Exploring Longitudinal Cough, Breath, and Voice Data for COVID-19 Progression Prediction via Sequential Deep Learning: Model Development and Validation (preprint)

Recent work has shown the potential of using audio data (eg, cough, breathing, and voice) in the screening for COVID-19. However, these approaches only focus on one-off detection and detect the infection given the current audio sample, but do not monitor disease progression in COVID-19. Limited exploration has been put forward to continuously monitor COVID-19 progression, especially recovery, through longitudinal audio data. Tracking disease progression characteristics could lead to more timely treatment. The primary objective of this study is to explore the potential of longitudinal audio samples over time for COVID-19 progression prediction and, especially, recovery trend prediction using sequential deep learning techniques. Crowdsourced respiratory audio data, including breathing, cough, and voice samples, from 212 individuals over 5-385 days were analyzed. We developed a deep learning-enabled tracking tool using gated recurrent units (GRUs) to detect COVID-19 progression by exploring the audio dynamics of the individuals' historical audio biomarkers. The investigation comprised 2 parts: (1) COVID-19 detection in terms of positive and negative (healthy) tests, and (2) longitudinal disease progression prediction over time in terms of probability of positive tests. The strong performance for COVID-19 detection, yielding an AUROC of 0.79, a sensitivity of 0.75, and a specificity of 0.71 supported the effectiveness of the approach compared to methods that do not leverage longitudinal dynamics. We further examined the predicted disease progression trajectory, displaying high consistency with test results with a correlation of 0.75 in the test cohort and 0.86 in a subset of the test cohort who reported recovery. Our findings suggest that monitoring COVID-19 evolution via longitudinal audio data has potential in the tracking of individuals' disease progression and recovery.

Sounds of COVID-19: exploring realistic performance of audio-based digital testing (preprint)

Researchers have been battling with the question of how we can identify Coronavirus disease (COVID-19) cases efficiently, affordably and at scale. Recent work has shown how audio based approaches, which collect respiratory audio data (cough, breathing and voice) can be used for testing, however there is a lack of exploration of how biases and methodological decisions impact these tools' performance in practice. In this paper, we explore the realistic performance of audio-based digital testing of COVID-19. To investigate this, we collected a large crowdsourced respiratory audio dataset through a mobile app, alongside recent COVID-19 test result and symptoms intended as a ground truth. Within the collected dataset, we selected 5,240 samples from 2,478 participants and split them into different participant-independent sets for model development and validation. Among these, we controlled for potential confounding factors (such as demographics and language). The unbiased model takes features extracted from breathing, coughs, and voice signals as predictors and yields an AUC-ROC of 0.71 (95\% CI: 0.65$-$0.77). We further explore different unbalanced distributions to show how biases and participant splits affect performance. Finally, we discuss how the realistic model presented could be integrated in clinical practice to realize continuous, ubiquitous, sustainable and affordable testing at population scale.

Uncertainty-Aware COVID-19 Detection from Imbalanced Sound Data (preprint)

Recently, sound-based COVID-19 detection studies have shown great promise to achieve scalable and prompt digital pre-screening. However, there are still two unsolved issues hindering the practice. First, collected datasets for model training are often imbalanced, with a considerably smaller proportion of users tested positive, making it harder to learn representative and robust features. Second, deep learning models are generally overconfident in their predictions. Clinically, false predictions aggravate healthcare costs. Estimation of the uncertainty of screening would aid this. To handle these issues, we propose an ensemble framework where multiple deep learning models for sound-based COVID-19 detection are developed from different but balanced subsets from original data. As such, data are utilized more effectively compared to traditional up-sampling and down-sampling approaches: an AUC of 0.74 with a sensitivity of 0.68 and a specificity of 0.69 is achieved. Simultaneously, we estimate uncertainty from the disagreement across multiple models. It is shown that false predictions often yield higher uncertainty, enabling us to suggest the users with certainty higher than a threshold to repeat the audio test on their phones or to take clinical tests if digital diagnosis still fails. This study paves the way for a more robust sound-based COVID-19 automated screening system.