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Multilingual Semantic Resources and Parallel Corpora in the Biomedical Domain: the CLEF-ER Challenge

Dietrich Rebholz-Schuhmann, Simon Clematide, Fabio Rinaldi, Senay Kafkas, Erik M. van Mulligen, Quoc-Chinh Bui, Johannes Hellrich, Ian Lewin, David Milward, Michael Poprat, Antonio Jimeno-Yepes, Udo Hahn (+1 others)
2013 Conference and Labs of the Evaluation Forum  
This main objective of the CLEF-ER challenge involves parallel corpora in English and other languages.  ...  In preparation of the CLEF-ER challenge, the documents have been annotated with terminologies in English and non-English languages (de, fr, es, and nl) and the pre-existing terminological resource has  ...  Acknowledgement This work was funded by the European Commission STREP grant number 296410 ("Mantra", FP7-ICT-2011-4.1).  ... 
dblp:conf/clef/Rebholz-SchuhmannCRKMBHLMPJHK13a fatcat:xpzdujrgpbbzzl7xmrjget6i64

Introduction to the CLEF2013 Labs and Workshop

Roberto Navigli, Dan Tufis
2013 Conference and Labs of the Evaluation Forum  
The three challenging tasks of the ImageCLEF 2013 were:  Photo Annotation and Retrieval: semantic concept detection using private collection data, and large-scale annotation using general Web data;   ...  In 2010 CLEF was launched in a new format, as a conference with research presentations, panels, poster and demo sessions and laboratory evaluation workshops.  ...  authors, whose effort, enthusiasm and creativity provided new energy to this new edition of CLEF, the lab and workshop organisers, the colleagues and friends involved in running the labs, and all the  ... 
dblp:conf/clef/NavigliT13 fatcat:kg76ulv4inf2jhfzxbqfsqywzm

Semantic transference for enriching multilingual biomedical knowledge resources

María Pérez, Rafael Berlanga
2015 Journal of Biomedical Informatics  
Biomedical knowledge resources (KRs) are mainly expressed in English, and many applications using them suffer from the scarcity of knowledge in non-English languages.  ...  The goal of the present work is to take maximum profit from existing multilingual biomedical KRs lexicons to enrich their non-English counterparts.  ...  The work was supported by the R&D project TIN2014-55335-R from the Spanish Ministry of Economy and Competitiveness (MINECO) and by the UJI INNOVA project 13I346 in collaboration with ActualMed.  ... 
doi:10.1016/j.jbi.2015.08.026 pmid:26386313 fatcat:5stczql3sngnbp67wuyd7u5hvu

Machine Translation for Entity Recognition across Languages in Biomedical Documents

Giuseppe Attardi, Andrea Buzzelli, Daniele Sartiano
2013 Conference and Labs of the Evaluation Forum  
We report on our experiments for the CLEF 2013 Entity Recognition Challenge. Our approach is based on a combination of machine translation and NE tagging techniques.  ...  The model is used for tagging entities in sentences in the target language with the proper semantic group and the entity dictionary is used for associating CUIs to each of them.  ...  Partial support for this work was provided by project RIS (POR RIS of the Regione Toscana, CUP n° 6408.30122011.026000160).  ... 
dblp:conf/clef/AttardiBS13 fatcat:ddecrlt4urflplkm7qfjlmqtwu

Multilingual Named-Entity Recognition from Parallel Corpora

Andreea Bodnari, Aurélie Névéol, Özlem Uzuner, Pierre Zweigenbaum, Peter Szolovits
2013 Conference and Labs of the Evaluation Forum  
We present a named-entity recognition (NER) system for parallel multilingual text. Our system handles three languages (i.e., English, French, and Spanish) and is tailored to the biomedical domain.  ...  Each language model benefits from the external knowledge extracted from biomedical and general domain resources.  ...  Our data consists of parallel multilingual corpora in English (en), French (fr), and Spanish (es).  ... 
dblp:conf/clef/BodnariNUZS13 fatcat:6gg5sqncsjervc52ldtlumuz6u

Semantic annotation in biomedicine: the current landscape

Jelena Jovanović, Ebrahim Bagheri
2017 Journal of Biomedical Semantics  
The abundance and unstructured nature of biomedical texts, be it clinical or research content, impose significant challenges for the effective and efficient use of information and knowledge stored in such  ...  Over the last dozen years, the biomedical research community has invested significant efforts in the development of biomedical semantic annotation technology.  ...  Funding The second author graciously acknowledges funding from The Natural Sciences and Engineering Research Council of Canada (NSERC).  ... 
doi:10.1186/s13326-017-0153-x pmid:28938912 pmcid:PMC5610427 fatcat:jby2gq576vfdfmf4lsusahjrrm

LIMSI @ CLEF eHealth 2015 - Task 1b

Eva D'hondt, François Morlane-Hondère, Leonardo Campillos Llanos, Dhouha Bouamor, Swen Ribeiro, Thomas Lavergne
2015 Conference and Labs of the Evaluation Forum  
This paper presents LIMSI's participation in the Clinical Named Entity Recognition task at the CLEF eHealth 2015 workshop.  ...  Our system is based on the combination of three classifiers: two CRFs to detect entities' boundaries and a SVM to identify their semantic class.  ...  Acknowledgments This work was supported by the French National Agency for Research under grant Accordys 8 ANR-12-CORD-0007.  ... 
dblp:conf/clef/DhondtMLBRL15 fatcat:oxko6vmmhbgmxgehgpxcmqpsmq

