Lara Orlandic

A Multimodal Dataset for Automatic Edge-AI Cough Detection

David Atienza Alonso, Lara Orlandic, Tomas Teijeiro Campo, Jérôme Paul Rémy Thevenot

Counting the number of times a patient coughs per day is an essential biomarker in determining treatment efficacy for novel antitussive therapies and personalizing patient care. There is a need for wearable devices that employ multimodal sensors to perform accurate, privacy-preserving, automatic cough counting algorithms directly on the device in an edge-AI fashion. To advance this research field, we contribute the first publicly accessible cough counting dataset of multimodal biosignals. The database contains nearly 4 hours of biosignal data, with both acoustic and kinematic modalities, covering 4,300 annotated cough events. Furthermore, several non-cough sounds (i.e. breathing, laughing, and throat clearing), background noises (i.e. music, traffic, bystander coughing) and motion scenarios (i.e. sitting, walking) mimicking daily life activities are also present, which the research community can use to accelerate ML algorithm development. For detailed information about using this dataset to train edge-AI models and example code, please refer to our public Git repository: https://github.com/esl-epfl/edge-ai-cough-count/

Zenodo2023

A Multimodal Dataset for Automatic Edge-AI Cough Detection

David Atienza Alonso, Lara Orlandic, Tomas Teijeiro Campo, Jérôme Paul Rémy Thevenot

Counting the number of times a patient coughs per day is an essential biomarker in determining treatment efficacy for novel antitussive therapies and personalizing patient care. Automatic cough counting tools must provide accurate information, while running on a lightweight, portable device that protects the patient’s privacy. Several devices and algorithms have been developed for cough counting, but many use only error-prone audio signals, rely on offline processing that compromises data privacy, or utilize processing and memory-intensive neural networks that require more hardware resources than can fit on a wearable device. Therefore, there is a need for wearable devices that employ multimodal sensors to perform accurate, privacy-preserving, automatic cough counting algorithms directly on the device in an edge Artificial Intelligence (edge-AI) fashion. To advance this research field, we contribute the first publicly accessible cough counting dataset of multimodal biosignals. The database contains nearly 4 hours of biosignal data, with both acoustic and kinematic modalities, covering 4,300 annotated cough events from 15 subjects. Furthermore, a variety of non-cough sounds and motion scenarios mimicking daily life activities are also present, which the research community can use to accelerate machine learning (ML) algorithm development. A technical validation of the dataset reveals that it represents a wide variety of signal-to- noise ratios, which can be expected in a real-life use case, as well as consistency across experimental trials. Finally, to demonstrate the usability of the dataset, we train a simple cough vs non-cough signal classifier that obtains a 91% sensitivity, 92% specificity, and 80% precision on unseen test subject data. Such edge-friendly AI algorithms have the potential to provide continuous ambulatory monitoring of the numerous chronic cough patients.

2023

A Semi-Supervised Algorithm for Improving the Consistency of Crowdsourced Datasets: The COVID-19 Case Study on Respiratory Disorder Classification

David Atienza Alonso, Lara Orlandic, Tomas Teijeiro Campo

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.

2022

The COUGHVID crowdsourcing dataset: A corpus for the study of large-scale cough analysis algorithms

David Atienza Alonso, Lara Orlandic, Tomas Teijeiro Campo

Overview 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. The COUGHVID dataset provides over 30,000 crowdsourced cough recordings representing a wide range of subject ages, genders, geographic locations, and COVID-19 statuses. Furthermore, 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. 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. Private Set and Testing Protocol Researchers interested in testing their models on the private test dataset should contact us at coughvid@epfl.ch, briefly explaining the type of validation they wish to make, and their obtained results obtained through cross-validation with the public data. Then, access to the unlabeled recordings will be provided, and the researchers should send the predictions of their models on these recordings. Finally, the performance metrics of the predictions will be sent to the researchers. The private testing data is not included in any file within our Zenodo record, and it can only be accessed by contacting the COUGHVID team at the aforementioned e-mail address. New Semi-Supervised Labeling The third version of the COUGHVID dataset contains thousands of additional recordings obtained through October 2021. Additionally, the recordings containing coughs were re-labeled according to a semi-supervised learning algorithm that combined the user labels with those of the expert physicians, which were modeled using ML and expanded on the previously unlabeled data. These labels can be found in the "status_SSL" column of the "metadata_compiled.csv" file. For more information about the data collection, pre-processing, validation, and data structure, please refer to the following publication: https://www.nature.com/articles/s41597-021-00937-4 The cough pre-processing and feature extraction code is available from the following c4science repository: https://c4science.ch/diffusion/10770/

EPFL Infoscience2021

Wearable and Continuous Prediction of Passage of Time Perception for Monitoring Mental Health

Adriana Arza Valdes, David Atienza Alonso, Lara Orlandic

A person’s passage of time perception (POTP) is strongly linked to their mental state and stress response, and can therefore provide an easily quantifiable means of continuous mental health monitoring. In this work, we develop a custom experiment and Machine Learning (ML) models for predicting POTP from biomarkers acquired from wearable biosensors. We first confirm that individuals experience time passing slower than usual during fear or sadness (p = 0.046) and faster than usual during cognitive tasks (p = 2 x10^-5). Then, we group together the experimental segments associated with fast, slow, and normal POTP, and train a ML model to classify between these states based on a person’s biomarkers. The classifier had a weighted average F-1 score of 79%, with the fast-passing time class having the highest F-1 score of 93%. Next, we classify each individual’s POTP regardless of the task at hand, achieving an F-1 score of 77.1% when distinguishing time passing faster rather than slower than usual. In the two classifiers, biomarkers derived from the respiration, electrocardiogram, skin conductance, and skin temperature signals contributed most to the classifier output, thus enabling real-time POTP monitoring using noninvasive, wearable biosensors.

