Des sources neuronales aux signaux EEG : modèle et interprétation des activités épileptiques

This work deals with the interpretation of electrophysiological patients recorded in epileptic patients candidate to surgery. This issue is addressed through a physiologically relevant model for the generation of scalp and intracerebral electroencephalographic (EEG) signals. The proposed model is based on a spatiotemporal representation of the sources of brain activity, which combines a distributed dipole source model and a model of coupled neuronal populations. Signals recorded by sensors (scalp and intracerebral) are then computed by solving the forward problem in the head volume conductor. In this paper, the EEG generation model is used to study the influence of some source-related parameters (spatial extent, position, synchronization) on simulated signals, during epileptic transient activity (interictal spikes). Results show that the model allows for studying, on the one hand, the relationship between the spatiotemporal organization of neuronal sources and the properties of the observed signals and, on the other hand, the relationship between surface and depth EEG signals.     

EEG source localization: comparative study of classical and neural network methods.

We address the problem of estimating biopotential sources within the brain, based on EEG signals observed on the scalp. This problem, known as the inverse problem of electrophysiology, has no closed-form solution, and requires iterative techniques such as the Levenberg-Marquardt (LM) algorithm. Considering the nonlinear nature of the inverse problem, and the low signal to noise ratio inherent in EEG signals, a backpropagation neural network (BPN) has been recently proposed as a solution. The technique has not been properly compared with classical techniques such as the LM method, or with more recent neural network techniques such as the Radial Basis Function (RBF) network. In this paper, we provide improved strategies based on BPN and consider RBF networks in solving the inverse problem. We compare the performances of BPN, RBF and a hybrid technique with that of the classical LM method.     

On the Usage of Linear Regression Models to Reconstruct Limb Kinematics from Low Frequency EEG Signals

Several works have reported on the reconstruction of 2D/3D limb kinematics from low-frequency EEG signals using linear regression models based on positive correlation values between the recorded and the reconstructed trajectories. This paper describes the mathematical properties of the linear model and the correlation evaluation metric that may lead to a misinterpretation of the results of this type of decoders. Firstly, the use of a linear regression model to adjust the two temporal signals (EEG and velocity profiles) implies that the relevant component of the signal used for decoding (EEG) has to be in the same frequency range as the signal to be decoded (velocity profiles). Secondly, the use of a correlation to evaluate the fitting of two trajectories could lead to overly-optimistic results as this metric is invariant to scale. Also, the correlation has a non-linear nature that leads to higher values for sinus/cosinus-like signals at low frequencies. Analysis of these properties on the reconstruction results was carried out through an experiment performed in line with previous studies, where healthy participants executed predefined reaching movements of the hand in 3D space. While the correlations of limb velocity profiles reconstructed from low-frequency EEG were comparable to studies in this domain, a systematic statistical analysis revealed that these results were not above the chance level. The empirical chance level was estimated using random assignments of recorded velocity profiles and EEG signals, as well as combinations of randomly generated synthetic EEG with recorded velocity profiles and recorded EEG with randomly generated synthetic velocity profiles. The analysis shows that the positive correlation results in this experiment cannot be used as an indicator of successful trajectory reconstruction based on a neural correlate. Several directions are herein discussed to address the misinterpretation of results as well as the implications on previous invasive and non-invasive works.     

Iterative reconstruction of cryo-electron tomograms using nonuniform fast Fourier transforms

Algorithms for three-dimensional (3D) reconstruction of objects based on their projections are essential in various biological and medical imaging modalities. In cryo-electron tomography (CET) a major challenge for reconstruction is the limited range of projection angles, which manifests itself as a “missing wedge” of data in Fourier space making the reconstruction problem ill-posed. Here, we apply an iterative reconstruction method that makes use of nonuniform fast Fourier transform (NUFFT) to the reconstruction of cryo-electron tomograms. According to several measures the reconstructions are superior to those obtained using conventional methods, most notably weighted backprojection. Most importantly, we show that it is possible to fill in partially the unsampled region in Fourier space with meaningful information without making assumptions about the data or applying prior knowledge. As a consequence, particles of known structure can be localized with higher confidence in cryotomograms and subtomogram averaging yields higher resolution densities.     

