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Overview of the TREC 2018 Precision Medicine Track

Kirk Roberts, Dina Demner-Fushman, Ellen M. Voorhees, William R. Hersh, Steven Bedrick, Alexander J. Lazar
2018 Text Retrieval Conference  
DDF is supported by the Intramural Research Program of the U.S. National Library of Medicine, NIH.  ...  KR is supported by the National Institutes of Health (NIH) grant 2R00LM012104-02 and the Cancer Prevention and Research Institute of Texas (CPRIT) grant RP170668.  ...  This started with the TREC 2017 Precision Medicine track and continued with the 2018 track described here.  ... 
dblp:conf/trec/RobertsDVHBL18 fatcat:pxcvu5tkirfwdcrg2o5vvmo5vy

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

TREC 2019 Precision Medicine - Medical University of Graz

Pilar López-Úbeda, José Antonio Vera-Ramos, Pablo López-García
2019 Text Retrieval Conference  
In this paper we report on our participation in the TREC 2019 Precision Medicine track (team name: imi_mug ).  ...  We submitted 5 fully automatic runs to the biomedical articles subtask, two of them with treatments.  ...  Acknowledgments This work was partially supported by the Spanish government via the projects RTI2018-094653-B-C21 (LIVING-LANG) and TIN2015-65136-C2-1-R (REDES).  ... 
dblp:conf/trec/Lopez-UbedaVL19 fatcat:ecad3wwj5nfnvpug2prw7ts6eu

CSIRO at 2019 TREC Precision Medicine Track

Maciej Rybinski, Sarvnaz Karimi, Cécile Paris
2019 Text Retrieval Conference  
TREC Precision Medicine track focuses on search tasks tailored for oncologists.  ...  Some of our submitted runs score in top ten runs reported by the organisers.  ...  We also acknowledge the contributions of our colleagues over the years to develop the A2A underlying system.  ... 
dblp:conf/trec/RybinskiKP19 fatcat:x5bnzzsq2bfexgwrqte4dymkqi

Overview of the TREC 2019 Precision Medicine Track

Kirk Roberts, Dina Demner-Fushman, Ellen M. Voorhees, William R. Hersh, Steven Bedrick, Alexander J. Lazar, Shubham Pant, Funda Meric-Bernstam
2019 Text Retrieval Conference  
DDF is supported by the Intramural Research Program of the U.S. National Library of Medicine, NIH.  ...  KR is supported by the National Institutes of Health (NIH) grant 2R00LM012104-02 and the Cancer Prevention and Research Institute of Texas (CPRIT) grant RP170668.  ...  This started with the TREC 2017 Precision Medicine track, continued in 2018, and further continues with the 2019 track described here.  ... 
dblp:conf/trec/RobertsDVHBLPM19 fatcat:z57hhfbvnnfexkawpix5zap5xe

Networks and Shared Tasks in Clinical Text Mining [chapter]

Hercules Dalianis
2018 Clinical Text Mining  
Accessed 2018-01-11. 2 TREC Medical track, http://trec.nist.gov/data/medical.html. Accessed 2018-01-11. 3 TREC Precision Medicine/Clinical Decision Support Track, http://www.trec-cds.org.  ...  -The CDS track deals with retrieval of relevant documents for clinical decision making and support it is also called the Precision Medicine track. • The ShARe/CLEF eHealth 4 tasks, which consist of: -Normalisation  ... 
doi:10.1007/978-3-319-78503-5_11 fatcat:bob7cb2zxvgffg6rqqj7gvbjee

Simple but Effective Knowledge-Based Query Reformulations for Precision Medicine Retrieval

Stefano Marchesin, Giorgio Maria Di Nunzio, Maristella Agosti
2021 Information  
The experimental analyses on different test collections for Precision Medicine IR show the effectiveness of the developed techniques.  ...  The query reformulations proposed are used to increase the probability of retrieving relevant documents through the addition to, or the removal from, the original query of highly specific terms.  ...  Preliminary Study: TREC Precision Medicine 2018 In this section, we describe the preliminary study we performed on the TREC PM 2018 Clinical Trials Track.  ... 
doi:10.3390/info12100402 fatcat:b2tiwkuyf5hzrfkst2oesitn74

Team Cat-Garfield at TREC 2018 Precision Medicine Track

Xuesi Zhou, Xin Chen, Jian Song, Gang Zhao, Ji Wu
2018 Text Retrieval Conference  
This paper describes the system designed for the TREC 2018 Precision Medicine Track by the Team Cat-Garfield from Tsinghua University.  ...  utilized the qrels of TREC 2017 Precision Medicine Track as annotated data to train a classifier for precision medicine-relatedness of biomedical articles, named PM Classifier.  ...  Same as the track in 2017, TREC 2018 Precision Medicine Track focuses on the retrieval of biomedical articles and clinical trials which can provide useful precision medicine-related information to clinicians  ... 
dblp:conf/trec/ZhouCSZW18 fatcat:ygbpqsljlrglxean5pulkmdyga

