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Cross-lingual Candidate Search for Biomedical Concept Normalization [article]

Roland Roller, Madeleine Kittner, Dirk Weissenborn, Ulf Leser
2018 arXiv   pre-print
To overcome the limitations of non-English terminologies we propose a cross-lingual candidate search for concept normalization using a character-based neural translation model trained on a multilingual  ...  Biomedical concept normalization links concept mentions in texts to a semantically equivalent concept in a biomedical knowledge base.  ...  In this work, we present a sequential cross-lingual candidate search for biomedical concept normalization.  ... 
arXiv:1805.01646v1 fatcat:ohcpjeltpbgndgqnkz6bj2f6aa

Cross-lingual Unified Medical Language System entity linking in online health communities

Yonatan Bitton, Raphael Cohen, Tamar Schifter, Eitan Bachmat, Michael Elhadad, Noémie Elhadad
2020 JAMIA Journal of the American Medical Informatics Association  
Conclusions Cross-lingual UMLS entity linking from Hebrew is possible and improves search performance across communities.  ...  When tagging and normalizing terms in queries from the Camoni search logs, UMLS-normalized queries improved search results in 46% of the cases.  ...  Xu et al 15 introduce a model to identify cross-lingual candidates for concept normalization using a character-based neural translation model trained on a multilingual biomedical terminology.  ... 
doi:10.1093/jamia/ocaa150 pmid:32910823 fatcat:pjnexvgv5rcydfpgdljfrzbequ

CODER: Knowledge infused cross-lingual medical term embedding for term normalization [article]

Zheng Yuan and Zhengyun Zhao and Haixia Sun and Jiao Li and Fei Wang and Sheng Yu
2021 arXiv   pre-print
CODER is designed for medical term normalization by providing close vector representations for different terms that represent the same or similar medical concepts with cross-lingual support.  ...  This paper proposes CODER: contrastive learning on knowledge graphs for cross-lingual medical term representation.  ...  The scalar output from the classifier is then used as a measure of similarity to rank the candidate concepts for normalization.  ... 
arXiv:2011.02947v3 fatcat:lyecgcxewzghhgsm3ujsy74o3u

Biomedical term normalization of EHRs with UMLS [article]

Naiara Perez, Montse Cuadros, German Rigau
2018 arXiv   pre-print
This paper presents a novel prototype for biomedical term normalization of electronic health record excerpts with the Unified Medical Language System (UMLS) Metathesaurus.  ...  Despite being multilingual and cross-lingual by design, we first focus on processing clinical text in Spanish because there is no existing tool for this language and for this specific purpose.  ...  The tool is multilingual and cross-lingual by design, but we first focus on Spanish EHR processing because there is no existing tool for this language and for this specific purpose.  ... 
arXiv:1802.02870v2 fatcat:a6yhzysrk5hytprq7ojh3w5yui

A Cross-Lingual Similarity Measure for Detecting Biomedical Term Translations

Danushka Bollegala, Georgios Kontonatsios, Sophia Ananiadou, Neil R. Smalheiser
2015 PLoS ONE  
We propose a cross-lingual similarity measure for detecting most similar translation candidates for a biomedical term specified in one language (source) from another language (target).  ...  Bilingual dictionaries for technical terms such as biomedical terms are an important resource for machine translation systems as well as for humans who would like to understand a concept described in a  ...  Evaluating Cross-Lingual Similarity Measurement Cross-Lingual Biomedical Terms Dataset.  ... 
doi:10.1371/journal.pone.0126196 pmid:26030738 pmcid:PMC4452086 fatcat:r6n43auqazgl5ey2ufwf6jq5ni

Analyzing transfer learning impact in biomedical cross-lingual named entity recognition and normalization

Renzo M. Rivera-Zavala, Paloma Martínez
2021 BMC Bioinformatics  
For the entity normalization task, the extended Bi-LSTM-CRF model achieves an F-score of 72.85% and the BERT model achieves 79.97%.  ...  Embeddings based on word, concepts, senses, etc. other than those for English are required to improve NER tasks in other languages.  ...  Abbreviation Dictionary [28] for normalizing biomedical entities.  ... 
doi:10.1186/s12859-021-04247-9 pmid:34920703 pmcid:PMC8680060 fatcat:dsavlikunvc4zeejhsl74hteo4

Scientific Discovery by Machine Intelligence: A New Avenue for Drug Research [article]

Carlo A. Trugenberger
2015 arXiv   pre-print
I will describe the methodology and a first successful experiment for the discovery of new biomarkers and phenotypes for diabetes and obesity on the basis of PubMed abstracts, public clinical trials and  ...  this vision I will introduce a totally new approach to drug research, namely that of identifying relevant information by employing a self-organizing semantic engine to text mine large repositories of biomedical  ...  the concept "biomarker/phenotype for D&O".  ... 
arXiv:1506.07116v1 fatcat:ciuab5j5xbhknpdplkkg7cji7e

A Survey of Techniques for Constructing Chinese Knowledge Graphs and Their Applications

Tianxing Wu, Guilin Qi, Cheng Li, Meng Wang
2018 Sustainability  
We first describe the background of OBOR, and then introduce the concept and development history of knowledge graph and typical Chinese knowledge graphs.  ...  In recent years, knowledge graph has been widely applied in different kinds of applications, such as semantic search, question answering, knowledge management and so on.  ...  To find as many new cross-lingual links as possible, the method adopts an iteration framework which allows the concept annotation and cross-lingual link prediction to mutually reinforce.  ... 
doi:10.3390/su10093245 fatcat:wrqgfkwfanfejnffn6nyr4nqbq

