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Overview of the TREC 2020 Precision Medicine Track

Kirk Roberts, Dina Demner-Fushman, Ellen M Voorhees, Steven Bedrick, William R Hersh
2020
However, the micro-targeting of patients greatly increases the space of treatment options, which results in fundamental difficulties with putting the findings of precision medicine into practice (Frey  ...  Generally speaking, the issues that are taken into consideration for precision medicine are the genomic, environmental, and lifestyle contexts of the patient.  ...  DDF is supported by the Intramural Research Program of the U.S. National Library of Medicine, NIH.  ... 
pmid:34849513 pmcid:PMC8629152 fatcat:insdyrwthjhp5mscerecnuksda

Addressing the Search Challenges of Precision Medicine with Information Retrieval Systems and Physician Readers

Kate Fultz Hollis, Kirk Roberts, Steven Bedrick, William R Hersh
2020 Studies in Health Technology and Informatics  
In 2017, the TREC Precision Medicine (Roberts et al., 2017) track grew from the Clinical Decision Support track and focused on a narrower problem domain of precision oncology.  ...  The Text REtrieval Conference (TREC), co-sponsored by the National Institute of Standards and Technology (NIST) in the US and US Department of Defense, was started in 1992.  ...  Acknowledgements KFH, KR, SB, and WTH and other organizers are grateful to the National Institute of Standards and Technology (NIST) for funding the assessment process for TREC.  ... 
doi:10.3233/shti200274 pmid:32570495 fatcat:uboe2c5am5a65jppi6j7depism

Aliababa DAMO Academy at TREC Precision Medicine 2020: State-of-the-art Evidence Retriever for Precision Medicine with Expert-in-the-loop Active Learning

Qiao Jin, Chuanqi Tan, Mosha Chen, Ming Yan, Songfang Huang, Ningyu Zhang, Xiaozhong Liu
2020 Text Retrieval Conference  
This paper describes the submissions of Alibaba DAMO Academy to the TREC Precision Medicine (PM) Track in 2020, which achieve state-of-the-art performance in the evidence quality assessment.  ...  The focus of the TREC PM Track is to retrieve academic papers that report critical clinical evidence for or against a given treatment in a population specified by its disease and gene mutation.  ...  Conclusions In this paper, we present the winning solution in the phase 2 of TREC Precision Medicine 2020.  ... 
dblp:conf/trec/JinJTCYHZL20 fatcat:a3rtcfs7gfd6habzsg73r7zlcm

CSIROmed at TREC Precision Medicine 2020

Maciej Rybinski, Sarvnaz Karimi
2020 Text Retrieval Conference  
TREC Precision Medicine (PM) focuses on providing highquality evidence from the biomedical literature for clinicians treating cancer patients.  ...  We examined two mechanisms for incorporating the treatment within the query formulation strategy for DFR: (1) a concatenation of disease, gene and treatment fields; and (2) a concatenation of disease and  ...  In the official evaluation of TREC Precision Medicine 2020 FIL-non-augmented was the best performing run in R-prec and P@10, and second best in infNDCG.  ... 
dblp:conf/trec/RybinskiK20 fatcat:ezkdhgwrwbguxgz26jdgkvy7iy

BIT.UA@TREC 2020 Precision Medicine Track

Tiago Almeida, Sérgio Matos
2020 Text Retrieval Conference  
The TREC Precision Medicine and the previous CDS track have produced a variety of approaches on document retrieval to support clinical decisions.  ...  In phase 2 we achieved a best score of 0.3289 nDCG@30, four percentage points above the reported median. Our source code is available from https://github.com/T-Almeida/TREC-PM-2020.  ...  for Science and Technology, in the context of the project UIDB/00127/2020.  ... 
dblp:conf/trec/AlmeidaM20a fatcat:pwwt65dr3zf4nnvvdlrs2zn3fu

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
This paper provides a comprehensive overview of the structure and results of TREC-COVID.  ...  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 TREC Precision Medicine track (2017-2020) [19] [20] [21] [22] refined that focus to oncologists interested in treating cancer patients with actionable gene mutations.  ... 
arXiv:2104.09632v1 fatcat:fy24bnbejvgx5oiwcty6ty2vpi

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

Ellen Voorhees
2020 arXiv   pre-print
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.  ...  It builds on a history of biomedical TREC tracks [1, 7, 3, 2] , and specifically on the Genomics, Clinical Decision Support, and Precision Medicine tracks that focused on retrieval from the scientific  ... 
arXiv:2005.04474v1 fatcat:2rxtbwccgvgvfjuvf6lb45bdtq

A2A: a platform for research in biomedical literature search

Maciej Rybinski, Sarvnaz Karimi, Vincent Nguyen, Cecile Paris
2020 BMC Bioinformatics  
Our setup is guided by the NIST setup of the relevant TREC evaluation tasks in genomics, clinical decision support, and precision medicine.  ...  Background Finding relevant literature is crucial for many biomedical research activities and in the practice of evidence-based medicine.  ...  About this supplement This article has been published as part of BMC Bioinformatics Volume 21 Supplement 19 2020: Proceedings from the Joint NETTAB/BBCC 2019 Conference.  ... 
doi:10.1186/s12859-020-03894-8 pmid:33349237 fatcat:dy45nsg2mvf3nlwrxf4s5wpe3a

