Neonatal Seizure Detection using Convolutional Neural Networks

This study presents a novel end-to-end architecture that learns hierarchical representations from raw EEG data using fully convolutional deep neural networks for the task of neonatal seizure detection. The deep neural network acts as both feature extractor and classifier, allowing for end-to-end optimization of the seizure detector. The designed system is evaluated on a large dataset of continuous unedited multi-channel neonatal EEG totaling 835 hours and comprising of 1389 seizures. The proposed deep architecture, with sample-level filters, achieves an accuracy that is comparable to the state-of-the-art SVM-based neonatal seizure detector, which operates on a set of carefully designed hand-crafted features. The fully convolutional architecture allows for the localization of EEG waveforms and patterns that result in high seizure probabilities for further clinical examination.Comment: IEEE International Workshop on Machine Learning for Signal Processin

Dynamic classifiers for neonatal brain monitoring

Brain injury due to lack of oxygen or impaired blood flow around the time of birth, may cause long term neurological dysfunction or death in severe cases. The treatments need to be initiated as soon as possible and tailored according to the nature of the injury to achieve best outcomes. The Electroencephalogram (EEG) currently provides the best insight into neurological activities. However, its interpretation presents formidable challenge for the neurophsiologists. Moreover, such expertise is not widely available particularly around the clock in a typical busy Neonatal Intensive Care Unit (NICU). Therefore, an automated computerized system for detecting and grading the severity of brain injuries could be of great help for medical staff to diagnose and then initiate on-time treatments. In this study, automated systems for detection of neonatal seizures and grading the severity of Hypoxic-Ischemic Encephalopathy (HIE) using EEG and Heart Rate (HR) signals are presented. It is well known that there is a lot of contextual and temporal information present in the EEG and HR signals if examined at longer time scale. The systems developed in the past, exploited this information either at very early stage of the system without any intelligent block or at very later stage where presence of such information is much reduced. This work has particularly focused on the development of a system that can incorporate the contextual information at the middle (classifier) level. This is achieved by using dynamic classifiers that are able to process the sequences of feature vectors rather than only one feature vector at a time

Spontaanien aktiviteettipurskeiden automaattinen tunnistus keskosten aivosähkökäyrästä

Very preterm infants may require neonatal intensive care for several months, and the developmental outcome of the care depends on how well brain function can be managed. Direct monitoring of brain function with electroencephalography (EEG) is currently not a part of routine care, since it is perceived challenging due to difficulties in its interpretation. Therefore, automated methods for EEG interpretation are needed in order to make brain monitoring part of the routine in neonatal intensive care. This thesis investigates the detection of spontaneous activity transients (SATs), which form the majority of brain activity in preterm infants. Using manual markings by three doctors in 18 short recordings of preterm EEG, I show that SATs can be recognized by doctors in a consistent manner. A commercially available algorithm is then tested for its ability to detect SATs automatically. The performance of the algorithm is clearly insufficient and therefore it is developed further. The parameters of the new, streamlined algorithm are optimized using unanimous markings by the three doctors as a gold standard. Estimates for the performance of the algorithm on unseen data are obtained by running the optimization 18 times, each time leaving out one of the recordings. The algorithm is then run on the EEG left out from the optimization using the optimized parameters. The estimated performance of the algorithm is found to be excellent, with sensitivity of 96.6 +- 2.8 % and specificity of 95.1 +- 5.6 %. Segmentation of the EEG into SATs and periods between SATs is a starting point for further analysis. One promising direction for future studies is to use SAT%, the proportion of time covered by SATs, to detect cycles of different vigilance stages in preterm infants. Such cyclicity could become a marker of the brain's wellbeing. The algorithm presented in this thesis may contribute to better care of preterm infants.Erittäin ennenaikaisesti syntyneet keskoset saattavat tarvita teho-osastohoitoa jopa kuukausien ajan. Hoidon vaikutus lapsen kehitykseen riippuu paljon siitä, kuinka hyvin aivojen hoito onnistuu. Aivojen toiminnan jatkuva valvonta elektroenkefalografian (EEG) avulla ei vielä kuulu tavanomaiseen hoitokäytäntöön, koska EEG:n tulkintaa pidetään vaikeana. EEG:n tulkintaan tarvitaankin automaattisia menetelmiä, jotta aivojen tarkkailusta tulisi osa vastasyntyneiden tehohoidon rutiinia. Tässä työssä tutkitaan spontaanien aktiviteettipurskeiden tunnistamista (engl. spontaneous activity transient, SAT). Keskosten aivotoiminta muodostuu suurelta osin aktiviteettipurskeista. Käyttämällä kolmen lääkärin käsin tehtyjä merkintöjä aktiviteettipurskeista 18 lyhyessä keskosilta mitatussa EEG:ssä todistan, että lääkärit tunnistavat aktiviteettipurskeet johdonmukaisesti. Tämän jälkeen testaan, sopiiko eräs myynnissä oleva algoritmi aktiviteettipurskeiden automaattiseen tunnistukseen. Algoritmin suorituskyky ei ole riittävä, joten kehitän siitä paremman version. Uuden, parannellun algoritmin parametrit optimoidaan käyttämällä opetusaineistona niitä EEGjaksoja, joiden luokittelusta kaikki kolme lääkäriä olivat yhtä mieltä. Algoritmin suorituskykyä arvioidaan suorittamalla optimointi 18 kertaa siten, että kullakin kerralla yksi mittauksista jätetään pois opetusaineistosta. Optimoitua menetelmää käytetään sitten aktiviteettipurskeiden tunnistamiseen poisjätetyssä mittauksessa. Algoritmin arvioitu suorituskyky on erinomainen; sen sensitiivisyys on 96,6 +- 2,8 % ja spesifisyys 95,1 +- 5,6 %. EEG:n segmentointi aktiviteettipurskeisiin ja niiden välisiin jaksoihin tarjoaa pohjan jatkoanalyysille. Aktiviteettipurskeiden osuutta EEG:stä (SAT%) voidaan mahdollisesti käyttää keskosen vireystilan vaihtelujen seuraamiseen. Vireystilojen säännöllinen vaihtelu saattaa olla merkki aivojen hyvinvoinnista. Tässä työssä esitelty algoritmi voi osaltaan edesauttaa keskosten hoidon kehittymistä entistä paremmaksi

