Semi-automated Annotation of Signal Events in Clinical EEG Data
Temple University（天普大学）
Scott Yang, Silvia Lopez, Meysam Golmohammadi, Iyad Obeid, Joseph Picone
备注：
Published in IEEE Signal Processing in Medicine and Biology Symposium. Philadelphia, Pennsylvania, USA
发表信息：
S. Yang, S. Lopez, M. Golmohammadi, I. Obeid and J. Picone, "Semi-automated annotation of signal events in clinical EEG data," 2016 IEEE Signal Processing in Medicine and Biology Symposium (SPMB), Philadelphia, PA, 2016, pp. 1-5
To be effective, state of the art machine learning technology needs large amounts of annotated data. There are numerous compelling applications in healthcare that can benefit from high performance automated decision support systems provided by deep learning technology, but they lack the comprehensive data resources required to apply sophisticated machine learning models. Further, for economic reasons, it is very difficult to justify the creation of large annotated corpora for these applications. Hence, automated annotation techniques become increasingly important. In this study, we investigated the effectiveness of using an active learning algorithm to automatically annotate a large EEG corpus. The algorithm is designed to annotate six types of EEG events. Two model training schemes, namely threshold-based and volume-based, are evaluated. In the threshold-based scheme the threshold of confidence scores is optimized in the initial training iteration, whereas for the volume-based scheme only a certain amount of data is preserved after each iteration. Recognition performance is improved 2% absolute and the system is capable of automatically annotating previously unlabeled data. Given that the interpretation of clinical EEG data is an exceedingly difficult task, this study provides some evidence that the proposed method is a viable alternative to expensive manual annotation.
EEG-Language Pretraining for Highly Label-Efficient Clinical Phenotyping
Charité – Universitätsmedizin Berlin, Department of Psychiatry and Psychotherapy, Berlin, Germany（柏林查理医院医学大学精神病与心理治疗系）；Hertie Institute for AI in Brain Health, University of Tübingen, Germany（图宾根大学健康人工智能研究所）
Identifying abnormal patterns in electroencephalography (EEG) remains the cornerstone of diagnosing several neurological diseases. The current clinical EEG review process relies heavily on expert visual review, which is unscalable and error-prone. In an effort to augment the expert review process, there is a significant interest in mining population-level EEG patterns using unsupervised approaches. Current approaches rely either on two-dimensional decompositions (e.g., principal and independent component analyses) or deep representation learning (e.g., auto-encoders, self-supervision). However…
X, the Moonshot Factory（X，登月工厂）；DeepMind（深度心智）；Florida State University（佛罗里达州立大学）
Despite extensive standardization, diagnostic interviews for mental health disorders encompass substantial subjective judgment. Previous studies have demonstrated that EEG-based neural measures can function as reliable objective correlates of depression, or even predictors of depression and its course. However, their clinical utility has not been fully realized because of 1) the lack of automated ways to deal with the inherent noise associated with EEG data at scale, and 2) the lack of knowledge of which aspects of the EEG signal may be markers of a clinical disorder. Here we adapt an unsuperv…
Objective: A clinical decision support tool that automatically interprets EEGs can reduce time to diagnosis and enhance real-time applications such as ICU monitoring. Clinicians have indicated that a sensitivity of 95% with a specificity below 5% was the minimum requirement for clinical acceptance. We propose a highperformance classification system based on principles of big data and machine learning. Methods: A hybrid machine learning system that uses hidden Markov models (HMM) for sequential decoding and deep learning networks for postprocessing is proposed. These algorithms were trained and…
Université Paris-Saclay（巴黎萨克雷大学）；Inria（法国国家信息与自动化研究所）；CEA（法国原子能和替代能源委员会）；InteraXon Inc.（InteraXon公司）；University of Helsinki（赫尔辛基大学）；Max Planck Institute for Human Cognitive and Brain Sciences（马克斯·普朗克人类认知与脑科学研究所）
Objective. Supervised learning paradigms are often limited by the amount of labeled data that is available. This phenomenon is particularly problematic in clinically-relevant data, such as electroencephalography (EEG), where labeling can be costly in terms of specialized expertise and human processing time. Consequently, deep learning architectures designed to learn on EEG data have yielded relatively shallow models and performances at best similar to those of traditional feature-based approaches. However, in most situations, unlabeled data is available in abundance. By extracting information …
Bayesian uncertainty-aware deep learning with noisy labels: Tackling annotation ambiguity in EEG seizure detection
