EEG/MEG Sparse Source Imaging and Its Application in Epilepsy

This dissertation is a summary of my Ph.D. work on the development of sparse source imaging technologies based on electroencephalography (EEG) and magneto-encephalography (MEG) and their application to noninvasively reconstruct brain activation from external surface measurements. Conventional sparse source imaging (SSI) methods using the ℓ1-norm regularization to enforce sparseness in the original source domain leads to over-focused solutions and causes bias in estimating spatially extended brain sources. I address the over-focused issue in the ℓ1-norm regularization technique framework by exploring sparseness in the transform domains. First, I apply a SSI method that uses the variation transform, i.e. V-SSI, on clinical MEG interictal recordings from partial epilepsy patients. Estimated epileptic sources by V-SSI are validated using clinical pre-surgical evaluation data and surgical outcomes. Second, I implement a novel face-based wavelet transform, which can efficiently compress brain activation signals into sparse representations on a multi-resolution cortical source model, into the SSI technology framework. The proposed wavelet-based SSI (W-SSI) demonstrates a significantly improved ability in inferring both brain source locations and extents as compared with conventional ℓ2-norm regularizations in obtaining EEG/MEG inverse solutions and other SSI technologies. Furthermore, the face-based wavelet also indicates better performance than a previously reported vertex-based wavelet in W-SSI. I evaluate the W-SSI method and conduct the comparison studies using both simulations and real data collected from partial epilepsy patients. Lastly, I further propose the concept of using multiple transforms in the SSI technology framework and investigated a new SSI method by enforcing sparseness in both variation and face-based wavelet domains, termed as VW-SSI. I conduct simulation studies, which demonstrate that VW-SSI has significantly better detection accuracies in both source locations and extents than conventional ℓ2-norm regularizations and other SSI methods, including SSI, V-SSI, and W-SSI. I further validate the VW-SSI method using clinical MEG data from both language and motor experiments collected from epilepsy patients again to localize their important functional brain areas. The results indicate that VW-SSI provides a performance advantage in detecting neural phenomena that have been extremely difficult to recognize by other EEG/MEG inverse solutions. It thus suggests that the sparse source imaging technique is promising to serve as a non-invasive tool in assisting pre-surgical planning for partial epilepsy patients

Electromagnetic Source Imaging via a Data-Synthesis-Based Convolutional Encoder-Decoder Network

Electromagnetic source imaging (ESI) requires solving a highly ill-posed inverse problem. To seek a unique solution, traditional ESI methods impose various forms of priors that may not accurately reflect the actual source properties, which may hinder their broad applications. To overcome this limitation, in this paper a novel data-synthesized spatio-temporally convolutional encoder-decoder network method termed DST-CedNet is proposed for ESI. DST-CedNet recasts ESI as a machine learning problem, where discriminative learning and latent-space representations are integrated in a convolutional encoder-decoder network (CedNet) to learn a robust mapping from the measured electroencephalography/magnetoencephalography (E/MEG) signals to the brain activity. In particular, by incorporating prior knowledge regarding dynamical brain activities, a novel data synthesis strategy is devised to generate large-scale samples for effectively training CedNet. This stands in contrast to traditional ESI methods where the prior information is often enforced via constraints primarily aimed for mathematical convenience. Extensive numerical experiments as well as analysis of a real MEG and Epilepsy EEG dataset demonstrate that DST-CedNet outperforms several state-of-the-art ESI methods in robustly estimating source signals under a variety of source configurations.Comment: 15 pages, 14 figures, and journa

