Selection of features for patient-independent detection of seizure events using scalp EEG signals

A Shallow Autoencoder Framework for Epileptic Seizure Detection in EEG Signals

This paper presents a trainable hybrid approach involving a shallow autoencoder (AE) and a conventional classifier for epileptic seizure detection. The signal segments of a channel of electroencephalogram (EEG) (EEG epochs) are classified as epileptic and non-epileptic by employing its encoded AE representation as a feature vector. Analysis on a single channel-basis and the low computational complexity of the algorithm allow its use in body sensor networks and wearable devices using one or few EEG channels for wearing comfort. This enables the extended diagnosis and monitoring of epileptic patients at home. The encoded representation of EEG signal segments is obtained based on training the shallow AE to minimize the signal reconstruction error. Extensive experimentation with classifiers has led us to propose two versions of our hybrid method: (a) one yielding the best classification performance compared to the reported methods using the k-nearest neighbor (kNN) classifier and (b) the second with a hardware-friendly architecture and yet with the best classification performance compared to other reported methods in this category using a support-vector machine (SVM) classifier. The algorithm is evaluated on the Children's Hospital Boston, Massachusetts Institute of Technology (CHB-MIT), and University of Bonn EEG datasets. The proposed method achieves 98.85% accuracy, 99.29% sensitivity, and 98.86% specificity on the CHB-MIT dataset using the kNN classifier. The best figures using the SVM classifier for accuracy, sensitivity, and specificity are 99.19%, 96.10%, and 99.19%, respectively. Our experiments establish the superiority of using an AE approach with a shallow architecture to generate a low-dimensionality yet effective EEG signal representation capable of high-performance abnormal seizure activity detection at a single-channel EEG level and with a fine granularity of 1 s EEG epochs.

Patient-independent seizure detection based on long-term iEEG and a novel lightweight CNN

Objective.Patient-dependent seizure detection based on intracranial electroencephalography (iEEG) has made significant progress. However, due to the difference in the locations and number of iEEG electrodes used for each patient, patient-independent seizure detection based on iEEG has not been carried out. Additionally, current seizure detection algorithms based on deep learning have outperformed traditional machine learning algorithms in many performance metrics. However, they still have shortcomings of large memory footprints and slow inference speed.Approach.To solve the above problems of the current study, we propose a novel lightweight convolutional neural network model combining the Convolutional Block Attention Module (CBAM). Its performance for patient-independent seizure detection is evaluated on two long-term continuous iEEG datasets: SWEC-ETHZ and TJU-HH. Finally, we reproduce four other patient-independent methods to compare with our method and calculate the memory footprints and inference speed for all methods.Main results.Our method achieves 83.81% sensitivity (SEN) and 85.4% specificity (SPE) on the SWEC-ETHZ dataset and 86.63% SEN and 92.21% SPE on the TJU-HH dataset. In particular, it takes only 11 ms to infer 10 min iEEG (128 channels), and its memory footprint is only 22 kB. Compared to baseline methods, our method not only achieves better patient-independent seizure detection performance but also has a smaller memory footprint and faster inference speed.Significance.To our knowledge, this is the first iEEG-based patient-independent seizure detection study. This facilitates the application of seizure detection algorithms to the future clinic.

Supervised Machine Learning and Deep Learning Techniques for Epileptic Seizure Recognition Using EEG Signals-A Systematic Literature Review

Electroencephalography (EEG) is a complicated, non-stationary signal that requires extensive preprocessing and feature extraction approaches to be accurately analyzed. In recent times, Deep learning (DL) has shown great promise in exploiting the characteristics of EEG signals as it can learn relevant features from raw data autonomously. Although studies involving DL have become more common in the last two years, the topic of whether DL truly delivers advantages over conventional Machine learning (ML) methodologies remains unsettled. This study aims to present a detailed overview of the main challenges in the field of seizure detection, prediction, and classification utilizing EEG data, and the approaches taken to solve them using ML and DL methods. A systematic review was conducted surveying peer-reviewed publications published between 2017 and 16 July 2022 using two scientific databases (Web of Science and Scopus) totaling 6822 references after discarding duplicate publications. Whereas 2262 articles were screened based on the title, abstract, and keywords, only 214 were eligible for full-text assessment. A total of 91 papers have been included in this survey after meeting the eligible inclusion and exclusion criteria. The most significant findings from the review are summarized, and several important concepts involving ML and DL for seizure detection, prediction, and classification are discussed in further depth. This review aims to learn more about the different approaches for identifying different types and stages of epileptic seizures, which may then be employed to enhance the lives of epileptic patients in the future, as well as aid experts in the field.

