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Distant Supervision for Medical Concept Normalization

Nikhil Pattisapu, Vivek Anand, Sangameshwar Patil, Girish Palshikar, Vasudeva Varma
2020 Journal of Biomedical Informatics  
We consider the task of Medical Concept Normalization (MCN) which aims to map informal medical phrases such as "loosing weight" to formal medical concepts, such as "Weight loss".  ...  We extend this idea by computationally creating a distant dataset from patient discussion forums.  ...  [7] also employ CNNs and RNNs for normalizing medical concepts.  ... 
doi:10.1016/j.jbi.2020.103522 pmid:32783923 pmcid:PMC7415240 fatcat:7b5p2goaxzda7nuoveuhlzqfla

Knowledge-guided Text Structuring in Clinical Trials [article]

Yingcheng Sun, Kenneth Loparo
2019 arXiv   pre-print
entities, attributes and relations that are more complex for parsing.  ...  Previous research has focused on extracting information from eligibility criteria, with usually a single pair of medical entity and attribute, but seldom considering other kinds of free text with multiple  ...  and Valx [7] for numeric expression extraction and normalization.  ... 
arXiv:1912.12380v1 fatcat:6d4bj5pprfew3dhwkjnuy2pske

Making the most of limited training data using distant supervision

Roland Roller, Mark Stevenson
2015 Proceedings of BioNLP 15  
The approach uses a form of distant supervision but does not require an external knowledge base.  ...  Supervised machine learning techniques have proved to be the most effective approach to this problem.  ...  Acknowledgements The authors are grateful to the Engineering and Physical Sciences Research Council for supporting the work described in this paper (EP/J008427/1).  ... 
doi:10.18653/v1/w15-3802 dblp:conf/bionlp/RollerS15 fatcat:scmytke3avh75e7wdiohuqofui

Ranking Medical Terms to Support Expansion of Lay Language Resources for Patient Comprehension of Electronic Health Record Notes: Adapted Distant Supervision Approach

Jinying Chen, Abhyuday N Jagannatha, Samah J Fodeh, Hong Yu
2017 JMIR Medical Informatics  
Medical terms are a major obstacle for patients to comprehend their electronic health record (EHR) notes.  ...  Methods: Adapted distant supervision uses distant supervision from consumer health vocabulary and transfer learning to adapt itself to solve the problem of ranking EHR terms in the target domain.  ...  supervision-supervised distant supervision. b (page number not for citation purposes)  ... 
doi:10.2196/medinform.8531 pmid:29089288 pmcid:PMC5686421 fatcat:yvf2gbrnr5cxzplh2x2czo3m3a

Held-out versus Gold Standard: Comparison of Evaluation Strategies for Distantly Supervised Relation Extraction from Medline abstracts

Roland Roller, Mark Stevenson
2015 Proceedings of the Sixth International Workshop on Health Text Mining and Information Analysis  
Distant supervision is a useful technique for creating relation classifiers in the absence of labelled data.  ...  A new evaluation data set for these relations is made available.  ...  Acknowledgments The authors are grateful to the Engineering and Physical Sciences Research Council (EP/J008427/1) for funding the research described in this paper.  ... 
doi:10.18653/v1/w15-2612 dblp:conf/acl-louhi/RollerS15 fatcat:3ecp3i66jndl3kanvwil5isk4i

Distant Supervision with Transductive Learning for Adverse Drug Reaction Identification from Electronic Medical Records

Siriwon Taewijit, Thanaruk Theeramunkong, Mitsuru Ikeda
2017 Journal of Healthcare Engineering  
In this study, we propose automatic data labeling by distant supervision where knowledge bases are exploited to assign an entity-level relation label for each drug-event pair in texts, and then, we use  ...  patterns for characterizing ADR relation.  ...  We firstly present the formal definition of distant supervision and then formulate the problem using MIL concept.  ... 
doi:10.1155/2017/7575280 pmid:29090077 pmcid:PMC5635478 fatcat:pdroxylgljaoragkwuqkucwq4q

Improving Broad-Coverage Medical Entity Linking with Semantic Type Prediction and Large-Scale Datasets [article]

Shikhar Vashishth, Denis Newman-Griffis, Rishabh Joshi, Ritam Dutt, Carolyn Rose
2021 arXiv   pre-print
Medical entity linking is the task of identifying and standardizing medical concepts referred to in an unstructured text.  ...  We make our source code and datasets publicly available for medical entity linking research.  ...  Distant supervision for relation extrac- tion without labeled data.  ... 
arXiv:2005.00460v3 fatcat:yn3teuimcbaa5objz6bzsmxw6q

A Deep Representation Empowered Distant Supervision Paradigm for Clinical Information Extraction [article]

Yanshan Wang, Sunghwan Sohn, Sijia Liu, Feichen Shen, Liwei Wang, Elizabeth J. Atkinson, Shreyasee Amin, Hongfang Liu
2018 arXiv   pre-print
Materials and Methods: We propose a distant supervision paradigm empowered by deep representation for extracting information from clinical text.  ...  Results: The results indicate that CNN is the best fit to the proposed distant supervision paradigm.  ...  Methods Distant Supervision Paradigm We now describe the deep representation empowered distant supervision paradigm for clinical information extraction from clinical text.  ... 
arXiv:1804.07814v1 fatcat:mbem63ckanfj3mlbogn3n2axmu

