The year 2020 has seen an unprecedented COVID-19 pandemic due to the outbreak of a novel strain of coronavirus in 180 countries. In a desperate effort to discover new drugs and vaccines for COVID-19, many scientists are working around the clock. Their valuable time and effort may benefit from computer-based mining of a large volume of health science literature that is a treasure trove of information. In this paper, we have developed a graph-based model using abstracts of 10,683 scientific articles to find key information on three topics: transmission, drug types, and genome research related to coronavirus. A subgraph is built for each of the three topics to extract more topic-focused information. Within each subgraph, we use a betweenness centrality measurement to rank order the importance of keywords related to drugs, diseases, pathogens, hosts of pathogens, and biomolecules. The results reveal intriguing information about antiviral drugs (Chloroquine, Amantadine, Dexamethasone), pathogen-hosts (pigs, bats, macaque, cynomolgus), viral pathogens (zika, dengue, malaria, and several viruses in the coronaviridae virus family), and proteins and therapeutic mechanisms (oligonucleotide, interferon, glycoprotein) in connection with the core topic of coronavirus. The categorical summary of these keywords and topics may be a useful reference to expedite and recommend new and alternative directions for COVID-19 research.
We created this EVIDENCEMINER system for automatic textual evidence mining in COVID-19 literature. EVIDENCEMINER is a web-based system that lets users query a natural language statement and automatically retrieves textual evidence from a background corpora for life sciences. It is constructed in a completely automated way without any human effort for training data annotation. EVIDENCEMINER is supported by novel data-driven methods for distantly supervised named entity recognition and open information extraction. The named entities and meta-patterns are pre-computed and indexed offline to suppo…
COVID-19 is one of the most important topic these days, specifically on search engines and news. While fake news are easily shared, scientific papers are reliable sources where information can be extracted. With about 24,000 scientific publications on COVID-19 and related research on PUBMED, automatic computer-assisted analysis is required. In this paper, we develop two methodologies to get insights on specific sub-topics of interest and latest research sub-topics. They rely on natural language processing and graph-based visualizations. We run these methodologies on two cases: the virus origin…
The novel coronavirus (SARS-CoV-2) which causes COVID-19 is an ongoing pandemic. There are ongoing studies with up to hundreds of publications uploaded to databases daily. We are exploring the use-case of artificial intelligence and natural language processing in order to efficiently sort through these publications. We demonstrate that clinical trial information, preclinical studies, and a general topic model can be used as text mining data intelligence tools for scientists all over the world to use as a resource for their own research. To evaluate our method, several metrics are used to measu…
The Coronavirus pandemic created a global crisis that prompted immediate large-scale action, including economic shutdowns and mobility restrictions. These actions have had devastating effects on the economy, but some positive effects on the environment. As the world recovers from the pandemic, we ask the following question: What is the public attitude towards climate action during COVID-19 recovery and beyond? We answer this question by analyzing discussions on the Twitter social media platform. We find that most discussions support climate action and point out lessons learned during pandemic …
University of Delaware（特拉华大学）；Clemson University（克莱姆森大学）；Charter School of Wilmington（威尔明顿特许学校）；University of S. Carolina（南卡罗来纳大学）
In 2020, the White House released the, "Call to Action to the Tech Community on New Machine Readable COVID-19 Dataset," wherein artificial intelligence experts are asked to collect data and develop text mining techniques that can help the science community answer high-priority scientific questions related to COVID-19. The Allen Institute for AI and collaborators announced the availability of a rapidly growing open dataset of publications, the COVID-19 Open Research Dataset (CORD-19). As the pace of research accelerates, biomedical scientists struggle to stay current. To expedite their investig…