A polygenic stacking classifier revealed the complicated platelet transcriptomic landscape of adult immune thrombocytopenia

Immune thrombocytopenia (ITP) is an autoimmune disease with the typical symptom of a low platelet count in blood. ITP demonstrated age and sex biases in both occurrences and prognosis, and adult ITP was mainly induced by the living environments. The current diagnosis guideline lacks the integration of molecular heterogenicity. This study recruited the largest cohort of platelet transcriptome samples. A comprehensive procedure of feature selection, feature engineering, and stacking classification was carried out to detect the ITP biomarkers using RNA sequencing (RNA-seq) transcriptomes. The 40 detected biomarkers were loaded to train the final ITP detection model, with an overall accuracy 0.974. The biomarkers suggested that ITP onset may be associated with various transcribed components, including protein-coding genes, long intergenic non-coding RNA (lincRNA) genes, and pseudogenes with apparent transcriptions. The delivered ITP detection model may also be utilized as a complementary ITP diagnosis tool. The code and the example dataset is freely available on http://www.healthinformaticslab.org/supp/resources.php

Bridging the Gap Between Patient-specific and Patient-independent Seizure Prediction via Knowledge Distillation

Deep neural networks (DNN) have shown unprecedented success in various brain-machine interface (BMI) applications such as epileptic seizure prediction. However, existing approaches typically train models in a patient-specific fashion due to the highly personalized characteristics of epileptic signals. Therefore, only a limited number of labeled recordings from each subject can be used for training. As a consequence, current DNN based methods demonstrate poor generalization ability to some extent due to the insufficiency of training data. On the other hand, patient-independent models attempt to utilize more patient data to train a universal model for all patients by pooling patient data together. Despite different techniques applied, results show that patient-independent models perform worse than patient-specific models due to high individual variation across patients. A substantial gap thus exists between patient-specific and patient-independent models. In this paper, we propose a novel training scheme based on knowledge distillation which makes use of a large amount of data from multiple subjects. It first distills informative features from signals of all available subjects with a pre-trained general model. A patient-specific model can then be obtained with the help of distilled knowledge and additional personalized data. The proposed training scheme significantly improves the performance of patient-specific seizure predictors and bridges the gap between patient-specific and patient-independent predictors. Five state-of-the-art seizure prediction methods are trained on the CHB-MIT sEEG database with our proposed scheme. The resulting accuracy, sensitivity, and false prediction rate show that our proposed training scheme consistently improves the prediction performance of state-of-the-art methods by a large margin.

A CNN based coronavirus disease prediction system for chest X-rays

Coronavirus disease (COVID-19) proliferated globally in early 2020, causing existential dread in the whole world. Radiography is crucial in the clinical staging and diagnosis of COVID-19 and offers high potential to improve healthcare plans for tackling the pandemic. However high variations in infection characteristics and low contrast between normal and infected regions pose great challenges in preparing radiological reports. To address these challenges, this study presents CODISC-CNN (CNN based Coronavirus DIsease Prediction System for Chest X-rays) that can automatically extract the features from chest X-ray images for the disease prediction. However, to get the infected region of X-ray, edges of the images are detected by applying image preprocessing. Furthermore, to attenuate the shortage of labeled datasets data augmentation has been adapted. Extensive experiments have been performed to classify X-ray images into two classes (Normal and COVID), three classes (Normal, COVID, and Virus Bacteria), and four classes (Normal, COVID, and Virus Bacteria, and Virus Pneumonia) with the accuracy of 97%, 89%, and 84% respectively. The proposed CNN-based model outperforms many cutting-edge classification models and boosts state-of-the-art performance.

A Novel Permutation Entropy-Based EEG Channel Selection for Improving Epileptic Seizure Prediction

The key research aspects of detecting and predicting epileptic seizures using electroencephalography (EEG) signals are feature extraction and classification. This paper aims to develop a highly effective and accurate algorithm for seizure prediction. Efficient channel selection could be one of the solutions as it can decrease the computational loading significantly. In this research, we present a patient-specific optimization method for EEG channel selection based on permutation entropy (PE) values, employing K nearest neighbors (KNNs) combined with a genetic algorithm (GA) for epileptic seizure prediction. The classifier is the well-known support vector machine (SVM), and the CHB-MIT Scalp EEG Database is used in this research. The classification results from 22 patients using the channels selected to the patient show a high prediction rate (average 92.42%) compared to the SVM testing results with all channels (71.13%). On average, the accuracy, sensitivity, and specificity with selected channels are improved by 10.58%, 23.57%, and 5.56%, respectively. In addition, four patient cases validate over 90% accuracy, sensitivity, and specificity rates with just a few selected channels. The corresponding standard deviations are also smaller than those used by all channels, demonstrating that tailored channels are a robust way to optimize the seizure prediction.

