 95% have been achieved during labour, thus helping to provide non-invasive transparency to fetal intrapartum welfare. Performance analysis and evaluation processes involved more than 30 critical cases classified as “fetal under stress in labour” recorded in a London hospital database and used both transbadominal ECG electrodes and fetal scalp electrodes. The latter facilitates detection of the instantaneous fetal heart rate which is then used as the Reference Fetal Heart Rate in the assessment of the classification rate of each of the above mentioned techniques. It will be shown that the fetal heartbeats are completely masked by uterine activity and noise artefacts in all the recorded transabdominal maternal ECG signals. The fetal scalp electrode was, therefore, deemed necessary to provide the highest accurate measure of fetal heart functionality (from the hospital viewpoint), and in the assessment of the three non-invasive techniques presented in this thesis. The techniques may also be used during gestation and as early as 10 weeks

Apport de nouvelles techniques dans l’évaluation de patients candidats à une chirurgie d’épilepsie : résonance magnétique à haut champ, spectroscopie proche infrarouge et magnétoencéphalographie

L'épilepsie constitue le désordre neurologique le plus fréquent après les maladies cérébrovasculaires. Bien que le contrôle des crises se fasse généralement au moyen d'anticonvulsivants, environ 30 % des patients y sont réfractaires. Pour ceux-ci, la chirurgie de l'épilepsie s'avère une option intéressante, surtout si l’imagerie par résonance magnétique (IRM) cérébrale révèle une lésion épileptogène bien délimitée. Malheureusement, près du quart des épilepsies partielles réfractaires sont dites « non lésionnelles ». Chez ces patients avec une IRM négative, la délimitation de la zone épileptogène doit alors reposer sur la mise en commun des données cliniques, électrophysiologiques (EEG de surface ou intracrânien) et fonctionnelles (tomographie à émission monophotonique ou de positrons). La faible résolution spatiale et/ou temporelle de ces outils de localisation se traduit par un taux de succès chirurgical décevant. Dans le cadre de cette thèse, nous avons exploré le potentiel de trois nouvelles techniques pouvant améliorer la localisation du foyer épileptique chez les patients avec épilepsie focale réfractaire considérés candidats potentiels à une chirurgie d’épilepsie : l’IRM à haut champ, la spectroscopie proche infrarouge (SPIR) et la magnétoencéphalographie (MEG). Dans une première étude, nous avons évalué si l’IRM de haut champ à 3 Tesla (T), présentant théoriquement un rapport signal sur bruit plus élevé que l’IRM conventionnelle à 1,5 T, pouvait permettre la détection des lésions épileptogènes subtiles qui auraient été manquées par cette dernière. Malheureusement, l’IRM 3 T n’a permis de détecter qu’un faible nombre de lésions épileptogènes supplémentaires (5,6 %) d’où la nécessité d’explorer d’autres techniques. Dans les seconde et troisième études, nous avons examiné le potentiel de la SPIR pour localiser le foyer épileptique en analysant le comportement hémodynamique au cours de crises temporales et frontales. Ces études ont montré que les crises sont associées à une augmentation significative de l’hémoglobine oxygénée (HbO) et l’hémoglobine totale au niveau de la région épileptique. Bien qu’une activation contralatérale en image miroir puisse être observée sur la majorité des crises, la latéralisation du foyer était possible dans la plupart des cas. Une augmentation surprenante de l’hémoglobine désoxygénée a parfois pu être observée suggérant qu’une hypoxie puisse survenir même lors de courtes crises focales. Dans la quatrième et dernière étude, nous avons évalué l’apport de la MEG dans l’évaluation des patients avec épilepsie focale réfractaire considérés candidats potentiels à une chirurgie. Il s’est avéré que les localisations de sources des pointes épileptiques interictales par la MEG ont eu un impact majeur sur le plan de traitement chez plus des deux tiers des sujets ainsi que sur le devenir postchirurgical au niveau du contrôle des crises.Epilepsy is the most common chronic neurological disorder after stroke. The major form of treatment is long-term drug therapy to which approximately 30% of patients are unfortunately refractory to. Brain surgery is recommended when medication fails, especially if magnetic resonance imaging (MRI) can identify a well-defined epileptogenic lesion. Unfortunately, close to a quarter of patients have nonlesional refractory focal epilepsy. For these MRI-negative cases, identification of the epileptogenic zone rely heavily on remaining tools: clinical history, video-electroencephalography (EEG) monitoring, ictal single-photon emission computed tomography (SPECT), and a positron emission tomography (PET). Unfortunately, the limited spatial and/or temporal resolution of these localization techniques translates into poor surgical outcome rates. In this thesis, we explore three relatively novel techniques to improve the localization of the epileptic focus for patients with drug-resistant focal epilepsy who are potential candidates for epilepsy surgery: high-field 3 Tesla (T) MRI, near-infrared spectroscopy (NIRS) and magnetoencephalography (MEG). In the first study, we evaluated if high-field 3T MRI, providing a higher signal to noise ratio, could help detect subtle epileptogenic lesions missed by conventional 1.5T MRIs. Unfortunately, we show that the former was able to detect an epileptogenic lesion in only 5.6% of cases of 1.5T MRI-negative epileptic patients, emphasizing the need for additional techniques. In the second and third studies, we evaluated the potential of NIRS in localizing the epileptic focus by analyzing the hemodynamic behavior of temporal and frontal lobe seizures respectively. We show that focal seizures are associated with significant increases in oxygenated haemoglobin (HbO) and total haemoglobin (HbT) over the epileptic area. While a contralateral mirror-like activation was seen in the majority of seizures, lateralization of the epileptic focus was possible most of the time. In addition, an unexpected increase in deoxygenated haemoglobin (HbR) was noted in some seizures, suggesting possible hypoxia even during relatively brief focal seizures. In the fourth and last study, the utility of MEG in the evaluation of nonlesional drug-refractory focal epileptic patients was studied. It was found that MEG source localization of interictal epileptic spikes had an impact both on patient management for over two thirds of patients and their surgical outcome