Hidden pattern discovery on event related potential EEG signals

EEG signals are important to capture brain disorders. They are useful for analyzing the cognitive activity of the brain and diagnosing types of seizure and potential mental health problems. The Event Related Potential can be measured through the EEG signal. However, it is always difficult to interpret due to its low amplitude and sensitivity to changes of the mental activity. In this paper, we propose a novel approach to incrementally detect the pattern of this kind of EEG signal. This approach successfully summarizes the whole stream of the EEG signal by finding the correlations across the electrodes and discriminates the signals corresponding to various tasks into different patterns. It is also able to detect the transition period between different EEG signals and identify the electrodes which contribute the most to these signals. The experimental results show that the proposed method allows the significant meaning of the EEG signal to be obtained from the extracted pattern.     

A probabilistic framework for a physiological representation of dynamically evolving sleep state

This work presents a probabilistic method for mapping human sleep electroencephalogram (EEG) signals onto a state space based on a biologically plausible mathematical model of the cortex. From a noninvasive EEG signal, this method produces physiologically meaningful pathways of the cortical state over a night of sleep. We propose ways in which these pathways offer insights into sleep-related conditions, functions, and complex pathologies. To address explicitly the noisiness of the EEG signal and the stochastic nature of the mathematical model, we use a probabilistic Bayesian framework to map each EEG epoch to a distribution of likelihoods over all model sleep states. We show that the mapping produced from human data robustly separates rapid eye movement sleep (REM) from slow wave sleep (SWS). A Hidden Markov Model (HMM) is incorporated to improve the path results using the prior knowledge that cortical physiology has temporal continuity.     

Correlation dimension based lossless compression of EEG signals

Transmission of long duration EEG signals without loss of information is essential for telemedicine based applications. In this work, a lossless compression scheme for EEG signals based on neural network predictors using the concept of correlation dimension (CD) is proposed. EEG signals which are considered as irregular time series of chaotic processes can be characterized by the non-linear dynamic parameter CD which is a measure of the correlation among the EEG samples. The EEG samples are first divided into segments of 1 s duration and for each segment, the value of CD is calculated. Blocks of EEG samples are then constructed such that each block contains segments with closer CD values. By arranging the EEG samples in this fashion, the accuracy of the predictor is improved as it makes use of highly correlated samples. As a result, the magnitude of the prediction error decreases leading to less number of bits for transmission. Experiments are conducted using EEG signals recorded under different physiological conditions. Different neural network predictors as well as classical predictors are considered. Experimental results show that the proposed CD based preprocessing scheme improves the compression performance of the predictors significantly.     

Local discriminative spatial patterns for movement-related potentials-based EEG classification

A novel discriminant method, termed local discriminative spatial patterns (LDSP), is proposed for movement-related potentials (MRPs)-based single-trial electroencephalogram (EEG) classification. Different from conventional discriminative spatial patterns (DSP), LDSP explicitly considers local structure of EEG trials in the construction of scatter matrices in the Fisher-like criterion. The underlying manifold structure of two-dimensional spatio-temporal EEG signals contains more discriminative information. LDSP is an extension to DSP in the sense that DSP can be formulated as a special case of LDSP. By constructing an adjacency matrix, LDSP is calculated as a generalized eigenvalue problem, and so is computationally straightforward. Experiments on MRPs-based single-trial EEG classification show the effectiveness of the proposed LDSP method.     