Enabling Prescription-based Health Apps [article]

Venet Osmani, Stefano Forti, Oscar Mayora, Diego Conforti
2017 arXiv   pre-print
We also describe three important aspects of health app prescription and how medical information is automatically encoded through the TreC framework and is prescribed as a personalised app, ready to be  ...  Our framework is based on an existing PHR ecosystem called TreC, uniquely positioned between healthcare provider and the patients, which is being used by over 70.000 patients in Trentino region in Northern  ...  ACKNOWLEDGEMENTS We would like to acknowledge the contribution of the following people: Stefano Cavallari, Luca Vettoretto, Barbara Purin, Marco Dianti, Flavio Berloffa, Claudio Eccher and Enrico Piras  ... 
arXiv:1706.09407v1 fatcat:eolv4pmkobbdhbjpfsqnpfvsiy

Extracting Concepts for Precision Oncology from the Biomedical Literature [article]

Nicholas Greenspan and Yuqi Si and Kirk Roberts
2020 arXiv   pre-print
The best-performing model achieved a precision of 63.8%, a recall of 71.9%, and an F1 of 67.1.  ...  Finally, we propose additional directions for research for improving extraction performance and utilizing the NLP system in downstream precision oncology applications.  ...  IR systems were evaluated for this task in the TREC Precision Medicine tracks.  ... 
arXiv:2010.00074v1 fatcat:rgq6yymifrd7jdb4r7knzm2w74

Patient Cohort Retrieval using Transformer Language Models [article]

Sarvesh Soni, Kirk Roberts
2020 arXiv   pre-print
The task of CR requires the extraction of relevant documents from the electronic health records (EHRs) on the basis of a given query.  ...  Given the recent advancements in the field of document retrieval, we map the task of CR to a document retrieval task and apply various deep neural models implemented for the general domain tasks.  ...  National Library of Medicine, National Institutes of Health (NIH), under award R00LM012104, and the Cancer Prevention and Research Institute of Texas (CPRIT), under award RP170668.  ... 
arXiv:2009.05121v1 fatcat:aggnzkq32fgpjgpnyfy6ywmje4

NLM at TREC 2020 Health Misinformation and Deep Learning Tracks

Yassine Mrabet, Mourad Sarrouti, Asma Ben Abacha, Soumya Gayen, Travis R. Goodwin, Alastair R. Rae, Willie Rogers, Dina Demner-Fushman
2020 Text Retrieval Conference  
This paper describes the participation of the National Library of Medicine to TREC 2020. Our main focus was the health misinformation track.  ...  We also participated to the Deep Learning track to both evaluate and enhance our deep re-ranking baselines for information retrieval.  ...  Acknowledgments This work was supported by the intramural research program at the U.S. National Library of Medicine, National Institutes of Health.  ... 
dblp:conf/trec/MrabetSAGGRRD20 fatcat:pmsm6gk3avfstmqbohpoxp5feu

Patient Cohort Retrieval using Transformer Language Models

Sarvesh Soni, Kirk Roberts
2021 AMIA Annual Symposium Proceedings  
The task ofCR requires the extraction of relevant documents from the electronic health records (EHRs) on the basis of a given query.  ...  Given the recent advancements in the field of document retrieval, we map the task of CR to a document retrieval task and apply various deep neural models implemented for the general domain tasks.  ...  National Library of Medicine, National Institutes of Health (NIH), under award R00LM012104, and the Cancer Prevention and Research Institute of Texas (CPRIT), under award RP170668.  ... 
pmid:33936491 pmcid:PMC8075458 fatcat:ir2cz5gxjzckzoi7ufeqd5amua

Literature-Augmented Clinical Outcome Prediction [article]

Aakanksha Naik, Sravanthi Parasa, Sergey Feldman, Lucy Lu Wang, Tom Hope
2022 arXiv   pre-print
Our approach boosts predictive performance on three important clinical tasks in comparison to strong recent LM baselines, increasing F1 by up to 5 points and precision@Top-K by a large margin of over 25%  ...  The authors would like to thank the members of the Semantic Scholar team, and the anonymous reviewers for their helpful feedback on this work.  ...  Our goal is to improve models for clinical outcome prediction 2 Since 2017, the focus has switched to TREC-PM (precision medicine) tracks where articles are retrieved based on short structured queries  ... 
arXiv:2111.08374v2 fatcat:jj5yqs24yfasrdilxmf2xuuxhm

Getting Insights from a Large Corpus of Scientific Papers on Specialisted Comprehensive Topics – the Case of COVID-19 [article]

Bernard Dousset, Josiane Mothe
2020 arXiv   pre-print
We run these methodologies on two cases: the virus origin and the uses of existing drugs.  ...  COVID-19 is one of the most important topic these days, specifically on search engines and news.  ...  Like the other TREC tracks 6 , TREC-COVID aims at gathering research teams in information retrieval to evaluate search engines on specific tasks.  ... 
arXiv:2005.00485v1 fatcat:56waormjxjfhnb6j63e5ly7bwe
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