Jožef Stefan International Postgraduate School（约瑟夫·斯特凡国际研究生院）；Jožef Stefan Institute（约瑟夫·斯特凡研究所）；University of Ljubljana（卢布尔雅那大学）；University of Nova Gorica（新戈里察大学）；Temida d.o.o（Temida有限责任公司）
The abundance of literature related to the widespread COVID-19 pandemic is beyond manual inspection of a single expert. Development of systems, capable of automatically processing tens of thousands of scientific publications with the aim to enrich existing empirical evidence with literature-based associations is challenging and relevant. We propose a system for contextualization of empirical expression data by approximating relations between entities, for which representations were learned from one of the largest COVID-19-related literature corpora. In order to exploit a larger scientific cont…
Bangladesh University of Engineering and Technology（孟加拉国工程技术大学）；Hamad Bin Khalifa University（哈马德·本·哈利法大学）
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…
During the COVID-19 pandemic, the scientific literature related to SARS-COV-2 has been growing dramatically, both in terms of the number of publications and of its impact on people's life. This literature encompasses a varied set of sensible topics, ranging from vaccination, to protective equipment efficacy, to lockdown policy evaluation. Up to now, hundreds of thousands of papers have been uploaded on online repositories and published in scientific journals. As a result, the development of digital methods that allow an in-depth exploration of this growing literature has become a relevant issu…
Microsoft Developer Relations（微软开发者关系部）；Higher School of Economics（高等经济学院）；Phystech Lyceum（物理技术学院附属中学）
Since the beginning of COVID pandemic, there have been around 700000 scientific papers published on the subject. A human researcher cannot possibly get acquainted with such a huge text corpus -- and therefore developing AI-based tools to help navigating this corpus and deriving some useful insights from it is highly needed. In this paper, we will use Text Analytics for Health pre-trained service together with some cloud tools to extract some knowledge from scientific papers, gain insights, and build a tool to help researcher navigate the paper collection in a meaningful way.
SRM University, Andhra Pradesh（SRM大学（安得拉邦））；University of Huddersfield（哈德斯菲尔德大学）
The novel coronavirus disease (COVID-19) began in Wuhan, China, in late 2019 and to date has infected over 148M people worldwide, resulting in 3.12M deaths. On March 10, 2020, the World Health Organisation (WHO) declared it as a global pandemic. Many academicians and researchers started to publish papers describing the latest discoveries on covid-19. The large influx of publications made it hard for other researchers to go through a large amount of data and find the appropriate one that helps their research. So, the proposed model attempts to extract relavent titles from the large corpus of re…
Diachronic text mining has frequently been applied to long-term linguistic surveys of word meaning and usage shifts over time. In this paper we apply short-term diachronic text mining to a rapidly growing corpus of scientific publications on COVID-19 captured in the CORD-19 dataset in order to identify co-occurrences and analyze the behavior of potential candidate treatments. We used a data set associated with a COVID-19 drug re-purposing study from Oak Ridge National Laboratory. This study identified existing candidate coronavirus treatments, including drugs and approved compounds, which had …
In recent years, several research articles have been published in the field of corona-virus caused diseases like severe acute respiratory syndrome (SARS), middle east respiratory syndrome (MERS) and COVID-19. In the presence of numerous research articles, extracting best-suited articles is time-consuming and manually impractical. The objective of this paper is to extract the activity and trends of corona-virus related research articles using machine learning approaches. The COVID-19 open research dataset (CORD-19) is used for experiments, whereas several target-tasks along with explanations ar…
