A Python-based Brain-Computer Interface Package for Neural Data Analysis

Anowar, Md Hasan, A Python-based Brain-Computer Interface Package for Neural Data Analysis. Master of Science (MS), December, 2020, 70 pp., 4 tables, 23 figures, 74 references. Although a growing amount of research has been dedicated to neural engineering, only a handful of software packages are available for brain signal processing. Popular brain-computer interface packages depend on commercial software products such as MATLAB. Moreover, almost every brain-computer interface software is designed for a specific neuro-biological signal; there is no single Python-based package that supports motor imagery, sleep, and stimulated brain signal analysis. The necessity to introduce a brain-computer interface package that can be a free alternative for commercial software has motivated me to develop a toolbox using the python platform. In this thesis, the structure of MEDUSA, a brain-computer interface toolbox, is presented. The features of the toolbox are demonstrated with publicly available data sources. The MEDUSA toolbox provides a valuable tool to biomedical engineers and computational neuroscience researchers

Closed-loop modulation of local slow oscillations in human NREM sleep.

Slow-wave sleep is the deep non-rapid eye-movement (NREM) sleep stage that is most relevant for the recuperative function of sleep. Its defining property is the presence of slow oscillations (<2 Hz) in the scalp electroencephalogram (EEG). Slow oscillations are generated by a synchronous back and forth between highly active UP-states and silent DOWN-states in neocortical neurons. Growing evidence suggests that closed-loop sensory stimulation targeted at UP-states of EEG-defined slow oscillations can enhance the slow oscillatory activity, increase sleep depth, and boost sleep's recuperative functions. However, several studies failed to replicate such findings. Failed replications might be due to the use of conventional closed-loop stimulation algorithms that analyze the signal from one single electrode and thereby neglect the fact that slow oscillations vary with respect to their origins, distributions, and trajectories on the scalp. In particular, conventional algorithms nonspecifically target functionally heterogeneous UP-states of distinct origins. After all, slow oscillations at distinct sites of the scalp have been associated with distinct functions. Here we present a novel EEG-based closed-loop stimulation algorithm that allows targeting UP- and DOWN-states of distinct cerebral origins based on topographic analyses of the EEG: the topographic targeting of slow oscillations (TOPOSO) algorithm. We present evidence that the TOPOSO algorithm can detect and target local slow oscillations with specific, predefined voltage maps on the scalp in real-time. When compared to a more conventional, single-channel-based approach, TOPOSO leads to fewer but locally more specific stimulations in a simulation study. In a validation study with napping participants, TOPOSO targets auditory stimulation reliably at local UP-states over frontal, sensorimotor, and centro-parietal regions. Importantly, auditory stimulation temporarily enhanced the targeted local state. However, stimulation then elicited a standard frontal slow oscillation rather than local slow oscillations. The TOPOSO algorithm is suitable for the modulation and the study of the functions of local slow oscillations