Department of Electrical and Computer Engineering, Johns Hopkins University（约翰霍普金斯大学电气与计算机工程系）；Department of Electrical and Computer Engineering, Boston University（波士顿大学电气与计算机工程系）
Medical Center – University of Freiburg（弗莱堡大学医学中心）；University of Freiburg（弗莱堡大学）；Machine Learning Lab（机器学习实验室）；Neuromedical AI Lab（神经医学人工智能实验室）；Neurorobotics Lab（神经机器人学实验室）
Machine learning (ML) methods have the potential to automate clinical EEG analysis. They can be categorized into feature-based (with handcrafted features), and end-to-end approaches (with learned features). Previous studies on EEG pathology decoding have typically analyzed a limited number of features, decoders, or both. For a I) more elaborate feature-based EEG analysis, and II) in-depth comparisons of both approaches, here we first develop a comprehensive feature-based framework, and then compare this framework to state-of-the-art end-to-end methods. To this aim, we apply the proposed featur…
Window Stacking Meta-Models for Clinical EEG Classification
University of the West of England（西英格兰大学）；University College London Hospitals NHS Foundation Trust（伦敦大学学院医院NHS基金会信托）；North Bristol NHS Trust（北布里斯托尔NHS信托）
Resting state electroencephalogram (EEG) abnormalities in clinically high-risk individuals (CHR), clinically stable first-episode patients with schizophrenia (FES), healthy controls (HC) suggest alterations in neural oscillatory activity. However, few studies directly compare these anomalies among each types. Therefore, this study investigated whether these electrophysiological characteristics differentiate clinical populations from one another, and from non-psychiatric controls. To address this question, resting EEG power and coherence were assessed in 40 clinically high-risk individuals (CHR…
University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）；Mayo Clinic（梅奥诊所）
The recent availability of large datasets in bio-medicine has inspired the development of representation learning methods for multiple healthcare applications. Despite advances in predictive performance, the clinical utility of such methods is limited when exposed to real-world data. This study develops model diagnostic measures to detect potential pitfalls before deployment without assuming access to external data. Specifically, we focus on modeling realistic data shifts in electrophysiological signals (EEGs) via data transforms and extend the conventional task-based evaluations with analyses…
Electroencephalograms (EEG) are often contaminated by artifacts which make interpreting them more challenging for clinicians. Hence, automated artifact recognition systems have the potential to aid the clinical workflow. In this abstract, we share the first results on applying various machine learning algorithms to the recently released world's largest open-source artifact recognition dataset. We envision that these results will serve as a benchmark for researchers who might work with this dataset in future.
Effective analysis of EEG signals for potential clinical applications remains a challenging task. So far, the analysis and conditioning of EEG have largely remained sex-neutral. This paper employs a machine learning approach to explore the evidence of sex effects on EEG signals, and confirms the generality of these effects by achieving successful sex prediction of resting-state EEG signals. We have found that the brain connectivity represented by the coherence between certain sensor channels are good predictors of sex.
Electroencephalogram (EEG) monitoring and objective seizure identification is an essential clinical investigation for some patients with epilepsy. Accurate annotation is done through a time-consuming process by EEG specialists. Computer-assisted systems for seizure detection currently lack extensive clinical utility due to retrospective, patient-specific, and/or irreproducible studies that result in low sensitivity or high false positives in clinical tests. We aim to significantly reduce the time and resources on data annotation by demonstrating a continental generalization of seizure detectio…
Modern deep learning holds a great potential to transform clinical practice on human sleep. Teaching a machine to carry out routine tasks would be a tremendous reduction in workload for clinicians. Sleep staging, a fundamental step in sleep practice, is a suitable task for this and will be the focus in this article. Recently, automatic sleep staging systems have been trained to mimic manual scoring, leading to similar performance to human sleep experts, at least on scoring of healthy subjects. Despite tremendous progress, we have not seen automatic sleep scoring adopted widely in clinical envi…
Tokyo University of Agriculture and Technology（东京农工大学）；Juntendo University Nerima Hospital（顺天堂大学练马医院）
