The recent outbreak of the novel coronavirus is wreaking havoc on the world and researchers are struggling to effectively combat it. One reason why the fight is difficult is due to the lack of information and knowledge. In this work, we outline our effort to contribute to shrinking this knowledge vacuum by creating covidAsk, a question answering (QA) system that combines biomedical text mining and QA techniques to provide answers to questions in real-time. Our system also leverages information retrieval (IR) approaches to provide entity-level answers that are complementary to QA models. Evaluation of covidAsk is carried out by using a manually created dataset called COVID-19 Questions which is based on information from various sources, including the CDC and the WHO. We hope our system will be able to aid researchers in their search for knowledge and information not only for COVID-19, but for future pandemics as well.
Ever since the COVID-19 pandemic broke out, the academic and scientific research community, as well as industry and governments around the world have joined forces in an unprecedented manner to fight the threat. Clinicians, biologists, chemists, bioinformaticians, nurses, data scientists, and all of the affiliated relevant disciplines have been mobilized to help discover efficient treatments for the infected population, as well as a vaccine solution to prevent further the virus spread. In this combat against the virus responsible for the pandemic, key for any advancements is the timely, accurate, peer-reviewed, and efficient communication of any novel research findings. In this paper we present a novel framework to address the information need of filtering efficiently the scientific bibliography for relevant literature around COVID-19. The contributions of the paper are summarized in the following: we define and describe the information need that encompasses the major requirements for COVID-19 articles relevancy, we present and release an expert-curated benchmark set for the task, and we analyze the performance of several state-of-the-art machine learning classifiers that may distinguish the relevant from the non-relevant COVID-19 literature.
The Covid-19 pandemic urged the scientific community to join efforts at an unprecedented scale, leading to faster than ever dissemination of data and results, which in turn motivated more research works. This paper presents and discusses information retrieval models aimed at addressing the challenge of searching the large number of publications that stem from these studies. The model presented, based on classical baselines followed by an interaction based neural ranking model, was evaluated and evolved within the TREC Covid challenge setting. Results on this dataset show that, when starting with a strong baseline, our light neural ranking model can achieve results that are comparable to other model architectures that use very large number of parameters.
A dataset of COVID-19-related scientific literature is compiled, combining the articles from several online libraries and selecting those with open access and full text available. Then, hierarchical nonnegative matrix factorization is used to organize literature related to the novel coronavirus into a tree structure that allows researchers to search for relevant literature based on detected topics. We discover eight major latent topics and 52 granular subtopics in the body of literature, related to vaccines, genetic structure and modeling of the disease and patient studies, as well as related diseases and virology. In order that our tool may help current researchers, an interactive website is created that organizes available literature using this hierarchical structure.
The COVID-19 pandemic is the worst pandemic to strike the world in over a century. Crucial to stemming the tide of the SARS-CoV-2 virus is communicating to vulnerable populations the means by which they can protect themselves. To this end, the collaborators forming the Translation Initiative for COvid-19 (TICO-19) have made test and development data available to AI and MT researchers in 35 different languages in order to foster the development of tools and resources for improving access to information about COVID-19 in these languages. In addition to 9 high-resourced, ”pivot” languages, the team is targeting 26 lesser resourced languages, in particular languages of Africa, South Asia and South-East Asia, whose populations may be the most vulnerable to the spread of the virus. The same data is translated into all of the languages represented, meaning that testing or development can be done for any pairing of languages in the set. Further, the team is converting the test and development data into translation memories (TMXs) that can be used by localizers from and to any of the languages.
The ongoing COVID-19 pandemic has raised concerns for many regarding personal and public health implications, financial security and economic stability. Alongside many other unprecedented challenges, there are increasing concerns over social isolation and mental health. We introduce Expressive Interviewing – an interview-style conversational system that draws on ideas from motivational interviewing and expressive writing. Expressive Interviewing seeks to encourage users to express their thoughts and feelings through writing by asking them questions about how COVID-19 has impacted their lives. We present relevant aspects of the system’s design and implementation as well as quantitative and qualitative analyses of user interactions with the system. In addition, we conduct a comparative evaluation with a general purpose dialogue system for mental health that shows our system potential in helping users to cope with COVID-19 issues.
