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Exploring semantic deep learning for building reliable and reusable one health knowledge from PubMed systematic reviews and veterinary clinical notes

Mercedes Arguello-Casteleiro, Robert Stevens, Julio Des-Diz, Chris Wroe, Maria Jesus Fernandez-Prieto, Nava Maroto, Diego Maseda-Fernandez, George Demetriou, Simon Peters, Peter-John M. Noble, Phil H. Jones, Jo Dukes-McEwan (+3 others)
2019 Journal of Biomedical Semantics  
We used a Semantic Deep Learning approach that combines the Semantic Web technologies and Deep Learning to acquire and validate knowledge about 11 well-known medical conditions mined from two sets of unstructured  ...  We also create ontological modules and illustrate how the extracted knowledge can be queried. The evaluation was performed using the content within BMJ Best Practice.  ...  Acknowledgements Thanks to Tim Furmston (University of Manchester) for help with software and e-infrastructure, and to the medical consultants from the Hospital do Salnés (Spain) for their support and  ... 
doi:10.1186/s13326-019-0212-6 pmid:31711540 pmcid:PMC6849172 fatcat:vfm3gd524ng3xprcra2z356lha

LINNAEUS: A species name identification system for biomedical literature

Martin Gerner, Goran Nenadic, Casey M Bergman
2010 BMC Bioinformatics  
The task of recognizing and identifying species names in biomedical literature has recently been regarded as critical for a number of applications in text and data mining, including gene name recognition  ...  When compared against our manually annotated corpus, LINNAEUS performs with 94% recall and 97% precision at the mention level, and 98% recall and 90% precision at the document level.  ...  This system includes a dictionary-based term search combined with filters to remove common English words, and then ranks species based on their mention frequency in the abstract or main text.  ... 
doi:10.1186/1471-2105-11-85 pmid:20149233 pmcid:PMC2836304 fatcat:eru576q7u5befdadlzwjhw3mqi

The Use of Ontology in Retrieval: A Study on Textual, Multilingual and Multimedia Retrieval

Muhammad Nabeel Asim, Muhammad Wasim, Muhammad Usman Ghani Khan, Nasir Mahmood, Waqar Mahmood
2019 IEEE Access  
This paper reviews modern ontology-based information retrieval methods for textual, multimedia, and cross-lingual data types.  ...  Ontologies are not only being extensively employed in the semantic Web to store unstructured information in an organized and structured way but it has also raised the performance of diverse information  ...  to search in the extended Wordnet for relevant annotation.  ... 
doi:10.1109/access.2019.2897849 fatcat:ei2zxyxdjndbvgzzue2indwqy4

BioCreative II Workshop Proceedings

Lynette, Martin, Alfonso
2007 Zenodo  
81 Combined Conditional Random Fields and n-Gram Language Models for Gene Mention Recognition 85 Tackling the BioCreative2 Gene Mention task with Conditional Random Fields and Syntactic Parsing 89 Named  ...  : Gene/protein annotation tool by Alma Bioinformatics 131 Peregrine: Lightweight gene name normalization by dictionary lookup 135 Gene Mention and Gene Normalization Based on Machine Learning and Online  ...  The expert annotation of the data sets was performed by Jeff Colombe; Marc Colosimo provided the second set of annotations for the interannotator agreement study. Acknowledgements: Dr.  ... 
doi:10.5281/zenodo.4274543 fatcat:3sa3fvgngffjrblxzgswof42tq

Message from the general chair

Benjamin C. Lee
2015 2015 IEEE International Symposium on Performance Analysis of Systems and Software (ISPASS)  
Joint Learning for Coreference Resolution with Markov Logic Resolving "This-issue" Anaphora Varada Kolhatkar and Graeme Hirst Saturday 12:00pm-12:30pm -202 A (ICC) We annotate and resolve a particular  ...  We propose a candidate ranking model for "this-issue" anaphora resolution that explores different "issue"-specific and general abstract-anaphora features. The model is not restricted to nominal  ...  We present a new neural network architecture which 1) learns word embeddings that better capture the semantics of words by incorporating both local and global document context, and 2) accounts for homonymy  ... 
doi:10.1109/ispass.2015.7095776 dblp:conf/ispass/Lee15 fatcat:ehbed6nl6barfgs6pzwcvwxria

TED-MWE: a bilingual parallel corpus with MWE annotation [chapter]

Johanna Monti, Federico Sangati, Mihael Arcan
Proceedings of the Second Italian Conference on Computational Linguistics CLiC-it 2015  
We are grateful to our annotators, in particular to Valentina Azer, Marta Benenti, Martina Brignolo, Enrico Grosso and Maurizio Stranisci.  ...  We are particularly grateful to Manuela Cherchi, Erika Ibba, Anna De Santis, Giuseppe Casu, Jessica Ladu, Ilaria Del Rio, Elisa Virdis, Gino Castangia for their annotation work.  ...  and search by linguistic annotations (e.g.  ... 
doi:10.4000/books.aaccademia.1514 fatcat:blsozns23nawtjt6rdt2pumjzm

Why TEI stand-off annotation doesn't quite work

Piotr Bański
Proceedings of Balisage: The Markup Conference 2010   unpublished
For example, relevant documents that are useful for cross-lingual retrieval, based on page-ranked search results, might not contain any parallel sentences.  ...  Then by searching the index we can obtain a ranked list of English texts, in terms of comparability. Those document pairs are returned as the output of the search engine.  ...  , examine, reveal, investigate", which seem to point to a level of high abstraction for the meaning of this word, with a behaviour partly comparable to what was observed for the word "natura".  ... 
doi:10.4242/balisagevol5.banski01 fatcat:am7p7jpr6bd6znxw4f3ew5p6va

