Saliva-based detection of COVID-19 infection in a real-world setting using reagent-free Raman spectroscopy and machine learning

ABSTRACT: SIGNIFICANCE: The primary method of COVID-19 detection is reverse transcription polymerase chain reaction (RT-PCR) testing. PCR test sensitivity may decrease as more variants of concern arise and reagents may become less specific to the virus. AIM: We aimed to develop a reagent-free way to detect COVID-19 in a real-world setting with minimal constraints on sample acquisition. The machine learning (ML) models involved could be frequently updated to include spectral information about variants without needing to develop new reagents. APPROACH: We present a workflow for collecting, preparing, and imaging dried saliva supernatant droplets using a non-invasive, label-free technique-Raman spectroscopy-to detect changes in the molecular profile of saliva associated with COVID-19 infection. RESULTS: We used an innovative multiple instance learning-based ML approach and droplet segmentation to analyze droplets. Amongst all confounding factors, we discriminated between COVID-positive and COVID-negative individuals yielding receiver operating coefficient curves with an area under curve (AUC) of 0.8 in both males (79% sensitivity and 75% specificity) and females (84% sensitivity and 64% specificity). Taking the sex of the saliva donor into account increased the AUC by 5%. CONCLUSION: These findings may pave the way for new rapid Raman spectroscopic screening tools for COVID-19 and other infectious diseases

Multi-instance learning with discriminative bag mapping

© 1989-2012 IEEE. Multi-instance learning (MIL) is a useful tool for tackling labeling ambiguity in learning because it allows a bag of instances to share one label. Bag mapping transforms a bag into a single instance in a new space via instance selection and has drawn significant attention recently. To date, most existing work is based on the original space, using all instances inside each bag for bag mapping, and the selected instances are not directly tied to an MIL objective. As a result, it is difficult to guarantee the distinguishing capacity of the selected instances in the new bag mapping space. In this paper, we propose a discriminative mapping approach for multi-instance learning (MILDM) that aims to identify the best instances to directly distinguish bags in the new mapping space. Accordingly, each instance bag can be mapped using the selected instances to a new feature space, and hence any generic learning algorithm, such as an instance-based learning algorithm, can be used to derive learning models for multi-instance classification. Experiments and comparisons on eight different types of real-world learning tasks (including 14 data sets) demonstrate that MILDM outperforms the state-of-The-Art bag mapping multi-instance learning approaches. Results also confirm that MILDM achieves balanced performance between runtime efficiency and classification effectiveness