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Searching for Scientific Evidence in a Pandemic: An Overview of TREC-COVID [article]

Kirk Roberts, Tasmeer Alam, Steven Bedrick, Dina Demner-Fushman, Kyle Lo, Ian Soboroff, Ellen Voorhees, Lucy Lu Wang, William R Hersh
2021 arXiv   pre-print
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.  ...  INTRODUCTION The Coronavirus Disease 2019 (COVID- 19) pandemic has resulted in an enormous demand for and supply of evidence-based information.  ... 
arXiv:2104.09632v1 fatcat:fy24bnbejvgx5oiwcty6ty2vpi

TREC-COVID: Constructing a Pandemic Information Retrieval Test Collection [article]

Ellen Voorhees
2020 arXiv   pre-print
TREC-COVID, in creating a test collection around COVID-19 literature, is building infrastructure to support new research and technologies in pandemic search.  ...  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.  ...  Structure of TREC-COVID Each round of TREC-COVID is structured as an independent community evaluation challenge much like a typical TREC track.  ... 
arXiv:2005.04474v1 fatcat:2rxtbwccgvgvfjuvf6lb45bdtq

Artificial Intelligence (AI) in Action: Addressing the COVID-19 Pandemic with Natural Language Processing (NLP) [article]

Qingyu Chen, Robert Leaman, Alexis Allot, Ling Luo, Chih-Hsuan Wei, Shankai Yan, Zhiyong Lu
2021 arXiv   pre-print
The COVID-19 pandemic has had a significant impact on society, both because of the serious health effects of COVID-19 and because of public health measures implemented to slow its spread.  ...  Many of these difficulties are fundamentally information needs; attempts to address these needs have caused an information overload for both researchers and the public.  ...  Acknowledgement This research is supported by the NIH Intramural Research Program, National Library of Medicine. Literature Cited  ... 
arXiv:2010.16413v2 fatcat:cxzxmnnbfrednpto4zkpnemltm

TREC-COVID: Rationale and Structure of an Information Retrieval Shared Task for COVID-19

Kirk Roberts, Tasmeer Alam, Steven Bedrick, Dina Demner-Fushman, Kyle Lo, Ian Soboroff, Ellen Voorhees, Lucy Lu Wang, William R Hersh
2020 JAMIA Journal of the American Medical Informatics Association  
TREC-COVID is an information retrieval (IR) shared task initiated to support clinicians and clinical research during the COVID-19 pandemic.  ...  This article describes how all these were addressed for the particular requirements of developing IR systems under a pandemic situation.  ...  Contributions The authors are organizers of TREC-COVID. KER initially drafted the manuscript. All authors reviewed and approved the manuscript.  ... 
doi:10.1093/jamia/ocaa091 pmid:32365190 pmcid:PMC7239098 fatcat:rhqp7cvirrgvpfcyz7zji4z67u

Artificial Intelligence in Action: Addressing the COVID-19 Pandemic with Natural Language Processing

Qingyu Chen, Robert Leaman, Alexis Allot, Ling Luo, Chih-Hsuan Wei, Shankai Yan, Zhiyong Lu
2021 Annual Review of Biomedical Data Science  
The COVID-19 (coronavirus disease 2019) pandemic has had a significant impact on society, both because of the serious health effects of COVID-19 and because of public health measures implemented to slow  ...  Many of these difficulties are fundamentally information needs; attempts to address these needs have caused an information overload for both researchers and the public.  ...  ACKNOWLEDGMENTS This research is supported by the NIH Intramural Research Program, National Library of Medicine.  ... 
doi:10.1146/annurev-biodatasci-021821-061045 pmid:34465169 fatcat:gxtcwu5ih5gx3la6ea4674pnmu

Covidex: Neural Ranking Models and Keyword Search Infrastructure for the COVID-19 Open Research Dataset [article]

Edwin Zhang, Nikhil Gupta, Raphael Tang, Xiao Han, Ronak Pradeep, Kuang Lu, Yue Zhang, Rodrigo Nogueira, Kyunghyun Cho, Hui Fang, Jimmy Lin
2020 arXiv   pre-print
We present Covidex, a search engine that exploits the latest neural ranking models to provide information access to the COVID-19 Open Research Dataset curated by the Allen Institute for AI.  ...  These techniques have been evaluated in the ongoing TREC-COVID challenge: Our infrastructure and baselines have been adopted by many participants, including some of the highest-scoring runs in rounds 1  ...  Acknowledgments This research was supported in part by the Canada First Research Excellence Fund, the Natural Sciences and Engineering Research Council (NSERC) of Canada, CIFAR AI & COVID-19 Catalyst Funding  ... 
arXiv:2007.07846v1 fatcat:obes7d2ybzc6nedmu6tsyfykmq

Incident Streams 2020: TRECIS in the Time of COVID-19

Cody Buntain, Richard McCreadie, Ian Soboroff
2020 Text Retrieval Conference  
This paper describes how the 2020 edition of TREC-IS has addressed these dual issues by introducing a new COVID-19-specific task for evaluating generalization of existing COVID-19 annotation and system  ...  TREC-IS has also continued expanding its set of target crises, adding 29 new events and expanding the collection of event types to include explosions, fires, and general storms, making for a total of 9  ...  Any mention of products, companies or services in this paper is for explanatory and scientific purposes and does not imply an endorsement or recommendation of those companies, products, or services.  ... 
dblp:conf/trec/BuntainMS20 fatcat:kcjf33b3ojdelhsdlcjh7kgywm

Text mining approaches for dealing with the rapidly expanding literature on COVID-19