Electroencephalography (EEG) is essential for the diagnosis of epilepsy, but it requires expertise and experience to identify abnormalities. It is thus crucial to develop automated models for the detection of abnormalities in EEGs related to epilepsy. This paper describes the development of a novel class of compact convolutional neural networks (CNNs) for detecting abnormal patterns and electrodes in EEGs for epilepsy. The designed model is inspired by a CNN developed for brain-computer interfacing called multichannel EEGNet (mEEGNet). Unlike the EEGNet, the proposed model, mEEGNet, has the sa…
Frankfurt Institute for Advanced Studies (FIAS)（法兰克福高等研究院）；Goethe University Frankfurt（法兰克福大学）；Center for Personalized Translational Epilepsy Research (CePTER)（个性化转化癫痫研究中心）
Epilepsy is the fourth most common neurological disorder, affecting about 1% of the population at all ages. As many as 60% of people with epilepsy experience focal seizures which originate in a certain brain area and are limited to part of one cerebral hemisphere. In focal epilepsy patients, a precise surgical removal of the seizure onset zone can lead to effective seizure control or even a seizure-free outcome. Thus, correct identification of the seizure onset zone is essential. For clinical evaluation purposes, electroencephalography (EEG) recordings are commonly used. However, their interpr…
Electroencephalography (EEG) during sleep is used by clinicians to evaluate various neurological disorders. In sleep medicine, it is relevant to detect macro-events (> 10s) such as sleep stages, and micro-events (<2s) such as spindles and K-complexes. Annotations of such events require a trained sleep expert, a time consuming and tedious process with a large inter-scorer variability. Automatic algorithms have been developed to detect various types of events but these are event-specific. We propose a deep learning method that jointly predicts locations, durations and types of events in EEG time…
Automatic detection of abnormal clinical EEG: comparison of a finetuned foundation model with two deep learning models
BioSerenity；Université de Lille（里尔大学）；CHU de Lille（里尔大学医院）；Hôpital Universitaire de Bruxelles（布鲁塞尔大学医院）；Université Libre de Bruxelles（布鲁塞尔自由大学）；Yale University School of Medicine（耶鲁大学医学院）；Université de Lorraine（洛林大学）；CHRU-Nancy（南锡大学地区医院）；CHU Grenoble Alpes（格勒诺布尔大学医院）；Université Grenoble Alpes（格勒诺布尔阿尔卑斯大学）；Jolt Capital
Clinical Feasibility of Smartphone-based EEG in Kenya
BrainCapture；Technical University of Denmark（丹麦技术大学）；Kenyatta University Teaching, Referral and Research Hospital（肯雅塔大学教学、转诊和研究中心医院）；Copenhagen University Hospital Rigshospitalet（哥本哈根大学医院利格什皮塔莱特医院）；Children's Hospital Srebrnjak（斯雷布伦亚克儿童医院）；"Prof. Dr. Alexandru Obregia" Psychiatry Hospital（亚历山大·奥布雷吉亚教授博士精神病医院）；Danish Epilepsy Center, Filadelfia（丹麦癫痫中心菲拉德尔菲亚）；University of Copenhagen（哥本哈根大学）
The diagnosis of Alzheimer's disease (AD) in routine clinical practice is most commonly based on subjective clinical interpretations. Quantitative electroencephalography (QEEG) measures have been shown to reflect neurodegenerative processes in AD and might qualify as affordable and thereby widely available markers to facilitate the objectivization of AD assessment. Here, we present a novel framework combining Riemannian tangent space mapping and elastic net regression for the development of brain atrophy markers. While most AD QEEG studies are based on small sample sizes and psychological test…
Automated seizure detection using clinical electroencephalograms is a challenging machine learning problem because the multichannel signal often has an extremely low signal to noise ratio. Events of interest such as seizures are easily confused with signal artifacts (e.g, eye movements) or benign variants (e.g., slowing). Commercially available systems suffer from unacceptably high false alarm rates. Deep learning algorithms that employ high dimensional models have not previously been effective due to the lack of big data resources. In this paper, we use the TUH EEG Seizure Corpus to evaluate …
University of Belgrade（贝尔格莱德大学）；Amsterdam Health and Technology Institute（阿姆斯特丹健康与技术研究所）；HealthInc；Universidad Complutense（康普顿斯大学）
In this paper, we aimed at reviewing present literature on employing nonlinear analysis in combination with machine learning methods, in depression detection or prediction task. We are focusing on an affordable data-driven approach, applicable for everyday clinical practice, and in particular, those based on electroencephalographic (EEG) recordings. Among those studies utilizing EEG, we are discussing a group of applications used for detecting the depression based on the resting state EEG (detection studies) and interventional studies (using stimulus in their protocols or aiming to predict the…
Bharati Vidyapeeth’s College of Engineering（巴拉蒂维迪亚佩特工程学院）
The electroencephalogram (EEG) is one of the most precious technologies to understand the happenings inside our brain and further understand our body's happenings. Automatic prediction of oncoming seizures using the EEG signals helps the doctors and clinical experts and reduces their workload. This paper proposes an end-to-end deep learning algorithm to fully automate seizure prediction's laborious task without any heavy pre-processing on the EEG data or feature engineering. The proposed deep learning network is a blend of signal processing and deep learning pipeline, which automates the seizu…