2021

The COUGHVID crowdsourcing dataset: A corpus for the study of large-scale cough analysis algorithms

David Atienza Alonso, Lara Orlandic, Tomas Teijeiro Campo

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.

2020

Towards Continuous and Ambulatory Blood Pressure Monitoring: Methods for Efficient Data Acquisition for Pulse Transit Time Estimation

Lara Orlandic

We developed a prototype for measuring physiological data for pulse transit time (PTT) estimation that will be used for ambulatory blood pressure (BP) monitoring. The device is comprised of an embedded system with multimodal sensors that streams high-throughput data to a custom Android application. The primary focus of this paper is on the hardware–software codesign that we developed to address the challenges associated with reliably recording data over Bluetooth on a resource-constrained platform. In particular, we developed a lossless compression algorithm that is based on optimally selective Huffman coding and Huffman prefixed coding, which yields virtually identical compression ratios to the standard algorithm, but with a 67–99% reduction in the size of the compression tables. In addition, we developed a hybrid software–hardware flow control method to eliminate microcontroller (MCU) interrupt-latency related data loss when multi-byte packets are sent from the phone to the embedded system via a Bluetooth module at baud rates exceeding 115,200 bit/s. The empirical error rate obtained with the proposed method with the baud rate set to 460,800 bit/s was identically equal to 0%. Our robust and computationally efficient physiological data acquisition system will enable field experiments that will drive the development of novel algorithms for PTT-based continuous BP monitoring.

2020

REWARD: Design, Optimization, and Evaluation of a Real-Time Relative-Energy Wearable R-Peak Detection Algorithm *

Adriana Arza Valdes, David Atienza Alonso, Elisabetta De Giovanni, Lara Orlandic, Jean-Marc Vesin, Sasan Yazdani

Wearable devices are an unobtrusive, cost-effective means of continuous ambulatory monitoring of chronic cardiovascular diseases. However, on these resource-constrained systems, electrocardiogram (ECG) processing algorithms must consume minimal power and memory, yet robustly provide accurate physiological information. This work presents REWARD, the Relative-Energy-based WeArable R-Peak Detection algorithm, which is a novel ECG R-peak detection mechanism based on a nonlinear filtering method called Relative-Energy (Rel-En). REWARD is designed and optimized for real-time execution on wearable systems. Then, this novel algorithm is compared against three state-of-the-art real-time R-peak detection algorithms in terms of accuracy, memory footprint, and energy consumption. The Physionet QT and NST Databases were employed to evaluate the algorithms' accuracy and robustness to noise, respectively. Then, a 32-bit ARM Cortex-M3-based microcontroller was used to measure the energy usage, computational burden, and memory footprint of the four algorithms. REWARD consumed at least 63% less energy and 32% less RAM than the other algorithms while obtaining comparable accuracy results. Therefore, REWARD would be a suitable choice of R-peak detection mechanism for wearable devices that perform more complex ECG analysis, whose algorithms require additional energy and memory resources.

2019

REWARD: Design, Optimization, and Evaluation of a Real-Time Relative-Energy Wearable R-Peak Detection Algorithm

Adriana Arza Valdes, David Atienza Alonso, Elisabetta De Giovanni, Lara Orlandic, Jean-Marc Vesin, Sasan Yazdani

Wearable devices are an unobtrusive, cost-effective means of continuous ambulatory monitoring of chronic cardiovascular diseases. However, on these resource-constrained systems, electrocardiogram (ECG) processing algorithms must consume minimal power and memory, yet robustly provide accurate physiological information. This work presents REWARD, the Relative-Energy-based WeArable R-Peak Detection algorithm, which is a novel ECG R-peak detection mechanism based on a nonlinear filtering method called Relative-Energy (Rel-En). REWARD is designed and optimized for real-time execution on wearable systems. Then, this novel algorithm is compared against three state-of-the-art real-time R-peak detection algorithms in terms of accuracy, memory footprint, and energy consumption. The Physionet QT and NST Databases were employed to evaluate the algorithms’ accuracy and robustness to noise, respectively. Then, a 32-bit ARM Cortex-M3-based microcontroller was used to measure the energy usage, computational burden, and memory footprint of the four algorithms. REWARD consumed at least 63% less energy and 32% less RAM than the other algorithms while obtaining comparable accuracy results. Therefore, REWARD would be a suitable choice of R-peak detection mechanism for wearable devices that perform more complex ECG analysis, whose algorithms require additional energy and memory resources.