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Register a new userSciSight: Combining faceted navigation and research group detection for COVID-19 exploratory scientific search
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Added by
Tom Hope
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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The COVID-19 pandemic has sparked unprecedented mobilization of scientists, generating a deluge of papers that makes it hard for researchers to keep track and explore new directions. Search engines are designed for targeted queries, not for discovery of connections across a corpus. In this paper, we present SciSight, a system for exploratory search of COVID-19 research integrating two key capabilities: first, exploring associations between biomedical facets automatically extracted from papers (e.g., genes, drugs, diseases, patient outcomes); second, combining textual and network information to search and visualize groups of researchers and their ties. SciSight has so far served over $15K$ users with over $42K$ page views and $13%$ returns.
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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.
Searching for concepts in science and technology is often a difficult task. To facilitate concept search, different types of human-generated metadata have been created to define the content of scientific and technical disclosures. Classification schemes such as the International Patent Classification (IPC) and MEDLINEs MeSH are structured and controlled, but require trained experts and central management to restrict ambiguity (Mork, 2013). While unstructured tags of folksonomies can be processed to produce a degree of structure (Kalendar, 2010; Karampinas, 2012; Sarasua, 2012; Bragg, 2013) the freedom enjoyed by the crowd typically results in less precision (Stock 2007). Existing classification schemes suffer from inflexibility and ambiguity. Since humans understand language, inference, implication, abstraction and hence concepts better than computers, we propose to harness the collective wisdom of the crowd. To do so, we propose a novel classification scheme that is sufficiently intuitive for the crowd to use, yet powerful enough to facilitate search by analogy, and flexible enough to deal with ambiguity. The system will enhance existing classification information. Linking up with the semantic web and computer intelligence, a Citizen Science effort (Good, 2013) would support innovation by improving the quality of granted patents, reducing duplicitous research, and stimulating problem-oriented solution design. A prototype of our design is in preparation. A crowd-sourced fuzzy and faceted classification scheme will allow for better concept search and improved access to prior art in science and technology.
In this study, we investigate the scientific research response from the early stages of the pandemic, and we review key findings on how the early warning systems developed in previous epidemics responded to contain the virus. The data records are analysed with commutable statistical methods, including R Studio, Bibliometrix package, and the Web of Science data mining tool. We identified few different clusters, containing references to exercise, inflammation, smoking, obesity and many additional factors. From the analysis on Covid-19 and vaccine, we discovered that although the USA is leading in volume of scientific research on Covid 19 vaccine, the leading 3 research institutions (Fudan, Melbourne, Oxford) are not based in the USA. Hence, it is difficult to predict which country would be first to produce a Covid 19 vaccine.
We present Covidex, a search engine that exploits the latest neural ranking models to provide information access to the COVID-19 Open Research Dataset curated by the Allen Institute for AI. Our system has been online and serving users since late March 2020. The Covidex is the user application component of our three-pronged strategy to develop technologies for helping domain experts tackle the ongoing global pandemic. In addition, we provide robust and easy-to-use keyword search infrastructure that exploits mature fusion-based methods as well as standalone neural ranking models that can be incorporated into other applications. These techniques have been evaluated in the ongoing TREC-COVID challenge: Our infrastructure and baselines have been adopted by many participants, including some of the highest-scoring runs in rounds 1, 2, and 3. In round 3, we report the highest-scoring run that takes advantage of previous training data and the second-highest fully automatic run.
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.
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