C-Trend parameters and possibilities of federated learning

Abstract. In this observational study, federated learning, a cutting-edge approach to machine learning, was applied to one of the parameters provided by C-Trend Technology developed by Cerenion Oy. The aim was to compare the performance of federated learning to that of conventional machine learning. Additionally, the potential of federated learning for resolving the privacy concerns that prevent machine learning from realizing its full potential in the medical field was explored. Federated learning was applied to burst-suppression ratio’s machine learning and it was compared to the conventional machine learning of burst-suppression ratio calculated on the same dataset. A suitable aggregation method was developed and used in the updating of the global model. The performance metrics were compared and a descriptive analysis including box plots and histograms was conducted. As anticipated, towards the end of the training, federated learning’s performance was able to approach that of conventional machine learning. The strategy can be regarded to be valid because the performance metric values remained below the set test criterion levels. With this strategy, we will potentially be able to make use of data that would normally be kept confidential and, as we gain access to more data, eventually develop machine learning models that perform better. Federated learning has some great advantages and utilizing it in the context of qEEGs’ machine learning could potentially lead to models, which reach better performance by receiving data from multiple institutions without the difficulties of privacy restrictions. Some possible future directions include an implementation on heterogeneous data and on larger data volume.C-Trend-teknologian parametrit ja federoidun oppimisen mahdollisuudet. Tiivistelmä. Tässä havainnointitutkimuksessa federoitua oppimista, koneoppimisen huippuluokan lähestymistapaa, sovellettiin yhteen Cerenion Oy:n kehittämään C-Trend-teknologian tarjoamaan parametriin. Tavoitteena oli verrata federoidun oppimisen suorituskykyä perinteisen koneoppimisen suorituskykyyn. Lisäksi tutkittiin federoidun oppimisen mahdollisuuksia ratkaista yksityisyyden suojaan liittyviä rajoitteita, jotka estävät koneoppimista hyödyntämästä täyttä potentiaaliaan lääketieteen alalla. Federoitua oppimista sovellettiin purskevaimentumasuhteen koneoppimiseen ja sitä verrattiin purskevaimentumasuhteen laskemiseen, johon käytettiin perinteistä koneoppimista. Kummankin laskentaan käytettiin samaa dataa. Sopiva aggregointimenetelmä kehitettiin, jota käytettiin globaalin mallin päivittämisessä. Suorituskykymittareiden tuloksia verrattiin keskenään ja tehtiin kuvaileva analyysi, johon sisältyi laatikkokuvioita ja histogrammeja. Odotetusti opetuksen loppupuolella federoidun oppimisen suorituskyky pystyi lähestymään perinteisen koneoppimisen suorituskykyä. Menetelmää voidaan pitää pätevänä, koska suorituskykymittarin arvot pysyivät alle asetettujen testikriteerien tasojen. Tämän menetelmän avulla voimme ehkä hyödyntää dataa, joka normaalisti pidettäisiin salassa, ja kun saamme lisää dataa käyttöömme, voimme lopulta kehittää koneoppimismalleja, jotka saavuttavat paremman suorituskyvyn. Federoidulla oppimisella on joitakin suuria etuja, ja sen hyödyntäminen qEEG:n koneoppimisen yhteydessä voisi mahdollisesti johtaa malleihin, jotka saavuttavat paremman suorituskyvyn saamalla tietoja useista eri lähteistä ilman yksityisyyden suojaan liittyviä rajoituksia. Joitakin mahdollisia tulevia suuntauksia ovat muun muassa heterogeenisen datan ja suurempien tietomäärien käyttö

Ultra-high precision grinding of BK7 glass

With the increase in the application of ultra-precision manufactured parts and the absence of much participation of researchers in ultra-high precision grinding of optical glasses which has a high rate of demand in the industries, it becomes imperative to garner a full understanding of the production of these precision optics using the above-listed technology. Single point inclined axes grinding configuration and Box-Behnken experimental design was developed and applied to the ultra-high precision grinding of BK7 glass. A high sampling acoustic emission monitoring system was implemented to monitor the process. The research tends to monitor the ultra-high precision grinding of BK7 glass using acoustic emission which has proven to be an effective sensing technique to monitor grinding processes. Response surface methodology was adopted to analyze the effect of the interaction between the machining parameters: feed, speed, depth of cut and the generated surface roughness. Furthermore, back propagation Artificial Neural Network was also implemented through careful feature extraction and selection process. The proposed models are aimed at creating a database guide to the ultra-high precision grinding of precision optics

Towards electrodeless EMG linear envelope signal recording for myo-activated prostheses control

After amputation, the residual muscles of the limb may function in a normal way, enabling the electromyogram (EMG) signals recorded from them to be used to drive a replacement limb. These replacement limbs are called myoelectric prosthesis. The prostheses that use EMG have always been the first choice for both clinicians and engineers. Unfortunately, due to the many drawbacks of EMG (e.g. skin preparation, electromagnetic interferences, high sample rate, etc.); researchers have aspired to find suitable alternatives. One proposes the dry-contact, low-cost sensor based on a force-sensitive resistor (FSR) as a valid alternative which instead of detecting electrical events, detects mechanical events of muscle. FSR sensor is placed on the skin through a hard, circular base to sense the muscle contraction and to acquire the signal. Similarly, to reduce the output drift (resistance) caused by FSR edges (creep) and to maintain the FSR sensitivity over a wide input force range, signal conditioning (Voltage output proportional to force) is implemented. This FSR signal acquired using FSR sensor can be used directly to replace the EMG linear envelope (an important control signal in prosthetics applications). To find the best FSR position(s) to replace a single EMG lead, the simultaneous recording of EMG and FSR output is performed. Three FSRs are placed directly over the EMG electrodes, in the middle of the targeted muscle and then the individual (FSR1, FSR2 and FSR3) and combination of FSR (e.g. FSR1+FSR2, FSR2-FSR3) is evaluated. The experiment is performed on a small sample of five volunteer subjects. The result shows a high correlation (up to 0.94) between FSR output and EMG linear envelope. Consequently, the usage of the best FSR sensor position shows the ability of electrode less FSR-LE to proportionally control the prosthesis (3-D claw). Furthermore, FSR can be used to develop a universal programmable muscle signal sensor that can be suitable to control the myo-activated prosthesis

