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Register a new userAugmenting Physiological Time Series Data: A Case Study for Sleep Apnea Detection
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Supervised machine learning applications in the health domain often face the problem of insufficient training datasets. The quantity of labelled data is small due to privacy concerns and the cost of data acquisition and labelling by a medical expert. Furthermore, it is quite common that collected data are unbalanced and getting enough data to personalize models for individuals is very expensive or even infeasible. This paper addresses these problems by (1) designing a recurrent Generative Adversarial Network to generate realistic synthetic data and to augment the original dataset, (2) enabling the generation of balanced datasets based on heavily unbalanced dataset, and (3) to control the data generation in such a way that the generated data resembles data from specific individuals. We apply these solutions for sleep apnea detection and study in the evaluation the performance of four well-known techniques, i.e., K-Nearest Neighbour, Random Forest, Multi-Layer Perceptron, and Support Vector Machine. All classifiers exhibit in the experiments a consistent increase in sensitivity and a kappa statistic increase by between 0.007 and 0.182.
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Internet of Things (IoT) enabled wearable sensors for health monitoring are widely used to reduce the cost of personal healthcare and improve quality of life. The sleep apnea-hypopnea syndrome, characterized by the abnormal reduction or pause in breathing, greatly affects the quality of sleep of an individual. This paper introduces a novel method for apnea detection (pause in breathing) from electrocardiogram (ECG) signals obtained from wearable devices. The novelty stems from the high resolution of apnea detection on a second-by-second basis, and this is achieved using a 1-dimensional convolutional neural network for feature extraction and detection of sleep apnea events. The proposed method exhibits an accuracy of 99.56% and a sensitivity of 96.05%. This model outperforms several lower resolution state-of-the-art apnea detection methods. The complexity of the proposed model is analyzed. We also analyze the feasibility of model pruning and binarization to reduce the resource requirements on a wearable IoT device. The pruned model with 80% sparsity exhibited an accuracy of 97.34% and a sensitivity of 86.48%. The binarized model exhibited an accuracy of 75.59% and sensitivity of 63.23%. The performance of low complexity patient-specific models derived from the generic model is also studied to analyze the feasibility of retraining existing models to fit patient-specific requirements. The patient-specific models on average exhibited an accuracy of 97.79% and sensitivity of 92.23%. The source code for this work is made publicly available.
Deep learning performs remarkably well on many time series analysis tasks recently. The superior performance of deep neural networks relies heavily on a large number of training data to avoid overfitting. However, the labeled data of many real-world time series applications may be limited such as classification in medical time series and anomaly detection in AIOps. As an effective way to enhance the size and quality of the training data, data augmentation is crucial to the successful application of deep learning models on time series data. In this paper, we systematically review different data augmentation methods for time series. We propose a taxonomy for the reviewed methods, and then provide a structured review for these methods by highlighting their strengths and limitations. We also empirically compare different data augmentation methods for different tasks including time series anomaly detection, classification, and forecasting. Finally, we discuss and highlight five future directions to provide useful research guidance.
With recent advancements in deep learning methods, automatically learning deep features from the original data is becoming an effective and widespread approach. However, the hand-crafted expert knowledge-based features are still insightful. These expert-curated features can increase the models generalization and remind the model of some data characteristics, such as the time interval between two patterns. It is particularly advantageous in tasks with the clinically-relevant data, where the data are usually limited and complex. To keep both implicit deep features and expert-curated explicit features together, an effective fusion strategy is becoming indispensable. In this work, we focus on a specific clinical application, i.e., sleep apnea detection. In this context, we propose a contrastive learning-based cross attention framework for sleep apnea detection (named ConCAD). The cross attention mechanism can fuse the deep and expert features by automatically assigning attention weights based on their importance. Contrastive learning can learn better representations by keeping the instances of each class closer and pushing away instances from different classes in the embedding space concurrently. Furthermore, a new hybrid loss is designed to simultaneously conduct contrastive learning and classification by integrating a supervised contrastive loss with a cross-entropy loss. Our proposed framework can be easily integrated into standard deep learning models to utilize expert knowledge and contrastive learning to boost performance. As demonstrated on two public ECG dataset with sleep apnea annotation, ConCAD significantly improves the detection performance and outperforms state-of-art benchmark methods.
In this work, a dense recurrent convolutional neural network (DRCNN) was constructed to detect sleep disorders including arousal, apnea and hypopnea using Polysomnography (PSG) measurement channels provided in the 2018 Physionet challenge database. Our model structure is composed of multiple dense convolutional units (DCU) followed by a bidirectional long-short term memory (LSTM) layer followed by a softmax output layer. The sleep events including sleep stages, arousal regions and multiple types of apnea and hypopnea are manually annotated by experts which enables us to train our proposed network using a multi-task learning mechanism. Three binary cross-entropy loss functions corresponding to sleep/wake, target arousal and apnea-hypopnea/normal detection tasks are summed up to generate our overall network loss function that is optimized using the Adam method. Our model performance was evaluated using two metrics: the area under the precision-recall curve (AUPRC) and the area under the receiver operating characteristic curve (AUROC). To measure our model generalization, 4-fold cross-validation was also performed. For training, our model was applied to full night recording data. Finally, the average AUPRC and AUROC values associated with the arousal detection task were 0.505 and 0.922, respectively on our testing dataset. An ensemble of four models trained on different data folds improved the AUPRC and AUROC to 0.543 and 0.931, respectively. Our proposed algorithm achieved the first place in the official stage of the 2018 Physionet challenge for detecting sleep arousals with AUPRC of 0.54 on the blind testing dataset.
Time-series anomaly detection is a popular topic in both academia and industrial fields. Many companies need to monitor thousands of temporal signals for their applications and services and require instant feedback and alerts for potential incidents in time. The task is challenging because of the complex characteristics of time-series, which are messy, stochastic, and often without proper labels. This prohibits training supervised models because of lack of labels and a single model hardly fits different time series. In this paper, we propose a solution to address these issues. We present an automated model selection framework to automatically find the most suitable detection model with proper parameters for the incoming data. The model selection layer is extensible as it can be updated without too much effort when a new detector is available to the service. Finally, we incorporate a customized tuning algorithm to flexibly filter anomalies to meet customers criteria. Experiments on real-world datasets show the effectiveness of our solution.
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