Finding Nonlinear Relationships in Functional Magnetic Resonance Imaging Data with Genetic Programming

The human brain is a complex, nonlinear dynamic chaotic system that is poorly understood. When faced with these difficult to understand systems, it is common to observe the system and develop models such that the underlying system might be deciphered. When observing neurological activity within the brain with functional magnetic resonance imaging (fMRI), it is common to develop linear models of functional connectivity; however, these models are incapable of describing the nonlinearities we know to exist within the system. A genetic programming (GP) system was developed to perform symbolic regression on recorded fMRI data. Symbolic regression makes fewer assumptions than traditional linear tools and can describe nonlinearities within the system. Although GP is a powerful form of machine learning that has many drawbacks (computational cost, overfitting, stochastic), it may provide new insights into the underlying system being studied. The contents of this thesis are presented in an integrated article format. For all articles, data from the Human Connectome Project were used. In the first article, nonlinear models for 507 subjects performing a motor task were created. These nonlinear models generated by GP contained fewer ROI than what would be found with traditional, linear tools. It was found that the generated nonlinear models would not fit the data as well as the linear models; however, when compared to linear models containing a similar number of ROI, the nonlinear models performed better. Ten subjects performing 7 tasks were studied in article two. After improvements to the GP system, the generated nonlinear models outperformed the linear models in many cases and were never significantly worse than the linear models. Forty subjects performing 7 tasks were studied in article three. Newly generated nonlinear models were applied to unseen data from the same subject performing the same task (intrasubject generalization) and many nonlinear models generalized to unseen data better than the linear models. The nonlinear models were applied to unseen data from other subjects performing the same task (intersubject generalization) and were not capable of generalizing as well as the linear