Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userUncertainty-Aware COVID-19 Detection from Imbalanced Sound Data
145
0
0.0
(
0
)
Added by
Tong Xia
Publication date
2021
fields
Informatics Engineering
and research's language is
English
Ask ChatGPT about the research
No Arabic abstract
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.
rate research
Read More
Audio signals generated by the human body (e.g., sighs, breathing, heart, digestion, vibration sounds) have routinely been used by clinicians as indicators to diagnose disease or assess disease progression. Until recently, such signals were usually collected through manual auscultation at scheduled visits. Research has now started to use digital technology to gather bodily sounds (e.g., from digital stethoscopes) for cardiovascular or respiratory examination, which could then be used for automatic analysis. Some initial work shows promise in detecting diagnostic signals of COVID-19 from voice and coughs. In this paper we describe our data analysis over a large-scale crowdsourced dataset of respiratory sounds collected to aid diagnosis of COVID-19. We use coughs and breathing to understand how discernible COVID-19 sounds are from those in asthma or healthy controls. Our results show that even a simple binary machine learning classifier is able to classify correctly healthy and COVID-19 sounds. We also show how we distinguish a user who tested positive for COVID-19 and has a cough from a healthy user with a cough, and users who tested positive for COVID-19 and have a cough from users with asthma and a cough. Our models achieve an AUC of above 80% across all tasks. These results are preliminary and only scratch the surface of the potential of this type of data and audio-based machine learning. This work opens the door to further investigation of how automatically analysed respiratory patterns could be used as pre-screening signals to aid COVID-19 diagnosis.
Audio classification using breath and cough samples has recently emerged as a low-cost, non-invasive, and accessible COVID-19 screening method. However, no application has been approved for official use at the time of writing due to the stringent reliability and accuracy requirements of the critical healthcare setting. To support the development of the Machine Learning classification models, we performed an extensive comparative investigation and ranking of 15 audio features, including less well-known ones. The results were verified on two independent COVID-19 sound datasets. By using the identified top-performing features, we have increased the COVID-19 classification accuracy by up to 17% on the Cambridge dataset, and up to 10% on the Coswara dataset, compared to the original baseline accuracy without our feature ranking.
Rapidly scaling screening, testing and quarantine has shown to be an effective strategy to combat the COVID-19 pandemic. We consider the application of deep learning techniques to distinguish individuals with COVID from non-COVID by using data acquirable from a phone. Using cough and context (symptoms and meta-data) represent such a promising approach. Several independent works in this direction have shown promising results. However, none of them report performance across clinically relevant data splits. Specifically, the performance where the development and test sets are split in time (retrospective validation) and across sites (broad validation). Although there is meaningful generalization across these splits the performance significantly varies (up to 0.1 AUC score). In addition, we study the performance of symptomatic and asymptomatic individuals across these three splits. Finally, we show that our model focuses on meaningful features of the input, cough bouts for cough and relevant symptoms for context. The code and checkpoints are available at https://github.com/WadhwaniAI/cough-against-covid
Testing capacity for COVID-19 remains a challenge globally due to the lack of adequate supplies, trained personnel, and sample-processing equipment. These problems are even more acute in rural and underdeveloped regions. We demonstrate that solicited-cough sounds collected over a phone, when analysed by our AI model, have statistically significant signal indicative of COVID-19 status (AUC 0.72, t-test,p <0.01,95% CI 0.61-0.83). This holds true for asymptomatic patients as well. Towards this, we collect the largest known(to date) dataset of microbiologically confirmed COVID-19 cough sounds from 3,621 individuals. When used in a triaging step within an overall testing protocol, by enabling risk-stratification of individuals before confirmatory tests, our tool can increase the testing capacity of a healthcare system by 43% at disease prevalence of 5%, without additional supplies, trained personnel, or physical infrastructure
We present an experimental investigation into the effectiveness of transfer learning and bottleneck feature extraction in detecting COVID-19 from audio recordings of cough, breath and speech. This type of screening is non-contact, does not require specialist medical expertise or laboratory facilities and can be deployed on inexpensive consumer hardware. We use datasets that contain recordings of coughing, sneezing, speech and other noises, but do not contain COVID-19 labels, to pre-train three deep neural networks: a CNN, an LSTM and a Resnet50. These pre-trained networks are subsequently either fine-tuned using smaller datasets of coughing with COVID-19 labels in the process of transfer learning, or are used as bottleneck feature extractors. Results show that a Resnet50 classifier trained by this transfer learning process delivers optimal or near-optimal performance across all datasets achieving areas under the receiver operating characteristic (ROC AUC) of 0.98, 0.94 and 0.92 respectively for all three sound classes (coughs, breaths and speech). This indicates that coughs carry the strongest COVID-19 signature, followed by breath and speech. Our results also show that applying transfer learning and extracting bottleneck features using the larger datasets without COVID-19 labels led not only to improve performance, but also to minimise the standard deviation of the classifier AUCs among the outer folds of the leave-$p$-out cross-validation, indicating better generalisation. We conclude that deep transfer learning and bottleneck feature extraction can improve COVID-19 cough, breath and speech audio classification, yielding automatic classifiers with higher accuracy.
suggested questions
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