We describe a set of experiments for building a temporal mental health dynamics system. We utilise a pre-existing methodology for distant- supervision of mental health data mining from social media platforms and deploy the system during the global COVID-19 pandemic as a case study. Despite the challenging nature of the task, we produce encouraging results, both explicit to the global pandemic and implicit to a global phenomenon, Christmas Depres- sion, supported by the literature. We propose a methodology for providing insight into tem- poral mental health dynamics to be utilised for strategic decision-making.
The COVID-19 pandemic, like many of the disease outbreaks that have preceded it, is likely to have a profound effect on mental health. Understanding its impact can inform strategies for mitigating negative consequences. In this work, we seek to better understand the effects of COVID-19 on mental health by examining discussions within mental health support communities on Reddit. First, we quantify the rate at which COVID-19 is discussed in each community, or subreddit, in order to understand levels of pandemic-related discussion. Next, we examine the volume of activity in order to determine whether the number of people discussing mental health has risen. Finally, we analyze how COVID-19 has influenced language use and topics of discussion within each subreddit.
Public health surveillance and tracking virus via social media can be a useful digital tool for contact tracing and preventing the spread of the virus. Nowadays, large volumes of COVID-19 tweets can quickly be processed in real-time to offer information to researchers. Nonetheless, due to the absence of labeled data for COVID-19, the preliminary supervised classifier or semi-supervised self-labeled methods will not handle non-spherical data with adequate accuracy. With the seasonal influenza and novel Coronavirus having many similar symptoms, we propose using few shot learning to fine-tune a semi-supervised model built on unlabeled COVID-19 and previously labeled influenza dataset that can provide in- sights into COVID-19 that have not been investigated. The experimental results show the efficacy of the proposed model with an accuracy of 86%, identification of Covid-19 related discussion using recently collected tweets.
Our ability to limit the future spread of COVID-19 will in part depend on our understanding of the psychological and sociological processes that lead people to follow or reject coronavirus health behaviors. We argue that the virus has taken on heterogeneous meanings in communities across the United States and that these disparate meanings shaped communities’ response to the virus during the early, vital stages of the outbreak in the U.S. Using word embeddings, we demonstrate that counties where residents socially distanced less on average (as measured by residential mobility) more semantically associated the virus in their COVID discourse with concepts of fraud, the political left, and more benign illnesses like the flu. We also show that the different meanings the virus took on in different communities explains a substantial fraction of what we call the “”Trump Gap”, or the empirical tendency for more Trump-supporting counties to socially distance less. This work demonstrates that community-level processes of meaning-making in part determined behavioral responses to the COVID-19 pandemic and that these processes can be measured unobtrusively using Twitter.
The ongoing pandemic has heightened the need for developing tools to flag COVID-19-related misinformation on the internet, specifically on social media such as Twitter. However, due to novel language and the rapid change of information, existing misinformation detection datasets are not effective for evaluating systems designed to detect misinformation on this topic. Misinformation detection can be divided into two sub-tasks: (i) retrieval of misconceptions relevant to posts being checked for veracity, and (ii) stance detection to identify whether the posts Agree, Disagree, or express No Stance towards the retrieved misconceptions. To facilitate research on this task, we release COVIDLies (https://ucinlp.github.io/covid19 ), a dataset of 6761 expert-annotated tweets to evaluate the performance of misinformation detection systems on 86 different pieces of COVID-19 related misinformation. We evaluate existing NLP systems on this dataset, providing initial benchmarks and identifying key challenges for future models to improve upon.