Artificial Intelligence Algorithms for Natural Language Processing and the Semantic Web Ontology Learning [article]

Bryar A. Hassan, Tarik A. Rashid
2021 arXiv   pre-print
For this, 32 heterogeneous and multi-featured datasets were used to examine their performance using internal and external clustering measures, and to measure the sensitivity of their performance towards  ...  Evolutionary clustering algorithms have considered as the most popular and widely used evolutionary algorithms for minimising optimisation and practical problems in nearly all fields.  ...  This balance can produce a wide range of numerical values necessary for the local and global searches.  ... 
arXiv:2108.13772v1 fatcat:mgexism7vfcdfgai62qmndz6cm

Automatic Correction of Real-Word Errors in Spanish Clinical Texts

Daniel Bravo-Candel, Jésica López-Hernández, José Antonio García-Díaz, Fernando Molina-Molina, Francisco García-Sánchez
2021 Sensors  
Moreover, GloVe and Word2Vec pretrained word embeddings were used to study their performance.  ...  For that, different types of error were generated in correct sentences by using rules.  ...  In addition, commonly misspelled terms such as 'alot' were localized and corrected. Stanford Named Entity Recognition was used to avoid misclassification of person names as errors.  ... 
doi:10.3390/s21092893 pmid:33919018 fatcat:sdac7vet3ja5pmtphp76qa4gqu

The CompWHoB Corpus: Computational Construction, Annotation and Linguistic Analysis of the White House Press Briefings Corpus [chapter]

Fabrizio Esposito, Pierpaolo Basile, Francesco Cutugno, Marco Venuti
Proceedings of the Second Italian Conference on Computational Linguistics CLiC-it 2015  
We are grateful to our annotators, in particular to Valentina Azer, Marta Benenti, Martina Brignolo, Enrico Grosso and Maurizio Stranisci.  ...  We are particularly grateful to Manuela Cherchi, Erika Ibba, Anna De Santis, Giuseppe Casu, Jessica Ladu, Ilaria Del Rio, Elisa Virdis, Gino Castangia for their annotation work.  ...  and search by linguistic annotations (e.g.  ... 
doi:10.4000/books.aaccademia.1467 fatcat:sglsur3fwvdofejg5uhboqk4ie

Galectin-1 Couples Glycobiology to Inflammation in Osteoarthritis through the Activation of an NF-κB–Regulated Gene Network

Stefan Toegel, Daniela Weinmann, Sabine André, Sonja M. Walzer, Martin Bilban, Sebastian Schmidt, Catharina Chiari, Reinhard Windhager, Christoph Krall, Idriss M. Bennani-Baiti, Hans-Joachim Gabius
2016 Journal of Immunology  
Friday, and W. Notelecs are gratefully acknowledged. We thank B. Rodriguez-Molina, R. Gruebl-Barabas, and M. Cezanne for excellent technical assistance. S. Nuernberger and C.  ...  Albrecht are gratefully acknowledged for support. Disclosures The authors have no financial conflicts of interest. References  ...  Pearson's correlation coefficients were calculated for each patient separately, and the Wilcoxon signed-rank test was performed to test whether the median correlation coefficient was different from 0.  ... 
doi:10.4049/jimmunol.1501165 pmid:26792806 fatcat:l4pllpjfubaz3iqdlmjopjrxyi

Organizing subject access to cultural heritage in Swedish online museums

Koraljka Golub, Pawel Michal Ziolkowski, Goran Zlodi
2021 Journal of Documentation  
for these museums; especially so in subject searching, which is the most complex and yet the most common type of search.  ...  for the end user.  ...  In addition, a number of functionalities related to display, ranking and navigation of search results are listed. Full-text searching is not enough.  ... 
doi:10.1108/jd-05-2021-0094 fatcat:kgk45ptz75hiveyjjqmklk47ru

Thesauri and ontologies in digital libraries

Dagobert Soergel
2005 Proceedings of the 5th ACM/IEEE-CS joint conference on Digital libraries - JCDL '05  
hierarchies and guided facet analysis) and with finding good search terms (through query term mapping and query term expansion -synonyms and hierarchic inclusion).  ...  , and hierarchy) for topic clarification and hierarchic query term expansion).  ...  Inclusive (hierarchically expanded) searching. Enhanced ranking algorithms based on concept and term relationships.  ... 
doi:10.1145/1065385.1065526 dblp:conf/jcdl/Soergel05 fatcat:zpmxl5d3qjaldawhnm7d57xrpa

Wikipedia in Action: Ontological Knowledge in Text Categorization

Maciej Janik, Krys J. Kochut
2008 2008 IEEE International Conference on Semantic Computing  
ACKNOWLEDGEMENTS We are grateful to all national and international academic, industry, and business partners in the GEXI cooperations for the innovative constructive work and the Science and High Performance  ...  Supercomputing Centre (SHPSC) for long-term support of collaborative research and the LX Project for providing suitable resources.  ...  It has been used in forensic investigation [9, 10] for better estimation and narrow down the forensic search.  ... 
doi:10.1109/icsc.2008.53 dblp:conf/semco/JanikK08 fatcat:wzj4ievka5ft3ayxxghzck2vjq

On Social Machines for Algorithmic Regulation [article]

Nello Cristianini, Teresa Scantamburlo
2019 arXiv   pre-print
After showing how all the building blocks of algorithmic regulation are already well in place, we discuss possible implications for human autonomy and social order.  ...  We take seriously recent proposals for algorithmic regulation of society, and we identify the existing technologies that can be used to implement them, most of them originally introduced in business contexts  ...  NC and TS were supported by the ERC Advanced Grant ThinkBIG.  ... 
arXiv:1904.13316v1 fatcat:gnq2qkbltnhvheivon4hx3znjy
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