Analysis of sleep EEG signal

Cílem této práce byl vývoj programu pro automatickou detekci arousalu v signálu spánkového EEG s použitím metod časově-frekvenční analýzy. Předmětem studie bylo 13 celonočních polysomnografických nahrávek (čtyři svody EEG, EMG, EKG a EOG), tj. celkově více než 100 hodin záznamu. Jednalo se o část dat z dřívějších výzkumných prací expertní lékařky v problematice spánku Dr. Emilie Sforzy, Ženeva, Švýcarsko, která rovněž poskytla základní hodnocení těchto dat. V záznamech bylo celkem označeno 1551 arousal událostí. Pro usnadnění výběru konkrétní metody časově-frekvenční analýzy byla následně vytvořena sada nástrojů pro vizualizaci jednotlivých signálů a jejich různých časově-frekvenčních vyjádření. S ohledem na závěry vizuální analýzy, charakter signálu EEG a efektivitu výpočetních metod byla pro analýzu vybrána waveletová transformace s mateřskou vlnkou Daubechies řádu 6. Jednotlivé svody EEG byly dekomponovány do šesti frekvenčních pásem. Z takto odvozených signálů a signálu EMG byly následně stanoveny ukazatele možné přítomnosti události arousalu. Tyto ukazatele byly dále váhovány lineárním klasifikátorem, jehož hodnoty vah byly optimalizovány pomocí genetického algoritmu. Na základě hodnoty lineárního klasifikátoru bylo rozhodnuto o přítomnosti události arousalu v daném svodě EEG – arousal byl detekován, jestliže hodnota klasifikátoru překročila danou mez na dobu více než 3 a méně než 30 vteřin. V celém záznamu pak byl arousal označen, byl-li detekován alespoň v jednom ze svodů EEG. Následně byly odvozeny míry senzitivity a selektivity detekce, jež byly rovněž základem pro stanovení fitness funkce genetického algoritmu. Pro učení genetického algoritmu byly vybrány první čtyři záznamy. Na základě takto optimalizovaných vah vznikl program pro automatickou detekci, který na celém souboru 13 záznamů dosáhl ve srovnání s expertním hodnocením míry senzitivity 76,09%, selektivity 53,26% a specificity 97,66%.The aim of this study was to develop an automatic detection program for scoring the sleep EEG arousals, based on one of time-frequency analysis methods. The subject of the study was 13 overnight polysomnographic recordings (four leads of EEG, EMG, ECG and EOG), i.e over 100 hours in total. It was a subset of data used in former studies by sleep expert Dr. Emilia Sforza, Geneva, Switzerland, who also provided baseline arousal scoring. Total number of 1551 arousal events were marked in the recordings. Next, several tools for recordings' visualization were developed to facilitate the decision on methods of analysis. Following the conclusions made after extensive visualization of input recordings in different time-frequency representations and regarding the character of EEG as neuroelectric waveforms and computing efficiency, discrete wavelet decomposition with Daubechies order 6 mother wavelet was chosen. The EEG signals were decomposed into six frequency bands. The results together with EMG recordings were used to evaluate a set of indices describing EEG and EMG changes accompanying arousals. These indices were weighted to form linear classifier of microarousal suspicion in each EEG lead – a microarousal was marked as present when it remained suspect in period of 3 to 30 seconds. Outputs of four EEG channels were then integrated to report final outcome. Based on sensitivity and selectivity measures the algorithm was optimized by genetic algorithm. The subject of tuning were the linear classifier parameters and first four of 13 recordings were selected as training data. A microarousal detection program emerged on basis of the tuned algorithm and resulted in average sensitivity of 76,09 %, selectivity of 53,26 % and 97,66 % specificity over all 13 recordings compared to expert visual scorings.

