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• Jorge Miguel Silva, Diogo Pratas, Tânia Caetano, Sérgio Matos. Feature-Based Classification of Archaeal Sequences Using Compression-Based Methods. Proceedings of the 10th Iberian Conference on Pattern Recognition and Image Analysis, IbPRIA, Aveiro, Portugal, p. 309-320, May 2022
• Jorge Miguel Silva, Diogo Pratas, Tania Caetano, Sérgio Matos. Archaea Taxonomic Classification. Proceedings of the 27th Portuguese Conference on Pattern Recognition, RecPad 2021, Évora, Portugal, November 2021
• 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
• João Figueira Silva, Sérgio Matos. Patient Trajectory Modelling in Longitudinal Data: A Review on Existing Solutions. The 2021 34th IEEE International Symposium on Computer-based Medical Systems (CBMS), Aveiro, Portugal, June 2021
• João Almeida, João Figueira Silva, Sérgio Matos, José Luís Oliveira. A Recommender System to Help Refining Clinical Research Studies. 31st Medical Informatics Europe conference, Studies in health technology and informatics, May 2021
• Jorge Miguel Silva, Diogo Pratas, Sérgio Matos. Comparison and Evaluation of Information-based Measures in Images. Proceedings of the 26th Portuguese Conference on Pattern Recognition, RecPad 2020, Évora, Portugal, October 2020
• Tiago Almeida, Sérgio Matos. Calling Attention to Passages for Biomedical Question Answering. 42nd European Conference on Information Retrieval, ECIR 2020, Online event, p. 69-77, April 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
• João Almeida, Sérgio Matos. Rule-based extraction of family history information from clinical notes. The 35th ACM/SIGAPP Symposium On Applied Computing, Online event, p. 670–675, March 2020
• João Almeida, João Figueira Silva, Alejandro Sierra, Sérgio Matos, José Luís Oliveira. Enhancing Decision-making Systems with Relevant Patient Information by Leveraging Clinical Notes. Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 5: HEALTHINF, vol. 5, p. 254-262, February 2020
• Jorge Miguel Silva, Diogo Pratas, Sérgio Matos. Evaluation of Statistical Complexity in Viral Genome Sequences. 25th Portuguese Conference on Pattern Recognition, RECPAD2019, Porto, Portugal, October 2019
• 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
• Micael Pedrosa, Jorge Miguel Silva, Sérgio Matos, Carlos Costa. SCREEN-DR - Software Architecture for the Diabetic Retinopathy Screening. Studies in health technology and informatics, vol. 247, p. 396-400, 2018
• Vitor Pereira, Sérgio Matos, José Luís Oliveira. Automated ICD-9-CM medical coding of diabetic patient's clinical reports. Proceedings of the First International Conference on Data Science, E-learning and Information Systems, Madrid, October 2018
• Pedro Matos, Sérgio Matos. Recognition of genetic mutations in text using deep learning. Proceedings of the First International Conference on Data Science, E-learning and Information Systems, Madrid, October 2018
• Jorge Miguel Silva, António Guerra, João Figueira Silva, Carlos Costa, Sérgio Matos. A Novel 3D-CNN Approach For Ejection Fraction Classification in Transthoracic Echocardiography. International Journal of Computer Assisted Radiology and Surgery, Berlin, Germany, vol. 13 (Supp1), p. S131--S132, June 2018
• João Figueira Silva, Jorge Miguel Silva, António Guerra, Sérgio Matos, Carlos Costa. Ejection Fraction Classification in Transthoracic Echocardiography Using a Deep Learning Approach. 2018 IEEE 31st International Symposium on Computer-Based Medical Systems (CBMS), Karlstad, Sweden, p. 123-128, June 2018
• Carlos Costa, Micael Pedrosa, Jorge Miguel Silva, Sérgio Matos. Research PACS for diabetic retinopathy screening. International Journal of Computer Assisted Radiology and Surgery, Berlin, Germany, vol. 13 (Supp1), p. S32--S33, June 2018