The scientific community is facing one of its greatest challenges in solving a global health problem: COVID-19 pandemic. This situation has generated an unprecedented volume of publications. What is the volume, in terms of publications, of research on COVID-19? The general objective of this research work is to obtain a global vision of the daily growth of scientific production on COVID-19 in different databases (Dimensions, Web of Science Core Collection, Scopus-Elsevier, Pubmed and eight repositories). In relation to the results obtained, Dimensions indexes a total of 9435 publications (69% w…
The University of Melbourne（墨尔本大学）；IBM Research Australia（IBM澳大利亚研究院）
We present COVID-SEE, a system for medical literature discovery based on the concept of information exploration, which builds on several distinct text analysis and natural language processing methods to structure and organise information in publications, and augments search by providing a visual overview supporting exploration of a collection to identify key articles of interest. We developed this system over COVID-19 literature to help medical professionals and researchers explore the literature evidence, and improve findability of relevant information. COVID-SEE is available at http://covid-…
School of Information and Communication Engineering, Hainan University（海南大学信息与通信工程学院）；School of Computer Science and Cyberspace Security, Hainan University（海南大学计算机与网络空间安全学院）；University of Chinese Academy of Sciences（中国科学院大学）；National University of Defense Technology（国防科技大学）；Department of Mathematics and Computer Science, Northeastern State University（东北州立大学数学与计算机科学系）
With the spread and development of new epidemics, it is of great reference value to identify the changing trends of epidemics in public emotions. We designed and implemented the COVID-19 public opinion monitoring system based on time series thermal new word mining. A new word structure discovery scheme based on the timing explosion of network topics and a Chinese sentiment analysis method for the COVID-19 public opinion environment is proposed. Establish a "Scrapy-Redis-Bloomfilter" distributed crawler framework to collect data. The system can judge the positive and negative emotions of the re…
The workshop "Mining Scientific Papers: Computational Linguistics and Bibliometrics" (CLBib 2015), co-located with the 15th International Society of Scientometrics and Informetrics Conference (ISSI 2015), brought together researchers in Bibliometrics and Computational Linguistics in order to study the ways Bibliometrics can benefit from large-scale text analytics and sense mining of scientific papers, thus exploring the interdisciplinarity of Bibliometrics and Natural Language Processing (NLP). The goals of the workshop were to answer questions like: How can we enhance author network analysis …
The outbreak of covid-19 started many months ago, the reported origin was in Wuhan Market, China. Fastly, this virus was propagated to other countries because the access to international travels is affordable and many countries have a distance of some flight hours, besides borders were a constant flow of people. By the other hand, Internet users have the habits of sharing content using Social Networks and issues, problems, thoughts about Covdid-19 were not an exception. Therefore, it is possible to analyze Social Network interaction from one city, country to understand the impact generated by …
We present an overview of the TREC-COVID Challenge, an information retrieval (IR) shared task to evaluate search on scientific literature related to COVID-19. The goals of TREC-COVID include the construction of a pandemic search test collection and the evaluation of IR methods for COVID-19. The challenge was conducted over five rounds from April to July, 2020, with participation from 92 unique teams and 556 individual submissions. A total of 50 topics (sets of related queries) were used in the evaluation, starting at 30 topics for Round 1 and adding 5 new topics per round to target emerging to…
CSIRO Data61（澳大利亚联邦科学与工业研究组织 Data61）；The Australian National University（澳大利亚国立大学）
Finding answers related to a pandemic of a novel disease raises new challenges for information seeking and retrieval, as the new information becomes available gradually. TREC COVID search track aims to assist in creating search tools to aid scientists, clinicians, policy makers and others with similar information needs in finding reliable answers from the scientific literature. We experiment with different ranking algorithms as part of our participation in this challenge. We propose a novel method for neural retrieval, and demonstrate its effectiveness on the TREC COVID search.