Automation of Sleep Staging

This thesis primarily covers the automation problem for sleep versus awake detection, which is sometimes accomplished by differentiating the various sleep stages prior to clustering. This thesis documents various experimentation into areas where the performance can be improved, including classifer design and feature selection from EEG, EOG and Context. In terms of classifers, it was found that the neural network MLP outperforms the continuous Hidden Markov Model with an accuracy of 91.91%, and additional performance requires better feature sets and more training data. Improved EEG features based on time frequency representation were optimized to differentiate Awake with 93.52% sensitivity and 94.60% specificity, differentiate REM with 96.12% sensitivity and 93.63% specificity, differentiate Stages II and III with 96.81% sensitivity and 89.28% specificity, and differentiate Stages III and IV with 93.60% sensitivity and 90.43% specificity. Due to the limited data set, an example of applying contextual information using a One-Cycle-Duo-Direction model was built and shown to improve EEG features by up to 10%. This level of performance is comparable if not superior to the human scorer accuracy of 88% to 94%. This thesis improved some aspects of sleep staging automation, but due to the limitations on resources, the full potential of these improvements could not be demonstrated. To further develop these improvements, additional data sets customized by sleep staging experts is crucial

Deep learning for automated sleep monitoring

Wearable electroencephalography (EEG) is a technology that is revolutionising the longitudinal monitoring of neurological and mental disorders, improving the quality of life of patients and accelerating the relevant research. As sleep disorders and other conditions related to sleep quality affect a large part of the population, monitoring sleep at home, over extended periods of time could have significant impact on the quality of life of people who suffer from these conditions. Annotating the sleep architecture of patients, known as sleep stage scoring, is an expensive and time-consuming process that cannot scale to a large number of people. Using wearable EEG and automating sleep stage scoring is a potential solution to this problem. In this thesis, we propose and evaluate two deep learning algorithms for automated sleep stage scoring using a single channel of EEG. In our first method, we use time-frequency analysis for extracting features that closely follow the guidelines that human experts follow, combined with an ensemble of stacked sparse autoencoders as our classification algorithm. In our second method, we propose a convolutional neural network (CNN) architecture for automatically learning filters that are specific to the problem of sleep stage scoring. We achieved state-of-the-art results (mean F1-score 84%; range 82-86%) with our first method and comparably good results with the second (mean F1-score 81%; range 79-83%). Both our methods effectively account for the skewed performance that is usually found in the literature due to sleep stage duration imbalance. We propose a filter analysis and visualisation methodology for CNNs to understand the filters that CNNs learn. Our results indicate that our CNN was able to robustly learn filters that closely follow the sleep scoring guidelines.Open Acces

Automatic Sleep EEG Pattern Detection

Analýza mozkové aktivity je jednou z klícových vyšetrovacích metod v moderní spánkové medicíne a výzkumu.nalysis of recorded brain activity is one of the main investigation methods in modern sleep medicine and research

From End to End: Gaining, Sorting, and Employing High-Density Neural Single Unit Recordings

The meaning behind neural single unit activity has constantly been a challenge, so it will persist in the foreseeable future. As one of the most sourced strategies, detecting neural activity in high-resolution neural sensor recordings and then attributing them to their corresponding source neurons correctly, namely the process of spike sorting, has been prevailing so far. Support from ever-improving recording techniques and sophisticated algorithms for extracting worthwhile information and abundance in clustering procedures turned spike sorting into an indispensable tool in electrophysiological analysis. This review attempts to illustrate that in all stages of spike sorting algorithms, the past 5 years innovations' brought about concepts, results, and questions worth sharing with even the non-expert user community. By thoroughly inspecting latest innovations in the field of neural sensors, recording procedures, and various spike sorting strategies, a skeletonization of relevant knowledge lays here, with an initiative to get one step closer to the original objective: deciphering and building in the sense of neural transcript