Efficient discovery and exploration of biomedical literature has grown in importance in the context of the COVID-19 pandemic, and topic-based methods such as latent Dirichlet allocation (LDA) are a useful tool for this purpose. In this study we compare traditional topic models based on word tokens with topic models based on medical concepts, and propose several ways to improve topic coherence and specificity.
The global pandemic of COVID-19 has made the public pay close attention to related news, covering various domains, such as sanitation, treatment, and effects on education. Meanwhile, the COVID-19 condition is very different among the countries (e.g., policies and development of the epidemic), and thus citizens would be interested in news in foreign countries. We build a system for worldwide COVID-19 information aggregation containing reliable articles from 10 regions in 7 languages sorted by topics. Our reliable COVID-19 related website dataset collected through crowdsourcing ensures the quality of the articles. A neural machine translation module translates articles in other languages into Japanese and English. A BERT-based topic-classifier trained on our article-topic pair dataset helps users find their interested information efficiently by putting articles into different categories.
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 snippets from existing literature given a query. We also propose query-focused abstractive and extractive multi-document summarization methods, to provide more relevant information related to the question. We further conduct quantitative experiments that show consistent improvements on various metrics for each module. We have launched our website CAiRE-COVID for broader use by the medical community, and have open-sourced the code for our system, to bootstrap further study by other researches.
We present a Question Answering (QA) system that won one of the tasks of the Kaggle CORD-19 Challenge, according to the qualitative evaluation of experts. The system is a combination of an Information Retrieval module and a reading comprehension module that finds the answers in the retrieved passages. In this paper we present a quantitative and qualitative analysis of the system. The quantitative evaluation using manually annotated datasets contradicted some of our design choices, e.g. the fact that using QuAC for fine-tuning provided better answers over just using SQuAD. We analyzed this mismatch with an additional A/B test which showed that the system using QuAC was indeed preferred by users, confirming our intuition. Our analysis puts in question the suitability of automatic metrics and its correlation to user preferences. We also show that automatic metrics are highly dependent on the characteristics of the gold standard, such as the average length of the answers.
We release a multilingual neural machine translation model, which can be used to translate text in the biomedical domain. The model can translate from 5 languages (French, German, Italian, Korean and Spanish) into English. It is trained with large amounts of generic and biomedical data, using domain tags. Our benchmarks show that it performs near state-of-the-art both on news (generic domain) and biomedical test sets, and that it outperforms the existing publicly released models. We believe that this release will help the large-scale multilingual analysis of the digital content of the COVID-19 crisis and of its effects on society, economy, and healthcare policies. We also release a test set of biomedical text for Korean-English. It consists of 758 sentences from official guidelines and recent papers, all about COVID-19.
Public sentiment (the opinion, attitude or feeling that the public expresses) is a factor of interest for government, as it directly influences the implementation of policies. Given the unprecedented nature of the COVID-19 crisis, having an up-to-date representation of public sentiment on governmental measures and announcements is crucial. In this paper, we analyse Dutch public sentiment on governmental COVID-19 measures from text data collected across three online media sources (Twitter, Reddit and Nu.nl) from February to September 2020. We apply sentiment analysis methods to analyse polarity over time, as well as to identify stance towards two specific pandemic policies regarding social distancing and wearing face masks. The presented preliminary results provide valuable insights into the narratives shown in vast social media text data, which help understand the influence of COVID-19 measures on the general public.
Social media is a rich source where we can learn about people’s reactions to social issues. As COVID-19 has significantly impacted on people’s lives, it is essential to capture how people react to public health interventions and understand their concerns. In this paper, we aim to investigate people’s reactions and concerns about COVID-19 in North America, especially focusing on Canada. We analyze COVID-19 related tweets using topic modeling and aspect-based sentiment analysis, and interpret the results with public health experts. We compare timeline of topics discussed with timing of implementation of public health interventions for COVID-19. We also examine people’s sentiment about COVID-19 related issues. We discuss how the results can be helpful for public health agencies when designing a policy for new interventions. Our work shows how Natural Language Processing (NLP) techniques could be applied to public health questions with domain expert involvement.
