Analysis of Signal Decomposition and Stain Separation methods for biomedical applications

Nowadays, the biomedical signal processing and classification and medical image interpretation play an essential role in the detection and diagnosis of several human diseases. The problem of high variability and heterogeneity of information, which is extracted from digital data, can be addressed with signal decomposition and stain separation techniques which can be useful approaches to highlight hidden patterns or rhythms in biological signals and specific cellular structures in histological color images, respectively. This thesis work can be divided into two macro-sections. In the first part (Part I), a novel cascaded RNN model based on long short-term memory (LSTM) blocks is presented with the aim to classify sleep stages automatically. A general workflow based on single-channel EEG signals is developed to enhance the low performance in staging N1 sleep without reducing the performances in the other sleep stages (i.e. Wake, N2, N3 and REM). In the same context, several signal decomposition techniques and time-frequency representations are deployed for the analysis of EEG signals. All extracted features are analyzed by using a novel correlation-based timestep feature selection and finally the selected features are fed to a bidirectional RNN model. In the second part (Part II), a fully automated method named SCAN (Stain Color Adaptive Normalization) is proposed for the separation and normalization of staining in digital pathology. This normalization system allows to standardize digitally, automatically and in a few seconds, the color intensity of a tissue slide with respect to that of a target image, in order to improve the pathologist’s diagnosis and increase the accuracy of computer-assisted diagnosis (CAD) systems. Multiscale evaluation and multi-tissue comparison are performed for assessing the robustness of the proposed method. In addition, a stain normalization based on a novel mathematical technique, named ICD (Inverse Color Deconvolution) is developed for immunohistochemical (IHC) staining in histopathological images. In conclusion, the proposed techniques achieve satisfactory results compared to state-of-the-art methods in the same research field. The workflow proposed in this thesis work and the developed algorithms can be employed for the analysis and interpretation of other biomedical signals and for digital medical image analysis

Multilayer brain network combined with deep convolutional neural network for detecting major depressive disorder

Acknowledgements This work was supported in part by the National Natural Science Foundation of China under Grants Nos. 61922062 and 61873181.Peer reviewedPostprin

A review of automated sleep stage scoring based on physiological signals for the new millennia

Background and Objective: Sleep is an important part of our life. That importance is highlighted by the multitude of health problems which result from sleep disorders. Detecting these sleep disorders requires an accurate interpretation of physiological signals. Prerequisite for this interpretation is an understanding of the way in which sleep stage changes manifest themselves in the signal waveform. With that understanding it is possible to build automated sleep stage scoring systems. Apart from their practical relevance for automating sleep disorder diagnosis, these systems provide a good indication of the amount of sleep stage related information communicated by a specific physiological signal. Methods: This article provides a comprehensive review of automated sleep stage scoring systems, which were created since the year 2000. The systems were developed for Electrocardiogram (ECG), Electroencephalogram (EEG), Electrooculogram (EOG), and a combination of signals. Results: Our review shows that all of these signals contain information for sleep stage scoring. Conclusions: The result is important, because it allows us to shift our research focus away from information extraction methods to systemic improvements, such as patient comfort, redundancy, safety and cost

Automatic neonatal sleep stage classification:A comparative study

Sleep is an essential feature of living beings. For neonates, it is vital for their mental and physical development. Sleep stage cycling is an important parameter to assess neonatal brain and physical development. Therefore, it is crucial to administer newborn's sleep in the neonatal intensive care unit (NICU). Currently, Polysomnography (PSG) is used as a gold standard method for classifying neonatal sleep patterns, but it is expensive and requires a lot of human involvement. Over the last two decades, multiple researchers are working on automatic sleep stage classification algorithms using electroencephalography (EEG), electrocardiography (ECG), and video. In this study, we present a comprehensive review of existing algorithms for neonatal sleep, their limitations and future recommendations. Additionally, a brief comparison of the extracted features, classification algorithms and evaluation parameters is reported in the proposed study

Machine learning with ensemble stacking model for automated sleep staging using dual-channel EEG signal

Abstract Sleep staging is an important part of diagnosing the different types of sleep-related disorders because any discrepancies in the sleep scoring process may cause serious health problems such as misinterpretations of sleep patterns, medication errors, and improper diagnosis. The best way of analyzing sleep staging is visual interpretations of the polysomnography (PSG) signals recordings from the patients, which is a quite tedious task, requires more domain experts, and time-consuming process. This proposed study aims to develop a new automated sleep staging system using the brain EEG signals. Based on a new automated sleep staging system based on an ensemble learning stacking model that integrates Random Forest (RF) and eXtreme Gradient Boosting (XGBoosting). Additionally, this proposed methodology considers the subjects' age, which helps analyze the S1 sleep stage properly. In this study, both linear (time and frequency) and non-linear features are extracted from the pre-processed signals. The most relevant features are selected using the ReliefF weight algorithm. Finally, the selected features are classified through the proposed two-layer stacking model. The proposed methodology performance is evaluated using the two most popular datasets, such as the Sleep-EDF dataset (S-EDF) and Sleep Expanded-EDF database (SE-EDF) under the Rechtschaffen & Kales (R&K) sleep scoring rules. The performance of the proposed method is also compared with the existing published sleep staging methods. The comparison results signify that the proposed sleep staging system has an excellent improvement in classification accuracy for the six-two sleep states classification. In the S-EDF dataset, the overall accuracy and Cohen's kappa coefficient score obtained by the proposed model is (91.10%, 0.87) and (90.68%, 0.86) with inclusion and exclusion of age feature using the Fpz-Cz channel, respectively. Similarly, the Pz-Oz channel's performance is (90.56%, 0.86) with age feature and (90.11%, 0.86) without age feature. The performed results with the SE-EDF dataset using Fpz-Cz channel is (81.32%, 0.77) and (81.06%, 0.76), using Pz-Oz channel with the inclusion and exclusion of the age feature, respectively. Similarly the model achieved an overall accuracy of 96.67% (CT-6), 96.60% (CT-5), 96.28% (CT-4),96.30% (CT-3) and 97.30% (CT-2) for with 16 selected features using S-EDF database. Similarly the model reported an overall accuracy of 85.85%, 84.98%, 85.51%, 85.37% and 87.40% for CT-6 to CT-2 with 18 selected features using SE-EDF database

