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Effective Crowd-Annotation of Participants, Interventions, and Outcomes in the Text of Clinical Trial Reports

Markus Zlabinger, Marta Sabou, Sebastian Hofstätter, Allan Hanbury
2020 Findings of the Association for Computational Linguistics: EMNLP 2020   unpublished
The search for Participants, Interventions, and Outcomes (PIO) in clinical trial reports is a critical task in Evidence Based Medicine.  ...  approach of annotating entire abstracts of trial reports as one task-instance (i.e.  ...  1 ) in clinical trial reports.  ... 
doi:10.18653/v1/2020.findings-emnlp.274 fatcat:3dm2rirucfazhdrldvkq3jvz3q

A Corpus with Multi-Level Annotations of Patients, Interventions and Outcomes to Support Language Processing for Medical Literature

Benjamin Nye, Junyi Jessy Li, Roma Patel, Yinfei Yang, Iain J Marshall, Ani Nenkova, Byron C Wallace
2018 Association for Computational Linguistics (ACL). Annual Meeting Conference Proceedings  
Annotations include demarcations of text spans that describe the Patient population enrolled, the Interventions studied and to what they were Compared, and the Outcomes measured (the 'PICO' elements).  ...  We present a corpus of 5,000 richly annotated abstracts of medical articles describing clinical randomized controlled trials.  ...  Acknowledgements This work was supported in part by the National Cancer Institute (NCI) of the National Institutes of Health (NIH), award number UH2CA203711.  ... 
pmid:30305770 pmcid:PMC6174533 fatcat:zdcgrj6exvbg5oeidm5j3n7hbe

A Corpus with Multi-Level Annotations of Patients, Interventions and Outcomes to Support Language Processing for Medical Literature [article]

Benjamin Nye, Junyi Jessy Li, Roma Patel, Yinfei Yang, Iain J. Marshall, Ani Nenkova, Byron C. Wallace
2018 arXiv   pre-print
Annotations include demarcations of text spans that describe the Patient population enrolled, the Interventions studied and to what they were Compared, and the Outcomes measured (the 'PICO' elements).  ...  We present a corpus of 5,000 richly annotated abstracts of medical articles describing clinical randomized controlled trials.  ...  Acknowledgements This work was supported in part by the National Cancer Institute (NCI) of the National Institutes of Health (NIH), award number UH2CA203711.  ... 
arXiv:1806.04185v1 fatcat:s2nt6pzlqjc6jpzhsfehly3rwy

A Corpus with Multi-Level Annotations of Patients, Interventions and Outcomes to Support Language Processing for Medical Literature

Benjamin Nye, Junyi Jessy Li, Roma Patel, Yinfei Yang, Iain Marshall, Ani Nenkova, Byron Wallace
2018 Proceedings of the 56th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)  
Annotations include demarcations of text spans that describe the Patient population enrolled, the Interventions studied and to what they were Compared, and the Outcomes measured (the 'PICO' elements).  ...  We present a corpus of 5,000 richly annotated abstracts of medical articles describing clinical randomized controlled trials.  ...  Acknowledgements This work was supported in part by the National Cancer Institute (NCI) of the National Institutes of Health (NIH), award number UH2CA203711.  ... 
doi:10.18653/v1/p18-1019 dblp:conf/acl/NenkovaLYMWNP18 fatcat:27u3zpeutbhq5oxpukkkiph5jq

Trialstreamer: a living, automatically updated database of clinical trial reports [article]

Iain J Marshall, Benjamin Nye, Joël Kuiper, Anna Noel-Storr, Rachel Marshall, Rory Maclean, Frank Soboczenski, Ani Nenkova, James Thomas, Byron C Wallace
2020 medRxiv   pre-print
We combine machine learning and rule-based methods to extract information from the RCT abstracts, including free-text descriptions of trial populations, interventions and outcomes (the 'PICO') and map  ...  We describe the development and evaluation of a system to automatically find and categorize all new RCT reports.  ...  This work makes use of data created by Cochrane, Cochrane Crowd, and Clinical Hedges at MacMaster University, and the Unified Medial Language System (UMLS) from the National Library of Medicine, which  ... 
doi:10.1101/2020.05.15.20103044 fatcat:r2vysomogrg3fhz64xai62kelq

