Rui Antunes

Subject	Biomedical information extraction with natural language processing and machine learning methods
Advisor	Sérgio Matos
Group	Biomedical Informatics and Technologies
Status	PhD student
Starts	2015/10/19
Ends	2022/06/30
Country	Portugal
Projects
Past projects	IF/01694/2013/CP1162/CT0018, SOCA - Smart Open Campus
Events	HEALTHINF2019, INForum 2017, PACBB'2017, RecPad2016
Proposals
Personal page	https://orcid.org/0000-0003-3533-8872

Publications

Articles in international journals listed in the ISI

• Jorge Miguel Silva, Diogo Pratas, Rui Antunes, Sérgio Matos, Armando J. Pinho. Automatic analysis of artistic paintings using information-based measures. Pattern Recognition, p. 107864, February 2021 [IF 2018: 5.165 (Q1, 10/202)]
• Rui Antunes, Sérgio Matos. Extraction of chemical–protein interactions from the literature using neural networks and narrow instance representation. Database, vol. 2019, no. baz095, October 2019 [IF 2018: 3.683 (Q1, 7/59)]
• Rezarta Islamaj Doğan, Sun Kim, Andrew Chatr-aryamontri, Chih-Hsuan Wei, Donald C Comeau, Rui Antunes, Sérgio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C Panyam, Karin Verspoor, Hongfang Liu, Yanshan Wang, Zhuang Liu, Berna Altınel, Zehra Melce Hüsünbeyi, Arzucan Özgür, Aris Fergadis, Chen-Kai Wang, Hong-Jie Dai, Tung Tran, Ramakanth Kavuluru, Ling Luo, Albert Steppi, Jinfeng Zhang, Jinchan Qu, Zhiyong Lu. Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. Database, vol. 2019, no. bay147, January 2019 [IF 2018: 3.683 (Q1, 7/59)]
• Sérgio Matos, Rui Antunes. Protein-protein interaction article classification using a convolutional recurrent neural network with pre-trained word embeddings. Journal of Integrative Bioinformatics, vol. 14, no. 4, December 2017
• Rui Antunes, Sérgio Matos. Supervised learning and knowledge-based approaches applied to biomedical word sense disambiguation. Journal of Integrative Bioinformatics, vol. 14, no. 4, December 2017

Articles in conference proceedings

• Tiago Almeida, Rui Antunes, João Figueira Silva, João Almeida, Sérgio Matos. Chemical detection and indexing in PubMed full text articles using deep learning and rule-based methods. Proceedings of the BioCreative VII Challenge Evaluation Workshop, Online event, p. 119-123, November 2021
• Rui Antunes, Tiago Almeida, João Figueira Silva, Sérgio Matos. Chemical–protein relation extraction in PubMed abstracts using BERT and neural networks. Proceedings of the BioCreative VII Challenge Evaluation Workshop, Online event, p. 76-79, November 2021
• João Figueira Silva, Tiago Almeida, Rui Antunes, João Almeida, Sérgio Matos. Drug mention recognition in Twitter posts using a deep learning approach. Proceedings of the BioCreative VII Challenge Evaluation Workshop, Online event, p. 210-213, November 2021
• Alina Trifan, Rui Antunes, José Luís Oliveira. Machine learning for depression screening in online communities. 14th International Conference on Practical Applications of Computational Biology & Bioinformatics, PACBB 2020, L'Aquila, Italy, October 2020
• João Figueira Silva, Rui Antunes, João Almeida, Sérgio Matos. Clinical concept normalization on medical records using word embeddings and heuristics. 30th Medical Informatics Europe conference, MIE 2020, Studies in health technology and informatics, vol. 270, p. 93-97, April 2020
• Alina Trifan, Rui Antunes, Sérgio Matos, José Luís Oliveira. Understanding depression from psycholinguistic patterns in social media texts. 42nd European Conference on Information Retrieval, ECIR 2020, Online event, April 2020
• Rui Antunes, João Figueira Silva, Sérgio Matos. Evaluating semantic textual similarity in clinical sentences using deep learning and sentence embeddings. The 35th ACM/SIGAPP Symposium On Applied Computing, Online event, March 2020
• Rui Antunes, João Figueira Silva, Arnaldo Pereira, Sérgio Matos. Rule-based and machine learning hybrid system for patient cohort selection. Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 5: HEALTHINF, Prague, Czech Republic, p. 59-67, February 2019
• Rui Antunes, Sérgio Matos. Evaluation of word embedding vector averaging functions for biomedical word sense disambiguation. INForum 2017 - Atas do Nono Simpósio de Informática, Aveiro, p. 25-30, October 2017
• Sérgio Matos, Rui Antunes. Identifying relevant literature for precision medicine using deep neural networks. Proceedings of the BioCreative VI Challenge Evaluation Workshop, Bethesda, MA, USA, p. 99-101, October 2017
• Rui Antunes, Sérgio Matos. Biomedical word sense disambiguation with word embeddings. 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, PACBB 2017, Porto, p. 273-279, June 2017
• Rui Antunes, Sérgio Matos. Machine learning with word embeddings applied to biomedical concept disambiguation. Proceedings of the 22nd Portuguese Conference on Pattern Recognition, RecPad 2016, Aveiro, p. 77-78, October 2016

Masters thesis

• Rui Antunes. Genomics music. Masters Thesis, University of Aveiro, July 2015