Tomas Teijeiro

William Andrew Simon, Una Pale, Tomas Teijeiro et al.

HyperDimensional Computing (HDC) as a machine learning paradigm is highly interesting for applications involving continuous, semi-supervised learning for long-term monitoring. However, its accuracy is not yet on par with other Machine Learning (ML) approaches. Frameworks enabling fast design space exploration to find practical algorithms are necessary to make HD computing competitive with other ML techniques. To this end, we introduce HDTorch, an open-source, PyTorch-based HDC library with CUDA extensions for hypervector operations. We demonstrate HDTorch's utility by analyzing four HDC benchmark datasets in terms of accuracy, runtime, and memory consumption, utilizing both classical and online HD training methodologies. We demonstrate average (training)/inference speedups of (111x/68x)/87x for classical/online HD, respectively. Moreover, we analyze the effects of varying hyperparameters on runtime and accuracy. Finally, we demonstrate how HDTorch enables exploration of HDC strategies applied to large, real-world datasets. We perform the first-ever HD training and inference analysis of the entirety of the CHB-MIT EEG epilepsy database. Results show that the typical approach of training on a subset of the data does not necessarily generalize to the entire dataset, an important factor when developing future HD models for medical wearable devices.

Saleh Baghersalimi, Alireza Amirshahi, Farnaz Forooghifar et al.

Integrating low-power wearable Internet of Things (IoT) systems into routine health monitoring is an ongoing challenge. Recent advances in the computation capabilities of wearables make it possible to target complex scenarios by exploiting multiple biosignals and using high-performance algorithms, such as Deep Neural Networks (DNNs). There is, however, a trade-off between performance of the algorithms and the low-power requirements of IoT platforms with limited resources. Besides, physically larger and multi-biosignal-based wearables bring significant discomfort to the patients. Consequently, reducing power consumption and discomfort is necessary for patients to use IoT devices continuously during everyday life. To overcome these challenges, in the context of epileptic seizure detection, we propose a many-to-one signals knowledge distillation approach targeting single-biosignal processing in IoT wearable systems. The starting point is to get a highly-accurate multi-biosignal DNN, then apply our approach to develop a single-biosignal DNN solution for IoT systems that achieves an accuracy comparable to the original multi-biosignal DNN. To assess the practicality of our approach to real-life scenarios, we perform a comprehensive simulation experiment analysis on several state-of-the-art edge computing platforms, such as Kendryte K210 and Raspberry Pi Zero.

Una Pale, Tomas Teijeiro, David Atienza

The healthcare landscape is moving from the reactive interventions focused on symptoms treatment to a more proactive prevention, from one-size-fits-all to personalized medicine, and from centralized to distributed paradigms. Wearable IoT devices and novel algorithms for continuous monitoring are essential components of this transition. Hyperdimensional (HD) computing is an emerging ML paradigm inspired by neuroscience research with various aspects interesting for IoT devices and biomedical applications. Here we explore the not yet addressed topic of optimal encoding of spatio-temporal data, such as electroencephalogram (EEG) signals, and all information it entails to the HD vectors. Further, we demonstrate how the HD computing framework can be used to perform feature selection by choosing an adequate encoding. To the best of our knowledge, this is the first approach to performing feature selection using HD computing in the literature. As a result, we believe it can support the ML community to further foster the research in multiple directions related to feature and channel selection, as well as model interpretability.

Lara Orlandic, Tomas Teijeiro, David Atienza

Cough audio signal classification is a potentially useful tool in screening for respiratory disorders, such as COVID-19. Since it is dangerous to collect data from patients with such contagious diseases, many research teams have turned to crowdsourcing to quickly gather cough sound data, as it was done to generate the COUGHVID dataset. The COUGHVID dataset enlisted expert physicians to diagnose the underlying diseases present in a limited number of uploaded recordings. However, this approach suffers from potential mislabeling of the coughs, as well as notable disagreement between experts. In this work, we use a semi-supervised learning (SSL) approach to improve the labeling consistency of the COUGHVID dataset and the robustness of COVID-19 versus healthy cough sound classification. First, we leverage existing SSL expert knowledge aggregation techniques to overcome the labeling inconsistencies and sparsity in the dataset. Next, our SSL approach is used to identify a subsample of re-labeled COUGHVID audio samples that can be used to train or augment future cough classification models. The consistency of the re-labeled data is demonstrated in that it exhibits a high degree of class separability, 3x higher than that of the user-labeled data, despite the expert label inconsistency present in the original dataset. Furthermore, the spectral differences in the user-labeled audio segments are amplified in the re-labeled data, resulting in significantly different power spectral densities between healthy and COVID-19 coughs, which demonstrates both the increased consistency of the new dataset and its explainability from an acoustic perspective. Finally, we demonstrate how the re-labeled dataset can be used to train a cough classifier. This SSL approach can be used to combine the medical knowledge of several experts to improve the database consistency for any diagnostic classification task.