University of Copenhagen（哥本哈根大学）；Aalborg University（奥尔堡大学）
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 D…
Since the emergence of the worldwide pandemic of COVID-19, relevant research has been published at a dazzling pace, which yields an abundant amount of big data in biomedical literature. Due to the high volum of relevant literature, it is practically impossible to follow up the research manually. Topic modeling is a well-known unsupervised learning that aims to reveal latent topics from text data. In this paper, we propose a novel analytical framework for estimating topic interactions and effective visualization to improve topics' relationships. We first estimate topic-word distributions using …
Allen Institute for Artificial Intelligence（艾伦人工智能研究所）；Paul G. Allen School for Computer Science & Engineering, University of Washington（华盛顿大学保罗·G·艾伦计算机科学与工程学院）；Information School, University of Washington（华盛顿大学信息学院）；Microsoft Research（微软研究院）；University of California, Berkeley（加利福尼亚大学伯克利分校）
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…
The coronavirus disease (COVID-19) has claimed the lives of over 350,000 people and infected more than 6 million people worldwide. Several search engines have surfaced to provide researchers with additional tools to find and retrieve information from the rapidly growing corpora on COVID-19. These engines lack extraction and visualization tools necessary to retrieve and interpret complex relations inherent to scientific literature. Moreover, because these engines mainly rely upon semantic information, their ability to capture complex global relationships across documents is limited, which reduc…
Future works in scientific articles are valuable for researchers and they can guide researchers to new research directions or ideas. In this paper, we mine the future works in scientific articles in order to 1) provide an insight for future work analysis and 2) facilitate researchers to search and browse future works in a research area. First, we study the problem of future work extraction and propose a regular expression based method to address the problem. Second, we define four different categories for the future works by observing the data and investigate the multi-class future work classi…
Georgetown University（乔治城大学）；Allen Institute for AI（艾伦人工智能研究所）
With worldwide concerns surrounding the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), there is a rapidly growing body of literature on the virus. Clinicians, researchers, and policy-makers need a way to effectively search these articles. In this work, we present a search system called SLEDGE, which utilizes SciBERT to effectively re-rank articles. We train the model on a general-domain answer ranking dataset, and transfer the relevance signals to SARS-CoV-2 for evaluation. We observe SLEDGE's effectiveness as a strong baseline on the TREC-COVID challenge (topping the learderboa…
Literature analysis facilitates researchers better understanding the development of science and technology. The conventional literature analysis focuses on the topics, authors, abstracts, keywords, references, etc., and rarely pays attention to the content of papers. In the field of machine learning, the involved methods (M) and datasets (D) are key information in papers. The extraction and mining of M and D are useful for discipline analysis and algorithm recommendation. In this paper, we propose a novel entity recognition model, called MDER, and constructe datasets from the papers of the PAK…
Institute of Mathematics and Computer Science (ICMC) University of São Paulo (USP)（圣保罗大学数学与计算机科学研究所）；National University of Moquegua（莫克瓜国立大学）
During the last decade, Peruvian government started to invest and promote Science and Technology through Concytec(National Council of Science and Technology). Many programs are oriented to support research projects, expenses for paper presentation, organization of conferences/ events and more. Concytec created a National Directory of Researchers(DINA) where professionals can create and add curriculum vitae, Concytec can provide official title of Researcher following some criterion for the evaluation. The actual paper aims to conduct an exploratory analysis over the curriculum vitae of Peruvian…
TREC-COVID is a community evaluation designed to build a test collection that captures the information needs of biomedical researchers using the scientific literature during a pandemic. One of the key characteristics of pandemic search is the accelerated rate of change: the topics of interest evolve as the pandemic progresses and the scientific literature in the area explodes. The COVID-19 pandemic provides an opportunity to capture this progression as it happens. TREC-COVID, in creating a test collection around COVID-19 literature, is building infrastructure to support new research and techno…
As the COVID-19 pandemic continues its march around the world, an unprecedented amount of open data is being generated for genetics and epidemiological research. The unparalleled rate at which many research groups around the world are releasing data and publications on the ongoing pandemic is allowing other scientists to learn from local experiences and data generated in the front lines of the COVID-19 pandemic. However, there is a need to integrate additional data sources that map and measure the role of social dynamics of such a unique world-wide event into biomedical, biological, and epidem…
Georgetown University（乔治城大学）；Allen Institute for AI（艾伦人工智能研究所）
With worldwide concerns surrounding the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), there is a rapidly growing body of scientific literature on the virus. Clinicians, researchers, and policy-makers need to be able to search these articles effectively. In this work, we present a zero-shot ranking algorithm that adapts to COVID-related scientific literature. Our approach filters training data from another collection down to medical-related queries, uses a neural re-ranking model pre-trained on scientific text (SciBERT), and filters the target document collection. This approach …
Jožef Stefan Institute（约瑟夫·斯蒂芬研究所）；Jožef Stefan International Postgraduate School（约瑟夫·斯蒂芬国际研究生院）；University of Maribor（马里博尔大学）
The COVID-19 pandemic triggered a wave of novel scientific literature that is impossible to inspect and study in a reasonable time frame manually. Current machine learning methods offer to project such body of literature into the vector space, where similar documents are located close to each other, offering an insightful exploration of scientific papers and other knowledge sources associated with COVID-19. However, to start searching, such texts need to be appropriately annotated, which is seldom the case due to the lack of human resources. In our system, the current body of COVID-19-related …
The scientific papers dealing with the novel betacoronavirus SARS-CoV-2 and the coronavirus disease 2019 (COVID-19) caused by this virus, published in 2020 and recorded in the database PUBMED, were retrieved on April 27, 2020. About 20\% of the records contain Medical Subject Headings (MeSH), keywords assigned to records in the course of the indexing process in order to summarise the articles' contents. The temporal sequence of the first occurrences of the keywords was determined, thus giving insight into the growth of the knowledge base of the pandemic.