Patient-Specific Epileptic Seizure Prediction in Long-Term Scalp EEG Signal Using Multivariate Statistical Process Control

An accurate epileptic seizure prediction algorithm can alleviate the problem and reduce risks in the life of a patient suffering from epilepsy. The main motive of this work is to propose a model which can predict seizures well in advance of its occurrence. Multivariate statistical process control (MSPC) has been used for seizure predictions in long-term scalp EEG signal. It has been observed that excessive neuronal activity in the preictal period of seizure changes the electrical characteristic from chaotic to rhythmic behavior. These changes have been utilized for prediction. Eight temporal based features are used for predicting the seizures by using multivariate statistical process control, which is widely known as an anomaly monitoring method. 90 seizures from the CHB-MIT EEG data of ten patients are analyzed.ResultThe results of the proposed method demonstrated that 80 seizures out of 90 in preictal period were correctly predicted prior to the seizure onset, thereby giving a sensitivity of 88.89%. The false positive rate is observed to 0.39 per hour.ConclusionThis study proposed a temporal based patient-specific epileptic seizure prediction method using MSPC in long-term scalp EEG signals. It also provides the possibility of realizing an EEG-based epileptic seizure prediction system which requires less computational power.SignificanceThe proposed method does not require preictal data for modeling. The extracted features are computationally easy. The tested result shows good accuracy on the CHB-MIT data base.     

Application of recurrence quantification analysis for the automated identification of epileptic EEG signals

Epilepsy is a common neurological disorder that is characterized by the recurrence of seizures. Electroencephalogram (EEG) signals are widely used to diagnose seizures. Because of the non-linear and dynamic nature of the EEG signals, it is difficult to effectively decipher the subtle changes in these signals by visual inspection and by using linear techniques. Therefore, non-linear methods are being researched to analyze the EEG signals. In this work, we use the recorded EEG signals in Recurrence Plots (RP), and extract Recurrence Quantification Analysis (RQA) parameters from the RP in order to classify the EEG signals into normal, ictal, and interictal classes. Recurrence Plot (RP) is a graph that shows all the times at which a state of the dynamical system recurs. Studies have reported significantly different RQA parameters for the three classes. However, more studies are needed to develop classifiers that use these promising features and present good classification accuracy in differentiating the three types of EEG segments. Therefore, in this work, we have used ten RQA parameters to quantify the important features in the EEG signals.These features were fed to seven different classifiers: Support vector machine (SVM), Gaussian Mixture Model (GMM), Fuzzy Sugeno Classifier, K-Nearest Neighbor (KNN), Naive Bayes Classifier (NBC), Decision Tree (DT), and Radial Basis Probabilistic Neural Network (RBPNN). Our results show that the SVM classifier was able to identify the EEG class with an average efficiency of 95.6%, sensitivity and specificity of 98.9% and 97.8%, respectively.     

A synchronization-desynchronization code for natural communication signals

Synchronous spiking of neural populations is hypothesized to play important computational roles in forming neural assemblies and solving the binding problem. Although the opposite phenomenon of desynchronization is well known from EEG studies, it is largely neglected on the neuronal level. We here provide an example of in vivo recordings from weakly electric fish demonstrating that, depending on the social context, different types of natural communication signals elicit transient desynchronization as well as synchronization of the electroreceptor population without changing the mean firing rate. We conclude that, in general, both positive and negative changes in the degree of synchrony can be the relevant signals for neural information processing.     

Seizure source localization using a hybrid second order blind identification and extended rival penalized competitive learning algorithm

Localization of seizure sources prior to neurosurgery is crucial. In this paper, a new method is proposed to localize the seizure sources from multi-channel electroencephalogram (EEG) signals. Blind source separation based on second order blind identification (SOBI) is primarily applied to estimate the brain source signals in each window of the EEG signals. A new clustering method based on rival penalized competitive learning (RPCL) is then developed to cluster the rows of the estimated unmixing matrices in all the windows. The algorithm also includes pre and post-processing stages. By multiplying each cluster center to the EEG signals, the brain signal sources are approximated. According to a complexity value measure, the main seizure source signal is separated from the others. This signal is projected back to the electrodes’ space and is subjected to the dipole source localization using a single dipole model. The simulation results verify the accuracy of the system. In addition, correct localization of the seizure source is consistent with the clinical tests derived using the simultaneous intracranial recordings.     