A protocol for the systematic review and meta-analysis of studies in which cannabinoids were tested for antinociceptive effects in animal models of pathological or injury-related persistent pain

Nadia Soliman, Andrea G. Hohmann, Simon Haroutounian, Kimberley Wever, Andrew S.C. Rice, David P. Finn
2019 PAIN Reports  
Data will be extracted for pain-associated behavioural outcomes, study design, and the reporting of measures to avoid bias.  ...  The evaluation of the preclinical evidence will quantify the antinociceptive effects of cannabinoids on pain behaviour in animal models of pathological pain in an effort to quantify the presence and prevalence  ...  Acknowledgements The authors thank Dr Emily Sena and Dr Jing Liao of CAMARDES, The University of Edinburgh, for their guidance in how machine learning and text mining can be used to improve the efficiency  ... 
doi:10.1097/pr9.0000000000000766 pmid:31579857 pmcid:PMC6727996 fatcat:q6pa4l23afd6xivygpprfpu4y4

Crowdsourcing in health and medical research: a systematic review

Cheng Wang, Larry Han, Gabriella Stein, Suzanne Day, Cedric Bien-Gund, Allison Mathews, Jason J. Ong, Pei-Zhen Zhao, Shu-Fang Wei, Jennifer Walker, Roger Chou, Amy Lee (+3 others)
2020 Infectious Diseases of Poverty  
Although crowdsourcing is effective at improving behavioral outcomes, more research is needed to understand effects on clinical outcomes and costs.  ...  Crowdsourcing is used increasingly in health and medical research. Crowdsourcing is the process of aggregating crowd wisdom to solve a problem.  ...  The SIHI network is supported by TDR, the Special Programme for Research and Training in Tropical Disease, co-sponsored by  ... 
doi:10.1186/s40249-020-0622-9 pmid:31959234 fatcat:vrijmeonejeqdjah5zlza2gmci

A practical guide to preclinical systematic review and meta-analysis

Nadia Soliman, Andrew S.C. Rice, Jan Vollert
2020 Pain  
Rice are part of the European Quality In  ...  Acknowledgements The authors thank Dr Emily Sena for her constructive feedback on the manuscript. The work is funded by the BBSRC (grant number BB/M011178/ 1). J. Vollert and A.S.C.  ...  A MA can be used to combine the outcome data of individual studies to estimate the overall intervention effect.  ... 
doi:10.1097/j.pain.0000000000001974 pmid:33449500 fatcat:5efzm4563zbkjk7hrcawrqkkai

MS2: Multi-Document Summarization of Medical Studies [article]

Jay DeYoung, Iz Beltagy, Madeleine van Zuylen, Bailey Kuehl, Lucy Lu Wang
2021 arXiv   pre-print
To assess the effectiveness of any medical intervention, researchers must conduct a time-intensive and highly manual literature review.  ...  We formulate our summarization inputs and targets in both free text and structured forms and modify a recently proposed metric to assess the quality of our system's generated summaries.  ...  We thank Ani Nenkova, Byron Wallace, Dan Weld, the reviewers, and members of the Semantic Scholar team for their valuable feedback.  ... 
arXiv:2104.06486v3 fatcat:2omphxpttzf5dovokqfpnzhxgm

Machine learning to help researchers evaluate biases in clinical trials: a prospective, randomized user study

Frank Soboczenski, Thomas A. Trikalinos, Joël Kuiper, Randolph G. Bias, Byron C. Wallace, Iain J. Marshall
2019 BMC Medical Informatics and Decision Making  
We conducted a user study of RobotReviewer, evaluating time saved and usability of the tool.  ...  Assessing risks of bias in randomized controlled trials (RCTs) is an important but laborious task when conducting systematic reviews.  ...  Acknowledgements We would like to express our gratitude to the systematic review authors who volunteered to take part in the user study, and also to Cochrane Crowd, the EPPI Centre, and the Society for  ... 
doi:10.1186/s12911-019-0814-z pmid:31068178 pmcid:PMC6505190 fatcat:lna2oofhszhv3ihpp3ta2cgw5m

