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1

Combining MEDLINE and publisher data to create parallel corpora for the automatic translation of biomedical text

Antonio Jimeno Yepes, Élise Prieur-Gaston, Aurélie Névéol

Journal:

BMC Bioinformatics

Year:

2013

Language:

english

File:

PDF, 249 KB

english, 2013

2

A representation model for biological entities by fusing structured axioms with unstructured texts

Lou, Peiliang, Dong, YuXin, Yepes, Antonio Jimeno, Li, Chen, Wren, Jonathan

Journal:

Year:

2020

File:

PDF, 558 KB

2020

3

Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation

Antonio J Jimeno-Yepes, Bridget T McInnes, Alan R Aronson

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 566 KB

english, 2011

4

Studying the correlation between different word sense disambiguation methods and summarization effectiveness in biomedical texts

Laura Plaza, Antonio J Jimeno-Yepes, Alberto Díaz, Alan R Aronson

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 419 KB

english, 2011

5

Collocation analysis for UMLS knowledge-based word sense disambiguation

Antonio Jimeno-Yepes, Bridget T Mclnnes, Alan R Aronson

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 339 KB

english, 2011

6

Ontology refinement for improved information retrieval

Antonio Jimeno-Yepes, Rafael Berlanga-Llavori, Dietrich Rebholz-Schuhmann

Journal:

Information Processing & Management

Year:

2010

Language:

english

File:

PDF, 200 KB

english, 2010

7

Measuring prediction capacity of individual verbs for the identification of protein interactions

Dietrich Rebholz-Schuhmann, Antonio Jimeno-Yepes, Miguel Arregui, Harald Kirsch

Journal:

Journal of Biomedical Informatics

Year:

2010

Language:

english

File:

PDF, 216 KB

english, 2010

8

Reuse of terminological resources for efficient ontological engineering in Life Sciences

Antonio Jimeno-Yepes, Ernesto Jiménez-Ruiz, Rafael Berlanga-Llavori, Dietrich Rebholz-Schuhmann

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 548 KB

english, 2009

9

Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb

Kevin Nagel, Antonio Jimeno-Yepes, Dietrich Rebholz-Schuhmann

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 2.70 MB

english, 2009

10

Knowledge-based biomedical word sense disambiguation: comparison of approaches

Antonio J Jimeno-Yepes, Alan R Aronson

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 702 KB

english, 2010

11

Assessment of NER solutions against the first and second CALBC Silver Standard Corpus

Dietrich Rebholz-Schuhmann, Antonio Jimeno Yepes, Chen Li, Senay Kafkas, Ian Lewin, Ning Kang, Peter Corbett, David Milward, Ekaterina Buyko, Elena Beisswanger, Kerstin Hornbostel, Alexandre Kouznetso

Journal:

Journal of Biomedical Semantics

Year:

2011

Language:

english

File:

PDF, 423 KB

english, 2011

12

MeSH indexing based on automatically generated summaries

Antonio J Jimeno-Yepes, Laura Plaza, James G Mork, Alan R Aronson…

Journal:

BMC Bioinformatics

Year:

2013

Language:

english

File:

PDF, 309 KB

english, 2013

13

GeneRIF indexing: sentence selection based on machine learning

Antonio J Jimeno-Yepes, J Caitlin Sticco, James G Mork…

Journal:

BMC Bioinformatics

Year:

2013

Language:

english

File:

PDF, 241 KB

english, 2013

14

[IEEE 2010 International Conference on Machine Learning and Applications (ICMLA) - Washington, DC, USA (2010.12.12-2010.12.14)] 2010 Ninth International Conference on Machine Learning and Applications - Query Expansion for UMLS Metathesaurus Disambiguation Based on Automatic Corpus Extraction

Yepes, Antonio Jimeno, Aronson, Alan R.

Year:

2010

Language:

english

File:

PDF, 153 KB

english, 2010

15

[IEEE 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society - Minneapolis, MN (2009.09.3-2009.09.6)] 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society - Exploitation of ontological resources for scientific literature analysis: Searching genes and related diseases

Jimeno-Yepes, A., Berlanga-Llavori, R., Rebholz-Schuhmann, D.