IBI at TREC 2018: Precision Medicine Track

Francesco Ronzano, Emilio Centeno, Judith Pérez-Granado, Laura I. Furlong
2018 Text Retrieval Conference  
In this paper, we present and discuss the biomedical scientific Information Retrieval strategy we developed in the context of our participation to the Precision Medicine Track of the Text Retrieval Conference  ...  2018.  ...  In this regard, in the context of the Text Retrieval Conference 2018 (TREC), the Precision Medicine Track (PM Track) has been organized.  ... 
dblp:conf/trec/RonzanoCPF18 fatcat:73s3iqgjqza7bi4jkktv4cr5uu

DUTIR at TREC 2019: Precision Medicine Track

Jingkun Feng, Zhihao Yang, Zhiqiang Liu, Ling Luo, Hongfei Lin, Jian Wang
2019 Text Retrieval Conference  
This paper describes the system developed for the TREC 2019 Precision Medicine Track by the Team DUTIR from Dalian University of Technology.  ...  The performance of our system is above the median for the scientific abstracts subtask and below median for the clinical trials subtask.  ...  INTRODUCTION The 2019 Text Retrieval Conference (TREC) Precision Medicine (PM) track continues the prior 2017 [1] and 2018 [2] Precision Medicine tracks, which aims to retrieve biomedical articles  ... 
dblp:conf/trec/FengYLLLW19 fatcat:aiarmr7kljgpthvtqaewosfvra

Team UVA_ART at TREC 2018 Precision Medicine Track: Graph-based Concept Expansion and NLP for Document Relevance Boosting

Sean Mullane, Kasi Vegesana, Valentina Baljak
2018 Text Retrieval Conference  
This paper describes the UVA_ART* team entries in the TREC 2018 workshop series Precision Medicine Track. We submitted 5 runs for the Scientific Abstracts task.  ...  Our approach used an exclusivity-based relatedness measure defined on the UMLS Metathesaurus ontologies to add context to our queries.  ...  The TREC 2018 Precision Medicine track aims to encourage research into precision medicine, oncology in particular, to provide better solutions to physicians and researchers.  ... 
dblp:conf/trec/MullaneVB18 fatcat:w3ww6mvhozhhdbdmdqzse3fveq

The University of Padua IMS Research Group at TREC 2018 Precision Medicine Track

Maristella Agosti, Giorgio Maria Di Nunzio, Stefano Marchesin
2018 Text Retrieval Conference  
We report on the participation of the Information Management System (IMS) Research Group of the University of Padua in the second task of the Precision Medicine Track at TREC 2018: the Clinical Trials  ...  This initial set of experiments lays the ground for a deeper study on the effectiveness of (automatic) knowledge-based expansion techniques in the context of precision medicine.  ...  Final Remarks In this paper, we presented the results of our participation in the TREC 2018 Precision Medicine Track.  ... 
dblp:conf/trec/AgostiN018 fatcat:73nrvszdsnhubn5jyfcnqqg7re

CSIRO at 2017 TREC Precision Medicine Track

Vincent Nguyen, Sarvnaz Karimi, Sara Falamaki, Diego Mollá Aliod, Cécile Paris, Stephen Wan
2017 Text Retrieval Conference  
We report on our participation as the CSIROmed 1 team in the TREC 2017 Precision Medicine track.  ...  Our results show that boosting the gene variant in the query increases the relevance of the retrieved results.  ...  Funding for the team to participate in TREC was provided by the Decision Sciences Research Program of CSIRO Data61.  ... 
dblp:conf/trec/NguyenKFAPW17 fatcat:zl6e3szjdrbvnc6xrzlsrgegwu

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  ...  We participated in the TREC PM as CSIROmed team, experimenting with neural ranking for precision medicine.  ... 
dblp:conf/trec/RybinskiK20 fatcat:ezkdhgwrwbguxgz26jdgkvy7iy

UTD HLTRI at TREC 2018: Precision Medicine Track

Stuart J. Taylor, Sanda M. Harabagiu, Travis R. Goodwin
2018 Text Retrieval Conference  
In this paper, we describe the system designed for the TREC 2018 Precision Medicine track by the University of Texas at Dallas (UTD) Human Language Technology Research Institute (HLTRI).  ...  , along with two "hidden" aspects encoding the need that retrieved documents be within the domain of precision medicine and that retrieved documents have a focus on treatment.  ...  Conclusion In this paper, we described our system designed for the TREC 2018 Precision Medicine track.  ... 
dblp:conf/trec/TaylorHG18 fatcat:efgb4umbq5bsfl3srix7rw7qwy
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