Una Pale, Tomas Teijeiro, David Atienza

Epilepsy is a chronic neurological disorder with a significant prevalence. However, there is still no adequate technological support to enable epilepsy detection and continuous outpatient monitoring in everyday life. Hyperdimensional (HD) computing is an interesting alternative for wearable devices, characterized by a much simpler learning process and also lower memory requirements. In this work, we demonstrate a few additional aspects in which HD computing, and the way its models are built and stored, can be used for further understanding, comparing, and creating more advanced machine learning models for epilepsy detection. These possibilities are not feasible with other state-of-the-art models, such as random forests or neural networks. We compare inter-subject similarity of models per different classes (seizure and non-seizure), then study the process of creation of generalized models from personalized ones, and in the end, how to combine personalized and generalized models to create hybrid models. This results in improved epilepsy detection performance. We also tested knowledge transfer between models created on two different datasets. Finally, all those examples could be highly interesting not only from an engineering perspective to create better models for wearables, but also from a neurological perspective to better understand individual epilepsy patterns.

Tomas Teijeiro, Jamie M. Taylor, Ali Hashemian et al.

We propose the use of machine learning techniques to find optimal quadrature rules for the construction of stiffness and mass matrices in isogeometric analysis (IGA). We initially consider 1D spline spaces of arbitrary degree spanned over uniform and non-uniform knot sequences, and then the generated optimal rules are used for integration over higher-dimensional spaces using tensor product sense. The quadrature rule search is posed as an optimization problem and solved by a machine learning strategy based on gradient-descent. However, since the optimization space is highly non-convex, the success of the search strongly depends on the number of quadrature points and the parameter initialization. Thus, we use a dynamic programming strategy that initializes the parameters from the optimal solution over the spline space with a lower number of knots. With this method, we found optimal quadrature rules for spline spaces when using IGA discretizations with up to 50 uniform elements and polynomial degrees up to 8, showing the generality of the approach in this scenario. For non-uniform partitions, the method also finds an optimal rule in a reasonable number of test cases. We also assess the generated optimal rules in two practical case studies, namely, the eigenvalue problem of the Laplace operator and the eigenfrequency analysis of freeform curved beams, where the latter problem shows the applicability of the method to curved geometries. In particular, the proposed method results in savings with respect to traditional Gaussian integration of up to 44% in 1D, 68% in 2D, and 82% in 3D spaces.

Una Pale, Tomas Teijeiro, David Atienza

Epilepsy is a chronic neurological disorder that affects a significant portion of the human population and imposes serious risks in the daily life of patients. Despite advances in machine learning and IoT, small, nonstigmatizing wearable devices for continuous monitoring and detection in outpatient environments are not yet available. Part of the reason is the complexity of epilepsy itself, including highly imbalanced data, multimodal nature, and very subject-specific signatures. However, another problem is the heterogeneity of methodological approaches in research, leading to slower progress, difficulty comparing results, and low reproducibility. Therefore, this article identifies a wide range of methodological decisions that must be made and reported when training and evaluating the performance of epilepsy detection systems. We characterize the influence of individual choices using a typical ensemble random-forest model and the publicly available CHB-MIT database, providing a broader picture of each decision and giving good-practice recommendations, based on our experience, where possible.

Lara Orlandic, Jonathan Dan, Jerome Thevenot et al.

Chronic cough disorders are widespread and challenging to assess because they rely on subjective patient questionnaires about cough frequency. Wearable devices running Machine Learning (ML) algorithms are promising for quantifying daily coughs, providing clinicians with objective metrics to track symptoms and evaluate treatments. However, there is a mismatch between state-of-the-art metrics for cough counting algorithms and the information relevant to clinicians. Most works focus on distinguishing cough from non-cough samples, which does not directly provide clinically relevant outcomes such as the number of cough events or their temporal patterns. In addition, typical metrics such as specificity and accuracy can be biased by class imbalance. We propose using event-based evaluation metrics aligned with clinical guidelines on significant cough counting endpoints. We use an ML classifier to illustrate the shortcomings of traditional sample-based accuracy measurements, highlighting their variance due to dataset class imbalance and sample window length. We also present an open-source event-based evaluation framework to test algorithm performance in identifying cough events and rejecting false positives. We provide examples and best practice guidelines in event-based cough counting as a necessary first step to assess algorithm performance with clinical relevance.