Reconstructing Resting State Networks from EEG

Resting state networks (RSNs) have been found in human brains during awake resting states. RSNs are composed of spatially distributed regions in which spontaneous activity fluctuations are temporally and dynamically correlated. In contrast to task-related brain activities, RSNs reflect intrinsic functional organizations and rhythms of the human brain when it is not engaged in any task and/or disturbed by external stimuli. To date, RSNs have been widely studied using functional magnetic resonance imaging (fMRI), which has identified various RSNs associated with different brain functions. More recently, due to the advantage of millisecond temporal resolution, both electroencephalography (EEG) and magnetoencephalography (MEG) have been used to investigate RSNs and their electrophysiological underpinnings. Despite these advantages, current RSN studies using EEG/MEG, as compared with those using fMRI, are still at their infant stage in many aspects, such as the quality of spatial pattern reconstructions and the reliability of detections. These limitations require further studies to obtain accurate reconstructions of RSNs directly from EEG/MEG data. My research aims to develop, optimize, and validate a variety of computational and analytical frameworks to reconstruct and investigate RSNs based on EEG data. In this dissertation, several studies have been conducted as outlined below. Firstly, a comparison in defining RSNs at the sensor space and at the source space was performed to evaluate the accuracy in reconstructing RSN spatial patterns. Results from both simulated and experimental data indicated that the analysis in the source space performed better in reconstructing various features of RSNs. Secondly, a new computational framework for reconstructing RSNs with human EEG data was developed. The proposed framework utilized independent component analysis (ICA) on short-time Fourier transformed inverse source maps imaged from EEG data and statistical correlation analysis to generate cortical tomography of electrophysiological RSNs. The proposed framework was validated using three sets of experimental data. The results indicated that the framework is reliable and efficient in the reconstruction of RSNs. Thirdly, an advanced inverse source imaging (ISI) method was used in the established framework discussed above to improve the spatial estimation of RSNs. The comparison between the new and conventional frameworks suggested that the ISI method significantly improved the accuracy of spatial estimations of RSNs. Fourthly, an ICA-based framework was used to assess RSN alternations under different conditions, which has been the model to identify imaging biomarkers, for example, for diseased patients as compared with healthy control. The results from both simulated and experimental data indicated that the framework could detect RSN alternations due to condition differences. My results further suggest that the framework could provide a finer resolution in detecting RSN changes as a contrast for multi-level (more than 2) condition differences, which can be used to study the difference, for example, among patients with a long history of a certain disorder, a short history, and healthy control. Overall, the findings of this dissertation study provided insights into the underlying electrophysiological basis of RSNs. More importantly, this study developed new frameworks that can be used as powerful tools for future investigations of more characteristics of RSNs, in particular for those not available in fMRI, e.g., spectral patterns

Sparse algorithms for EEG source localization

Source localization using EEG is important in diagnosing various physiological and psychiatric diseases related to the brain. The high temporal resolution of EEG helps medical professionals assess the internal physiology of the brain in a more informative way. The internal sources are obtained from EEG by an inversion process. The number of sources in the brain outnumbers the number of measurements. In this article, a comprehensive review of the state of the art sparse source localization methods in this field is presented. A recently developed method, certainty based reduced sparse solution (CARSS), is implemented and is examined. A vast comparative study is performed using a sixty four channel setup involving two source spaces. The first source space has 5004 sources and the other has 2004 sources. Four test cases with one, three, five, and seven simulated active sources are considered. Two noise levels are also being added to the noiseless data. The CARSS is also evaluated. The results are examined. A real EEG study is also attempted.Comment: Published in Medical & Biological Engineering & Computing, Springer on Oct 02, 202

