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Brown University at TREC Precision Medicine 2018

Prakrit Baruah, Riya Dulepet, Kyle Qian, Carsten Eickhoff
2018 Text Retrieval Conference  
This paper describes Brown University's submission to the TREC 2018 Precision Medicine (PM) track. This report details our efforts to query processing and retrieval modeling.  ...  The empirical evaluation is based on 50 synthetic precision oncology patients and shows solid retrieval performance.  ...  Conclusion This report describes Brown University's entry to the TREC 2018 Precision Medicine Track, ranking scientific abstracts and clinical trial descriptions in response to structured precision oncology  ... 
dblp:conf/trec/BaruahDQE18 fatcat:uloklguikfbylact3ykawsuctm

Brown University at TREC Precision Medicine 2019

Abdullah Ahmed, Gil Alon, Bashar Zaidat, Isaac Nathoo, Hwai-Liang Tung, Charles Wang, Carsten Eickhoff
2019 Text Retrieval Conference  
This paper describes Brown University's submission to the TREC 2019 Precision Medicine (PM) track.  ...  Conclusion In this paper, we provide an overview of Brown University's contribution to the TREC 2019 Precision Medicine Track.  ...  In this paper we present a patient-centric information retrieval system which may be applied in precision medicine.  ... 
dblp:conf/trec/AhmedAZNTWE19 fatcat:mzplno2o3vb7jchanotflkvrmu

The Impact of a Search Engine on Clinical Decisions Under Time and System Effectiveness Constraints: Research Protocol (Preprint)

Anton van der Vegt, Guido Zuccon, Bevan Koopman, Anthony Deacon
2018 JMIR Research Protocols  
All data collected in this study will be made available at the University of Queensland's UQ eSpace public data repository. DERR1-10.2196/12803.  ...  An evidence-based medicine approach expects that clinicians will seek and apply the best available evidence to answer clinical questions.  ...  Also, to Harrisen Scells for his helpful technical input for the design of Taskiir and the IELab team (ielab.io) at The University of Queensland for Taskiir system testing.  ... 
doi:10.2196/12803 pmid:31140437 pmcid:PMC6658292 fatcat:4lnykcshb5cublfhbhfssc55aq

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 thank the members of Korea University for the helpful comments and Kyle Lo (Allen Institute for Artificial Intelligence) for the insightful discussion.  ...  First, users can input any type of question in the search box located at the top.  ...  Table 5 shows the results on TREC-COVID.  ... 
arXiv:2006.15830v2 fatcat:36sbtup3rrgdtkqrqnw2i67qhi

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

2019 Database: The Journal of Biological Databases and Curation  
The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods.  ...  Brown 66 , Brian P. Dalrymple 67 , David J. Harvey 68 , Grace Ng 69 , Sebastiaan Werten 70 , Mark Bleackley 71 , Zhanwu Dai 72 , Raman Dhariwal 73 , Yael Gelfer 74 , Marcus D.  ...  Department of Radiology, Institute of Medical Science, The University of Tokyo, Japan; 571. Family Medicine, Faculty of Medicine, Çukurova University, Adana, Turkey; 572.  ... 
doi:10.1093/database/baz085 pmid:33326193 pmcid:PMC7291946 fatcat:floik5bx6bdxpnvxnl64ryqhou

Pretrained Transformers for Text Ranking: BERT and Beyond

Andrew Yates, Rodrigo Nogueira, Jimmy Lin
2021 Proceedings of the 14th ACM International Conference on Web Search and Data Mining  
The Precision Medicine Track, which began in TREC 2017 [Roberts et al., 2017] and continues to this day, focuses on clinical information seeking scenarios in the context of evidence-based medicine.  ...  , Precision@10 is capped at 0.2.  ... 
doi:10.1145/3437963.3441667 fatcat:6teqmlndtrgfvk5mneq5l7ecvq

Interpreting Neural Networks With Nearest Neighbors [article]

Eric Wallace, Shi Feng, Jordan Boyd-Graber
2018 arXiv   pre-print
The authors would like to thank the members of the CLIP lab at the University of Maryland and the anonymous reviewers for their feedback.  ...  Introduction The growing use of neural networks in sensitive domains such as medicine, finance, and security raises concerns about human trust in these machine learning systems.  ...  The conformity score uses the representations at each neural network layer, and therefore, a prediction only receives high conformity if it largely agrees with the training data at all representation levels  ... 
arXiv:1809.02847v2 fatcat:lp5bqugwhzfk3ixongbt4vmkz4

Interpreting Neural Networks with Nearest Neighbors

Eric Wallace, Shi Feng, Jordan Boyd-Graber
2018 Proceedings of the 2018 EMNLP Workshop BlackboxNLP: Analyzing and Interpreting Neural Networks for NLP  
The authors would like to thank the members of the CLIP lab at the University of Maryland and the anonymous reviewers for their feedback.  ...  Introduction The growing use of neural networks in sensitive domains such as medicine, finance, and security raises concerns about human trust in these machine learning systems.  ...  We use k = 75 nearest neighbors at each layer. The empirical results are robust to the choice of k.  ... 
doi:10.18653/v1/w18-5416 dblp:conf/emnlp/WallaceFB18 fatcat:uwytppt2s5g4rlccf27wx5ymke