Seizure detection from multi-channel EEG using entropy-based dynamic graph embedding

An epileptic seizure is a chronic disease with sudden abnormal discharge of brain neurons, which leads to transient brain dysfunction. To detect epileptic seizures, we propose a novel idea based on a dynamic graph embedding model. The dynamic graph is built by identifying the correlation among the multi-channel EEG signals. Graph entropy measurement is exploited to calculate the similarity among the graph at each time interval and construct the graph embedding space. Since the abnormal electrical brain activity causes the epileptic seizure, the graph entropy during the seizure time interval is different from other time intervals. Therefore, we propose an entropy-based dynamic graph embedding model to cluster the graphs, and the graphs with epileptic seizures are discriminated. We applied the proposed approach to the Children Hospital Boston-Massachusetts Institute of Technology Scalp EEG database. The results have shown that the proposed approach outperformed the baselines by 1.4% with respect to accuracy.

Classifying Single Channel Epileptic EEG data based on Sparse Representation using Shallow Autoencoder

Patient independent epileptic seizure detection algorithm for scalp electroencephalogram (EEG) data is pro- posed in this paper. Principal motivation of this work is to integrate neural and conventional machine learning methods to develop a classification system which can advance the current wearable health systems in terms of computational complexity and accuracy. Being based on processing a single channel EEG processing, the approach is suitable for usage with small wireless sensors. A shallow autoencoder model is utilized for sparse representation of the EEG signal followed by k-nearest neighbor (kNN) classifier to categorize the data as epileptic or non-epileptic. Using a single EEG channel an optimum sparsity level is explored in the encoded sample. Attaining an accuracy, sensitivity and specificity of 98.85%, 99.29% and 98.86% respectively, for CHB-MIT scalp EEG database, proposed classification method outperforms state of- the-art seizure detection methodologies. Experiments has shown that this performance was possible by using a sparsity level of 4 in the auto-encoder. Furthermore, use of shallow learning instead of deep learning approach for generation of sparse but effective representation is computationally lighter than many other feature extraction and preprocessing methods.

Geometric Deep Learning for Subject-Independent Epileptic Seizure Prediction using Scalp EEG Signals

Recently, researchers in the biomedical community have introduced deep learning-based epileptic seizure prediction models using electroencephalograms (EEGs) that can anticipate an epileptic seizure by differentiating between the pre-ictal and interictal stages of the subjects brain. Despite having the appearance of a typical anomaly detection task, this problem is complicated by subject-specific characteristics in EEG data. Therefore, studies that investigate seizure prediction widely employ subject-specific models. However, this approach is not suitable in situations where a target subject has limited (or no) data for training. Subject-independent models can address this issue by learning to predict seizures from multiple subjects, and therefore are of greater value in practice. In this study, we propose a subject-independent seizure predictor using Geometric Deep Learning (GDL). In the first stage of our GDL-based method we use graphs derived from physical connections in the EEG grid. We subsequently seek to synthesize subject-specific graphs using deep learning. The models proposed in both stages achieve state-of-the-art performance using a one-hour early seizure prediction window on two benchmark datasets (CHB-MIT-EEG: 95.38% with 23 subjects and Siena-EEG: 96.05% with 15 subjects). To the best of our knowledge, this is the first study that proposes synthesizing subject-specific graphs for seizure prediction. Furthermore, through model interpretation we outline how this method can potentially contribute towards Scalp EEG-based seizure localization.

Computational pan-cancer characterization of model-based quantitative transcription regulations dysregulated in regional lymph node metastasis

Cancer is one of the major causes of mortality worldwide. Regional lymph node metastasis is an important mechanism during the spread of human cancers, in which transcription regulation plays an essential role. This study formulated a regression-model-based quantitative transcription regulation (mqTrans) between one mRNA gene and multiple transcription factors (TFs). Computational pan-cancer screening was carried out to detect the quantitative dysregulation of transcription regulation in the regional lymph node metastasis of 18 cancer types. Only a few metastasis-dysregulated mqTrans models were shared among the cancer types. The mRNA genes of the metastasis-dysregulated mqTrans models were not differentially expressed in regional lymph node metastasis. The experimental data suggested that mqTrans technology provided a complementary approach to the evaluation of transcription regulation mechanisms and may facilitate its quantitative investigation in other phenotypes.

