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Register a new userCOVID-19Base: A knowledgebase to explore biomedical entities related to COVID-19
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Added by
Md. Tawkat Islam Khondaker
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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We are presenting COVID-19Base, a knowledgebase highlighting the biomedical entities related to COVID-19 disease based on literature mining. To develop COVID-19Base, we mine the information from publicly available scientific literature and related public resources. We considered seven topic-specific dictionaries, including human genes, human miRNAs, human lncRNAs, diseases, Protein Databank, drugs, and drug side effects, are integrated to mine all scientific evidence related to COVID-19. We have employed an automated literature mining and labeling system through a novel approach to measure the effectiveness of drugs against diseases based on natural language processing, sentiment analysis, and deep learning. To the best of our knowledge, this is the first knowledgebase dedicated to COVID-19, which integrates such large variety of related biomedical entities through literature mining. Proper investigation of the mined biomedical entities along with the identified interactions among those, reported in COVID-19Base, would help the research community to discover possible ways for the therapeutic treatment of COVID-19.
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This report describes the participation of two Danish universities, University of Copenhagen and Aalborg University, in the international search engine competition on COVID-19 (the 2020 TREC-COVID Challenge) organised by the U.S. National Institute of Standards and Technology (NIST) and its Text Retrieval Conference (TREC) division. The aim of the competition was to find the best search engine strategy for retrieving precise biomedical scientific information on COVID-19 from the largest, at that point in time, dataset of curated scientific literature on COVID-19 -- the COVID-19 Open Research Dataset (CORD-19). CORD-19 was the result of a call to action to the tech community by the U.S. White House in March 2020, and was shortly thereafter posted on Kaggle as an AI competition by the Allen Institute for AI, the Chan Zuckerberg Initiative, Georgetown Universitys Center for Security and Emerging Technology, Microsoft, and the National Library of Medicine at the US National Institutes of Health. CORD-19 contained over 200,000 scholarly articles (of which more than 100,000 were with full text) about COVID-19, SARS-CoV-2, and related coronaviruses, gathered from curated biomedical sources. The TREC-COVID challenge asked for the best way to (a) retrieve accurate and precise scientific information, in response to some queries formulated by biomedical experts, and (b) rank this information decreasingly by its relevance to the query. In this document, we describe the TREC-COVID competition setup, our participation to it, and our resulting reflections and lessons learned about the state-of-art technology when faced with the acute task of retrieving precise scientific information from a rapidly growing corpus of literature, in response to highly specialised queries, in the middle of a pandemic.
The world has seen in 2020 an unprecedented global outbreak of SARS-CoV-2, a new strain of coronavirus, causing the COVID-19 pandemic, and radically changing our lives and work conditions. Many scientists are working tirelessly to find a treatment and a possible vaccine. Furthermore, governments, scientific institutions and companies are acting quickly to make resources available, including funds and the opening of large-volume data repositories, to accelerate innovation and discovery aimed at solving this pandemic. In this paper, we develop a novel automated theme-based visualisation method, combining advanced data modelling of large corpora, information mapping and trend analysis, to provide a top-down and bottom-up browsing and search interface for quick discovery of topics and research resources. We apply this method on two recently released publications datasets (Dimensions COVID-19 dataset and the Allen Institute for AIs CORD-19). The results reveal intriguing information including increased efforts in topics such as social distancing; cross-domain initiatives (e.g. mental health and education); evolving research in medical topics; and the unfolding trajectory of the virus in different territories through publications. The results also demonstrate the need to quickly and automatically enable search and browsing of large corpora. We believe our methodology will improve future large volume visualisation and discovery systems but also hope our visualisation interfaces will currently aid scientists, researchers, and the general public to tackle the numerous issues in the fight against the COVID-19 pandemic.
What are the latent questions on some textual data? In this work, we investigate using question generation models for exploring a collection of documents. Our method, dubbed corpus2question, consists of applying a pre-trained question generation model over a corpus and aggregating the resulting questions by frequency and time. This technique is an alternative to methods such as topic modelling and word cloud for summarizing large amounts of textual data. Results show that applying corpus2question on a corpus of scientific articles related to COVID-19 yields relevant questions about the topic. The most frequent questions are what is covid 19 and what is the treatment for covid. Among the 1000 most frequent questions are what is the threshold for herd immunity and what is the role of ace2 in viral entry. We show that the proposed method generated similar questions for 13 of the 27 expert-made questions from the CovidQA question answering dataset. The code to reproduce our experiments and the generated questions are available at: https://github.com/unicamp-dl/corpus2question
COVID-19 pandemic has generated what public health officials called an infodemic of misinformation. As social distancing and stay-at-home orders came into effect, many turned to social media for socializing. This increase in social media usage has made it a prime vehicle for the spreading of misinformation. This paper presents a mechanism to detect COVID-19 health-related misinformation in social media following an interdisciplinary approach. Leveraging social psychology as a foundation and existing misinformation frameworks, we defined misinformation themes and associated keywords incorporated into the misinformation detection mechanism using applied machine learning techniques. Next, using the Twitter dataset, we explored the performance of the proposed methodology using multiple state-of-the-art machine learning classifiers. Our method shows promising results with at most 78% accuracy in classifying health-related misinformation versus true information using uni-gram-based NLP feature generations from tweets and the Decision Tree classifier. We also provide suggestions on alternatives for countering misinformation and ethical consideration for the study.
Information overload is a prevalent challenge in many high-value domains. A prominent case in point is the explosion of the biomedical literature on COVID-19, which swelled to hundreds of thousands of papers in a matter of months. In general, biomedical literature expands by two papers every minute, totalling over a million new papers every year. Search in the biomedical realm, and many other vertical domains is challenging due to the scarcity of direct supervision from click logs. Self-supervised learning has emerged as a promising direction to overcome the annotation bottleneck. We propose a general approach for vertical search based on domain-specific pretraining and present a case study for the biomedical domain. Despite being substantially simpler and not using any relevance labels for training or development, our method performs comparably or better than the best systems in the official TREC-COVID evaluation, a COVID-related biomedical search competition. Using distributed computing in modern cloud infrastructure, our system can scale to tens of millions of articles on PubMed and has been deployed as Microsoft Biomedical Search, a new search experience for biomedical literature: https://aka.ms/biomedsearch.
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