Medical students' preparedness for professional activities in early clerkships

Josefin Bosch, Asja Maaz, Tanja Hitzblech, Ylva Holzhausen, Harm Peters
2017 BMC Medical Education  
Methods: Medical students from a competency-based undergraduate curriculum were surveyed about preparedness for 21 professional activities and level of perceived supervision during their early clerkships  ...  Conclusions: The applied three-dimensional concept of preparedness and the task-specific approach provided a detailed and meaningful view on medical students' workplace participation and experiences in  ...  Chen for critically reviewing the manuscript and Olle ten Cate for reviewing an earlier version of the manuscript.  ... 
doi:10.1186/s12909-017-0971-7 pmid:28830418 pmcid:PMC5568232 fatcat:r3e7mciywrer3mipkxsgpolfgu

Initial Experiments for Pharmacovigilance Analysis in Social Media Using Summaries of Product Characteristics

Leonardo Campillos-Llanos, Cyril Grouin, Agnès Lillo-Le Louët, Pierre Zweigenbaum
2019 Studies in Health Technology and Informatics  
We report initial experiments for analyzing social media through an NLP annotation tool on web posts about medications of current interests (baclofen, levothyroxine and vaccines) and summaries of product  ...  We conducted supervised experiments on a subset of messages annotated by experts according to positive or negative misuse; results ranged from 0.62 to 0.91 of F-score.  ...  Paris 13) for the data, and the pharmacovigilance team for annotating those posts.  ... 
doi:10.3233/shti190183 pmid:31437885 fatcat:bgqaxngmkbglvdctbj73zbv2fy

Making a Case for Entrustable Professional Activities for Nurse Practitioners in Emergency Care

K. Sue Hoyt, Elda G. Ramirez, Jean A. Proehl
2017 Advanced Emergency Nursing Journal  
with heavy to light supervision or no supervision at all.  ...  The Association of American Medical Colleges established a taxonomy of competency domains (entrustable professional activities [EPAs]) that are applicable for other health care providers, including nursing  ...  Academicians must use structural entrustment decisions as a way for these students to execute EPAs with distant supervision.  ... 
doi:10.1097/tme.0000000000000146 pmid:28463862 fatcat:5vweos3bcjaejgwkbwwyp5t3qe

Hybrid Approaches for our Participation to the n2c2 Challenge on Cohort Selection for Clinical Trials [article]

Xavier Tannier, Nicolas Paris, Hugo Cisneros, Christel Daniel, Matthieu Doutreligne, Catherine Duclos, Nicolas Griffon, Claire Hassen-Khodja, Ivan Lerner, Adrien Parrot, Éric Sadou, Cyrina Saussol (+1 others)
2020 arXiv   pre-print
The terminology-based method is very efficient when medical concepts carry most of the relevant information.  ...  The second method is a terminology-based approach where a medical expert selects the appropriate concepts, and a procedure is defined to search the terms and check the structural or temporal constraints  ...  a big "silver standard" dataset suitable for supervised learning (Section 4.2) and a terminology-based approach where a medical expert selects the appropriate concepts (Section 4.3).  ... 
arXiv:1903.07879v2 fatcat:4g7p6waw5nhm7kyanxm5onk7tm

EMSContExt: EMS Protocol-Driven Concept Extraction for Cognitive Assistance in Emergency Response

Sarah Masud Preum, Sile Shu, Homa Alemzadeh, John A. Stankovic
Hence, we develop EMSContExt, a weakly-supervised concept extraction approach for EMS concepts.  ...  Our experimental results show that EMSContExt achieves 0.85 recall and 0.82 F1-score for EMS concept extraction and significantly outperforms MetaMap, a state-of-the-art medical concept extraction tool  ...  Some existing works address the low training resources issue utilizing distant or weak supervision.  ... 
doi:10.1609/aaai.v34i08.7048 fatcat:wsltv773g5bm7o2sne3rjowgte

BioRel: towards large-scale biomedical relation extraction

Rui Xing, Jie Luo, Tengwei Song
2020 BMC Bioinformatics  
Then, we assign each sentence a relation label by using distant supervision.  ...  We construct BioRel, a large-scale dataset for biomedical relation extraction problem, by using Unified Medical Language System as knowledge base and Medline as corpus.  ...  Acknowledgements We would like to thank all of the reviewers for their comments on the manuscript.  ... 
doi:10.1186/s12859-020-03889-5 pmid:33323106 fatcat:ngugz4tvvzdanjlmo4hvnwfmbm

Two Level Self-Supervised Relation Extraction From Medline Using UMLS

Huda Banuqitah, Fathy Eassa, Kamal Jambi, Maysoon Abulkhair
2016 International Journal of Data Mining & Knowledge Management Process  
In this paper, we propose a Two-level model for Self-supervised relation extraction from MEDLINE using Unified Medical Language System (UMLS) Knowledge base.  ...  The model uses a Self-supervised Approach for Relation Extraction (RE) by constructing enhanced training examples using information from UMLS.  ...  There are some works done in Self-supervised approach outside the biomedical domain. Mintz and others in [12] use Freebase to provide distant supervision for relation extraction.  ... 
doi:10.5121/ijdkp.2016.6302 fatcat:wctvqzwozjbb5deshlajclrdey
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