Multidisciplinary treatment strategy for early rectal cancer A review

Gyung Mo Son, In Young Lee, Sung Hwan Cho, Byung-Soo Park, Hyun Sung Kim, Su Bum Park, Hyung Wook Kim, Sang Bo Oh, Tae Un Kim, Dong Hoon Shin
2021 Precision and Future Medicine  
radiologic, endoscopic and pathologic evaluation to predict the risk of lymph node metastasis and local recurrence has been evolving to determine the optimal treatment strategy in the patient-tailored medicine  ...  The classification of capillary patterns using magnifying endoscopy can be performed more precisely.  ...  to dark brown relative to back ground; sometimes patchy whiter areas Vessles None, or isolated lacy vessels may be present coursing across the lesion Brown vessels surrounding white structures Has area  ... 
doi:10.23838/pfm.2021.00163 fatcat:2wa4xmojsng2zbulz2r3uvoune

Applications of Clinical Text Mining [chapter]

Hercules Dalianis
2018 Clinical Text Mining  
Accessed 2018-01-11. 2 Evidence-based medicine is a concept within medicine meaning that the treatment of the patient should follow scientific results from well-designed research.  ...  In TREC 2013, the tasks were similar to the previous Text REtrieval Conferences (TREC) using patient records as document collections.  ...  The official name of the shared task in precision medicine was TREC 2014 Clinical Decision Support Track. Precision medicine means customised treatment to each individual patient.  ... 
doi:10.1007/978-3-319-78503-5_10 fatcat:qctgcc6uo5hefdwmq6scrwnwma

Pretrained Transformers for Text Ranking: BERT and Beyond [article]

Jimmy Lin, Rodrigo Nogueira, Andrew Yates
2021 arXiv   pre-print
Often, precision is evaluated at a cutoff k, notated as Precision@k or abbreviated as P@k.  ...  National Library of Medicine (NLM) had been publishing since 1879.  ... 
arXiv:2010.06467v3 fatcat:obla6reejzemvlqhvgvj77fgoy

Screening Pathways through China, the Asia Pacific Region, the World

Wiley, Webster, Loeber, on behalf of ISNS two thousand nineteen, Local Organising Committee
2019 International Journal of Neonatal Screening  
The International Society for Neonatal Screening (ISNS) has met regularly at both international meetings and those of the various chapters[...]  ...  Until Dec. 2018, four confirmed cases had complete their follow-up exams at the age of 6 months old.  ...  We have assessed the assay accuracy, precision and linearity.  ... 
doi:10.3390/ijns5030026 pmid:33072985 pmcid:PMC7510188 fatcat:3y6yescmijgatfyypjxzpeosma

Fentanyl Induces Cerebellar Internal Granular Cell Layer Apoptosis in Healthy Newborn Pigs

Hemmen Sabir, John Dingley, Emma Scull-Brown, Ela Chakkarapani, Marianne Thoresen
2018 Frontiers in Neurology  
Methods: Thirteen healthy pigs (<median 12 h old) were randomized into (1) 24 h of intravenous fentanyl at normothermia (NTFe, n = 6) or (2) non-ventilated controls at normothermia (NTCTR, n = 7).  ...  Rectal temperature (Trec) was maintained at 38.5 ± 0.2°C using a servo-controlled (CritiCool, MTRE, Yavne, Israel) mat containing circulating water.  ...  Input from the cerebellar cortex has a major role in the functioning of the cerebellum (coordination, precision, and accurate timing).  ... 
doi:10.3389/fneur.2018.00294 pmid:29765353 pmcid:PMC5938373 fatcat:6pfvdzi5hbfx7oodvf4ytrbzfq

Abstracts for the 42nd Human Genetics Society of Australasia Annual Scientific Meeting Sydney, New South Wales August 4–7, 2018

2018 Twin Research and Human Genetics  
Plenary 15 THE POWER OF MYCODE: SOMEDAY IS TODAY Amy Curry Sturm Geisinger, Genomic Medicine Institute, Danville, Pennsylvania, USA The MyCode Community Health Initiative is a precision medicine project  ...  Zero Childhood Cancer demonstrates the potential of a precision medicine model approach to enhance clinical outcomes for HR childhood cancers.  ...  Supplementation with citrate (800 mg/kg/day) commenced at age 5.5 years of age.  ... 
doi:10.1017/thg.2018.51 pmid:30284531 fatcat:2fzkr56iwndxfhcpcuuwtxymkm

2019 CIS Annual Meeting: Immune Deficiency & Dysregulation North American Conference

2019 Journal of Clinical Immunology  
1 Genetic Counselor, Co-Director of Personalized Medicine, Division of Hematology/Oncology/BMT and the Institute for Genomic Medicine, Nationwide Childrens Hospital 2 Genetic Counselor, Division of Hematology  ...  Raif Geha and Janet Chou at the Division of Immunology, Allergy, Rheumatology and Dermatology, Boston Children's Hospital, Harvard Medical School. The following grants are acknowledged: 1.  ...  Methods: Eligible subjects included patients less than 21 years seen at the University of Michigan between January 2010-July 2018.  ... 
doi:10.1007/s10875-019-00597-5 pmid:30809743 fatcat:ophhlkvazzhjxl4t4eoct3tfna
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