Brain Dynamics Based Automated Epileptic Seizure Detection

abstract: Approximately 1% of the world population suffers from epilepsy. Continuous long-term electroencephalographic (EEG) monitoring is the gold-standard for recording epileptic seizures and assisting in the diagnosis and treatment of patients with epilepsy. However, this process still requires that seizures are visually detected and marked by experienced and trained electroencephalographers. The motivation for the development of an automated seizure detection algorithm in this research was to assist physicians in such a laborious, time consuming and expensive task. Seizures in the EEG vary in duration (seconds to minutes), morphology and severity (clinical to subclinical, occurrence rate) within the same patient and across patients. The task of seizure detection is also made difficult due to the presence of movement and other recording artifacts. An early approach towards the development of automated seizure detection algorithms utilizing both EEG changes and clinical manifestations resulted to a sensitivity of 70-80% and 1 false detection per hour. Approaches based on artificial neural networks have improved the detection performance at the cost of algorithm's training. Measures of nonlinear dynamics, such as Lyapunov exponents, have been applied successfully to seizure prediction. Within the framework of this MS research, a seizure detection algorithm based on measures of linear and nonlinear dynamics, i.e., the adaptive short-term maximum Lyapunov exponent (ASTLmax) and the adaptive Teager energy (ATE) was developed and tested. The algorithm was tested on long-term (0.5-11.7 days) continuous EEG recordings from five patients (3 with intracranial and 2 with scalp EEG) and a total of 56 seizures, producing a mean sensitivity of 93% and mean specificity of 0.048 false positives per hour. The developed seizure detection algorithm is data-adaptive, training-free and patient-independent. It is expected that this algorithm will assist physicians in reducing the time spent on detecting seizures, lead to faster and more accurate diagnosis, better evaluation of treatment, and possibly to better treatments if it is incorporated on-line and real-time with advanced neuromodulation therapies for epilepsy.Dissertation/ThesisM.S. Electrical Engineering 201

Accurate wearable heart rate monitoring during physical exercises using PPG

Objective: The challenging task of heart rate (HR) estimation from the photoplethysmographic (PPG) signal, during intensive physical exercises is tackled in this paper. Methods: The study presents a detailed analysis of a novel algorithm (WFPV) that exploits a Wiener filter to attenuate the motion artifacts, a phase vocoder to refine the HR estimate and user-adaptive postprocessing to track the subject physiology. Additionally, an offline version of the HR estimation algorithm that uses Viterbi decoding is designed for scenarios that do not require online HR monitoring (WFPV+VD). The performance of the HR estimation systems is rigorously compared with existing algorithms on the publically available database of 23 PPG recordings. Results: On the whole dataset of 23 PPG recordings, the algorithms result in average absolute errors of 1.97 and 1.37 BPM in the online and offline modes, respectively. On the test dataset of 10 PPG recordings which were most corrupted with motion artifacts, WFPV has an error of 2.95 BPM on its own and 2.32 BPM in an ensemble with 2 existing algorithms. Conclusion: The error rate is significantly reduced when compared with the state-of-the art PPG-based HR estimation methods. Significance: The proposed system is shown to be accurate in the presence of strong motion artifacts and in contrast to existing alternatives has very few free parameters to tune. The algorithm has a low computational cost and can be used for fitness tracking and health monitoring in wearable devices. The Matlab implementation of the algorithm is provided online