Object-based Modeling of Audio for Coding and Source Separation

This thesis studies several data decomposition algorithms for obtaining an object-based representation of an audio signal. The estimation of the representation parameters are coupled with audio-specific criteria, such as the spectral redundancy, sparsity, perceptual relevance and spatial position of sounds. The objective is to obtain an audio signal representation that is composed of meaningful entities called audio objects that reflect the properties of real-world sound objects and events. The estimation of the object-based model is based on magnitude spectrogram redundancy using non-negative matrix factorization with extensions to multichannel and complex-valued data. The benefits of working with object-based audio representations over the conventional time-frequency bin-wise processing are studied. The two main applications of the object-based audio representations proposed in this thesis are spatial audio coding and sound source separation from multichannel microphone array recordings. In the proposed spatial audio coding algorithm, the audio objects are estimated from the multichannel magnitude spectrogram. The audio objects are used for recovering the content of each original channel from a single downmixed signal, using time-frequency filtering. The perceptual relevance of modeling the audio signal is considered in the estimation of the parameters of the object-based model, and the sparsity of the model is utilized in encoding its parameters. Additionally, a quantization of the model parameters is proposed that reflects the perceptual relevance of each quantized element. The proposed object-based spatial audio coding algorithm is evaluated via listening tests and comparing the overall perceptual quality to conventional time-frequency block-wise methods at the same bitrates. The proposed approach is found to produce comparable coding efficiency while providing additional functionality via the object-based coding domain representation, such as the blind separation of the mixture of sound sources in the encoded channels. For the sound source separation from multichannel audio recorded by a microphone array, a method combining an object-based magnitude model and spatial covariance matrix estimation is considered. A direction of arrival-based model for the spatial covariance matrices of the sound sources is proposed. Unlike the conventional approaches, the estimation of the parameters of the proposed spatial covariance matrix model ensures a spatially coherent solution for the spatial parameterization of the sound sources. The separation quality is measured with objective criteria and the proposed method is shown to improve over the state-of-the-art sound source separation methods, with recordings done using a small microphone array

Audio source separation for music in low-latency and high-latency scenarios

Aquesta tesi proposa mètodes per tractar les limitacions de les tècniques existents de separació de fonts musicals en condicions de baixa i alta latència. En primer lloc, ens centrem en els mètodes amb un baix cost computacional i baixa latència. Proposem l'ús de la regularització de Tikhonov com a mètode de descomposició de l'espectre en el context de baixa latència. El comparem amb les tècniques existents en tasques d'estimació i seguiment dels tons, que són passos crucials en molts mètodes de separació. A continuació utilitzem i avaluem el mètode de descomposició de l'espectre en tasques de separació de veu cantada, baix i percussió. En segon lloc, proposem diversos mètodes d'alta latència que milloren la separació de la veu cantada, gràcies al modelatge de components específics, com la respiració i les consonants. Finalment, explorem l'ús de correlacions temporals i anotacions manuals per millorar la separació dels instruments de percussió i dels senyals musicals polifònics complexes.Esta tesis propone métodos para tratar las limitaciones de las técnicas existentes de separación de fuentes musicales en condiciones de baja y alta latencia. En primer lugar, nos centramos en los métodos con un bajo coste computacional y baja latencia. Proponemos el uso de la regularización de Tikhonov como método de descomposición del espectro en el contexto de baja latencia. Lo comparamos con las técnicas existentes en tareas de estimación y seguimiento de los tonos, que son pasos cruciales en muchos métodos de separación. A continuación utilizamos y evaluamos el método de descomposición del espectro en tareas de separación de voz cantada, bajo y percusión. En segundo lugar, proponemos varios métodos de alta latencia que mejoran la separación de la voz cantada, gracias al modelado de componentes que a menudo no se toman en cuenta, como la respiración y las consonantes. Finalmente, exploramos el uso de correlaciones temporales y anotaciones manuales para mejorar la separación de los instrumentos de percusión y señales musicales polifónicas complejas.This thesis proposes specific methods to address the limitations of current music source separation methods in low-latency and high-latency scenarios. First, we focus on methods with low computational cost and low latency. We propose the use of Tikhonov regularization as a method for spectrum decomposition in the low-latency context. We compare it to existing techniques in pitch estimation and tracking tasks, crucial steps in many separation methods. We then use the proposed spectrum decomposition method in low-latency separation tasks targeting singing voice, bass and drums. Second, we propose several high-latency methods that improve the separation of singing voice by modeling components that are often not accounted for, such as breathiness and consonants. Finally, we explore using temporal correlations and human annotations to enhance the separation of drums and complex polyphonic music signals