Feature Selection Techniques for the Analysis of Discriminative Features in Temporal and Frontal Lobe Epilepsy: A Comparative Study

Background:

Because about 30% of epileptic patients suffer from refractory epilepsy, an efficient automatic seizure prediction tool is in great demand to improve their life quality.

Methods:

In this work, time-domain discriminating preictal and interictal features were efficiently extracted from the intracranial electroencephalogram of twelve patients, i.e., six with temporal and six with frontal lobe epilepsy. The performance of three types of feature selection methods was compared using Matthews’s correlation coefficient (MCC).

Results:

Kruskal Wallis, a non-parametric approach, was found to perform better than the other approaches due to a simple and less resource consuming strategy as well as maintaining the highest MCC score. The impact of dividing the electroencephalogram signals into various sub-bands was investigated as well. The highest performance of Kruskal Wallis may suggest considering the importance of univariate features like complexity and interquartile ratio (IQR), along with autoregressive (AR) model parameters and the maximum (MAX) cross-correlation to efficiently predict epileptic seizures.

Conclusion:

The proposed approach has the potential to be implemented on a low power device by considering a few simple time domain characteristics for a specific sub-band. It should be noted that, as there is not a great deal of literature on frontal lobe epilepsy, the results of this work can be considered promising.

Personalized EEG Feature Selection for Low-Complexity Seizure Monitoring

Approximately, one third of patients with epilepsy are refractory to medical therapy and thus can be at high risk of injuries and sudden unexpected death. A low-complexity electroencephalography (EEG)-based seizure monitoring algorithm is critically important for daily use, especially for wearable monitoring platforms. This paper presents a personalized EEG feature selection approach, which is the key to achieve a reliable seizure monitoring with a low computational cost. We advocate a two-step, personalized feature selection strategy to enhance monitoring performances for each patient. In the first step, linear discriminant analysis (LDA) is applied to find a few seizure-indicative channels. Then in the second step, least absolute shrinkage and selection operator (LASSO) method is employed to select a discriminative subset of both frequency and time domain features (spectral powers and entropy). A personalization strategy is further customized to find the best settings (number of channels and features) that yield the highest classification scores for each subject. Experimental results of analyzing 23 subjects in CHB-MIT database are quite promising. We have achieved an average F-1 score of 88% with excellent sensitivity and specificity using not more than 7 features extracted from at most 3 channels.

Severity Detection for the Coronavirus Disease 2019 (COVID-19) Patients Using a Machine Learning Model Based on the Blood and Urine Tests

The recent outbreak of the coronavirus disease-2019 (COVID-19) caused serious challenges to the human society in China and across the world. COVID-19 induced pneumonia in human hosts and carried a highly inter-person contagiousness. The COVID-19 patients may carry severe symptoms, and some of them may even die of major organ failures. This study utilized the machine learning algorithms to build the COVID-19 severeness detection model. Support vector machine (SVM) demonstrated a promising detection accuracy after 32 features were detected to be significantly associated with the COVID-19 severeness. These 32 features were further screened for inter-feature redundancies. The final SVM model was trained using 28 features and achieved the overall accuracy 0.8148. This work may facilitate the risk estimation of whether the COVID-19 patients would develop the severe symptoms. The 28 COVID-19 severeness associated biomarkers may also be investigated for their underlining mechanisms how they were involved in the COVID-19 infections.

Severity Detection for the Coronavirus Disease 2019 (COVID-19) Patients Using a Machine Learning Model Based on the Blood and Urine Tests

The recent outbreak of the coronavirus disease-2019 (COVID-19) caused serious challenges to the human society in China and across the world. COVID-19 induced pneumonia in human hosts and carried a highly inter-person contagiousness. The COVID-19 patients may carry severe symptoms, and some of them may even die of major organ failures. This study utilized the machine learning algorithms to build the COVID-19 severeness detection model. Support vector machine (SVM) demonstrated a promising detection accuracy after 32 features were detected to be significantly associated with the COVID-19 severeness. These 32 features were further screened for inter-feature redundancies. The final SVM model was trained using 28 features and achieved the overall accuracy 0.8148. This work may facilitate the risk estimation of whether the COVID-19 patients would develop the severe symptoms. The 28 COVID-19 severeness associated biomarkers may also be investigated for their underlining mechanisms how they were involved in the COVID-19 infections.