Data-efficient Deep Learning Approach for Single-Channel EEG-Based Sleep Stage Classification with Model Interpretability

Sleep, a fundamental physiological process, occupies a significant portion of our lives. Accurate classification of sleep stages serves as a crucial tool for evaluating sleep quality and identifying probable sleep disorders. Our work introduces a novel methodology that utilizes a SE-Resnet-Bi-LSTM architecture to classify sleep into five separate stages. The classification process is based on the analysis of single-channel electroencephalograms (EEGs). The suggested framework consists of two fundamental elements: a feature extractor that utilizes SE-ResNet, and a temporal context encoder that uses stacks of Bi-LSTM units. The effectiveness of our approach is substantiated by thorough assessments conducted on three different datasets, namely SleepEDF-20, SleepEDF-78, and SHHS. The proposed methodology achieves significant model performance, with Macro-F1 scores of 82.5, 78.9, and 81.9 for the respective datasets. We employ 1D-GradCAM visualization as a methodology to elucidate the decision-making process inherent in our model in the realm of sleep stage classification. This visualization method not only provides valuable insights into the model's classification rationale but also aligns its outcomes with the annotations made by sleep experts. One notable feature of our research lies in the incorporation of an efficient training approach, which adeptly upholds the model's resilience in terms of performance. The experimental evaluations provide a comprehensive evaluation of the effectiveness of our proposed model in comparison to the existing approaches, highlighting its potential for practical applications

A real-time Brain-Computer Interface (BCI) framework for sleep state stimulation using a deep-learning technique: proposal

Sleep disturbance can cause mental illnesses such as depression, hypertension, metabolic syndrome, and cognitive impairment. To date, various methods have been proposed as intervention measures for sleep disturbance, including taking a short mid-day nap. Falling asleep depends on several external factors, such as the ambience, temperature, sound, and lighting. On top of that, the factors that affect the quality and period of falling asleep can be subjective. The attempt to provide feedback based on the configuration of those external factors is time-consuming. Additionally, if those external factors are incorrectly configured, the intended short nap as a solution may have the opposite effects. As such, research on real-time sleep analysis plays an important role. However, the current study on deep-learning techniques regarding the sleep analysis that can give real-time results is still scarce compared to the offline sleep analysis. Therefore, this study aims to design and develop a real-time BCI framework for sleep state stimulation

A Real-Time Brain-Computer Interface (BCI) framework for sleep state stimulation using a deep-learning technique: proposal

Abstract— Sleep disturbance can cause mental illnesses such as depression, hypertension, metabolic syndrome, and cognitive impairment. To date, various methods have been proposed as intervention measures for sleep disturbance, including taking a short mid-day nap. Falling asleep depends on several external factors, such as the ambience, temperature, sound, and lighting. On top of that, the factors that affect the quality and period of falling asleep can be subjective. The attempt to provide feedback based on the configuration of those external factors is time-consuming. Additionally, if those external factors are incorrectly configured, the intended short nap as a solution may have the opposite effects. As such, research on real-time sleep analysis plays an important role. However, the current study on deep-learning techniques regarding the sleep analysis that can give real-time results is still scarce compared to the offline sleep analysis. Therefore, this study aims to design and develop a real-time BCI framework for sleep state stimulation

A hybrid deep learning scheme for multi-channel sleep stage classification

Sleep stage classification plays a significant role in the accurate diagnosis and treatment of sleep-related diseases. This study aims to develop an efficient deep learning based scheme for correctly identifying sleep stages using multi-biological signals such as electroencephalography (EEG), electrocardiogram (ECG), electromyogram (EMG), and electrooculogram (EOG). Most of the prior studies in sleep stage classification focus on hand-crafted feature extraction methods. Traditional hand-crafted feature extraction methods choose features manually from raw data, which is tedious, and these features are limited in their ability to balance efficiency and accuracy. Moreover, most of the existing works on sleep staging are either single channel (a single-lead EEG may not contain enough information) or only EEG signal based which can not reveal more complicated physical features for reliable classification of various sleep stages. This study proposes an approach to combine Convolutional Neural Networks (CNNs) and Gated Recurrent Units (GRUs) that can discover hidden features from multi-biological signal data to recognize the different sleep stages efficiently. In the proposed scheme, the CNN is designed to extract concealed features from the multi-biological signals, and the GRU is employed to automatically learn the transition rules among different sleep stages. After that, the softmax layers are used to classify various sleep stages. The proposed method was tested on two publicly available databases: Sleep Heart Health Study (SHHS) and St. Vincent’s University Hospital/University College Dublin Sleep Apnoea (UCDDB). The experimental results reveal that the proposed model yields better performance compared to state-of-the-art works. Our proposed scheme will assist in building a new system to deal with multi-channel or multi-modal signal processing tasks in various applications