Fostering Multilinguality in the UMLS: A Computational Approach to Terminology Expansion for Multiple Languages

Johannes Hellrich, Udo Hahn
2014 AMIA Annual Symposium Proceedings  
We here report on efforts to computationally support the maintenance and extension of multilingual biomedical terminology resources.  ...  Our main idea is to treat term acquisition as a classification problem guided by term alignment in parallel multilingual corpora, using termhood information coming from of a named entity recognition system  ...  Both the corpora and the UMLS version we used were taken from the CLEF-ER 2013 challenge material. b,6 Corpus Set-Up We started by merging the MEDLINE and EMEA parallel corpora, resulting in one single  ... 
pmid:25954371 pmcid:PMC4419887 fatcat:kt7x4paa6vdefj5vdqf2qcr47y

Clinical Natural Language Processing in languages other than English: opportunities and challenges

Aurélie Névéol, Hercules Dalianis, Sumithra Velupillai, Guergana Savova, Pierre Zweigenbaum
2018 Journal of Biomedical Semantics  
Finally, we identify major challenges and opportunities that will affect the impact of NLP on clinical practice and public health studies in a context that encompasses English as well as other languages  ...  other than English, and (3) clinical informatics researchers and practitioners looking for resources in their languages in order to apply NLP techniques and tools to clinical practice and/or investigation  ...  Multilingual corpora are used for terminological resource construction [64] with parallel [65] [66] [67] or comparable [68, 69] corpora, as a contribution to bridging the gap between the scope of  ... 
doi:10.1186/s13326-018-0179-8 pmid:29602312 pmcid:PMC5877394 fatcat:xas3ynaltjeuhgdymutha7akvi

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

Roland Roller, Madeleine Kittner, Dirk Weissenborn, Ulf Leser
2018 arXiv   pre-print
Biomedical concept normalization links concept mentions in texts to a semantically equivalent concept in a biomedical knowledge base.  ...  Concept normalization of non-English biomedical text is even more challenging as non-English resources tend to be much smaller and contain less synonyms.  ...  Acknowledgements This research was supported by the German Federal Ministry of Economics and Energy (BMWi) through the project MACSS (01MD16011F) and the German Federal Ministry of Education and Research  ... 
arXiv:1805.01646v1 fatcat:ohcpjeltpbgndgqnkz6bj2f6aa

An overview of event extraction and its applications [article]

Jiangwei Liu, Liangyu Min, Xiaohong Huang
2021 arXiv   pre-print
This study provides a comprehensive overview of the state-of-the-art event extraction methods and their applications from text, including closed-domain and open-domain event extraction.  ...  With the rapid development of information technology, online platforms have produced enormous text resources.  ...  We summarize these popular corpora inThe texts in the TimeBANK corpus [31] cover various media sources of the news domain.  ... 
arXiv:2111.03212v1 fatcat:o3oagnjrybh3vapvvp7twgjtuu

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
In this survey, we provide a comprehensive description of recent neural entity linking (EL) systems developed since 2015 as a result of the "deep learning revolution" in NLP.  ...  The vast variety of modifications of this general neural entity linking architecture are grouped by several common themes: joint entity recognition and linking, models for global linking, domain-independent  ...  The work of Artem Shelmanov in the current study (preparation of sections related to application of entity linking to neural language models, entity ranking, contextmention encoding, and overall harmonization  ... 
arXiv:2006.00575v3 fatcat:ra3kwc4tmbfhlmgtlevkcshcqq

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  
In the context of text ranking, these models produce high quality results across many domains, tasks, and settings.  ...  The combination of transformers and self-supervised pretraining has, without exaggeration, revolutionized the fields of natural language processing (NLP), information retrieval (IR), and beyond.  ...  Acknowledgements 129 Acknowledgements This research was supported in part by the Canada First Research Excellence Fund and the Natural Sciences and Engineering Research Council (NSERC) of Canada.  ... 
doi:10.1145/3437963.3441667 fatcat:6teqmlndtrgfvk5mneq5l7ecvq

Analyzing Non-Textual Content Elements to Detect Academic Plagiarism

Norman Meuschke, Bela Gipp, Harald Reiterer, Michael L. Nelson
2021 Zenodo  
Detection approaches proposed so far analyze lexical, syntactical, and semantic text similarity. These approaches find copied, moderately reworded, and literally translated text.  ...  To improve the identification of plagiarism in disciplines like mathematics, physics, and engineering, the thesis presents the first plagiarism detection approach that analyzes the similarity of mathematical  ...  [408] , [412] . combined and rearranged data from six multilingual parallel and comparable corpora 7 .  ... 
doi:10.5281/zenodo.4913344 fatcat:xmpaahvwuva53l5l5i2gaidvi4

Challenges for annotating images for sense disambiguation

Cecilia Ovesdotter Alm, Nicolas Loeff, David A. Forsyth
2006 Proceedings of the Workshop on Frontiers in Linguistically Annotated Corpora 2006 - LAC '06   unpublished
The views expressed are not necessarily endorsed by the sponsors. We also thank anonymous reviewers for improvements in the final version. Acknowledgment.  ...  Martha Palmer, Daniel Gildea, and Paul Kingsbury. 2005 Acknowledgement This research was supported, in part, by the National Science Foundation under Grant CNI-0551615.  ...  Thus merging resources may present opportunities for constructing nearly parallel resources, which in turn could prove useful for a multilingual application.  ... 
doi:10.3115/1641991.1641992 fatcat:anbt5zqbzjb5lpyqdzy6hwpehq
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