Lara Orlandic, Tomas Teijeiro, David Atienza

Cough audio signal classification has been successfully used to diagnose a variety of respiratory conditions, and there has been significant interest in leveraging Machine Learning (ML) to provide widespread COVID-19 screening. However, there is currently no validated database of cough sounds with which to train such ML models. The COUGHVID dataset provides over 20,000 crowdsourced cough recordings representing a wide range of subject ages, genders, geographic locations, and COVID-19 statuses. First, we filtered the dataset using our open-sourced cough detection algorithm. Second, experienced pulmonologists labeled more than 2,000 recordings to diagnose medical abnormalities present in the coughs, thereby contributing one of the largest expert-labeled cough datasets in existence that can be used for a plethora of cough audio classification tasks. Finally, we ensured that coughs labeled as symptomatic and COVID-19 originate from countries with high infection rates, and that their expert labels are consistent. As a result, the COUGHVID dataset contributes a wealth of cough recordings for training ML models to address the world's most urgent health crises.

Una Pale, Tomas Teijeiro, David Atienza

Wearable and unobtrusive monitoring and prediction of epileptic seizures has the potential to significantly increase the life quality of patients, but is still an unreached goal due to challenges of real-time detection and wearable devices design. Hyperdimensional (HD) computing has evolved in recent years as a new promising machine learning approach, especially when talking about wearable applications. But in the case of epilepsy detection, standard HD computing is not performing at the level of other state-of-the-art algorithms. This could be due to the inherent complexity of the seizures and their signatures in different biosignals, such as the electroencephalogram (EEG), the highly personalized nature, and the disbalance of seizure and non-seizure instances. In the literature, different strategies for improved learning of HD computing have been proposed, such as iterative (multi-pass) learning, multi-centroid learning and learning with sample weight ("OnlineHD"). Yet, most of them have not been tested on the challenging task of epileptic seizure detection, and it stays unclear whether they can increase the HD computing performance to the level of the current state-of-the-art algorithms, such as random forests. Thus, in this paper, we implement different learning strategies and assess their performance on an individual basis, or in combination, regarding detection performance and memory and computational requirements. Results show that the best-performing algorithm, which is a combination of multi-centroid and multi-pass, can indeed reach the performance of the random forest model on a highly unbalanced dataset imitating a real-life epileptic seizure detection application.

Elisabetta De Giovanni, Tomas Teijeiro, Grégoire P. Millet et al.

Objective: Continuous monitoring of biosignals via wearable sensors has quickly expanded in the medical and wellness fields. At rest, automatic detection of vital parameters is generally accurate. However, in conditions such as high-intensity exercise, sudden physiological changes occur to the signals, compromising the robustness of standard algorithms. Methods: Our method, called BayeSlope, is based on unsupervised learning, Bayesian filtering, and non-linear normalization to enhance and correctly detect the R peaks according to their expected positions in the ECG. Furthermore, as BayeSlope is computationally heavy and can drain the device battery quickly, we propose an online design that adapts its robustness to sudden physiological changes, and its complexity to the heterogeneous resources of modern embedded platforms. This method combines BayeSlope with a lightweight algorithm, executed in cores with different capabilities, to reduce the energy consumption while preserving the accuracy. Results: BayeSlope achieves an F1 score of 99.3% in experiments during intense cycling exercise with 20 subjects. Additionally, the online adaptive process achieves an F1 score of 99% across five different exercise intensities, with a total energy consumption of 1.55+-0.54~mJ. Conclusion: We propose a highly accurate and robust method, and a complete energy-efficient implementation in a modern ultra-low-power embedded platform to improve R peak detection in challenging conditions, such as during high-intensity exercise. Significance: The experiments show that BayeSlope outperforms a state-of-the-art algorithm up to 8.4% in F1 score, while our online adaptive method can reach energy savings up to 38.7% on modern heterogeneous wearable platforms.