Modeling of movement-related potentials using a fractal approach

In bio-signal applications, classification performance depends greatly on feature extraction, which is also the case for electroencephalogram (EEG) based applications. Feature extraction, and consequently classification of EEG signals is not an easy task due to their inherent low signal-to-noise ratios and artifacts. EEG signals can be treated as the output of a non-linear dynamical (chaotic) system in the human brain and therefore they can be modeled by their dimension values. In this study, the variance fractal dimension technique is suggested for the modeling of movement-related potentials (MRPs). Experimental data sets consist of EEG signals recorded during the movements of right foot up, lip pursing and a simultaneous execution of these two tasks. The experimental results and performance tests show that the proposed modeling method can efficiently be applied to MRPs especially in the binary approached brain computer interface applications aiming to assist severely disabled people such as amyotrophic lateral sclerosis patients in communication and/or controlling devices.     

A New Method for Nonlinear Dynamic Analysis of the Multi-kinetics Neural Mass Model

ObjectiveThe aim was to use a new method to analyze the nonlinear dynamic characteristics of the multi-kinetics neural mass model. We hope that this new method can be as an auxiliary judgment tool for the diagnosis of brain diseases and the identification of brain activity states.MethodsWe apply the Lorenz plot to analyze the nonlinear dynamic characteristics of electroencephalogram (EEG) signals from the multi-kinetics neural mass models. The standard deviations in two orthogonal directions of the Lorenz plot are further used to quantify the nonlinear dynamic characteristics of EEG signals.ResultsThe results show that the normalized signal frequency power spectrum may not be able to distinguish normal EEG signals and epileptiform spikes, but the Lorenz plot can distinguish the normal EEG signals and epileptiform spikes effectively. For EEG signals with multi-rhythms, the Lorenz plot of all the simulated signals are oval, but the value of SD1/SD2 increases monotonically when the multi-rhythm EEG signals change from low frequency to high frequency.ConclusionThe Lorenz plot of EEG signals with different rhythms presents different distribution. It is an effective nonlinear analysis method for EEG signals.     

Bayesian inference for stationary points in Gaussian process regression models for event-related potentials analysis

Stationary points embedded in the derivatives are often critical for a model to be interpretable and may be considered as key features of interest in many applications. We propose a semiparametric Bayesian model to efficiently infer the locations of stationary points of a nonparametric function, which also produces an estimate of the function. We use Gaussian processes as a flexible prior for the underlying function and impose derivative constraints to control the function's shape via conditioning. We develop an inferential strategy that intentionally restricts estimation to the case of at least one stationary point, bypassing possible mis-specifications in the number of stationary points and avoiding the varying dimension problem that often brings in computational complexity. We illustrate the proposed methods using simulations and then apply the method to the estimation of event-related potentials derived from electroencephalography (EEG) signals. We show how the proposed method automatically identifies characteristic components and their latencies at the individual level, which avoids the excessive averaging across subjects that is routinely done in the field to obtain smooth curves. By applying this approach to EEG data collected from younger and older adults during a speech perception task, we are able to demonstrate how the time course of speech perception processes changes with age.     

Algorithmic approaches to clonal reconstruction in heterogeneous cell populations

Background: The reconstruction of clonal haplotypes and their evolutionary history in evolving populations is a common problem in both microbial evolutionary biology and cancer biology. The clonal theory of evolution provides a theoretical framework for modeling the evolution of clones.Results: In this paper, we review the theoretical framework and assumptions over which the clonal reconstruction problem is formulated. We formally define the problem and then discuss the complexity and solution space of the problem. Various methods have been proposed to find the phylogeny that best explains the observed data. We categorize these methods based on the type of input data that they use (space-resolved or time-resolved), and also based on their computational formulation as either combinatorial or probabilistic. It is crucial to understand the different types of input data because each provides essential but distinct information for drastically reducing the solution space of the clonal reconstruction problem. Complementary information provided by single cell sequencing or from whole genome sequencing of randomly isolated clones can also improve the accuracy of clonal reconstruction. We briefly review the existing algorithms and their relationships. Finally we summarize the tools that are developed for either directly solving the clonal reconstruction problem or a related computational problem.Conclusions: In this review, we discuss the various formulations of the problem of inferring the clonal evolutionary history from allele frequeny data, review existing algorithms and catergorize them according to their problem formulation and solution approaches. We note that most of the available clonal inference algorithms were developed for elucidating tumor evolution whereas clonal reconstruction for unicellular genomes are less addressed. We conclude the review by discussing more open problems such as the lack of benchmark datasets and comparison of performance between available tools.     

