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Register a new userCOVID-19 Detection in Cough, Breath and Speech using Deep Transfer Learning and Bottleneck Features
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Added by
Madhurananda Pahar
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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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.
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We present a machine learning based COVID-19 cough classifier which can discriminate COVID-19 positive coughs from both COVID-19 negative and healthy coughs recorded on a smartphone. This type of screening is non-contact, easy to apply, and can reduce the workload in testing centres as well as limit transmission by recommending early self-isolation to those who have a cough suggestive of COVID-19. The datasets used in this study include subjects from all six continents and contain both forced and natural coughs, indicating that the approach is widely applicable. The publicly available Coswara dataset contains 92 COVID-19 positive and 1079 healthy subjects, while the second smaller dataset was collected mostly in South Africa and contains 18 COVID-19 positive and 26 COVID-19 negative subjects who have undergone a SARS-CoV laboratory test. Both datasets indicate that COVID-19 positive coughs are 15%-20% shorter than non-COVID coughs. Dataset skew was addressed by applying the synthetic minority oversampling technique (SMOTE). A leave-$p$-out cross-validation scheme was used to train and evaluate seven machine learning classifiers: LR, KNN, SVM, MLP, CNN, LSTM and Resnet50. Our results show that although all classifiers were able to identify COVID-19 coughs, the best performance was exhibited by the Resnet50 classifier, which was best able to discriminate between the COVID-19 positive and the healthy coughs with an area under the ROC curve (AUC) of 0.98. An LSTM classifier was best able to discriminate between the COVID-19 positive and COVID-19 negative coughs, with an AUC of 0.94 after selecting the best 13 features from a sequential forward selection (SFS). Since this type of cough audio classification is cost-effective and easy to deploy, it is potentially a useful and viable means of non-contact COVID-19 screening.
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
Deep clustering (DC) and utterance-level permutation invariant training (uPIT) have been demonstrated promising for speaker-independent speech separation. DC is usually formulated as two-step processes: embedding learning and embedding clustering, which results in complex separation pipelines and a huge obstacle in directly optimizing the actual separation objectives. As for uPIT, it only minimizes the chosen permutation with the lowest mean square error, doesnt discriminate it with other permutations. In this paper, we propose a discriminative learning method for speaker-independent speech separation using deep embedding features. Firstly, a DC network is trained to extract deep embedding features, which contain each sources information and have an advantage in discriminating each target speakers. Then these features are used as the input for uPIT to directly separate the different sources. Finally, uPIT and DC are jointly trained, which directly optimizes the actual separation objectives. Moreover, in order to maximize the distance of each permutation, the discriminative learning is applied to fine tuning the whole model. Our experiments are conducted on WSJ0-2mix dataset. Experimental results show that the proposed models achieve better performances than DC and uPIT for speaker-independent speech separation.
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
Cross-speaker style transfer is crucial to the applications of multi-style and expressive speech synthesis at scale. It does not require the target speakers to be experts in expressing all styles and to collect corresponding recordings for model training. However, the performances of existing style transfer methods are still far behind real application needs. The root causes are mainly twofold. Firstly, the style embedding extracted from single reference speech can hardly provide fine-grained and appropriate prosody information for arbitrary text to synthesize. Secondly, in these models the content/text, prosody, and speaker timbre are usually highly entangled, its therefore not realistic to expect a satisfied result when freely combining these components, such as to transfer speaking style between speakers. In this paper, we propose a cross-speaker style transfer text-to-speech (TTS) model with explicit prosody bottleneck. The prosody bottleneck builds up the kernels accounting for speaking style robustly, and disentangles the prosody from content and speaker timbre, therefore guarantees high quality cross-speaker style transfer. Evaluation result shows the proposed method even achieves on-par performance with source speakers speaker-dependent (SD) model in objective measurement of prosody, and significantly outperforms the cycle consistency and GMVAE-based baselines in objective and subjective evaluations.
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