• 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. Extracting Chemical-Protein Interactions using Long Short-Term Memory Networks. Proceedings of the VI BioCreative Challenge Evaluation Workshop, Bethesda, MA, USA, p. 151-154, 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
• Sérgio Matos. Improving Document Prioritization for Protein-Protein Interaction Extraction Using Shallow Linguistics and Word Embeddings. 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, Porto, p. 43-49, June 2017
• André Santos, Sérgio Matos. Neji: DIY web services for biomedical concept recognition. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, Barcelona, Spain, p. 191-195, April 2017
• André Santos, Sérgio Matos. Neji: Recognition of Chemical and Gene Mentions in Patent Texts. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, Barcelona, Spain, p. 54-60, April 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
• André Santos, Sérgio Matos, David Campos, José Luís Oliveira. A Curation Pipeline and Web-Services for PDF Documents. Proceedings of the 7th International Symposium on Semantic Mining in Biomedicine, Potsdam, Germany, August 2016
• Eriksson Monteiro, Pedro Sernadela, Sérgio Matos, Carlos Costa, José Luís Oliveira. Semantic Knowledge Base Construction from Radiology Reports. Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies, Rome, Italy, p. 345-352, February 2016
• Pedro Sernadela, Sérgio Matos, José Luís Oliveira. Ann2RDF: moving annotations to semantic web,. 17th International Conference on Information Integration and Web-based Applications & Services (iiWAS 2015), Brussels, Belgium, December 2015
• Sérgio Matos, David Campos, Renato Pinho, Raquel Silva, Matthew Mort, David N. Cooper, José Luís Oliveira. Assisted Mining and Curation of Genomic Variants using Egas. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, Sevilla, Spain, p. 396-402, September 2015
• Sérgio Matos, José Sequeira, David Campos, José Luís Oliveira. Identification of chemical and gene mentions in patent texts using feature-rich conditional random fields. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, Sevilla, Spain, p. 76-81, September 2015
• Sérgio Matos, André Santos, David Campos, José Luís Oliveira. Neji: a BioC compatible framework for biomedical concept recognition. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, Sevilla, Spain, p. 17-21, September 2015
• Sérgio Matos, José Sequeira, José Luís Oliveira. BioinformaticsUA: Machine Learning and Rule-Based Recognition of Disorders and Clinical Attributes from Patient Notes. Proceedings of the 9th International Workshop on Semantic Evaluation (SemEval 2015), Denver, Colorado (USA), p. 422-426, June 2015
• Carlos Ferreira, Sérgio Matos, Carlos Costa. Long-Term Prefetching for Cloud Medical Imaging Repositories. 26th Medical Informatics Europe Conference (MIE2015), Madrid, Spain, May 2015
• Pedro Sernadela, Pedro Lopes, David Campos, Sérgio Matos, José Luís Oliveira. A Semantic Layer for Unifying and Exploring Biomedical Document Curation Results. Bioinformatics and Biomedical Engineering, Proceeedings of the Third International Conference, IWBBIO, Part I, Granada, Spain, vol. Part I, p. 8-17, April 2015
• Carlos Viana Ferreira, Sérgio Matos, Carlos Costa. Incremental learning versus batch learning for classification of user's behaviour in medical imaging. 8th International Conference on health informatics (HealthInf), January 2015
• Sérgio Matos, Tiago Nunes, José Luís Oliveira. BioinformaticsUA: Concept Recognition in Clinical Narratives Using a Modular and Highly Efficient Text Processing Framework. Proceedings of the 8th International Workshop on Semantic Evaluation (SemEval 2014), Dublin, Ireland, p. 135–139, August 2014