We describe the application of data mining algorithms to research problems in astronomy. We posit that data mining has always been fundamental to astronomical research, since data mining is the basis of evidence-based discovery, including classification, clustering, and novelty discovery. These algorithms represent a major set of computational tools for discovery in large databases, which will be increasingly essential in the era of data-intensive astronomy. Historical examples of data mining in astronomy are reviewed, followed by a discussion of one of the largest data-producing projects anti…
Univ. of Maryland, Baltimore County（马里兰大学巴尔的摩县分校）；Booz Allen Hamilton（博思艾伦汉密尔顿）
The world has faced the devastating outbreak of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), or COVID-19, in 2020. Research in the subject matter was fast-tracked to such a point that scientists were struggling to keep up with new findings. With this increase in the scientific literature, there arose a need for organizing those documents. We describe an approach to organize and visualize the scientific literature on or related to COVID-19 using machine learning techniques so that papers on similar topics are grouped together. By doing so, the navigation of topics and related p…
Coronavirus disease (COVID-19) has been declared as a pandemic by WHO with thousands of cases being reported each day. Numerous scientific articles are being published on the disease raising the need for a service which can organize, and query them in a reliable fashion. To support this cause we present AWS CORD-19 Search (ACS), a public, COVID-19 specific, neural search engine that is powered by several machine learning systems to support natural language based searches. ACS with capabilities such as document ranking, passage ranking, question answering and topic classification provides a sca…
The COVID-19 pandemic has gained worldwide attention and allowed fake news, such as ``COVID-19 is the flu,'' to spread quickly and widely on social media. Combating this coronavirus infodemic demands effective methods to detect fake news. To this end, we propose a method to infer news credibility from hashtags involved in news dissemination on social media, motivated by the tight connection between hashtags and news credibility observed in our empirical analyses. We first introduce a new graph that captures all (direct and \textit{indirect}) relationships among hashtags. Then, a language-indep…
University of Washington（华盛顿大学）；Allen Institute for Artificial Intelligence（艾伦人工智能研究所）；Swedish Medical Group（瑞典医疗集团）；Microsoft Research（微软研究院）；The Hebrew University of Jerusalem（耶路撒冷希伯来大学）
The COVID-19 pandemic has spawned a diverse body of scientific literature that is challenging to navigate, stimulating interest in automated tools to help find useful knowledge. We pursue the construction of a knowledge base (KB) of mechanisms -- a fundamental concept across the sciences encompassing activities, functions and causal relations, ranging from cellular processes to economic impacts. We extract this information from the natural language of scientific papers by developing a broad, unified schema that strikes a balance between relevance and breadth. We annotate a dataset of mechanism…
We present CAiRE-COVID, a real-time question answering (QA) and multi-document summarization system, which won one of the 10 tasks in the Kaggle COVID-19 Open Research Dataset Challenge, judged by medical experts. Our system aims to tackle the recent challenge of mining the numerous scientific articles being published on COVID-19 by answering high priority questions from the community and summarizing salient question-related information. It combines information extraction with state-of-the-art QA and query-focused multi-document summarization techniques, selecting and highlighting evidence sni…
University of Waterloo（滑铁卢大学）；New York University（纽约大学）；Facebook AI Research（Facebook人工智能研究院）