The COVID-19 outbreak is an ongoing worldwide pandemic that was announced as a global health crisis in March 2020. Due to the enormous challenges and high stakes of this pandemic, governments have implemented a wide range of policies aimed at containing the spread of the virus and its negative effect on multiple aspects of our life. Public responses to various intervention measures imposed over time can be explored by analyzing the social media. Due to the shortage of available labeled data for this new and evolving domain, we apply data distillation methodology to labeled datasets from related tasks and a very small manually labeled dataset. Our experimental results show that data distillation outperforms other data augmentation methods on our task.
With the increasing number of publications about COVID-19, it is a challenge to extract personalized knowledge suitable for each researcher. This work aims to build a new semantic-based pipeline for recommending biomedical entities to scientific researchers. To this end, we developed a pipeline that creates an implicit feedback matrix based on Named Entity Recognition (NER) on a corpus of documents, using multidisciplinary ontologies for recognizing and linking the entities. Our hypothesis is that by using ontologies from different fields in the NER phase, we can improve the results for state-of-the-art collaborative-filtering recommender systems applied to the dataset created. The tests performed using the COVID-19 Open Research Dataset (CORD-19) dataset show that when using four ontologies, the results for precision@k, for example, reach the 80%, whereas when using only one ontology, the results for precision@k drops to 20%, for the same users. Furthermore, the use of multi-fields entities may help in the discovery of new items, even if the researchers do not have items from that field in their set of preferences.
Coronavirus Disease of 2019 (COVID-19) created dire consequences globally and triggered an intense scientific effort from different domains. The resulting publications created a huge text collection in which finding the studies related to a biomolecule of interest is challenging for general purpose search engines because the publications are rich in domain specific terminology. Here, we present Vapur: an online COVID-19 search engine specifically designed to find related protein - chemical pairs. Vapur is empowered with a relation-oriented inverted index that is able to retrieve and group studies for a query biomolecule with respect to its related entities. The inverted index of Vapur is automatically created with a BioNLP pipeline and integrated with an online user interface. The online interface is designed for the smooth traversal of the current literature by domain researchers and is publicly available at https://tabilab.cmpe.boun.edu.tr/vapur/.
This paper presents the preliminary results of an ongoing project that analyzes the growing body of scientific research published around the COVID-19 pandemic. In this research, a general-purpose semantic model is used to double annotate a batch of $500$ sentences that were manually selected by the researchers from the CORD-19 corpus. Afterwards, a baseline text-mining pipeline is designed and evaluated via a large batch of $100,959$ sentences. We present a qualitative analysis of the most interesting facts automatically extracted and highlight possible future lines of development. The preliminary results show that general-purpose semantic models are a useful tool for discovering fine-grained knowledge in large corpora of scientific documents.
The COVID-19 pandemic has thrown natural life out of gear across the globe. Strict measures are deployed to curb the spread of the virus that is causing it, and the most effective of them have been social isolation. This has led to wide-spread gloom and depression across society but more so among the young and the elderly. There are currently more than 200 million college students in 186 countries worldwide, affected due to the pandemic. The mode of education has changed suddenly, with the rapid adaptation of e-learning, whereby teaching is undertaken remotely and on digital platforms. This study presents insights gathered from social media posts that were posted by students and young adults during the COVID times. Using statistical and NLP techniques, we analyzed the behavioural issues reported by users themselves in their posts in depression related communities on Reddit. We present methodologies to systematically analyze content using linguistic techniques to find out the stress-inducing factors. Online education, losing jobs, isolation from friends and abusive families emerge as key stress factors
The coronavirus disease of 2019 (COVID-19) has a huge impact on economies and societies around the world. While governments are taking extreme measures to reduce the spread of the virus, people are getting affected by these new measures. With restrictions like lockdown and social distancing, it became important to understand the emotional response of the public towards the pandemic. In this paper, we study the reaction of Saudi Arabia citizens towards the pandemic. We utilize a collection of Arabic tweets that were sent during 2020, primarily through hashtags that were originated from Saudi Arabia. Our results showed that people had kept a positive reaction towards the pandemic. This positive reaction was at its highest at the beginning of the COVID-19 crisis and started to decline as time passes. Overall, the results showed that people were so supportive of each other through this pandemic. This research can help researchers and policymakers in understanding the emotional effect of a pandemic on societies.