• Tiago Nunes, Sérgio Matos, José Luís Oliveira. Extracting sentences describing biomolecular events from the biomedical literature. 11th International Symposium on Distributed Computing and Artificial Intelligence (DCAI'14), Salamanca, Spain, June 2014
• David Campos, Sérgio Matos, José Luís Oliveira. Chemical name recognition with harmonized feature-rich conditional random fields. Fourth BioCreative Challenge Evaluation Workshop, vol. 2, p. 82-87, October 2013
• David Campos, Jóni Lourenço, Tiago Nunes, Rui Vitorino, Pedro Domingues, Sérgio Matos, José Luís Oliveira. Egas - Collaborative Biomedical Annotation as a Service. Fourth BioCreative Challenge Evaluation Workshop, vol. 1, p. 254-259, October 2013
• David Campos, Sérgio Matos, José Luís Oliveira. Neji: a tool for heterogeneous biomedical concept identification. Proceedings of the BioLINK SIG, ISMB/ECCB, Berlin, Germany, p. 28-31, July 2013
• Víctor M. Prieto, Sérgio Matos, Manuel Álvarez, Fidel Cacheda, José Luís Oliveira. Analysing Relevant Diseases From Iberian Tweets. Proc. of the 7th Int. Conf. on Practical Applications of Computational Biology and Bioinformatics, PACBB 2013, Salamanca, Spain, May 2013
• Sérgio Matos, Hugo Araújo, José Luís Oliveira. Structuring and Exploring the Biomedical Literature Using Latent Semantics. 10th International Symposium on Distributed Computing and Artificial Intelligence (DCAI'13), Salamanca, Spain, May 2013
• José Carlos Santos, Sérgio Matos. Predicting Flu Incidence from Portuguese Tweets. International Work-Conference on Bioinformatics and Biomedical Engineering, Granada, Spain, March 2013
• José Carlos Santos, Sérgio Matos. Extracting Health Information From Portuguese Tweets. Proc. of the 18th Portuguese Conf. on Pattern Recognition, RecPad 2012, Coimbra, Portugal, October 2012
• Sérgio Matos, José Luís Oliveira. Prioritizing Literature Search Results Using a Training Set of Classified Documents. Proc. of the 5th Int. Conf. on Practical Applications of Computational Biology and Bioinformatics, PACBB 2011, April 2011
• David Campos, D. Rebholz-Schuhman, Sérgio Matos, José Luís Oliveira. A CRF-based approach to harmonize heterogeneous gene/protein annotations. Proceedings of the Second CALBC workshop, p. 17-18, March 2011
• David Campos, Sérgio Matos, José Luís Oliveira. Annotating the CALBC corpus with a machine learning harmonization approach. Proceedings of the Second CALBC workshop, p. 43-45, March 2011
• David Campos, Sérgio Matos, José Luís Oliveira. Recognition of Gene/Protein names using Conditional Random Fields. Proceedings of the International Conference on Knowledge Discovery and Information Retrieval 2010 (KDIR2010), Valencia, Spain, October 2010
• Sérgio Matos, David Campos, José Luís Oliveira. Vector-space models and terminologies in gene normalization and document classification. Proceedings of BioCreative III Workshop, Bethesda, Maryland, USA, p. 119-124, September 2010
• Sérgio Matos, Joel Arrais, José Luís Oliveira. Expanding Gene-based PubMed Queries. Proceedings of the 4th International Workshop on Practical Applications of Computational Biology and Bioinformatics 2010 (IWPACBB 2010), Guimarães, Portugal, vol. 74, p. 61-68, June 2010
• Joel Arrais, João Pereira, Pedro Lopes, Sérgio Matos, José Luís Oliveira. Improving cross mapping in biomedical databases. 4th International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2010), June 2010
• Sérgio Matos, Joel Arrais, João Maia-Rodrigues, José Luís Oliveira. QuExT: a concept-based query expansion approach for literature retrieval from MEDLINE. Jornadas de Bioinformática (JB 2009), Lisbon, Portugal, 2009
• Sérgio Matos, Anabela Barreiro, José Luís Oliveira. Syntactic Parsing for Bio-molecular Event Detection from Scientific Literature. 14th Portuguese Conference on Artificial Intelligence, Aveiro, Portugal, vol. 5816, p. 79-85, October 2009