Artefact detection and removal algorithms for EEG diagnostic systems

The electroencephalogram (EEG) is a medical technology that is used in the monitoring of the brain and in the diagnosis of many neurological illnesses. Although coarse in its precision, the EEG is a non-invasive tool that requires minimal set-up times, and is suitably unobtrusive and mobile to allow continuous monitoring of the patient, either in clinical or domestic environments. Consequently, the EEG is the current tool-of-choice with which to continuously monitor the brain where temporal resolution, ease-of- use and mobility are important. Traditionally, EEG data are examined by a trained clinician who identifies neurological events of interest. However, recent advances in signal processing and machine learning techniques have allowed the automated detection of neurological events for many medical applications. In doing so, the burden of work on the clinician has been significantly reduced, improving the response time to illness, and allowing the relevant medical treatment to be administered within minutes rather than hours. However, as typical EEG signals are of the order of microvolts (μV ), contamination by signals arising from sources other than the brain is frequent. These extra-cerebral sources, known as artefacts, can significantly distort the EEG signal, making its interpretation difficult, and can dramatically disimprove automatic neurological event detection classification performance. This thesis therefore, contributes to the further improvement of auto- mated neurological event detection systems, by identifying some of the major obstacles in deploying these EEG systems in ambulatory and clinical environments so that the EEG technologies can emerge from the laboratory towards real-world settings, where they can have a real-impact on the lives of patients. In this context, the thesis tackles three major problems in EEG monitoring, namely: (i) the problem of head-movement artefacts in ambulatory EEG, (ii) the high numbers of false detections in state-of-the-art, automated, epileptiform activity detection systems and (iii) false detections in state-of-the-art, automated neonatal seizure detection systems. To accomplish this, the thesis employs a wide range of statistical, signal processing and machine learning techniques drawn from mathematics, engineering and computer science. The first body of work outlined in this thesis proposes a system to automatically detect head-movement artefacts in ambulatory EEG and utilises supervised machine learning classifiers to do so. The resulting head-movement artefact detection system is the first of its kind and offers accurate detection of head-movement artefacts in ambulatory EEG. Subsequently, addtional physiological signals, in the form of gyroscopes, are used to detect head-movements and in doing so, bring additional information to the head- movement artefact detection task. A framework for combining EEG and gyroscope signals is then developed, offering improved head-movement arte- fact detection. The artefact detection methods developed for ambulatory EEG are subsequently adapted for use in an automated epileptiform activity detection system. Information from support vector machines classifiers used to detect epileptiform activity is fused with information from artefact-specific detection classifiers in order to significantly reduce the number of false detections in the epileptiform activity detection system. By this means, epileptiform activity detection which compares favourably with other state-of-the-art systems is achieved. Finally, the problem of false detections in automated neonatal seizure detection is approached in an alternative manner; blind source separation techniques, complimented with information from additional physiological signals are used to remove respiration artefact from the EEG. In utilising these methods, some encouraging advances have been made in detecting and removing respiration artefacts from the neonatal EEG, and in doing so, the performance of the underlying diagnostic technology is improved, bringing its deployment in the real-world, clinical domain one step closer

Human Intracranial High Frequency Oscillation Detection Using Time Frequency Analysis and Its Relation to the Seizure Onset Zone

One third of the patients diagnosed with focal epilepsy do not respond to antiepileptic drugs. For these patients the possible diagnosis options to give seizure freedom or at least reduce seizure frequencies significantly would be surgical resection or seizure interrupting implantable devices. The success of these procedures depends on accurate detection of the region causing seizure also known as epileptic zone. This requires detail pre-surgical evaluation including Invasive Video Electroencephalographic Monitoring (IVEM). The resulting great volume of intracranial Electroencephalography (iEEG) signal is visually examined by an expert epileptologist which can be time consuming, extremely complex, and not always effective. We have introduced an automated method to help the epileptologist analyze the iEEG signals. Literature suggest that signals recorded from brain regions subject to seizure activity produce a short durational high gamma ripple activity in the iEEG called High Frequency Oscillations (HFOs). The algorithm presented in this thesis uses an automated time-frequency space analysis method to detect HFOs and distinguish them from high frequency artifacts. As HFOs are short-lived high frequency oscillations, the time-frequency space analysis method chosen should have good time and frequency resolution capabilities. The Stockwell transform was used for this purpose which is a variable window version of the Short Time Fourier Transform (STFT). We have modified the detection algorithm to analyze the multi-channel iEEG data obtained from patients monitored at the Spectrum Health Epilepsy Monitoring Unit (EMU) and found that the electrode site recordings exhibiting higher HFO rate are within the Seizure Onset Zone (SOZ) determined by visual examination of the iEEG recordings by the epileptologist. These electrodes also continue to show higher HFO rate throughout the entire study. The HFO analysis presented in this thesis suggests that HFO detection and identification may be used to reduce IVEM monitoring time by aiding the neurosurgeon delineating the epileptic zone in relatively shorter time. This will lead to better surgical outcome or succesful implantation of the seizure intervention devices