Since the classification of COVID-19 as a global pandemic, there have been many attempts to treat and contain the virus. Although there is no specific antiviral treatment recommended for COVID-19, there are several drugs that can potentially help with symptoms. In this work, we mined a large twitter dataset of 424 million tweets of COVID-19 chatter to identify discourse around drug mentions. While seemingly a straightforward task, due to the informal nature of language use in Twitter, we demonstrate the need of machine learning alongside traditional automated methods to aid in this task. By applying these complementary methods, we are able to recover almost 15% additional data, making misspelling handling a needed task as a pre-processing step when dealing with social media data.
Iran, along with China, South Korea, and Italy was among the countries that were hit hard in the first wave of the COVID-19 spread. Twitter is one of the widely-used online platforms by Iranians inside and abroad for sharing their opinion, thoughts, and feelings about a wide range of issues. In this study, using more than 530,000 original tweets in Persian/Farsi on COVID-19, we analyzed the topics discussed among users, who are mainly Iranians, to gauge and track the response to the pandemic and how it evolved over time. We applied a combination of manual annotation of a random sample of tweets and topic modeling tools to classify the contents and frequency of each category of topics. We identified the top 25 topics among which living experience under home quarantine emerged as a major talking point. We additionally categorized the broader content of tweets that shows satire, followed by news, is the dominant tweet type among Iranian users. While this framework and methodology can be used to track public response to ongoing developments related to COVID-19, a generalization of this framework can become a useful framework to gauge Iranian public reaction to ongoing policy measures or events locally and internationally.
The COVID-19 pandemic has been accompanied by such an explosive increase in media coverage and scientific publications that researchers find it difficult to keep up. We are presenting a publicly available pipeline to perform named entity recognition and normalisation in parallel to help find relevant publications and to aid in downstream NLP tasks such as text summarisation. In our approach, we are using a dictionary-based system for its high recall in conjunction with two models based on BioBERT for their accuracy. Their outputs are combined according to different strategies depending on the entity type. In addition, we are using a manually crafted dictionary to increase performance for new concepts related to COVID-19. We have previously evaluated our work on the CRAFT corpus, and make the output of our pipeline available on two visualisation platforms.
In a recent project, the Language Application Grid was augmented to support the mining of scientific publications. The results of that ef- fort have now been repurposed to focus on Covid-19 literature, including modification of the LAPPS Grid “AskMe” query and retrieval engine. We describe the AskMe system and discuss its functionality as compared to other query engines available to search covid-related publications.
Understanding scientific articles related to COVID-19 requires broad knowledge about concepts such as symptoms, diseases and medicine. Given the very large and ever-growing scientific articles related to COVID-19, it is a daunting task even for experts to recognize the large set of concepts mentioned in these articles. In this paper, we address the problem of concept wikification for COVID-19, which is to automatically recognize mentions of concepts related to COVID-19 in text and resolve them into Wikipedia titles. We develop an approach to curate a COVID-19 concept wikification dataset by mining Wikipedia text and the associated intra-Wikipedia links. We also develop an end-to-end system for concept wikification for COVID-19. Preliminary experiments show very encouraging results. Our dataset, code and pre-trained model are available at github.com/panlybero/Covid19_wikification.
Topic models can facilitate search, navigation, and knowledge discovery in large document collections. However, automatic generation of topic models can produce results that fail to meet the needs of users. We advocate for a set of user-focused desiderata in topic modeling for the COVID-19 literature, and describe an effort in progress to develop a curated topic model for COVID-19 articles informed by subject matter expertise and the way medical researchers engage with medical literature.