Una Pale, Tomas Teijeiro, David Atienza

Long-term monitoring of patients with epilepsy presents a challenging problem from the engineering perspective of real-time detection and wearable devices design. It requires new solutions that allow continuous unobstructed monitoring and reliable detection and prediction of seizures. A high variability in the electroencephalogram (EEG) patterns exists among people, brain states, and time instances during seizures, but also during non-seizure periods. This makes epileptic seizure detection very challenging, especially if data is grouped under only seizure and non-seizure labels. Hyperdimensional (HD) computing, a novel machine learning approach, comes in as a promising tool. However, it has certain limitations when the data shows a high intra-class variability. Therefore, in this work, we propose a novel semi-supervised learning approach based on a multi-centroid HD computing. The multi-centroid approach allows to have several prototype vectors representing seizure and non-seizure states, which leads to significantly improved performance when compared to a simple 2-class HD model. Further, real-life data imbalance poses an additional challenge and the performance reported on balanced subsets of data is likely to be overestimated. Thus, we test our multi-centroid approach with three different dataset balancing scenarios, showing that performance improvement is higher for the less balanced dataset. More specifically, up to 14% improvement is achieved on an unbalanced test set with 10 times more non-seizure than seizure data. At the same time, the total number of sub-classes is not significantly increased compared to the balanced dataset. Thus, the proposed multi-centroid approach can be an important element in achieving a high performance of epilepsy detection with real-life data balance or during online learning, where seizures are infrequent.

Una Pale, Tomas Teijeiro, David Atienza

Hyperdimensional computing is a promising novel paradigm for low-power embedded machine learning. It has been applied on different biomedical applications, and particularly on epileptic seizure detection. Unfortunately, due to differences in data preparation, segmentation, encoding strategies, and performance metrics, results are hard to compare, which makes building upon that knowledge difficult. Thus, the main goal of this work is to perform a systematic assessment of the HD computing framework for the detection of epileptic seizures, comparing different feature approaches mapped to HD vectors. More precisely, we test two previously implemented features as well as several novel approaches with HD computing on epileptic seizure detection. We evaluate them in a comparable way, i.e., with the same preprocessing setup, and with the identical performance measures. We use two different datasets in order to assess the generalizability of our conclusions. The systematic assessment involved three primary aspects relevant for potential wearable implementations: 1) detection performance, 2) memory requirements, and 3) computational complexity. Our analysis shows a significant difference in detection performance between approaches, but also that the ones with the highest performance might not be ideal for wearable applications due to their high memory or computational requirements. Furthermore, we evaluate a post-processing strategy to adjust the predictions to the dynamics of epileptic seizures, showing that performance is significantly improved in all the approaches and also that after post-processing, differences in performance are much smaller between approaches.

Valentin Gabeff, Tomas Teijeiro, Marina Zapater et al.

While Deep Learning (DL) is often considered the state-of-the art for Artificial Intelligence-based medical decision support, it remains sparsely implemented in clinical practice and poorly trusted by clinicians due to insufficient interpretability of neural network models. We have tackled this issue by developing interpretable DL models in the context of online detection of epileptic seizure, based on EEG signal. This has conditioned the preparation of the input signals, the network architecture, and the post-processing of the output in line with the domain knowledge. Specifically, we focused the discussion on three main aspects: 1) how to aggregate the classification results on signal segments provided by the DL model into a larger time scale, at the seizure-level; 2) what are the relevant frequency patterns learned in the first convolutional layer of different models, and their relation with the delta, theta, alpha, beta and gamma frequency bands on which the visual interpretation of EEG is based; and 3) the identification of the signal waveforms with larger contribution towards the ictal class, according to the activation differences highlighted using the DeepLIFT method. Results show that the kernel size in the first layer determines the interpretability of the extracted features and the sensitivity of the trained models, even though the final performance is very similar after post-processing. Also, we found that amplitude is the main feature leading to an ictal prediction, suggesting that a larger patient population would be required to learn more complex frequency patterns. Still, our methodology was successfully able to generalize patient inter-variability for the majority of the studied population with a classification F1-score of 0.873 and detecting 90% of the seizures.

Tomas Teijeiro, Paulo Felix

This paper presents a software implementation of a general framework for time series interpretation based on abductive reasoning. The software provides a data model and a set of algorithms to make inference to the best explanation of a time series, resulting in a description in multiple abstraction levels of the processes underlying the time series. As a proof of concept, a comprehensive knowledge base for the electrocardiogram (ECG) domain is provided, so it can be used directly as a tool for ECG analysis. This tool has been successfully validated in several noteworthy problems, such as heartbeat classification or atrial fibrillation detection.