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Register a new userPandemic Drugs at Pandemic Speed: Infrastructure for Accelerating COVID-19 Drug Discovery with Hybrid Machine Learning- and Physics-based Simulations on High Performance Computers
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Added by
Agastya Bhati
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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The race to meet the challenges of the global pandemic has served as a reminder that the existing drug discovery process is expensive, inefficient and slow. There is a major bottleneck screening the vast number of potential small molecules to shortlist lead compounds for antiviral drug development. New opportunities to accelerate drug discovery lie at the interface between machine learning methods, in this case developed for linear accelerators, and physics-based methods. The two in silico methods, each have their own advantages and limitations which, interestingly, complement each other. Here, we present an innovative infrastructural development that combines both approaches to accelerate drug discovery. The scale of the potential resulting workflow is such that it is dependent on supercomputing to achieve extremely high throughput. We have demonstrated the viability of this workflow for the study of inhibitors for four COVID-19 target proteins and our ability to perform the required large-scale calculations to identify lead antiviral compounds through repurposing on a variety of supercomputers.
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COVID-19 has claimed more 1 million lives and resulted in over 40 million infections. There is an urgent need to identify drugs that can inhibit SARS-CoV-2. In response, the DOE recently established the Medical Therapeutics project as part of the National Virtual Biotechnology Laboratory, and tasked it with creating the computational infrastructure and methods necessary to advance therapeutics development. We discuss innovations in computational infrastructure and methods that are accelerating and advancing drug design. Specifically, we describe several methods that integrate artificial intelligence and simulation-based approaches, and the design of computational infrastructure to support these methods at scale. We discuss their implementation and characterize their performance, and highlight science advances that these capabilities have enabled.
Coronavirus disease (COVID-19) is an infectious disease caused by a newly discovered coronavirus. It is similar to influenza viruses and raises concerns through alarming levels of spread and severity resulting in an ongoing pandemic worldwide. Within eight months (by August 2020), it infected 24.0 million persons worldwide and over 824 thousand have died. Drones or Unmanned Aerial Vehicles (UAVs) are very helpful in handling the COVID-19 pandemic. This work investigates the drone-based systems, COVID-19 pandemic situations, and proposes an architecture for handling pandemic situations in different scenarios using real-time and simulation-based scenarios. The proposed architecture uses wearable sensors to record the observations in Body Area Networks (BANs) in a push-pull data fetching mechanism. The proposed architecture is found to be useful in remote and highly congested pandemic areas where either the wireless or Internet connectivity is a major issue or chances of COVID-19 spreading are high. It collects and stores the substantial amount of data in a stipulated period and helps to take appropriate action as and when required. In real-time drone-based healthcare system implementation for COVID-19 operations, it is observed that a large area can be covered for sanitization, thermal image collection, and patient identification within a short period (2 KMs within 10 minutes approx.) through aerial route. In the simulation, the same statistics are observed with an addition of collision-resistant strategies working successfully for indoor and outdoor healthcare operations. Further, open challenges are identified and promising research directions are highlighted.
Background: The COVID-19 pandemic has uncovered the potential of digital misinformation in shaping the health of nations. The deluge of unverified information that spreads faster than the epidemic itself is an unprecedented phenomenon that has put millions of lives in danger. Mitigating this Infodemic requires strong health messaging systems that are engaging, vernacular, scalable, effective and continuously learn the new patterns of misinformation. Objective: We created WashKaro, a multi-pronged intervention for mitigating misinformation through conversational AI, machine translation and natural language processing. WashKaro provides the right information matched against WHO guidelines through AI, and delivers it in the right format in local languages. Methods: We theorize (i) an NLP based AI engine that could continuously incorporate user feedback to improve relevance of information, (ii) bite sized audio in the local language to improve penetrance in a country with skewed gender literacy ratios, and (iii) conversational but interactive AI engagement with users towards an increased health awareness in the community. Results: A total of 5026 people who downloaded the app during the study window, among those 1545 were active users. Our study shows that 3.4 times more females engaged with the App in Hindi as compared to males, the relevance of AI-filtered news content doubled within 45 days of continuous machine learning, and the prudence of integrated AI chatbot Satya increased thus proving the usefulness of an mHealth platform to mitigate health misinformation. Conclusion: We conclude that a multi-pronged machine learning application delivering vernacular bite-sized audios and conversational AI is an effective approach to mitigate health misinformation.
The objective of the study is to examine coronavirus disease (COVID-19) related discussions, concerns, and sentiments that emerged from tweets posted by Twitter users. We analyze 4 million Twitter messages related to the COVID-19 pandemic using a list of 25 hashtags such as coronavirus, COVID-19, quarantine from March 1 to April 21 in 2020. We use a machine learning approach, Latent Dirichlet Allocation (LDA), to identify popular unigram, bigrams, salient topics and themes, and sentiments in the collected Tweets. Popular unigrams include virus, lockdown, and quarantine. Popular bigrams include COVID-19, stay home, corona virus, social distancing, and new cases. We identify 13 discussion topics and categorize them into five different themes, such as public health measures to slow the spread of COVID-19, social stigma associated with COVID-19, coronavirus news cases and deaths, COVID-19 in the United States, and coronavirus cases in the rest of the world. Across all identified topics, the dominant sentiments for the spread of coronavirus are anticipation that measures that can be taken, followed by a mixed feeling of trust, anger, and fear for different topics. The public reveals a significant feeling of fear when they discuss the coronavirus new cases and deaths than other topics. The study shows that Twitter data and machine learning approaches can be leveraged for infodemiology study by studying the evolving public discussions and sentiments during the COVID-19. Real-time monitoring and assessment of the Twitter discussion and concerns can be promising for public health emergency responses and planning. Already emerged pandemic fear, stigma, and mental health concerns may continue to influence public trust when there occurs a second wave of COVID-19 or a new surge of the imminent pandemic.
The ongoing COVID-19 global pandemic is affecting every facet of human lives (e.g., public health, education, economy, transportation, and the environment). This novel pandemic and citywide implemented lockdown measures are affecting virus transmission, peoples travel patterns, and air quality. Many studies have been conducted to predict the COVID-19 diffusion, assess the impacts of the pandemic on human mobility and air quality, and assess the impacts of lockdown measures on viral spread with a range of Machine Learning (ML) techniques. This review study aims to analyze results from past research to understand the interactions among the COVID-19 pandemic, lockdown measures, human mobility, and air quality. The critical review of prior studies indicates that urban form, peoples socioeconomic and physical conditions, social cohesion, and social distancing measures significantly affect human mobility and COVID-19 transmission. during the COVID-19 pandemic, many people are inclined to use private transportation for necessary travel purposes to mitigate coronavirus-related health problems. This review study also noticed that COVID-19 related lockdown measures significantly improve air quality by reducing the concentration of air pollutants, which in turn improves the COVID-19 situation by reducing respiratory-related sickness and deaths of people. It is argued that ML is a powerful, effective, and robust analytic paradigm to handle complex and wicked problems such as a global pandemic. This study also discusses policy implications, which will be helpful for policymakers to take prompt actions to moderate the severity of the pandemic and improve urban environments by adopting data-driven analytic methods.
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