Year:

2009

Language:

english

File:

PDF, 383 KB

english, 2009

16

Knowledge based word-concept model estimation and refinement for biomedical text mining

Jimeno Yepes, Antonio, Berlanga, Rafael

Journal:

Journal of Biomedical Informatics

Year:

2015

Language:

english

File:

PDF, 903 KB

english, 2015

17

[IEEE 2011 22nd International Conference on Database and Expert Systems Applications (DEXA) - Toulouse, France (2011.08.29-2011.09.2)] 2011 22nd International Workshop on Database and Expert Systems Applications - Preliminary Results for Biomedical Word Sense Disambiguation Based on Semantic Clustering

Martin-Wanton, Tamara, Berlanga-Llavori, Rafael, Jimeno-Yepes, Antonio

Year:

2011

Language:

english

File:

PDF, 269 KB

english, 2011

18

CALBC SILVER STANDARD CORPUS

REBHOLZ-SCHUHMANN, DIETRICH, YEPES, ANTONIO JOSÉ JIMENO, VAN MULLIGEN, ERIK M., KANG, NING, KORS, JAN, MILWARD, DAVID, CORBETT, PETER, BUYKO, EKATERINA, BEISSWANGER, ELENA, HAHN, UDO

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.14 MB

english, 2010

19

Feature engineering for MEDLINE citation categorization with MeSH

Jimeno Yepes, Antonio Jose, Plaza, Laura, Carrillo-de-Albornoz, Jorge, Mork, James G, Aronson, Alan R

Journal:

BMC Bioinformatics

Year:

2015

Language:

english

File:

PDF, 708 KB

english, 2015

20

BioC interoperability track overview

Comeau, D. C., Batista-Navarro, R. T., Dai, H.-J., Islamaj Do an, R., Jimeno Yepes, A., Khare, R., Lu, Z., Marques, H., Mattingly, C. J., Neves, M., Peng, Y., Rak, R., Rinaldi, F., Tsai, R. T.-H., Ver

Journal:

Year:

2014

Language:

english

File:

PDF, 422 KB

english, 2014

21

Combining Evidence, Specificity, and Proximity towards the Normalization of Gene Ontology Terms in Text

Gaudan, S., Jimeno Yepes, A., Lee, V., Rebholz-Schuhmann, D.

Journal:

EURASIP Journal on Bioinformatics and Systems Biology

Year:

2008

Language:

english

File:

PDF, 746 KB

english, 2008

22

Annotating the biomedical literature for the human variome

Verspoor, K., Jimeno Yepes, A., Cavedon, L., McIntosh, T., Herten-Crabb, A., Thomas, Z., Plazzer, J.-P.

Journal:

Year:

2013

Language:

english

File:

PDF, 370 KB

english, 2013

23

PCorral--interactive mining of protein interactions from MEDLINE

Li, C., Jimeno-Yepes, A., Arregui, M., Kirsch, H., Rebholz-Schuhmann, D.

Journal:

Year:

2013

Language:

english

File:

PDF, 569 KB

english, 2013

24

[ACM Press the 2nd ACM SIGHIT symposium - Miami, Florida, USA (2012.01.28-2012.01.30)] Proceedings of the 2nd ACM SIGHIT symposium on International health informatics - IHI '12 - Knowledge-based and knowledge-lean methods combined in unsupervised word sense disambiguation

Jimeno Yepes, Antonio, Aronson, Alan R.

Year:

2012

Language:

english

File:

PDF, 437 KB

english, 2012

25

[ACM Press the 2nd ACM SIGHIT symposium - Miami, Florida, USA (2012.01.28-2012.01.30)] Proceedings of the 2nd ACM SIGHIT symposium on International health informatics - IHI '12 - MEDLINE MeSH indexing

Jimeno Yepes, Antonio, Mork, James G., Wilkowski, BartBomiej, Demner Fushman, Dina, Aronson, Alan R.

Year:

2012

Language:

english

File:

PDF, 591 KB

english, 2012

26

[ACM Press the WSDM '09 Workshop - Barcelona, Spain (2009.02.09-2009.02.09)] Proceedings of the WSDM '09 Workshop on Exploiting Semantic Annotations in Information Retrieval - ESAIR '09 - Terminological cleansing for improved information retrieval based on ontological terms

Jimeno-Yepes, Antonio, Berlanga-Llavori, Rafael, Rebholz-Schuhmann, Dietrich

Year:

2009

Language:

english

File:

PDF, 178 KB

english, 2009

27

[ACM Press the ACM Ninth International Workshop - Melbourne, Australia (2015.10.23-2015.10.23)] Proceedings of the ACM Ninth International Workshop on Data and Text Mining in Biomedical Informatics - DTMBIO '15 - Identification and Analysis of Medical Entity Co-occurrences in Twitter

MacKinlay, Andrew, Jimeno Yepes, Antonio, Han, Bo

Year:

2015

Language:

english

File:

PDF, 385 KB

english, 2015

28

[ACM Press the ACM International Conference - Como, Italy (2016.05.16-2016.05.19)] Proceedings of the ACM International Conference on Computing Frontiers - CF '16 - Decoding EEG and LFP signals using deep learning

Nurse, Ewan, Mashford, Benjamin S., Yepes, Antonio Jimeno, Kiral-Kornek, Isabell, Harrer, Stefan, Freestone, Dean R.