We release a dataset of over 2,100 COVID19 related Frequently asked Question-Answer pairs scraped from over 40 trusted websites. We include an additional 24, 000 questions pulled from online sources that have been aligned by experts with existing answered questions from our dataset. This paper describes our efforts in collecting the dataset and summarizes the resulting data. Our dataset is automatically updated daily and available at https://github.com/JHU-COVID-QA/ scraping-qas. So far, this data has been used to develop a chatbot providing users information about COVID-19. We encourage others to build analytics and tools upon this dataset as well.
The number of unique terms in the scientific literature used to refer to either SARS-CoV-2 or COVID-19 is remarkably large and has continued to increase rapidly despite well-established standardized terms. This high degree of term variation makes high recall identification of these important entities difficult. In this manuscript we present an extensive dictionary of terms used in the literature to refer to SARS-CoV-2 and COVID-19. We use a rule-based approach to iteratively generate new term variants, then locate these variants in a large text corpus. We compare our dictionary to an extensive collection of terminological resources, demonstrating that our resource provides a substantial number of additional terms. We use our dictionary to analyze the usage of SARS-CoV-2 and COVID-19 terms over time and show that the number of unique terms continues to grow rapidly. Our dictionary is freely available at https://github.com/ncbi-nlp/CovidTermVar.
To combat misinformation regarding COVID- 19 during this unprecedented pandemic, we propose a conversational agent that answers questions related to COVID-19. We adapt the Poly-encoder (Humeau et al., 2020) model for informational retrieval from FAQs. We show that after fine-tuning, the Poly-encoder can achieve a higher F1 score. We make our code publicly available for other researchers to use.
With the rapid development of COVID-19 around the world, people are requested to maintain “social distance” and “stay at home”. In this scenario, extensive social interactions transfer to cyberspace, especially on social media platforms like Twitter and Sina Weibo. People generate posts to share information, express opinions and seek help during the pandemic outbreak, and these kinds of data on social media are valuable for studies to prevent COVID-19 transmissions, such as early warning and outbreaks detection. Therefore, in this paper, we release a novel and fine-grained large-scale COVID-19 social media dataset collected from Sina Weibo, named Weibo-COV, contains more than 40 million posts ranging from December 1, 2019 to April 30, 2020. Moreover, this dataset includes comprehensive information nuggets like post-level information, interactive information, location information, and repost network. We hope this dataset can promote studies of COVID-19 from multiple perspectives and enable better and rapid researches to suppress the spread of this pandemic.
In this paper, we present an iterative graph-based approach for the detection of symptoms of COVID-19, the pathology of which seems to be evolving. More generally, the method can be applied to finding context-specific words and texts (e.g. symptom mentions) in large imbalanced corpora (e.g. all tweets mentioning }#COVID-19). Given the novelty of COVID-19, we also test if the proposed approach generalizes to the problem of detecting Adverse Drug Reaction (ADR). We find that the approach applied to Twitter data can detect symptom mentions substantially before to their being reported by the Centers for Disease Control (CDC).
As social distancing, self-quarantines, and travel restrictions have shifted a lot of pandemic conversations to social media so does the spread of hate speech. While recent machine learning solutions for automated hate and offensive speech identification are available on Twitter, there are issues with their interpretability. We propose a novel use of learned feature importance which improves upon the performance of prior state-of-the-art text classification techniques, while producing more easily interpretable decisions. We also discuss both technical and practical challenges that remain for this task.
As people communicate on social media during COVID-19, it can be an invaluable source of useful and up-to-date information. However, the large volume and noise-to-signal ratio of social media can make this impractical. We present a prototype dashboard for the real-time classification, geolocation and interactive visualization of COVID-19 tweets that addresses these issues. We also describe a novel L2 classification layer that outperforms linear layers on a dataset of respiratory virus tweets.