Unsupervised machine learning framework for discriminating major variants of concern during COVID-19.

Due to the high mutation rate of the virus, the COVID-19 pandemic evolved rapidly. Certain variants of the virus, such as Delta and Omicron emerged with altered viral properties leading to severe transmission and death rates. These variants burdened the medical systems worldwide with a major impact to travel, productivity, and the world economy. Unsupervised machine learning methods have the ability to compress, characterize, and visualize unlabelled data. This paper presents a framework that utilizes unsupervised machine learning methods to discriminate and visualize the associations between major COVID-19 variants based on their genome sequences. These methods comprise a combination of selected dimensionality reduction and clustering techniques. The framework processes the RNA sequences by performing a k-mer analysis on the data and further visualises and compares the results using selected dimensionality reduction methods that include principal component analysis (PCA), t-distributed stochastic neighbour embedding (t-SNE), and uniform manifold approximation projection (UMAP). Our framework also employs agglomerative hierarchical clustering to visualize the mutational differences among major variants of concern and country-wise mutational differences for selected variants (Delta and Omicron) using dendrograms. We also provide country-wise mutational differences for selected variants via dendrograms. We find that the proposed framework can effectively distinguish between the major variants and has the potential to identify emerging variants in the future.

CoviRx: A User-Friendly Interface for Systematic Down-Selection of Repurposed Drug Candidates for COVID-19

Although various vaccines are now commercially available, they have not been able to stop the spread of COVID-19 infection completely. An excellent strategy to get safe, effective, and affordable COVID-19 treatments quickly is to repurpose drugs that are already approved for other diseases. The process of developing an accurate and standardized drug repurposing dataset requires considerable resources and expertise due to numerous commercially available drugs that could be potentially used to address the SARS-CoV-2 infection. To address this bottleneck, we created the CoviRx.org platform. CoviRx is a user-friendly interface that allows analysis and filtering of large quantities of data, which is onerous to curate manually for COVID-19 drug repurposing. Through CoviRx, the curated data have been made open source to help combat the ongoing pandemic and encourage users to submit their findings on the drugs they have evaluated, in a uniform format that can be validated and checked for integrity by authenticated volunteers. This article discusses the various features of CoviRx, its design principles, and how its functionality is independent of the data it displays. Thus, in the future, this platform can be extended to include any other disease beyond COVID-19.

COVID-19 sentiment analysis via deep learning during the rise of novel cases

Social scientists and psychologists take interest in understanding how people express emotions and sentiments when dealing with catastrophic events such as natural disasters, political unrest, and terrorism. The COVID-19 pandemic is a catastrophic event that has raised a number of psychological issues such as depression given abrupt social changes and lack of employment. Advancements of deep learning-based language models have been promising for sentiment analysis with data from social networks such as Twitter. Given the situation with COVID-19 pandemic, different countries had different peaks where rise and fall of new cases affected lock-downs which directly affected the economy and employment. During the rise of COVID-19 cases with stricter lock-downs, people have been expressing their sentiments in social media. This can provide a deep understanding of human psychology during catastrophic events. In this paper, we present a framework that employs deep learning-based language models via long short-term memory (LSTM) recurrent neural networks for sentiment analysis during the rise of novel COVID-19 cases in India. The framework features LSTM language model with a global vector embedding and state-of-art BERT language model. We review the sentiments expressed for selective months in 2020 which covers the major peak of novel cases in India. Our framework utilises multi-label sentiment classification where more than one sentiment can be expressed at once. Our results indicate that the majority of the tweets have been positive with high levels of optimism during the rise of the novel COVID-19 cases and the number of tweets significantly lowered towards the peak. We find that the optimistic, annoyed and joking tweets mostly dominate the monthly tweets with much lower portion of negative sentiments. The predictions generally indicate that although the majority have been optimistic, a significant group of population has been annoyed towards the way the pandemic was handled by the authorities. (PsycInfo Database Record (c) 2022 APA, all rights reserved)

COVID-19 sentiment analysis via deep learning during the rise of novel cases.

Social scientists and psychologists take interest in understanding how people express emotions and sentiments when dealing with catastrophic events such as natural disasters, political unrest, and terrorism. The COVID-19 pandemic is a catastrophic event that has raised a number of psychological issues such as depression given abrupt social changes and lack of employment. Advancements of deep learning-based language models have been promising for sentiment analysis with data from social networks such as Twitter. Given the situation with COVID-19 pandemic, different countries had different peaks where rise and fall of new cases affected lock-downs which directly affected the economy and employment. During the rise of COVID-19 cases with stricter lock-downs, people have been expressing their sentiments in social media. This can provide a deep understanding of human psychology during catastrophic events. In this paper, we present a framework that employs deep learning-based language models via long short-term memory (LSTM) recurrent neural networks for sentiment analysis during the rise of novel COVID-19 cases in India. The framework features LSTM language model with a global vector embedding and state-of-art BERT language model. We review the sentiments expressed for selective months in 2020 which covers the major peak of novel cases in India. Our framework utilises multi-label sentiment classification where more than one sentiment can be expressed at once. Our results indicate that the majority of the tweets have been positive with high levels of optimism during the rise of the novel COVID-19 cases and the number of tweets significantly lowered towards the peak. We find that the optimistic, annoyed and joking tweets mostly dominate the monthly tweets with much lower portion of negative sentiments. The predictions generally indicate that although the majority have been optimistic, a significant group of population has been annoyed towards the way the pandemic was handled by the authorities.

Bayesian neural networks for stock price forecasting before and during COVID-19 pandemic.

Recently, there has been much attention in the use of machine learning methods, particularly deep learning for stock price prediction. A major limitation of conventional deep learning is uncertainty quantification in predictions which affect investor confidence. Bayesian neural networks feature Bayesian inference for providing inference (training) of model parameters that provides a rigorous methodology for uncertainty quantification in predictions. Markov Chain Monte Carlo (MCMC) sampling methods have been prominent in implementing inference of Bayesian neural networks; however certain limitations existed due to a large number of parameters and the need for better computational resources. Recently, there has been much progress in the area of Bayesian neural networks given the use of Langevin gradients with parallel tempering MCMC that can be implemented in a parallel computing environment. The COVID-19 pandemic had a drastic impact in the world economy and stock markets given different levels of lockdowns due to rise and fall of daily infections. It is important to investigate the performance of related forecasting models during the COVID-19 pandemic given the volatility in stock markets. In this paper, we use novel Bayesian neural networks for multi-step-ahead stock price forecasting before and during COVID-19. We also investigate if the pre-COVID-19 datasets are useful of modelling stock price forecasting during COVID-19. Our results indicate due to high volatility in the stock-price during COVID-19, it is more challenging to provide forecasting. However, we found that Bayesian neural networks could provide reasonable predictions with uncertainty quantification despite high market volatility during the first peak of the COVID-19 pandemic.