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 learderboard with an nDCG@10 of 0.6844). Insights provided by a detailed analysis provide some potential future directions to explore, including the importance of filtering by date and the potential of neural methods that rely more heavily on count signals. We release the code to facilitate future work on this critical task at https://github.com/Georgetown-IR-Lab/covid-neural-ir
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 …
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-…
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.
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…
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…
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…
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…
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…
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…
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…
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…
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…
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 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…
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…
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…
Neural rankers based on deep pretrained language models (LMs) have been shown to improve many information retrieval benchmarks. However, these methods are affected by their the correlation between pretraining domain and target domain and rely on massive fine-tuning relevance labels. Directly applying pretraining methods to specific domains may result in suboptimal search quality because specific domains may have domain adaption problems, such as the COVID domain. This paper presents a search system to alleviate the special domain adaption problem. The system utilizes the domain-adaptive pretra…
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…
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…
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 …
In the absence of sufficient medication for COVID patients due to the increased demand, disused drugs have been employed or the doses of those available were modified by hospital pharmacists. Some evidences for the use of alternative drugs can be found in the existing scientific literature that could assist in such decisions. However, exploiting large corpus of documents in an efficient manner is not easy, since drugs may not appear explicitly related in the texts and could be mentioned under different brand names. Drugs4Covid combines word embedding techniques and semantic web technologies to…
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…
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.
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…
Coronavirus disease (COVID-19) is an infectious disease, which is caused by the SARS-CoV-2 virus. Due to the growing literature on COVID-19, it is hard to get precise, up-to-date information about the virus. Practitioners, front-line workers, and researchers require expert-specific methods to stay current on scientific knowledge and research findings. However, there are a lot of research papers being written on the subject, which makes it hard to keep up with the most recent research. This problem motivates us to propose the design of the COVID-19 Search Engine (CO-SE), which is an algorithmic…
Boğaziçi University（博加齐奇大学）；F. Hoffmann-La Roche AG（Hoffmann - La Roche 有限公司）
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 stud…
Wofford College（沃福德学院）；University of California, Los Angeles（加州大学洛杉矶分校）；California State University Channel Islands（加州州立大学海峡群岛分校）；LWS Research（LWS研究公司）
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 …
During the current century, each major coronavirus outbreak has triggered a quick surge of academic publications on this topic. The spike in research publications following the 2019 Novel Coronavirus (Covid-19), however, has been like no other. The global crisis caused by the Covid-19 pandemic has mobilised scientific efforts in an unprecedented way. In less than five months, more than 12,000 research items have been indexed while the number increasing every day. With the crisis affecting all aspects of life, research on Covid-19 seems to have become a focal point of interest across many acade…