Sparse and Redundant Representations for Inverse Problems and Recognition

Sparse and redundant representation of data enables the description of signals as linear combinations of a few atoms from a dictionary. In this dissertation, we study applications of sparse and redundant representations in inverse problems and object recognition. Furthermore, we propose two novel imaging modalities based on the recently introduced theory of Compressed Sensing (CS). This dissertation consists of four major parts. In the first part of the dissertation, we study a new type of deconvolution algorithm that is based on estimating the image from a shearlet decomposition. Shearlets provide a multi-directional and multi-scale decomposition that has been mathematically shown to represent distributed discontinuities such as edges better than traditional wavelets. We develop a deconvolution algorithm that allows for the approximation inversion operator to be controlled on a multi-scale and multi-directional basis. Furthermore, we develop a method for the automatic determination of the threshold values for the noise shrinkage for each scale and direction without explicit knowledge of the noise variance using a generalized cross validation method. In the second part of the dissertation, we study a reconstruction method that recovers highly undersampled images assumed to have a sparse representation in a gradient domain by using partial measurement samples that are collected in the Fourier domain. Our method makes use of a robust generalized Poisson solver that greatly aids in achieving a significantly improved performance over similar proposed methods. We will demonstrate by experiments that this new technique is more flexible to work with either random or restricted sampling scenarios better than its competitors. In the third part of the dissertation, we introduce a novel Synthetic Aperture Radar (SAR) imaging modality which can provide a high resolution map of the spatial distribution of targets and terrain using a significantly reduced number of needed transmitted and/or received electromagnetic waveforms. We demonstrate that this new imaging scheme, requires no new hardware components and allows the aperture to be compressed. Also, it presents many new applications and advantages which include strong resistance to countermesasures and interception, imaging much wider swaths and reduced on-board storage requirements. The last part of the dissertation deals with object recognition based on learning dictionaries for simultaneous sparse signal approximations and feature extraction. A dictionary is learned for each object class based on given training examples which minimize the representation error with a sparseness constraint. A novel test image is then projected onto the span of the atoms in each learned dictionary. The residual vectors along with the coefficients are then used for recognition. Applications to illumination robust face recognition and automatic target recognition are presented

Advancing models of the visual system using biologically plausible unsupervised spiking neural networks

Spikes are thought to provide a fundamental unit of computation in the nervous system. The retina is known to use the relative timing of spikes to encode visual input, whereas primary visual cortex (V1) exhibits sparse and irregular spiking activity – but what do these different spiking patterns represent about sensory stimuli? To address this question, I set out to model the retina and V1 using a biologically-realistic spiking neural network (SNN), exploring the idea that temporal prediction underlies the sensory transformation of natural inputs. Firstly, I trained a recurrently-connected SNN of excitatory and inhibitory units to predict the sensory future in natural movies under metabolic-like constraints. This network exhibited V1-like spike statistics, simple and complex cell-like tuning, and - advancing prior studies - key physiological and tuning differences between excitatory and inhibitory neurons. Secondly, I modified this spiking network to model the retina to explore its role in visual processing. I found the model optimized for efficient prediction to capture retina-like receptive fields and - in contrast to previous studies - various retinal phenomena, such as latency coding, response omissions, and motion-tuning properties. Notably, the temporal prediction model also more accurately predicts retinal ganglion cell responses to natural images and movies across various animal species. Lastly, I developed a new method to accelerate the simulation and training of SNNs, obtaining a 10-50 times speedup, with performance on a par with the standard training approach on supervised classification benchmarks and for fitting electrophysiological recordings of cortical neurons. The retina and V1 models lay the foundation for developing normative models of increasing biological realism and link sensory processing to spiking activity, suggesting that temporal prediction is an underlying function of visual processing. This is complemented by a new approach to drastically accelerate computational research using SNNs