We present the Neural Covidex, a search engine that exploits the latest neural ranking architectures to provide information access to the COVID-19 Open Research Dataset curated by the Allen Institute for AI. This web application exists as part of a suite of tools that we have developed over the past few weeks to help domain experts tackle the ongoing global pandemic. We hope that improved information access capabilities to the scientific literature can inform evidence-based decision making and insight generation. This paper describes our initial efforts and offers a few thoughts about lessons …
State University of New York at Buffalo（纽约州立大学布法罗分校）
The Covid-19 pandemic has caused a spur in the medical research literature. With new research advances in understanding the virus, there is a need for robust text mining tools which can process, extract and present answers from the literature in a concise and consumable way. With a DialoGPT based multi-turn conversation generation module, and BM-25 \& neural embeddings based ensemble information retrieval module, in this paper we present a conversational system, which can retrieve and answer coronavirus-related queries from the rich medical literature, and present it in a conversational settin…
University of Maribor（马里博尔大学）；General Hospital Murska Sobota（穆尔斯卡索博塔综合医院）
A COVID-19 pandemic has already proven itself to be a global challenge. It proves how vulnerable humanity can be. It has also mobilized researchers from different sciences and different countries in the search for a way to fight this potentially fatal disease. In line with this, our study analyses the abstracts of papers related to COVID-19 and coronavirus-related-research using association rule text mining in order to find the most interestingness words, on the one hand, and relationships between them on the other. Then, a method, called information cartography, was applied for extracting str…
The COVID-19 global pandemic has resulted in international efforts to understand, track, and mitigate the disease, yielding a significant corpus of COVID-19 and SARS-CoV-2-related publications across scientific disciplines. As of May 2020, 128,000 coronavirus-related publications have been collected through the COVID-19 Open Research Dataset Challenge. Here we present CO-Search, a retriever-ranker semantic search engine designed to handle complex queries over the COVID-19 literature, potentially aiding overburdened health workers in finding scientific answers during a time of crisis. The retri…
The COVID-19 pandemic has resulted in a tremendous need for access to the latest scientific information, primarily through the use of text mining and search tools. This has led to both corpora for biomedical articles related to COVID-19 (such as the CORD-19 corpus (Wang et al., 2020)) as well as search engines to query such data. While most research in search engines is performed in the academic field of information retrieval (IR), most academic search engines$\unicode{x2013}$though rigorously evaluated$\unicode{x2013}$are sparsely utilized, while major commercial web search engines (e.g., Goo…
Pune Institute of Computer Technology（浦那计算机技术学院）；Indian Institute of Technology Madras（马德拉斯印度理工学院）
Social media platforms like Facebook, Twitter, and Instagram have enabled connection and communication on a large scale. It has revolutionized the rate at which information is shared and enhanced its reach. However, another side of the coin dictates an alarming story. These platforms have led to an increase in the creation and spread of fake news. The fake news has not only influenced people in the wrong direction but also claimed human lives. During these critical times of the Covid19 pandemic, it is easy to mislead people and make them believe in fatal information. Therefore it is important …
The amount of scientific papers published every day is daunting and constantly increasing. Keeping up with literature represents a challenge. If one wants to start exploring new topics it is hard to have a big picture without reading lots of articles. Furthermore, as one reads through literature, making mental connections is crucial to ask new questions which might lead to discoveries. In this work, I present a web tool which uses a Text Mining strategy to transform large collections of unstructured biomedical articles into structured data. Generated results give a quick overview on complex to…