University of California Los Angeles（加州大学洛杉矶分校）；Philips Research（飞利浦研究院）
Sleep is particularly important to the health of infants, children, and adolescents, and sleep scoring is the first step to accurate diagnosis and treatment of potentially life-threatening conditions. But pediatric sleep is severely under-researched compared to adult sleep in the context of machine learning for health, and sleep scoring algorithms developed for adults usually perform poorly on infants. Here, we present the first automated sleep scoring results on a recent large-scale pediatric sleep study dataset that was collected during standard clinical care. We develop a transformer-based …
The Epilepsies are a common, chronic neurological disorder affecting more than 50 million individuals across the globe. It is characterized by unprovoked, recurring (similar or different type) seizures which are commonly diagnosed through clinical EEGs. Good-quality, open-access and free EEG data can act as a catalyst for on-going state-of-the-art (SOTA) research works for detection, prediction and management of epilepsy and seizures. They can also aid in improving the quality of life (QOL) of these diseased individuals and contribute research in healthcare multimedia, data analytics and Artif…
A Simple Review of EEG Foundation Models: Datasets, Advancements and Future Perspectives
The College of Computer Science, Zhejiang University, Hangzhou, China.（浙江大学计算机科学学院）；The MOE Frontiers Science Center for Brain and Brain-Machine Integration, Zhejiang University, Hangzhou, China.（脑科学与脑机接口前沿科学中心）；The Nanhu Brain-Computer Interface Institute, Hangzhou, China.（南湖脑机接口研究院）；The Qiushi Academy for Advanced Studies, Hangzhou, China.（启石先进研究院）
Wavelet quantile normalization (WQN) is a nonparametric algorithm designed to efficiently remove transient artifacts from single-channel EEG in real-time clinical monitoring. Today, EEG monitoring machines suspend their output when artifacts in the signal are detected. Removing unpredictable EEG artifacts would thus allow to improve the continuity of the monitoring. We analyze the WQN algorithm which consists in transporting wavelet coefficient distributions of an artifacted epoch into a reference, uncontaminated signal distribution. We show that the algorithm regularizes the signal. To confir…
Electroencephalography (EEG) analysis extracts critical information from brain signals, which has provided fundamental support for various applications, including brain-disease diagnosis and brain-computer interface. However, the real-time processing of large-scale EEG signals at high energy efficiency has placed great challenges for electronic processors on edge computing devices. Here, we propose the EEG opto-processor based on diffractive photonic computing units (DPUs) to effectively process the extracranial and intracranial EEG signals and perform epileptic seizure detection. The signals …
Northern Arizona University（北亚利桑那大学）；Ngee Ann Polytechnic（义安理工学院）；Singapore University of Social Sciences（新加坡社会科学大学）；University of Malaya（马来亚大学）
Electroencephalogram (EEG) is a common base signal used to monitor brain activity and diagnose sleep disorders. Manual sleep stage scoring is a time-consuming task for sleep experts and is limited by inter-rater reliability. In this paper, we propose an automatic sleep stage annotation method called SleepEEGNet using a single-channel EEG signal. The SleepEEGNet is composed of deep convolutional neural networks (CNNs) to extract time-invariant features, frequency information, and a sequence to sequence model to capture the complex and long short-term context dependencies between sleep epochs an…
In this article, we propose a sparse spectra graph convolutional network (SSGCNet) for solving Epileptic EEG signal classification problems. The aim is to achieve a lightweight deep learning model without losing model classification accuracy. We propose a weighted neighborhood field graph (WNFG) to represent EEG signals, which reduces the redundant edges between graph nodes. WNFG has lower time complexity and memory usage than the conventional solutions. Using the graph representation, the sequential graph convolutional network is based on a combination of sparse weight pruning technique and t…
Electroencephalogram (EEG) based brain-computer interface (BCI) systems are useful tools for clinical purposes like neural prostheses. In this study, we collected EEG signals related to grasp motions. Five healthy subjects participated in this experiment. They executed and imagined five sustained-grasp actions. We proposed a novel data augmentation method that increases the amount of training data using labels obtained from electromyogram (EMG) signals analysis. For implementation, we recorded EEG and EMG simultaneously. The data augmentation over the original EEG data concluded higher classif…