Application of a dissimilarity index of EEG and its sub-bands on prediction of induced epileptic seizures from rat's EEG signals

ObjectiveEpileptic seizures are defined as manifest of excessive and hyper-synchronous activity of neurons in the cerebral cortex that cause frequent malfunction of the human central nervous system. Therefore, finding precursors and predictors of epileptic seizure is of utmost clinical relevance to reduce the epileptic seizure induced nervous system malfunction consequences. Researchers for this purpose may even guide us to a deep understanding of the seizure generating mechanisms. The goal of this paper is to predict epileptic seizures in epileptic rats.MethodsSeizures were induced in rats using pentylenetetrazole (PTZ) model. EEG signals in interictal, preictal, ictal and postictal periods were then recorded and analyzed to predict epileptic seizures. Epileptic seizures were predicted by calculating an index in consecutive windows of EEG signal and comparing the index with a threshold. In this work, a newly proposed dissimilarity index called Bhattacharyya Based Dissimilarity Index (BBDI), dynamical similarity index and fuzzy similarity index were investigated.ResultsBBDI, dynamical similarity index and fuzzy similarity index were examined on case and control groups and compared to each other. The results show that BBDI outperforms dynamical and fuzzy similarity indices. In order to improve the results, EEG sub-bands were also analyzed. The best result achieved when the proposed dissimilarity index was applied on Delta sub-band that predicts epileptic seizures in all rats with a mean of 299.5 s.ConclusionThe dissimilarity of neural network activity between reference window and present window of EEG signal has a significant increase prior to an epileptic seizure and the proposed dissimilarity index (BBDI) can reveal this variation to predict epileptic seizures. In addition, analyzing EEG sub-bands results in more accurate information about constituent neuronal activities underlying the EEG since certain changes in EEG signal may be amplified when each sub-band is analyzed separately.SignificanceThis paper presents application of a dissimilarity index (BBDI) on EEG signals and its sub-bands to predict PTZ-induced epileptic seizures in rats. Based on the results of this work, BBDI will predict epileptic seizures more accurately and more reliably compared to current indices that increases epileptic patient comfort and improves patient outcomes.     

Constructing logical models of gene regulatory networks by integrating transcription factor-DNA interactions with expression data: an entropy-based approach

Models of gene regulatory networks (GRNs) attempt to explain the complex processes that determine cells' behavior, such as differentiation, metabolism, and the cell cycle. The advent of high-throughput data generation technologies has allowed researchers to fit theoretical models to experimental data on gene-expression profiles. GRNs are often represented using logical models. These models require that real-valued measurements be converted to discrete levels, such as on/off, but the discretization often introduces inconsistencies into the data. Dimitrova et al. posed the problem of efficiently finding a parsimonious resolution of the introduced inconsistencies. We show that reconstruction of a logical GRN that minimizes the errors is NP-complete, so that an efficient exact algorithm for the problem is not likely to exist. We present a probabilistic formulation of the problem that circumvents discretization of expression data. We phrase the problem of error reduction as a minimum entropy problem, develop a heuristic algorithm for it, and evaluate its performance on mouse embryonic stem cell data. The constructed model displays high consistency with prior biological knowledge. Despite the oversimplification of a discrete model, we show that it is superior to raw experimental measurements and demonstrates a highly significant level of identical regulatory logic among co-regulated genes. A software implementing the method is freely available at: http://acgt.cs.tau.ac.il/modent.