Discovery of novel biomarkers and phenotypes by semantic technologies

Carlo A Trugenberger, Christoph Wälti, David Peregrim, Mark E Sharp, Svetlana Bureeva
2013 BMC Bioinformatics  
Amongst these were many interesting candidates with a high potential, although noticeable noise (uninteresting or obvious terms) was generated.  ...  However, there is an even larger source of valuable information available that can potentially be tapped for such discoveries: repositories constituted by research documents.  ...  Acknowledgements The authors wish to thank Matthew Wiener, Matthew Walker, Paul Ziegler, and Guochun Xie of Merck Research Labs for helpful comments on manuscript drafts.  ... 
doi:10.1186/1471-2105-14-51 pmid:23402646 pmcid:PMC3605201 fatcat:abn5vckzqjbbtpk7jao2lx7a5m

Bisociative Literature-Based Discovery: Lessons Learned and New Word Embedding Approach

Nada Lavrač, Matej Martinc, Senja Pollak, Maruša Pompe Novak, Bojan Cestnik
2020 New generation computing  
The paper addresses also new prospects in bisociative literature-based discovery, proposing an advanced embeddings-based technology for cross-domain literature mining.  ...  This paper outlines several outlier-based literature mining approaches to bridging term detection and the lessons learned from selected biomedical literature-based discovery applications.  ...  On the other hand, research in cross-lingual embeddings [8] has demonstrated the ability of aligning embeddings spaces across languages, which can be used as a basis for finding analogies across corpora  ... 
doi:10.1007/s00354-020-00108-w fatcat:ypxsjir5tjamdn7fenzxd7oqky

Discovery of Novel Biomarkers by Text Mining: A New Avenue for Drug Research?

Carlo A Trugenberger David Peregrim
2013 Journal of Molecular Biomarkers & Diagnosis  
Citation: Trugenberger CA, Peregrim D (2013) Discovery of Novel Biomarkers by Text Mining: A New Avenue for Drug Research? J Mol Biomark Diagn S3: 004.  ...  However, there is an even larger source of valuable information available that can potentially be tapped for discoveries: repositories constituted by research documents.  ...  the accelerated recognition of collocated expressions The words/phrases with almost the same meaning are collected into cross-lingual synonym groups (microscopic semantic clouds) and systematically linked  ... 
doi:10.4172/2155-9929.s3-004 fatcat:2nllv7vyvvb3xebqpewfokv3ne

An IR-Based Approach Utilizing Query Expansion for Plagiarism Detection in MEDLINE

Rao Muhammad Adeel Nawab, Mark Stevenson, Paul Clough
2017 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
Various approaches to Word Sense Disambiguation are investigated to deal with cases where there are multiple Concept Unique Identifiers (CUIs) for a given term.  ...  A scalable approach based on Information Retrieval is used to perform candidate document selection -the identification of a subset of potential source documents given a suspicious text -from MEDLINE.  ...  (related to biomedical and health), concept names and relationships between concepts.  ... 
doi:10.1109/tcbb.2016.2542803 pmid:26992177 fatcat:koibe2amdzcwdo3ygxf34brjni

Neural Entity Linking: A Survey of Models Based on Deep Learning [article]

Ozge Sevgili, Artem Shelmanov, Mikhail Arkhipov, Alexander Panchenko, Chris Biemann
2021 arXiv   pre-print
techniques including zero-shot and distant supervision methods, and cross-lingual approaches.  ...  We distill generic architectural components of a neural EL system, like candidate generation and entity ranking, and summarize prominent methods for each of them.  ...  and linking mentions of drugs, symptoms, diseases to concepts in biomedical ontologies.  ... 
arXiv:2006.00575v3 fatcat:ra3kwc4tmbfhlmgtlevkcshcqq

Empowering industrial research with shared biomedical vocabularies

Lee Harland, Christopher Larminie, Susanna-Assunta Sansone, Sorana Popa, M. Scott Marshall, Michael Braxenthaler, Michael Cantor, Wendy Filsell, Mark J. Forster, Enoch Huang, Andreas Matern, Mark Musen (+6 others)
2011 Drug Discovery Today  
The life science industries (including pharmaceuticals, agrochemicals and consumer goods) are exploring new business models for research and development that focus on external partnerships.  ...  We also thank Therese Vachon (Novartis), Hilary Vass (AstraZeneca) and Phoebe Roberts (Pfizer) for suggestions and corrections. We thank Anna Zhao-Wong (MSSO) for information regarding MedDRA.  ...  We thank the following participants for valuable contributions which provided the substrate for this perspective: Michael Ashburner, Susanna Lewis, Alan Ruttenberg, Barry Smith (OBO Foundry); Johanna McEntyre  ... 
doi:10.1016/j.drudis.2011.09.013 pmid:21963522 pmcid:PMC7098809 fatcat:rs35p6w34bgifaz7gcdta36mka

Component-Based Evaluation for Question Answering [chapter]

Teruko Mitamura, Eric Nyberg
2020 Evaluating Information Retrieval and Access Tasks  
the component-based evaluation of automatic question answering (QA) systems, which was pioneered in the NTCIR-7 ACLIA challenge and has became a fundamental part of QA system development, especially for  ...  We summarize the history of component evaluation for QA and describe more recent work at Carnegie Mellon (on TREC Genomics, BioASQ, and LiveQA datasets) which has descended directly from our experiences  ...  Shared Data Schema and Tracks In order to combine a Cross-Lingual Information Retrieval (CLIR) module with a cross-lingual Question Answering (CLQA) system for module-based evaluation, we defined five  ... 
doi:10.1007/978-981-15-5554-1_8 fatcat:3pklke6ulvh7xjlxwxxzctgfue
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