AWS CORD-19 Search: A Neural Search Engine for COVID-19 Literature
Parminder Bhatia, Lan Liu, Kristjan Arumae, Nima Pourdamghani, Suyog Deshpande, Ben Snively, Mona Mona, Colby Wise, George Price, Shyam Ramaswamy, Xiaofei Ma, R… 展开作者
Parminder Bhatia, Lan Liu, Kristjan Arumae, Nima Pourdamghani, Suyog Deshpande, Ben Snively, Mona Mona, Colby Wise, George Price, Shyam Ramaswamy, Xiaofei Ma, Ramesh Nallapati, Zhiheng Huang, Bing Xiang, Taha Kass-Hout
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 scalable solution to COVID-19 researchers and policy makers in their search and discovery for answers to high priority scientific questions. We present a quantitative evaluation and qualitative analysis of the system against other leading COVID-19 search platforms. ACS is top performing across these systems yielding quality results which we detail with relevant examples in this work.
The novel coronavirus disease 2019 (COVID-19) began in Wuhan, China in late 2019 and to date has infected over 14M people worldwide, resulting in over 750,000 deaths. On March 10, 2020 the World Health Organization (WHO) declared the outbreak a global pandemic. Many academics and researchers, not restricted to the medical domain, began publishing papers describing new discoveries. However, with the large influx of publications, it was hard for these individuals to sift through the large amount of data and make sense of the findings. The White House and a group of industry research labs, lead b…
University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
We created this CORD-NER dataset with comprehensive named entity recognition (NER) on the COVID-19 Open Research Dataset Challenge (CORD-19) corpus (2020-03-13). This CORD-NER dataset covers 75 fine-grained entity types: In addition to the common biomedical entity types (e.g., genes, chemicals and diseases), it covers many new entity types related explicitly to the COVID-19 studies (e.g., coronaviruses, viral proteins, evolution, materials, substrates and immune responses), which may benefit research on COVID-19 related virus, spreading mechanisms, and potential vaccines. CORD-NER annotation i…
We describe our participation in all five rounds of the TREC 2020 COVID Track (TREC-COVID). The goal of TREC-COVID is to contribute to the response to the COVID-19 pandemic by identifying answers to many pressing questions and building infrastructure to improve search systems [8]. All five rounds of this Track challenged participants to perform a classic ad-hoc search task on the new data collection CORD-19. Our solution addressed this challenge by applying the Continuous Active Learning model (CAL) and its variations. Our results showed us to be amongst the top scoring manual runs and we rema…
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…
Previous work established skip-gram word2vec models could be used to mine knowledge in the materials science literature for the discovery of thermoelectrics. Recent transformer architectures have shown great progress in language modeling and associated fine-tuned tasks, but they have yet to be adapted for drug discovery. We present a RoBERTa transformer-based method that extends the masked language token prediction using query-target conditioning to treat the specificity challenge. The transformer discovery method entails several benefits over the word2vec method including domain-specific (ant…
This paper presents a project, named VIDAR-19, able to extract automatically diseases from the CORD-19 dataset, and also diseases which might be considered as risk factors. The project relies on the ICD-11 classification of diseases maintained by the WHO. This nomenclature is used as a data source of the extraction mechanism, and also as the repository for the results. Developed for the COVID-19, the project has the ability to extract diseases at risk and to calculate relevant indicators. The outcome of the project is presented in a dashboard which enables the user to explore graphically disea…
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…
Indian Institute of Technology Kharagpur（印度理工学院卡哈拉格普尔分校）；University of Manchester（曼彻斯特大学）；University of Technology Sydney（悉尼科技大学）
Increasing number of COVID-19 research literatures cause new challenges in effective literature screening and COVID-19 domain knowledge aware Information Retrieval. To tackle the challenges, we demonstrate two tasks along withsolutions, COVID-19 literature retrieval, and question answering. COVID-19 literature retrieval task screens matching COVID-19 literature documents for textual user query, and COVID-19 question answering task predicts proper text fragments from text corpus as the answer of specific COVID-19 related questions. Based on transformer neural network, we provided solutions to i…
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…
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 2019 (COVID-19) has infected more than one million individuals all over the world and caused more than 55,000 deaths, as of April 3 in 2020. Radiological findings are important sources of information in guiding the diagnosis and treatment of COVID-19. However, the existing studies on how radiological findings are correlated with COVID-19 are conducted separately by different hospitals, which may be inconsistent or even conflicting due to population bias. To address this problem, we develop natural language processing methods to analyze a large collection of COVID-19 literat…
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…
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…
University of Illinois, Urbana Champaign（伊利诺伊大学厄巴纳-香槟分校）；IBM Research AI（IBM研究院人工智能部门）
End-to-end question answering (QA) requires both information retrieval (IR) over a large document collection and machine reading comprehension (MRC) on the retrieved passages. Recent work has successfully trained neural IR systems using only supervised question answering (QA) examples from open-domain datasets. However, despite impressive performance on Wikipedia, neural IR lags behind traditional term matching approaches such as BM25 in more specific and specialized target domains such as COVID-19. Furthermore, given little or no labeled data, effective adaptation of QA systems can also be ch…
Following the global COVID-19 pandemic, the number of scientific papers studying the virus has grown massively, leading to increased interest in automated literate review. We present a clinical text mining system that improves on previous efforts in three ways. First, it can recognize over 100 different entity types including social determinants of health, anatomy, risk factors, and adverse events in addition to other commonly used clinical and biomedical entities. Second, the text processing pipeline includes assertion status detection, to distinguish between clinical facts that are present, …
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…
We are developing semantic visualization techniques in order to enhance exploration and enable discovery over large datasets of complex networks of relations. Semantic visualization is a method of enabling exploration and discovery over large datasets of complex networks by exploiting the semantics of the relations in them. This involves (i) NLP to extract named entities, relations and knowledge graphs from the original data; (ii) indexing the output and creating representations for all relevant entities and relations that can be visualized in many different ways, e.g., as tag clouds, heat map…
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…