State of the evidence: a survey of global disparities in clinical trials

Iain James Marshall, Veline L'Esperance, Rachel Marshall, James Thomas, Anna Noel-Storr, Frank Soboczenski, Benjamin Nye, Ani Nenkova, Byron C Wallace
2021 BMJ Global Health  
RCTs recruited a median of 72 participants (IQR 32-195). 82% of RCTs were conducted by researchers in the top fifth of countries by socio-economic development.  ...  We use machine learning to monitor PubMed daily, and find and analyse RCT reports.  ...  Acknowledgements We are enormously grateful to the volunteers from the Cochrane Crowd, who labelled hundreds of thousands of articles manually, enabling us to develop the machine learning system.  ... 
doi:10.1136/bmjgh-2020-004145 pmid:33402333 pmcid:PMC7786802 fatcat:z4q5i7getvh5ppqhnzuudbtu24

Improving the Science of Annotation for Natural Language Processing: The Use of the Single-Case Study for Piloting Annotation Projects

Kylie Anglin, Arielle Boguslav, Todd Hall
2022 Journal of Data Science  
In this paper, we demonstrate the application of the single-case study in an applied experiment and argue that future researchers should incorporate the design into the pilot stage of annotation projects  ...  Researchers need guidance on how to obtain maximum efficiency and accuracy when annotating training data for text classification applications.  ...  Study Corpus and Participants Our corpus of coaching conversations comes from prior studies of the impact of a short (5-minute) coaching intervention on teachers-in-training.  ... 
doi:10.6339/22-jds1054 fatcat:zev6rsfpp5hghglsyubg24jhlm

Are Patients With Longer Emergency Department Wait Times Less Likely to Consent to Research?

Alexander T. Limkakeng, Seth W. Glickman, Frances Shofer, Giselle Mani, Weiying Drake, Debbie Freeman, Simon Ascher, Ricardo Pietrobon, Charles B. Cairns
2012 Academic Emergency Medicine  
The objective of this study was to assess the effect of ED wait times on patient participation in ED clinical research.  ...  An analysis of association between patient wait times for the outcome of consent to participate was performed using a multivariate logistic regression model.  ...  To our knowledge, this is the first study examining the effects of wait times on ED clinical research participation.  ... 
doi:10.1111/j.1553-2712.2012.01310.x pmid:22506943 fatcat:re3mkx4t7bcbpkjrcl7azwxjom

State of the evidence: a survey of global disparities in clinical trials [article]

Iain J Marshall, Veline L'Esperance, Rachel Marshall, James Thomas, Anna Noel-Storr, Frank Soboczenski, Benjamin Nye, Ani Nenkova, Byron C Wallace
2020 medRxiv   pre-print
RCTs recruited a median of 72 participants (interquartile range 32-195). 82% of RCTs were conducted by researchers in the top fifth of countries by socio-economic development.  ...  We conducted a comprehensive global study investigating the number of randomised controlled trials (RCTs) published on different health conditions, and how this compares with the global disease burden  ...  Acknowledgements We are enormously grateful to the volunteers from the Cochrane Crowd, who labelled hundreds of thousands of articles manually, enabling us to develop the machine learning system.  ... 
doi:10.1101/2020.10.08.20209353 fatcat:rmi26rucrzdgdneppdxkfprvma

Detect and Classify – Joint Span Detection and Classification for Health Outcomes [article]

Michael Abaho, Danushka Bollegala, Paula Williamson, Susanna Dodd
2021 arXiv   pre-print
A health outcome is a measurement or an observation used to capture and assess the effect of a treatment.  ...  the goal is to classify a text into a pre-defined set of categories depending on an outcome that is mentioned somewhere in that text.  ...  We use this alignment for data augmentation in a low-resource setting. 3. We investigate the document-level contributions by a piece of text (e.g. an abstract) for predictions made at the token-level.  ... 
arXiv:2104.07789v2 fatcat:3dluowmkanbx3agojewgf4ek7e
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