Lucy Lu Wang, Kyle Lo
2020 Briefings in Bioinformatics  
We compile a list of 39 systems that provide functionality such as search, discovery, visualization and summarization over the COVID-19 literature.  ...  a basis for comparing the performance of different systems.  ...  An overview of these resources is provided in Table 1 .  ... 
doi:10.1093/bib/bbaa296 pmid:33279995 fatcat:np267ckskrbyjcilgetknqon7m

COVID-19 Pandemic and Immune Boost Up: The Synergistic Role of Nutrients

A. K. Obidul Huq, Ielias Uddin, Md. Tazul Islam, Eyad Ahmed, Mohammad Abu Bakr Siddique, A.N.M. Bazlur Rahim, Mesbah Uddin Talukder, Shireen Nigar, Nusrat Abedin, Mahjabeen Arjoo
2021 Current Research in Nutrition and Food Science Journal  
Based on current published evidence, this review article specifies the role of different nutrients in the possible prevention and management of COVID-19 and viral infections.  ...  World Health Organization (WHO) declared a global public health emergency due to the recent spread of COVID-19 throughout the world. Millions of people are affected daily and thousands died.  ...  Evidence based management nu12051466. guideline for the COVID-19 pandemic - 9. Liang W, Guan W, Chen R, Wang W, Review article.  ... 
doi:10.12944/crnfsj.9.3.04 fatcat:cwdnu2xdjrc4znv33qrhvnlvvq

AWS CORD-19 Search: A Neural Search Engine for COVID-19 Literature [article]

Parminder Bhatia, Lan Liu, Kristjan Arumae, Nima Pourdamghani, Suyog Deshpande, Ben Snively, Mona Mona, Colby Wise, George Price, Shyam Ramaswamy, Xiaofei Ma, Ramesh Nallapati (+3 others)
2020 arXiv   pre-print
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.  ...  (no topic) Use of quarantine in the control of SARS in Singapore "The main lesson to learn from the SARS outbreak is the capability of an emerging infection to cause a pandemic in a short span of time  ... 
arXiv:2007.09186v3 fatcat:vnjo7klajfe3dfy2mlwzuoqli4

Answering Questions on COVID-19 in Real-Time [article]

Jinhyuk Lee, Sean S. Yi, Minbyul Jeong, Mujeen Sung, Wonjin Yoon, Yonghwa Choi, Miyoung Ko, Jaewoo Kang
2020 arXiv   pre-print
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.  ...  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 thank the members of Korea University for the helpful comments and Kyle Lo (Allen Institute for Artificial Intelligence) for the insightful discussion.  ... 
arXiv:2006.15830v2 fatcat:36sbtup3rrgdtkqrqnw2i67qhi

Domain-Specific Pretraining for Vertical Search: Case Study on Biomedical Literature [article]

Yu Wang, Jinchao Li, Tristan Naumann, Chenyan Xiong, Hao Cheng, Robert Tinn, Cliff Wong, Naoto Usuyama, Richard Rogahn, Zhihong Shen, Yang Qin, Eric Horvitz (+3 others)
2021 arXiv   pre-print
A prominent case in point is the explosion of the biomedical literature on COVID-19, which swelled to hundreds of thousands of papers in a matter of months.  ...  a COVID-related biomedical search competition.  ...  We thank colleagues at the Cleveland Clinic Foundation for composing and sharing a sample of COVID-19-centric queries spanning a broad range of biomedical topics.  ... 
arXiv:2106.13375v1 fatcat:7q5x7agh3zcfjglpxs7bkdsrje

BEIR: A Heterogenous Benchmark for Zero-shot Evaluation of Information Retrieval Models [article]

Nandan Thakur, Nils Reimers, Andreas Rücklé, Abhishek Srivastava, Iryna Gurevych
2021 arXiv   pre-print
To address this, and to facilitate researchers to broadly evaluate the effectiveness of their models, we introduce Benchmarking-IR (BEIR), a robust and heterogeneous evaluation benchmark for information  ...  In contrast, dense and sparse-retrieval models are computationally more efficient but often underperform other approaches, highlighting the considerable room for improvement in their generalization capabilities  ...  TREC-COVID [65] is an ad-hoc search challenge based on the CORD-19 dataset containing scientific articles related to the COVID-19 pandemic [69] .  ... 
arXiv:2104.08663v4 fatcat:fow5uqghbzggjclobtv7bpjtaa

RRF102: Meeting the TREC-COVID Challenge with a 100+ Runs Ensemble [article]

Michael Bendersky and Honglei Zhuang and Ji Ma and Shuguang Han and Keith Hall and Ryan McDonald
2020 arXiv   pre-print
In this paper, we report the results of our participation in the TREC-COVID challenge.  ...  The submitted ensemble runs achieved state-of-the-art performance in rounds 4 and 5 of the TREC-COVID challenge.  ...  Acknowledgments We thank the TREC-COVID challenge organizers for their tremendous investment of time and effort in smooth execution of all the evaluation rounds.  ... 
arXiv:2010.00200v1 fatcat:wptmhsg3rnfatlf66qhgtsjml4

Multistage BiCross encoder for multilingual access to COVID-19 health information

Iknoor Singh, Carolina Scarton, Kalina Bontcheva, Balaraman Ravindran
2021 PLoS ONE  
This has motivated the need for accurate semantic search and retrieval of reliable COVID-19 information across millions of documents, in multiple languages.  ...  The Coronavirus (COVID-19) pandemic has led to a rapidly growing 'infodemic' of health information online.  ...  Recently, the TREC-COVID challenge [26] invited participants to develop information retrieval systems for scientific literature containing tens of thousands of scholarly articles related to COVID-19.  ... 
doi:10.1371/journal.pone.0256874 pmid:34492073 fatcat:wl5ozj47s5aajpilg7jobwxhka
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