Year:

2016

Language:

english

File:

PDF, 837 KB

english, 2016

29

[IEEE 2016 International Joint Conference on Neural Networks (IJCNN) - Vancouver, BC, Canada (2016.7.24-2016.7.29)] 2016 International Joint Conference on Neural Networks (IJCNN) - Weighted Population Code for low power neuromorphic image classification

Yepes, Antonio Jimeno, Tang, Jianbin, Saxena, Shreya, Brosch, Tobias, Amir, Arnon

Year:

2016

Language:

english

File:

PDF, 265 KB

english, 2016

30

Word embeddings and recurrent neural networks based on Long-Short Term Memory nodes in supervised biomedical word sense disambiguation

Yepes, Antonio Jimeno

Journal:

Journal of Biomedical Informatics

Year:

2017

Language:

english

File:

PDF, 1.05 MB

english, 2017

31

[IEEE 2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE) - Washington, DC (2017.10.23-2017.10.25)] 2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE) - Knowledge-Based Biomedical Word Sense Disambiguation with Neural Concept Embeddings

Sabbir, Akm, Jimeno-Yepes, Antonio, Kavuluru, Ramakanth

Year:

2017

Language:

english

File:

PDF, 341 KB

english, 2017

32

Stage-based Variation in the Effect of Primary Tumor Side on All Stages of Colorectal Cancer Recurrence and Survival

Lee, Margaret M., MacKinlay, Andrew, Semira, Christine, Schieber, Christine, Jimeno Yepes, Antonio Jose, Lee, Belinda, Wong, Rachel, Hettiarachchige, Chathurika K.H., Gunn, Natalie, Tie, Jeanne, Wong,

Journal:

Clinical Colorectal Cancer

Year:

2018

Language:

english

File:

PDF, 599 KB

english, 2018

33

[ACM Press the 5th Spanish Conference - Zaragoza, Spain (2018.06.26-2018.06.27)] Proceedings of the 5th Spanish Conference on Information Retrieval - CERI '18 - Coarse-grained Semantic Characterization of Large Knowledge Resources

Berlanga, Rafael, Yepes, Antonio Jimeno, Pérez, María, Lanza-Cruz, Indira

Year:

2018

Language:

english

File:

PDF, 283 KB

english, 2018

34

BioNorm: Deep learning based event normalization for the curation of reaction databases

Lou, Peiliang, Yepes, Antonio Jimeno, Zhang, Zai, Zheng, Qinghua, Zhang, Xiangrong, Li, Chen, Wren, Jonathan

Journal:

Year:

2019

Language:

english

File:

PDF, 2.22 MB

english, 2019

35

[IEEE 2019 International Conference on Document Analysis and Recognition (ICDAR) - Sydney, Australia (2019.9.20-2019.9.25)] 2019 International Conference on Document Analysis and Recognition (ICDAR) - PubLayNet: Largest Dataset Ever for Document Layout Analysis

Zhong, Xu, Tang, Jianbin, Jimeno Yepes, Antonio

Year:

2019

Language:

english

File:

PDF, 2.77 MB

english, 2019

36

Combining Social Media and FDA Adverse Event Reporting System to Detect Adverse Drug Reactions

Li, Ying, Jimeno Yepes, Antonio, Xiao, Cao

Journal:

Year:

2020

File:

PDF, 1016 KB

2020

37

[IEEE 2020 International Joint Conference on Neural Networks (IJCNN) - Glasgow, United Kingdom (2020.7.19-2020.7.24)] 2020 International Joint Conference on Neural Networks (IJCNN) - Forget Me Not: Reducing Catastrophic Forgetting for Domain Adaptation in Reading Comprehension

Xu, Ying, Zhong, Xu, Yepes, Antonio Jose Jimeno, Lau, Jey Han

Year:

2020

File:

PDF, 881 KB

2020

38

Adverse drug event detection using reason assignments in FDA drug labels

Sutphin, Corey, Lee, Kahyun, Yepes, Antonio Jimeno, Uzuner, Ãzlem, McInnes, Bridget T.

Journal:

Journal of Biomedical Informatics

Year:

2020

File:

PDF, 1.15 MB

2020